Psyllid ID: psy4122

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160--
Protein Sequence
MTIAINSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQVETL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEccccccHHHHHHHHHHHHccccEEEEcccccccccccccEEEEccEEEEEEcHHHHHHHHccEEEEEccccccccHHHHHHHHHHccEEEEccccEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHcccEEEEEEEccccHHHHHcccccccccEEEEccHHHHHHHcccEEEEccccccccccHHHHHHHHHcccEEcccccEEccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mtiainsqEYVRFTLIYLFSVNTDALTQDWLSHLRWILQkdnmsqdvfligkpgslRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQVETL
Flexible Loop (DISEMBL)
mtiainsqeyVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYIclsrdtteadikqrrEIVNGtaiyydqsavrAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGrflvsastydkllqvetl
Low Complexity Region (SEG)
MTIAINSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAernvlpvlnnllenreMHLEDGRFLVSASTYDKLLQVETL
Disordered region (IsUnstruct)
****INSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKL******
Disordered Region (DISOPRED)
*************TLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQVE**
Disordered Region (DISEMBL)
MTIAINSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQVETL
Disordered Region (DISPRO)
MTIAINSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQ****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTIAINSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQVETL
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	162	2.2.26 [Sep-21-2011]
A3KMH1	1905	von Willebrand factor A d	no	N/A	0.839	0.071	0.755	4e-56
B0R0T1	1896	von Willebrand factor A d	yes	N/A	0.845	0.072	0.746	1e-55
Q8CC88	1905	von Willebrand factor A d	no	N/A	0.851	0.072	0.741	2e-55

>sp|A3KMH1|VWA8_HUMAN von Willebrand factor A domain-containing protein 8 OS=Homo sapiens GN=VWA8 PE=1 SV=2

 Score =  216 bits (550), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 105/139 (75%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 82  SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 141

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 142 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 201

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLL+  T
Sbjct: 202 DGRFLMSAERYDKLLRDHT 220

Homo sapiens (taxid: 9606)

>sp|B0R0T1|VWA8_DANRE von Willebrand factor A domain-containing protein 8 OS=Danio rerio GN=si:dkey-18l1.1 PE=4 SV=1

 Score =  214 bits (546), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 103/138 (74%), Positives = 116/138 (84%)

Query: 24  DALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTE 83
           +AL Q    HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEY+ LSRDTTE
Sbjct: 75  EALPQMVTQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYVALSRDTTE 134

Query: 84  ADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED 143
            D+KQRREI +GTA Y DQ AVRAA EGR+L+LEG+EKAERNVLPVLNNLLENREM LED
Sbjct: 135 TDLKQRREIRSGTAFYIDQCAVRAATEGRILVLEGLEKAERNVLPVLNNLLENREMQLED 194

Query: 144 GRFLVSASTYDKLLQVET 161
           GRFL+SA  YDKLL+  T
Sbjct: 195 GRFLMSAHRYDKLLEEHT 212

Danio rerio (taxid: 7955)

>sp|Q8CC88|VWA8_MOUSE von Willebrand factor A domain-containing protein 8 OS=Mus musculus GN=Vwa8 PE=2 SV=2

 Score =  214 bits (546), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 103/139 (74%), Positives = 115/139 (82%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+  Q  + HLRW++QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 81  SDSPAQSIVQHLRWLMQKDLLGQDVFLIGPPGPLRRSVAMQYLELTKREVEYIALSRDTT 140

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR L+LEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 141 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLVLEGLEKAERNVLPVLNNLLENREMQLE 200

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 201 DGRFLMSAERYDKLLQDHT 219

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	162
363729456	1904	PREDICTED: uncharacterized protein KIAA0	0.851	0.072	0.755	2e-55
326914135	1872	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.851	0.073	0.755	2e-55
296203808	1909	PREDICTED: uncharacterized protein KIAA0	0.839	0.071	0.762	4e-55
426236691	1935	PREDICTED: von Willebrand factor A domai	0.839	0.070	0.762	4e-55
332241809	1905	PREDICTED: LOW QUALITY PROTEIN: von Will	0.839	0.071	0.762	6e-55
449484533	1883	PREDICTED: LOW QUALITY PROTEIN: von Will	0.851	0.073	0.748	6e-55
338715471	2159	PREDICTED: uncharacterized protein KIAA0	0.839	0.062	0.755	6e-55
297274349	1906	PREDICTED: uncharacterized protein KIAA0	0.839	0.071	0.762	6e-55
355754660	1905	hypothetical protein EGM_08435 [Macaca f	0.839	0.071	0.762	6e-55
355700958	1851	hypothetical protein EGK_09273, partial	0.839	0.073	0.762	6e-55

>gi|363729456|ref|XP_425624.3| PREDICTED: uncharacterized protein KIAA0564-like [Gallus gallus]

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 105/139 (75%), Positives = 118/139 (84%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           TD+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 76  TDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 135

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI +G+A Y DQ AVRAA EGR+L+LEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 136 ETDLKQRREIRDGSAFYLDQCAVRAATEGRILVLEGLEKAERNVLPVLNNLLENREMQLE 195

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 196 DGRFLMSAERYDKLLQDHT 214

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326914135|ref|XP_003203383.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein KIAA0564-like [Meleagris gallopavo]

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 105/139 (75%), Positives = 118/139 (84%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           TD+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 46  TDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 105

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI +G+A Y DQ AVRAA EGR+L+LEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 106 ETDLKQRREIRDGSAFYLDQCAVRAATEGRILVLEGLEKAERNVLPVLNNLLENREMQLE 165

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 166 DGRFLMSAERYDKLLQDHT 184

Source: Meleagris gallopavo

Species: Meleagris gallopavo

Genus: Meleagris

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|296203808|ref|XP_002749063.1| PREDICTED: uncharacterized protein KIAA0564 [Callithrix jacchus]

 Score =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 106/139 (76%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 85  SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 144

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 145 ETDLKQRREIREGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 204

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 205 DGRFLMSAERYDKLLQDHT 223

Source: Callithrix jacchus

Species: Callithrix jacchus

Genus: Callithrix

Family: Cebidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|426236691|ref|XP_004012301.1| PREDICTED: von Willebrand factor A domain-containing protein 8 [Ovis aries]

 Score =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 106/139 (76%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 112 SDSLAQSVIQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 171

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 172 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 231

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 232 DGRFLMSAERYDKLLQDHT 250

Source: Ovis aries

Species: Ovis aries

Genus: Ovis

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|332241809|ref|XP_003270072.1| PREDICTED: LOW QUALITY PROTEIN: von Willebrand factor A domain-containing protein 8 [Nomascus leucogenys]

 Score =  218 bits (556), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 106/139 (76%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 82  SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 141

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 142 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 201

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 202 DGRFLMSAERYDKLLQDHT 220

Source: Nomascus leucogenys

Species: Nomascus leucogenys

Genus: Nomascus

Family: Hylobatidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449484533|ref|XP_004175140.1| PREDICTED: LOW QUALITY PROTEIN: von Willebrand factor A domain-containing protein 8 [Taeniopygia guttata]

 Score =  218 bits (556), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 104/139 (74%), Positives = 118/139 (84%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           T++L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 55  TESLAQSVVHHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 114

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI +G+A Y DQ AVRAA EGR+L+LEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 115 ETDLKQRREIRDGSAFYLDQCAVRAATEGRILVLEGLEKAERNVLPVLNNLLENREMQLE 174

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 175 DGRFLMSADRYDKLLQEHT 193

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|338715471|ref|XP_001493080.3| PREDICTED: uncharacterized protein KIAA0564-like [Equus caballus]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 105/139 (75%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D++ Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELTQREVEYI LSRDTT
Sbjct: 334 SDSVAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTQREVEYIALSRDTT 393

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR L+LEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 394 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLVLEGLEKAERNVLPVLNNLLENREMQLE 453

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 454 DGRFLMSAERYDKLLQDHT 472

Source: Equus caballus

Species: Equus caballus

Genus: Equus

Family: Equidae

Order: Perissodactyla

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|297274349|ref|XP_001091849.2| PREDICTED: uncharacterized protein KIAA0564 isoform 2 [Macaca mulatta]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 106/139 (76%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 83  SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 142

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 143 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 202

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 203 DGRFLMSAERYDKLLQDHT 221

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|355754660|gb|EHH58561.1| hypothetical protein EGM_08435 [Macaca fascicularis]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 106/139 (76%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 82  SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 141

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 142 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 201

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 202 DGRFLMSAERYDKLLQDHT 220

Source: Macaca fascicularis

Species: Macaca fascicularis

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|355700958|gb|EHH28979.1| hypothetical protein EGK_09273, partial [Macaca mulatta]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 106/139 (76%), Positives = 116/139 (83%)

Query: 23  TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
           +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct: 28  SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 87

Query: 83  EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE 142
           E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKAERNVLPVLNNLLENREM LE
Sbjct: 88  ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 147

Query: 143 DGRFLVSASTYDKLLQVET 161
           DGRFL+SA  YDKLLQ  T
Sbjct: 148 DGRFLMSAERYDKLLQDHT 166

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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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	162
UNIPROTKB|F1NXF1	1357	F1NXF1 "Uncharacterized protei	0.919	0.109	0.610	3.1e-40
UNIPROTKB|I3LJL2	406	LOC100511470 "Uncharacterized	0.858	0.342	0.624	3.7e-39
UNIPROTKB|F1MIM5	958	Bt.110663 "Uncharacterized pro	0.858	0.145	0.633	6.1e-39
UNIPROTKB|A3KMH1	1905	VWA8 "von Willebrand factor A	0.858	0.072	0.640	1.3e-38
UNIPROTKB|F1MIT3	1828	Bt.110663 "Uncharacterized pro	0.858	0.076	0.633	2e-38
ZFIN|ZDB-GENE-070912-407	1903	vwa8 "von Willebrand factor A	0.851	0.072	0.630	2.7e-38
UNIPROTKB|F1PD22	1904	VWA8 "Uncharacterized protein"	0.858	0.073	0.618	5.6e-38
MGI|MGI:1919008	1905	Vwa8 "von Willebrand factor A	0.858	0.072	0.625	7.2e-38
RGD|1308772	1905	Vwa8 "von Willebrand factor A	0.833	0.070	0.629	8.3e-37
FB|FBgn0040234	1386	c12.2 "c12.2" [Drosophila mela	0.901	0.105	0.549	2.9e-36

UNIPROTKB|F1NXF1 F1NXF1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 441 (160.3 bits), Expect = 3.1e-40, P = 3.1e-40
 Identities = 94/154 (61%), Positives = 109/154 (70%)

Query:     8 QEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL 67
             Q Y +F+    F V TD+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLEL
Sbjct:    23 QNYRKFS----FKV-TDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLEL 77

Query:    68 TQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXX 127
             T+REVEYI LSRDTTE D+KQRREI +G+A Y DQ AVRAA EGR+L+LEG+EKA     
Sbjct:    78 TKREVEYIALSRDTTETDLKQRREIRDGSAFYLDQCAVRAATEGRILVLEGLEKAERNVL 137

Query:   128 XXXXXXXXXXXMHLEDGRFLVSASTYDKLLQVET 161
                        M LEDGRFL+SA  YDKLLQ  T
Sbjct:   138 PVLNNLLENREMQLEDGRFLMSAERYDKLLQDHT 171

GO:0016887 "ATPase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

UNIPROTKB|I3LJL2 LOC100511470 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 88/141 (62%), Positives = 100/141 (70%)

Query:    23 TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
             +D++ Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct:    82 SDSVAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 141

Query:    83 EADIKQRREIVNGTAIYYDQS--AVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMH 140
             E D+KQRREI  GTA Y DQ   AVRAA EGR L+LEG+EKA                M 
Sbjct:   142 ETDLKQRREIRAGTAFYIDQKQCAVRAATEGRTLVLEGLEKAERNVLPVLNNLLENREMQ 201

Query:   141 LEDGRFLVSASTYDKLLQVET 161
             LEDGRFL+SA  YDKLLQ  T
Sbjct:   202 LEDGRFLMSAERYDKLLQDHT 222

GO:0016887 "ATPase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1MIM5 Bt.110663 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 426 (155.0 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 88/139 (63%), Positives = 99/139 (71%)

Query:    23 TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
             +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT++E EYI LSRDTT
Sbjct:     2 SDSLAQSVIQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKKEAEYIALSRDTT 61

Query:    83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLE 142
             E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKA                M LE
Sbjct:    62 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 121

Query:   143 DGRFLVSASTYDKLLQVET 161
             DGRFL+SA  YDKLLQ  T
Sbjct:   122 DGRFLMSAERYDKLLQDHT 140

GO:0005524 "ATP binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

UNIPROTKB|A3KMH1 VWA8 "von Willebrand factor A domain-containing protein 8" [Homo sapiens (taxid:9606)]

 Score = 428 (155.7 bits), Expect = 1.3e-38, P = 1.3e-38
 Identities = 89/139 (64%), Positives = 100/139 (71%)

Query:    23 TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
             +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct:    82 SDSLAQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 141

Query:    83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLE 142
             E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKA                M LE
Sbjct:   142 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 201

Query:   143 DGRFLVSASTYDKLLQVET 161
             DGRFL+SA  YDKLL+  T
Sbjct:   202 DGRFLMSAERYDKLLRDHT 220

GO:0016887 "ATPase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005576 "extracellular region" evidence=IEA

UNIPROTKB|F1MIT3 Bt.110663 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 426 (155.0 bits), Expect = 2.0e-38, P = 2.0e-38
 Identities = 88/139 (63%), Positives = 99/139 (71%)

Query:    23 TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
             +D+L Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT++E EYI LSRDTT
Sbjct:     2 SDSLAQSVIQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKKEAEYIALSRDTT 61

Query:    83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLE 142
             E D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKA                M LE
Sbjct:    62 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 121

Query:   143 DGRFLVSASTYDKLLQVET 161
             DGRFL+SA  YDKLLQ  T
Sbjct:   122 DGRFLMSAERYDKLLQDHT 140

GO:0005739 "mitochondrion" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

ZFIN|ZDB-GENE-070912-407 vwa8 "von Willebrand factor A domain containing 8" [Danio rerio (taxid:7955)]

 Score = 425 (154.7 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 87/138 (63%), Positives = 100/138 (72%)

Query:    24 DALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTE 83
             +AL Q    HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT+REVEY+ LSRDTTE
Sbjct:    75 EALPQMVTQHLRWIMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYVALSRDTTE 134

Query:    84 ADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLED 143
              D+KQRREI +GTA Y DQ AVRAA EGR+L+LEG+EKA                M LED
Sbjct:   135 TDLKQRREIRSGTAFYIDQCAVRAATEGRILVLEGLEKAERNVLPVLNNLLENREMQLED 194

Query:   144 GRFLVSASTYDKLLQVET 161
             GRFL+SA  YDKLL+  T
Sbjct:   195 GRFLMSAHRYDKLLEEHT 212

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1PD22 VWA8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 422 (153.6 bits), Expect = 5.6e-38, P = 5.6e-38
 Identities = 86/139 (61%), Positives = 101/139 (72%)

Query:    23 TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
             +D++ Q  + HL+W++QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct:    81 SDSVVQSVIQHLKWMMQKDLLGQDVFLIGPPGPLRRSIAMQYLELTKREVEYIALSRDTT 140

Query:    83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLE 142
             E+D+KQRREI  GTA Y DQ AVRAA EGR LILEG+EKA                M LE
Sbjct:   141 ESDLKQRREIRAGTAFYIDQCAVRAATEGRTLILEGLEKAERNVLPVLNNLLENREMQLE 200

Query:   143 DGRFLVSASTYDKLLQVET 161
             DGRFL+S+  YDKLLQ  T
Sbjct:   201 DGRFLMSSERYDKLLQDHT 219

GO:0005739 "mitochondrion" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

MGI|MGI:1919008 Vwa8 "von Willebrand factor A domain containing 8" [Mus musculus (taxid:10090)]

 Score = 421 (153.3 bits), Expect = 7.2e-38, P = 7.2e-38
 Identities = 87/139 (62%), Positives = 99/139 (71%)

Query:    23 TDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT 82
             +D+  Q  + HLRW++QKD + QDVFLIG PG LRRS+AM YLELT+REVEYI LSRDTT
Sbjct:    81 SDSPAQSIVQHLRWLMQKDLLGQDVFLIGPPGPLRRSVAMQYLELTKREVEYIALSRDTT 140

Query:    83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLE 142
             E D+KQRREI  GTA Y DQ AVRAA EGR L+LEG+EKA                M LE
Sbjct:   141 ETDLKQRREIRAGTAFYIDQCAVRAATEGRTLVLEGLEKAERNVLPVLNNLLENREMQLE 200

Query:   143 DGRFLVSASTYDKLLQVET 161
             DGRFL+SA  YDKLLQ  T
Sbjct:   201 DGRFLMSAERYDKLLQDHT 219

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005524 "ATP binding" evidence=IEA

GO:0005576 "extracellular region" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0008150 "biological_process" evidence=ND

GO:0016887 "ATPase activity" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

RGD|1308772 Vwa8 "von Willebrand factor A domain containing 8" [Rattus norvegicus (taxid:10116)]

 Score = 411 (149.7 bits), Expect = 8.3e-37, P = 8.3e-37
 Identities = 85/135 (62%), Positives = 97/135 (71%)

Query:    27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADI 86
             +Q  + HLRWI+QKD + QDVFLIG PG LRRS+AM YLELT++EVEYI LSRDTTE D+
Sbjct:    85 SQSVVQHLRWIMQKDLLGQDVFLIGPPGPLRRSVAMQYLELTKQEVEYIALSRDTTETDL 144

Query:    87 KQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXXXXXXXXXXXXXMHLEDGRF 146
             KQRREI  GTA Y DQ AVRAA EGR L+LEG+EKA                M LEDGRF
Sbjct:   145 KQRREIRAGTAFYIDQCAVRAATEGRTLVLEGLEKAERNVLPVLNNLLENREMQLEDGRF 204

Query:   147 LVSASTYDKLLQVET 161
             L+SA  YDKLL+  T
Sbjct:   205 LMSAERYDKLLRDHT 219

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISO

GO:0016887 "ATPase activity" evidence=IEA

FB|FBgn0040234 c12.2 "c12.2" [Drosophila melanogaster (taxid:7227)]

 Score = 404 (147.3 bits), Expect = 2.9e-36, P = 2.9e-36
 Identities = 83/151 (54%), Positives = 106/151 (70%)

Query:     8 QEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL 67
             Q+YV++      S  T  L+Q  L HLRW+LQKD + QD+FL+G+PG LRR LAM +LEL
Sbjct:    62 QQYVKYA-----SDGTLQLSQSALHHLRWMLQKDALRQDMFLLGQPGPLRRQLAMQFLEL 116

Query:    68 TQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAXXXXX 127
             TQREVEY+ LSRDTTE+D+KQRREI +  AI++DQ AVRAA+ GRVL+L+G+E A     
Sbjct:   117 TQREVEYVALSRDTTESDLKQRREINDRAAIFHDQGAVRAALNGRVLVLDGVEHAERNVL 176

Query:   128 XXXXXXXXXXXMHLEDGRFLVSASTYDKLLQ 158
                        MHLE G+FL+S   YDKLL+
Sbjct:   177 PILNNLLENREMHLESGKFLMSPERYDKLLE 207

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005524 "ATP binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B0R0T1	VWA8_DANRE	No assigned EC number	0.7463	0.8456	0.0722	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	162
pfam07728	135	pfam07728, AAA_5, AAA domain (dynein-related subfa	1e-33

>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily)

 Score =  114 bits (288), Expect = 1e-33
 Identities = 45/110 (40%), Positives = 63/110 (57%), Gaps = 1/110 (0%)

Query: 46  DVFLIGKPGSLRRSLAMSYLE-LTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA 104
            V L+G PG+ +  LA      L+ R V Y+ L+RDTTE D+K RR I  G A + D   
Sbjct: 1   GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60

Query: 105 VRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYD 154
           VRAA EG + +L+ I +A  +VL  L +LL+ R + L +G  LV A+   
Sbjct: 61  VRAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDG 110

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 135

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	162
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.95
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.93
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.93
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	99.9
PF07726	131	AAA_3: ATPase family associated with various cellu	99.88
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	99.87
COG0714	329	MoxR-like ATPases [General function prediction onl	99.87
PHA02244	383	ATPase-like protein	99.87
KOG1808|consensus	1856		99.85
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.74
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.6
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.6
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.58
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.58
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.58
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.56
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.55
PRK13531	498	regulatory ATPase RavA; Provisional	99.54
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.51
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.49
KOG2004|consensus	906		99.48
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.46
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.46
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.45
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.45
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.44
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.43
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.4
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.38
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	99.36
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.36
COG0606	490	Predicted ATPase with chaperone activity [Posttran	99.35
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.35
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.35
KOG2028|consensus	554		99.34
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.34
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.34
PRK09862	506	putative ATP-dependent protease; Provisional	99.34
CHL00095	821	clpC Clp protease ATP binding subunit	99.33
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.32
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.32
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.3
PRK13342	413	recombination factor protein RarA; Reviewed	99.29
PF00004	132	AAA: ATPase family associated with various cellula	99.28
smart00350	509	MCM minichromosome maintenance proteins.	99.28
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	99.28
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.27
PRK10865	857	protein disaggregation chaperone; Provisional	99.22
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.21
PHA02544	316	44 clamp loader, small subunit; Provisional	99.19
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.19
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.18
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.17
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.15
PRK13341	725	recombination factor protein RarA/unknown domain f	99.12
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.11
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.11
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.1
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.09
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.09
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.08
PRK04195	482	replication factor C large subunit; Provisional	99.08
PLN03025	319	replication factor C subunit; Provisional	99.08
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.07
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.07
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.07
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.06
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.06
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.06
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.05
KOG1051|consensus	898		99.05
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	99.04
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.03
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.02
KOG0743|consensus	457		99.01
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.01
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.0
CHL00181	287	cbbX CbbX; Provisional	99.0
COG2204	464	AtoC Response regulator containing CheY-like recei	98.99
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.99
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.98
KOG0733|consensus	802		98.98
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.97
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.97
smart00382	148	AAA ATPases associated with a variety of cellular	98.96
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	98.96
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.95
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.94
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.94
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.93
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.93
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.92
PRK12377	248	putative replication protein; Provisional	98.92
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.91
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.91
PRK08084	235	DNA replication initiation factor; Provisional	98.9
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.9
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.89
PRK08116	268	hypothetical protein; Validated	98.89
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.89
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.88
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.88
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.87
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.87
CHL00195	489	ycf46 Ycf46; Provisional	98.86
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.86
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.85
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.85
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.84
CHL00176	638	ftsH cell division protein; Validated	98.84
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.84
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.84
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.83
PRK07952	244	DNA replication protein DnaC; Validated	98.83
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.83
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.82
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.82
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.81
KOG0989|consensus	346		98.81
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.81
PRK08181	269	transposase; Validated	98.8
PRK06620	214	hypothetical protein; Validated	98.8
PF13173	128	AAA_14: AAA domain	98.8
PRK15115	444	response regulator GlrR; Provisional	98.79
PRK12402	337	replication factor C small subunit 2; Reviewed	98.79
PRK10865	857	protein disaggregation chaperone; Provisional	98.79
KOG0734|consensus	752		98.79
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.78
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.77
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.77
KOG0727|consensus	408		98.77
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.76
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	98.76
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.75
KOG0745|consensus	564		98.75
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	98.75
PRK06893	229	DNA replication initiation factor; Validated	98.73
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.73
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.73
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.72
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.72
PRK06526	254	transposase; Provisional	98.72
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.72
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.71
CHL00095	821	clpC Clp protease ATP binding subunit	98.71
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.7
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.69
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.69
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.69
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.69
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	98.69
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.69
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.68
KOG1969|consensus	877		98.68
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.67
PRK08939	306	primosomal protein DnaI; Reviewed	98.67
KOG0478|consensus	804		98.67
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.66
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	98.66
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.66
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.66
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.65
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.64
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	98.64
PRK08727	233	hypothetical protein; Validated	98.64
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.63
PRK06921	266	hypothetical protein; Provisional	98.63
PRK13765	637	ATP-dependent protease Lon; Provisional	98.62
KOG1808|consensus	1856		98.62
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.62
PRK05642	234	DNA replication initiation factor; Validated	98.62
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.61
PRK09183	259	transposase/IS protein; Provisional	98.6
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.6
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.6
KOG0480|consensus	764		98.6
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.58
CHL00206	2281	ycf2 Ycf2; Provisional	98.58
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	98.57
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.56
KOG0738|consensus	491		98.56
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.54
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.54
KOG0737|consensus	386		98.54
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	98.52
PRK06835	329	DNA replication protein DnaC; Validated	98.51
KOG0733|consensus	802		98.51
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.51
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.51
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.5
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	98.49
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.49
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.48
KOG0731|consensus	774		98.48
KOG0991|consensus	333		98.47
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.46
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.46
KOG0735|consensus	952		98.45
PRK08058	329	DNA polymerase III subunit delta'; Validated	98.45
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.44
KOG0742|consensus	630		98.44
KOG0730|consensus	693		98.44
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.43
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.4
KOG0477|consensus	854		98.4
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	98.4
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.4
PRK09087	226	hypothetical protein; Validated	98.38
PRK12422	445	chromosomal replication initiation protein; Provis	98.36
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.36
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.36
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.35
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.35
KOG0739|consensus	439		98.31
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	98.31
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.3
KOG0651|consensus	388		98.27
PHA00729	226	NTP-binding motif containing protein	98.25
KOG0726|consensus	440		98.25
KOG0741|consensus	744		98.25
PRK04296	190	thymidine kinase; Provisional	98.23
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.22
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	98.22
KOG0736|consensus	953		98.21
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.21
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	98.21
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.2
KOG0652|consensus	424		98.19
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.18
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	98.17
KOG0741|consensus	744		98.15
PRK13947	171	shikimate kinase; Provisional	98.13
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.13
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	98.11
KOG0729|consensus	435		98.11
PRK00131	175	aroK shikimate kinase; Reviewed	98.11
PRK10536	262	hypothetical protein; Provisional	98.11
KOG0728|consensus	404		98.08
PRK08118	167	topology modulation protein; Reviewed	98.08
KOG3347|consensus	176		98.07
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.07
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	98.07
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.06
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	98.06
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	98.06
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	98.06
PHA02774	613	E1; Provisional	98.05
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.04
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	98.04
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.03
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.03
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	98.03
PRK03839	180	putative kinase; Provisional	98.02
cd01128	249	rho_factor Transcription termination factor rho is	98.02
KOG2170|consensus	344		98.01
PRK13695	174	putative NTPase; Provisional	98.01
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	98.0
PRK00625	173	shikimate kinase; Provisional	97.99
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	97.98
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	97.98
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.98
PRK14530	215	adenylate kinase; Provisional	97.96
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.96
PRK13949	169	shikimate kinase; Provisional	97.95
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.94
PRK14532	188	adenylate kinase; Provisional	97.94
PRK13946	184	shikimate kinase; Provisional	97.93
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.91
PRK03731	171	aroL shikimate kinase II; Reviewed	97.91
KOG0730|consensus	693		97.91
PRK07261	171	topology modulation protein; Provisional	97.91
COG4178	604	ABC-type uncharacterized transport system, permeas	97.9
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.9
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.89
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.89
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.89
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.89
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	97.88
PRK14531	183	adenylate kinase; Provisional	97.87
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.87
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	97.86
PRK06217	183	hypothetical protein; Validated	97.86
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.86
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.86
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.86
KOG0482|consensus	721		97.85
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.85
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.84
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.83
KOG0481|consensus	729		97.83
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	97.82
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.81
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	97.81
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	97.81
PHA02624	647	large T antigen; Provisional	97.81
PRK06762	166	hypothetical protein; Provisional	97.81
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.8
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.8
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.79
PRK04132	846	replication factor C small subunit; Provisional	97.79
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.78
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	97.78
PRK05057	172	aroK shikimate kinase I; Reviewed	97.77
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.77
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.77
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.77
PLN02165	334	adenylate isopentenyltransferase	97.76
PRK02496	184	adk adenylate kinase; Provisional	97.75
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.75
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.74
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	97.74
PRK05917	290	DNA polymerase III subunit delta'; Validated	97.73
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.73
KOG0744|consensus	423		97.73
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.72
PRK14528	186	adenylate kinase; Provisional	97.72
KOG0740|consensus	428		97.72
cd03246	173	ABCC_Protease_Secretion This family represents the	97.71
PLN02199	303	shikimate kinase	97.71
KOG0990|consensus	360		97.71
PF13245	76	AAA_19: Part of AAA domain	97.71
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	97.71
TIGR00767	415	rho transcription termination factor Rho. Members	97.69
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.68
PRK13948	182	shikimate kinase; Provisional	97.68
PRK04182	180	cytidylate kinase; Provisional	97.68
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.67
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.67
PTZ00088	229	adenylate kinase 1; Provisional	97.67
KOG0058|consensus	716		97.67
PRK05973	237	replicative DNA helicase; Provisional	97.66
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	97.66
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.66
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.66
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	97.65
PF07931	174	CPT: Chloramphenicol phosphotransferase-like prote	97.64
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	97.64
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	97.64
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.64
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.63
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	97.63
PRK04841	903	transcriptional regulator MalT; Provisional	97.62
TIGR02533	486	type_II_gspE general secretory pathway protein E.	97.62
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.62
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.61
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	97.61
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.61
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	97.6
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.59
PRK14527	191	adenylate kinase; Provisional	97.59
PRK06696	223	uridine kinase; Validated	97.58
PRK08233	182	hypothetical protein; Provisional	97.57
PRK15455	644	PrkA family serine protein kinase; Provisional	97.56
PRK00279	215	adk adenylate kinase; Reviewed	97.56
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.56
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	97.55
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.55
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	97.55
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	97.55
PLN02674	244	adenylate kinase	97.54
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.52
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	97.52
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	97.52
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.51
PRK06547	172	hypothetical protein; Provisional	97.51
cd03115	173	SRP The signal recognition particle (SRP) mediates	97.5
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	97.5
PLN02200	234	adenylate kinase family protein	97.5
PRK13851	344	type IV secretion system protein VirB11; Provision	97.49
PRK01184	184	hypothetical protein; Provisional	97.48
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	97.47
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	97.46
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	97.46
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.46
PF05729	166	NACHT: NACHT domain	97.45
PRK10436	462	hypothetical protein; Provisional	97.45
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.45
PRK14526	211	adenylate kinase; Provisional	97.45
PRK07132	299	DNA polymerase III subunit delta'; Validated	97.44
PRK04040	188	adenylate kinase; Provisional	97.44
PHA02530	300	pseT polynucleotide kinase; Provisional	97.43
PRK13975	196	thymidylate kinase; Provisional	97.43
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	97.42
PRK05541	176	adenylylsulfate kinase; Provisional	97.41
PRK10646	153	ADP-binding protein; Provisional	97.41
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	97.41
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	97.41
PRK00300	205	gmk guanylate kinase; Provisional	97.4
PRK09825	176	idnK D-gluconate kinase; Provisional	97.4
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	97.39
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.39
PRK14529	223	adenylate kinase; Provisional	97.39
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	97.37
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	97.37
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	97.36
PRK13764	602	ATPase; Provisional	97.36
PRK00889	175	adenylylsulfate kinase; Provisional	97.35
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.34
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	97.33
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.33
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	97.33
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	97.33
KOG0735|consensus	952		97.33
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.32
PRK05480	209	uridine/cytidine kinase; Provisional	97.31
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.3
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.29
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	97.29
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.29
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	97.29
KOG1970|consensus	634		97.28
TIGR00235	207	udk uridine kinase. Model contains a number of lon	97.27
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.26
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	97.25
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.25
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.25
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	97.24
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	97.24
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.24
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.24
KOG1942|consensus	456		97.23
PRK14738	206	gmk guanylate kinase; Provisional	97.23
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.22
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.22
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.21
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	97.21
KOG0479|consensus	818		97.21
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	97.2
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.2
PLN02459	261	probable adenylate kinase	97.2
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	97.19
PHA02653	675	RNA helicase NPH-II; Provisional	97.19
PRK12608	380	transcription termination factor Rho; Provisional	97.19
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.19
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.18
PRK04328	249	hypothetical protein; Provisional	97.18
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	97.17
COG0802	149	Predicted ATPase or kinase [General function predi	97.17
PRK12339	197	2-phosphoglycerate kinase; Provisional	97.17
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	97.17
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.17
COG4525	259	TauB ABC-type taurine transport system, ATPase com	97.16
KOG0060|consensus	659		97.15
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	97.13
PRK09376	416	rho transcription termination factor Rho; Provisio	97.13
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	97.13
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	97.13
PRK14974	336	cell division protein FtsY; Provisional	97.12
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.12
PRK08356	195	hypothetical protein; Provisional	97.12
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	97.11
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	97.11
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	97.1
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.1
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	97.1
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.1
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	97.09
PRK07667	193	uridine kinase; Provisional	97.09
PRK11545	163	gntK gluconate kinase 1; Provisional	97.08
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	97.08
PRK08099	399	bifunctional DNA-binding transcriptional repressor	97.06
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.06
COG1485	367	Predicted ATPase [General function prediction only	97.06
KOG0732|consensus	1080		97.06
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	97.05
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.05
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.05
PRK06067	234	flagellar accessory protein FlaH; Validated	97.04
PF00005	137	ABC_tran: ABC transporter This structure is on hol	97.04
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	97.04
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	97.04
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.04
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	97.04
PRK14730	195	coaE dephospho-CoA kinase; Provisional	97.03
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	97.03
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.03
KOG0927|consensus	614		97.03
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.02
PRK13973	213	thymidylate kinase; Provisional	97.01
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.01
PRK06761	282	hypothetical protein; Provisional	97.0
PRK09302	509	circadian clock protein KaiC; Reviewed	97.0
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.0
PLN03130	1622	ABC transporter C family member; Provisional	97.0
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	96.99
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	96.99
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	96.98
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	96.98
PRK06851	367	hypothetical protein; Provisional	96.98
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.98
KOG0922|consensus	674		96.98
KOG0736|consensus	953		96.98
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.98
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.96
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.96
PRK13808	333	adenylate kinase; Provisional	96.95
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.94
PF13555	62	AAA_29: P-loop containing region of AAA domain	96.94
cd01673	193	dNK Deoxyribonucleoside kinase (dNK) catalyzes the	96.94
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.93

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.95  E-value=1.9e-27  Score=202.39  Aligned_cols=124  Identities=15%  Similarity=0.182  Sum_probs=110.8

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCe--EEEeccHHHHHhhcC
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGT--AIYYDQSAVRAAIEG  111 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~--~~~~~gpl~~A~~~G  111 (162)
                      .++.++..+++++|+||||||||++++++|+.+|+|+.+++++++++..||+|...+  ++|.  +.|++||+..|+++|
T Consensus        56 ~vl~~l~~~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g  135 (327)
T TIGR01650        56 AICAGFAYDRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHN  135 (327)
T ss_pred             HHHHHHhcCCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCC
Confidence            355555568899999999999999999999999999999999999999999997554  3553  899999999999999


Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhc-CCeEEEcC-CcEEecCcchHhhhhh
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLE-NREMHLED-GRFLVSASTYDKLLQV  159 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle-~r~l~l~~-g~~i~~~~~f~~~~~~  159 (162)
                      .|+++||||+++|+++++|+++|| +|++++++ ++.+.+||+|+.++=+
T Consensus       136 ~illlDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~  185 (327)
T TIGR01650       136 VALCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATA  185 (327)
T ss_pred             eEEEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEee
Confidence            999999999999999999999999 57999986 7777799999988743

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.93  E-value=7.2e-26  Score=186.83  Aligned_cols=132  Identities=18%  Similarity=0.160  Sum_probs=115.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe-------------
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI-------------   92 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~-------------   92 (162)
                      .|+.+.+.++.++.....+.|++|+||||||||++|+++|+.+|.|+..++|+++++.+|++|.+.-             
T Consensus         3 ~t~~~~~l~~~~l~~l~~g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~   82 (262)
T TIGR02640         3 ETDAVKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHN   82 (262)
T ss_pred             CCHHHHHHHHHHHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHH
Confidence            4778888888888888889999999999999999999999999999999999999999999985321             


Q ss_pred             -----ecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC----CcEEecCcchHhhh
Q psy4122          93 -----VNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED----GRFLVSASTYDKLL  157 (162)
Q Consensus        93 -----~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~----g~~i~~~~~f~~~~  157 (162)
                           ......|.+||+..|+++|++|+|||||++++++++.|+++||+|.+.+++    +..+..|++|+.+.
T Consensus        83 ~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIa  156 (262)
T TIGR02640        83 VVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIF  156 (262)
T ss_pred             hhhhhcccceeecCchHHHHHHcCCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEE
Confidence                 124568999999999999999999999999999999999999999999986    35666888887653

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.93  E-value=7.8e-27  Score=173.77  Aligned_cols=101  Identities=37%  Similarity=0.487  Sum_probs=90.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCcc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERN  125 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~  125 (162)
                      ||+|+||||||||++|+.+|+.++.++..++++.+++.+||+|.+...++.+.|.+|++++|+++|.|++|||||+++++
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a~~~   80 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRAPPE   80 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG--HH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccCCHH
Confidence            69999999999999999999999999999999999999999998888899999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCeEEEcCCcE
Q psy4122         126 VLPVLNNLLENREMHLEDGRF  146 (162)
Q Consensus       126 v~~~L~~lle~r~l~l~~g~~  146 (162)
                      +++.|++++|++++.++++..
T Consensus        81 v~~~L~~ll~~~~~~~~~~~~  101 (139)
T PF07728_consen   81 VLESLLSLLEERRIQLPEGGE  101 (139)
T ss_dssp             HHHTTHHHHSSSEEEE-TSSS
T ss_pred             HHHHHHHHHhhCcccccCCCc
Confidence            999999999999999886443

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=99.90  E-value=7.2e-24  Score=203.57  Aligned_cols=152  Identities=16%  Similarity=0.197  Sum_probs=135.1

Q ss_pred             cceeceeeeecccCCCC-------CCHHHHHHHHHHHHhc-CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccC
Q psy4122           9 EYVRFTLIYLFSVNTDA-------LTQDWLSHLRWILQKD-NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRD   80 (162)
Q Consensus         9 ~y~~~~~~~~~~~~~~~-------~~~~~~~~L~~i~~~~-~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~   80 (162)
                      .|+.||+||...++...       +||-+-..+-.+..+. ...-|+|+.||+.+|||+++..+|..+|+.+.+++-|+.
T Consensus       845 ~yi~f~hyw~~~g~~~veeq~hyIiTPfVqkn~ln~~Ra~s~~~fP~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEH  924 (4600)
T COG5271         845 SYIAFCHYWKHGGSFPVEEQEHYIITPFVQKNYLNTMRAASLSNFPLLIQGPTSSGKTSMILYLARETGHKFVRINNHEH  924 (4600)
T ss_pred             cHHHHHHHHHhcCCCchhhcceeEecHHHHHHHHHHHHHHhhcCCcEEEecCCCCCcchHHHHHHHHhCccEEEecCccc
Confidence            59999999988766553       6898888665555543 355699999999999999999999999999999999999


Q ss_pred             CChhhhcceeEe-ecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc-CCeEEEcC-CcEEecCcchHhhh
Q psy4122          81 TTEADIKQRREI-VNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE-NREMHLED-GRFLVSASTYDKLL  157 (162)
Q Consensus        81 ~~~~dL~g~~~~-~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle-~r~l~l~~-g~~i~~~~~f~~~~  157 (162)
                      |+.++.+|.+.. .+|+..|++|.|+.|+|+|.|++|||+|.||.+|+++||++|| +|++.||+ -..++|||+|+.|+
T Consensus       925 TdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIVLDELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFA 1004 (4600)
T COG5271         925 TDLQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVLDELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFA 1004 (4600)
T ss_pred             chHHHHhhceeecCCCceeeehhHHHHHHhcCcEEEeeccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEe
Confidence            999999998765 5699999999999999999999999999999999999999998 58999997 78899999999988


Q ss_pred             hhh
Q psy4122         158 QVE  160 (162)
Q Consensus       158 ~~~  160 (162)
                      -|.
T Consensus      1005 TQN 1007 (4600)
T COG5271        1005 TQN 1007 (4600)
T ss_pred             ecC
Confidence            653

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.88  E-value=2.1e-22  Score=151.18  Aligned_cols=102  Identities=20%  Similarity=0.262  Sum_probs=77.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEee--cCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIV--NGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~--~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |+||+|+||+|||++|+++|+.+|..+.++++++|+.++||+|.....  .+.+.|.+||+.     .+++++|||||++
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif-----~~ill~DEiNrap   75 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIF-----TNILLADEINRAP   75 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT------SSEEEEETGGGS-
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhh-----hceeeecccccCC
Confidence            799999999999999999999999999999999999999999976554  588999999965     4799999999999


Q ss_pred             ccHHHHHHHhhcCCeEEE-------cCCcEEecCcc
Q psy4122         124 RNVLPVLNNLLENREMHL-------EDGRFLVSAST  152 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l-------~~g~~i~~~~~  152 (162)
                      |.++++|++++++|++.+       |+...++++.|
T Consensus        76 pktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqN  111 (131)
T PF07726_consen   76 PKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQN  111 (131)
T ss_dssp             HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-
T ss_pred             HHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecC
Confidence            999999999999998875       45666666655

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=99.87  E-value=2e-22  Score=193.89  Aligned_cols=133  Identities=22%  Similarity=0.282  Sum_probs=123.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee--EeecCeEEEeccHH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR--EIVNGTAIYYDQSA  104 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~--~~~~G~~~~~~gpl  104 (162)
                      +|.+...+++++.+...++|++|.|.||+|||+|+.++|+.+|..+.++++++.|+.-||.|..  ..++|.+.|.|.|+
T Consensus      1526 spTT~~Nl~rVlRAmqv~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapf 1605 (4600)
T COG5271        1526 SPTTTVNLRRVLRAMQVGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPF 1605 (4600)
T ss_pred             CCchHHhHHHHHHHHhcCCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHH
Confidence            7999999999999999999999999999999999999999999999999999999999999944  34679999999999


Q ss_pred             HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC-CeEEEcC-CcEEecCcchHhhhhh
Q psy4122         105 VRAAIEGRVLILEGIEKAERNVLPVLNNLLEN-REMHLED-GRFLVSASTYDKLLQV  159 (162)
Q Consensus       105 ~~A~~~G~vlllDEId~a~~~v~~~L~~lle~-r~l~l~~-g~~i~~~~~f~~~~~~  159 (162)
                      +.|||.|+|++|||+|.|+.+|++.||..||+ |+..||+ ...+..||+|+-|+-|
T Consensus      1606 L~amr~G~WVlLDEiNLaSQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaq 1662 (4600)
T COG5271        1606 LHAMRDGGWVLLDEINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQ 1662 (4600)
T ss_pred             HHHhhcCCEEEeehhhhhHHHHHHHHHHHHhhccccccccccceeeccCCeeeeeec
Confidence            99999999999999999999999999999996 5789997 7788899999987644

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.87  E-value=2.6e-22  Score=170.12  Aligned_cols=112  Identities=20%  Similarity=0.159  Sum_probs=101.2

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEee-----cCeEEEeccHH
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIV-----NGTAIYYDQSA  104 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~-----~G~~~~~~gpl  104 (162)
                      ..+.+..++.++..+.|++|.||||||||.+|+++|+.++.++.+++|+++++++|++|.+.+.     .+.+.|.+||+
T Consensus        29 ~~~~~~~~l~a~~~~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl  108 (329)
T COG0714          29 DEEVIELALLALLAGGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPL  108 (329)
T ss_pred             cHHHHHHHHHHHHcCCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCc
Confidence            3445566667777899999999999999999999999999999999999999999999966543     78899999999


Q ss_pred             HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         105 VRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       105 ~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      ..+++  +++++||||+++|+++++|+++|+++++++++
T Consensus       109 ~~~~~--~ill~DEInra~p~~q~aLl~~l~e~~vtv~~  145 (329)
T COG0714         109 FAAVR--VILLLDEINRAPPEVQNALLEALEERQVTVPG  145 (329)
T ss_pred             ccccc--eEEEEeccccCCHHHHHHHHHHHhCcEEEECC
Confidence            99887  89999999999999999999999999998875

>PHA02244 ATPase-like protein

Probab=99.87  E-value=6.5e-22  Score=170.90  Aligned_cols=140  Identities=15%  Similarity=0.165  Sum_probs=112.2

Q ss_pred             eceeeeecccCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeE
Q psy4122          12 RFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRRE   91 (162)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~   91 (162)
                      +.....-+.-+....+|.+......+......+.|+||+||||||||++|+++|+.++.|+.+++.  .++..++.|.  
T Consensus        87 ~~~~l~~~d~~~ig~sp~~~~~~~ri~r~l~~~~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~--l~d~~~L~G~--  162 (383)
T PHA02244         87 PAGDISGIDTTKIASNPTFHYETADIAKIVNANIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNA--IMDEFELKGF--  162 (383)
T ss_pred             CcCchhhCCCcccCCCHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhCCCEEEEec--ChHHHhhccc--
Confidence            334444444444455677777777777777788999999999999999999999999999887763  3445566652  


Q ss_pred             eecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcCCcEEecCcchHhhh
Q psy4122          92 IVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLL  157 (162)
Q Consensus        92 ~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~g~~i~~~~~f~~~~  157 (162)
                       .++...|++||+++|+++|++|+||||++++++++..|+++++++.+.+.++ .+.+|++|+.++
T Consensus       163 -i~~~g~~~dgpLl~A~~~GgvLiLDEId~a~p~vq~~L~~lLd~r~l~l~g~-~i~~h~~FRlIA  226 (383)
T PHA02244        163 -IDANGKFHETPFYEAFKKGGLFFIDEIDASIPEALIIINSAIANKFFDFADE-RVTAHEDFRVIS  226 (383)
T ss_pred             -ccccccccchHHHHHhhcCCEEEEeCcCcCCHHHHHHHHHHhccCeEEecCc-EEecCCCEEEEE
Confidence             2333479999999999999999999999999999999999999998888755 577888888775

>KOG1808|consensus

Probab=99.85  E-value=3.1e-21  Score=189.29  Aligned_cols=149  Identities=19%  Similarity=0.228  Sum_probs=135.4

Q ss_pred             eceeeeecccCCC-------CCCHHHHHHHHHHHHhcCCC-CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCCh
Q psy4122          12 RFTLIYLFSVNTD-------ALTQDWLSHLRWILQKDNMS-QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTE   83 (162)
Q Consensus        12 ~~~~~~~~~~~~~-------~~~~~~~~~L~~i~~~~~~g-~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~   83 (162)
                      +|+++|+.++...       .+|+.....+..|..+...| .|+||.||+|||||++++.+|+.+|+.+.+++.|.+|+.
T Consensus       400 ~~~~~~i~~gs~~~~~~~~~i~T~~vq~~la~~~~a~~~~~~pillqG~tssGKtsii~~la~~~g~~~vrinnhehtd~  479 (1856)
T KOG1808|consen  400 RFEGYWIPSGSELTSEATHYIITPRVQKNLADLARAISSGKFPILLQGPTSSGKTSIIKELARATGKNIVRINNHEHTDL  479 (1856)
T ss_pred             ccceeecCCCCccccccceeeccHHHHHHHHHHHHHHhcCCCCeEEecCcCcCchhHHHHHHHHhccCceehhccccchH
Confidence            7899999887544       37899999999999888877 599999999999999999999999999999999999999


Q ss_pred             hhhccee-EeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC-CeEEEcC-CcEEecCcchHhhhhhh
Q psy4122          84 ADIKQRR-EIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN-REMHLED-GRFLVSASTYDKLLQVE  160 (162)
Q Consensus        84 ~dL~g~~-~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~-r~l~l~~-g~~i~~~~~f~~~~~~~  160 (162)
                      .+++|++ ...+|+..|.+|+++.|+++|.|+++||+|.|+.+++++|++++++ |++.+|+ -+.+.+|++|..++++.
T Consensus       480 qeyig~y~~~~~g~l~freg~LV~Alr~G~~~vlD~lnla~~dvL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn  559 (1856)
T KOG1808|consen  480 QEYIGTYVADDNGDLVFREGVLVQALRNGDWIVLDELNLAPHDVLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQN  559 (1856)
T ss_pred             HHHHHhhhcCCCCCeeeehhHHHHHHHhCCEEEeccccccchHHHHHHHhhhhhhccccccccceeeccCcchhhhhhcc
Confidence            9999955 4578999999999999999999999999999999999999999997 9999998 55677888899888764

>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=99.74  E-value=1.1e-17  Score=136.31  Aligned_cols=99  Identities=13%  Similarity=0.251  Sum_probs=72.7

Q ss_pred             HHHHHHHHHHHHhcCC-C---CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKDNM-S---QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~-g---~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ++.+..++-++++... +   .|++|+||||+||||||+.+|+.+|.++...+...-....||.               .
T Consensus        30 ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k~~dl~---------------~   94 (233)
T PF05496_consen   30 EHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEKAGDLA---------------A   94 (233)
T ss_dssp             HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--SCHHHH---------------H
T ss_pred             HHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhhHHHHH---------------H
Confidence            6677777766665432 2   3799999999999999999999999998877664333356665               3


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ++..+.++.||+||||||+++.+++.|++.+|++.+.+
T Consensus        95 il~~l~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idi  132 (233)
T PF05496_consen   95 ILTNLKEGDILFIDEIHRLNKAQQEILLPAMEDGKIDI  132 (233)
T ss_dssp             HHHT--TT-EEEECTCCC--HHHHHHHHHHHHCSEEEE
T ss_pred             HHHhcCCCcEEEEechhhccHHHHHHHHHHhccCeEEE
Confidence            45567889999999999999999999999999999855

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.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=99.60  E-value=1.1e-15  Score=122.99  Aligned_cols=113  Identities=20%  Similarity=0.270  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEE--EEeccCCCh------hhhcceeEe------------ecCeEEEecc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEY--ICLSRDTTE------ADIKQRREI------------VNGTAIYYDQ  102 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~--v~~~~~~~~------~dL~g~~~~------------~~G~~~~~~g  102 (162)
                      .++|+||+||||||||++|+.++.++......  +....-.+.      ..++..+.+            .+|...+.+|
T Consensus        21 G~h~lLl~GppGtGKTmlA~~l~~lLP~l~~~e~le~~~i~s~~~~~~~~~~~~~~Pfr~phhs~s~~~liGgg~~~~PG  100 (206)
T PF01078_consen   21 GGHHLLLIGPPGTGKTMLARRLPSLLPPLTEEEALEVSKIYSVAGLGPDEGLIRQRPFRAPHHSASEAALIGGGRPPRPG  100 (206)
T ss_dssp             CC--EEEES-CCCTHHHHHHHHHHCS--CCEECCESS--S-TT---S---EEEE---EEEE-TT--HHHHHEEGGGEEE-
T ss_pred             CCCCeEEECCCCCCHHHHHHHHHHhCCCCchHHHhhhccccccccCCCCCceecCCCcccCCCCcCHHHHhCCCcCCCcC
Confidence            46899999999999999999999887532111  111111001      111111111            1233355666


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc-CCcEEecCcchHhhh
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE-DGRFLVSASTYDKLL  157 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~-~g~~i~~~~~f~~~~  157 (162)
                      -+  +..|+|||+|||++.+++++++.|.+.+|+|++.+. .|..+.-+.+|..++
T Consensus       101 ei--slAh~GVLflDE~~ef~~~vld~Lr~ple~g~v~i~R~~~~~~~Pa~f~lv~  154 (206)
T PF01078_consen  101 EI--SLAHRGVLFLDELNEFDRSVLDALRQPLEDGEVTISRAGGSVTYPARFLLVA  154 (206)
T ss_dssp             CG--GGGTTSEEEECETTTS-HHHHHHHHHHHHHSBEEEEETTEEEEEB--EEEEE
T ss_pred             HH--HHhcCCEEEechhhhcCHHHHHHHHHHHHCCeEEEEECCceEEEecccEEEE
Confidence            55  556999999999999999999999999999999997 488888888887653

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=99.60  E-value=2.7e-15  Score=130.31  Aligned_cols=96  Identities=20%  Similarity=0.250  Sum_probs=76.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH--h-
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA--A-  108 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A--~-  108 (162)
                      .-|++|+++.... +++|+|||||||||||+.+|..++.+++.++.. .....|+..              .+-+|  . 
T Consensus        37 ~~lrr~v~~~~l~-SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv-~~gvkdlr~--------------i~e~a~~~~  100 (436)
T COG2256          37 KPLRRAVEAGHLH-SMILWGPPGTGKTTLARLIAGTTNAAFEALSAV-TSGVKDLRE--------------IIEEARKNR  100 (436)
T ss_pred             chHHHHHhcCCCc-eeEEECCCCCCHHHHHHHHHHhhCCceEEeccc-cccHHHHHH--------------HHHHHHHHH
Confidence            3577888876655 899999999999999999999999998877664 224566652              22222  1 


Q ss_pred             --hcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         109 --IEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       109 --~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                        ....+|++|||+|++...|+.|++.+|+|.+++.+
T Consensus       101 ~~gr~tiLflDEIHRfnK~QQD~lLp~vE~G~iilIG  137 (436)
T COG2256         101 LLGRRTILFLDEIHRFNKAQQDALLPHVENGTIILIG  137 (436)
T ss_pred             hcCCceEEEEehhhhcChhhhhhhhhhhcCCeEEEEe
Confidence              22479999999999999999999999999999865

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.58  E-value=4.4e-15  Score=137.93  Aligned_cols=99  Identities=21%  Similarity=0.291  Sum_probs=84.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC---CceEEEEec---cCCChhhhcceeEeecCeEEEecc-HHHHHhhcC--cEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLS---RDTTEADIKQRREIVNGTAIYYDQ-SAVRAAIEG--RVLIL  116 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~---~~~~~~dL~g~~~~~~G~~~~~~g-pl~~A~~~G--~vlll  116 (162)
                      ..|+.||+|||||.||+++|..+.   ..+.++.++   +..+.+.|+|.   ..|...|.+| -|++|+|+.  .|++|
T Consensus       523 sFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIGa---PPGYVGyeeGG~LTEaVRr~PySViLl  599 (786)
T COG0542         523 SFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGA---PPGYVGYEEGGQLTEAVRRKPYSVILL  599 (786)
T ss_pred             EEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhCC---CCCCceeccccchhHhhhcCCCeEEEe
Confidence            368899999999999999999886   678888887   45568889984   5666666664 578999876  59999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCeEEEcCCcEE
Q psy4122         117 EGIEKAERNVLPVLNNLLENREMHLEDGRFL  147 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~l~l~~g~~i  147 (162)
                      |||.+|+|+|++.|+++||+|+++-..|+.+
T Consensus       600 DEIEKAHpdV~nilLQVlDdGrLTD~~Gr~V  630 (786)
T COG0542         600 DEIEKAHPDVFNLLLQVLDDGRLTDGQGRTV  630 (786)
T ss_pred             chhhhcCHHHHHHHHHHhcCCeeecCCCCEE
Confidence            9999999999999999999999998877665

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=99.58  E-value=6.5e-15  Score=123.48  Aligned_cols=99  Identities=18%  Similarity=0.249  Sum_probs=83.6

Q ss_pred             HHHHHHHHHHHHhcCCC----CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKDNMS----QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g----~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      +...++|+-.+++...+    .|+||+||||.||||||..+|..+|..+...+...--.+.||.               .
T Consensus        32 ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~gDla---------------a   96 (332)
T COG2255          32 EKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPGDLA---------------A   96 (332)
T ss_pred             HHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccChhhHH---------------H
Confidence            67888888777664422    3899999999999999999999999998877666554577776               5


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ++..+.+|.|++||||||+++.+-+.|++.||+-++-+
T Consensus        97 iLt~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI  134 (332)
T COG2255          97 ILTNLEEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDI  134 (332)
T ss_pred             HHhcCCcCCeEEEehhhhcChhHHHHhhhhhhheeEEE
Confidence            67778999999999999999999999999999988754

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.58  E-value=3.4e-15  Score=127.84  Aligned_cols=95  Identities=16%  Similarity=0.230  Sum_probs=75.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh-------CCceE------------------------EEEeccCCChhhhcceeE--
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT-------QREVE------------------------YICLSRDTTEADIKQRRE--   91 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l-------g~p~~------------------------~v~~~~~~~~~dL~g~~~--   91 (162)
                      .++||.|+||+|||++|+.+|.++       +.|+.                        .++++.+++.+.|+|...  
T Consensus        30 ~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~  109 (334)
T PRK13407         30 GGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIE  109 (334)
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCCcccccCCccccCCCCCCcceeecchhhh
Confidence            599999999999999999999998       32211                        122445556666777432  


Q ss_pred             --eecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122          92 --IVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus        92 --~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                        +..|.+.+++|++.+|  ++|+|++||||++++++++.|.++|+++++.+
T Consensus       110 ~~l~~g~~~~~~G~l~~A--~~GiL~lDEInrl~~~~q~~Lle~mee~~v~v  159 (334)
T PRK13407        110 RALTRGEKAFEPGLLARA--NRGYLYIDEVNLLEDHIVDLLLDVAQSGENVV  159 (334)
T ss_pred             hhhhcCCeeecCCceEEc--CCCeEEecChHhCCHHHHHHHHHHHHcCCeEE
Confidence              3468899999998654  78999999999999999999999999998755

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.56  E-value=2.3e-14  Score=126.76  Aligned_cols=105  Identities=19%  Similarity=0.187  Sum_probs=79.9

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-----ceEEEEeccCCChhhhcceeEeecCeEEEeccHHHH-
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-----EVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVR-  106 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-----p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~-  106 (162)
                      .++.++..+..+++++|+||||||||++|+++|..++.     .+..+++|...+.+|+++...-.+....+.+|++.+ 
T Consensus       183 ~le~l~~~L~~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~  262 (459)
T PRK11331        183 TIETILKRLTIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNF  262 (459)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHH
Confidence            34455555667899999999999999999999988753     355788999999999985322223457788998743 


Q ss_pred             ---Hhh---cCcEEEEeCCCCCCcc-HHHHHHHhhcCC
Q psy4122         107 ---AAI---EGRVLILEGIEKAERN-VLPVLNNLLENR  137 (162)
Q Consensus       107 ---A~~---~G~vlllDEId~a~~~-v~~~L~~lle~r  137 (162)
                         |..   ++.+|+||||||++.+ +...|.++||++
T Consensus       263 ~~~A~~~p~~~~vliIDEINRani~kiFGel~~lLE~~  300 (459)
T PRK11331        263 CQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHD  300 (459)
T ss_pred             HHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhcccc
Confidence               332   3579999999999976 588889999853

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.55  E-value=7.8e-15  Score=114.68  Aligned_cols=94  Identities=26%  Similarity=0.261  Sum_probs=66.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC----ceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR----EVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEK  121 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~----p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~  121 (162)
                      +++|.||+|||||.+|+++|+.+..    ++.++.++.-++..+....  + .......  +......+++||+||||+|
T Consensus         5 ~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~--~-~~l~~~~--~~~v~~~~~gVVllDEidK   79 (171)
T PF07724_consen    5 NFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESS--V-SKLLGSP--PGYVGAEEGGVVLLDEIDK   79 (171)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCH--C-HHHHHHT--TCHHHHHHHTEEEEETGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhh--h-hhhhhcc--cceeeccchhhhhhHHHhh
Confidence            6899999999999999999999995    7888888754442111100  0 0000000  1112345667999999999


Q ss_pred             CCc-----------cHHHHHHHhhcCCeEEEcCC
Q psy4122         122 AER-----------NVLPVLNNLLENREMHLEDG  144 (162)
Q Consensus       122 a~~-----------~v~~~L~~lle~r~l~l~~g  144 (162)
                      +++           +|++.|++++|++.+.-..|
T Consensus        80 a~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g  113 (171)
T PF07724_consen   80 AHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYG  113 (171)
T ss_dssp             CSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTC
T ss_pred             ccccccccchhhHHHHHHHHHHHhcccceecccc
Confidence            999           99999999999999986655

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.54  E-value=2e-14  Score=128.16  Aligned_cols=105  Identities=22%  Similarity=0.243  Sum_probs=78.9

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEeccCCChhhhcceeEe----ecCeE-EEeccHH
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR--EVEYICLSRDTTEADIKQRREI----VNGTA-IYYDQSA  104 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~~~~~~~~dL~g~~~~----~~G~~-~~~~gpl  104 (162)
                      +.++.++.+...+.|+||+||||||||++|+.+|...+.  ++....+. -++++||+|...+    ..|.+ .+..|++
T Consensus        27 ~vI~lll~aalag~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~-fttp~DLfG~l~i~~~~~~g~f~r~~~G~L  105 (498)
T PRK13531         27 HAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTR-FSTPEEVFGPLSIQALKDEGRYQRLTSGYL  105 (498)
T ss_pred             HHHHHHHHHHccCCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeee-ecCcHHhcCcHHHhhhhhcCchhhhcCCcc
Confidence            445566667778999999999999999999999998764  44444443 1257799884322    24554 3555654


Q ss_pred             HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         105 VRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       105 ~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|    .++++|||+++++.+++.|+++|++|.++.
T Consensus       106 ~~A----~lLfLDEI~rasp~~QsaLLeam~Er~~t~  138 (498)
T PRK13531        106 PEA----EIVFLDEIWKAGPAILNTLLTAINERRFRN  138 (498)
T ss_pred             ccc----cEEeecccccCCHHHHHHHHHHHHhCeEec
Confidence            333    599999999999999999999999999876

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.51  E-value=6.7e-14  Score=130.69  Aligned_cols=97  Identities=21%  Similarity=0.266  Sum_probs=77.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCC---ChhhhcceeEeecCeEEEec-cHHHHHhhc--CcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDT---TEADIKQRREIVNGTAIYYD-QSAVRAAIE--GRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~---~~~dL~g~~~~~~G~~~~~~-gpl~~A~~~--G~vlllDEI  119 (162)
                      ++||+||||||||.+|+.+|+.++.++.++.|+.-+   +.++|+|.+   .|...+.. |.+.++++.  .+|++||||
T Consensus       490 ~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~---~gyvg~~~~g~L~~~v~~~p~sVlllDEi  566 (758)
T PRK11034        490 SFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAP---PGYVGFDQGGLLTDAVIKHPHAVLLLDEI  566 (758)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCC---CCcccccccchHHHHHHhCCCcEEEeccH
Confidence            589999999999999999999999999999887533   367777742   34333333 467777654  369999999


Q ss_pred             CCCCccHHHHHHHhhcCCeEEEcCCc
Q psy4122         120 EKAERNVLPVLNNLLENREMHLEDGR  145 (162)
Q Consensus       120 d~a~~~v~~~L~~lle~r~l~l~~g~  145 (162)
                      +++++++++.|+++||+|.++-..|+
T Consensus       567 eka~~~v~~~LLq~ld~G~ltd~~g~  592 (758)
T PRK11034        567 EKAHPDVFNLLLQVMDNGTLTDNNGR  592 (758)
T ss_pred             hhhhHHHHHHHHHHHhcCeeecCCCc
Confidence            99999999999999999998765554

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.49  E-value=1.2e-13  Score=126.87  Aligned_cols=89  Identities=22%  Similarity=0.319  Sum_probs=74.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee-EeecCeEEEeccHHHHHhhc----CcEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR-EIVNGTAIYYDQSAVRAAIE----GRVLILE  117 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~-~~~~G~~~~~~gpl~~A~~~----G~vlllD  117 (162)
                      .|--+||+||||+|||+|++.+|+.+|+++.++++.+-.+.+++.|++ +..|.    .+|-++++|++    ..+++||
T Consensus       349 kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRRTYIGa----mPGrIiQ~mkka~~~NPv~LLD  424 (782)
T COG0466         349 KGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGA----MPGKIIQGMKKAGVKNPVFLLD  424 (782)
T ss_pred             CCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhcccccccccc----CChHHHHHHHHhCCcCCeEEee
Confidence            444689999999999999999999999999999999888899999944 43332    46678888764    4789999


Q ss_pred             CCCCCCcc----HHHHHHHhhc
Q psy4122         118 GIEKAERN----VLPVLNNLLE  135 (162)
Q Consensus       118 EId~a~~~----v~~~L~~lle  135 (162)
                      |||+++.+    -.++|+.+||
T Consensus       425 EIDKm~ss~rGDPaSALLEVLD  446 (782)
T COG0466         425 EIDKMGSSFRGDPASALLEVLD  446 (782)
T ss_pred             chhhccCCCCCChHHHHHhhcC
Confidence            99998876    4789999998

>KOG2004|consensus

Probab=99.48  E-value=1.5e-13  Score=126.19  Aligned_cols=105  Identities=18%  Similarity=0.232  Sum_probs=84.8

Q ss_pred             CHHHHHHHHHHHHhc----CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee-EeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKD----NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR-EIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~----~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~-~~~~G~~~~~~  101 (162)
                      .+-..+.|+.+....    ..|+-+||+||||+|||++++.+|+++|+.+.++++.+-++.+|+.|++ +..+.    .+
T Consensus       417 ~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRRTYVGA----MP  492 (906)
T KOG2004|consen  417 EDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGA----MP  492 (906)
T ss_pred             HHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhcccceeeecc----CC
Confidence            344555666666543    3567899999999999999999999999999999999999999999943 44332    56


Q ss_pred             cHHHHHhhc----CcEEEEeCCCCCCc----cHHHHHHHhhc
Q psy4122         102 QSAVRAAIE----GRVLILEGIEKAER----NVLPVLNNLLE  135 (162)
Q Consensus       102 gpl~~A~~~----G~vlllDEId~a~~----~v~~~L~~lle  135 (162)
                      |-+++|++.    ..+++|||||+...    |-.++|+.+||
T Consensus       493 GkiIq~LK~v~t~NPliLiDEvDKlG~g~qGDPasALLElLD  534 (906)
T KOG2004|consen  493 GKIIQCLKKVKTENPLILIDEVDKLGSGHQGDPASALLELLD  534 (906)
T ss_pred             hHHHHHHHhhCCCCceEEeehhhhhCCCCCCChHHHHHHhcC
Confidence            788888864    57999999999776    45789999998

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.46  E-value=3.5e-13  Score=112.18  Aligned_cols=96  Identities=17%  Similarity=0.226  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHHhcC----CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHH
Q psy4122          29 DWLSHLRWILQKDN----MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA  104 (162)
Q Consensus        29 ~~~~~L~~i~~~~~----~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl  104 (162)
                      +.++.|+.++....    ...+++|+||||||||++|+++|+.++.++............++.               ..
T Consensus        11 ~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~---------------~~   75 (305)
T TIGR00635        11 KVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLA---------------AI   75 (305)
T ss_pred             HHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHH---------------HH
Confidence            34555666665321    224799999999999999999999999887655544332333333               23


Q ss_pred             HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         105 VRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       105 ~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      ..++..+.+++||||++++++.++.|.++++++..
T Consensus        76 l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~  110 (305)
T TIGR00635        76 LTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRL  110 (305)
T ss_pred             HHhcccCCEEEEehHhhhCHHHHHHhhHHHhhhhe
Confidence            45667789999999999999999999999987664

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.46  E-value=3.6e-13  Score=125.34  Aligned_cols=97  Identities=21%  Similarity=0.250  Sum_probs=76.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccC---CChhhhcceeEeecCeEEEecc-HHHHHhhc--CcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRD---TTEADIKQRREIVNGTAIYYDQ-SAVRAAIE--GRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~---~~~~dL~g~~~~~~G~~~~~~g-pl~~A~~~--G~vlllDEI  119 (162)
                      +++|+||||||||++|+.+|+.++.++.++.++.-   .+.+.++|.+   .|...+.++ .+.++++.  .+|++||||
T Consensus       486 ~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~---~gyvg~~~~~~l~~~~~~~p~~VvllDEi  562 (731)
T TIGR02639       486 SFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAP---PGYVGFEQGGLLTEAVRKHPHCVLLLDEI  562 (731)
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCC---CCCcccchhhHHHHHHHhCCCeEEEEech
Confidence            37999999999999999999999999988888643   2456677642   333334443 46777754  379999999


Q ss_pred             CCCCccHHHHHHHhhcCCeEEEcCCc
Q psy4122         120 EKAERNVLPVLNNLLENREMHLEDGR  145 (162)
Q Consensus       120 d~a~~~v~~~L~~lle~r~l~l~~g~  145 (162)
                      +++++++++.|++++|+|.++...|+
T Consensus       563 eka~~~~~~~Ll~~ld~g~~~d~~g~  588 (731)
T TIGR02639       563 EKAHPDIYNILLQVMDYATLTDNNGR  588 (731)
T ss_pred             hhcCHHHHHHHHHhhccCeeecCCCc
Confidence            99999999999999999998754443

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.45  E-value=6.4e-14  Score=127.73  Aligned_cols=107  Identities=16%  Similarity=0.175  Sum_probs=83.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEeccCCChhhhcceeE----eecCeEEEeccHHHHHhhcCcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR--EVEYICLSRDTTEADIKQRRE----IVNGTAIYYDQSAVRAAIEGRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~~~~~~~~dL~g~~~----~~~G~~~~~~gpl~~A~~~G~vlllDEI  119 (162)
                      +|||.|+||+|||++|+.++..++.  |+..+++  ..+...|.|...    +.+|.+.|++|++.+|  +|++|+||||
T Consensus        18 ~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~--~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A--~~GvL~lDEi   93 (589)
T TIGR02031        18 GVAIRARAGTGKTALARALAEILPPIMPFVELPL--GVTEDRLIGGIDVEESLAGGQRVTQPGLLDEA--PRGVLYVDMA   93 (589)
T ss_pred             eEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCc--ccchhhcccchhhhhhhhcCcccCCCCCeeeC--CCCcEeccch
Confidence            8999999999999999999998875  4555554  456677777533    3468888999998765  8899999999


Q ss_pred             CCCCccHHHHHHHhhcCCeEEEc-CCcEEecCcchHhh
Q psy4122         120 EKAERNVLPVLNNLLENREMHLE-DGRFLVSASTYDKL  156 (162)
Q Consensus       120 d~a~~~v~~~L~~lle~r~l~l~-~g~~i~~~~~f~~~  156 (162)
                      |++++++++.|..+|+++.+++. +|.....+.+|+.+
T Consensus        94 ~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lI  131 (589)
T TIGR02031        94 NLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALI  131 (589)
T ss_pred             hhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEE
Confidence            99999999999999999998775 34444334444443

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.45  E-value=2.2e-13  Score=116.86  Aligned_cols=96  Identities=15%  Similarity=0.196  Sum_probs=74.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh-------CCceE-------------E------------------EEeccCCChhh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT-------QREVE-------------Y------------------ICLSRDTTEAD   85 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l-------g~p~~-------------~------------------v~~~~~~~~~d   85 (162)
                      ..+++|.|++|+|||++++.++..+       +.|+.             +                  ..+...++.++
T Consensus        25 ~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~  104 (337)
T TIGR02030        25 IGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDR  104 (337)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhhcccccccccCCCCcCCCCCCCcccc
Confidence            3589999999999999999999887       33322             0                  12222344557


Q ss_pred             hcceeE----eecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122          86 IKQRRE----IVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus        86 L~g~~~----~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      |+|...    +..|..++++|++.+|  ++++|+|||||++++.+++.|..+|+++.+.+
T Consensus       105 l~G~~d~~~~l~~g~~~~~~GlL~~A--~~GvL~lDEi~~L~~~~Q~~Ll~~l~~g~~~v  162 (337)
T TIGR02030       105 VCGTLDIERALTEGVKAFEPGLLARA--NRGILYIDEVNLLEDHLVDVLLDVAASGWNVV  162 (337)
T ss_pred             eecchhHhhHhhcCCEEeecCcceec--cCCEEEecChHhCCHHHHHHHHHHHHhCCeEE
Confidence            777433    3478999999987655  78999999999999999999999999887554

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.44  E-value=2.1e-13  Score=106.30  Aligned_cols=114  Identities=13%  Similarity=0.098  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEEe
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIYY  100 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~~  100 (162)
                      +.+.+.++.+-.......||+|+|++||||+.+|+.+.+..   +.|+..++|..-..   .++|.|... .-.|.....
T Consensus         6 ~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~~~~e~~LFG~~~~~~~~~~~~~   85 (168)
T PF00158_consen    6 PAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPEELLESELFGHEKGAFTGARSDK   85 (168)
T ss_dssp             HHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-HHHHHHHHHEBCSSSSTTTSSEB
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhcchhhhhhhcccccccccccccc
Confidence            44444444444444456799999999999999999999765   46888899973321   234556311 112333344


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      .|.+..  .+||.|+||||+.++++++..|..+|+++.+.-.+
T Consensus        86 ~G~l~~--A~~GtL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g  126 (168)
T PF00158_consen   86 KGLLEQ--ANGGTLFLDEIEDLPPELQAKLLRVLEEGKFTRLG  126 (168)
T ss_dssp             EHHHHH--TTTSEEEEETGGGS-HHHHHHHHHHHHHSEEECCT
T ss_pred             CCceee--ccceEEeecchhhhHHHHHHHHHHHHhhchhcccc
Confidence            565544  48899999999999999999999999998876543

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.43  E-value=9.4e-13  Score=111.54  Aligned_cols=97  Identities=18%  Similarity=0.232  Sum_probs=73.2

Q ss_pred             HHHHHHHHHHHHhc----CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKD----NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~----~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ....+.++.++.+.    ....+++|+||||||||++|+.+|+.++..+...+.......+++.               .
T Consensus        31 ~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~~~~l~---------------~   95 (328)
T PRK00080         31 EKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLA---------------A   95 (328)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccChHHHH---------------H
Confidence            55666676666542    2234899999999999999999999999887665554332333333               3


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      +..++..+.+++||||+++++++.+.|.+.++++.+
T Consensus        96 ~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~  131 (328)
T PRK00080         96 ILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRL  131 (328)
T ss_pred             HHHhcccCCEEEEecHhhcchHHHHHHHHHHHhcce
Confidence            445567889999999999999999999999997754

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.40  E-value=1.3e-13  Score=120.97  Aligned_cols=103  Identities=19%  Similarity=0.179  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeE--eecCeEEEeccHHHHHhhcCcEEEEeCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRRE--IVNGTAIYYDQSAVRAAIEGRVLILEGIEK  121 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~--~~~G~~~~~~gpl~~A~~~G~vlllDEId~  121 (162)
                      ..++||+||||||||++|+.+|..++.|+..+.++.-+ ...++|...  +..+...-.++.+.  ...+++|+|||||+
T Consensus       108 ~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~-~~gyvG~d~e~~l~~l~~~~~~~~~--~a~~gIi~iDEIdk  184 (412)
T PRK05342        108 KSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLT-EAGYVGEDVENILLKLLQAADYDVE--KAQRGIVYIDEIDK  184 (412)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcc-cCCcccchHHHHHHHHHHhccccHH--HcCCcEEEEechhh
Confidence            35899999999999999999999999998877775322 222222100  00000000001111  23678999999999


Q ss_pred             CCcc--------------HHHHHHHhhcCCeEEEcC-CcEEec
Q psy4122         122 AERN--------------VLPVLNNLLENREMHLED-GRFLVS  149 (162)
Q Consensus       122 a~~~--------------v~~~L~~lle~r~l~l~~-g~~i~~  149 (162)
                      +++.              ++..|+.+||...+.+++ |.+..+
T Consensus       185 l~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~~~gg~~~~  227 (412)
T PRK05342        185 IARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHP  227 (412)
T ss_pred             hccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeCCCCCcCcC
Confidence            9764              899999999988888864 444333

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.38  E-value=8.5e-13  Score=121.21  Aligned_cols=94  Identities=15%  Similarity=0.246  Sum_probs=74.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC---------------------------------CceEEEEeccCCChhhhcceeE-
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ---------------------------------REVEYICLSRDTTEADIKQRRE-   91 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg---------------------------------~p~~~v~~~~~~~~~dL~g~~~-   91 (162)
                      +|||.|++|||||++|+.++..+.                                 .+..++.++.+.+...|+|... 
T Consensus        27 ~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d~  106 (633)
T TIGR02442        27 GVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLDI  106 (633)
T ss_pred             eEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhcccccccCCCCeeeCCCCCcHHHcCCcccH
Confidence            799999999999999999999982                                 0112344555666777887532 


Q ss_pred             ---eecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122          92 ---IVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus        92 ---~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                         +..|...+..|++.+  .++++|+||||+++++++++.|+.+|+++.+.+
T Consensus       107 ~~~l~~g~~~~~~G~L~~--A~~GiL~lDEi~~l~~~~q~~Ll~~le~g~~~v  157 (633)
T TIGR02442       107 ERALREGEKAFQPGLLAE--AHRGILYIDEVNLLDDHLVDVLLDAAAMGVNRV  157 (633)
T ss_pred             HHHhhcCCeeecCcceee--cCCCeEEeChhhhCCHHHHHHHHHHHhcCCEEE
Confidence               345777788887754  488999999999999999999999999997655

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=99.36  E-value=7.5e-12  Score=102.30  Aligned_cols=101  Identities=14%  Similarity=0.063  Sum_probs=78.4

Q ss_pred             cCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEe
Q psy4122          21 VNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        21 ~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~  100 (162)
                      .+....||.+.+....|..++.......+.||+|||||+.++.+|+.+|+++..++|.+.++...+-.            
T Consensus         9 ~~rlv~Tplt~r~~~~l~~al~~~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~r------------   76 (231)
T PF12774_consen    9 SPRLVITPLTDRCFLTLTQALSLNLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSR------------   76 (231)
T ss_dssp             -------HHHHHHHHHHHHHHCTTTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHH------------
T ss_pred             CCCceechHHHHHHHHHHHHhccCCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHH------------
Confidence            34556799999999999999988888899999999999999999999999999999999988876641            


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                        -+.-+...|.|+.+||+|+.+.++++++-+.+.
T Consensus        77 --il~G~~~~GaW~cfdefnrl~~~vLS~i~~~i~  109 (231)
T PF12774_consen   77 --ILKGLAQSGAWLCFDEFNRLSEEVLSVISQQIQ  109 (231)
T ss_dssp             --HHHHHHHHT-EEEEETCCCSSHHHHHHHHHHHH
T ss_pred             --HHHHHhhcCchhhhhhhhhhhHHHHHHHHHHHH
Confidence              233345679999999999999999998866554

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.36  E-value=1.3e-12  Score=112.71  Aligned_cols=99  Identities=13%  Similarity=0.235  Sum_probs=74.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC-------c-------------------------------eEEEEeccCCChhhhc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR-------E-------------------------------VEYICLSRDTTEADIK   87 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~-------p-------------------------------~~~v~~~~~~~~~dL~   87 (162)
                      .++|.|++|||||++++.++..+..       |                               ...+.+....+.++|+
T Consensus        40 ~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~  119 (350)
T CHL00081         40 GVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSDPELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVC  119 (350)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCCChhhhchhhhhhhcccccccceeccccceecCCCCchhhcc
Confidence            7999999999999999999877632       1                               1122333345666677


Q ss_pred             cee----EeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc-CCcE
Q psy4122          88 QRR----EIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE-DGRF  146 (162)
Q Consensus        88 g~~----~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~-~g~~  146 (162)
                      |..    .+.+|...+++|++.+|  ++++|++||||++++++++.|..+++++...+. +|..
T Consensus       120 G~iD~~~al~~g~~~~~~GlL~~A--~~GiL~lDEInrL~~~~Q~~LLeam~e~~~~ier~G~s  181 (350)
T CHL00081        120 GTIDIEKALTEGVKAFEPGLLAKA--NRGILYVDEVNLLDDHLVDILLDSAASGWNTVEREGIS  181 (350)
T ss_pred             CcccHHHHhhcCcccccCCeeeec--CCCEEEecChHhCCHHHHHHHHHHHHhCCeEEeeCCee
Confidence            643    23467777888887765  899999999999999999999999999876664 3443

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=99.35  E-value=4.4e-13  Score=118.64  Aligned_cols=110  Identities=19%  Similarity=0.266  Sum_probs=80.1

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce--EE-------------------------EEeccCCChhhhcceeEe
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV--EY-------------------------ICLSRDTTEADIKQRREI   92 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~--~~-------------------------v~~~~~~~~~dL~g~~~~   92 (162)
                      +...|+|++++||||||||.||+.+..++--=.  +.                         ..-|...+..+|      
T Consensus       194 AAAGgHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s~~g~~~~~~~~~~~rPFr~PHHsaS~~aL------  267 (490)
T COG0606         194 AAAGGHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSLAGDLHEGCPLKIHRPFRAPHHSASLAAL------  267 (490)
T ss_pred             HHhcCCcEEEecCCCCchHHhhhhhcccCCCCChHHHHHHHHHhhhcccccccCccceeCCccCCCccchHHHH------
Confidence            344589999999999999999998886663100  00                         011111122222      


Q ss_pred             ecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC-CcEEecCcchHhhh
Q psy4122          93 VNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED-GRFLVSASTYDKLL  157 (162)
Q Consensus        93 ~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~-g~~i~~~~~f~~~~  157 (162)
                      .+|...+.+|+...  .|+|||||||+-++..+++++|.+.||++++.|.. +..+.=+.+|+.+.
T Consensus       268 vGGG~~p~PGeIsL--AH~GVLFLDElpef~~~iLe~LR~PLE~g~i~IsRa~~~v~ypa~Fqlv~  331 (490)
T COG0606         268 VGGGGVPRPGEISL--AHNGVLFLDELPEFKRSILEALREPLENGKIIISRAGSKVTYPARFQLVA  331 (490)
T ss_pred             hCCCCCCCCCceee--ecCCEEEeeccchhhHHHHHHHhCccccCcEEEEEcCCeeEEeeeeEEhh
Confidence            24556777777644  59999999999999999999999999999999974 66777777887764

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.35  E-value=2.3e-12  Score=113.28  Aligned_cols=88  Identities=18%  Similarity=0.256  Sum_probs=61.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH---------hhcCcEEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA---------AIEGRVLI  115 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A---------~~~G~vll  115 (162)
                      .++||+||||||||++|+.+|+.++.|+..+.+..- +...+.|..         ..+.+..+         ...+++|+
T Consensus       117 ~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L-~~~gyvG~d---------~e~~L~~~~~~~~~~l~~a~~gIV~  186 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTLARILNVPFAIADATTL-TEAGYVGED---------VENILLKLLQAADYDVEKAQKGIIY  186 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhc-ccccccccc---------HHHHHHHHHHhCcccHHhcccceEE
Confidence            479999999999999999999999999876665432 222222210         01122222         12457999


Q ss_pred             EeCCCCCCc--------------cHHHHHHHhhcCCeEEEc
Q psy4122         116 LEGIEKAER--------------NVLPVLNNLLENREMHLE  142 (162)
Q Consensus       116 lDEId~a~~--------------~v~~~L~~lle~r~l~l~  142 (162)
                      |||||++++              ++++.|+.+||.....++
T Consensus       187 lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~~v~  227 (413)
T TIGR00382       187 IDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVP  227 (413)
T ss_pred             ecccchhchhhccccccccccchhHHHHHHHHhhccceecc
Confidence            999999987              699999999974444443

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>TIGR00368 Mg chelatase-related protein

Probab=99.35  E-value=1.4e-12  Score=116.98  Aligned_cols=121  Identities=19%  Similarity=0.230  Sum_probs=76.0

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce--EEEEeccCCChhhh------cceeE------------ee
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV--EYICLSRDTTEADI------KQRRE------------IV   93 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~--~~v~~~~~~~~~dL------~g~~~------------~~   93 (162)
                      .+.+..+...+++++|+||||||||++++.++.++..--  +.+....-.+....      +..++            +.
T Consensus       201 ~~al~~aa~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~~g~~~~~~~~~~~Pf~~p~~s~s~~~~~  280 (499)
T TIGR00368       201 KRALEIAAAGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSLVGKLIDRKQIKQRPFRSPHHSASKPALV  280 (499)
T ss_pred             HhhhhhhccCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccchhhhccccccccCCccccccccchhhhh
Confidence            334444555678999999999999999999997653210  11111111000000      00000            11


Q ss_pred             cCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC-CcEEecCcchHhh
Q psy4122          94 NGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED-GRFLVSASTYDKL  156 (162)
Q Consensus        94 ~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~-g~~i~~~~~f~~~  156 (162)
                      +|.....+|.+.  ..++++|+|||++.+++++++.|.++||++++.+.. |..+.-+.+|+.+
T Consensus       281 ggg~~~~pG~i~--lA~~GvLfLDEi~e~~~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlI  342 (499)
T TIGR00368       281 GGGPIPLPGEIS--LAHNGVLFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPARFQLV  342 (499)
T ss_pred             CCccccchhhhh--ccCCCeEecCChhhCCHHHHHHHHHHHHcCcEEEEecCcceeccCCeEEE
Confidence            343445566554  458999999999999999999999999999987753 4334344455544

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>KOG2028|consensus

Probab=99.34  E-value=1.8e-12  Score=112.47  Aligned_cols=111  Identities=14%  Similarity=0.314  Sum_probs=77.5

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce-EEEEecc-CCChhhhcceeEeecCeEEEeccHHHHH-hh
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV-EYICLSR-DTTEADIKQRREIVNGTAIYYDQSAVRA-AI  109 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~-~~v~~~~-~~~~~dL~g~~~~~~G~~~~~~gpl~~A-~~  109 (162)
                      .|+..++..... .++||||||||||+||+.++.-...+. .++.++. .....|+.+-         |++..=.+. -+
T Consensus       152 llrs~ieq~~ip-SmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~t~dvR~i---------fe~aq~~~~l~k  221 (554)
T KOG2028|consen  152 LLRSLIEQNRIP-SMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAKTNDVRDI---------FEQAQNEKSLTK  221 (554)
T ss_pred             HHHHHHHcCCCC-ceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccchHHHHHH---------HHHHHHHHhhhc
Confidence            456666654443 799999999999999999998777663 3455553 2335566531         111110111 14


Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcCCcEEecCcchHh
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDK  155 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~g~~i~~~~~f~~  155 (162)
                      ...||+||||+|++..+++.+++.+|+|.+++.+...-  .|.|+.
T Consensus       222 rkTilFiDEiHRFNksQQD~fLP~VE~G~I~lIGATTE--NPSFql  265 (554)
T KOG2028|consen  222 RKTILFIDEIHRFNKSQQDTFLPHVENGDITLIGATTE--NPSFQL  265 (554)
T ss_pred             ceeEEEeHHhhhhhhhhhhcccceeccCceEEEecccC--CCccch
Confidence            55799999999999999999999999999999765433  667764

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.34  E-value=5e-12  Score=119.55  Aligned_cols=98  Identities=23%  Similarity=0.339  Sum_probs=73.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEecc---CCChhhhcceeEeecCeEEE-eccHHHHHhhcC--cEEEEe
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICLSR---DTTEADIKQRREIVNGTAIY-YDQSAVRAAIEG--RVLILE  117 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~---~~~~~dL~g~~~~~~G~~~~-~~gpl~~A~~~G--~vlllD  117 (162)
                      ++|.||||||||++|+.+|+.+   ...+.++.++.   ..+.+.|+|.+   .|...+ +.|.+..++++.  ++|+||
T Consensus       599 ~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~g~~---~gyvg~~~~g~L~~~v~~~p~svvllD  675 (852)
T TIGR03345       599 FLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSP---PGYVGYGEGGVLTEAVRRKPYSVVLLD  675 (852)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhccccCCC---CCcccccccchHHHHHHhCCCcEEEEe
Confidence            7999999999999999999887   34556666653   23345566632   233333 235677887654  699999


Q ss_pred             CCCCCCccHHHHHHHhhcCCeEEEcCCcEE
Q psy4122         118 GIEKAERNVLPVLNNLLENREMHLEDGRFL  147 (162)
Q Consensus       118 EId~a~~~v~~~L~~lle~r~l~l~~g~~i  147 (162)
                      ||+++++++++.|.+++++|.++-..|+.+
T Consensus       676 Eieka~~~v~~~Llq~ld~g~l~d~~Gr~v  705 (852)
T TIGR03345       676 EVEKAHPDVLELFYQVFDKGVMEDGEGREI  705 (852)
T ss_pred             chhhcCHHHHHHHHHHhhcceeecCCCcEE
Confidence            999999999999999999999877666543

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>TIGR00763 lon ATP-dependent protease La

Probab=99.34  E-value=2.9e-12  Score=119.98  Aligned_cols=91  Identities=21%  Similarity=0.305  Sum_probs=67.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH----hhcCcEEEEeC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA----AIEGRVLILEG  118 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A----~~~G~vlllDE  118 (162)
                      .+.+++|+||||||||++|+.+|+.++.++.++++....+.+++.+....--|.   ..|.+.++    .....+++|||
T Consensus       346 ~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~---~~g~i~~~l~~~~~~~~villDE  422 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGA---MPGRIIQGLKKAKTKNPLFLLDE  422 (775)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCC---CCchHHHHHHHhCcCCCEEEEec
Confidence            345799999999999999999999999999999987766778887632111111   12344444    34557999999


Q ss_pred             CCCCCcc----HHHHHHHhhcC
Q psy4122         119 IEKAERN----VLPVLNNLLEN  136 (162)
Q Consensus       119 Id~a~~~----v~~~L~~lle~  136 (162)
                      ||++.++    ..++|+++||.
T Consensus       423 idk~~~~~~~~~~~aLl~~ld~  444 (775)
T TIGR00763       423 IDKIGSSFRGDPASALLEVLDP  444 (775)
T ss_pred             hhhcCCccCCCHHHHHHHhcCH
Confidence            9999774    45888888873

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=99.34  E-value=1.7e-12  Score=116.50  Aligned_cols=121  Identities=21%  Similarity=0.246  Sum_probs=79.2

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce--EEEEeccCCC-------hhhhcceeE-----------ee
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV--EYICLSRDTT-------EADIKQRRE-----------IV   93 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~--~~v~~~~~~~-------~~dL~g~~~-----------~~   93 (162)
                      ++.+..+...|++++|+||||||||++++.++..+...-  +.+.+..-.+       ...+..++.           +.
T Consensus       200 ~~al~laa~~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~  279 (506)
T PRK09862        200 KRGLEITAAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMV  279 (506)
T ss_pred             HhhhheeccCCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhhccccccCCcCCCCccCCCccchHHHHh
Confidence            334444455788999999999999999999997764211  1122211000       111211110           12


Q ss_pred             cCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC-CcEEecCcchHhh
Q psy4122          94 NGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED-GRFLVSASTYDKL  156 (162)
Q Consensus        94 ~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~-g~~i~~~~~f~~~  156 (162)
                      +|.....+|.+  +..+||+|+||||+++++++++.|.+.||++.+.+.. |..+.-+.+|+.+
T Consensus       280 GGg~~~~pG~l--~~A~gGvLfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lI  341 (506)
T PRK09862        280 GGGAIPGPGEI--SLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPARFQLV  341 (506)
T ss_pred             CCCceehhhHh--hhccCCEEecCCchhCCHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEE
Confidence            45555565654  5569999999999999999999999999999998864 5444445566544

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.33  E-value=5.6e-12  Score=118.75  Aligned_cols=98  Identities=17%  Similarity=0.268  Sum_probs=73.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccC---CChhhhcceeEeecCeEEEec-cHHHHHhhcC--cEEEEe
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRD---TTEADIKQRREIVNGTAIYYD-QSAVRAAIEG--RVLILE  117 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~---~~~~dL~g~~~~~~G~~~~~~-gpl~~A~~~G--~vlllD  117 (162)
                      ++|.||||||||++|+.+|+.+   +.++.++.++.-   .+.+.|+|.+   .|...+.+ |.+..+++..  .|+++|
T Consensus       542 ~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~g~~---~gyvg~~~~~~l~~~~~~~p~~VvllD  618 (821)
T CHL00095        542 FLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSP---PGYVGYNEGGQLTEAVRKKPYTVVLFD  618 (821)
T ss_pred             EEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccHHHhcCCC---CcccCcCccchHHHHHHhCCCeEEEEC
Confidence            7899999999999999999876   345666666532   2355666642   34333433 3577787665  699999


Q ss_pred             CCCCCCccHHHHHHHhhcCCeEEEcCCcEE
Q psy4122         118 GIEKAERNVLPVLNNLLENREMHLEDGRFL  147 (162)
Q Consensus       118 EId~a~~~v~~~L~~lle~r~l~l~~g~~i  147 (162)
                      ||+++++++++.|++++|+|+++...|+.+
T Consensus       619 eieka~~~v~~~Llq~le~g~~~d~~g~~v  648 (821)
T CHL00095        619 EIEKAHPDIFNLLLQILDDGRLTDSKGRTI  648 (821)
T ss_pred             ChhhCCHHHHHHHHHHhccCceecCCCcEE
Confidence            999999999999999999998876655543

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.32  E-value=8.6e-12  Score=117.07  Aligned_cols=91  Identities=22%  Similarity=0.334  Sum_probs=74.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc----CcEEEEeC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE----GRVLILEG  118 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~----G~vlllDE  118 (162)
                      .|..++|+||||||||++++.+|+.+++++.++++....+.+++.|....--|.   .+|.+.+++++    +.+++|||
T Consensus       348 ~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~---~~G~~~~~l~~~~~~~~villDE  424 (784)
T PRK10787        348 KGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGS---MPGKLIQKMAKVGVKNPLFLLDE  424 (784)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccchhccCCC---CCcHHHHHHHhcCCCCCEEEEEC
Confidence            456799999999999999999999999999999998877888888754322222   35677777654    45899999


Q ss_pred             CCCCCccH----HHHHHHhhcC
Q psy4122         119 IEKAERNV----LPVLNNLLEN  136 (162)
Q Consensus       119 Id~a~~~v----~~~L~~lle~  136 (162)
                      ||+++++.    .++|++++|.
T Consensus       425 idk~~~~~~g~~~~aLlevld~  446 (784)
T PRK10787        425 IDKMSSDMRGDPASALLEVLDP  446 (784)
T ss_pred             hhhcccccCCCHHHHHHHHhcc
Confidence            99999886    5999999985

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.32  E-value=9.6e-12  Score=117.59  Aligned_cols=96  Identities=21%  Similarity=0.276  Sum_probs=73.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccC---CChhhhcceeEeecCeEEEe-ccHHHHHhhc--CcEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRD---TTEADIKQRREIVNGTAIYY-DQSAVRAAIE--GRVLIL  116 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~---~~~~dL~g~~~~~~G~~~~~-~gpl~~A~~~--G~vlll  116 (162)
                      +++|.||||||||++|+.+|+.+   +.++.++.++.-   ...+.|+|.+   .|.+.+. .|.+..+++.  ..+|+|
T Consensus       597 ~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~g~~---~g~~g~~~~g~l~~~v~~~p~~vlll  673 (852)
T TIGR03346       597 SFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAP---PGYVGYEEGGQLTEAVRRKPYSVVLF  673 (852)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhcCCC---CCccCcccccHHHHHHHcCCCcEEEE
Confidence            48999999999999999999877   457777777632   2345666643   3433343 3567777754  369999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCeEEEcCC
Q psy4122         117 EGIEKAERNVLPVLNNLLENREMHLEDG  144 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~l~l~~g  144 (162)
                      |||+++++++++.|+++||+|.++...|
T Consensus       674 Deieka~~~v~~~Ll~~l~~g~l~d~~g  701 (852)
T TIGR03346       674 DEVEKAHPDVFNVLLQVLDDGRLTDGQG  701 (852)
T ss_pred             eccccCCHHHHHHHHHHHhcCceecCCC
Confidence            9999999999999999999998875433

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>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=99.30  E-value=1.2e-11  Score=89.00  Aligned_cols=90  Identities=17%  Similarity=0.167  Sum_probs=59.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIE  120 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId  120 (162)
                      +.+++++||||||||++++.++..+   +.++.++.++...............    .+..-..........++++||++
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~lilDe~~   94 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF----LVRLLFELAEKAKPGVLFIDEID   94 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhh----hHhHHHHhhccCCCeEEEEeChh
Confidence            6789999999999999999999988   7788777776443332222100000    00000111123456899999999


Q ss_pred             CCCccHHHHHHHhhcCC
Q psy4122         121 KAERNVLPVLNNLLENR  137 (162)
Q Consensus       121 ~a~~~v~~~L~~lle~r  137 (162)
                      .+++.....+...++..
T Consensus        95 ~~~~~~~~~~~~~i~~~  111 (151)
T cd00009          95 SLSRGAQNALLRVLETL  111 (151)
T ss_pred             hhhHHHHHHHHHHHHhc
Confidence            99887777777777654

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.29  E-value=1.8e-11  Score=107.05  Aligned_cols=93  Identities=19%  Similarity=0.289  Sum_probs=68.3

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH-----
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA-----  107 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A-----  107 (162)
                      .|+.++..... .+++|+||||||||++|+.+|..++.++..+++.. ....++..              .+..+     
T Consensus        26 ~L~~~i~~~~~-~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~-~~~~~ir~--------------ii~~~~~~~~   89 (413)
T PRK13342         26 PLRRMIEAGRL-SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVT-SGVKDLRE--------------VIEEARQRRS   89 (413)
T ss_pred             HHHHHHHcCCC-ceEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccc-ccHHHHHH--------------HHHHHHHhhh
Confidence            37777765443 38999999999999999999999998877766542 12223221              01111     


Q ss_pred             hhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         108 AIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       108 ~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..++.+|+||||++++++.++.|+..++++.+.+
T Consensus        90 ~g~~~vL~IDEi~~l~~~~q~~LL~~le~~~iil  123 (413)
T PRK13342         90 AGRRTILFIDEIHRFNKAQQDALLPHVEDGTITL  123 (413)
T ss_pred             cCCceEEEEechhhhCHHHHHHHHHHhhcCcEEE
Confidence            1155799999999999999999999999887655

>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=99.28  E-value=4.8e-12  Score=91.61  Aligned_cols=82  Identities=22%  Similarity=0.182  Sum_probs=55.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc--CcEEEEeCCCCCCc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE--GRVLILEGIEKAER  124 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~--G~vlllDEId~a~~  124 (162)
                      +||+||||||||++|+.+|+.++.++..+.+....+.  ..+     ..... ...-+.+|...  ..+++|||+|...+
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~--~~~-----~~~~~-i~~~~~~~~~~~~~~vl~iDe~d~l~~   72 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISS--YAG-----DSEQK-IRDFFKKAKKSAKPCVLFIDEIDKLFP   72 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTS--STT-----HHHHH-HHHHHHHHHHTSTSEEEEEETGGGTSH
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccc--ccc-----ccccc-cccccccccccccceeeeeccchhccc
Confidence            6899999999999999999999999877777633210  000     00000 01123333334  37999999999888


Q ss_pred             cH-----------HHHHHHhhcC
Q psy4122         125 NV-----------LPVLNNLLEN  136 (162)
Q Consensus       125 ~v-----------~~~L~~lle~  136 (162)
                      +.           ++.|...+++
T Consensus        73 ~~~~~~~~~~~~~~~~L~~~l~~   95 (132)
T PF00004_consen   73 KSQPSSSSFEQRLLNQLLSLLDN   95 (132)
T ss_dssp             HCSTSSSHHHHHHHHHHHHHHHT
T ss_pred             ccccccccccccccceeeecccc
Confidence            76           7778887773

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 ....

>smart00350 MCM minichromosome maintenance proteins

Probab=99.28  E-value=9.7e-12  Score=111.59  Aligned_cols=93  Identities=14%  Similarity=0.261  Sum_probs=69.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |+||+|+||+|||++|+.++....+.. +... ...+...|.+....  ..|.+..+.|++..|  ++|+++|||+|+++
T Consensus       238 ~vLL~G~pGtGKs~lar~l~~~~~r~~-~~~~-~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A--~~Gil~iDEi~~l~  313 (509)
T smart00350      238 NILLLGDPGTAKSQLLKYVEKTAPRAV-YTTG-KGSSAVGLTAAVTRDPETREFTLEGGALVLA--DNGVCCIDEFDKMD  313 (509)
T ss_pred             eEEEeCCCChhHHHHHHHHHHHcCcce-EcCC-CCCCcCCccccceEccCcceEEecCccEEec--CCCEEEEechhhCC
Confidence            899999999999999999999886542 2221 11222233321111  246677788877654  89999999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEc
Q psy4122         124 RNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~  142 (162)
                      ++.+..|+++||.+.+.+.
T Consensus       314 ~~~q~~L~e~me~~~i~i~  332 (509)
T smart00350      314 DSDRTAIHEAMEQQTISIA  332 (509)
T ss_pred             HHHHHHHHHHHhcCEEEEE
Confidence            9999999999999998775

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=99.28  E-value=3.8e-12  Score=116.08  Aligned_cols=110  Identities=19%  Similarity=0.228  Sum_probs=93.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee----EeecCeEEEeccHHHHHhhcCcEEEEeCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR----EIVNGTAIYYDQSAVRAAIEGRVLILEGIEK  121 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~----~~~~G~~~~~~gpl~~A~~~G~vlllDEId~  121 (162)
                      -|+|.|++|++||++++.++.++..+.-++.+|...+...|+|.-    .+..|...+++|-+.+  .++|||+|||+|+
T Consensus        27 Gv~i~g~~G~~ks~~~r~l~~llp~~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGlla~--Ah~GvL~lDe~n~  104 (584)
T PRK13406         27 GVVLRARAGPVRDRWLAALRALLPAGTPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLLAE--ADGGVLVLAMAER  104 (584)
T ss_pred             eEEEEcCCCcHHHHHHHHHHHhcCCCCCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCceee--ccCCEEEecCccc
Confidence            499999999999999999999997744567888888899999853    3456787788887654  5999999999999


Q ss_pred             CCccHHHHHHHhhcCCeEEEc-CCcEEecCcchHhhh
Q psy4122         122 AERNVLPVLNNLLENREMHLE-DGRFLVSASTYDKLL  157 (162)
Q Consensus       122 a~~~v~~~L~~lle~r~l~l~-~g~~i~~~~~f~~~~  157 (162)
                      +++.+++.|.+.||+|.+++. +|..+..+.+|..++
T Consensus       105 ~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIa  141 (584)
T PRK13406        105 LEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVA  141 (584)
T ss_pred             CCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEe
Confidence            999999999999999999996 577777777887654

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.27  E-value=3.1e-11  Score=103.08  Aligned_cols=113  Identities=17%  Similarity=0.219  Sum_probs=78.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+..+.+-.......||+|+|++||||+.+|+.+....   +.|+..++|.....   .+.|.|... .-.|....
T Consensus         5 S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~~~l~~~lfG~~~g~~~ga~~~   84 (329)
T TIGR02974         5 SNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHEAGAFTGAQKR   84 (329)
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCChHHHHHHHhccccccccCcccc
Confidence            455555555555555567899999999999999999988654   46889999973321   233444210 01122222


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|-+..  .+||.|+||||+.++++++..|..+|+++.+.-
T Consensus        85 ~~G~~~~--a~gGtL~Ldei~~L~~~~Q~~Ll~~l~~~~~~~  124 (329)
T TIGR02974        85 HQGRFER--ADGGTLFLDELATASLLVQEKLLRVIEYGEFER  124 (329)
T ss_pred             cCCchhh--CCCCEEEeCChHhCCHHHHHHHHHHHHcCcEEe
Confidence            3344433  378999999999999999999999999887643

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.22  E-value=4.6e-11  Score=113.16  Aligned_cols=93  Identities=17%  Similarity=0.246  Sum_probs=69.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccC---CChhhhcceeEeecCeEEEec-cHHHHHhhc--CcEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRD---TTEADIKQRREIVNGTAIYYD-QSAVRAAIE--GRVLIL  116 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~---~~~~dL~g~~~~~~G~~~~~~-gpl~~A~~~--G~vlll  116 (162)
                      +++|+||||||||++|+.+|..+   +.++.++.|+.-   ...+.|+|.+   .|...+.+ |.+..+++.  +++|+|
T Consensus       600 ~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~LiG~~---pgy~g~~~~g~l~~~v~~~p~~vLll  676 (857)
T PRK10865        600 SFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAP---PGYVGYEEGGYLTEAVRRRPYSVILL  676 (857)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHHhCCC---CcccccchhHHHHHHHHhCCCCeEEE
Confidence            58999999999999999999876   346666776532   2345566632   33333333 346666654  479999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         117 EGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      |||+++++++++.|.+++++|.++-
T Consensus       677 DEieka~~~v~~~Ll~ile~g~l~d  701 (857)
T PRK10865        677 DEVEKAHPDVFNILLQVLDDGRLTD  701 (857)
T ss_pred             eehhhCCHHHHHHHHHHHhhCceec
Confidence            9999999999999999999988764

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.21  E-value=4.1e-11  Score=104.88  Aligned_cols=112  Identities=16%  Similarity=0.106  Sum_probs=78.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH----hCCceEEEEeccC---CChhhhcceeE-eecCeEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL----TQREVEYICLSRD---TTEADIKQRRE-IVNGTAI   98 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~----lg~p~~~v~~~~~---~~~~dL~g~~~-~~~G~~~   98 (162)
                      +++..+.++.+-..--.+.|||+.|++|+||+.+|++++..    .+.|+..+||..-   .-.++|.|... .-.|...
T Consensus        84 ~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~eLFG~~kGaftGa~~  163 (403)
T COG1221          84 SPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQG  163 (403)
T ss_pred             CHHHHHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHHHHhccccceeecccC
Confidence            45555555555554447899999999999999999988743    3668999999732   22444666211 0011111


Q ss_pred             EeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEE
Q psy4122          99 YYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMH  140 (162)
Q Consensus        99 ~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~  140 (162)
                      =+.|-+  ...+||.|+||||.++|+..+..|..+||+|++.
T Consensus       164 ~k~Glf--e~A~GGtLfLDEI~~LP~~~Q~kLl~~le~g~~~  203 (403)
T COG1221         164 GKAGLF--EQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYR  203 (403)
T ss_pred             CcCchh--eecCCCEEehhhhhhCCHhHHHHHHHHHHcCceE
Confidence            111222  2248999999999999999999999999999997

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.19  E-value=2e-10  Score=95.98  Aligned_cols=122  Identities=15%  Similarity=0.210  Sum_probs=86.3

Q ss_pred             eecCCccceeceeeeecccCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC
Q psy4122           3 IAINSQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT   82 (162)
Q Consensus         3 ~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~   82 (162)
                      |-++|+|+.=++.|-+.+.......+...+.++..+........++|+||||+|||++++.+|+.++.++..+++.. ..
T Consensus         2 ~~~~~~~~~w~~kyrP~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~~-~~   80 (316)
T PHA02544          2 ITVNPNEFMWEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD-CR   80 (316)
T ss_pred             cccCCCCCcceeccCCCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEeccCc-cc
Confidence            45788888888888777777777788888899888876444434555899999999999999999988877777754 22


Q ss_pred             hhhhcceeEeecCeEEEeccHHHHHh---hcCcEEEEeCCCCC-CccHHHHHHHhhcC
Q psy4122          83 EADIKQRREIVNGTAIYYDQSAVRAA---IEGRVLILEGIEKA-ERNVLPVLNNLLEN  136 (162)
Q Consensus        83 ~~dL~g~~~~~~G~~~~~~gpl~~A~---~~G~vlllDEId~a-~~~v~~~L~~lle~  136 (162)
                      ...+...  +.         .+....   ....+++|||+++. ..+.++.|..+++.
T Consensus        81 ~~~i~~~--l~---------~~~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~  127 (316)
T PHA02544         81 IDFVRNR--LT---------RFASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEA  127 (316)
T ss_pred             HHHHHHH--HH---------HHHHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHh
Confidence            1111100  00         011111   24579999999999 66788888888885

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.19  E-value=1.9e-10  Score=97.91  Aligned_cols=115  Identities=16%  Similarity=0.182  Sum_probs=80.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+......+.||+|+|++||||+++|+.+....   +.|+..++|....+   .++++|... .-.|...-
T Consensus        12 S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~~~~~~~lfg~~~~~~~g~~~~   91 (326)
T PRK11608         12 ANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKR   91 (326)
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCHHHHHHHHccccccccCCcccc
Confidence            566666666666666677899999999999999999988665   36888888874321   233444210 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      ..|.+.  ..+||.|+||||+.++++++..|..+++++.+.-.+
T Consensus        92 ~~g~l~--~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g  133 (326)
T PRK11608         92 HPGRFE--RADGGTLFLDELATAPMLVQEKLLRVIEYGELERVG  133 (326)
T ss_pred             cCCchh--ccCCCeEEeCChhhCCHHHHHHHHHHHhcCcEEeCC
Confidence            123332  347899999999999999999999999988765433

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.18  E-value=1e-10  Score=105.94  Aligned_cols=111  Identities=16%  Similarity=0.078  Sum_probs=77.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH-----------hCCceEEEEeccCCC---hhhhcceeEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL-----------TQREVEYICLSRDTT---EADIKQRREI   92 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~-----------lg~p~~~v~~~~~~~---~~dL~g~~~~   92 (162)
                      ++.+.+..+.+...-....||||.|++||||+.+|+.+...           .+.|+..++|..-.+   .++|.|.   
T Consensus       225 S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e~lleseLFG~---  301 (538)
T PRK15424        225 SPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEAELFGY---  301 (538)
T ss_pred             CHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCChhhHHHHhcCC---
Confidence            45444444444333445679999999999999999999876           467899999974322   3445552   


Q ss_pred             ecCeE-----EEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122          93 VNGTA-----IYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus        93 ~~G~~-----~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      ..|.+     .-..|-+-  ..+||.|+||||+.++++++..|..+|+++++.-.
T Consensus       302 ~~gaftga~~~~~~Gl~e--~A~gGTLfLdeI~~Lp~~~Q~kLl~~L~e~~~~r~  354 (538)
T PRK15424        302 EEGAFTGSRRGGRAGLFE--IAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRV  354 (538)
T ss_pred             ccccccCccccccCCchh--ccCCCEEEEcChHhCCHHHHHHHHhhhhcCeEEec
Confidence            22211     11222222  24789999999999999999999999999887543

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.17  E-value=1.6e-10  Score=103.97  Aligned_cols=115  Identities=14%  Similarity=0.130  Sum_probs=79.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+-.......||+|+|++||||+++|+.++...   +.|+..++|....+   .+.|.|... .-.|....
T Consensus       202 s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~~~~~~~lfg~~~~~~~~~~~~  281 (534)
T TIGR01817       202 SPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGAIAQ  281 (534)
T ss_pred             CHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCHHHHHHHHcCCCCCccCCCCcC
Confidence            566666666555555567799999999999999999999764   56899999974322   234444210 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      ..|.+..  .+||.|+||||+.++++++..|..+++++.+.-.+
T Consensus       282 ~~g~~~~--a~~GtL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~  323 (534)
T TIGR01817       282 RKGRFEL--ADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVG  323 (534)
T ss_pred             CCCcccc--cCCCeEEEechhhCCHHHHHHHHHHHhcCcEEECC
Confidence            2232322  36899999999999999999999999998875433

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.15  E-value=1.6e-10  Score=105.76  Aligned_cols=111  Identities=14%  Similarity=0.055  Sum_probs=80.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeEeecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRREIVNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~~~~G~~~~~  100 (162)
                      ++.+.+.++.+-.....+.||+|.|++||||+++|+++.+..   +.|+..++|..-..   .++|+|...  ++...-.
T Consensus       331 s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~~~~~~elfg~~~--~~~~~~~  408 (638)
T PRK11388        331 SPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDR--TDSENGR  408 (638)
T ss_pred             CHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCChHHHHHHhcCCCC--cCccCCC
Confidence            566666666666666667799999999999999999998765   46899999974332   355666421  1111111


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .|.+.  ..+||.|+||||+.++++++..|..+|+++.+.-
T Consensus       409 ~g~~~--~a~~GtL~ldei~~l~~~~Q~~Ll~~l~~~~~~~  447 (638)
T PRK11388        409 LSKFE--LAHGGTLFLEKVEYLSPELQSALLQVLKTGVITR  447 (638)
T ss_pred             CCcee--ECCCCEEEEcChhhCCHHHHHHHHHHHhcCcEEe
Confidence            12222  2478999999999999999999999999988753

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.12  E-value=2.6e-10  Score=106.33  Aligned_cols=101  Identities=16%  Similarity=0.219  Sum_probs=68.2

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcC
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEG  111 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G  111 (162)
                      ..|+.++..... .+++|+||||||||++|+.+|+..+.++..+++. .....++...  +...    .  ........+
T Consensus        41 ~~L~~~i~~~~~-~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~-~~~i~dir~~--i~~a----~--~~l~~~~~~  110 (725)
T PRK13341         41 RLLRRAIKADRV-GSLILYGPPGVGKTTLARIIANHTRAHFSSLNAV-LAGVKDLRAE--VDRA----K--ERLERHGKR  110 (725)
T ss_pred             HHHHHHHhcCCC-ceEEEECCCCCCHHHHHHHHHHHhcCcceeehhh-hhhhHHHHHH--HHHH----H--HHhhhcCCc
Confidence            456777765444 3899999999999999999999988776655543 1112222100  0000    0  000111245


Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      .+|+|||||+++.+.++.|.+.++++.+.+-
T Consensus       111 ~IL~IDEIh~Ln~~qQdaLL~~lE~g~IiLI  141 (725)
T PRK13341        111 TILFIDEVHRFNKAQQDALLPWVENGTITLI  141 (725)
T ss_pred             eEEEEeChhhCCHHHHHHHHHHhcCceEEEE
Confidence            6999999999999999999999999887663

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.11  E-value=1e-10  Score=99.90  Aligned_cols=102  Identities=20%  Similarity=0.223  Sum_probs=68.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH------hhcCcEEEEeC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA------AIEGRVLILEG  118 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A------~~~G~vlllDE  118 (162)
                      -|+||+||+|||||-||+.+|+.++.|+...-+... |.+-.+|.... +     .=-.|+.|      -.+.|+++|||
T Consensus        98 SNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtL-TEAGYVGEDVE-N-----illkLlqaadydV~rAerGIIyIDE  170 (408)
T COG1219          98 SNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTL-TEAGYVGEDVE-N-----ILLKLLQAADYDVERAERGIIYIDE  170 (408)
T ss_pred             ccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccch-hhccccchhHH-H-----HHHHHHHHcccCHHHHhCCeEEEec
Confidence            389999999999999999999999999764433211 22223331000 0     00011222      23668999999


Q ss_pred             CCCCCc--------------cHHHHHHHhhcCCeEEEc-CCcEEecCcch
Q psy4122         119 IEKAER--------------NVLPVLNNLLENREMHLE-DGRFLVSASTY  153 (162)
Q Consensus       119 Id~a~~--------------~v~~~L~~lle~r~l~l~-~g~~i~~~~~f  153 (162)
                      ||+...              .|+.+|+.++|.-...+| .|.+=+|+.+|
T Consensus       171 IDKIarkSeN~SITRDVSGEGVQQALLKiiEGTvasVPPqGGRKHP~Qe~  220 (408)
T COG1219         171 IDKIARKSENPSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPQQEF  220 (408)
T ss_pred             hhhhhccCCCCCcccccCchHHHHHHHHHHcCceeccCCCCCCCCCccce
Confidence            998644              379999999998888886 46676666654

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.11  E-value=5.9e-10  Score=99.99  Aligned_cols=113  Identities=13%  Similarity=0.148  Sum_probs=79.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+-.....+.||+|+|++||||+.+|+.+....   +.|+..++|..-.+   .++|.|... .-.|...-
T Consensus       193 s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~~~~e~~lfG~~~g~~~ga~~~  272 (509)
T PRK05022        193 SPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAFTGAISN  272 (509)
T ss_pred             CHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCChHHHHHHhcCccccccCCCccc
Confidence            566666666665555567899999999999999999999764   56899999974322   234555210 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|.+.  ..+||.|+||||+.++++++..|..+++++.+.-
T Consensus       273 ~~g~~~--~a~gGtL~ldeI~~L~~~~Q~~Ll~~l~~~~~~~  312 (509)
T PRK05022        273 RSGKFE--LADGGTLFLDEIGELPLALQAKLLRVLQYGEIQR  312 (509)
T ss_pred             CCcchh--hcCCCEEEecChhhCCHHHHHHHHHHHhcCCEee
Confidence            223332  3478999999999999999999999999988744

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.10  E-value=4e-10  Score=101.79  Aligned_cols=112  Identities=21%  Similarity=0.218  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEecc-CCC----hhhhccee--
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSR-DTT----EADIKQRR--   90 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~-~~~----~~dL~g~~--   90 (162)
                      ....+.++..+.+ ....|++|+||||||||++|+.+++..          +.++..+.|.. .++    .+.+++..  
T Consensus        71 s~~i~~l~~al~~-~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~  149 (531)
T TIGR02902        71 EEGIKALKAALCG-PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDERGIADPLIGSVHD  149 (531)
T ss_pred             HHHHHHHHHHHhC-CCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEccccccCCccccchhhcCCccc
Confidence            3444555544322 234699999999999999999997642          24556666642 111    12333321  


Q ss_pred             Eeec--------CeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122          91 EIVN--------GTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus        91 ~~~~--------G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      .+..        |...-..|.+.+  .+|++|+||||+++++++++.|+.+||++.+.+.
T Consensus       150 p~~~~~~~~g~~g~~~~~~G~l~~--a~gG~L~IdEI~~L~~~~q~~LL~~Le~~~~~~~  207 (531)
T TIGR02902       150 PIYQGAGPLGIAGIPQPKPGAVTR--AHGGVLFIDEIGELHPVQMNKLLKVLEDRKVFLD  207 (531)
T ss_pred             chhccccccccCCcccccCchhhc--cCCcEEEEechhhCCHHHHHHHHHHHHhCeeeec
Confidence            1100        111112333333  3789999999999999999999999999887764

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.09  E-value=5.8e-10  Score=89.38  Aligned_cols=88  Identities=17%  Similarity=0.231  Sum_probs=64.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ....+..++.+......+.+++|+||+|||||+|++.+++..   +.++.++++.....  .+                 
T Consensus        25 ~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~~--~~-----------------   85 (227)
T PRK08903         25 NAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLL--AF-----------------   85 (227)
T ss_pred             cHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhHH--HH-----------------
Confidence            456677777766644456699999999999999999999764   56666666643211  11                 


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                        .-..++.+|+|||++.++++.+..|..+++
T Consensus        86 --~~~~~~~~liiDdi~~l~~~~~~~L~~~~~  115 (227)
T PRK08903         86 --DFDPEAELYAVDDVERLDDAQQIALFNLFN  115 (227)
T ss_pred             --hhcccCCEEEEeChhhcCchHHHHHHHHHH
Confidence              012356899999999999988888888885

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.09  E-value=5.2e-10  Score=100.02  Aligned_cols=110  Identities=14%  Similarity=0.100  Sum_probs=65.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce--EEEEeccCCChhhhc-c----eeEeecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV--EYICLSRDTTEADIK-Q----RREIVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~--~~v~~~~~~~~~dL~-g----~~~~~~G~~~~   99 (162)
                      -+.....|+.++.....++.++|+||+|||||++|+.+|+.++..-  ....|+.-.+-.++. +    ...+...+..=
T Consensus        23 Qe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas~~g  102 (484)
T PRK14956         23 QDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASNRG  102 (484)
T ss_pred             hHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhhccc
Confidence            3567788998888777666689999999999999999999887531  000111000000110 0    00011000000


Q ss_pred             ecc--HHHHHh----h--cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         100 YDQ--SAVRAA----I--EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       100 ~~g--pl~~A~----~--~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .+-  -+...+    .  ...|+||||+|+++.+.+++|+..||+
T Consensus       103 Vd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEE  147 (484)
T PRK14956        103 IENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEE  147 (484)
T ss_pred             HHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhc
Confidence            000  011111    1  225999999999999999999999997

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.08  E-value=4e-10  Score=101.84  Aligned_cols=110  Identities=16%  Similarity=0.102  Sum_probs=75.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCC---hhhhcceeEeecCeEE--
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTT---EADIKQRREIVNGTAI--   98 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~---~~dL~g~~~~~~G~~~--   98 (162)
                      ++.+.+..+.+-.......||||.|++||||+.+|+.+...   .+.|+..++|..-.+   .++|.|.   +.|.+.  
T Consensus       218 S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~e~lleseLFG~---~~gaftga  294 (526)
T TIGR02329       218 SAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGY---EEGAFTGA  294 (526)
T ss_pred             CHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCChhHHHHHhcCC---cccccccc
Confidence            45444444444333345679999999999999999999865   456899999874322   3445552   222211  


Q ss_pred             ---EeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122          99 ---YYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus        99 ---~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                         ...|-+-  ..+||.|+||||+.+|++++..|..+|+++++.-
T Consensus       295 ~~~~~~Gl~e--~A~gGTLfLdeI~~Lp~~~Q~~Ll~~L~~~~~~r  338 (526)
T TIGR02329       295 RRGGRTGLIE--AAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVR  338 (526)
T ss_pred             cccccccchh--hcCCceEEecChHhCCHHHHHHHHHHHhcCcEEe
Confidence               1122222  2478999999999999999999999999988754

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK04195 replication factor C large subunit; Provisional

Probab=99.08  E-value=5e-10  Score=99.76  Aligned_cols=105  Identities=17%  Similarity=0.140  Sum_probs=70.9

Q ss_pred             CCHHHHHHHHHHHHhcCC---CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          26 LTQDWLSHLRWILQKDNM---SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~---g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      -.+...+.|+.++..+..   .+++||+||||||||++|+.+|+.++.++..++.+...+...+... .......    .
T Consensus        18 g~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r~~~~i~~~-i~~~~~~----~   92 (482)
T PRK04195         18 GNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERV-AGEAATS----G   92 (482)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEcccccccHHHHHHH-HHHhhcc----C
Confidence            467788889988887764   4589999999999999999999999998877776532222222110 0000000    0


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCc----cHHHHHHHhhcCC
Q psy4122         103 SAVRAAIEGRVLILEGIEKAER----NVLPVLNNLLENR  137 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~----~v~~~L~~lle~r  137 (162)
                      ++..  ....+|+|||+|.+..    ..+..|..+++..
T Consensus        93 sl~~--~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~~  129 (482)
T PRK04195         93 SLFG--ARRKLILLDEVDGIHGNEDRGGARAILELIKKA  129 (482)
T ss_pred             cccC--CCCeEEEEecCcccccccchhHHHHHHHHHHcC
Confidence            0000  2457999999999876    5678888888743

>PLN03025 replication factor C subunit; Provisional

Probab=99.08  E-value=7.3e-10  Score=93.66  Aligned_cols=103  Identities=17%  Similarity=0.253  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh-CCc--eEEEEecc-C-CChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT-QRE--VEYICLSR-D-TTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l-g~p--~~~v~~~~-~-~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      ....++.|+.++..... .|++|+||||||||++|+.+|+.+ +..  ...+.++. + .....+...  ++.    +..
T Consensus        18 ~~~~~~~L~~~~~~~~~-~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~~~~~~vr~~--i~~----~~~   90 (319)
T PLN03025         18 NEDAVSRLQVIARDGNM-PNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRNK--IKM----FAQ   90 (319)
T ss_pred             cHHHHHHHHHHHhcCCC-ceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecccccccHHHHHHH--HHH----HHh
Confidence            46678888888775443 379999999999999999999876 321  12233331 1 111111100  000    000


Q ss_pred             cHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .+....-....+++|||+|++..+.++.|+..+|.
T Consensus        91 ~~~~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~  125 (319)
T PLN03025         91 KKVTLPPGRHKIVILDEADSMTSGAQQALRRTMEI  125 (319)
T ss_pred             ccccCCCCCeEEEEEechhhcCHHHHHHHHHHHhc
Confidence            00000001236999999999999999999999984

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.07  E-value=2.2e-10  Score=95.90  Aligned_cols=82  Identities=16%  Similarity=0.321  Sum_probs=52.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh--hcCcEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA--IEGRVL  114 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~--~~G~vl  114 (162)
                      +.|++|+||||||||++|+.+|+.+..       ++..+++      +++++..  . |...   ......+  ..|++|
T Consensus        58 ~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~------~~l~~~~--~-g~~~---~~~~~~~~~a~~gvL  125 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR------DDLVGQY--I-GHTA---PKTKEILKRAMGGVL  125 (284)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH------HHHhHhh--c-ccch---HHHHHHHHHccCcEE
Confidence            348999999999999999998876632       3443433      3444311  1 1110   1111122  257899


Q ss_pred             EEeCCCCC---------CccHHHHHHHhhcCC
Q psy4122         115 ILEGIEKA---------ERNVLPVLNNLLENR  137 (162)
Q Consensus       115 llDEId~a---------~~~v~~~L~~lle~r  137 (162)
                      +|||++.+         +.++++.|.++|+++
T Consensus       126 ~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~  157 (284)
T TIGR02880       126 FIDEAYYLYRPDNERDYGQEAIEILLQVMENQ  157 (284)
T ss_pred             EEechhhhccCCCccchHHHHHHHHHHHHhcC
Confidence            99999966         356788999999865

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.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.07  E-value=7.4e-10  Score=102.45  Aligned_cols=113  Identities=15%  Similarity=0.215  Sum_probs=77.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+-.....+.||+|+|++|||||++|+.+....   +.|+..++|.....   .+++.|... .-.|...-
T Consensus       382 S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~~~~~~~lfg~~~~~~~g~~~~  461 (686)
T PRK15429        382 SEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQ  461 (686)
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCChhHhhhhhcCcccccccccccc
Confidence            565655555555444566799999999999999999998754   56888899874321   334555211 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|-+  ...+||.|+||||+.++++++..|..+|+++.+.-
T Consensus       462 ~~g~l--e~a~~GtL~Ldei~~L~~~~Q~~L~~~l~~~~~~~  501 (686)
T PRK15429        462 RIGRF--ELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFER  501 (686)
T ss_pred             hhhHH--HhcCCCeEEEechhhCCHHHHHHHHHHHHhCCEEe
Confidence            12223  23578999999999999999999999999887654

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.07  E-value=2.2e-10  Score=100.26  Aligned_cols=108  Identities=11%  Similarity=0.154  Sum_probs=81.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE----EEEe---------------------------------ccCCChhh-hc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE----YICL---------------------------------SRDTTEAD-IK   87 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~----~v~~---------------------------------~~~~~~~d-L~   87 (162)
                      .+|+.|+.|+|||++++++|.++.--..    .++|                                 .++++..| ++
T Consensus        40 gvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvv  119 (423)
T COG1239          40 GALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDDPEEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLV  119 (423)
T ss_pred             eeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCChhhhhHHHHhhccccccccccceecceecCCCccchhhhc
Confidence            6999999999999999999998842110    0111                                 23444555 77


Q ss_pred             ceeE----eecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC-eEEEcCCcEEecCcchHh
Q psy4122          88 QRRE----IVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENR-EMHLEDGRFLVSASTYDK  155 (162)
Q Consensus        88 g~~~----~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r-~l~l~~g~~i~~~~~f~~  155 (162)
                      |...    +++|...|++|-|.+|  ++||+++||+|.++..++++|+.+++.| +.+=.+|-.+.++.+|-.
T Consensus       120 GslDi~ka~~~g~~af~PGlLa~A--nRGIlYvDEvnlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvl  190 (423)
T COG1239         120 GSLDIEKALEEGPKAFQPGLLARA--NRGILYVDEVNLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLL  190 (423)
T ss_pred             cccCHHHHHhcCccccCCcchhhc--cCCEEEEeccccccHHHHHHHHHHHHhCCceeeeCceeeccCccEEE
Confidence            7433    3468889998888766  8999999999999999999999999998 444456777777777643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.06  E-value=1e-09  Score=98.10  Aligned_cols=107  Identities=16%  Similarity=0.146  Sum_probs=64.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+.++........++|+||||||||++|+.+|+.++..       +..+..+...   +..++.   .+...+
T Consensus        19 q~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~---el~aa~   95 (472)
T PRK14962         19 QDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVI---ELDAAS   95 (472)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccE---EEeCcc
Confidence            356677888888766655568999999999999999999988642       2111100000   000111   010000


Q ss_pred             EEEecc--HHHH------HhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVR------AAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~------A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+.  .+..      ...+..+++|||++++..+.++.|+..+|+
T Consensus        96 ~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~  143 (472)
T PRK14962         96 NRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEE  143 (472)
T ss_pred             cCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHh
Confidence            000000  0000      112346999999999999999999999987

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.06  E-value=7e-10  Score=88.10  Aligned_cols=92  Identities=15%  Similarity=0.178  Sum_probs=63.7

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      .....++.|+.++... .+.+++|+||+|||||++|++++...   +.++.++.+.....  +..               
T Consensus        21 ~~~~~~~~l~~~~~~~-~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~~--~~~---------------   82 (226)
T TIGR03420        21 GNAELLAALRQLAAGK-GDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQ--ADP---------------   82 (226)
T ss_pred             CcHHHHHHHHHHHhcC-CCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHHH--hHH---------------
Confidence            3567888888876543 35589999999999999999999765   45666666642211  000               


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccH--HHHHHHhhc
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNV--LPVLNNLLE  135 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v--~~~L~~lle  135 (162)
                      -+...+...++|+|||++.++.+.  +..|..+++
T Consensus        83 ~~~~~~~~~~lLvIDdi~~l~~~~~~~~~L~~~l~  117 (226)
T TIGR03420        83 EVLEGLEQADLVCLDDVEAIAGQPEWQEALFHLYN  117 (226)
T ss_pred             HHHhhcccCCEEEEeChhhhcCChHHHHHHHHHHH
Confidence            122233455799999999998755  777777765

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.06  E-value=3.4e-10  Score=93.08  Aligned_cols=84  Identities=17%  Similarity=0.224  Sum_probs=51.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC-----ceEEEEeccCCChhhhcceeEeecCeEEEe-ccHHHHHhhcCcEEEEeC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR-----EVEYICLSRDTTEADIKQRREIVNGTAIYY-DQSAVRAAIEGRVLILEG  118 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~-----p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~-~gpl~~A~~~G~vlllDE  118 (162)
                      .|++|+||||||||++|+.+|+.+..     .-..+.+    +.+++.+.+.   |.+.-. .+.+-+  ..|++|+|||
T Consensus        43 ~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~----~~~~l~~~~~---g~~~~~~~~~~~~--a~~~VL~IDE  113 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEV----ERADLVGEYI---GHTAQKTREVIKK--ALGGVLFIDE  113 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEe----cHHHhhhhhc---cchHHHHHHHHHh--ccCCEEEEec
Confidence            47999999999999999999987521     1112222    2344544211   111000 011112  2478999999


Q ss_pred             CCCCC--------ccHHHHHHHhhcCC
Q psy4122         119 IEKAE--------RNVLPVLNNLLENR  137 (162)
Q Consensus       119 Id~a~--------~~v~~~L~~lle~r  137 (162)
                      ++++.        .++++.|...+|+.
T Consensus       114 ~~~L~~~~~~~~~~~~i~~Ll~~~e~~  140 (261)
T TIGR02881       114 AYSLARGGEKDFGKEAIDTLVKGMEDN  140 (261)
T ss_pred             hhhhccCCccchHHHHHHHHHHHHhcc
Confidence            99865        35778888888865

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.

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.05  E-value=5.5e-10  Score=100.41  Aligned_cols=117  Identities=16%  Similarity=0.195  Sum_probs=86.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccC---CChhhhcceeEeecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRD---TTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~---~~~~dL~g~~~~~~G~~~~~  100 (162)
                      +|.+++.++..-..-...-+|||.|.+||||.-+|+.+....   +.|+..++|.+-   .=.++|.|          |+
T Consensus       251 S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFG----------ye  320 (560)
T COG3829         251 SPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFG----------YE  320 (560)
T ss_pred             CHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCHHHHHHHHhC----------cC
Confidence            677777777665544455689999999999999999998654   668999999733   22566666          22


Q ss_pred             ccHHHHH----------hhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC-------CcEEecCcch
Q psy4122         101 DQSAVRA----------AIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED-------GRFLVSASTY  153 (162)
Q Consensus       101 ~gpl~~A----------~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~-------g~~i~~~~~f  153 (162)
                      .|+++-|          +.+||.||||||+.+|...|+.|+++|+++++.=-+       .-||+++-|-
T Consensus       321 ~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~  390 (560)
T COG3829         321 KGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNR  390 (560)
T ss_pred             CccccccccCCCCcceeeccCCeEEehhhccCCHHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCc
Confidence            3333333          347899999999999999999999999999985432       4456665543

>KOG1051|consensus

Probab=99.05  E-value=3.8e-10  Score=106.61  Aligned_cols=98  Identities=22%  Similarity=0.248  Sum_probs=72.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh-CCce--EEEEeccCCChhhhcceeEeecCeEEEecc-HHHHHhhcC--cEEEEeCCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT-QREV--EYICLSRDTTEADIKQRREIVNGTAIYYDQ-SAVRAAIEG--RVLILEGIE  120 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l-g~p~--~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g-pl~~A~~~G--~vlllDEId  120 (162)
                      ++|.||.|+|||.||+++|+.+ |-.-  .++-+++-++.+.++|.+   +|-..+..| -+++|++..  .|+++|||+
T Consensus       594 flflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskligsp---~gyvG~e~gg~LteavrrrP~sVVLfdeIE  670 (898)
T KOG1051|consen  594 FLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSP---PGYVGKEEGGQLTEAVKRRPYSVVLFEEIE  670 (898)
T ss_pred             EEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhccCCC---cccccchhHHHHHHHHhcCCceEEEEechh
Confidence            7999999999999999999876 4333  334343333345666532   233333333 688999765  689999999


Q ss_pred             CCCccHHHHHHHhhcCCeEEEcCCcEE
Q psy4122         121 KAERNVLPVLNNLLENREMHLEDGRFL  147 (162)
Q Consensus       121 ~a~~~v~~~L~~lle~r~l~l~~g~~i  147 (162)
                      +|++++++.|.+++|+|+++-..|+.|
T Consensus       671 kAh~~v~n~llq~lD~GrltDs~Gr~V  697 (898)
T KOG1051|consen  671 KAHPDVLNILLQLLDRGRLTDSHGREV  697 (898)
T ss_pred             hcCHHHHHHHHHHHhcCccccCCCcEe
Confidence            999999999999999999987777654

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=99.04  E-value=1.9e-10  Score=98.18  Aligned_cols=95  Identities=19%  Similarity=0.347  Sum_probs=69.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      -|+||+|+||+|||.|.+.++....+-+ +.+. ..++...|.....-  .+|....+.|+++.|  +||++.|||+|++
T Consensus        58 ihiLlvGdpg~gKS~ll~~~~~~~pr~v-~~~g-~~~s~~gLta~~~~d~~~~~~~leaGalvla--d~GiccIDe~dk~  133 (331)
T PF00493_consen   58 IHILLVGDPGTGKSQLLKYVAKLAPRSV-YTSG-KGSSAAGLTASVSRDPVTGEWVLEAGALVLA--DGGICCIDEFDKM  133 (331)
T ss_dssp             --EEEECSCHHCHHHHHHCCCCT-SSEE-EEEC-CGSTCCCCCEEECCCGGTSSECEEE-HHHHC--TTSEEEECTTTT-
T ss_pred             cceeeccchhhhHHHHHHHHHhhCCceE-EECC-CCcccCCccceeccccccceeEEeCCchhcc--cCceeeecccccc
Confidence            3899999999999999998776654432 3333 34556666543221  245666678888776  9999999999999


Q ss_pred             CccHHHHHHHhhcCCeEEEcC
Q psy4122         123 ERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       123 ~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +.+....|+++||.+.+.+..
T Consensus       134 ~~~~~~~l~eaMEqq~isi~k  154 (331)
T PF00493_consen  134 KEDDRDALHEAMEQQTISIAK  154 (331)
T ss_dssp             -CHHHHHHHHHHHCSCEEECT
T ss_pred             cchHHHHHHHHHHcCeeccch
Confidence            999999999999999998875

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.03  E-value=5.5e-10  Score=96.44  Aligned_cols=85  Identities=18%  Similarity=0.173  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..+-|||+||||||||-||+++|+.++..|.++..++-  .+.++|     .|.- .+..-+.-|= +...++|+||||.
T Consensus       184 PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSEl--VqKYiG-----EGaR-lVRelF~lArekaPsIIFiDEIDA  255 (406)
T COG1222         184 PPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSEL--VQKYIG-----EGAR-LVRELFELAREKAPSIIFIDEIDA  255 (406)
T ss_pred             CCCceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHH--HHHHhc-----cchH-HHHHHHHHHhhcCCeEEEEechhh
Confidence            44569999999999999999999999999888877533  334443     2210 0111122222 3357999999987


Q ss_pred             CCc-----------cHHHHHHHhhc
Q psy4122         122 AER-----------NVLPVLNNLLE  135 (162)
Q Consensus       122 a~~-----------~v~~~L~~lle  135 (162)
                      ...           +|+-.+.+||.
T Consensus       256 Ig~kR~d~~t~gDrEVQRTmleLL~  280 (406)
T COG1222         256 IGAKRFDSGTSGDREVQRTMLELLN  280 (406)
T ss_pred             hhcccccCCCCchHHHHHHHHHHHH
Confidence            433           56666666654

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.02  E-value=2.4e-09  Score=92.76  Aligned_cols=49  Identities=18%  Similarity=0.203  Sum_probs=39.0

Q ss_pred             cHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcCC-------cEEecCcc
Q psy4122         102 QSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDG-------RFLVSAST  152 (162)
Q Consensus       102 gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~g-------~~i~~~~~  152 (162)
                      |.+.+|  +.|++-++|+.+++.+.+..|+.+++++.+.++++       ..|+++.|
T Consensus       230 G~l~~a--NrGi~~f~Ei~K~~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sN  285 (361)
T smart00763      230 GALNRA--NRGILEFVEMFKADIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSN  285 (361)
T ss_pred             Cccccc--cCceEEEeehhcCCHHHHHHHhhhhhcceEecCCcccccccceEEEEeCC
Confidence            444443  66899999999999999999999999999988643       45666554

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>KOG0743|consensus

Probab=99.01  E-value=1.9e-09  Score=95.07  Aligned_cols=61  Identities=18%  Similarity=0.331  Sum_probs=54.1

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      -||+||||||||+++.++|..+++.++.+++.+-...+||.               -|+.+.....||||++||.+
T Consensus       238 YLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr---------------~LL~~t~~kSIivIEDIDcs  298 (457)
T KOG0743|consen  238 YLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLR---------------HLLLATPNKSILLIEDIDCS  298 (457)
T ss_pred             ceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCcHHHH---------------HHHHhCCCCcEEEEeecccc
Confidence            79999999999999999999999999999998666667775               57777788899999999876

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.01  E-value=2.1e-09  Score=96.75  Aligned_cols=107  Identities=11%  Similarity=0.127  Sum_probs=66.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+.++......+.+||+||+|||||++|+.+|+.++.+       |-.+..+..+   ...|++   .+...+
T Consensus        21 q~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~---eidaas   97 (509)
T PRK14958         21 QAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLF---EVDAAS   97 (509)
T ss_pred             CHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEE---EEcccc
Confidence            477888999888876666567999999999999999999988643       1110000000   001111   111110


Q ss_pred             EEEecc--HHHHHh----h--cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRAA----I--EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A~----~--~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+.  .+...+    .  ...|++|||+|+++++..+.|+..||+
T Consensus        98 ~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEe  145 (509)
T PRK14958         98 RTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEE  145 (509)
T ss_pred             cCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhc
Confidence            000000  111111    1  225999999999999999999999996

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.00  E-value=3.2e-09  Score=98.09  Aligned_cols=107  Identities=13%  Similarity=0.148  Sum_probs=66.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+.++......+.+||+||+|||||++|+.+|+.++..       |..+..+...   ...|++   .+...+
T Consensus        20 Qe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDvi---EIDAAs   96 (702)
T PRK14960         20 QNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLI---EIDAAS   96 (702)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceE---Eecccc
Confidence            367788888888876666677999999999999999999998752       1111000000   001121   011110


Q ss_pred             EEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..=.+.  .+...+      ....++||||+++++++..+.|+..||+
T Consensus        97 ~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEE  144 (702)
T PRK14960         97 RTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEE  144 (702)
T ss_pred             cCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhc
Confidence            000000  011111      1236999999999999999999999997

>CHL00181 cbbX CbbX; Provisional

Probab=99.00  E-value=4.6e-10  Score=94.25  Aligned_cols=83  Identities=14%  Similarity=0.303  Sum_probs=52.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC---C----ceEEEEeccCCChhhhcceeEeecCeEEE-eccHHHHHhhcCcEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ---R----EVEYICLSRDTTEADIKQRREIVNGTAIY-YDQSAVRAAIEGRVLI  115 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg---~----p~~~v~~~~~~~~~dL~g~~~~~~G~~~~-~~gpl~~A~~~G~vll  115 (162)
                      +.|++|+||||||||++|+.+|..+.   .    ++  +.++    .++|.+.+  . |.+.- ..+.+.+  ..|++|+
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~--~~v~----~~~l~~~~--~-g~~~~~~~~~l~~--a~ggVLf  127 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHL--LTVT----RDDLVGQY--I-GHTAPKTKEVLKK--AMGGVLF  127 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCce--EEec----HHHHHHHH--h-ccchHHHHHHHHH--ccCCEEE
Confidence            45799999999999999999998652   1    22  2222    33454321  1 11100 0011112  2478999


Q ss_pred             EeCCCCC---------CccHHHHHHHhhcCC
Q psy4122         116 LEGIEKA---------ERNVLPVLNNLLENR  137 (162)
Q Consensus       116 lDEId~a---------~~~v~~~L~~lle~r  137 (162)
                      |||++..         .+++++.|..+||++
T Consensus       128 IDE~~~l~~~~~~~~~~~e~~~~L~~~me~~  158 (287)
T CHL00181        128 IDEAYYLYKPDNERDYGSEAIEILLQVMENQ  158 (287)
T ss_pred             EEccchhccCCCccchHHHHHHHHHHHHhcC
Confidence            9999875         457889999999864

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=98.99  E-value=1.4e-09  Score=96.76  Aligned_cols=117  Identities=15%  Similarity=0.140  Sum_probs=81.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEeccCC---Chhhhccee-EeecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLSRDT---TEADIKQRR-EIVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~~~~---~~~dL~g~~-~~~~G~~~~   99 (162)
                      +|.+.+..+.+-+.-...-+||+.|++||||-.+|+++.....   .|+..++|..-.   =.++|.|+- .--.|...=
T Consensus       147 S~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~l~ESELFGhekGAFTGA~~~  226 (464)
T COG2204         147 SPAMQQLRRLIAKVAPSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLLESELFGHEKGAFTGAITR  226 (464)
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHHHHHHHhhcccccCcCCcccc
Confidence            5655555555544444566999999999999999999997654   599999997432   245566621 000111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcCCc
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGR  145 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~g~  145 (162)
                      +.|-+-  ..+||.|+||||..+|.++|..|+.+|++|++.--+|+
T Consensus       227 r~G~fE--~A~GGTLfLDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~  270 (464)
T COG2204         227 RIGRFE--QANGGTLFLDEIGEMPLELQVKLLRVLQEREFERVGGN  270 (464)
T ss_pred             cCccee--EcCCceEEeeccccCCHHHHHHHHHHHHcCeeEecCCC
Confidence            112221  14789999999999999999999999999998765543

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.99  E-value=3.4e-10  Score=107.06  Aligned_cols=93  Identities=18%  Similarity=0.301  Sum_probs=65.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeE---eecCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRRE---IVNGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~---~~~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      ||||+|+||||||.+|+.+++...+... .+. ...+...+.+...   ...|.+..+.|+++.  ..||+++|||++++
T Consensus       494 hVLLvGDPGTGKSqLAr~Ih~lspR~~y-tsG-~~~s~vgLTa~~~~~d~~tG~~~le~GaLvl--AdgGtL~IDEidkm  569 (915)
T PTZ00111        494 NVLLCGDPGTAKSQLLHYTHLLSPRSIY-TSG-KSSSSVGLTASIKFNESDNGRAMIQPGAVVL--ANGGVCCIDELDKC  569 (915)
T ss_pred             eEEEeCCCCccHHHHHHHHHHhCCcccc-CCC-CCCccccccchhhhcccccCcccccCCcEEE--cCCCeEEecchhhC
Confidence            8999999999999999999987644321 111 1111112222111   123555556666654  47899999999999


Q ss_pred             CccHHHHHHHhhcCCeEEEc
Q psy4122         123 ERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       123 ~~~v~~~L~~lle~r~l~l~  142 (162)
                      +++.+..|+++||.+.+.+.
T Consensus       570 s~~~Q~aLlEaMEqqtIsI~  589 (915)
T PTZ00111        570 HNESRLSLYEVMEQQTVTIA  589 (915)
T ss_pred             CHHHHHHHHHHHhCCEEEEe
Confidence            99999999999999998765

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.98  E-value=2.7e-09  Score=96.08  Aligned_cols=111  Identities=9%  Similarity=0.069  Sum_probs=74.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+-.......||+|+|++||||+++|+++....   +.|+..++|..-.+   .++|.|... --.|....
T Consensus       210 s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~~~~~e~elFG~~~~~~~~~~~~  289 (520)
T PRK10820        210 SPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGAYPNALEG  289 (520)
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCCHHHHHHHhcCCCCCCcCCcccC
Confidence            455555554444444467799999999999999999987653   46888888874322   234555210 00011111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      ..|-+..  .+|+.|+||||+.++++++..|..+++++.+
T Consensus       290 ~~g~~e~--a~~GtL~LdeI~~L~~~~Q~~Ll~~l~~~~~  327 (520)
T PRK10820        290 KKGFFEQ--ANGGSVLLDEIGEMSPRMQAKLLRFLNDGTF  327 (520)
T ss_pred             CCChhhh--cCCCEEEEeChhhCCHHHHHHHHHHHhcCCc
Confidence            2333322  4689999999999999999999999998764

>KOG0733|consensus

Probab=98.98  E-value=1e-09  Score=100.01  Aligned_cols=100  Identities=15%  Similarity=0.150  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHHhcCC-----------CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCe
Q psy4122          28 QDWLSHLRWILQKDNM-----------SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGT   96 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~-----------g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~   96 (162)
                      ..++..|..|+..+..           .+-+||.||||||||+||+++|..+|.|+..++..      +++..  +.+-+
T Consensus       196 d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isAp------eivSG--vSGES  267 (802)
T KOG0733|consen  196 DKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAP------EIVSG--VSGES  267 (802)
T ss_pred             HHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecch------hhhcc--cCccc
Confidence            5566667666654322           22489999999999999999999999998766553      33321  11111


Q ss_pred             EEEeccHHHHHhhc-CcEEEEeCCCCCCcc-----------HHHHHHHhhc
Q psy4122          97 AIYYDQSAVRAAIE-GRVLILEGIEKAERN-----------VLPVLNNLLE  135 (162)
Q Consensus        97 ~~~~~gpl~~A~~~-G~vlllDEId~a~~~-----------v~~~L~~lle  135 (162)
                      ..=.+.-+-+|... ..++||||||.+.|.           +.+-|+..||
T Consensus       268 EkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD  318 (802)
T KOG0733|consen  268 EKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMD  318 (802)
T ss_pred             HHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhh
Confidence            00011133445433 468999999998774           4566777777

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

Probab=98.97  E-value=5.5e-10  Score=81.21  Aligned_cols=97  Identities=18%  Similarity=0.234  Sum_probs=63.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh--------CCceEEEEeccCCChhhhcceeE------eec-CeEEEeccHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT--------QREVEYICLSRDTTEADIKQRRE------IVN-GTAIYYDQSAVRAA  108 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l--------g~p~~~v~~~~~~~~~dL~g~~~------~~~-G~~~~~~gpl~~A~  108 (162)
                      +..++++||||+|||+++++++..+        +.++..+.+....+..++.....      ... .+..--...+.+++
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            4579999999999999999999877        66777788876666666653110      011 11000002344455


Q ss_pred             hcC-c-EEEEeCCCCC-CccHHHHHHHhhcCCeEE
Q psy4122         109 IEG-R-VLILEGIEKA-ERNVLPVLNNLLENREMH  140 (162)
Q Consensus       109 ~~G-~-vlllDEId~a-~~~v~~~L~~lle~r~l~  140 (162)
                      .+. . +|+|||++.+ +.++++.|..+.++..+.
T Consensus        84 ~~~~~~~lviDe~~~l~~~~~l~~l~~l~~~~~~~  118 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHLFSDEFLEFLRSLLNESNIK  118 (131)
T ss_dssp             HHCTEEEEEEETTHHHHTHHHHHHHHHHTCSCBEE
T ss_pred             HhcCCeEEEEeChHhcCCHHHHHHHHHHHhCCCCe
Confidence            444 3 7899999999 999999999998855553

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.97  E-value=4.4e-09  Score=90.66  Aligned_cols=107  Identities=12%  Similarity=0.116  Sum_probs=64.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE--EEec-----cCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY--ICLS-----RDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~--v~~~-----~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+......+.++|+||+|+|||++|+.+|+.++.+...  -.|.     ..+   ...|+.   .+..++
T Consensus        21 q~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~---~~~~~~   97 (363)
T PRK14961         21 QKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLI---EIDAAS   97 (363)
T ss_pred             hHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceE---Eecccc
Confidence            477788888888765555557999999999999999999988632100  0000     000   000111   011111


Q ss_pred             EEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ....+.  .+...+      ....+++|||+++++.+.++.|+..+|+
T Consensus        98 ~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe  145 (363)
T PRK14961         98 RTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEE  145 (363)
T ss_pred             cCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhc
Confidence            000000  111111      1235999999999999999999999996

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.96  E-value=8.8e-10  Score=78.12  Aligned_cols=89  Identities=19%  Similarity=0.105  Sum_probs=51.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEeccCCChhhh------cceeEeecCeEEEeccHHHHHhhcC-cE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSRDTTEADI------KQRREIVNGTAIYYDQSAVRAAIEG-RV  113 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~~~~~~dL------~g~~~~~~G~~~~~~gpl~~A~~~G-~v  113 (162)
                      +.+++|+||||||||++++.+|..++.+   +.++.+.........      ............-....+..|-... .+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            4689999999999999999999998876   555555422221111      0000000000000011122222333 89


Q ss_pred             EEEeCCCCCCccHHHHHHH
Q psy4122         114 LILEGIEKAERNVLPVLNN  132 (162)
Q Consensus       114 lllDEId~a~~~v~~~L~~  132 (162)
                      +++||+++........+..
T Consensus        82 iiiDei~~~~~~~~~~~~~  100 (148)
T smart00382       82 LILDEITSLLDAEQEALLL  100 (148)
T ss_pred             EEEECCcccCCHHHHHHHH
Confidence            9999999988877665443

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.

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=98.96  E-value=2.6e-09  Score=95.42  Aligned_cols=109  Identities=16%  Similarity=0.157  Sum_probs=83.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccC---CChhhhcceeEeecCeEEE
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRD---TTEADIKQRREIVNGTAIY   99 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~---~~~~dL~g~~~~~~G~~~~   99 (162)
                      .+|.+...++.+-.-....-+|||.|.+||||--+|+++.+..   ..|+..+||..-   .-.++|.|.          
T Consensus       228 ~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESELFGH----------  297 (550)
T COG3604         228 RSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESELFGH----------  297 (550)
T ss_pred             cCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccchHHHHHHHhcc----------
Confidence            3777777777665544456689999999999999999998765   578999999733   336778773          


Q ss_pred             eccHHHHH---------hhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcCC
Q psy4122         100 YDQSAVRA---------AIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDG  144 (162)
Q Consensus       100 ~~gpl~~A---------~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~g  144 (162)
                      +.|+++-|         +.+||.|+||||-.+|.+++..|+.+|++|++.=-+|
T Consensus       298 eKGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL~lQaKLLRvLQegEieRvG~  351 (550)
T COG3604         298 EKGAFTGAINTRRGRFELADGGTLFLDEIGELPLALQAKLLRVLQEGEIERVGG  351 (550)
T ss_pred             cccccccchhccCcceeecCCCeEechhhccCCHHHHHHHHHHHhhcceeecCC
Confidence            22233222         3578999999999999999999999999999965443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.95  E-value=3.4e-09  Score=100.45  Aligned_cols=109  Identities=17%  Similarity=0.132  Sum_probs=65.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE-----EEEeccCCChhhhcc--eeEeecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE-----YICLSRDTTEADIKQ--RREIVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~-----~v~~~~~~~~~dL~g--~~~~~~G~~~~   99 (162)
                      -...++.|+.++......+.+||+||||||||++|+.||+.++.+..     ...|+.-....+...  -..+ ++....
T Consensus        21 Qe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEi-dAas~~   99 (944)
T PRK14949         21 QSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEV-DAASRT   99 (944)
T ss_pred             cHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEe-cccccc
Confidence            36778888888887666645689999999999999999998875310     011110000111000  0001 111000


Q ss_pred             -ec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         100 -YD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       100 -~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       .+  .-+...+      ....|+||||+++++++.++.|+..||+
T Consensus       100 kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEE  145 (944)
T PRK14949        100 KVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEE  145 (944)
T ss_pred             CHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhc
Confidence             00  0111111      1235999999999999999999999996

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.94  E-value=4e-09  Score=96.86  Aligned_cols=97  Identities=16%  Similarity=0.152  Sum_probs=62.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccC-CChhh----hcceeEe-----------ecCeE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRD-TTEAD----IKQRREI-----------VNGTA   97 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~-~~~~d----L~g~~~~-----------~~G~~   97 (162)
                      ..+++|+||||||||++|+.++...          +.++..+++... .+..+    +++....           .-|..
T Consensus       175 ~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~  254 (615)
T TIGR02903       175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVP  254 (615)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCC
Confidence            4589999999999999999988655          234555665421 12222    2221000           00111


Q ss_pred             EEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122          98 IYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus        98 ~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      ...++.+..  .+|++|+|||++.++++.+..|..+++++++.+.
T Consensus       255 ~~~~g~v~~--asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~  297 (615)
T TIGR02903       255 EPKTGLVTD--AHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFS  297 (615)
T ss_pred             chhcCchhh--cCCCeEEEeccccCCHHHHHHHHHHHhhCeEEee
Confidence            112222222  2678999999999999999999999999876553

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.94  E-value=6.1e-09  Score=94.55  Aligned_cols=108  Identities=12%  Similarity=0.131  Sum_probs=65.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEE-ec--cCCChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYIC-LS--RDTTEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~-~~--~~~~~~dL~g~~~~~~G~   96 (162)
                      -+..++.|+..+......+.+||+||+|||||++|+.+|+.++..       +-.+. |.  ......|++.   +...+
T Consensus        21 q~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlie---idaas   97 (546)
T PRK14957         21 QQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIE---IDAAS   97 (546)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEE---eeccc
Confidence            366777888888765555458899999999999999999987641       11110 00  0001112211   10000


Q ss_pred             -EEEec-cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          97 -AIYYD-QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        97 -~~~~~-gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                       ..-.+ ..+...+      .+..+++|||+++++.+.++.|+..||+.
T Consensus        98 ~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEep  146 (546)
T PRK14957         98 RTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEP  146 (546)
T ss_pred             ccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcC
Confidence             00000 0111111      13369999999999999999999999973

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.93  E-value=7e-09  Score=93.46  Aligned_cols=125  Identities=14%  Similarity=0.193  Sum_probs=72.2

Q ss_pred             cceeceeeee-cccCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE------EEEec--c
Q psy4122           9 EYVRFTLIYL-FSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE------YICLS--R   79 (162)
Q Consensus         9 ~y~~~~~~~~-~~~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~------~v~~~--~   79 (162)
                      .|..+.+-|= .+-....--+...+.|+..+......+.+||+||+|||||++|+.+|+.++....      ...|+  .
T Consensus         7 ~y~~la~kyRP~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~   86 (507)
T PRK06645          7 QYIPFARKYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCT   86 (507)
T ss_pred             cccchhhhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCCh
Confidence            5666655441 1111111246778888887766555568999999999999999999998865210      00000  0


Q ss_pred             ------CCChhhhcceeEeecCeEEEecc--HHHHH------hhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          80 ------DTTEADIKQRREIVNGTAIYYDQ--SAVRA------AIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        80 ------~~~~~dL~g~~~~~~G~~~~~~g--pl~~A------~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                            +..-.|++   .+...+..-++.  .+...      ..+..+++|||+++++.+.++.|+..+|+
T Consensus        87 ~C~~i~~~~h~Dv~---eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEe  154 (507)
T PRK06645         87 NCISFNNHNHPDII---EIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEE  154 (507)
T ss_pred             HHHHHhcCCCCcEE---EeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhh
Confidence                  00000111   011100000000  01111      12457999999999999999999999996

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.93  E-value=5.4e-09  Score=96.46  Aligned_cols=107  Identities=11%  Similarity=0.133  Sum_probs=66.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc------------eEEEEeccCC---ChhhhcceeE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE------------VEYICLSRDT---TEADIKQRRE   91 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p------------~~~v~~~~~~---~~~dL~g~~~   91 (162)
                      -+...+.|+.++......+.+||+||+|||||++|+.+|+.++..            |-.+..+..+   +..|++   .
T Consensus        21 Qe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDvi---E   97 (700)
T PRK12323         21 QEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYI---E   97 (700)
T ss_pred             cHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcce---E
Confidence            477888899998877776667999999999999999999988751            1101000000   001121   1


Q ss_pred             eecCeEEEecc--HHHHHh----hc--CcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          92 IVNGTAIYYDQ--SAVRAA----IE--GRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        92 ~~~G~~~~~~g--pl~~A~----~~--G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +...+..-++.  -+.+.+    ..  ..|+||||+|+++.+..+.|+..||+
T Consensus        98 IdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEE  150 (700)
T PRK12323         98 MDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEE  150 (700)
T ss_pred             ecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhcc
Confidence            11110000000  011111    12  25999999999999999999999997

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.92  E-value=3.2e-09  Score=92.74  Aligned_cols=113  Identities=12%  Similarity=0.110  Sum_probs=77.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+......+.++++.|++||||+++|+.+...   .+.|+..++|.....   .+.|.|... ...|....
T Consensus       149 S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~~~~~~~lfg~~~~~~~~~~~~  228 (457)
T PRK11361        149 SPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTL  228 (457)
T ss_pred             cHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCHHHHHHHhcCCCCCCCCCCCCC
Confidence            45556666666665666779999999999999999998765   356888888874321   233444210 01121111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|.+..  .+||+|+||||+.++++++..|..+++++.+.-
T Consensus       229 ~~g~~~~--a~~gtl~ld~i~~l~~~~q~~L~~~l~~~~~~~  268 (457)
T PRK11361        229 RQGLFER--ANEGTLLLDEIGEMPLVLQAKLLRILQEREFER  268 (457)
T ss_pred             CCCceEE--CCCCEEEEechhhCCHHHHHHHHHHHhcCcEEe
Confidence            2233222  368999999999999999999999999887654

>PRK12377 putative replication protein; Provisional

Probab=98.92  E-value=3.3e-09  Score=87.65  Aligned_cols=99  Identities=23%  Similarity=0.325  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHhcCC-CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhccee--EeecCeEEEeccH
Q psy4122          30 WLSHLRWILQKDNM-SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRR--EIVNGTAIYYDQS  103 (162)
Q Consensus        30 ~~~~L~~i~~~~~~-g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~--~~~~G~~~~~~gp  103 (162)
                      .+...+.++..+.. ..+++|+||||||||+||.++|..+   |..+.++++.      +++...  ...++.   ...-
T Consensus        86 a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~------~l~~~l~~~~~~~~---~~~~  156 (248)
T PRK12377         86 ALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVP------DVMSRLHESYDNGQ---SGEK  156 (248)
T ss_pred             HHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHH------HHHHHHHHHHhccc---hHHH
Confidence            45555555555443 2579999999999999999999766   5555544442      333210  011111   1113


Q ss_pred             HHHHhhcCcEEEEeCC--CCCCccHHHHHHHhhcCC
Q psy4122         104 AVRAAIEGRVLILEGI--EKAERNVLPVLNNLLENR  137 (162)
Q Consensus       104 l~~A~~~G~vlllDEI--d~a~~~v~~~L~~lle~r  137 (162)
                      +.+.+.+-.+|+|||+  .+.++...+.|.++++.|
T Consensus       157 ~l~~l~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R  192 (248)
T PRK12377        157 FLQELCKVDLLVLDEIGIQRETKNEQVVLNQIIDRR  192 (248)
T ss_pred             HHHHhcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHH
Confidence            5677788899999999  556777889999999865

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.91  E-value=4.6e-09  Score=91.65  Aligned_cols=100  Identities=18%  Similarity=0.195  Sum_probs=68.9

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEeccCCC---hhhhcceeE-eecCeEEEeccHHHHHhhcCcEE
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLSRDTT---EADIKQRRE-IVNGTAIYYDQSAVRAAIEGRVL  114 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~~~gpl~~A~~~G~vl  114 (162)
                      ....++++.|++||||+++|+.+....+   .|+..++|..-.+   .+.|.|... .-.|......|.+..  .+||.|
T Consensus       160 ~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~--a~~gtl  237 (445)
T TIGR02915       160 PSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTLGKIEY--AHGGTL  237 (445)
T ss_pred             CCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCChHHHHHHhcCCCCCCcCCCccCCCCceeE--CCCCEE
Confidence            3567999999999999999999987654   5778888874321   233344210 001211222232322  368999


Q ss_pred             EEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         115 ILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       115 llDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +||||+.++++++..|..+++++.+.-.+
T Consensus       238 ~l~~i~~l~~~~q~~l~~~l~~~~~~~~~  266 (445)
T TIGR02915       238 FLDEIGDLPLNLQAKLLRFLQERVIERLG  266 (445)
T ss_pred             EEechhhCCHHHHHHHHHHHhhCeEEeCC
Confidence            99999999999999999999998765443

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.91  E-value=1e-08  Score=92.09  Aligned_cols=101  Identities=18%  Similarity=0.208  Sum_probs=65.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEE---------------EEec--cCCC
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEY---------------ICLS--RDTT   82 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~---------------v~~~--~~~~   82 (162)
                      -+...+.|+..+......+++||+||+|+|||++|+.+|+.++.       |+-.               +.++  ..+.
T Consensus        18 Qe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~~   97 (491)
T PRK14964         18 QDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTS   97 (491)
T ss_pred             cHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCCC
Confidence            36778888888877666678999999999999999999987742       1111               1111  1111


Q ss_pred             hhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        83 ~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..++..   +.+ ..  ...|+   ..+..++||||++.++.+.++.|+..||+
T Consensus        98 vddIR~---Iie-~~--~~~P~---~~~~KVvIIDEah~Ls~~A~NaLLK~LEe  142 (491)
T PRK14964         98 VDDIKV---ILE-NS--CYLPI---SSKFKVYIIDEVHMLSNSAFNALLKTLEE  142 (491)
T ss_pred             HHHHHH---HHH-HH--Hhccc---cCCceEEEEeChHhCCHHHHHHHHHHHhC
Confidence            112110   000 00  00010   12447999999999999999999999996

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.90  E-value=5.7e-09  Score=84.92  Aligned_cols=97  Identities=18%  Similarity=0.265  Sum_probs=63.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      +...+..++.+.... .+.+++|+||+|||||||+.++++..   |..+.++.+.....   .             . .-
T Consensus        29 n~~a~~~l~~~~~~~-~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~---~-------------~-~~   90 (235)
T PRK08084         29 NDSLLAALQNALRQE-HSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAW---F-------------V-PE   90 (235)
T ss_pred             cHHHHHHHHHHHhCC-CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhh---h-------------h-HH
Confidence            456777777776544 34589999999999999999998754   34455555542110   0             0 01


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccH------HHHHHHhhcCC--eEEE
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNV------LPVLNNLLENR--EMHL  141 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v------~~~L~~lle~r--~l~l  141 (162)
                      +.+.+..-.+|+||||++.+.+.      ...++.+.|++  .+.+
T Consensus        91 ~~~~~~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~  136 (235)
T PRK08084         91 VLEGMEQLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLI  136 (235)
T ss_pred             HHHHhhhCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEE
Confidence            22333444789999999986543      56777887765  3544

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.90  E-value=9.7e-09  Score=89.56  Aligned_cols=109  Identities=11%  Similarity=0.062  Sum_probs=65.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE----------EEeccCCC-hhhhc-c----ee
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY----------ICLSRDTT-EADIK-Q----RR   90 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~----------v~~~~~~~-~~dL~-g----~~   90 (162)
                      -+...+.|+.++......+.++|+||||||||++|+.+|+.++.+-..          -.|. ... -.++. |    ..
T Consensus        21 q~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~-~c~~c~~~~~~~~~n~~   99 (397)
T PRK14955         21 QEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCG-ECESCRDFDAGTSLNIS   99 (397)
T ss_pred             hHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCC-CCHHHHHHhcCCCCCeE
Confidence            467788888888876666569999999999999999999988653100          0000 000 00000 0    00


Q ss_pred             EeecCeEEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          91 EIVNGTAIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        91 ~~~~G~~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .+.++...=.+.  -+...+      .+..++||||+++++.+.++.|+..+|+
T Consensus       100 ~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEe  153 (397)
T PRK14955        100 EFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEE  153 (397)
T ss_pred             eecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhc
Confidence            011111000000  011122      2346999999999999999999999996

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.89  E-value=7.1e-09  Score=95.71  Aligned_cols=106  Identities=16%  Similarity=0.209  Sum_probs=64.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+..++.|+..+......+.+||+||+|||||++|+.+|+.++..       |-.+..+..+   ...|++   .+ ++.
T Consensus        21 Qe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~i---ei-daa   96 (647)
T PRK07994         21 QEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLI---EI-DAA   96 (647)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCce---ee-ccc
Confidence            367788888888765555456899999999999999999988653       1100000000   001111   01 111


Q ss_pred             E-EEec--cHHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 A-IYYD--QSAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~-~~~~--gpl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      . .=.+  .-+...+    .+|  .|+||||+|+++.+.++.|+..||+
T Consensus        97 s~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEE  145 (647)
T PRK07994         97 SRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE  145 (647)
T ss_pred             ccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHc
Confidence            0 0000  0111111    122  5999999999999999999999997

>PRK08116 hypothetical protein; Validated

Probab=98.89  E-value=5.1e-09  Score=87.11  Aligned_cols=103  Identities=17%  Similarity=0.205  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHhcC----CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          30 WLSHLRWILQKDN----MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        30 ~~~~L~~i~~~~~----~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      .....+..+..+.    .+.+++|+|+||+|||+||.++|+.+   +.++.+++...-  ..++...  . ++...+...
T Consensus        96 a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~l--l~~i~~~--~-~~~~~~~~~  170 (268)
T PRK08116         96 AYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQL--LNRIKST--Y-KSSGKEDEN  170 (268)
T ss_pred             HHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHH--HHHHHHH--H-hccccccHH
Confidence            4445555555432    23459999999999999999999764   667666654311  1122211  1 111112223


Q ss_pred             HHHHHhhcCcEEEEeCC--CCCCccHHHHHHHhhcCC
Q psy4122         103 SAVRAAIEGRVLILEGI--EKAERNVLPVLNNLLENR  137 (162)
Q Consensus       103 pl~~A~~~G~vlllDEI--d~a~~~v~~~L~~lle~r  137 (162)
                      -+.+++.+..+|+|||+  ++..+..+..|..+++.|
T Consensus       171 ~~~~~l~~~dlLviDDlg~e~~t~~~~~~l~~iin~r  207 (268)
T PRK08116        171 EIIRSLVNADLLILDDLGAERDTEWAREKVYNIIDSR  207 (268)
T ss_pred             HHHHHhcCCCEEEEecccCCCCCHHHHHHHHHHHHHH
Confidence            46677788899999999  566777888888888854

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.89  E-value=3.4e-09  Score=79.17  Aligned_cols=80  Identities=21%  Similarity=0.280  Sum_probs=55.7

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCc
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGR  112 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~  112 (162)
                      .+-.......||+|+|++||||+++|+.++...+..   +..+.|.. +. .+                  +... .+|+
T Consensus        13 ~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~-~~-~~------------------~l~~-a~~g   71 (138)
T PF14532_consen   13 QLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCAS-LP-AE------------------LLEQ-AKGG   71 (138)
T ss_dssp             HHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHC-TC-HH------------------HHHH-CTTS
T ss_pred             HHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhh-Cc-HH------------------HHHH-cCCC
Confidence            333333456799999999999999999999877652   22222321 11 11                  2222 2888


Q ss_pred             EEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         113 VLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       113 vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .++|+||+.++++.+..|...+++
T Consensus        72 tL~l~~i~~L~~~~Q~~L~~~l~~   95 (138)
T PF14532_consen   72 TLYLKNIDRLSPEAQRRLLDLLKR   95 (138)
T ss_dssp             EEEEECGCCS-HHHHHHHHHHHHH
T ss_pred             EEEECChHHCCHHHHHHHHHHHHh
Confidence            999999999999999999999985

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.88  E-value=1.6e-08  Score=88.56  Aligned_cols=107  Identities=20%  Similarity=0.210  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHHhcC---------CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCC---------Chhhhcce
Q psy4122          28 QDWLSHLRWILQKDN---------MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDT---------TEADIKQR   89 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~---------~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~---------~~~dL~g~   89 (162)
                      +..++.|+.++....         ..+.+||+||+|+|||++|+.+|+.+..+-..-.++...         +-.|+.- 
T Consensus        11 ~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~~-   89 (394)
T PRK07940         11 EAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPDVRV-   89 (394)
T ss_pred             HHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEE-
Confidence            567788888888754         455699999999999999999998775431000000000         0111110 


Q ss_pred             eEeecCeEEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          90 REIVNGTAIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        90 ~~~~~G~~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       ...+|.....+.  .+.+.+      ....|++|||+++++++..+.|+..||+
T Consensus        90 -i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEe  143 (394)
T PRK07940         90 -VAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEE  143 (394)
T ss_pred             -eccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhc
Confidence             001122111111  111111      1225899999999999999999999997

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=98.88  E-value=3.8e-09  Score=98.53  Aligned_cols=89  Identities=13%  Similarity=0.222  Sum_probs=55.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeEEEecc--HHHHHh-hc-
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ--SAVRAA-IE-  110 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g--pl~~A~-~~-  110 (162)
                      .|++|+||||||||++|+.+|..+          +..+..+.      .+.++...... |  .|+..  .+...+ .+ 
T Consensus       204 ~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~------~~~l~a~~~~~-g--~~e~~l~~i~~~~~~~~  274 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLD------MGSLLAGTKYR-G--DFEERLKAVVSEIEKEP  274 (731)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEec------HHHHhhhcccc-c--hHHHHHHHHHHHHhccC
Confidence            489999999999999999999876          33333222      22333100000 1  11110  112222 22 


Q ss_pred             CcEEEEeCCCCCC---------ccHHHHHHHhhcCCeEEEc
Q psy4122         111 GRVLILEGIEKAE---------RNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       111 G~vlllDEId~a~---------~~v~~~L~~lle~r~l~l~  142 (162)
                      +.+|+|||||.+.         .++.+.|.+.|++|++.+-
T Consensus       275 ~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~g~i~~I  315 (731)
T TIGR02639       275 NAILFIDEIHTIVGAGATSGGSMDASNLLKPALSSGKLRCI  315 (731)
T ss_pred             CeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhCCCeEEE
Confidence            4689999999763         3568899999999988764

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.87  E-value=7.8e-09  Score=90.91  Aligned_cols=115  Identities=14%  Similarity=0.152  Sum_probs=75.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+..+.+-.....+.++++.|++||||+++|+.++...   +.|+..++|..-..   .++|.|... .-.|....
T Consensus       144 s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~~~~~~~lfg~~~g~~~~~~~~  223 (469)
T PRK10923        144 APAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTI  223 (469)
T ss_pred             CHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCHHHHHHHhcCCCCCCCCCCCcC
Confidence            344444444443333456799999999999999999998765   46888888863311   344444210 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      ..|-+..  .+||.++||||+.++++++..|..+++++++.-.+
T Consensus       224 ~~g~~~~--a~~Gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~~~  265 (469)
T PRK10923        224 RQGRFEQ--ADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVG  265 (469)
T ss_pred             CCCCeeE--CCCCEEEEeccccCCHHHHHHHHHHHhcCcEEeCC
Confidence            2222222  36889999999999999999999999998876543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.87  E-value=1.1e-08  Score=95.58  Aligned_cols=107  Identities=13%  Similarity=0.174  Sum_probs=65.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCCC---hhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDTT---EADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~~---~~dL~g~~~~~~G~   96 (162)
                      -+..++.|+..+......+.+||+||+|||||++++.||+.++..       |-.+..+..+.   ..|++   .+...+
T Consensus        21 Qe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~Dvi---EIDAas   97 (830)
T PRK07003         21 QEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYV---EMDAAS   97 (830)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEE---Eecccc
Confidence            477888888888766555567999999999999999999988753       11000000000   01111   111111


Q ss_pred             EEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+.  -+++.+      .+..|+||||+|+++.+..+.|+..||+
T Consensus        98 ~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEE  145 (830)
T PRK07003         98 NRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEE  145 (830)
T ss_pred             cccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHh
Confidence            000000  011111      1246999999999999999999999996

>CHL00195 ycf46 Ycf46; Provisional

Probab=98.86  E-value=5.5e-09  Score=93.74  Aligned_cols=73  Identities=16%  Similarity=0.105  Sum_probs=46.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..+.+||+||||||||.+|+++|+.++.|+..+.++.-  .+.++|.      +..-....+..|- ....||+|||||+
T Consensus       258 ~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l--~~~~vGe------se~~l~~~f~~A~~~~P~IL~IDEID~  329 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKL--FGGIVGE------SESRMRQMIRIAEALSPCILWIDEIDK  329 (489)
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHh--cccccCh------HHHHHHHHHHHHHhcCCcEEEehhhhh
Confidence            34679999999999999999999999999887766421  1111110      0000001121222 2457999999997


Q ss_pred             CC
Q psy4122         122 AE  123 (162)
Q Consensus       122 a~  123 (162)
                      +.
T Consensus       330 ~~  331 (489)
T CHL00195        330 AF  331 (489)
T ss_pred             hh
Confidence            53

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=98.86  E-value=9e-09  Score=85.90  Aligned_cols=110  Identities=18%  Similarity=0.237  Sum_probs=65.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEeccCCChhhhcc---eeEee-cCeEE
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSRDTTEADIKQ---RREIV-NGTAI   98 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~~~~~~dL~g---~~~~~-~G~~~   98 (162)
                      +|.++.+....|-.-...++|+||+||+|||||.+++.+-..+...   ...++++..|++..+..   ....+ .|. .
T Consensus        15 pT~dt~r~~~ll~~l~~~~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~-~   93 (272)
T PF12775_consen   15 PTVDTVRYSYLLDLLLSNGRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQLQKIIESKLEKRRGR-V   93 (272)
T ss_dssp             --HHHHHHHHHHHHHHHCTEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHHHHCCCTTECECTTE-E
T ss_pred             CcHHHHHHHHHHHHHHHcCCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHHHHHHhhcEEcCCCC-C
Confidence            4555555544333333468899999999999999999876555433   23566677666655432   11112 233 3


Q ss_pred             EeccHHHHHhhcCcEEEEeCCCCCCcc------HHHHHHHhhcCCeEEE
Q psy4122          99 YYDQSAVRAAIEGRVLILEGIEKAERN------VLPVLNNLLENREMHL  141 (162)
Q Consensus        99 ~~~gpl~~A~~~G~vlllDEId~a~~~------v~~~L~~lle~r~l~l  141 (162)
                      |  ||-   ..+.-++++|++|...+|      .++.|.+++|.+-+.-
T Consensus        94 ~--gP~---~~k~lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd  137 (272)
T PF12775_consen   94 Y--GPP---GGKKLVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYD  137 (272)
T ss_dssp             E--EEE---SSSEEEEEEETTT-S---TTS--HHHHHHHHHHHCSEEEC
T ss_pred             C--CCC---CCcEEEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCccc
Confidence            3  341   123358899999987654      5799999999776543

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.85  E-value=5.9e-09  Score=90.84  Aligned_cols=83  Identities=22%  Similarity=0.252  Sum_probs=52.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEE-eccHHHHHhh-cCcEEEEeCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIY-YDQSAVRAAI-EGRVLILEGIEK  121 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~-~~gpl~~A~~-~G~vlllDEId~  121 (162)
                      .+.+||+||||||||++|+++|..++.++..+.++      ++...+   -|...+ ....+..|-. .+++|+|||||.
T Consensus       165 p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~------~l~~~~---~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~  235 (389)
T PRK03992        165 PKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGS------ELVQKF---IGEGARLVRELFELAREKAPSIIFIDEIDA  235 (389)
T ss_pred             CCceEEECCCCCChHHHHHHHHHHhCCCEEEeehH------HHhHhh---ccchHHHHHHHHHHHHhcCCeEEEEechhh
Confidence            35699999999999999999999999997776554      232110   011000 0011222222 357999999998


Q ss_pred             C-----------CccHHHHHHHhhc
Q psy4122         122 A-----------ERNVLPVLNNLLE  135 (162)
Q Consensus       122 a-----------~~~v~~~L~~lle  135 (162)
                      +           +++++..|..++.
T Consensus       236 l~~~r~~~~~~~~~~~~~~l~~lL~  260 (389)
T PRK03992        236 IAAKRTDSGTSGDREVQRTLMQLLA  260 (389)
T ss_pred             hhcccccCCCCccHHHHHHHHHHHH
Confidence            6           3455666666663

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.85  E-value=2e-08  Score=90.76  Aligned_cols=107  Identities=14%  Similarity=0.164  Sum_probs=65.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+......+.+||+||+|||||++|+.+|+.++.+       +-.+..+..+   ...|++   .+..++
T Consensus        21 q~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~---ei~~~~   97 (527)
T PRK14969         21 QEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLI---EVDAAS   97 (527)
T ss_pred             cHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCcee---Eeeccc
Confidence            467788888888876666567999999999999999999988642       2111000000   011121   111110


Q ss_pred             EEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+.  -+...+      .+..++||||+|+++.+..+.|+..||+
T Consensus        98 ~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEe  145 (527)
T PRK14969         98 NTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEE  145 (527)
T ss_pred             cCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhC
Confidence            000000  011111      1236999999999999999999999997

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.84  E-value=1.8e-08  Score=95.38  Aligned_cols=107  Identities=13%  Similarity=0.089  Sum_probs=66.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEE-Eec----cCCChhhhcceeEeec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYI-CLS----RDTTEADIKQRREIVN   94 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v-~~~----~~~~~~dL~g~~~~~~   94 (162)
                      -+...+.|+.++......+.+||+||+|||||++|+.||+.++.       ||-.+ +|.    ..-..-|++   .+..
T Consensus        20 qe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~---eida   96 (824)
T PRK07764         20 QEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVT---EIDA   96 (824)
T ss_pred             cHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEE---Eecc
Confidence            36678889988887666656899999999999999999998863       22111 010    000011111   1111


Q ss_pred             CeEEEecc--HHHH-----Hh-hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          95 GTAIYYDQ--SAVR-----AA-IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        95 G~~~~~~g--pl~~-----A~-~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ++..=++.  -+.+     .+ ....|+||||+|+++.+.++.|+..||+
T Consensus        97 as~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEE  146 (824)
T PRK07764         97 ASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEE  146 (824)
T ss_pred             cccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhC
Confidence            11000000  0110     11 2346999999999999999999999996

>CHL00176 ftsH cell division protein; Validated

Probab=98.84  E-value=1.4e-08  Score=93.78  Aligned_cols=72  Identities=18%  Similarity=0.155  Sum_probs=45.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~a  122 (162)
                      .+++||+||||||||++|+++|...+.|+..++++.-.  +...|     .+.... ..-+.+|.. ...+|+|||||.+
T Consensus       216 p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~--~~~~g-----~~~~~v-r~lF~~A~~~~P~ILfIDEID~l  287 (638)
T CHL00176        216 PKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFV--EMFVG-----VGAARV-RDLFKKAKENSPCIVFIDEIDAV  287 (638)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHH--HHhhh-----hhHHHH-HHHHHHHhcCCCcEEEEecchhh
Confidence            34799999999999999999999999998777664211  11111     010000 011233332 2368999999887


Q ss_pred             C
Q psy4122         123 E  123 (162)
Q Consensus       123 ~  123 (162)
                      .
T Consensus       288 ~  288 (638)
T CHL00176        288 G  288 (638)
T ss_pred             h
Confidence            3

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.84  E-value=1.6e-08  Score=93.09  Aligned_cols=106  Identities=10%  Similarity=0.148  Sum_probs=65.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc------------eEEE-Eec--cCCChhhhcceeE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE------------VEYI-CLS--RDTTEADIKQRRE   91 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p------------~~~v-~~~--~~~~~~dL~g~~~   91 (162)
                      -+...+.|+.++......+.+||+||+|||||++|+.+|+.++..            |-.+ +|.  ..-...|++   .
T Consensus        21 Qe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~---e   97 (618)
T PRK14951         21 QEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYT---E   97 (618)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCcee---e
Confidence            467888999998877666567999999999999999999988641            1110 000  000001111   0


Q ss_pred             eecCeEEE-ecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          92 IVNGTAIY-YDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        92 ~~~G~~~~-~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      + ++.... .+.  -+.+.+      ....|++|||+|+++.+..+.|+..||+
T Consensus        98 l-daas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEE  150 (618)
T PRK14951         98 L-DAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEE  150 (618)
T ss_pred             c-CcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhccc
Confidence            1 111000 000  011111      1236999999999999999999999996

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.84  E-value=1.2e-08  Score=84.50  Aligned_cols=102  Identities=18%  Similarity=0.232  Sum_probs=67.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ....+..++...+.+..+++++|+||||+|||+||-++|..+   |..+.++.+...  .++|...  ..+|.   .+.-
T Consensus        88 ~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el--~~~Lk~~--~~~~~---~~~~  160 (254)
T COG1484          88 DKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDL--LSKLKAA--FDEGR---LEEK  160 (254)
T ss_pred             hHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHH--HHHHHHH--HhcCc---hHHH
Confidence            455666777777666678899999999999999999999654   555665555422  2333321  11122   1224


Q ss_pred             HHHHhhcCcEEEEeCCCC--CCccHHHHHHHhhc
Q psy4122         104 AVRAAIEGRVLILEGIEK--AERNVLPVLNNLLE  135 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~--a~~~v~~~L~~lle  135 (162)
                      +.+.+++-.+|||||+-.  ..+...+.+.+++.
T Consensus       161 l~~~l~~~dlLIiDDlG~~~~~~~~~~~~~q~I~  194 (254)
T COG1484         161 LLRELKKVDLLIIDDIGYEPFSQEEADLLFQLIS  194 (254)
T ss_pred             HHHHhhcCCEEEEecccCccCCHHHHHHHHHHHH
Confidence            667788899999999966  44434566666555

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.83  E-value=2.2e-08  Score=92.09  Aligned_cols=106  Identities=17%  Similarity=0.174  Sum_probs=64.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE--EEEecc-----CC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE--YICLSR-----DT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~--~v~~~~-----~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+.++........+||+||+|||||++|+.+|+.++.+-.  ...|+.     .+   ...|++   .+ ++.
T Consensus        21 Qe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~---eI-d~a   96 (624)
T PRK14959         21 QETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVV---EI-DGA   96 (624)
T ss_pred             CHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCceE---EE-ecc
Confidence            46778888888876655567889999999999999999998864210  000100     00   000111   01 110


Q ss_pred             -EEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 -AIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 -~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       ..-.+.  -+.+.+      ....++||||+++++.+.++.|+..||+
T Consensus        97 ~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEE  145 (624)
T PRK14959         97 SNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEE  145 (624)
T ss_pred             cccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhc
Confidence             000000  011111      1236999999999999999999999986

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.83  E-value=1.1e-08  Score=84.32  Aligned_cols=101  Identities=19%  Similarity=0.252  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHHhcCCC-CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhccee--EeecCeEEEecc
Q psy4122          29 DWLSHLRWILQKDNMS-QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRR--EIVNGTAIYYDQ  102 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g-~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~--~~~~G~~~~~~g  102 (162)
                      ..+..++..+.....+ .+++|.|+||||||+|+.++|..+   |..+.++.      ..+++...  ......  ....
T Consensus        83 ~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it------~~~l~~~l~~~~~~~~--~~~~  154 (244)
T PRK07952         83 NALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT------VADIMSAMKDTFSNSE--TSEE  154 (244)
T ss_pred             HHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE------HHHHHHHHHHHHhhcc--ccHH
Confidence            3566666666654432 489999999999999999999776   55555553      34444210  011111  1122


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCcc--HHHHHHHhhcCC
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERN--VLPVLNNLLENR  137 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~--v~~~L~~lle~r  137 (162)
                      .+.+.+..-.+|+|||+.....+  ..+.|+++++.|
T Consensus       155 ~~l~~l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~R  191 (244)
T PRK07952        155 QLLNDLSNVDLLVIDEIGVQTESRYEKVIINQIVDRR  191 (244)
T ss_pred             HHHHHhccCCEEEEeCCCCCCCCHHHHHHHHHHHHHH
Confidence            45666777889999999776544  456888898865

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.83  E-value=1e-08  Score=91.64  Aligned_cols=72  Identities=19%  Similarity=0.153  Sum_probs=45.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~a  122 (162)
                      .+.+||+||||||||++|+.+|...+.|+..+++.      ++...+  .+....-....+..|.. .+.+|+|||||.+
T Consensus        88 ~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~------~~~~~~--~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l  159 (495)
T TIGR01241        88 PKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGS------DFVEMF--VGVGASRVRDLFEQAKKNAPCIIFIDEIDAV  159 (495)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHH------HHHHHH--hcccHHHHHHHHHHHHhcCCCEEEEechhhh
Confidence            45799999999999999999999999997766543      222100  00000000112233332 3479999999886


Q ss_pred             C
Q psy4122         123 E  123 (162)
Q Consensus       123 ~  123 (162)
                      .
T Consensus       160 ~  160 (495)
T TIGR01241       160 G  160 (495)
T ss_pred             h
Confidence            4

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.82  E-value=2.6e-08  Score=92.44  Aligned_cols=107  Identities=15%  Similarity=0.167  Sum_probs=66.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce-------EEEEeccCCC---hhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV-------EYICLSRDTT---EADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~-------~~v~~~~~~~---~~dL~g~~~~~~G~   96 (162)
                      -...++.|+..+......+.+||+||+|||||++|+.+|+.++.+-       ..+..+..+.   ..|++   .+...+
T Consensus        21 Qe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~Dvl---EidaAs   97 (709)
T PRK08691         21 QEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLL---EIDAAS   97 (709)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceE---EEeccc
Confidence            4677888888888766666789999999999999999999886531       1111000000   11221   111111


Q ss_pred             EEEecc--HHHHH------hhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRA------AIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A------~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+.  -++..      ..+..++||||+++++.+..+.|+..||+
T Consensus        98 ~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEE  145 (709)
T PRK08691         98 NTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEE  145 (709)
T ss_pred             cCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHh
Confidence            000000  01111      12346999999999999999999999986

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.82  E-value=2.6e-09  Score=83.90  Aligned_cols=99  Identities=18%  Similarity=0.268  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcceeE--eecCeEEEecc
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQRRE--IVNGTAIYYDQ  102 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g~~~--~~~G~~~~~~g  102 (162)
                      ...+..+.. ......+++++|.||||+|||+||.+++..   .|.++.++...      +|+....  ..++.    ..
T Consensus        32 ~~~~~~l~~-~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~------~L~~~l~~~~~~~~----~~  100 (178)
T PF01695_consen   32 KAQIAQLAA-LEFIENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITAS------DLLDELKQSRSDGS----YE  100 (178)
T ss_dssp             --HHHHHHH-H-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHH------HHHHHHHCCHCCTT----HC
T ss_pred             HHHHHHHhc-CCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecC------ceeccccccccccc----hh
Confidence            444444422 223335789999999999999999999853   37777776653      4443111  11121    12


Q ss_pred             HHHHHhhcCcEEEEeCCCCC--CccHHHHHHHhhcCC
Q psy4122         103 SAVRAAIEGRVLILEGIEKA--ERNVLPVLNNLLENR  137 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a--~~~v~~~L~~lle~r  137 (162)
                      -+.+.+.+-.+|||||+-..  .+...+.|..+++.|
T Consensus       101 ~~~~~l~~~dlLilDDlG~~~~~~~~~~~l~~ii~~R  137 (178)
T PF01695_consen  101 ELLKRLKRVDLLILDDLGYEPLSEWEAELLFEIIDER  137 (178)
T ss_dssp             HHHHHHHTSSCEEEETCTSS---HHHHHCTHHHHHHH
T ss_pred             hhcCccccccEecccccceeeecccccccchhhhhHh
Confidence            35677888899999999654  445667777777754

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.81  E-value=3.1e-08  Score=89.26  Aligned_cols=106  Identities=13%  Similarity=0.057  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--eE--EEEeccCC-----ChhhhcceeEeecCeEE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--VE--YICLSRDT-----TEADIKQRREIVNGTAI   98 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--~~--~v~~~~~~-----~~~dL~g~~~~~~G~~~   98 (162)
                      +...+.|+.++.+...++.+||+||||||||++|+.+|+.++..  ..  .-.|+.-.     .-.|+.   .+...+..
T Consensus        20 ~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~---el~~~~~~   96 (504)
T PRK14963         20 EHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVL---EIDAASNN   96 (504)
T ss_pred             HHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceE---EecccccC
Confidence            56778888888877666556999999999999999999887531  00  00111000     000111   01000000


Q ss_pred             Eecc--HHHH------HhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          99 YYDQ--SAVR------AAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        99 ~~~g--pl~~------A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      =.+.  -+..      ...+..++||||+++++.+.++.|...+++
T Consensus        97 ~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEe  142 (504)
T PRK14963         97 SVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEE  142 (504)
T ss_pred             CHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHh
Confidence            0000  0111      112346999999999999999999999987

>KOG0989|consensus

Probab=98.81  E-value=5.4e-09  Score=88.81  Aligned_cols=104  Identities=14%  Similarity=0.222  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc----eEEEEeccCCChhhhcceeEeecCeEEEec--
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE----VEYICLSRDTTEADIKQRREIVNGTAIYYD--  101 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p----~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~--  101 (162)
                      ++++..|..-+.. ...-++|++||||||||+.|.++|++++-|    +..+..+    .+|-.|.-......-.|..  
T Consensus        42 e~vV~~L~~a~~~-~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~ln----aSderGisvvr~Kik~fakl~  116 (346)
T KOG0989|consen   42 EHVVQVLKNALLR-RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELN----ASDERGISVVREKIKNFAKLT  116 (346)
T ss_pred             HHHHHHHHHHHhh-cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhc----ccccccccchhhhhcCHHHHh
Confidence            5666667766665 333489999999999999999999988763    3333333    2233331101000000000  


Q ss_pred             ----cHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 ----QSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 ----gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                          ++.-.-..-=.+++|||.|.+..+.+++|...+|+
T Consensus       117 ~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~  155 (346)
T KOG0989|consen  117 VLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMED  155 (346)
T ss_pred             hccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhc
Confidence                00000000116999999999999999999999996

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.81  E-value=3.7e-08  Score=76.87  Aligned_cols=103  Identities=21%  Similarity=0.258  Sum_probs=58.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEE-Eec--cCCChhhhcceeEeecCeEEEec
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYI-CLS--RDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v-~~~--~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      +.|+..+......+.+||+||+|+|||++|+.+++.+..+       +... +|.  ..-...|+..  ....+...-.+
T Consensus         2 ~~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~--~~~~~~~~~~~   79 (188)
T TIGR00678         2 QQLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHR--LEPEGQSIKVD   79 (188)
T ss_pred             hHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEE--eccccCcCCHH
Confidence            3566666665555679999999999999999999876432       1000 000  0000001100  00001000000


Q ss_pred             c--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 Q--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .  .+...+      ....+++|||+++++++.++.|+..+|+
T Consensus        80 ~i~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~  122 (188)
T TIGR00678        80 QVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEE  122 (188)
T ss_pred             HHHHHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcC
Confidence            0  011111      1236999999999999999999999986

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK08181 transposase; Validated

Probab=98.80  E-value=1e-08  Score=85.64  Aligned_cols=101  Identities=17%  Similarity=0.133  Sum_probs=61.8

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcceeE--eecCeEEEe
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQRRE--IVNGTAIYY  100 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g~~~--~~~G~~~~~  100 (162)
                      ++......+...-.....+++++|+||||||||+|+.++|..   .|+.+.+++.      .+|+....  ..++.    
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~------~~L~~~l~~a~~~~~----  157 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRT------TDLVQKLQVARRELQ----  157 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeH------HHHHHHHHHHHhCCc----
Confidence            345555555433112235679999999999999999999853   3666665554      34442110  01111    


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCcc--HHHHHHHhhcC
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERN--VLPVLNNLLEN  136 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~--v~~~L~~lle~  136 (162)
                      .....+.+.+-.+|+|||+...+.+  ....|.++++.
T Consensus       158 ~~~~l~~l~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~  195 (269)
T PRK08181        158 LESAIAKLDKFDLLILDDLAYVTKDQAETSVLFELISA  195 (269)
T ss_pred             HHHHHHHHhcCCEEEEeccccccCCHHHHHHHHHHHHH
Confidence            1124455677789999999876554  34567777764

>PRK06620 hypothetical protein; Validated

Probab=98.80  E-value=2e-08  Score=80.96  Aligned_cols=89  Identities=17%  Similarity=0.172  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHhcCCC---CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHH
Q psy4122          28 QDWLSHLRWILQKDNMS---QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA  104 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g---~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl  104 (162)
                      ....+.++.+...+..+   .+++|+||||||||||++.+++..+..+  +.        +...           .+   
T Consensus        25 ~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~--~~--------~~~~-----------~~---   80 (214)
T PRK06620         25 DQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYI--IK--------DIFF-----------NE---   80 (214)
T ss_pred             HHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhccCCEE--cc--------hhhh-----------ch---
Confidence            45667777766544211   3599999999999999999888776421  11        0000           00   


Q ss_pred             HHHhhcCcEEEEeCCCCCCc-cHHHHHHHhhcCCeEEE
Q psy4122         105 VRAAIEGRVLILEGIEKAER-NVLPVLNNLLENREMHL  141 (162)
Q Consensus       105 ~~A~~~G~vlllDEId~a~~-~v~~~L~~lle~r~l~l  141 (162)
                       ..++...+++||||++... .....+|.+.|+|...+
T Consensus        81 -~~~~~~d~lliDdi~~~~~~~lf~l~N~~~e~g~~il  117 (214)
T PRK06620         81 -EILEKYNAFIIEDIENWQEPALLHIFNIINEKQKYLL  117 (214)
T ss_pred             -hHHhcCCEEEEeccccchHHHHHHHHHHHHhcCCEEE
Confidence             1124568999999997753 45666677778776444

>PF13173 AAA_14: AAA domain

Probab=98.80  E-value=2.4e-08  Score=73.70  Aligned_cols=83  Identities=13%  Similarity=0.196  Sum_probs=54.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC--CceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ--REVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIE  120 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg--~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId  120 (162)
                      ++.++|.||.|||||++++++++.+.  ....++++. +.....+.      ..+  .. .-+.+... +..+++||||+
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~-~~~~~~~~------~~~--~~-~~~~~~~~~~~~~i~iDEiq   71 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFD-DPRDRRLA------DPD--LL-EYFLELIKPGKKYIFIDEIQ   71 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhcccccceeeccC-CHHHHHHh------hhh--hH-HHHHHhhccCCcEEEEehhh
Confidence            46789999999999999999998776  445556554 21111111      000  00 01111121 45789999999


Q ss_pred             CCCccHHHHHHHhhcCC
Q psy4122         121 KAERNVLPVLNNLLENR  137 (162)
Q Consensus       121 ~a~~~v~~~L~~lle~r  137 (162)
                      +++ +....+..+.|++
T Consensus        72 ~~~-~~~~~lk~l~d~~   87 (128)
T PF13173_consen   72 YLP-DWEDALKFLVDNG   87 (128)
T ss_pred             hhc-cHHHHHHHHHHhc
Confidence            996 7888899999876

>PRK15115 response regulator GlrR; Provisional

Probab=98.79  E-value=2e-08  Score=87.63  Aligned_cols=113  Identities=17%  Similarity=0.149  Sum_probs=73.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+........++++.|++|+||+++|+.+....   +.|+..++|.....   .+.|.|... .-.|...-
T Consensus       140 s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~~~~~~~lfg~~~~~~~~~~~~  219 (444)
T PRK15115        140 SPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESELFGHARGAFTGAVSN  219 (444)
T ss_pred             CHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCHHHHHHHhcCCCcCCCCCCccC
Confidence            344444444443333345689999999999999999998764   46888888874311   223333110 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|-+.  ..+|+.|+||||+.++++++..|..+++++.+.-
T Consensus       220 ~~g~~~--~a~~gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~  259 (444)
T PRK15115        220 REGLFQ--AAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRP  259 (444)
T ss_pred             CCCcEE--ECCCCEEEEEccccCCHHHHHHHHHHHhhCCEEe
Confidence            122221  2367899999999999999999999999988743

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.79  E-value=3.7e-08  Score=82.45  Aligned_cols=109  Identities=9%  Similarity=0.141  Sum_probs=62.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-----ceEEEEeccCC--ChhhhcceeEe----ecC
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-----EVEYICLSRDT--TEADIKQRREI----VNG   95 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-----p~~~v~~~~~~--~~~dL~g~~~~----~~G   95 (162)
                      .+...+.|+..+..-.. .+++|+||||||||++|+.+|+.+..     ++..+++..-.  ....+...+..    ..+
T Consensus        20 ~~~~~~~L~~~~~~~~~-~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (337)
T PRK12402         20 QDEVVERLSRAVDSPNL-PHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTD   98 (337)
T ss_pred             CHHHHHHHHHHHhCCCC-ceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhh
Confidence            46677778777764322 28999999999999999999987642     23334442110  00000000000    000


Q ss_pred             -eEEEeccHHHHH-----------hhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          96 -TAIYYDQSAVRA-----------AIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        96 -~~~~~~gpl~~A-----------~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       ...-......+.           ..+..+|+|||++.++++.+..|..++++
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~  151 (337)
T PRK12402         99 KRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQ  151 (337)
T ss_pred             hhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHh
Confidence             000000001111           12346999999999999999999999884

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.79  E-value=1.2e-08  Score=96.91  Aligned_cols=102  Identities=17%  Similarity=0.280  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeEEEe
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~  100 (162)
                      ++.+..++.... ..+++|+||||||||++|+.+|...          +.++..+.++.........       |.  |.
T Consensus       187 i~~~i~iL~r~~-~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~-------g~--~e  256 (857)
T PRK10865        187 IRRTIQVLQRRT-KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYR-------GE--FE  256 (857)
T ss_pred             HHHHHHHHhcCC-cCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchh-------hh--hH
Confidence            444444443332 2389999999999999999999876          4444444333211000010       11  11


Q ss_pred             cc--HHHHH-hhc--CcEEEEeCCCCCCc--------cHHHHHHHhhcCCeEEEc
Q psy4122         101 DQ--SAVRA-AIE--GRVLILEGIEKAER--------NVLPVLNNLLENREMHLE  142 (162)
Q Consensus       101 ~g--pl~~A-~~~--G~vlllDEId~a~~--------~v~~~L~~lle~r~l~l~  142 (162)
                      ..  .+... .+.  ..+|+||||+.+..        +..+.|.+.+++|++.+-
T Consensus       257 ~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~g~l~~I  311 (857)
T PRK10865        257 ERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCV  311 (857)
T ss_pred             HHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhhcCCCeEE
Confidence            10  11222 222  35899999998753        368899999999988664

>KOG0734|consensus

Probab=98.79  E-value=3.2e-08  Score=89.49  Aligned_cols=70  Identities=19%  Similarity=0.189  Sum_probs=47.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhc-ceeEeecCeEEEeccHHHHHh--hcCcEEEEeCCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIK-QRREIVNGTAIYYDQSAVRAA--IEGRVLILEGIEK  121 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~-g~~~~~~G~~~~~~gpl~~A~--~~G~vlllDEId~  121 (162)
                      +-|||+||||||||.||+++|...|.|+.+.+.+   +.++.. |     -|..+-.  -|..|.  +...|++|||||.
T Consensus       338 KGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGS---EFdEm~VG-----vGArRVR--dLF~aAk~~APcIIFIDEiDa  407 (752)
T KOG0734|consen  338 KGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGS---EFDEMFVG-----VGARRVR--DLFAAAKARAPCIIFIDEIDA  407 (752)
T ss_pred             CceEEeCCCCCchhHHHHHhhcccCCCeEecccc---chhhhhhc-----ccHHHHH--HHHHHHHhcCCeEEEEechhh
Confidence            4699999999999999999999999998766554   233332 2     1111101  233444  3457999999987


Q ss_pred             CCc
Q psy4122         122 AER  124 (162)
Q Consensus       122 a~~  124 (162)
                      ...
T Consensus       408 vG~  410 (752)
T KOG0734|consen  408 VGG  410 (752)
T ss_pred             hcc
Confidence            543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.78  E-value=6.1e-08  Score=81.93  Aligned_cols=107  Identities=13%  Similarity=0.177  Sum_probs=63.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE--EEEecc-----CC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE--YICLSR-----DT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~--~v~~~~-----~~---~~~dL~g~~~~~~G~   96 (162)
                      .+..++.|+..+.....++.+||+||||+|||++|+.+|+.+..+-.  .-.|+.     ..   ...++.   .+.++.
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~---~~~~~~   95 (355)
T TIGR02397        19 QEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVI---EIDAAS   95 (355)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEE---Eeeccc
Confidence            46778888888876656656899999999999999999988753210  000000     00   000010   011100


Q ss_pred             EEEec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+  ..+..++      ....+++|||++.++.+.++.|+..+|+
T Consensus        96 ~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~~~~~~Ll~~le~  143 (355)
T TIGR02397        96 NNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSKSAFNALLKTLEE  143 (355)
T ss_pred             cCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCHHHHHHHHHHHhC
Confidence            00000  0122211      2336999999999999999999999986

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.77  E-value=4.7e-08  Score=90.01  Aligned_cols=108  Identities=12%  Similarity=0.090  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE----------EEeccCCC-hhhhc-c----eeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY----------ICLSRDTT-EADIK-Q----RRE   91 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~----------v~~~~~~~-~~dL~-g----~~~   91 (162)
                      +...+.|+.++......+.+||+||+|||||++|+.+|+.++.....          -.|. ... -..+. |    ...
T Consensus        22 e~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg-~C~sC~~~~~g~~~n~~~  100 (620)
T PRK14954         22 EHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCG-ECESCRDFDAGTSLNISE  100 (620)
T ss_pred             HHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCc-cCHHHHHHhccCCCCeEE
Confidence            67778888888776666679999999999999999999988653100          0010 000 00000 0    001


Q ss_pred             eecCeEEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          92 IVNGTAIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        92 ~~~G~~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +.+++..-.+.  -+...+      ....++||||+++++.+.++.|+..||+
T Consensus       101 ~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEe  153 (620)
T PRK14954        101 FDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEE  153 (620)
T ss_pred             ecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhC
Confidence            11111100000  011111      2346999999999999999999999997

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.77  E-value=4.8e-08  Score=89.38  Aligned_cols=107  Identities=13%  Similarity=0.072  Sum_probs=66.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEEEeccCCC-----hhhhcceeEeec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYICLSRDTT-----EADIKQRREIVN   94 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v~~~~~~~-----~~dL~g~~~~~~   94 (162)
                      -+...+.|+.++.+....+.+||+||+|||||++|+.+|+.++.       ||-.+..+..+.     ..|++   .+..
T Consensus        18 q~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~dvi---eida   94 (584)
T PRK14952         18 QEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSIDVV---ELDA   94 (584)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCceEE---Eecc
Confidence            46778889988887666545799999999999999999988873       222111111100     01221   1111


Q ss_pred             CeEEEecc--HHHH------HhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          95 GTAIYYDQ--SAVR------AAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        95 G~~~~~~g--pl~~------A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .+..=.+.  -+..      ......|+||||+++++.+.++.|+..||+
T Consensus        95 as~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEE  144 (584)
T PRK14952         95 ASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEE  144 (584)
T ss_pred             ccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhc
Confidence            11000000  0100      112447999999999999999999999997

>KOG0727|consensus

Probab=98.77  E-value=1.3e-08  Score=85.30  Aligned_cols=84  Identities=24%  Similarity=0.299  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc--CcEEEEeCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE--GRVLILEGIE  120 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~--G~vlllDEId  120 (162)
                      ..+-+||+||||||||.|++++|+.+...+.++..++-  ....+|     .|...-.  -+.+-.++  ..+++|||||
T Consensus       188 pprgvllygppg~gktml~kava~~t~a~firvvgsef--vqkylg-----egprmvr--dvfrlakenapsiifideid  258 (408)
T KOG0727|consen  188 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF--VQKYLG-----EGPRMVR--DVFRLAKENAPSIIFIDEID  258 (408)
T ss_pred             CCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHH--HHHHhc-----cCcHHHH--HHHHHHhccCCcEEEeehhh
Confidence            34569999999999999999999999888888776532  333443     1210000  01122233  3799999997


Q ss_pred             C-----------CCccHHHHHHHhhc
Q psy4122         121 K-----------AERNVLPVLNNLLE  135 (162)
Q Consensus       121 ~-----------a~~~v~~~L~~lle  135 (162)
                      .           +..+|+..|..+|.
T Consensus       259 aiatkrfdaqtgadrevqril~elln  284 (408)
T KOG0727|consen  259 AIATKRFDAQTGADREVQRILIELLN  284 (408)
T ss_pred             hHhhhhccccccccHHHHHHHHHHHH
Confidence            5           44568888888775

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.76  E-value=7.8e-08  Score=87.87  Aligned_cols=110  Identities=13%  Similarity=0.102  Sum_probs=65.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE---EEEeccCCC-hhhhc-c----eeEeecCe-
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE---YICLSRDTT-EADIK-Q----RREIVNGT-   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~---~v~~~~~~~-~~dL~-g----~~~~~~G~-   96 (162)
                      -+...+.|+..+.....++.+||+||+|||||++|+.+|+.++....   .-.|+ ... -..+. +    ...+...+ 
T Consensus        21 q~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~-~c~~c~~i~~~~~~d~~~i~~~~~   99 (585)
T PRK14950         21 QEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCG-TCEMCRAIAEGSAVDVIEMDAASH   99 (585)
T ss_pred             CHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCc-cCHHHHHHhcCCCCeEEEEecccc
Confidence            46778888887776666666799999999999999999988753110   00010 000 00000 0    00011100 


Q ss_pred             EEEec-cHHHHH------hhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          97 AIYYD-QSAVRA------AIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        97 ~~~~~-gpl~~A------~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ....+ ..+...      .....++||||+++++.+.++.|+..||+-
T Consensus       100 ~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEep  147 (585)
T PRK14950        100 TSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEP  147 (585)
T ss_pred             CCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcC
Confidence            00000 001111      123479999999999999999999999973

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=98.76  E-value=1.3e-08  Score=88.80  Aligned_cols=72  Identities=11%  Similarity=0.032  Sum_probs=45.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh------cCcEEEEeC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI------EGRVLILEG  118 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~------~G~vlllDE  118 (162)
                      .-++|+||||||||.+|+++|+.+|.++..++..      +|...+.=+...  -....+..|..      ...+|+|||
T Consensus       149 lgllL~GPPGcGKTllAraiA~elg~~~i~vsa~------eL~sk~vGEsEk--~IR~~F~~A~~~a~~~~aPcVLFIDE  220 (413)
T PLN00020        149 LILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAG------ELESENAGEPGK--LIRQRYREAADIIKKKGKMSCLFIND  220 (413)
T ss_pred             eEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHH------HhhcCcCCcHHH--HHHHHHHHHHHHhhccCCCeEEEEeh
Confidence            3489999999999999999999999997666554      333210000000  00112333321      347999999


Q ss_pred             CCCCCc
Q psy4122         119 IEKAER  124 (162)
Q Consensus       119 Id~a~~  124 (162)
                      ||..-+
T Consensus       221 IDA~~g  226 (413)
T PLN00020        221 LDAGAG  226 (413)
T ss_pred             hhhcCC
Confidence            997554

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.75  E-value=7.1e-08  Score=88.84  Aligned_cols=106  Identities=14%  Similarity=0.099  Sum_probs=65.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE----EEeccCCCh---------hhhcceeEee
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY----ICLSRDTTE---------ADIKQRREIV   93 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~----v~~~~~~~~---------~dL~g~~~~~   93 (162)
                      -+...+.|+.++........+||+||+|+|||++|+.+|+.++.....    -.|. ....         .|++   .+.
T Consensus        21 q~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg-~C~~C~~i~~g~h~D~~---ei~   96 (620)
T PRK14948         21 QEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCG-KCELCRAIAAGNALDVI---EID   96 (620)
T ss_pred             hHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCc-ccHHHHHHhcCCCccEE---EEe
Confidence            367788888888876666789999999999999999999988642100    0010 0000         0111   011


Q ss_pred             cCeEEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          94 NGTAIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        94 ~G~~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .....-.+.  -+...+      ....|+||||+++++.+.++.|+..||+
T Consensus        97 ~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEe  147 (620)
T PRK14948         97 AASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEE  147 (620)
T ss_pred             ccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhc
Confidence            110000000  011111      1236999999999999999999999996

>KOG0745|consensus

Probab=98.75  E-value=2.8e-08  Score=87.96  Aligned_cols=93  Identities=18%  Similarity=0.247  Sum_probs=62.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH-----hhcCcEEEEeCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA-----AIEGRVLILEGI  119 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A-----~~~G~vlllDEI  119 (162)
                      -||||.||+|+|||-||+.+|+.++.|+...-|... |-+-.+|...    ..+. .--+..|     -.+-|+++|||+
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtL-TQAGYVGeDV----Esvi-~KLl~~A~~nVekAQqGIVflDEv  300 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTL-TQAGYVGEDV----ESVI-QKLLQEAEYNVEKAQQGIVFLDEV  300 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHhCCCeEEecccch-hhcccccccH----HHHH-HHHHHHccCCHHHHhcCeEEEehh
Confidence            389999999999999999999999999876666422 2222222100    0000 0011222     135689999999


Q ss_pred             CCCCc--------------cHHHHHHHhhcCCeEEEcC
Q psy4122         120 EKAER--------------NVLPVLNNLLENREMHLED  143 (162)
Q Consensus       120 d~a~~--------------~v~~~L~~lle~r~l~l~~  143 (162)
                      |++..              .|+..|+.++|.-.+.+|+
T Consensus       301 DKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpe  338 (564)
T KOG0745|consen  301 DKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPE  338 (564)
T ss_pred             hhhcccCccccccccccchhHHHHHHHHhcccEEcccC
Confidence            99662              4899999999977777754

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=98.75  E-value=2.4e-08  Score=93.11  Aligned_cols=71  Identities=15%  Similarity=0.196  Sum_probs=45.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc-CcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE-GRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~-G~vlllDEId~a  122 (162)
                      .+.+||+||||||||++|+++|...+.++..+.+.      ++...+  .+.+.......+..|... ..+++|||||.+
T Consensus       487 ~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~------~l~~~~--vGese~~i~~~f~~A~~~~p~iifiDEid~l  558 (733)
T TIGR01243       487 PKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGP------EILSKW--VGESEKAIREIFRKARQAAPAIIFFDEIDAI  558 (733)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehH------HHhhcc--cCcHHHHHHHHHHHHHhcCCEEEEEEChhhh
Confidence            34699999999999999999999999998766553      333211  000000001123334333 479999999875

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK06893 DNA replication initiation factor; Validated

Probab=98.73  E-value=3.8e-08  Score=79.75  Aligned_cols=61  Identities=16%  Similarity=0.185  Sum_probs=42.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      .++|+||||||||||+.++|+.+   +..+.++.++..    +...             ..+.+.+++..+|+||||+..
T Consensus        41 ~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~----~~~~-------------~~~~~~~~~~dlLilDDi~~~  103 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKS----QYFS-------------PAVLENLEQQDLVCLDDLQAV  103 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHh----hhhh-------------HHHHhhcccCCEEEEeChhhh
Confidence            37999999999999999999764   456666655310    1100             023344566789999999986


Q ss_pred             C
Q psy4122         123 E  123 (162)
Q Consensus       123 ~  123 (162)
                      .
T Consensus       104 ~  104 (229)
T PRK06893        104 I  104 (229)
T ss_pred             c
Confidence            5

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.73  E-value=3.6e-08  Score=83.79  Aligned_cols=43  Identities=16%  Similarity=0.209  Sum_probs=31.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC---------CceEEEEeccCCChhhhc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ---------REVEYICLSRDTTEADIK   87 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg---------~p~~~v~~~~~~~~~dL~   87 (162)
                      .+++++||||||||++++.+++.+.         .++.+++|....+..++.
T Consensus        41 ~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~   92 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVL   92 (365)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHH
Confidence            4799999999999999999987653         345566766544544443

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.73  E-value=9.5e-08  Score=86.26  Aligned_cols=29  Identities=21%  Similarity=0.305  Sum_probs=26.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ..+.+||+||||||||++|+++|+.++.+
T Consensus       215 ~p~GILLyGPPGTGKT~LAKAlA~eL~~~  243 (512)
T TIGR03689       215 PPKGVLLYGPPGCGKTLIAKAVANSLAQR  243 (512)
T ss_pred             CCcceEEECCCCCcHHHHHHHHHHhhccc
Confidence            34579999999999999999999998876

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.72  E-value=7.7e-08  Score=87.85  Aligned_cols=107  Identities=14%  Similarity=0.145  Sum_probs=65.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+......+.+||+||+|+|||++|+.+|+.++.+       |-.+..+..+   +..|++   .+.+.+
T Consensus        21 q~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~---eid~~s   97 (576)
T PRK14965         21 QEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVF---EIDGAS   97 (576)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCee---eeeccC
Confidence            367778888888766555567999999999999999999988642       1111000000   001111   011100


Q ss_pred             EEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..-.+.  -+...+      .+..++||||+|+++.+..+.|+..||+
T Consensus        98 ~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEe  145 (576)
T PRK14965         98 NTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEE  145 (576)
T ss_pred             ccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHc
Confidence            000000  111111      2346999999999999999999999996

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=98.72  E-value=1.1e-08  Score=89.57  Aligned_cols=35  Identities=23%  Similarity=0.241  Sum_probs=30.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      .++.+||+||||||||++|+++|..++.++..+..
T Consensus       178 ~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~  212 (398)
T PTZ00454        178 PPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVG  212 (398)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEeh
Confidence            45679999999999999999999999998776654

>PRK06526 transposase; Provisional

Probab=98.72  E-value=6.2e-09  Score=86.12  Aligned_cols=84  Identities=17%  Similarity=0.187  Sum_probs=53.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeE--eecCeEEEeccHHHHHhhcCcEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRRE--IVNGTAIYYDQSAVRAAIEGRVLILE  117 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~--~~~G~~~~~~gpl~~A~~~G~vlllD  117 (162)
                      .+++++|+||||||||+|+.+++...   |+.+.++++      .+++....  ...|..    ....+.+..-.+|+||
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~------~~l~~~l~~~~~~~~~----~~~l~~l~~~dlLIID  166 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATA------AQWVARLAAAHHAGRL----QAELVKLGRYPLLIVD  166 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhH------HHHHHHHHHHHhcCcH----HHHHHHhccCCEEEEc
Confidence            36799999999999999999988643   565544333      33332100  011211    1233445556899999


Q ss_pred             CCCCCC--ccHHHHHHHhhcC
Q psy4122         118 GIEKAE--RNVLPVLNNLLEN  136 (162)
Q Consensus       118 EId~a~--~~v~~~L~~lle~  136 (162)
                      |++..+  +.....|..+++.
T Consensus       167 D~g~~~~~~~~~~~L~~li~~  187 (254)
T PRK06526        167 EVGYIPFEPEAANLFFQLVSS  187 (254)
T ss_pred             ccccCCCCHHHHHHHHHHHHH
Confidence            998765  5566778888764

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.72  E-value=4.3e-08  Score=83.85  Aligned_cols=121  Identities=15%  Similarity=0.219  Sum_probs=81.1

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH------HhCCceEEEEec---cCCChhhhcceeEeec---Ce
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE------LTQREVEYICLS---RDTTEADIKQRREIVN---GT   96 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~------~lg~p~~~v~~~---~~~~~~dL~g~~~~~~---G~   96 (162)
                      .++++++....  .+.-|+||.||+|.|||.||+.+-+      .+.-++..++|.   +|+..+.|.|.  .++   |.
T Consensus       195 rmieqierva~--rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfgh--vkgaftga  270 (531)
T COG4650         195 RMIEQIERVAI--RSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGH--VKGAFTGA  270 (531)
T ss_pred             HHHHHHHHHHh--hccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhh--hccccccc
Confidence            45555555543  3456999999999999999998764      344567777775   67677778773  221   11


Q ss_pred             EEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEE-EcCCcEEecCcchHhhh
Q psy4122          97 AIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMH-LEDGRFLVSASTYDKLL  157 (162)
Q Consensus        97 ~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~-l~~g~~i~~~~~f~~~~  157 (162)
                      -.-..| ++++ ..|++++||||.....+-+..|+..+|+++.. +...+.+  ..+|+.++
T Consensus       271 ~~~r~g-llrs-adggmlfldeigelgadeqamllkaieekrf~pfgsdr~v--~sdfqlia  328 (531)
T COG4650         271 RESREG-LLRS-ADGGMLFLDEIGELGADEQAMLLKAIEEKRFYPFGSDRQV--SSDFQLIA  328 (531)
T ss_pred             hhhhhh-hhcc-CCCceEehHhhhhcCccHHHHHHHHHHhhccCCCCCcccc--ccchHHhh
Confidence            111111 2232 47899999999999999999999999977653 2223333  56777664

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

Probab=98.71  E-value=9.4e-08  Score=77.75  Aligned_cols=109  Identities=11%  Similarity=0.139  Sum_probs=60.5

Q ss_pred             CHHHHHHHHHHHHhcCCCC-cEEEEcCCCchHHHHHHHHHHHhCC-ceEEEE-eccCCChhhhcce----eEee-cCeEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQ-DVFLIGKPGSLRRSLAMSYLELTQR-EVEYIC-LSRDTTEADIKQR----REIV-NGTAI   98 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~-~vlL~GppG~GKT~La~~lA~~lg~-p~~~v~-~~~~~~~~dL~g~----~~~~-~G~~~   98 (162)
                      ++...+.+..+......+. .++|+||+|+|||++++.++..+.. ...... ++...+..++...    .... .+...
T Consensus        25 ~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~  104 (269)
T TIGR03015        25 SKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLETEGRDK  104 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCH
Confidence            3444455555544433333 5889999999999999999988763 222222 2334455544321    0111 11100


Q ss_pred             -EeccHHH----HHhhcC--cEEEEeCCCCCCccHHHHHHHhhc
Q psy4122          99 -YYDQSAV----RAAIEG--RVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus        99 -~~~gpl~----~A~~~G--~vlllDEId~a~~~v~~~L~~lle  135 (162)
                       ..-..+.    .....|  .++++||++.++++.++.|..+.+
T Consensus       105 ~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~  148 (269)
T TIGR03015       105 AALLRELEDFLIEQFAAGKRALLVVDEAQNLTPELLEELRMLSN  148 (269)
T ss_pred             HHHHHHHHHHHHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhC
Confidence             0000111    111223  478999999999988888876655

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.71  E-value=2.8e-08  Score=93.88  Aligned_cols=102  Identities=15%  Similarity=0.233  Sum_probs=59.7

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC----------CceEEEEeccCCChhhhcceeEeecCeEEEe
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ----------REVEYICLSRDTTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg----------~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~  100 (162)
                      ++.+..++.... ..+++|+||||||||++|+.+|....          .++.  .++    ..+++..-.. .|  .|+
T Consensus       188 i~~~~~~L~r~~-~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~--~l~----~~~l~ag~~~-~g--e~e  257 (821)
T CHL00095        188 IERVIQILGRRT-KNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVI--TLD----IGLLLAGTKY-RG--EFE  257 (821)
T ss_pred             HHHHHHHHcccc-cCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEE--Eee----HHHHhccCCC-cc--HHH
Confidence            334444443332 23899999999999999999998753          2333  222    2344320000 01  122


Q ss_pred             cc--HHHHHhh-c-CcEEEEeCCCCCCc--------cHHHHHHHhhcCCeEEEc
Q psy4122         101 DQ--SAVRAAI-E-GRVLILEGIEKAER--------NVLPVLNNLLENREMHLE  142 (162)
Q Consensus       101 ~g--pl~~A~~-~-G~vlllDEId~a~~--------~v~~~L~~lle~r~l~l~  142 (162)
                      +-  .+...++ . +.+|+||||+.+-.        ++.+.|.+.+.+|++.+-
T Consensus       258 ~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~rg~l~~I  311 (821)
T CHL00095        258 ERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALARGELQCI  311 (821)
T ss_pred             HHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhCCCcEEE
Confidence            10  1222222 3 35889999975322        578899999999988764

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.70  E-value=9.7e-08  Score=87.64  Aligned_cols=107  Identities=15%  Similarity=0.135  Sum_probs=67.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEE------eccCCC---------hhhhcceeE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYIC------LSRDTT---------EADIKQRRE   91 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~------~~~~~~---------~~dL~g~~~   91 (162)
                      -+.+.+.|+..+......+.+||+||+|+|||++|+.+|+.++......+      .+....         -.|++   .
T Consensus        29 q~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~---e  105 (598)
T PRK09111         29 QEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVL---E  105 (598)
T ss_pred             cHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcCCCCceE---E
Confidence            57888899998887766668999999999999999999998864321110      000000         00111   0


Q ss_pred             eecCeEEEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          92 IVNGTAIYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        92 ~~~G~~~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +...+..=.+.  -+...+      ....++||||+++++.+..+.|+..||+
T Consensus       106 ~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEe  158 (598)
T PRK09111        106 MDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEE  158 (598)
T ss_pred             ecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHh
Confidence            10000000000  011111      2347999999999999999999999986

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.69  E-value=1.6e-07  Score=78.01  Aligned_cols=98  Identities=15%  Similarity=0.302  Sum_probs=60.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEecc--CCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSR--DTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~--~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      -....+.++..+..... .+++|+||||||||++++.+++.+..+   ...+.++.  .... +.+.. .+.        
T Consensus        22 ~~~~~~~l~~~i~~~~~-~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~-~~~~~-~i~--------   90 (319)
T PRK00440         22 QEEIVERLKSYVKEKNM-PHLLFAGPPGTGKTTAALALARELYGEDWRENFLELNASDERGI-DVIRN-KIK--------   90 (319)
T ss_pred             cHHHHHHHHHHHhCCCC-CeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEeccccccch-HHHHH-HHH--------
Confidence            35677777777765333 379999999999999999999876432   22233321  1111 00000 000        


Q ss_pred             cHHHHH--h--hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRA--A--IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A--~--~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       .+...  +  ....+++|||++.++.+.+..|..+++.
T Consensus        91 -~~~~~~~~~~~~~~vviiDe~~~l~~~~~~~L~~~le~  128 (319)
T PRK00440         91 -EFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEM  128 (319)
T ss_pred             -HHHhcCCCCCCCceEEEEeCcccCCHHHHHHHHHHHhc
Confidence             00000  0  1235999999999999989999999884

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.69  E-value=9.4e-08  Score=83.04  Aligned_cols=113  Identities=15%  Similarity=0.161  Sum_probs=75.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.....++.+........++++.|++|+||+++|+.+....   +.|+..++|.....   .+.|.|... .-.|....
T Consensus       145 s~~~~~~~~~i~~~~~~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~~~~~~~lfg~~~~~~~~~~~~  224 (441)
T PRK10365        145 SPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKR  224 (441)
T ss_pred             CHHHHHHHHHHhhccCCCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCHHHHHHHhcCCCCCCcCCCCcC
Confidence            444444455554434456789999999999999999998654   46788888874321   223333210 00111122


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|.+..|  +||.|+||||++++++++..|..+++++.+.-
T Consensus       225 ~~g~~~~a--~~gtl~ldei~~l~~~~q~~l~~~l~~~~~~~  264 (441)
T PRK10365        225 REGRFVEA--DGGTLFLDEIGDISPMMQVRLLRAIQEREVQR  264 (441)
T ss_pred             CCCceeEC--CCCEEEEeccccCCHHHHHHHHHHHccCcEEe
Confidence            23333333  78999999999999999999999999988654

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.69  E-value=1.1e-07  Score=87.27  Aligned_cols=106  Identities=13%  Similarity=0.161  Sum_probs=64.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEEEecc---CCChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYICLSR---DTTEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v~~~~---~~~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+......+.+|++||+|||||++|+.+|+.+..       |+-.+..+.   .....|++   .+ ++.
T Consensus        21 Qe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~Dii---eI-daa   96 (605)
T PRK05896         21 QELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIV---EL-DAA   96 (605)
T ss_pred             cHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCceE---Ee-ccc
Confidence            36677888887776655667899999999999999999998752       111110000   00001111   11 110


Q ss_pred             EEE-ec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIY-YD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~-~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ... .+  ..+...+      ....+++|||+++++.+..+.|+..||+
T Consensus        97 s~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEE  145 (605)
T PRK05896         97 SNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEE  145 (605)
T ss_pred             cccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHh
Confidence            000 00  0111111      1346999999999999999999999995

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.69  E-value=9.8e-09  Score=88.25  Aligned_cols=33  Identities=24%  Similarity=0.315  Sum_probs=28.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYIC   76 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~   76 (162)
                      .+.++|+||||||||++|+++|+.++.++..+.
T Consensus       156 p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~  188 (364)
T TIGR01242       156 PKGVLLYGPPGTGKTLLAKAVAHETNATFIRVV  188 (364)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhCCCCEEecc
Confidence            346999999999999999999999998876554

Many proteins may score above the trusted cutoff because an internal

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=98.69  E-value=7.9e-08  Score=89.71  Aligned_cols=85  Identities=16%  Similarity=0.155  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc-CcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE-GRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~-G~vlllDEId~  121 (162)
                      .++.++|+||||||||++++++|+.++.++..+++.      ++...+.-.... . ...-+-.|... ..+|+|||||.
T Consensus       211 ~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~------~i~~~~~g~~~~-~-l~~lf~~a~~~~p~il~iDEid~  282 (733)
T TIGR01243       211 PPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGP------EIMSKYYGESEE-R-LREIFKEAEENAPSIIFIDEIDA  282 (733)
T ss_pred             CCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecH------HHhcccccHHHH-H-HHHHHHHHHhcCCcEEEeehhhh
Confidence            456899999999999999999999999987766653      222110000000 0 00112223222 36999999987


Q ss_pred             CCc-----------cHHHHHHHhhc
Q psy4122         122 AER-----------NVLPVLNNLLE  135 (162)
Q Consensus       122 a~~-----------~v~~~L~~lle  135 (162)
                      +.+           .+++.|..+++
T Consensus       283 l~~~r~~~~~~~~~~~~~~Ll~~ld  307 (733)
T TIGR01243       283 IAPKREEVTGEVEKRVVAQLLTLMD  307 (733)
T ss_pred             hcccccCCcchHHHHHHHHHHHHhh
Confidence            643           25666777775

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.69  E-value=4e-08  Score=91.05  Aligned_cols=96  Identities=18%  Similarity=0.308  Sum_probs=73.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |+||+|+||+|||.|-+.+++...+-++  .-...++...|...-.-  ..|.++-+-|+|+.|  .+|++.|||+|+++
T Consensus       321 nILLvGDPgtaKSqlLk~v~~~aPr~vy--tsgkgss~~GLTAav~rd~~tge~~LeaGALVlA--D~Gv~cIDEfdKm~  396 (682)
T COG1241         321 HILLVGDPGTAKSQLLKYVAKLAPRGVY--TSGKGSSAAGLTAAVVRDKVTGEWVLEAGALVLA--DGGVCCIDEFDKMN  396 (682)
T ss_pred             eEEEcCCCchhHHHHHHHHHhhCCceEE--EccccccccCceeEEEEccCCCeEEEeCCEEEEe--cCCEEEEEeccCCC
Confidence            7999999999999999999998866543  22334455556542111  125555566666554  88999999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEcCCc
Q psy4122         124 RNVLPVLNNLLENREMHLEDGR  145 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~~g~  145 (162)
                      .+-..+|+..||...+.+..+.
T Consensus       397 ~~dr~aihEaMEQQtIsIaKAG  418 (682)
T COG1241         397 EEDRVAIHEAMEQQTISIAKAG  418 (682)
T ss_pred             hHHHHHHHHHHHhcEeeecccc
Confidence            9999999999999999998643

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.68  E-value=1.2e-07  Score=84.20  Aligned_cols=106  Identities=14%  Similarity=0.170  Sum_probs=65.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--------eEEE-Eecc---CCChhhhcceeEeec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--------VEYI-CLSR---DTTEADIKQRREIVN   94 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--------~~~v-~~~~---~~~~~dL~g~~~~~~   94 (162)
                      -+...+.|+..+......+.+||+||||+|||++|+.+|+.+..+        +..+ +|..   ..+ .+++   .+.+
T Consensus        22 q~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~-~d~~---~i~g   97 (451)
T PRK06305         22 QDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTS-LDVL---EIDG   97 (451)
T ss_pred             cHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCC-CceE---Eeec
Confidence            467778888888776666678999999999999999999887542        1100 0000   000 0111   1111


Q ss_pred             CeE-EEecc-HHHH------HhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          95 GTA-IYYDQ-SAVR------AAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        95 G~~-~~~~g-pl~~------A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ... .+.+- .+.+      ......++|+||+++++.+.++.|...+|+
T Consensus        98 ~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEe  147 (451)
T PRK06305         98 ASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEE  147 (451)
T ss_pred             cccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhc
Confidence            000 00000 0111      112347999999999999999999999997

>KOG1969|consensus

Probab=98.68  E-value=4.3e-08  Score=90.89  Aligned_cols=86  Identities=24%  Similarity=0.295  Sum_probs=64.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe-ecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI-VNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~-~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      +-+||.||||-||||||.-+|+.-|+.+..++.+.+-++..+..+..- ..-+      .++.|=.....||+||||-++
T Consensus       327 KilLL~GppGlGKTTLAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~------s~l~adsrP~CLViDEIDGa~  400 (877)
T KOG1969|consen  327 KILLLCGPPGLGKTTLAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNH------SVLDADSRPVCLVIDEIDGAP  400 (877)
T ss_pred             ceEEeecCCCCChhHHHHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhc------cccccCCCcceEEEecccCCc
Confidence            348999999999999999999999999999999887777766532100 0000      001111344689999999999


Q ss_pred             ccHHHHHHHhhcC
Q psy4122         124 RNVLPVLNNLLEN  136 (162)
Q Consensus       124 ~~v~~~L~~lle~  136 (162)
                      +...++|++++..
T Consensus       401 ~~~Vdvilslv~a  413 (877)
T KOG1969|consen  401 RAAVDVILSLVKA  413 (877)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999983

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.67  E-value=7.5e-08  Score=84.37  Aligned_cols=113  Identities=13%  Similarity=0.130  Sum_probs=75.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++...+.++.+........++++.|.+||||+++|+.+....   +.|+..++|.....   .+.+.|... .-.|....
T Consensus       140 s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~~~~~~~lfg~~~~~~~~~~~~  219 (463)
T TIGR01818       140 APAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTR  219 (463)
T ss_pred             CHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCHHHHHHHhcCCCCCCCCCcccC
Confidence            566666666665544456789999999999999999998764   45788888864311   233444210 00111111


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|.+.  ..+|+.|+||||+.++++++..|..+++++.+.-
T Consensus       220 ~~g~~~--~a~~gtl~l~ei~~l~~~~q~~ll~~l~~~~~~~  259 (463)
T TIGR01818       220 RQGRFE--QADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYR  259 (463)
T ss_pred             CCCcEE--ECCCCeEEEEchhhCCHHHHHHHHHHHhcCcEEE
Confidence            112111  2368899999999999999999999999887654

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.67  E-value=6e-08  Score=82.31  Aligned_cols=87  Identities=21%  Similarity=0.263  Sum_probs=56.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGI  119 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEI  119 (162)
                      .+++++|+||+|||||+|+.++|..+   |.++.++.+..-  ..+|...  ..+++  +  .-..+.+++-.+|+||||
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l--~~~lk~~--~~~~~--~--~~~l~~l~~~dlLiIDDi  226 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEF--IRELKNS--ISDGS--V--KEKIDAVKEAPVLMLDDI  226 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHH--HHHHHHH--HhcCc--H--HHHHHHhcCCCEEEEecC
Confidence            35689999999999999999999766   677776666421  2233221  11222  1  245677888899999999


Q ss_pred             CCC--CccHH-HHHHHhhcCC
Q psy4122         120 EKA--ERNVL-PVLNNLLENR  137 (162)
Q Consensus       120 d~a--~~~v~-~~L~~lle~r  137 (162)
                      ..-  .+.+. +.|..+++.|
T Consensus       227 G~e~~s~~~~~~ll~~Il~~R  247 (306)
T PRK08939        227 GAEQMSSWVRDEVLGVILQYR  247 (306)
T ss_pred             CCccccHHHHHHHHHHHHHHH
Confidence            654  33344 3455566544

>KOG0478|consensus

Probab=98.67  E-value=2.7e-08  Score=91.61  Aligned_cols=95  Identities=14%  Similarity=0.253  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      -|+||+|+||+|||.|.+.++++.-+-.+ .+. ...+..-|......  ..+.++-+-|+|+.  ..||++-|||+||+
T Consensus       463 INILL~GDPGtsKSqlLqyv~~l~pRg~y-TSG-kGsSavGLTayVtrd~dtkqlVLesGALVL--SD~GiCCIDEFDKM  538 (804)
T KOG0478|consen  463 INILLVGDPGTSKSQLLQYCHRLLPRGVY-TSG-KGSSAVGLTAYVTKDPDTRQLVLESGALVL--SDNGICCIDEFDKM  538 (804)
T ss_pred             ceEEEecCCCcCHHHHHHHHHHhCCccee-ecC-CccchhcceeeEEecCccceeeeecCcEEE--cCCceEEchhhhhh
Confidence            48999999999999999999999876543 333 23344444432222  23456666666544  48899999999999


Q ss_pred             CccHHHHHHHhhcCCeEEEcC
Q psy4122         123 ERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       123 ~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +.+..++|+++||..++.|+.
T Consensus       539 ~dStrSvLhEvMEQQTvSIAK  559 (804)
T KOG0478|consen  539 SDSTRSVLHEVMEQQTLSIAK  559 (804)
T ss_pred             hHHHHHHHHHHHHHhhhhHhh
Confidence            999999999999999887764

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.66  E-value=1.7e-07  Score=85.37  Aligned_cols=108  Identities=14%  Similarity=0.161  Sum_probs=66.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+.....++.+||+||+|||||++|+.+|+.++.+       |-.+..+...   ...|++   .+...+
T Consensus        21 q~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~---eidaas   97 (559)
T PRK05563         21 QEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDVI---EIDAAS   97 (559)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCeE---Eeeccc
Confidence            467788888888876667668899999999999999999987632       2111100000   011111   111100


Q ss_pred             EEEec--cHHHHH------hhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          97 AIYYD--QSAVRA------AIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        97 ~~~~~--gpl~~A------~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ..-.+  ..+...      .....|++|||++++..+..+.|+..||+-
T Consensus        98 ~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEep  146 (559)
T PRK05563         98 NNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEP  146 (559)
T ss_pred             cCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCC
Confidence            00000  001111      123469999999999999999999999963

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=98.66  E-value=2e-08  Score=84.23  Aligned_cols=85  Identities=14%  Similarity=0.240  Sum_probs=54.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~  121 (162)
                      +.++||++||||||||++|+++|...+.|+.-+.      +.+|+|.+. -+|....+ ....+|-+ ...+++|||+|.
T Consensus       150 APknVLFyGppGTGKTm~Akalane~kvp~l~vk------at~liGehV-Gdgar~Ih-ely~rA~~~aPcivFiDE~DA  221 (368)
T COG1223         150 APKNVLFYGPPGTGKTMMAKALANEAKVPLLLVK------ATELIGEHV-GDGARRIH-ELYERARKAAPCIVFIDELDA  221 (368)
T ss_pred             CcceeEEECCCCccHHHHHHHHhcccCCceEEec------hHHHHHHHh-hhHHHHHH-HHHHHHHhcCCeEEEehhhhh
Confidence            3469999999999999999999999999987554      346776321 12221111 12233332 347899999987


Q ss_pred             CC---------ccHHHHHHHhhc
Q psy4122         122 AE---------RNVLPVLNNLLE  135 (162)
Q Consensus       122 a~---------~~v~~~L~~lle  135 (162)
                      +.         -||.++.|.+|-
T Consensus       222 iaLdRryQelRGDVsEiVNALLT  244 (368)
T COG1223         222 IALDRRYQELRGDVSEIVNALLT  244 (368)
T ss_pred             hhhhhhHHHhcccHHHHHHHHHH
Confidence            43         355555555543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.66  E-value=6.3e-08  Score=91.89  Aligned_cols=102  Identities=12%  Similarity=0.238  Sum_probs=59.1

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeEEEe
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~  100 (162)
                      ++.+..++... ...+++|+||||||||++++.+|..+          +.++..+.+      ..++..... .|.  |.
T Consensus       182 i~~~~~~l~r~-~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~------~~l~a~~~~-~g~--~e  251 (852)
T TIGR03346       182 IRRTIQVLSRR-TKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDM------GALIAGAKY-RGE--FE  251 (852)
T ss_pred             HHHHHHHHhcC-CCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeH------HHHhhcchh-hhh--HH
Confidence            33344443332 23489999999999999999999875          333333322      222210000 011  11


Q ss_pred             cc--HHHHHh-h--cCcEEEEeCCCCCCc--------cHHHHHHHhhcCCeEEEc
Q psy4122         101 DQ--SAVRAA-I--EGRVLILEGIEKAER--------NVLPVLNNLLENREMHLE  142 (162)
Q Consensus       101 ~g--pl~~A~-~--~G~vlllDEId~a~~--------~v~~~L~~lle~r~l~l~  142 (162)
                      ..  .+.+.+ +  .+.+|+||||+.+..        ++.+.|.+.++++++.+-
T Consensus       252 ~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~g~i~~I  306 (852)
T TIGR03346       252 ERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCI  306 (852)
T ss_pred             HHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhhcCceEEE
Confidence            10  112222 2  245899999997642        477889999999888664

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.66  E-value=1.1e-07  Score=90.37  Aligned_cols=90  Identities=12%  Similarity=0.189  Sum_probs=52.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC---c-----eEEEEeccCCChhhhcceeEeecCeEEEecc--HHHHHh-hc--Cc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR---E-----VEYICLSRDTTEADIKQRREIVNGTAIYYDQ--SAVRAA-IE--GR  112 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~---p-----~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g--pl~~A~-~~--G~  112 (162)
                      +++|+||||||||++|+.+|..+..   |     ...+.++    .+.+...... .|  .|...  .+...+ ++  +.
T Consensus       210 n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~----l~~l~ag~~~-~g--e~e~~lk~ii~e~~~~~~~~  282 (852)
T TIGR03345       210 NPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLD----LGLLQAGASV-KG--EFENRLKSVIDEVKASPQPI  282 (852)
T ss_pred             ceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEee----hhhhhccccc-ch--HHHHHHHHHHHHHHhcCCCe
Confidence            8999999999999999999987632   1     1111111    1112100000 01  11110  122222 22  35


Q ss_pred             EEEEeCCCCCCc--------cHHHHHHHhhcCCeEEEc
Q psy4122         113 VLILEGIEKAER--------NVLPVLNNLLENREMHLE  142 (162)
Q Consensus       113 vlllDEId~a~~--------~v~~~L~~lle~r~l~l~  142 (162)
                      ||+||||+.+..        ++.+.|.+.+++|++.+-
T Consensus       283 ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~G~l~~I  320 (852)
T TIGR03345       283 ILFIDEAHTLIGAGGQAGQGDAANLLKPALARGELRTI  320 (852)
T ss_pred             EEEEeChHHhccCCCccccccHHHHhhHHhhCCCeEEE
Confidence            889999998753        455579999999998774

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.65  E-value=2.1e-07  Score=79.82  Aligned_cols=95  Identities=12%  Similarity=0.177  Sum_probs=62.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce----------EEEEeccC--CChhhhcceeEeec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV----------EYICLSRD--TTEADIKQRREIVN   94 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~----------~~v~~~~~--~~~~dL~g~~~~~~   94 (162)
                      -....+.++..++.....++++|+||||+|||++|+.+|+.++.+.          ..+.++..  ...+++.       
T Consensus        22 ~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~-------   94 (367)
T PRK14970         22 QSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIR-------   94 (367)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHHHH-------
Confidence            3566777777777655556799999999999999999999876421          11111110  0011111       


Q ss_pred             CeEEEeccHHHHH------hhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          95 GTAIYYDQSAVRA------AIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        95 G~~~~~~gpl~~A------~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                              .+.+.      .....++++||++.+.+..++.|+..+++
T Consensus        95 --------~l~~~~~~~p~~~~~kiviIDE~~~l~~~~~~~ll~~le~  134 (367)
T PRK14970         95 --------NLIDQVRIPPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEE  134 (367)
T ss_pred             --------HHHHHHhhccccCCcEEEEEeChhhcCHHHHHHHHHHHhC
Confidence                    11111      12346999999999999888999888886

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.64  E-value=1.6e-07  Score=85.67  Aligned_cols=106  Identities=14%  Similarity=0.197  Sum_probs=65.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCC---ChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDT---TEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~---~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+......+.+||+||+|+|||++|+.+|+.++.+       +-.+..+..+   ..-|++   .+ +|.
T Consensus        21 qe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv~---~i-dga   96 (563)
T PRK06647         21 QDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVI---EI-DGA   96 (563)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCeE---Ee-cCc
Confidence            467788888888876666668999999999999999999988642       2111000000   000111   01 111


Q ss_pred             E-EEecc--HHHH------HhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 A-IYYDQ--SAVR------AAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~-~~~~g--pl~~------A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      . .-.+.  -+..      ......+++|||+++++.+.++.|+..+|+
T Consensus        97 s~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEe  145 (563)
T PRK06647         97 SNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEE  145 (563)
T ss_pred             ccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhcc
Confidence            0 00000  0000      112346999999999999999999999996

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=98.64  E-value=8.6e-08  Score=79.50  Aligned_cols=95  Identities=18%  Similarity=0.244  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHhcCCCCc-EEEEcCCCchHHHHHHHHHHHhCCce----------------------EEEEeccCCChhh
Q psy4122          29 DWLSHLRWILQKDNMSQD-VFLIGKPGSLRRSLAMSYLELTQREV----------------------EYICLSRDTTEAD   85 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~-vlL~GppG~GKT~La~~lA~~lg~p~----------------------~~v~~~~~~~~~d   85 (162)
                      .....+......+....| +||.||||+|||++|..+|+.+....                      ..+.+++    +|
T Consensus         8 ~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~----s~   83 (325)
T COG0470           8 EAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNP----SD   83 (325)
T ss_pred             hHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecc----cc
Confidence            344444444443333346 99999999999999999998776221                      1222221    11


Q ss_pred             hcceeEeecCeEEEeccHHHHHh----------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          86 IKQRREIVNGTAIYYDQSAVRAA----------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        86 L~g~~~~~~G~~~~~~gpl~~A~----------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..+.      + .-.  ..++.+          ....+++|||+|.++++.+++|+..+|.
T Consensus        84 ~~~~------~-i~~--~~vr~~~~~~~~~~~~~~~kviiidead~mt~~A~nallk~lEe  135 (325)
T COG0470          84 LRKI------D-IIV--EQVRELAEFLSESPLEGGYKVVIIDEADKLTEDAANALLKTLEE  135 (325)
T ss_pred             cCCC------c-chH--HHHHHHHHHhccCCCCCCceEEEeCcHHHHhHHHHHHHHHHhcc
Confidence            1100      0 000  011111          1126899999999999999999999995

>PRK08727 hypothetical protein; Validated

Probab=98.64  E-value=2e-07  Score=75.82  Aligned_cols=88  Identities=20%  Similarity=0.265  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHH
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVR  106 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~  106 (162)
                      .+..++.+.... ...+++|+||+|||||||+.+++..   .|....++.+..      +...         +.  ...+
T Consensus        28 ~~~~~~~~~~~~-~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~------~~~~---------~~--~~~~   89 (233)
T PRK08727         28 LLAQLQALAAGQ-SSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQA------AAGR---------LR--DALE   89 (233)
T ss_pred             HHHHHHHHHhcc-CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHH------hhhh---------HH--HHHH
Confidence            445555444322 2347999999999999999998754   355555555432      1110         00  1234


Q ss_pred             HhhcCcEEEEeCCCCCCc--cHHHHHHHhhc
Q psy4122         107 AAIEGRVLILEGIEKAER--NVLPVLNNLLE  135 (162)
Q Consensus       107 A~~~G~vlllDEId~a~~--~v~~~L~~lle  135 (162)
                      .+..-.+|+|||++....  .....|..+++
T Consensus        90 ~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n  120 (233)
T PRK08727         90 ALEGRSLVALDGLESIAGQREDEVALFDFHN  120 (233)
T ss_pred             HHhcCCEEEEeCcccccCChHHHHHHHHHHH
Confidence            555668999999998753  33444555554

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.63  E-value=1.2e-07  Score=87.16  Aligned_cols=34  Identities=18%  Similarity=0.280  Sum_probs=31.4

Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +||+|+|||++.++++++..|..+|+++++.+.+
T Consensus       217 ngGtL~Ldei~~L~~~~q~~Ll~~L~~~~i~~~g  250 (608)
T TIGR00764       217 HKGVLYIDEIKTMPLEVQQYLLTALQDKKFPITG  250 (608)
T ss_pred             CCCEEEEEChHhCCHHHHHHHHHHHHhCcEEecC
Confidence            5799999999999999999999999999988754

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK06921 hypothetical protein; Provisional

Probab=98.63  E-value=1e-07  Score=79.23  Aligned_cols=83  Identities=17%  Similarity=0.216  Sum_probs=52.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEeccCCChhhhcceeEeecCeEEEe-ccHHHHHhhcCcEEEEeC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLSRDTTEADIKQRREIVNGTAIYY-DQSAVRAAIEGRVLILEG  118 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~-~gpl~~A~~~G~vlllDE  118 (162)
                      +.+++|+|+||+|||+|+.++|..+    |..+.++...      +++..  +...   |. .....+.+.+-.+|+|||
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~------~l~~~--l~~~---~~~~~~~~~~~~~~dlLiIDD  185 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFV------EGFGD--LKDD---FDLLEAKLNRMKKVEVLFIDD  185 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHH------HHHHH--HHHH---HHHHHHHHHHhcCCCEEEEec
Confidence            5689999999999999999999754    5555555542      22211  0000   00 012345667789999999


Q ss_pred             CCC-------CCccHHHHHHHhhcCC
Q psy4122         119 IEK-------AERNVLPVLNNLLENR  137 (162)
Q Consensus       119 Id~-------a~~~v~~~L~~lle~r  137 (162)
                      +..       +.+...+.|..+++.|
T Consensus       186 l~~~~~g~e~~t~~~~~~lf~iin~R  211 (266)
T PRK06921        186 LFKPVNGKPRATEWQIEQMYSVLNYR  211 (266)
T ss_pred             cccccCCCccCCHHHHHHHHHHHHHH
Confidence            944       3333456666766643

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=98.62  E-value=8.4e-08  Score=88.60  Aligned_cols=34  Identities=12%  Similarity=0.254  Sum_probs=31.1

Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +||+|+|||++.+++.++..|..+|+++++.+.+
T Consensus       226 nGGtL~LDei~~L~~~~q~~Llr~L~~~~i~i~g  259 (637)
T PRK13765        226 HKGVLFIDEINTLDLESQQSLLTAMQEKKFPITG  259 (637)
T ss_pred             CCcEEEEeChHhCCHHHHHHHHHHHHhCCEEecc
Confidence            5799999999999999999999999999987744

>KOG1808|consensus

Probab=98.62  E-value=3.2e-08  Score=98.89  Aligned_cols=106  Identities=26%  Similarity=0.323  Sum_probs=92.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVR  106 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~  106 (162)
                      +|.+...++..+.++...+++++.|+||+|||+++..++...|....+++....++..|+.|...-.+|.. |+|+|+..
T Consensus      1029 a~t~~~nl~~~l~~~~l~~p~~leg~sg~gktsl~~~l~~~~G~~~~r~nl~~qtdl~dl~g~~~pve~~~-~~d~ell~ 1107 (1856)
T KOG1808|consen 1029 APTTSENLRRVLRALGLPKPILLEGESGSGKTSLVLALGRLTGKWTIRLNLSDQTDLADLFGSDVPVEGEE-WEDSELLA 1107 (1856)
T ss_pred             ChHHHHHHHHHHHhccCCccccccCCCCCCccchhhhhhhhcccceeccccccccccchhcCccCCCCCcc-ccccHHHh
Confidence            68999999999999999999999999999999999999999999999888888888999998543222322 99999999


Q ss_pred             HhhcCcEEEEeCCCCCCccHHHHHHHhhcCCe-EEEc
Q psy4122         107 AAIEGRVLILEGIEKAERNVLPVLNNLLENRE-MHLE  142 (162)
Q Consensus       107 A~~~G~vlllDEId~a~~~v~~~L~~lle~r~-l~l~  142 (162)
                      |+++|         .|+.++...||..+|+|. ..++
T Consensus      1108 a~~~~---------l~sqsv~Eglna~~D~R~e~~i~ 1135 (1856)
T KOG1808|consen 1108 ADKNG---------LASQSVLEGLNACLDHRNEVFIA 1135 (1856)
T ss_pred             hhhcc---------ccchhhhhchhHhhhhhhhhhhh
Confidence            99999         789999999999999765 4553

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.62  E-value=3.2e-07  Score=83.25  Aligned_cols=101  Identities=16%  Similarity=0.232  Sum_probs=64.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ce---------------EEEEeccC--CC
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EV---------------EYICLSRD--TT   82 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~---------------~~v~~~~~--~~   82 (162)
                      -+...+.|+..+......+..||+||+|+|||++|+.+|+.+..       |+               ..+.+++.  ..
T Consensus        19 qe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas~~g   98 (535)
T PRK08451         19 QESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAASNRG   98 (535)
T ss_pred             cHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEeccccccC
Confidence            46777888888877666655689999999999999999988742       11               11111110  00


Q ss_pred             hhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          83 EADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        83 ~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..++...  +..  ..+  .|   .+....+++|||+++++++.+++|+..||+
T Consensus        99 Id~IRel--ie~--~~~--~P---~~~~~KVvIIDEad~Lt~~A~NALLK~LEE  143 (535)
T PRK08451         99 IDDIREL--IEQ--TKY--KP---SMARFKIFIIDEVHMLTKEAFNALLKTLEE  143 (535)
T ss_pred             HHHHHHH--HHH--Hhh--Cc---ccCCeEEEEEECcccCCHHHHHHHHHHHhh
Confidence            1111100  000  000  01   112346999999999999999999999996

>PRK05642 DNA replication initiation factor; Validated

Probab=98.62  E-value=2.6e-07  Score=75.18  Aligned_cols=90  Identities=17%  Similarity=0.182  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHhcC--CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          28 QDWLSHLRWILQKDN--MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~--~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      ....+.++.+.....  ...+++|+||+|||||||+.++++..   +..+.+++.      +++...           ..
T Consensus        27 ~~a~~~~~~~~~~~~~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~------~~~~~~-----------~~   89 (234)
T PRK05642         27 AAALGYVERLCEADAGWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL------AELLDR-----------GP   89 (234)
T ss_pred             HHHHHHHHHHhhccccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH------HHHHhh-----------hH
Confidence            445555555443211  12479999999999999999998643   455555544      233311           12


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCc--cHHHHHHHhh
Q psy4122         103 SAVRAAIEGRVLILEGIEKAER--NVLPVLNNLL  134 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~--~v~~~L~~ll  134 (162)
                      .+.+.+++..+|+||+++....  +....|..++
T Consensus        90 ~~~~~~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~  123 (234)
T PRK05642         90 ELLDNLEQYELVCLDDLDVIAGKADWEEALFHLF  123 (234)
T ss_pred             HHHHhhhhCCEEEEechhhhcCChHHHHHHHHHH
Confidence            3556677778999999987642  3334444444

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.61  E-value=3.4e-07  Score=82.22  Aligned_cols=108  Identities=14%  Similarity=0.110  Sum_probs=65.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEE-Eec--cCCChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYI-CLS--RDTTEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v-~~~--~~~~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+......+.+||+||+|+|||++|+.+|+.++.       ||..+ +|.  ...+..|+.   .+...+
T Consensus        21 q~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~---eidaas   97 (486)
T PRK14953         21 QEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLI---EIDAAS   97 (486)
T ss_pred             hHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEE---EEeCcc
Confidence            46777888888877655545688999999999999999998863       22111 110  000111221   111100


Q ss_pred             EEEec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          97 AIYYD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        97 ~~~~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ..=.+  ..+...+      ..-.+++|||++.++.+..+.|+..+++-
T Consensus        98 ~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEep  146 (486)
T PRK14953         98 NRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEP  146 (486)
T ss_pred             CCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcC
Confidence            00000  0111111      12369999999999999999999999863

>PRK09183 transposase/IS protein; Provisional

Probab=98.60  E-value=6e-08  Score=80.28  Aligned_cols=100  Identities=18%  Similarity=0.237  Sum_probs=58.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhccee--EeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQRR--EIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g~~--~~~~G~~~~~~  101 (162)
                      +...+..|..+.- ...+.+++|+||||||||+|+..++..   .|..+.++.+.      ++....  ....+.  +. 
T Consensus        86 ~~~~i~~L~~~~~-i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~------~l~~~l~~a~~~~~--~~-  155 (259)
T PRK09183         86 PQKQLQSLRSLSF-IERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAA------DLLLQLSTAQRQGR--YK-  155 (259)
T ss_pred             CHHHHHHHhcCCc-hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHH------HHHHHHHHHHHCCc--HH-
Confidence            3444455543211 335789999999999999999999754   46666655432      333110  001111  00 


Q ss_pred             cHHHHHhhcCcEEEEeCCCCCCc--cHHHHHHHhhcC
Q psy4122         102 QSAVRAAIEGRVLILEGIEKAER--NVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A~~~G~vlllDEId~a~~--~v~~~L~~lle~  136 (162)
                      ..+.+.+..-.+++|||+...+.  +..+.|.++++.
T Consensus       156 ~~~~~~~~~~dlLiiDdlg~~~~~~~~~~~lf~li~~  192 (259)
T PRK09183        156 TTLQRGVMAPRLLIIDEIGYLPFSQEEANLFFQVIAK  192 (259)
T ss_pred             HHHHHHhcCCCEEEEcccccCCCChHHHHHHHHHHHH
Confidence            01222244557999999987444  455567777753

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.60  E-value=2.2e-07  Score=79.85  Aligned_cols=91  Identities=19%  Similarity=0.143  Sum_probs=53.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhccee--Eeec---CeEEEeccH----HHHHhhc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRR--EIVN---GTAIYYDQS----AVRAAIE  110 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~--~~~~---G~~~~~~gp----l~~A~~~  110 (162)
                      .+++++||||+|||++++.+++.+     +..+.+++|....+..++....  .+.+   ....+....    +.+.+.+
T Consensus        56 ~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~  135 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDE  135 (394)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHh
Confidence            479999999999999999999766     4556777777665544433210  0100   011111011    2223322


Q ss_pred             -C--cEEEEeCCCCCC----ccHHHHHHHhhc
Q psy4122         111 -G--RVLILEGIEKAE----RNVLPVLNNLLE  135 (162)
Q Consensus       111 -G--~vlllDEId~a~----~~v~~~L~~lle  135 (162)
                       +  .+|+|||+|.+.    .+.+..|...++
T Consensus       136 ~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~  167 (394)
T PRK00411        136 RDRVLIVALDDINYLFEKEGNDVLYSLLRAHE  167 (394)
T ss_pred             cCCEEEEEECCHhHhhccCCchHHHHHHHhhh
Confidence             2  478899999875    445555555444

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=98.60  E-value=5.3e-08  Score=91.43  Aligned_cols=98  Identities=9%  Similarity=0.099  Sum_probs=55.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec-cCCChhhhcceeEeecCeEEEeccHHHHHhh--cCcEEEEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS-RDTTEADIKQRREIVNGTAIYYDQSAVRAAI--EGRVLILE  117 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~-~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~--~G~vlllD  117 (162)
                      ..|++|+||||||||++|+.+|...   +.|.....+. -..+...++... .--|.+...-..+...++  .+++|+||
T Consensus       207 ~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~-~~~Ge~e~rl~~l~~~l~~~~~~ILfID  285 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGT-KYRGDFEKRFKALLKQLEQDTNSILFID  285 (758)
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhccc-chhhhHHHHHHHHHHHHHhcCCCEEEec
Confidence            3489999999999999999999754   2232211111 011233333100 001111111112222222  24699999


Q ss_pred             CCCCC---------CccHHHHHHHhhcCCeEEEc
Q psy4122         118 GIEKA---------ERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       118 EId~a---------~~~v~~~L~~lle~r~l~l~  142 (162)
                      ||+.+         ..++.+.|.+++.++++.+.
T Consensus       286 EIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~vI  319 (758)
T PRK11034        286 EIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVI  319 (758)
T ss_pred             cHHHHhccCCCCCcHHHHHHHHHHHHhCCCeEEE
Confidence            99864         23466779999999988664

>KOG0480|consensus

Probab=98.60  E-value=7.1e-08  Score=88.34  Aligned_cols=94  Identities=11%  Similarity=0.248  Sum_probs=74.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee--EeecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR--EIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~--~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |||++|+||+|||.+.++.++...+.+  +.+..-++.+-|...-  ....|++..+-|+|..  ..+|++-|||+|++.
T Consensus       380 nv~iVGDPgt~KSQfLk~v~~fsPR~v--YtsGkaSSaAGLTaaVvkD~esgdf~iEAGALmL--ADnGICCIDEFDKMd  455 (764)
T KOG0480|consen  380 NVCIVGDPGTGKSQFLKAVCAFSPRSV--YTSGKASSAAGLTAAVVKDEESGDFTIEAGALML--ADNGICCIDEFDKMD  455 (764)
T ss_pred             eEEEeCCCCccHHHHHHHHhccCCcce--EecCcccccccceEEEEecCCCCceeeecCcEEE--ccCceEEechhcccC
Confidence            799999999999999999999887653  3344455566665421  1245888888887644  488999999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEcC
Q psy4122         124 RNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~~  143 (162)
                      -.-+.+|++.||...+.|..
T Consensus       456 ~~dqvAihEAMEQQtISIaK  475 (764)
T KOG0480|consen  456 VKDQVAIHEAMEQQTISIAK  475 (764)
T ss_pred             hHhHHHHHHHHHhheehhee
Confidence            98899999999999887764

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=98.58  E-value=5.6e-08  Score=86.24  Aligned_cols=35  Identities=23%  Similarity=0.222  Sum_probs=30.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      .++.++|+||||||||++|+++|..++.++..+..
T Consensus       216 ~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~  250 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLAKAVANETSATFLRVVG  250 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEec
Confidence            44579999999999999999999999988766543

>CHL00206 ycf2 Ycf2; Provisional

Probab=98.58  E-value=1.6e-07  Score=94.30  Aligned_cols=36  Identities=19%  Similarity=0.180  Sum_probs=32.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      ..+-+||+||||||||.||+++|...+.|+..+.++
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs 1664 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLN 1664 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHH
Confidence            345699999999999999999999999999888776

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=98.57  E-value=4.5e-08  Score=87.17  Aligned_cols=73  Identities=14%  Similarity=0.188  Sum_probs=48.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~a  122 (162)
                      .+.+||+||||||||.||+++|...+.++..+...      +|+..+.  +-+..-....+.+|- ....++++||||.+
T Consensus       276 ~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~------~l~sk~v--Gesek~ir~~F~~A~~~~p~iiFiDEiDs~  347 (494)
T COG0464         276 PKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGS------ELLSKWV--GESEKNIRELFEKARKLAPSIIFIDEIDSL  347 (494)
T ss_pred             CCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCH------HHhcccc--chHHHHHHHHHHHHHcCCCcEEEEEchhhh
Confidence            34699999999999999999999999998776664      3432111  000001112344554 34689999999875


Q ss_pred             Cc
Q psy4122         123 ER  124 (162)
Q Consensus       123 ~~  124 (162)
                      -+
T Consensus       348 ~~  349 (494)
T COG0464         348 AS  349 (494)
T ss_pred             hc
Confidence            43

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.56  E-value=9.3e-08  Score=87.20  Aligned_cols=119  Identities=16%  Similarity=0.120  Sum_probs=87.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh--CCceEEEEeccC---CChhhhcceeEeecCe--E
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT--QREVEYICLSRD---TTEADIKQRREIVNGT--A   97 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l--g~p~~~v~~~~~---~~~~dL~g~~~~~~G~--~   97 (162)
                      -..++....++++.+.....-|++|.|.||+||-.+++++....  .-|+..++|..-   .-.++|+|.   ..|.  .
T Consensus       317 ~~d~s~a~l~rk~~rv~~~~~pvll~GEtGtGKe~laraiH~~s~~~gpfvAvNCaAip~~liesELFGy---~~GafTg  393 (606)
T COG3284         317 LLDPSRATLLRKAERVAATDLPVLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIESELFGY---VAGAFTG  393 (606)
T ss_pred             ccCHHHHHHHHHHHHHhhcCCCeEecCCcchhHHHHHHHHHhcccccCCeEEEEeccchHHhhhHHHhcc---Ccccccc
Confidence            45788888888888877777899999999999999999998554  457888999732   234556552   2222  1


Q ss_pred             EEeccHHHH-HhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcCCcE
Q psy4122          98 IYYDQSAVR-AAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLEDGRF  146 (162)
Q Consensus        98 ~~~~gpl~~-A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~g~~  146 (162)
                      .+..|+.-+ -...|+.++||||.-+|-+.++.|+.+|++|+++=-+|++
T Consensus       394 a~~kG~~g~~~~A~gGtlFldeIgd~p~~~Qs~LLrVl~e~~v~p~g~~~  443 (606)
T COG3284         394 ARRKGYKGKLEQADGGTLFLDEIGDMPLALQSRLLRVLQEGVVTPLGGTR  443 (606)
T ss_pred             chhccccccceecCCCccHHHHhhhchHHHHHHHHHHHhhCceeccCCcc
Confidence            222232100 0136799999999999999999999999999987666654

>KOG0738|consensus

Probab=98.56  E-value=6.7e-08  Score=84.59  Aligned_cols=77  Identities=18%  Similarity=0.286  Sum_probs=52.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH------hhcCcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA------AIEGRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A------~~~G~vlllDEI  119 (162)
                      .|||+||||||||.||+++|...|.  .+++++..+-.+...|.      +     .-+++-      .....+||||||
T Consensus       247 gvLm~GPPGTGKTlLAKAvATEc~t--TFFNVSsstltSKwRGe------S-----EKlvRlLFemARfyAPStIFiDEI  313 (491)
T KOG0738|consen  247 GVLMVGPPGTGKTLLAKAVATECGT--TFFNVSSSTLTSKWRGE------S-----EKLVRLLFEMARFYAPSTIFIDEI  313 (491)
T ss_pred             eeeeeCCCCCcHHHHHHHHHHhhcC--eEEEechhhhhhhhccc------h-----HHHHHHHHHHHHHhCCceeehhhH
Confidence            5999999999999999999999984  46777655445555441      0     122222      234689999999


Q ss_pred             CCC------------CccHHHHHHHhhc
Q psy4122         120 EKA------------ERNVLPVLNNLLE  135 (162)
Q Consensus       120 d~a------------~~~v~~~L~~lle  135 (162)
                      |.+            +..+-+-|+-.+|
T Consensus       314 Dslcs~RG~s~EHEaSRRvKsELLvQmD  341 (491)
T KOG0738|consen  314 DSLCSQRGGSSEHEASRRVKSELLVQMD  341 (491)
T ss_pred             HHHHhcCCCccchhHHHHHHHHHHHHhh
Confidence            753            3345566666666

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.54  E-value=2.4e-07  Score=81.93  Aligned_cols=106  Identities=15%  Similarity=0.145  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEec
Q psy4122          28 QDWLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      ......++.+...-. ...+++|+||||||||||++++|..+     +..+.++++..-  ..++...  +.++..    
T Consensus       131 ~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~--~~~~~~~--~~~~~~----  202 (450)
T PRK00149        131 RLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKF--TNDFVNA--LRNNTM----  202 (450)
T ss_pred             HHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHH--HHHHHHH--HHcCcH----
Confidence            335555555554321 22479999999999999999999776     333445554321  2222221  111111    


Q ss_pred             cHHHHHhhcCcEEEEeCCCCCCc------cHHHHHHHhhcCC-eEEE
Q psy4122         102 QSAVRAAIEGRVLILEGIEKAER------NVLPVLNNLLENR-EMHL  141 (162)
Q Consensus       102 gpl~~A~~~G~vlllDEId~a~~------~v~~~L~~lle~r-~l~l  141 (162)
                      ..+.+.++.-.+|+||||+....      +....++.+.+++ .+.+
T Consensus       203 ~~~~~~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iii  249 (450)
T PRK00149        203 EEFKEKYRSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVL  249 (450)
T ss_pred             HHHHHHHhcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEE
Confidence            13445566778999999988644      2344455566554 3444

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.54  E-value=5.6e-07  Score=84.08  Aligned_cols=105  Identities=14%  Similarity=0.234  Sum_probs=64.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEE---Eec-----cCCChhhhcceeEeecCeEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYI---CLS-----RDTTEADIKQRREIVNGTAI   98 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v---~~~-----~~~~~~dL~g~~~~~~G~~~   98 (162)
                      -+...+.|+..+......+.+||+||+|||||++|+.+|+.+..+-...   .|.     .+.. .|++   .+ ++...
T Consensus        23 Qe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~-~Dvi---ei-daasn   97 (725)
T PRK07133         23 QDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNS-LDII---EM-DAASN   97 (725)
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCC-CcEE---EE-ecccc
Confidence            3667788888887665555679999999999999999998886431100   010     0000 0111   01 11000


Q ss_pred             E-ec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          99 Y-YD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        99 ~-~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      . .+  ..+...+      ....|++|||++.+..+.+++|+..||+
T Consensus        98 ~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEE  144 (725)
T PRK07133         98 NGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEE  144 (725)
T ss_pred             CCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhc
Confidence            0 00  0111222      1236999999999999999999999996

>KOG0737|consensus

Probab=98.54  E-value=6.8e-08  Score=83.63  Aligned_cols=65  Identities=17%  Similarity=0.292  Sum_probs=47.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh------hcCcEEEEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA------IEGRVLILE  117 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~------~~G~vlllD  117 (162)
                      .+.+||.||||||||.+|+++|...|..+.-+.++.-|+  +..|           +...+++|+      .++.+++||
T Consensus       127 ~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~--KWfg-----------E~eKlv~AvFslAsKl~P~iIFID  193 (386)
T KOG0737|consen  127 PKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTS--KWFG-----------EAQKLVKAVFSLASKLQPSIIFID  193 (386)
T ss_pred             CccceecCCCCchHHHHHHHHHHHcCCCcceeeccccch--hhHH-----------HHHHHHHHHHhhhhhcCcceeehh
Confidence            356999999999999999999999999987776654433  2222           111344543      467899999


Q ss_pred             CCCC
Q psy4122         118 GIEK  121 (162)
Q Consensus       118 EId~  121 (162)
                      |||-
T Consensus       194 Evds  197 (386)
T KOG0737|consen  194 EVDS  197 (386)
T ss_pred             hHHH
Confidence            9974

>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=98.52  E-value=5.2e-07  Score=70.34  Aligned_cols=96  Identities=15%  Similarity=0.220  Sum_probs=52.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe---ccCC-----Chhhh-ccee-Ee---------ecCeEEEe-c-
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL---SRDT-----TEADI-KQRR-EI---------VNGTAIYY-D-  101 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~---~~~~-----~~~dL-~g~~-~~---------~~G~~~~~-~-  101 (162)
                      +++|+|+||+||||+++.+.+.+   |.++.=+.+   ..+-     +..++ -|.. .+         .-|...+. + 
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l~~~~~~v~Gf~t~evr~~g~r~GF~iv~l~~g~~~~la~~~~~~~~~vgky~v~~e~   80 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEELKKKGLPVGGFYTEEVRENGRRIGFDIVDLNSGEEAILARVDFRSGPRVGKYFVDLES   80 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHHHHTCGGEEEEEEEEEETTSSEEEEEEEET-TS-EEEEEETTSS-SCECTTCEE-HHH
T ss_pred             CEEEECcCCCCHHHHHHHHHHHhhccCCccceEEeecccCCCceEEEEEEECcCCCccccccccccccccCCCEEEcHHH
Confidence            58999999999999999999888   666432211   1110     01112 1100 01         11322222 1 


Q ss_pred             ------cHHHHHhhcCcEEEEeCCCC---CCccHHHHHHHhhcCCeEEE
Q psy4122         102 ------QSAVRAAIEGRVLILEGIEK---AERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       102 ------gpl~~A~~~G~vlllDEId~---a~~~v~~~L~~lle~r~l~l  141 (162)
                            ..+..|+.+..++++|||-+   ..+.....+..+|+.+.-.|
T Consensus        81 fe~~~~~~L~~~~~~~~liviDEIG~mEl~~~~F~~~v~~~l~s~~~vi  129 (168)
T PF03266_consen   81 FEEIGLPALRNALSSSDLIVIDEIGKMELKSPGFREAVEKLLDSNKPVI  129 (168)
T ss_dssp             HHCCCCCCCHHHHHCCHEEEE---STTCCC-CHHHHHHHHHHCTTSEEE
T ss_pred             HHHHHHHHHHhhcCCCCEEEEeccchhhhcCHHHHHHHHHHHcCCCcEE
Confidence                  12334456678999999955   66778999999999654433

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.51  E-value=1.1e-07  Score=81.41  Aligned_cols=89  Identities=15%  Similarity=0.168  Sum_probs=55.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGI  119 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEI  119 (162)
                      .+.+++|+||||+|||+|+.++|..+   |+.+.+++...-  ...|... .. +......  .....+.+-.+|+||++
T Consensus       182 ~~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l--~~~l~~~-~~-~~~~~~~--~~~~~l~~~DLLIIDDl  255 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADEL--IEILREI-RF-NNDKELE--EVYDLLINCDLLIIDDL  255 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHH--HHHHHHH-Hh-ccchhHH--HHHHHhccCCEEEEecc
Confidence            34799999999999999999999765   555555544211  1112110 00 1110000  11466777899999999


Q ss_pred             CC--CCccHHHHHHHhhcCC
Q psy4122         120 EK--AERNVLPVLNNLLENR  137 (162)
Q Consensus       120 d~--a~~~v~~~L~~lle~r  137 (162)
                      ..  ..+...+.|..+++.|
T Consensus       256 G~e~~t~~~~~~Lf~iin~R  275 (329)
T PRK06835        256 GTEKITEFSKSELFNLINKR  275 (329)
T ss_pred             CCCCCCHHHHHHHHHHHHHH
Confidence            54  4555667777777744

>KOG0733|consensus

Probab=98.51  E-value=1.2e-07  Score=86.84  Aligned_cols=71  Identities=17%  Similarity=0.076  Sum_probs=45.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCCCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEKAER  124 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~a~~  124 (162)
                      -|||+||||||||-||+++|...|..+..+-..+.  ...++|      -+..-+..-+.+|= ....|+|+||||.+-|
T Consensus       547 GvLL~GPPGCGKTLlAKAVANEag~NFisVKGPEL--lNkYVG------ESErAVR~vFqRAR~saPCVIFFDEiDaL~p  618 (802)
T KOG0733|consen  547 GVLLCGPPGCGKTLLAKAVANEAGANFISVKGPEL--LNKYVG------ESERAVRQVFQRARASAPCVIFFDEIDALVP  618 (802)
T ss_pred             ceEEeCCCCccHHHHHHHHhhhccCceEeecCHHH--HHHHhh------hHHHHHHHHHHHhhcCCCeEEEecchhhcCc
Confidence            49999999999999999999999998765544321  122222      11111112233332 2347999999988655

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.51  E-value=1.7e-07  Score=81.53  Aligned_cols=87  Identities=11%  Similarity=0.085  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          30 WLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        30 ~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ....++.+...-. ...+++|+||+|+|||+|++++++.+     +..+.++++..-  ..++...  +..+.    -..
T Consensus       121 a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~--~~~~~~~--~~~~~----~~~  192 (405)
T TIGR00362       121 AHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKF--TNDFVNA--LRNNK----MEE  192 (405)
T ss_pred             HHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHH--HHHHHHH--HHcCC----HHH
Confidence            3444444444311 12378999999999999999999765     344555554311  1122211  11111    113


Q ss_pred             HHHHhhcCcEEEEeCCCCCCc
Q psy4122         104 AVRAAIEGRVLILEGIEKAER  124 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~  124 (162)
                      +.+.++...+|+||||+....
T Consensus       193 ~~~~~~~~dlLiiDDi~~l~~  213 (405)
T TIGR00362       193 FKEKYRSVDLLLIDDIQFLAG  213 (405)
T ss_pred             HHHHHHhCCEEEEehhhhhcC
Confidence            445566678999999998654

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).

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.51  E-value=9e-07  Score=81.52  Aligned_cols=107  Identities=9%  Similarity=0.158  Sum_probs=63.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--------eEEEE-ec--cCCChhhhcceeEeecC
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--------VEYIC-LS--RDTTEADIKQRREIVNG   95 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--------~~~v~-~~--~~~~~~dL~g~~~~~~G   95 (162)
                      -+...+.|+..+......+.+||+||+|+|||++|+.+|+.++..        |-.+. |.  .+...-++.   .+.+.
T Consensus        22 q~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~---~ld~~   98 (614)
T PRK14971         22 QEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIH---ELDAA   98 (614)
T ss_pred             cHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceE---Eeccc
Confidence            467777888888776666568999999999999999999987521        10000 00  000000010   01111


Q ss_pred             eEEEecc--HHHHH------hhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          96 TAIYYDQ--SAVRA------AIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        96 ~~~~~~g--pl~~A------~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +..-.+-  -+...      .....++||||+++++.+.++.|+..||+
T Consensus        99 ~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEe  147 (614)
T PRK14971         99 SNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEE  147 (614)
T ss_pred             ccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhC
Confidence            0000000  01100      11236999999999999999999999996

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=98.50  E-value=1.9e-07  Score=81.18  Aligned_cols=91  Identities=14%  Similarity=0.104  Sum_probs=60.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCc-----eEEEEeccCCChhhhcceeE--e-ecCeEEEeccHH----HHHhhc--
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQRE-----VEYICLSRDTTEADIKQRRE--I-VNGTAIYYDQSA----VRAAIE--  110 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p-----~~~v~~~~~~~~~dL~g~~~--~-~~G~~~~~~gpl----~~A~~~--  110 (162)
                      .|++++|+||||||..++.+++.+..+     +.+++|...-+.-.+.....  + .-..+.|.....    .+.+..  
T Consensus        43 ~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~  122 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKG  122 (366)
T ss_pred             ccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcC
Confidence            379999999999999999999887655     78899987777666553111  1 111222322222    233322  


Q ss_pred             C-cEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         111 G-RVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       111 G-~vlllDEId~a~~~v~~~L~~lle  135 (162)
                      + -+++|||+|.+-..-.+.|+.++.
T Consensus       123 ~~~IvvLDEid~L~~~~~~~LY~L~r  148 (366)
T COG1474         123 KTVIVILDEVDALVDKDGEVLYSLLR  148 (366)
T ss_pred             CeEEEEEcchhhhccccchHHHHHHh
Confidence            2 467899999977775577777765

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=98.49  E-value=5.9e-07  Score=83.04  Aligned_cols=72  Identities=15%  Similarity=0.135  Sum_probs=45.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~a  122 (162)
                      .+.++|+||||||||++++.+|...+.|+..+++..-.  +...+     .+..... ..+..|.. ...+++|||||.+
T Consensus       185 ~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~--~~~~g-----~~~~~~~-~~f~~a~~~~P~IifIDEiD~l  256 (644)
T PRK10733        185 PKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFV--EMFVG-----VGASRVR-DMFEQAKKAAPCIIFIDEIDAV  256 (644)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhH--Hhhhc-----ccHHHHH-HHHHHHHhcCCcEEEehhHhhh
Confidence            45699999999999999999999999998766654210  01111     0100000 01222322 3469999999887


Q ss_pred             C
Q psy4122         123 E  123 (162)
Q Consensus       123 ~  123 (162)
                      .
T Consensus       257 ~  257 (644)
T PRK10733        257 G  257 (644)
T ss_pred             h
Confidence            3

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.49  E-value=4.7e-07  Score=80.18  Aligned_cols=95  Identities=13%  Similarity=0.153  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH----hCCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL----TQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~----lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ...+..|..++.-...+.|+++.||+|||||+++..++..    .|         .-++.++|+..  +..        .
T Consensus       193 r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~l~~~~a~~sG---------~f~T~a~Lf~~--L~~--------~  253 (449)
T TIGR02688       193 RQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNNLSPYVILISG---------GTITVAKLFYN--IST--------R  253 (449)
T ss_pred             HHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHHHhHHHHHHcC---------CcCcHHHHHHH--HHH--------H
Confidence            3445556565555556789999999999999999987744    23         35667778742  101        2


Q ss_pred             HHHHhhcCcEEEEeCCCCCC----ccHHHHHHHhhcCCeEEE
Q psy4122         104 AVRAAIEGRVLILEGIEKAE----RNVLPVLNNLLENREMHL  141 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~----~~v~~~L~~lle~r~l~l  141 (162)
                      ....+..-.+|+|||+.-.+    .+..+.|...|+++...-
T Consensus       254 ~lg~v~~~DlLI~DEvgylp~~~~~~~v~imK~yMesg~fsR  295 (449)
T TIGR02688       254 QIGLVGRWDVVAFDEVATLKFAKPKELIGILKNYMESGSFTR  295 (449)
T ss_pred             HHhhhccCCEEEEEcCCCCcCCchHHHHHHHHHHHHhCceec
Confidence            23344556899999997633    347788999999888765

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.48  E-value=3.4e-07  Score=82.81  Aligned_cols=61  Identities=13%  Similarity=0.032  Sum_probs=45.6

Q ss_pred             eeeecccCCCCCCHHHHHHHHHHHHhcCCCC----cEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          15 LIYLFSVNTDALTQDWLSHLRWILQKDNMSQ----DVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~L~~i~~~~~~g~----~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      +|.+.+..+....+..++.++..++....+.    -++|.||||||||+.++.+|+.+|..+...
T Consensus        12 ky~P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew   76 (519)
T PF03215_consen   12 KYAPKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEW   76 (519)
T ss_pred             hcCCCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEe
Confidence            4444445555567778888887776654333    478899999999999999999999877654

>KOG0731|consensus

Probab=98.48  E-value=7.2e-08  Score=90.05  Aligned_cols=73  Identities=18%  Similarity=0.152  Sum_probs=46.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~a  122 (162)
                      .+-+||+||||||||-||+++|..-|.|+..++.++   .-+..     .++...=+..-+..|=. ...++++||||..
T Consensus       344 PkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSE---FvE~~-----~g~~asrvr~lf~~ar~~aP~iifideida~  415 (774)
T KOG0731|consen  344 PKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSE---FVEMF-----VGVGASRVRDLFPLARKNAPSIIFIDEIDAV  415 (774)
T ss_pred             cCceEEECCCCCcHHHHHHHHhcccCCceeeechHH---HHHHh-----cccchHHHHHHHHHhhccCCeEEEecccccc
Confidence            345999999999999999999999999987665542   22222     11110001111222222 2478999999875


Q ss_pred             Cc
Q psy4122         123 ER  124 (162)
Q Consensus       123 ~~  124 (162)
                      ..
T Consensus       416 ~~  417 (774)
T KOG0731|consen  416 GR  417 (774)
T ss_pred             cc
Confidence            43

>KOG0991|consensus

Probab=98.47  E-value=6.6e-07  Score=74.29  Aligned_cols=99  Identities=14%  Similarity=0.249  Sum_probs=65.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH-hCCceE----EEEeccCCChhhhccee-EeecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL-TQREVE----YICLSRDTTEADIKQRR-EIVNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~-lg~p~~----~v~~~~~~~~~dL~g~~-~~~~G~~~~~  100 (162)
                      +..+.+.|.-|....... |+++.||||||||+-+..+|+. +|....    .++.+.+-...-...+. .+...+.   
T Consensus        32 Ne~tv~rl~via~~gnmP-~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv---  107 (333)
T KOG0991|consen   32 NEDTVERLSVIAKEGNMP-NLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQKKV---  107 (333)
T ss_pred             CHHHHHHHHHHHHcCCCC-ceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHHHHHhhc---
Confidence            689999999999877665 8999999999999999999965 564321    22222211111110000 0000000   


Q ss_pred             ccHHHHHhhcC--cEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         101 DQSAVRAAIEG--RVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       101 ~gpl~~A~~~G--~vlllDEId~a~~~v~~~L~~lle  135 (162)
                            .+..|  .+++|||.|.+....+.+|.+.+|
T Consensus       108 ------~lp~grhKIiILDEADSMT~gAQQAlRRtME  138 (333)
T KOG0991|consen  108 ------TLPPGRHKIIILDEADSMTAGAQQALRRTME  138 (333)
T ss_pred             ------cCCCCceeEEEeeccchhhhHHHHHHHHHHH
Confidence                  01122  589999999999999999999988

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.46  E-value=4.5e-07  Score=80.37  Aligned_cols=100  Identities=14%  Similarity=0.137  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEeccHH
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA  104 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl  104 (162)
                      .....+.+...-....|++|+||||||||||+.++|+.+     +..+.++++..-  ..++...  +..+..    ..+
T Consensus       116 a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f--~~~~~~~--~~~~~~----~~f  187 (440)
T PRK14088        116 AYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKF--LNDLVDS--MKEGKL----NEF  187 (440)
T ss_pred             HHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHH--HHHHHHH--HhcccH----HHH
Confidence            334444444321112379999999999999999999764     233445544311  1222211  111111    123


Q ss_pred             HHHhh-cCcEEEEeCCCCCCc------cHHHHHHHhhcCC
Q psy4122         105 VRAAI-EGRVLILEGIEKAER------NVLPVLNNLLENR  137 (162)
Q Consensus       105 ~~A~~-~G~vlllDEId~a~~------~v~~~L~~lle~r  137 (162)
                      .+.++ ...+|+|||++....      +....++.+.+.+
T Consensus       188 ~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~  227 (440)
T PRK14088        188 REKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSG  227 (440)
T ss_pred             HHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcC
Confidence            33444 468999999987532      2344455555554

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.46  E-value=2.1e-07  Score=67.00  Aligned_cols=81  Identities=14%  Similarity=0.240  Sum_probs=52.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCcc-
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERN-  125 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~-  125 (162)
                      |+|+||||||||++++.+|..+.....      ......+.   ....+.-.|      ..+..-.++++||+.....+ 
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~------~~~~~~vy---~~~~~~~~w------~gY~~q~vvi~DD~~~~~~~~   65 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIG------EPTKDSVY---TRNPGDKFW------DGYQGQPVVIIDDFGQDNDGY   65 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhc------cCCCCcEE---eCCCccchh------hccCCCcEEEEeecCcccccc
Confidence            589999999999999999977754320      00011111   111122222      23455579999999887765 


Q ss_pred             ---HHHHHHHhhcCCeEEEc
Q psy4122         126 ---VLPVLNNLLENREMHLE  142 (162)
Q Consensus       126 ---v~~~L~~lle~r~l~l~  142 (162)
                         ....|.++++.-.+..+
T Consensus        66 ~~~~~~~l~~l~s~~~~~~~   85 (107)
T PF00910_consen   66 NYSDESELIRLISSNPFQPN   85 (107)
T ss_pred             chHHHHHHHHHHhcCCcccc
Confidence               67788888888777654

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>KOG0735|consensus

Probab=98.45  E-value=5.6e-07  Score=83.64  Aligned_cols=101  Identities=13%  Similarity=0.086  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHh------------cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecC
Q psy4122          28 QDWLSHLRWILQK------------DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~------------~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      .+....|+.+++.            +.....+||+||||||||.||.++|...+..+..+-..+-  .+..+|.-  +.+
T Consensus       673 ~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPEl--L~KyIGaS--Eq~  748 (952)
T KOG0735|consen  673 FEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKGPEL--LSKYIGAS--EQN  748 (952)
T ss_pred             HHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHHH--HHHHhccc--HHH
Confidence            4555666666541            2233469999999999999999999887765443333211  34444421  001


Q ss_pred             eEEEeccHHHHH-hhcCcEEEEeCCCCCCcc-----------HHHHHHHhhcC
Q psy4122          96 TAIYYDQSAVRA-AIEGRVLILEGIEKAERN-----------VLPVLNNLLEN  136 (162)
Q Consensus        96 ~~~~~~gpl~~A-~~~G~vlllDEId~a~~~-----------v~~~L~~lle~  136 (162)
                          +.--+.+| +....+|++||+|...|.           |.+-|+.-||.
T Consensus       749 ----vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG  797 (952)
T KOG0735|consen  749 ----VRDLFERAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDG  797 (952)
T ss_pred             ----HHHHHHHhhccCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhcc
Confidence                11123344 345689999999986662           56666666664

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=98.45  E-value=1.6e-06  Score=74.03  Aligned_cols=107  Identities=17%  Similarity=0.139  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce--EEEEec--------cCCChhhhcceeEeecCeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV--EYICLS--------RDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~--~~v~~~--------~~~~~~dL~g~~~~~~G~~   97 (162)
                      +...+.|+.++......+..||+||+|+||+++|+.+|+.+..+-  ....|.        ..-+-.|+.-  ...+|..
T Consensus        12 ~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~--i~~~~~~   89 (329)
T PRK08058         12 PVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHL--VAPDGQS   89 (329)
T ss_pred             HHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEE--ecccccc
Confidence            456778888887666665679999999999999999998764221  000000        0000011110  0011211


Q ss_pred             EEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          98 IYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        98 ~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .=.+.  .+.+.+      ....|++|||+++++.+.+++|+..||+
T Consensus        90 i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEE  136 (329)
T PRK08058         90 IKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEE  136 (329)
T ss_pred             CCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcC
Confidence            10110  011111      1236999999999999999999999996

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=98.44  E-value=2.4e-06  Score=65.91  Aligned_cols=107  Identities=16%  Similarity=0.236  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE-EEec--------cCCChhhhcceeEeec-Ce-
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY-ICLS--------RDTTEADIKQRREIVN-GT-   96 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~-v~~~--------~~~~~~dL~g~~~~~~-G~-   96 (162)
                      +...+.|..+++.....+.+||+||+|+||+++|..+|+.+--.-.. ..|.        ..-...|+.   .+.. +. 
T Consensus         3 ~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~---~~~~~~~~   79 (162)
T PF13177_consen    3 EEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFI---IIKPDKKK   79 (162)
T ss_dssp             HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEE---EEETTTSS
T ss_pred             HHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceE---EEeccccc
Confidence            45678888888887777778999999999999999999766322110 0000        000011111   0111 00 


Q ss_pred             -EEEecc--HHHHH-----hh-cCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          97 -AIYYDQ--SAVRA-----AI-EGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        97 -~~~~~g--pl~~A-----~~-~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                       ..-.+.  .+...     .. .-.+++|||+++++.+.+++|+..||+-
T Consensus        80 ~~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEep  129 (162)
T PF13177_consen   80 KSIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEP  129 (162)
T ss_dssp             SSBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHST
T ss_pred             chhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCC
Confidence             000000  01111     11 2369999999999999999999999964

...

>KOG0742|consensus

Probab=98.44  E-value=3.3e-07  Score=81.02  Aligned_cols=101  Identities=12%  Similarity=0.153  Sum_probs=66.2

Q ss_pred             CCHHHHHHHHHHHHhcCC-------CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeec--Ce
Q psy4122          26 LTQDWLSHLRWILQKDNM-------SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVN--GT   96 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~-------g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~--G~   96 (162)
                      +.|+....++++..+-..       -+|++++||||||||..|+.+|...|...-.++.. |.-+   +|+.....  --
T Consensus       359 L~psLe~Rie~lA~aTaNTK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGG-DVAP---lG~qaVTkiH~l  434 (630)
T KOG0742|consen  359 LHPSLEKRIEDLAIATANTKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGG-DVAP---LGAQAVTKIHKL  434 (630)
T ss_pred             cCHHHHHHHHHHHHHhcccccccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCC-Cccc---cchHHHHHHHHH
Confidence            579999999999865332       23799999999999999999999999875433322 2111   11100000  01


Q ss_pred             EEEeccHHHHHhhcCcEEEEeCCCC---------CCccHHHHHHHhhc
Q psy4122          97 AIYYDQSAVRAAIEGRVLILEGIEK---------AERNVLPVLNNLLE  135 (162)
Q Consensus        97 ~~~~~gpl~~A~~~G~vlllDEId~---------a~~~v~~~L~~lle  135 (162)
                      |.|-     +-.+.|-+|+|||.|.         ++.+.-+.||.+|=
T Consensus       435 FDWa-----kkS~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLf  477 (630)
T KOG0742|consen  435 FDWA-----KKSRRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLF  477 (630)
T ss_pred             HHHH-----hhcccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHH
Confidence            2221     2235677899999975         56677888888774

>KOG0730|consensus

Probab=98.44  E-value=1.5e-07  Score=86.39  Aligned_cols=85  Identities=14%  Similarity=0.119  Sum_probs=52.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..+-|||+||||||||++|+++|...+.++..+.+.+-  .+...|      -+.....--+-+|= ....|+++||||.
T Consensus       467 ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL--~sk~vG------eSEr~ir~iF~kAR~~aP~IiFfDEiDs  538 (693)
T KOG0730|consen  467 PPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPEL--FSKYVG------ESERAIREVFRKARQVAPCIIFFDEIDA  538 (693)
T ss_pred             CCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHH--HHHhcC------chHHHHHHHHHHHhhcCCeEEehhhHHh
Confidence            34569999999999999999999999999876655322  111222      00000000122221 1237999999986


Q ss_pred             CCc-----------cHHHHHHHhhc
Q psy4122         122 AER-----------NVLPVLNNLLE  135 (162)
Q Consensus       122 a~~-----------~v~~~L~~lle  135 (162)
                      ...           .|++.|+.-||
T Consensus       539 i~~~R~g~~~~v~~RVlsqLLtEmD  563 (693)
T KOG0730|consen  539 LAGSRGGSSSGVTDRVLSQLLTEMD  563 (693)
T ss_pred             HhhccCCCccchHHHHHHHHHHHcc
Confidence            432           36677777666

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=98.43  E-value=2e-06  Score=71.19  Aligned_cols=110  Identities=17%  Similarity=0.189  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC-CceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ-REVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA  108 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg-~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~  108 (162)
                      .+++.+..+..... .|+||+|+.|||||++++++..... ..+..+++..+    +|..-            ..+...+
T Consensus        39 l~~Nt~~Fl~G~pa-nnvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~----~L~~l------------~~l~~~l  101 (249)
T PF05673_consen   39 LIENTEQFLQGLPA-NNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKE----DLGDL------------PELLDLL  101 (249)
T ss_pred             HHHHHHHHHcCCCC-cceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHH----HhccH------------HHHHHHH
Confidence            33444444444333 3899999999999999999887653 34666766522    33210            0233333


Q ss_pred             h---cCcEEEEeCCCC-CCccHHHHHHHhhcCCeEEEcCCcEEecCcchHhh
Q psy4122         109 I---EGRVLILEGIEK-AERNVLPVLNNLLENREMHLEDGRFLVSASTYDKL  156 (162)
Q Consensus       109 ~---~G~vlllDEId~-a~~~v~~~L~~lle~r~l~l~~g~~i~~~~~f~~~  156 (162)
                      +   ..-||++|++.- ....--..|.++||.+--.-|+.-.+.++.|-+-+
T Consensus       102 ~~~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHL  153 (249)
T PF05673_consen  102 RDRPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHL  153 (249)
T ss_pred             hcCCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhc
Confidence            3   345899999843 44456788999999876666777777777776544

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.40  E-value=1e-06  Score=76.14  Aligned_cols=109  Identities=16%  Similarity=0.172  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEEEeccCCChhhhc--c-ee---Ee--
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYICLSRDTTEADIK--Q-RR---EI--   92 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v~~~~~~~~~dL~--g-~~---~~--   92 (162)
                      ....+.|...+.+....+.+||+||+|+|||++|+.+|+.+..       |....+.+.....-.++  | .+   .+  
T Consensus        29 ~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i~~~~hPdl~~l~~  108 (351)
T PRK09112         29 EEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQIAQGAHPNLLHITR  108 (351)
T ss_pred             HHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHHHcCCCCCEEEeec
Confidence            5566777777766555546999999999999999999987744       11100010111111111  0 00   01  


Q ss_pred             ----ecCe---EEEecc--HHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          93 ----VNGT---AIYYDQ--SAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        93 ----~~G~---~~~~~g--pl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                          ++|.   .+-++.  .+.+-+    ..|  .|++|||+++++++.++.|+..||+
T Consensus       109 ~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEE  167 (351)
T PRK09112        109 PFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEE  167 (351)
T ss_pred             ccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhc
Confidence                1111   000110  011111    123  5899999999999999999999996

>KOG0477|consensus

Probab=98.40  E-value=2.6e-07  Score=84.78  Aligned_cols=93  Identities=12%  Similarity=0.200  Sum_probs=65.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEee---cCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIV---NGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~---~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      ||||.|+||||||.+.++.++...+.+.  ......+..-|... ..+   .+....+-|+|+.  ..+||++|||+|++
T Consensus       484 nvLL~GDPGTaKSQFLKY~eK~s~RAV~--tTGqGASavGLTa~-v~KdPvtrEWTLEaGALVL--ADkGvClIDEFDKM  558 (854)
T KOG0477|consen  484 NVLLLGDPGTAKSQFLKYAEKTSPRAVF--TTGQGASAVGLTAY-VRKDPVTREWTLEAGALVL--ADKGVCLIDEFDKM  558 (854)
T ss_pred             eEEEecCCCccHHHHHHHHHhcCcceeE--eccCCccccceeEE-EeeCCccceeeeccCeEEE--ccCceEEeehhhhh
Confidence            6999999999999999999988877643  33334344344321 111   1233334444444  47899999999999


Q ss_pred             CccHHHHHHHhhcCCeEEEcC
Q psy4122         123 ERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       123 ~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +..=-..++..||...+.|..
T Consensus       559 ndqDRtSIHEAMEQQSISISK  579 (854)
T KOG0477|consen  559 NDQDRTSIHEAMEQQSISISK  579 (854)
T ss_pred             cccccchHHHHHHhcchhhhh
Confidence            998888899999988776643

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=98.40  E-value=1.3e-06  Score=76.28  Aligned_cols=93  Identities=13%  Similarity=0.176  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec---cCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS---RDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLIL  116 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~---~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlll  116 (162)
                      ...|+|+.|.+||||--+|++...+   .+.|+.-++|.   ++.-.++|.|+..=.+|+.    |-+-  ..+||.++|
T Consensus       226 lDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lPe~~aEsElFG~apg~~gk~----GffE--~AngGTVlL  299 (511)
T COG3283         226 LDAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLPEDAAESELFGHAPGDEGKK----GFFE--QANGGTVLL  299 (511)
T ss_pred             cCCCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeecCCCchhHhHHHHhcCCCCCCCcc----chhh--hccCCeEEe
Confidence            3469999999999999999977644   36788888886   3444677888533333432    2222  348999999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         117 EGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      |||-.++|..+..|+.+|.+|...-
T Consensus       300 DeIgEmSp~lQaKLLRFL~DGtFRR  324 (511)
T COG3283         300 DEIGEMSPRLQAKLLRFLNDGTFRR  324 (511)
T ss_pred             ehhhhcCHHHHHHHHHHhcCCceee
Confidence            9999999999999999999887754

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.40  E-value=1.3e-06  Score=83.27  Aligned_cols=89  Identities=17%  Similarity=0.175  Sum_probs=51.8

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh-------CCc---eEEEEeccCCChhhhcce--eEeec--CeEEEeccHHHH----Hh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT-------QRE---VEYICLSRDTTEADIKQR--REIVN--GTAIYYDQSAVR----AA  108 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l-------g~p---~~~v~~~~~~~~~dL~g~--~~~~~--G~~~~~~gpl~~----A~  108 (162)
                      +++.|+||||||..++.+.+.+       +.+   +.+++|....++..+...  ..+.+  ....|.-.-+..    .+
T Consensus       784 LYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L  863 (1164)
T PTZ00112        784 LYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQN  863 (1164)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhh
Confidence            4699999999999999997655       223   356777544444433210  00100  111111011111    11


Q ss_pred             h---c-CcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         109 I---E-GRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       109 ~---~-G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                      .   . -.+|+|||||.+....+.+|+.+++
T Consensus       864 ~k~~r~v~IIILDEID~L~kK~QDVLYnLFR  894 (1164)
T PTZ00112        864 KKDNRNVSILIIDEIDYLITKTQKVLFTLFD  894 (1164)
T ss_pred             hcccccceEEEeehHhhhCccHHHHHHHHHH
Confidence            1   1 1378999999998888888888776

>PRK09087 hypothetical protein; Validated

Probab=98.38  E-value=1.6e-06  Score=70.39  Aligned_cols=73  Identities=25%  Similarity=0.296  Sum_probs=45.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      +.+++|+||+|||||||++.+++..+..  ++...      ++.             + .++.++.. ++|+||+++..+
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~~~~--~i~~~------~~~-------------~-~~~~~~~~-~~l~iDDi~~~~  100 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKSDAL--LIHPN------EIG-------------S-DAANAAAE-GPVLIEDIDAGG  100 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhcCCE--EecHH------Hcc-------------h-HHHHhhhc-CeEEEECCCCCC
Confidence            3359999999999999999988765432  23221      111             0 12223333 689999998865


Q ss_pred             cc---HHHHHHHhhcCCeE
Q psy4122         124 RN---VLPVLNNLLENREM  139 (162)
Q Consensus       124 ~~---v~~~L~~lle~r~l  139 (162)
                      .+   ....+|.+.+++..
T Consensus       101 ~~~~~lf~l~n~~~~~g~~  119 (226)
T PRK09087        101 FDETGLFHLINSVRQAGTS  119 (226)
T ss_pred             CCHHHHHHHHHHHHhCCCe
Confidence            32   45555566665543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.36  E-value=5.1e-07  Score=80.23  Aligned_cols=72  Identities=18%  Similarity=0.188  Sum_probs=45.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEK  121 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~  121 (162)
                      .|++|+||+|+|||||+++++..+   +..+.+++...-  ..++...  +..+..    ..+...++.-.+|+||||+.
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f--~~~~~~~--l~~~~~----~~f~~~~~~~dvLiIDDiq~  213 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELF--TEHLVSA--IRSGEM----QRFRQFYRNVDALFIEDIEV  213 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHH--HHHHHHH--HhcchH----HHHHHHcccCCEEEEcchhh
Confidence            479999999999999999999765   555555554211  1122211  111210    12333355678999999998


Q ss_pred             CCc
Q psy4122         122 AER  124 (162)
Q Consensus       122 a~~  124 (162)
                      ...
T Consensus       214 l~~  216 (445)
T PRK12422        214 FSG  216 (445)
T ss_pred             hcC
Confidence            754

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.36  E-value=2.8e-06  Score=72.78  Aligned_cols=103  Identities=19%  Similarity=0.121  Sum_probs=57.3

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEE-Eec---cCCChhhhcceeEeecCeEEEec
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYI-CLS---RDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v-~~~---~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      ..+.++......+.+||.||+|+||+++|+.+|+.+...       +-.+ +|.   ....+ |+.--.....++.+=+|
T Consensus        11 ~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HP-D~~~i~~~~~~~~i~id   89 (328)
T PRK05707         11 LWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHP-DNFVLEPEEADKTIKVD   89 (328)
T ss_pred             HHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCC-CEEEEeccCCCCCCCHH
Confidence            344555554455568999999999999999999887531       1100 000   00001 11100000001100000


Q ss_pred             c--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 Q--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .  .+.+.+      ....|++|||+++++.+..++|+..||+
T Consensus        90 ~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEE  132 (328)
T PRK05707         90 QVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEE  132 (328)
T ss_pred             HHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhC
Confidence            0  011111      1236899999999999999999999997

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.36  E-value=1.3e-06  Score=80.41  Aligned_cols=104  Identities=16%  Similarity=0.219  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHhcCCC-CcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          30 WLSHLRWILQKDNMS-QDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g-~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      .....+.++...... -+++|+|++|||||||+.++|+.+     +..+.++++..-  ..++...  +.++..    .-
T Consensus       299 A~aaa~avae~~~~~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef--~~el~~a--l~~~~~----~~  370 (617)
T PRK14086        299 AHAAAVAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEF--TNEFINS--IRDGKG----DS  370 (617)
T ss_pred             HHHHHHHHHhCccccCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH--HHHHHHH--HHhccH----HH
Confidence            334445555443222 259999999999999999999765     344555555321  1223211  112211    12


Q ss_pred             HHHHhhcCcEEEEeCCCCCCcc------HHHHHHHhhcC-CeEEE
Q psy4122         104 AVRAAIEGRVLILEGIEKAERN------VLPVLNNLLEN-REMHL  141 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~------v~~~L~~lle~-r~l~l  141 (162)
                      +.+.++.-.+|+||||+....+      +...++.+.++ +.+.+
T Consensus       371 f~~~y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~III  415 (617)
T PRK14086        371 FRRRYREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVL  415 (617)
T ss_pred             HHHHhhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEE
Confidence            4445667789999999887442      44555566554 34544

>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=98.35  E-value=2e-06  Score=69.53  Aligned_cols=101  Identities=14%  Similarity=0.157  Sum_probs=61.0

Q ss_pred             CHHHHHHHHHHHHhcCC-CCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNM-SQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~-g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~  100 (162)
                      +....+..+.+...-.. ..+++|+||+|+|||||.+++++..     +..+.+++...-  ..++..  .+.++..   
T Consensus        16 N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f--~~~~~~--~~~~~~~---   88 (219)
T PF00308_consen   16 NELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEF--IREFAD--ALRDGEI---   88 (219)
T ss_dssp             THHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHH--HHHHHH--HHHTTSH---
T ss_pred             HHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHH--HHHHHH--HHHcccc---
Confidence            56667777777765322 2379999999999999999998754     233444443211  111110  0111111   


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCccH--HHHHHHhhc
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERNV--LPVLNNLLE  135 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~v--~~~L~~lle  135 (162)
                       ..+...++.-.+|+||+|+......  +..|..+++
T Consensus        89 -~~~~~~~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n  124 (219)
T PF00308_consen   89 -EEFKDRLRSADLLIIDDIQFLAGKQRTQEELFHLFN  124 (219)
T ss_dssp             -HHHHHHHCTSSEEEEETGGGGTTHHHHHHHHHHHHH
T ss_pred             -hhhhhhhhcCCEEEEecchhhcCchHHHHHHHHHHH
Confidence             1345566777999999999976643  555555554

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.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.35  E-value=6.5e-06  Score=69.39  Aligned_cols=100  Identities=15%  Similarity=0.197  Sum_probs=62.4

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce------EEEEecc----CCChhhhcceeEeecCeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV------EYICLSR----DTTEADIKQRREIVNGTA   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~------~~v~~~~----~~~~~dL~g~~~~~~G~~   97 (162)
                      +...+.|+..+......+..+++||+|+|||++|+.+|+.+....      ....+..    .....++..   +. ...
T Consensus        10 ~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~---~~-~~~   85 (313)
T PRK05564         10 ENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRN---II-EEV   85 (313)
T ss_pred             HHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHH---HH-HHH
Confidence            566777888887666666679999999999999999998763210      0111110    011111110   00 000


Q ss_pred             EEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          98 IYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        98 ~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                        ...|+   .....|++|||+++++.+..++|+..||+
T Consensus        86 --~~~p~---~~~~kv~iI~~ad~m~~~a~naLLK~LEe  119 (313)
T PRK05564         86 --NKKPY---EGDKKVIIIYNSEKMTEQAQNAFLKTIEE  119 (313)
T ss_pred             --hcCcc---cCCceEEEEechhhcCHHHHHHHHHHhcC
Confidence              00010   01336999999999999999999999996

>KOG0739|consensus

Probab=98.31  E-value=8.4e-07  Score=75.89  Aligned_cols=69  Identities=16%  Similarity=0.261  Sum_probs=43.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc--CcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE--GRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~--G~vlllDEId~a~  123 (162)
                      -+||+||||+|||.||+++|...+.-  +++++    .+||+..+.=+.-+  .+. .|....|+  ..+++|||||.+.
T Consensus       168 giLLyGPPGTGKSYLAKAVATEAnST--FFSvS----SSDLvSKWmGESEk--LVk-nLFemARe~kPSIIFiDEiDslc  238 (439)
T KOG0739|consen  168 GILLYGPPGTGKSYLAKAVATEANST--FFSVS----SSDLVSKWMGESEK--LVK-NLFEMARENKPSIIFIDEIDSLC  238 (439)
T ss_pred             eEEEeCCCCCcHHHHHHHHHhhcCCc--eEEee----hHHHHHHHhccHHH--HHH-HHHHHHHhcCCcEEEeehhhhhc
Confidence            38999999999999999999988844  55554    44555211000000  000 12222343  4799999998654

>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=98.31  E-value=7.7e-07  Score=64.00  Aligned_cols=26  Identities=31%  Similarity=0.384  Sum_probs=24.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +++.|+|||||||+|+.+|+.+|.++
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~   27 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPV   27 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeE
Confidence            68999999999999999999998763

...

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.30  E-value=3.9e-06  Score=72.87  Aligned_cols=41  Identities=12%  Similarity=0.067  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +...+.|...+......+.+||+||+|+||+++|..+|+.+
T Consensus        25 ~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~L   65 (365)
T PRK07471         25 AAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFL   65 (365)
T ss_pred             HHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            56667787777766666569999999999999999999876

>KOG0651|consensus

Probab=98.27  E-value=2.5e-06  Score=73.06  Aligned_cols=84  Identities=15%  Similarity=0.156  Sum_probs=52.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~a  122 (162)
                      .+-++|+||||+|||-+|+++|+.+|..+..+..++-  .++.+|.    .+.  ....-+..|-. ...++++||||..
T Consensus       166 Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~l--v~kyiGE----saR--lIRemf~yA~~~~pciifmdeiDAi  237 (388)
T KOG0651|consen  166 PKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSAL--VDKYIGE----SAR--LIRDMFRYAREVIPCIIFMDEIDAI  237 (388)
T ss_pred             CceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhhh--hhhhccc----HHH--HHHHHHHHHhhhCceEEeehhhhhh
Confidence            3458999999999999999999999998776655422  2233331    000  00001112221 2478999999863


Q ss_pred             -----------CccHHHHHHHhhc
Q psy4122         123 -----------ERNVLPVLNNLLE  135 (162)
Q Consensus       123 -----------~~~v~~~L~~lle  135 (162)
                                 +..++.-|..+++
T Consensus       238 gGRr~se~Ts~dreiqrTLMeLln  261 (388)
T KOG0651|consen  238 GGRRFSEGTSSDREIQRTLMELLN  261 (388)
T ss_pred             ccEEeccccchhHHHHHHHHHHHH
Confidence                       3457777777776

>PHA00729 NTP-binding motif containing protein

Probab=98.25  E-value=3.1e-06  Score=69.26  Aligned_cols=24  Identities=21%  Similarity=0.270  Sum_probs=22.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +++|+|+|||||||+|..+|..++
T Consensus        19 nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            899999999999999999999876

>KOG0726|consensus

Probab=98.25  E-value=7e-07  Score=76.21  Aligned_cols=69  Identities=20%  Similarity=0.239  Sum_probs=46.7

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH-HHHH----h--hcCcE
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS-AVRA----A--IEGRV  113 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp-l~~A----~--~~G~v  113 (162)
                      +...+-|+|+|+||+|||-||+++|..+..-+.++..      ++|++.+.        -+|| +++-    .  -...+
T Consensus       216 ikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvG------seLiQkyl--------GdGpklvRqlF~vA~e~apSI  281 (440)
T KOG0726|consen  216 IKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVG------SELIQKYL--------GDGPKLVRELFRVAEEHAPSI  281 (440)
T ss_pred             CCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhh------HHHHHHHh--------ccchHHHHHHHHHHHhcCCce
Confidence            3344569999999999999999999988777665544      35554221        1233 2222    2  23479


Q ss_pred             EEEeCCCCCC
Q psy4122         114 LILEGIEKAE  123 (162)
Q Consensus       114 lllDEId~a~  123 (162)
                      +||||||...
T Consensus       282 vFiDEIdAiG  291 (440)
T KOG0726|consen  282 VFIDEIDAIG  291 (440)
T ss_pred             EEeehhhhhc
Confidence            9999998754

>KOG0741|consensus

Probab=98.25  E-value=8.7e-07  Score=80.28  Aligned_cols=69  Identities=19%  Similarity=0.191  Sum_probs=50.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcC-cEEEEeCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEG-RVLILEGIEK  121 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G-~vlllDEId~  121 (162)
                      .+||.||||+|||+||-.+|...+.|+..+.     +++|++|.  .+..+..+....+-.|++.. .++++|+|.+
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~S~FPFvKii-----Spe~miG~--sEsaKc~~i~k~F~DAYkS~lsiivvDdiEr  609 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALSSDFPFVKII-----SPEDMIGL--SESAKCAHIKKIFEDAYKSPLSIIVVDDIER  609 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhhcCCCeEEEe-----ChHHccCc--cHHHHHHHHHHHHHHhhcCcceEEEEcchhh
Confidence            6999999999999999999999999987552     46677762  11222223334455666665 7899999976

>PRK04296 thymidine kinase; Provisional

Probab=98.23  E-value=6.1e-06  Score=65.11  Aligned_cols=94  Identities=9%  Similarity=0.014  Sum_probs=49.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChh--hhcceeEeecCeEEEec-cHHHHHhh--cC--cE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEA--DIKQRREIVNGTAIYYD-QSAVRAAI--EG--RV  113 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~--dL~g~~~~~~G~~~~~~-gpl~~A~~--~G--~v  113 (162)
                      |.-.+++||+|+|||+++..++...   |..+..+.-.-+....  .+..+-.+.-....|.. ..+...++  ++  .+
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            4457899999999999999888654   5554444221122211  11111001001111211 12223332  22  58


Q ss_pred             EEEeCCCCCCcc-HHHHHHHhhcCC
Q psy4122         114 LILEGIEKAERN-VLPVLNNLLENR  137 (162)
Q Consensus       114 lllDEId~a~~~-v~~~L~~lle~r  137 (162)
                      |+|||+..++.+ +.+.+..+-+.+
T Consensus        82 viIDEaq~l~~~~v~~l~~~l~~~g  106 (190)
T PRK04296         82 VLIDEAQFLDKEQVVQLAEVLDDLG  106 (190)
T ss_pred             EEEEccccCCHHHHHHHHHHHHHcC
Confidence            999999999777 555554445555

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.22  E-value=2.4e-06  Score=79.03  Aligned_cols=48  Identities=8%  Similarity=0.117  Sum_probs=37.8

Q ss_pred             CCHHHHHHHHHHHHhcCCC----CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          26 LTQDWLSHLRWILQKDNMS----QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g----~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..+..++.++.++.....+    +-++|+||||||||++++.+|..++..+.
T Consensus        88 ~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~  139 (637)
T TIGR00602        88 VHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQ  139 (637)
T ss_pred             CcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHH
Confidence            3567777788777765432    23999999999999999999999887653

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

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

Probab=98.22  E-value=3.2e-06  Score=67.16  Aligned_cols=95  Identities=16%  Similarity=0.065  Sum_probs=53.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcc-eeEeecCeEEEeccHHHHHhh--cCcEEEEeCCCCCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQ-RREIVNGTAIYYDQSAVRAAI--EGRVLILEGIEKAE  123 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g-~~~~~~G~~~~~~gpl~~A~~--~G~vlllDEId~a~  123 (162)
                      +++.|+||||||++++.++... .  .....++.  ...+.. .....+....+.+..+.....  .+..+++||+-.++
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~-~--~~~~~~~~--~~~~~~~~~~~~~~~~~~v~s~~~~~~~~~~~~~liiDE~~~~~   75 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR-L--VVTVISPT--IELYTEWLPDPPSKSVRTVDSFLKALVKPKSYDTLIIDEAQLLP   75 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc-c--cccccccc--ceeccccccccCCccccEEeEhhhcccccCcCCEEEEeccccCC
Confidence            4678999999999999998774 1  10000000  000000 000111122223332222222  37899999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEc-CCcE
Q psy4122         124 RNVLPVLNNLLENREMHLE-DGRF  146 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~-~g~~  146 (162)
                      +..+..|......+.+.+- |-.+
T Consensus        76 ~g~l~~l~~~~~~~~~~l~GDp~Q   99 (234)
T PF01443_consen   76 PGYLLLLLSLSPAKNVILFGDPLQ   99 (234)
T ss_pred             hHHHHHHHhhccCcceEEEECchh
Confidence            9888887777776666553 4333

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

>KOG0736|consensus

Probab=98.21  E-value=1.6e-06  Score=81.21  Aligned_cols=71  Identities=14%  Similarity=0.141  Sum_probs=44.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCCCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEKAER  124 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~a~~  124 (162)
                      -+||+||||||||-+|+++|......+..+...      +|+-.|  .+-+..=....+.+|= ....|+++||+|...|
T Consensus       707 GILLYGPPGTGKTLlAKAVATEcsL~FlSVKGP------ELLNMY--VGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP  778 (953)
T KOG0736|consen  707 GILLYGPPGTGKTLLAKAVATECSLNFLSVKGP------ELLNMY--VGQSEENVREVFERARSAAPCVIFFDELDSLAP  778 (953)
T ss_pred             eeEEECCCCCchHHHHHHHHhhceeeEEeecCH------HHHHHH--hcchHHHHHHHHHHhhccCCeEEEeccccccCc
Confidence            599999999999999999998887765544432      233110  1111000111233442 2457999999988666

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.21  E-value=2.1e-06  Score=76.35  Aligned_cols=106  Identities=12%  Similarity=0.187  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          30 WLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        30 ~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      .....+.+..... ...|++|+|++|||||||+.++++.+     +..+.++++..-  ..++...  +..+....  ..
T Consensus       126 A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f--~~~~~~~--l~~~~~~~--~~  199 (450)
T PRK14087        126 AFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEF--ARKAVDI--LQKTHKEI--EQ  199 (450)
T ss_pred             HHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHH--HHHHHHH--HHHhhhHH--HH
Confidence            4455555544221 12479999999999999999999754     233334433210  1112110  11110000  02


Q ss_pred             HHHHhhcCcEEEEeCCCCCC--ccHHHH----HHHhhcCC-eEEE
Q psy4122         104 AVRAAIEGRVLILEGIEKAE--RNVLPV----LNNLLENR-EMHL  141 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~--~~v~~~----L~~lle~r-~l~l  141 (162)
                      +.+.++.-.+|+||||+...  +..++.    ++.+.+++ .+.+
T Consensus       200 ~~~~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIl  244 (450)
T PRK14087        200 FKNEICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFF  244 (450)
T ss_pred             HHHHhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEE
Confidence            33345667899999998876  334444    44444544 3544

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.21  E-value=8e-07  Score=81.38  Aligned_cols=75  Identities=20%  Similarity=0.269  Sum_probs=50.7

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeec-CeEEEeccHHHHHhhcC-cEEEEeCC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVN-GTAIYYDQSAVRAAIEG-RVLILEGI  119 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~-G~~~~~~gpl~~A~~~G-~vlllDEI  119 (162)
                      ...+-++|+||||||||.||+++|...+.|+..++.+      |.+-.  ..+ |..+ ..-.+.+|-++. .+++||||
T Consensus       181 kiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS------~FVem--fVGvGAsR-VRdLF~qAkk~aP~IIFIDEi  251 (596)
T COG0465         181 KIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGS------DFVEM--FVGVGASR-VRDLFEQAKKNAPCIIFIDEI  251 (596)
T ss_pred             ccccceeEecCCCCCcHHHHHHHhcccCCCceeccch------hhhhh--hcCCCcHH-HHHHHHHhhccCCCeEEEehh
Confidence            3456799999999999999999999999998766554      22210  111 1111 112456665544 59999999


Q ss_pred             CCCCcc
Q psy4122         120 EKAERN  125 (162)
Q Consensus       120 d~a~~~  125 (162)
                      |.....
T Consensus       252 DAvGr~  257 (596)
T COG0465         252 DAVGRQ  257 (596)
T ss_pred             hhcccc
Confidence            886553

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.20  E-value=1.2e-05  Score=63.18  Aligned_cols=94  Identities=18%  Similarity=0.319  Sum_probs=55.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEeccCCC--------hhhhc-ceeE-e--ec------C-eEEEecc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSRDTT--------EADIK-QRRE-I--VN------G-TAIYYDQ  102 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~~~~--------~~dL~-g~~~-~--~~------G-~~~~~~g  102 (162)
                      ..+.++|+||+||||++..+|+.+...   +-=+-+.+-.+        ..||- |... +  .+      | ..+..++
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~gGkR~GF~Ivdl~tg~~~~la~~~~~~~rvGkY~V~v~~   85 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGKRIGFKIVDLATGEEGILARVGFSRPRVGKYGVNVEG   85 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeeecCCeEeeeEEEEccCCceEEEEEcCCCCcccceEEeeHHH
Confidence            468999999999999999999776443   21111111001        11121 1100 0  00      1 1122221


Q ss_pred             -------HHHHHhhcCcEEEEeCCCC---CCccHHHHHHHhhcCCe
Q psy4122         103 -------SAVRAAIEGRVLILEGIEK---AERNVLPVLNNLLENRE  138 (162)
Q Consensus       103 -------pl~~A~~~G~vlllDEId~---a~~~v~~~L~~lle~r~  138 (162)
                             .+-+|+++..++++|||-.   .++.+.+.+..+|+...
T Consensus        86 le~i~~~al~rA~~~aDvIIIDEIGpMElks~~f~~~ve~vl~~~k  131 (179)
T COG1618          86 LEEIAIPALRRALEEADVIIIDEIGPMELKSKKFREAVEEVLKSGK  131 (179)
T ss_pred             HHHHhHHHHHHHhhcCCEEEEecccchhhccHHHHHHHHHHhcCCC
Confidence                   2445667779999999954   67788999999998655

>KOG0652|consensus

Probab=98.19  E-value=6.8e-07  Score=75.40  Aligned_cols=73  Identities=14%  Similarity=0.182  Sum_probs=43.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..+-+|++||||+|||-+|++.|+.++..+..+..      .+|++. .+-+|. ..+.-++..|- +...+++|||+|.
T Consensus       204 pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAg------PQLVQM-fIGdGA-kLVRDAFaLAKEkaP~IIFIDElDA  275 (424)
T KOG0652|consen  204 PPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAG------PQLVQM-FIGDGA-KLVRDAFALAKEKAPTIIFIDELDA  275 (424)
T ss_pred             CCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcc------hHHHhh-hhcchH-HHHHHHHHHhhccCCeEEEEechhh
Confidence            34459999999999999999999988765442222      122211 111221 11112333333 3457999999986


Q ss_pred             CC
Q psy4122         122 AE  123 (162)
Q Consensus       122 a~  123 (162)
                      +.
T Consensus       276 IG  277 (424)
T KOG0652|consen  276 IG  277 (424)
T ss_pred             hc
Confidence            43

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.18  E-value=7.5e-06  Score=60.32  Aligned_cols=33  Identities=21%  Similarity=0.321  Sum_probs=25.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      .+++.||||+|||+++..++...   +.++.++.+.
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e   36 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIE   36 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECC
Confidence            36899999999999999998766   4555555553

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=98.17  E-value=8.2e-06  Score=70.50  Aligned_cols=105  Identities=14%  Similarity=0.164  Sum_probs=62.9

Q ss_pred             HHHHHHHHHhc--CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC-hhhhc-ceeEe--------ecCeEE
Q psy4122          31 LSHLRWILQKD--NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT-EADIK-QRREI--------VNGTAI   98 (162)
Q Consensus        31 ~~~L~~i~~~~--~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~-~~dL~-g~~~~--------~~G~~~   98 (162)
                      .+.+..+++++  ..+.++++.|+.|||||++.+++...+...-..+.+.+-|. ++.++ |..++        ......
T Consensus         7 ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~AA~~i~~G~T~hs~f~i~~~~~~~~   86 (364)
T PF05970_consen    7 RRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIAAFNIPGGRTIHSFFGIPINNNEKS   86 (364)
T ss_pred             HHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHHHHhccCCcchHHhcCccccccccc
Confidence            34444443333  45668999999999999999999877744322232222222 33344 31111        111111


Q ss_pred             Ee----ccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122          99 YY----DQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus        99 ~~----~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                      +.    ...+.+-+++-.+|++|||...+..+++.+...|.
T Consensus        87 ~~~~~~~~~~~~~l~~~~~lIiDEism~~~~~l~~i~~~lr  127 (364)
T PF05970_consen   87 QCKISKNSRLRERLRKADVLIIDEISMVSADMLDAIDRRLR  127 (364)
T ss_pred             cccccccchhhhhhhhheeeecccccchhHHHHHHHHHhhh
Confidence            11    11233445666899999999999999998887665

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>KOG0741|consensus

Probab=98.15  E-value=3.4e-07  Score=82.85  Aligned_cols=33  Identities=21%  Similarity=0.330  Sum_probs=27.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC-CceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ-REVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg-~p~~~v~~~   78 (162)
                      -+||+||||||||-+|+++...+| ++...++..
T Consensus       258 GiLLyGPPGTGKTLiARqIGkMLNArePKIVNGP  291 (744)
T KOG0741|consen  258 GILLYGPPGTGKTLIARQIGKMLNAREPKIVNGP  291 (744)
T ss_pred             eEEEECCCCCChhHHHHHHHHHhcCCCCcccCcH
Confidence            489999999999999999999886 455556553

>PRK13947 shikimate kinase; Provisional

Probab=98.13  E-value=2.5e-06  Score=65.02  Aligned_cols=28  Identities=14%  Similarity=0.136  Sum_probs=26.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|+|+||||||++++.+|+.+|.++.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~i   30 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFI   30 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEE
Confidence            7999999999999999999999999865

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

Probab=98.13  E-value=1.2e-05  Score=63.69  Aligned_cols=105  Identities=16%  Similarity=0.197  Sum_probs=58.0

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcce-----eEeec---
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQR-----REIVN---   94 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~-----~~~~~---   94 (162)
                      ++++=.+.++.++.+.  .+-.++.||||||||+++..++..+   |..+..+..... -..+|...     .++..   
T Consensus         2 L~~~Q~~a~~~~l~~~--~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~-Aa~~L~~~~~~~a~Ti~~~l~   78 (196)
T PF13604_consen    2 LNEEQREAVRAILTSG--DRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNK-AAKELREKTGIEAQTIHSFLY   78 (196)
T ss_dssp             S-HHHHHHHHHHHHCT--CSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHH-HHHHHHHHHTS-EEEHHHHTT
T ss_pred             CCHHHHHHHHHHHhcC--CeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHH-HHHHHHHhhCcchhhHHHHHh
Confidence            3555566777776531  2346778999999999999887554   444433333211 12222211     11100   


Q ss_pred             --CeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          95 --GTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        95 --G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                        ........+   ......++|+||...++...+..|...+..
T Consensus        79 ~~~~~~~~~~~---~~~~~~vliVDEasmv~~~~~~~ll~~~~~  119 (196)
T PF13604_consen   79 RIPNGDDEGRP---ELPKKDVLIVDEASMVDSRQLARLLRLAKK  119 (196)
T ss_dssp             EECCEECCSSC---C-TSTSEEEESSGGG-BHHHHHHHHHHS-T
T ss_pred             cCCcccccccc---cCCcccEEEEecccccCHHHHHHHHHHHHh
Confidence              000000000   034567999999999999999999998876

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=98.11  E-value=5.3e-06  Score=69.30  Aligned_cols=104  Identities=25%  Similarity=0.327  Sum_probs=72.4

Q ss_pred             CCHHHHHHHHHHHHhcCC-CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHH
Q psy4122          26 LTQDWLSHLRWILQKDNM-SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA  104 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~-g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl  104 (162)
                      +-+.+++++-+|...+.. +.|+||+|..|+||+++++..|...+..+..+.++..-+..|....  +        ...+
T Consensus        12 lf~~ai~hi~ri~RvL~~~~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y~~~~f~~d--L--------k~~~   81 (268)
T PF12780_consen   12 LFDEAIEHIARISRVLSQPRGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGYSIKDFKED--L--------KKAL   81 (268)
T ss_dssp             --HHHHHHHHHHHHHHCSTTEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTTHHHHHHHH--H--------HHHH
T ss_pred             eHHHHHHHHHHHHHHHcCCCCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCcCHHHHHHH--H--------HHHH
Confidence            357888888888877663 4599999999999999999999998877655544443333332210  0        0123


Q ss_pred             HHHhhcC--cEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         105 VRAAIEG--RVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       105 ~~A~~~G--~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      .+|-.+|  .+++++|-+-..+..++.+|.+|..|++
T Consensus        82 ~~ag~~~~~~vfll~d~qi~~~~fLe~in~LL~sGei  118 (268)
T PF12780_consen   82 QKAGIKGKPTVFLLTDSQIVDESFLEDINSLLSSGEI  118 (268)
T ss_dssp             HHHHCS-S-EEEEEECCCSSSCHHHHHHHHHHHCSS-
T ss_pred             HHHhccCCCeEEEecCcccchHhHHHHHHHHHhCCCC
Confidence            3444344  5788999888899999999999999976

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>KOG0729|consensus

Probab=98.11  E-value=3.7e-06  Score=71.18  Aligned_cols=72  Identities=14%  Similarity=0.115  Sum_probs=46.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh--hcCcEEEEeCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA--IEGRVLILEGIE  120 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~--~~G~vlllDEId  120 (162)
                      ..+-+||+||||+|||-.|+++|..++.-+.++..++.  .+..+|    ++...+  . -+....  ++..++++||||
T Consensus       210 ppkgvllygppgtgktl~aravanrtdacfirvigsel--vqkyvg----egarmv--r-elf~martkkaciiffdeid  280 (435)
T KOG0729|consen  210 PPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSEL--VQKYVG----EGARMV--R-ELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             CCCceEEeCCCCCchhHHHHHHhcccCceEEeehhHHH--HHHHhh----hhHHHH--H-HHHHHhcccceEEEEeeccc
Confidence            44569999999999999999999999988777766422  223332    111100  0 111112  344689999998


Q ss_pred             CCC
Q psy4122         121 KAE  123 (162)
Q Consensus       121 ~a~  123 (162)
                      .+.
T Consensus       281 aig  283 (435)
T KOG0729|consen  281 AIG  283 (435)
T ss_pred             ccc
Confidence            743

>PRK00131 aroK shikimate kinase; Reviewed

Probab=98.11  E-value=3.2e-06  Score=63.91  Aligned_cols=30  Identities=13%  Similarity=0.170  Sum_probs=27.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +..++|+|+||||||++++.+|+.+|.++.
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l~~~~~   33 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRLGYDFI   33 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhCCCEE
Confidence            568999999999999999999999998765

>PRK10536 hypothetical protein; Provisional

Probab=98.11  E-value=2.1e-05  Score=65.62  Aligned_cols=98  Identities=13%  Similarity=0.125  Sum_probs=59.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHH-Hh-CCceEEEEe-ccCCChhhhcce-eEe---------------------------
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLE-LT-QREVEYICL-SRDTTEADIKQR-REI---------------------------   92 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~-~l-g~p~~~v~~-~~~~~~~dL~g~-~~~---------------------------   92 (162)
                      ...++++||+|||||+||.++|. .+ +..+..+-+ ++..+..+.+|. +..                           
T Consensus        74 ~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p~~~pi~D~L~~~~~~~~~~~  153 (262)
T PRK10536         74 KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDIAEKFAPYFRPVYDVLVRRLGASFMQY  153 (262)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCCCHHHHHHHHHHHHHHHHHHHhChHHHHH
Confidence            56899999999999999999886 33 544554443 355555554441 100                           


Q ss_pred             ----ecCeEEEeccHHHHHh-hcCcEEEEeCCCCCCccHHHHHHHhhcCC-eEEE
Q psy4122          93 ----VNGTAIYYDQSAVRAA-IEGRVLILEGIEKAERNVLPVLNNLLENR-EMHL  141 (162)
Q Consensus        93 ----~~G~~~~~~gpl~~A~-~~G~vlllDEId~a~~~v~~~L~~lle~r-~l~l  141 (162)
                          ..|.....+-...+.- .+.+++++||...+.+..+..+..-+..+ .+++
T Consensus       154 ~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k~~ltR~g~~sk~v~  208 (262)
T PRK10536        154 CLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMKMFLTRLGENVTVIV  208 (262)
T ss_pred             HHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHHHHHhhcCCCCEEEE
Confidence                0122222211111110 13479999999999998888887776644 4444

>KOG0728|consensus

Probab=98.08  E-value=2.8e-06  Score=71.43  Aligned_cols=74  Identities=18%  Similarity=0.174  Sum_probs=48.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc-CcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE-GRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~-G~vlllDEId~  121 (162)
                      ..+-+||+||||+|||-||+++|+.....+.+++.++.  .+..+|     .|+. ....-++-|-.+ ..+++.||||.
T Consensus       180 QPKGvlLygppgtGktLlaraVahht~c~firvsgsel--vqk~ig-----egsr-mvrelfvmarehapsiifmdeids  251 (404)
T KOG0728|consen  180 QPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSEL--VQKYIG-----EGSR-MVRELFVMAREHAPSIIFMDEIDS  251 (404)
T ss_pred             CCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHH--HHHHhh-----hhHH-HHHHHHHHHHhcCCceEeeecccc
Confidence            34569999999999999999999988877776665422  333333     2221 111123334333 46899999987


Q ss_pred             CCc
Q psy4122         122 AER  124 (162)
Q Consensus       122 a~~  124 (162)
                      ..+
T Consensus       252 igs  254 (404)
T KOG0728|consen  252 IGS  254 (404)
T ss_pred             ccc
Confidence            644

>PRK08118 topology modulation protein; Reviewed

Probab=98.08  E-value=3.5e-06  Score=65.32  Aligned_cols=28  Identities=32%  Similarity=0.339  Sum_probs=26.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++++||||+||||+|+.+++.++.|+.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~   30 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVH   30 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCce
Confidence            5899999999999999999999999854

>KOG3347|consensus

Probab=98.07  E-value=4.8e-06  Score=64.66  Aligned_cols=33  Identities=33%  Similarity=0.519  Sum_probs=28.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      +-++|+.|-||||||++++++|+.+|.+  +++++
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~--~i~is   39 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLE--YIEIS   39 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCc--eEehh
Confidence            3489999999999999999999999987  44544

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.07  E-value=6e-06  Score=71.56  Aligned_cols=41  Identities=15%  Similarity=0.230  Sum_probs=35.7

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDT   81 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~   81 (162)
                      -...+|+|++||+|+|||.+|+.+|.+.|.|+..+....-|
T Consensus        47 EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATKfT   87 (444)
T COG1220          47 EVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFT   87 (444)
T ss_pred             ccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeeeee
Confidence            34568999999999999999999999999999988776433

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=98.07  E-value=1.9e-05  Score=61.03  Aligned_cols=29  Identities=14%  Similarity=0.139  Sum_probs=25.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      |+.++|.|+||+||||+++.+++.++.+.
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~~~~~   30 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVLAEPW   30 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhCCCc
Confidence            56789999999999999999999987764

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.06  E-value=3.3e-05  Score=66.37  Aligned_cols=105  Identities=14%  Similarity=0.054  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEec---------cCCChhhhcceeEeecC-eE
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR--EVEYICLS---------RDTTEADIKQRREIVNG-TA   97 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~~---------~~~~~~dL~g~~~~~~G-~~   97 (162)
                      .-++|...+.+....+-+|+.||+|+||+++|..+|+.+--  |-..-.|.         ..+.+ |+.--.+ +++ ..
T Consensus        10 ~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HP-D~~~i~p-~~~~~~   87 (334)
T PRK07993         10 DYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHP-DYYTLTP-EKGKSS   87 (334)
T ss_pred             HHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCC-CEEEEec-cccccc
Confidence            44556666666556667889999999999999999987732  10000110         00111 1110000 011 11


Q ss_pred             EEecc--HHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          98 IYYDQ--SAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        98 ~~~~g--pl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +-++.  -+.+.+    .+|  .|++||+.++++.+..++|+..||+
T Consensus        88 I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEE  134 (334)
T PRK07993         88 LGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEE  134 (334)
T ss_pred             CCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcC
Confidence            11110  011111    123  5999999999999999999999995

>cd01131 PilT Pilus retraction ATPase PilT

Probab=98.06  E-value=2.3e-05  Score=62.13  Aligned_cols=90  Identities=12%  Similarity=0.223  Sum_probs=49.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc--eEEEEeccCCChhhhc--ceeE-ee----c-CeEEEeccHHHHHhhc-CcEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE--VEYICLSRDTTEADIK--QRRE-IV----N-GTAIYYDQSAVRAAIE-GRVL  114 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p--~~~v~~~~~~~~~dL~--g~~~-~~----~-G~~~~~~gpl~~A~~~-G~vl  114 (162)
                      -+++.||+||||||++..++..+..+  ...+.+. +. . ++.  .... +.    + +...|.+ .+..|++. ..++
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e-~~-~-E~~~~~~~~~i~q~~vg~~~~~~~~-~i~~aLr~~pd~i   78 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIE-DP-I-EFVHESKRSLINQREVGLDTLSFEN-ALKAALRQDPDVI   78 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEc-CC-c-cccccCccceeeecccCCCccCHHH-HHHHHhcCCcCEE
Confidence            47899999999999999988777533  2223332 21 1 111  0001 11    1 1122221 34455654 5799


Q ss_pred             EEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         115 ILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       115 llDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ++||+.  .++....+......+...+
T Consensus        79 i~gEir--d~e~~~~~l~~a~~G~~v~  103 (198)
T cd01131          79 LVGEMR--DLETIRLALTAAETGHLVM  103 (198)
T ss_pred             EEcCCC--CHHHHHHHHHHHHcCCEEE
Confidence            999994  3444444445555665433

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.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=98.06  E-value=4.7e-06  Score=73.88  Aligned_cols=35  Identities=14%  Similarity=0.280  Sum_probs=31.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .++++|+||||||||++|+.+|..++.|+..+...
T Consensus        47 p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat   81 (441)
T TIGR00390        47 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEAT   81 (441)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCeEEEeecc
Confidence            36899999999999999999999999998877754

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=98.06  E-value=4.6e-06  Score=62.11  Aligned_cols=28  Identities=14%  Similarity=0.169  Sum_probs=25.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|+|+||||||++++.+|+.+|.++.
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~   28 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFV   28 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999998854

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PHA02774 E1; Provisional

Probab=98.05  E-value=2.3e-05  Score=71.86  Aligned_cols=91  Identities=14%  Similarity=0.285  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce-EEEEeccCCChhhhcceeEeecCeEEEeccHHHHH
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV-EYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA  107 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~-~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A  107 (162)
                      ..+..|+.+++..-....++|+||||||||+++..+++.++..+ .+++.+.                 -.| -.|+.  
T Consensus       419 ~fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s-----------------~Fw-Lqpl~--  478 (613)
T PHA02774        419 SFLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKS-----------------HFW-LQPLA--  478 (613)
T ss_pred             HHHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcc-----------------ccc-cchhc--
Confidence            56677777876543333699999999999999999999886443 3343311                 112 12443  


Q ss_pred             hhcCcEEEEeCCCCCC-ccHHHHHHHhhcCCeEEE
Q psy4122         108 AIEGRVLILEGIEKAE-RNVLPVLNNLLENREMHL  141 (162)
Q Consensus       108 ~~~G~vlllDEId~a~-~~v~~~L~~lle~r~l~l  141 (162)
                        ...+++|||+-... .-....|..+|+.+.+.|
T Consensus       479 --d~ki~vlDD~t~~~w~y~d~~Lrn~LdG~~v~l  511 (613)
T PHA02774        479 --DAKIALLDDATHPCWDYIDTYLRNALDGNPVSI  511 (613)
T ss_pred             --cCCEEEEecCcchHHHHHHHHHHHHcCCCccee
Confidence              44799999994332 334557899999886555

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.04  E-value=6.9e-05  Score=64.15  Aligned_cols=26  Identities=23%  Similarity=0.323  Sum_probs=24.1

Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      .|+++|+++.++++..+.|...||+.
T Consensus       115 kV~iiEp~~~Ld~~a~naLLk~LEep  140 (325)
T PRK08699        115 RVILIHPAESMNLQAANSLLKVLEEP  140 (325)
T ss_pred             eEEEEechhhCCHHHHHHHHHHHHhC
Confidence            68999999999999999999999974

>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=98.04  E-value=3.7e-06  Score=61.89  Aligned_cols=83  Identities=16%  Similarity=0.226  Sum_probs=44.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEE--Eec-------cHHHHHhhcCcEEEEe
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAI--YYD-------QSAVRAAIEGRVLILE  117 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~--~~~-------gpl~~A~~~G~vlllD  117 (162)
                      +++.|||||||||+|+.+++.++.    ..++.|.-...+.+.. .......  +.+       .-+..++..|.-+++|
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~----~~i~~D~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~vvd   76 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGA----VVISQDEIRRRLAGED-PPSPSDYIEAEERAYQILNAAIRKALRNGNSVVVD   76 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTE----EEEEHHHHHHHHCCSS-SGCCCCCHHHHHHHHHHHHHHHHHHHHTT-EEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCC----EEEeHHHHHHHHcccc-cccchhHHHHHHHHHHHHHHHHHHHHHcCCCceec
Confidence            689999999999999999999982    2232221112222200 0000000  110       1122445678888889


Q ss_pred             CCCCCCccHHHHHHHhhc
Q psy4122         118 GIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       118 EId~a~~~v~~~L~~lle  135 (162)
                      .-+... .....+..++.
T Consensus        77 ~~~~~~-~~r~~~~~~~~   93 (143)
T PF13671_consen   77 NTNLSR-EERARLRELAR   93 (143)
T ss_dssp             SS--SH-HHHHHHHHHHH
T ss_pred             cCcCCH-HHHHHHHHHHH
Confidence            776655 44455666665

...

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=98.03  E-value=1.1e-05  Score=70.48  Aligned_cols=48  Identities=17%  Similarity=0.241  Sum_probs=34.4

Q ss_pred             HHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEec
Q psy4122          31 LSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELTQR--EVEYICLS   78 (162)
Q Consensus        31 ~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~~   78 (162)
                      .-.+-+|++... .|+.+||.||||||||.||..+|+.+|.  |+..++.+
T Consensus        36 agiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgS   86 (398)
T PF06068_consen   36 AGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGS   86 (398)
T ss_dssp             HHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGG
T ss_pred             HHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEcccc
Confidence            334557777655 7889999999999999999999999984  55545444

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.03  E-value=6e-05  Score=64.20  Aligned_cols=109  Identities=17%  Similarity=0.199  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--eEE-EEec-cCCChhhhcc-eeEe-ecCeE----
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--VEY-ICLS-RDTTEADIKQ-RREI-VNGTA----   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--~~~-v~~~-~~~~~~dL~g-~~~~-~~G~~----   97 (162)
                      +...+.|+..+......+..|++||+|+||+++|..+|+.+-..  +-. .+|. ....-.|+.- .+.. .+|..    
T Consensus        10 ~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g~~~~~~   89 (314)
T PRK07399         10 PLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKLITAS   89 (314)
T ss_pred             HHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccccccccchh
Confidence            56677888888777666789999999999999999999876322  100 0010 0111122221 1000 01110    


Q ss_pred             --------------EEecc--HHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          98 --------------IYYDQ--SAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        98 --------------~~~~g--pl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                                    +-.+.  .+.+.+      ....|++||++++++.+..++|+..||+
T Consensus        90 ~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEE  150 (314)
T PRK07399         90 EAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEE  150 (314)
T ss_pred             hhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhC
Confidence                          00000  111111      1236999999999999999999999995

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

Probab=98.03  E-value=6.3e-05  Score=62.51  Aligned_cols=110  Identities=15%  Similarity=0.153  Sum_probs=62.0

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce-EEEEeccCCChhhhccee--Eee-cCeEEEec
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV-EYICLSRDTTEADIKQRR--EIV-NGTAIYYD  101 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~-~~v~~~~~~~~~dL~g~~--~~~-~G~~~~~~  101 (162)
                      .++...+.|++++..  .+..+++.||+|+||||+.+.+...+..+- ..+.+ +|...-.+-+..  .+. .....|.+
T Consensus        64 ~~~~~~~~l~~~~~~--~~GlilisG~tGSGKTT~l~all~~i~~~~~~iiti-Edp~E~~~~~~~q~~v~~~~~~~~~~  140 (264)
T cd01129          64 LKPENLEIFRKLLEK--PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITV-EDPVEYQIPGINQVQVNEKAGLTFAR  140 (264)
T ss_pred             CCHHHHHHHHHHHhc--CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEE-CCCceecCCCceEEEeCCcCCcCHHH
Confidence            467777777777642  233799999999999999998876665432 23333 232221222211  111 11122321


Q ss_pred             cHHHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         102 QSAVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       102 gpl~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                       .+..+++. ..+++++||.-  ++....+......|.+.+
T Consensus       141 -~l~~~lR~~PD~i~vgEiR~--~e~a~~~~~aa~tGh~v~  178 (264)
T cd01129         141 -GLRAILRQDPDIIMVGEIRD--AETAEIAVQAALTGHLVL  178 (264)
T ss_pred             -HHHHHhccCCCEEEeccCCC--HHHHHHHHHHHHcCCcEE
Confidence             34455664 47999999964  333343444445665544

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.

>PRK03839 putative kinase; Provisional

Probab=98.02  E-value=5.3e-06  Score=64.14  Aligned_cols=28  Identities=18%  Similarity=0.179  Sum_probs=25.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|+|+|||||||+++.+|+.++.++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~~~i   29 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGYEYV   29 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4899999999999999999999998864

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.02  E-value=1.1e-05  Score=66.71  Aligned_cols=49  Identities=14%  Similarity=0.198  Sum_probs=34.6

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eE-EEEeccC--CChhhhcc
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VE-YICLSRD--TTEADIKQ   88 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~-~v~~~~~--~~~~dL~g   88 (162)
                      ..-.|+.++++||+|||||+|++.+++.....   .. .+.+..+  .+..++..
T Consensus        12 ~i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~   66 (249)
T cd01128          12 PIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQR   66 (249)
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCccHHHHHH
Confidence            44568899999999999999999999877552   22 2232333  56666653

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>KOG2170|consensus

Probab=98.01  E-value=1.3e-05  Score=68.22  Aligned_cols=100  Identities=19%  Similarity=0.222  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEE--cCCCchHHHHHHHHHHHhCC---ceEEEEe-----c-cC-CChhhhcceeEeecC
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLI--GKPGSLRRSLAMSYLELTQR---EVEYICL-----S-RD-TTEADIKQRREIVNG   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~--GppG~GKT~La~~lA~~lg~---p~~~v~~-----~-~~-~~~~dL~g~~~~~~G   95 (162)
                      +..+..|+.-+..-...||+.|.  |+|||||+..++.+|+.+-+   ..-+|..     | ++ ...++..-  .+   
T Consensus        92 ~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~Yk~--eL---  166 (344)
T KOG2170|consen   92 QLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIEDYKE--EL---  166 (344)
T ss_pred             HHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHHHHH--HH---
Confidence            44555555555555566777664  99999999999999987632   1111111     1 11 11111110  00   


Q ss_pred             eEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122          96 TAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus        96 ~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                       -.|..+-+  +.-...++|+||+|++++..+++|.+.||
T Consensus       167 -~~~v~~~v--~~C~rslFIFDE~DKmp~gLld~lkpfLd  203 (344)
T KOG2170|consen  167 -KNRVRGTV--QACQRSLFIFDEVDKLPPGLLDVLKPFLD  203 (344)
T ss_pred             -HHHHHHHH--HhcCCceEEechhhhcCHhHHHHHhhhhc
Confidence             00111111  11234799999999999999999999999

>PRK13695 putative NTPase; Provisional

Probab=98.01  E-value=2.3e-05  Score=60.39  Aligned_cols=23  Identities=26%  Similarity=0.447  Sum_probs=20.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++|+|++|+|||++++.++..+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48899999999999999987654

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=98.00  E-value=6.2e-06  Score=73.18  Aligned_cols=35  Identities=14%  Similarity=0.280  Sum_probs=32.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .++++|+||||||||++|+.+|..++.|+..+.+.
T Consensus        50 ~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t   84 (443)
T PRK05201         50 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEAT   84 (443)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCChheeecch
Confidence            46899999999999999999999999999888765

>PRK00625 shikimate kinase; Provisional

Probab=97.99  E-value=7.2e-06  Score=64.22  Aligned_cols=29  Identities=17%  Similarity=0.209  Sum_probs=26.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      +++|+|.||||||++++.+|+.+|.++..
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id   30 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFD   30 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEE
Confidence            69999999999999999999999998653

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=97.98  E-value=4.1e-05  Score=58.93  Aligned_cols=26  Identities=12%  Similarity=0.169  Sum_probs=23.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +-++++||+||||||++++++..++.
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCc
Confidence            45789999999999999999988753

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.98  E-value=1.1e-05  Score=70.40  Aligned_cols=49  Identities=16%  Similarity=0.372  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhc-CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          30 WLSHLRWILQKD-NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        30 ~~~~L~~i~~~~-~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      ..-.+.+|++.- ..|+-+|+.||||||||.||..+|+.+|..+-+++++
T Consensus        50 AaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~is   99 (450)
T COG1224          50 AAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAIS   99 (450)
T ss_pred             hhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeec
Confidence            334456777766 5788999999999999999999999998544444443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.98  E-value=4.8e-05  Score=65.28  Aligned_cols=106  Identities=13%  Similarity=0.141  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEE-Eec---cCCChhhhcceeEeecCeE
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYI-CLS---RDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v-~~~---~~~~~~dL~g~~~~~~G~~   97 (162)
                      ..-+.|...+......+-.|+.||+|+||+++|+.+|+.+.-.       +-.+ +|.   .... .|+..-.. .+|+.
T Consensus         9 ~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~H-PD~~~i~p-~~~~~   86 (325)
T PRK06871          9 PTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNH-PDFHILEP-IDNKD   86 (325)
T ss_pred             HHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCC-CCEEEEcc-ccCCC
Confidence            3445566666655555678899999999999999999877431       1100 000   0111 11211000 01221


Q ss_pred             EEecc--HHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          98 IYYDQ--SAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        98 ~~~~g--pl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .=++.  -+.+.+    .+|  .|++||++++++....++|+..||+
T Consensus        87 I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEE  133 (325)
T PRK06871         87 IGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEE  133 (325)
T ss_pred             CCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcC
Confidence            11110  011111    123  5899999999999999999999995

>PRK14530 adenylate kinase; Provisional

Probab=97.96  E-value=8.6e-06  Score=65.00  Aligned_cols=30  Identities=20%  Similarity=0.279  Sum_probs=26.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +..++|+||||+||||+++.+|+.+|.+..
T Consensus         3 ~~~I~i~G~pGsGKsT~~~~La~~~~~~~i   32 (215)
T PRK14530          3 QPRILLLGAPGAGKGTQSSNLAEEFGVEHV   32 (215)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEE
Confidence            557999999999999999999999997643

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.96  E-value=2e-05  Score=59.56  Aligned_cols=42  Identities=14%  Similarity=0.073  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +.+.-+.+.+.+..++.++|.|+.|+|||++++.+++.+|.+
T Consensus         8 t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150         8 MDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             HHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            344444555555577889999999999999999999999865

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PRK13949 shikimate kinase; Provisional

Probab=97.95  E-value=8.8e-06  Score=63.19  Aligned_cols=28  Identities=18%  Similarity=0.240  Sum_probs=26.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|+|+||+|||++++.+|+.++.++.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~i   30 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFI   30 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCee
Confidence            6999999999999999999999998865

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.94  E-value=3.2e-05  Score=65.72  Aligned_cols=112  Identities=15%  Similarity=0.230  Sum_probs=64.8

Q ss_pred             CHHHHHHHHHHHHhcCCC--CcEEEEcCCCchHHHHHHHHHHHhC---------CceEEEEeccCCChhhhccee-----
Q psy4122          27 TQDWLSHLRWILQKDNMS--QDVFLIGKPGSLRRSLAMSYLELTQ---------REVEYICLSRDTTEADIKQRR-----   90 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g--~~vlL~GppG~GKT~La~~lA~~lg---------~p~~~v~~~~~~~~~dL~g~~-----   90 (162)
                      ....++.|++++..=...  .+++|+|++|.|||++++.|+....         .|+..+++.+.-+...+-...     
T Consensus        42 A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lg  121 (302)
T PF05621_consen   42 AKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALG  121 (302)
T ss_pred             HHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhC
Confidence            466777777777632211  2799999999999999999997653         467777777665555543210     


Q ss_pred             -EeecCeEEEe-ccHHHHHhhc--CcEEEEeCCCCC-------CccHHHHHHHhhcCCe
Q psy4122          91 -EIVNGTAIYY-DQSAVRAAIE--GRVLILEGIEKA-------ERNVLPVLNNLLENRE  138 (162)
Q Consensus        91 -~~~~G~~~~~-~gpl~~A~~~--G~vlllDEId~a-------~~~v~~~L~~lle~r~  138 (162)
                       +.......-. ......-++.  -.+|+|||++.+       ..++++.|..+-.+-+
T Consensus       122 aP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~  180 (302)
T PF05621_consen  122 APYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQ  180 (302)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccC
Confidence             1111111000 0111122322  368999999773       1245666666643333

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14532 adenylate kinase; Provisional

Probab=97.94  E-value=8.3e-06  Score=63.36  Aligned_cols=27  Identities=19%  Similarity=0.242  Sum_probs=24.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ++++.|||||||||+++.+|+.+|.+.
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~   28 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQ   28 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeE
Confidence            589999999999999999999998764

>PRK13946 shikimate kinase; Provisional

Probab=97.93  E-value=1.2e-05  Score=62.88  Aligned_cols=34  Identities=12%  Similarity=0.087  Sum_probs=29.8

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +.+..++++|+|.+|||||++++.+|+.+|.|+.
T Consensus         6 ~~~~~~~I~l~G~~GsGKsti~~~LA~~Lg~~~i   39 (184)
T PRK13946          6 AALGKRTVVLVGLMGAGKSTVGRRLATMLGLPFL   39 (184)
T ss_pred             hccCCCeEEEECCCCCCHHHHHHHHHHHcCCCeE
Confidence            3345678999999999999999999999999865

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.91  E-value=7.1e-05  Score=62.28  Aligned_cols=111  Identities=15%  Similarity=0.186  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-ceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-EVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA  108 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~  108 (162)
                      .+++-+..++..-+. ||||+|.-|+|||+|++++-...+. -..-+.++.    +||..-+.+.         -++++.
T Consensus        72 L~~NT~~F~~G~pAN-nVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k----~dl~~Lp~l~---------~~Lr~~  137 (287)
T COG2607          72 LVRNTEQFAEGLPAN-NVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDK----EDLATLPDLV---------ELLRAR  137 (287)
T ss_pred             HHHHHHHHHcCCccc-ceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcH----HHHhhHHHHH---------HHHhcC
Confidence            334444455444443 8999999999999999997766543 344566652    2343211000         234555


Q ss_pred             hcCcEEEEeCCCC-CCccHHHHHHHhhcCCeEEEcCCcEEecCcchH
Q psy4122         109 IEGRVLILEGIEK-AERNVLPVLNNLLENREMHLEDGRFLVSASTYD  154 (162)
Q Consensus       109 ~~G~vlllDEId~-a~~~v~~~L~~lle~r~l~l~~g~~i~~~~~f~  154 (162)
                      .+.-||+.|++.- -..+.-..|.++||.+----|+.-.+.+..|-+
T Consensus       138 ~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRR  184 (287)
T COG2607         138 PEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRR  184 (287)
T ss_pred             CceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCc
Confidence            5667899999843 445567888899987655555555555555443

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.91  E-value=1.3e-05  Score=61.24  Aligned_cols=30  Identities=20%  Similarity=0.315  Sum_probs=27.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      ++++|+|.+|||||++++.+|+.+|.|+..
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d   32 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVD   32 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEE
Confidence            579999999999999999999999998653

>KOG0730|consensus

Probab=97.91  E-value=2.2e-05  Score=72.41  Aligned_cols=84  Identities=14%  Similarity=0.157  Sum_probs=54.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEE-EeccHHHHHhhc--CcEEEEeCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAI-YYDQSAVRAAIE--GRVLILEGI  119 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~-~~~gpl~~A~~~--G~vlllDEI  119 (162)
                      ....+|++||||||||.+++++|+..+-.+..++++      +++..+   .|.+. .-...+.+|.++  +.+++||||
T Consensus       217 ~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~p------eli~k~---~gEte~~LR~~f~~a~k~~~psii~IdEl  287 (693)
T KOG0730|consen  217 PPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGP------ELISKF---PGETESNLRKAFAEALKFQVPSIIFIDEL  287 (693)
T ss_pred             CCCCccccCCCCCChHHHHHHHHHHhCceeEecccH------HHHHhc---ccchHHHHHHHHHHHhccCCCeeEeHHhH
Confidence            344689999999999999999999999665555543      343211   11110 000133444433  579999999


Q ss_pred             CCCCc----------cHHHHHHHhhc
Q psy4122         120 EKAER----------NVLPVLNNLLE  135 (162)
Q Consensus       120 d~a~~----------~v~~~L~~lle  135 (162)
                      |..-|          .+...|..+++
T Consensus       288 d~l~p~r~~~~~~e~Rv~sqlltL~d  313 (693)
T KOG0730|consen  288 DALCPKREGADDVESRVVSQLLTLLD  313 (693)
T ss_pred             hhhCCcccccchHHHHHHHHHHHHHh
Confidence            88665          36777888887

>PRK07261 topology modulation protein; Provisional

Probab=97.91  E-value=1.2e-05  Score=62.46  Aligned_cols=28  Identities=25%  Similarity=0.247  Sum_probs=25.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++++|+||+||||+|+.+++.++.|..
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i   29 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVL   29 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeE
Confidence            4899999999999999999999988743

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.90  E-value=1.8e-05  Score=72.71  Aligned_cols=105  Identities=12%  Similarity=0.147  Sum_probs=62.7

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe-------------------------ccC----CC
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL-------------------------SRD----TT   82 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~-------------------------~~~----~~   82 (162)
                      -.++.+-.....|+.+++.||+|||||+|.+++|.+..+--=.+++                         +++    .+
T Consensus       407 ~ll~~l~~~v~~G~~llI~G~SG~GKTsLlRaiaGLWP~g~G~I~~P~~~~~lflpQ~PY~p~GtLre~l~YP~~~~~~~  486 (604)
T COG4178         407 TLLSELNFEVRPGERLLITGESGAGKTSLLRALAGLWPWGSGRISMPADSALLFLPQRPYLPQGTLREALCYPNAAPDFS  486 (604)
T ss_pred             eeeccceeeeCCCCEEEEECCCCCCHHHHHHHHhccCccCCCceecCCCCceEEecCCCCCCCccHHHHHhCCCCCCCCC
Confidence            3444444456679999999999999999999999765321111111                         111    11


Q ss_pred             hhhhcc---eeEe------ecCeEEEec----c-----HHHHHh-hcCcEEEEeCC-CCCCccHHHHHHHhhcC
Q psy4122          83 EADIKQ---RREI------VNGTAIYYD----Q-----SAVRAA-IEGRVLILEGI-EKAERNVLPVLNNLLEN  136 (162)
Q Consensus        83 ~~dL~g---~~~~------~~G~~~~~~----g-----pl~~A~-~~G~vlllDEI-d~a~~~v~~~L~~lle~  136 (162)
                      .++|..   .-.+      -++...|.+    |     .+++.+ .+..+++|||. ...+++....|++++.+
T Consensus       487 d~~l~~vL~~vgL~~L~~rl~~~~~W~~vLS~GEqQRlafARilL~kP~~v~LDEATsALDe~~e~~l~q~l~~  560 (604)
T COG4178         487 DAELVAVLHKVGLGDLAERLDEEDRWDRVLSGGEQQRLAFARLLLHKPKWVFLDEATSALDEETEDRLYQLLKE  560 (604)
T ss_pred             hHHHHHHHHHcCcHHHHHHHhccCcHhhhcChhHHHHHHHHHHHHcCCCEEEEecchhccChHHHHHHHHHHHh
Confidence            122211   0000      012233432    1     233433 46789999999 66888999999999986

>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=97.90  E-value=4.1e-05  Score=62.86  Aligned_cols=109  Identities=16%  Similarity=0.176  Sum_probs=61.1

Q ss_pred             CHHHHHHHHHHHHhc-CCCCcEEEEcCCCchHHHHHHHHHHHhCCc-eEEEEeccCCChhhhccee--Ee--ecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKD-NMSQDVFLIGKPGSLRRSLAMSYLELTQRE-VEYICLSRDTTEADIKQRR--EI--VNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~-~~g~~vlL~GppG~GKT~La~~lA~~lg~p-~~~v~~~~~~~~~dL~g~~--~~--~~G~~~~~  100 (162)
                      .+...+.+..++... ..+.++++.|++|+||||+.+++...+... ...+.+ ++...-.+-+..  .+  ..+...+.
T Consensus       109 ~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~i-Ed~~E~~l~~~~~~~~~~~~~~~~~~  187 (270)
T PF00437_consen  109 SGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTI-EDPPELRLPGPNQIQIQTRRDEISYE  187 (270)
T ss_dssp             THHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEE-ESSS-S--SCSSEEEEEEETTTBSHH
T ss_pred             chhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhccccccceEEe-ccccceeecccceEEEEeecCcccHH
Confidence            344445555554433 245699999999999999999999887666 444444 332222222211  11  11222222


Q ss_pred             ccHHHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEE
Q psy4122         101 DQSAVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMH  140 (162)
Q Consensus       101 ~gpl~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~  140 (162)
                      + .+..++|. ..+++++||.-  +++... ...+..|...
T Consensus       188 ~-~l~~~LR~~pD~iiigEiR~--~e~~~~-~~a~~tGh~~  224 (270)
T PF00437_consen  188 D-LLKSALRQDPDVIIIGEIRD--PEAAEA-IQAANTGHLG  224 (270)
T ss_dssp             H-HHHHHTTS--SEEEESCE-S--CHHHHH-HHHHHTT-EE
T ss_pred             H-HHHHHhcCCCCcccccccCC--HhHHHH-HHhhccCCce
Confidence            1 24445664 47999999984  466666 5566666654

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 ....

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

Probab=97.89  E-value=5.7e-05  Score=66.65  Aligned_cols=80  Identities=20%  Similarity=0.286  Sum_probs=53.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc----------
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE----------  110 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~----------  110 (162)
                      .-|++|+||+|+|||||..++++..   +....++-++    .++...              +++.|+++          
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~----se~f~~--------------~~v~a~~~~~~~~Fk~~y  174 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLT----SEDFTN--------------DFVKALRDNEMEKFKEKY  174 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEecc----HHHHHH--------------HHHHHHHhhhHHHHHHhh
Confidence            3489999999999999999998654   3323333332    334332              44555554          


Q ss_pred             -CcEEEEeCCCCCCcc------HHHHHHHhhcCC-eEEE
Q psy4122         111 -GRVLILEGIEKAERN------VLPVLNNLLENR-EMHL  141 (162)
Q Consensus       111 -G~vlllDEId~a~~~------v~~~L~~lle~r-~l~l  141 (162)
                       -.+++||+|......      ....+|.+.+++ ++.+
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvl  213 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVL  213 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEE
Confidence             569999999775443      556677777765 5655

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.89  E-value=1.2e-05  Score=63.27  Aligned_cols=30  Identities=13%  Similarity=0.151  Sum_probs=27.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      .++.|+|++|+||||+.+++|+.++.++..
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D   32 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFID   32 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCccc
Confidence            589999999999999999999999999863

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

Probab=97.89  E-value=2.9e-05  Score=66.60  Aligned_cols=107  Identities=12%  Similarity=0.184  Sum_probs=57.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCC-C-hhhhcceeEee--cCeEEEeccHHHHHhh-------
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDT-T-EADIKQRREIV--NGTAIYYDQSAVRAAI-------  109 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~-~-~~dL~g~~~~~--~G~~~~~~gpl~~A~~-------  109 (162)
                      -+++.|.||||||.||-.++..+     +....++..+... . ..+.+......  .....-....+.+.+.       
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            46788999999999999999887     2333334443221 1 11111111100  0111111122333332       


Q ss_pred             cCcEEEEeCCCCCCc--------cHHHHHHHhhcCCe-EE-EcCCcEEecCcc
Q psy4122         110 EGRVLILEGIEKAER--------NVLPVLNNLLENRE-MH-LEDGRFLVSAST  152 (162)
Q Consensus       110 ~G~vlllDEId~a~~--------~v~~~L~~lle~r~-l~-l~~g~~i~~~~~  152 (162)
                      +=.++|+||.+++..        ...+.|..++.... ++ +-|..+.+.+.+
T Consensus        83 ~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~~kv~v~f~D~~Q~i~~~e  135 (352)
T PF09848_consen   83 KYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKRAKVVVFFYDENQSIRPSE  135 (352)
T ss_pred             cCCEEEEehhHhhhhccccccccccHHHHHHHHhcCCEEEEEEccccEeeccc
Confidence            348999999999988        23567777777543 32 235444444444

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

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=97.89  E-value=1.4e-05  Score=58.84  Aligned_cols=27  Identities=15%  Similarity=0.054  Sum_probs=24.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +.+.|+||||||++|+.+|+.+|.|+.
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~   28 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYL   28 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcee
Confidence            689999999999999999999998864

>TIGR03263 guanyl_kin guanylate kinase

Probab=97.88  E-value=9.2e-06  Score=62.41  Aligned_cols=27  Identities=19%  Similarity=0.240  Sum_probs=23.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      |+.++|+||+|||||++++.+++....
T Consensus         1 g~ii~l~G~~GsGKsTl~~~L~~~~~~   27 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTLVKALLEEDPN   27 (180)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHccCcc
Confidence            467899999999999999999986543

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.

>PRK14531 adenylate kinase; Provisional

Probab=97.87  E-value=1.6e-05  Score=62.02  Aligned_cols=29  Identities=17%  Similarity=0.269  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+.+++.||||+||||+++.+|+.+|.+.
T Consensus         2 ~~~i~i~G~pGsGKsT~~~~la~~~g~~~   30 (183)
T PRK14531          2 KQRLLFLGPPGAGKGTQAARLCAAHGLRH   30 (183)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            34799999999999999999999999874

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.87  E-value=0.00011  Score=62.13  Aligned_cols=104  Identities=14%  Similarity=0.158  Sum_probs=57.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEeccCCChhhhcc--eeEe--ecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR--EVEYICLSRDTTEADIKQ--RREI--VNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~~~~~~~~dL~g--~~~~--~~G~~~~~  100 (162)
                      ++...+.|+.++.   .++++++.|++|+||||++++++.....  |-.++..-+|...-.+.+  ...+  ..+...|.
T Consensus       118 ~~~~~~~L~~~v~---~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~~~~~~~~~~~~  194 (299)
T TIGR02782       118 TAAQRDVLREAVL---ARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQLRTSDDAISMT  194 (299)
T ss_pred             CHHHHHHHHHHHH---cCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEEEEecCCCCCHH
Confidence            4445566666654   4679999999999999999999987642  223333324432212211  0111  11211222


Q ss_pred             ccHHHHHhhcC-cEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         101 DQSAVRAAIEG-RVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       101 ~gpl~~A~~~G-~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      + .+..|+|.. .++++.||.-  ++....|+ .+..|
T Consensus       195 ~-~l~~aLR~~pD~iivGEiR~--~ea~~~l~-a~~tG  228 (299)
T TIGR02782       195 R-LLKATLRLRPDRIIVGEVRG--GEALDLLK-AWNTG  228 (299)
T ss_pred             H-HHHHHhcCCCCEEEEeccCC--HHHHHHHH-HHHcC
Confidence            1 234455554 7999999974  35555544 34444

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.

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

Probab=97.86  E-value=4e-05  Score=59.97  Aligned_cols=49  Identities=14%  Similarity=0.238  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      +++...+.|+..+..   ++.+++.||+|+||||+.+.++.........+.+
T Consensus        10 ~~~~~~~~l~~~v~~---g~~i~I~G~tGSGKTTll~aL~~~i~~~~~~i~i   58 (186)
T cd01130          10 FSPLQAAYLWLAVEA---RKNILISGGTGSGKTTLLNALLAFIPPDERIITI   58 (186)
T ss_pred             CCHHHHHHHHHHHhC---CCEEEEECCCCCCHHHHHHHHHhhcCCCCCEEEE
Confidence            578888888888764   7899999999999999999999887533333433

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.

>PRK06217 hypothetical protein; Validated

Probab=97.86  E-value=1.4e-05  Score=62.17  Aligned_cols=28  Identities=18%  Similarity=0.169  Sum_probs=25.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .|+|+|.+|+||||+++.+++.+|.|+.
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~   30 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHL   30 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEE
Confidence            5899999999999999999999998853

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.86  E-value=0.00013  Score=62.54  Aligned_cols=108  Identities=19%  Similarity=0.198  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc----eEEEEec----cCCChhhhcce--eEeecC--
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE----VEYICLS----RDTTEADIKQR--REIVNG--   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p----~~~v~~~----~~~~~~dL~g~--~~~~~G--   95 (162)
                      +...+.|...+......+-+||.||+|+||+++|..+|+.+.-.    +....+.    ....+ |+.--  .+.+.|  
T Consensus        10 ~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HP-D~~~i~~~p~~~~~k   88 (319)
T PRK08769         10 QRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHP-DLQLVSFIPNRTGDK   88 (319)
T ss_pred             HHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCC-CEEEEecCCCccccc
Confidence            34556666666655555569999999999999999999766321    1100000    11111 12100  000011  


Q ss_pred             --eEEEecc--HHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          96 --TAIYYDQ--SAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        96 --~~~~~~g--pl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                        ..+-+|.  .+.+.+    .+|  .|++||+.++++.+..++|+..||+
T Consensus        89 ~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEE  139 (319)
T PRK08769         89 LRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEE  139 (319)
T ss_pred             ccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhC
Confidence              0111111  011100    112  6999999999999999999999995

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.86  E-value=0.00013  Score=62.65  Aligned_cols=103  Identities=17%  Similarity=0.231  Sum_probs=55.7

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--eEEEEeccCCChhhhcceeE-e---ecC--eEEEeccHH
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--VEYICLSRDTTEADIKQRRE-I---VNG--TAIYYDQSA  104 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--~~~v~~~~~~~~~dL~g~~~-~---~~G--~~~~~~gpl  104 (162)
                      .+..++..  .+..+++.||+|+||||+.+.+...+..+  ...+.+ ++.-.-..-+... +   .-|  ...|.+ .+
T Consensus       113 ~l~~~~~~--~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~ti-Edp~E~~~~~~~~~i~q~evg~~~~~~~~-~l  188 (343)
T TIGR01420       113 VLRELAER--PRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITI-EDPIEYVHRNKRSLINQREVGLDTLSFAN-AL  188 (343)
T ss_pred             HHHHHHhh--cCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEE-cCChhhhccCccceEEccccCCCCcCHHH-HH
Confidence            34444432  24589999999999999999998876543  223333 2211101111000 1   112  122322 34


Q ss_pred             HHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         105 VRAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       105 ~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|++. ..++++||+.  .++...........|...+
T Consensus       189 ~~~lr~~pd~i~vgEir--d~~~~~~~l~aa~tGh~v~  224 (343)
T TIGR01420       189 RAALREDPDVILIGEMR--DLETVELALTAAETGHLVF  224 (343)
T ss_pred             HHhhccCCCEEEEeCCC--CHHHHHHHHHHHHcCCcEE
Confidence            556655 4799999996  4444444344455666544

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.86  E-value=0.00015  Score=62.03  Aligned_cols=107  Identities=15%  Similarity=0.154  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc------eEEE-Eec---cCCChhhhcceeEeecCeEE
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE------VEYI-CLS---RDTTEADIKQRREIVNGTAI   98 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p------~~~v-~~~---~~~~~~dL~g~~~~~~G~~~   98 (162)
                      ..-++|...+......+-+||.||.|+||+++|+.+|+.+.-.      +-.+ +|.   ..+. .|+.--.+.++|+.+
T Consensus        10 ~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~H-PD~~~i~p~~~~~~I   88 (319)
T PRK06090         10 PVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNH-PDLHVIKPEKEGKSI   88 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCC-CCEEEEecCcCCCcC
Confidence            3455666666666666679999999999999999999876321      1100 000   0001 122110000112211


Q ss_pred             Eecc--HHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          99 YYDQ--SAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        99 ~~~g--pl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      =+|.  .+.+.+    ..|  .|++||++++++.+..++|+..||+
T Consensus        89 ~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEE  134 (319)
T PRK06090         89 TVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEE  134 (319)
T ss_pred             CHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcC
Confidence            1111  011111    112  5999999999999999999999995

>KOG0482|consensus

Probab=97.85  E-value=1.1e-05  Score=72.92  Aligned_cols=94  Identities=17%  Similarity=0.358  Sum_probs=66.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcce--eEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQR--REIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~--~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |+||.|+||+-||.|.+++.++--+-+++  .....+-.-|...  +.-..|..+.+-|+|+.|  .+|++-|||+|++.
T Consensus       377 NicLmGDPGVAKSQLLkyi~rlapRgvYT--TGrGSSGVGLTAAVmkDpvTgEM~LEGGALVLA--D~GICCIDEfDKM~  452 (721)
T KOG0482|consen  377 NICLMGDPGVAKSQLLKYISRLAPRGVYT--TGRGSSGVGLTAAVMKDPVTGEMVLEGGALVLA--DGGICCIDEFDKMD  452 (721)
T ss_pred             eEEecCCCchhHHHHHHHHHhcCccccee--cCCCCCccccchhhhcCCCCCeeEeccceEEEc--cCceEeehhhhhhh
Confidence            69999999999999999999887665442  2222221112110  001235556666666544  78999999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEcC
Q psy4122         124 RNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~~  143 (162)
                      ..=-.+++.++|...+.|..
T Consensus       453 e~DRtAIHEVMEQQTISIaK  472 (721)
T KOG0482|consen  453 ESDRTAIHEVMEQQTISIAK  472 (721)
T ss_pred             hhhhHHHHHHHHhhhhhhhh
Confidence            99999999999988887753

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=97.85  E-value=2.5e-05  Score=70.76  Aligned_cols=102  Identities=15%  Similarity=0.189  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-------eEEEEeccCCC---hhhhcceeEeec---
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-------VEYICLSRDTT---EADIKQRREIVN---   94 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-------~~~v~~~~~~~---~~dL~g~~~~~~---   94 (162)
                      ......|+..+......+-.++.||-||||||+|+.+|+.++..       |-.+..+..++   ..|++-   ++.   
T Consensus        22 e~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~DviE---iDaASn   98 (515)
T COG2812          22 EHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVIE---IDAASN   98 (515)
T ss_pred             HHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCcccchh---hhhhhc
Confidence            45667777777766666678999999999999999999998754       22111111111   223331   111   


Q ss_pred             -C---------eEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          95 -G---------TAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        95 -G---------~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                       |         ...|.+.     -.+-.|++|||++..+....++|+.-||+-
T Consensus        99 ~gVddiR~i~e~v~y~P~-----~~ryKVyiIDEvHMLS~~afNALLKTLEEP  146 (515)
T COG2812          99 TGVDDIREIIEKVNYAPS-----EGRYKVYIIDEVHMLSKQAFNALLKTLEEP  146 (515)
T ss_pred             cChHHHHHHHHHhccCCc-----cccceEEEEecHHhhhHHHHHHHhcccccC
Confidence             1         1112211     112369999999999999999999999963

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.84  E-value=1.7e-05  Score=61.14  Aligned_cols=25  Identities=28%  Similarity=0.390  Sum_probs=23.3

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++++|+||+||||+++.+|+.+|.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~   26 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFT   26 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCe
Confidence            6899999999999999999999865

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.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.83  E-value=1.7e-05  Score=60.30  Aligned_cols=50  Identities=24%  Similarity=0.321  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhc--CCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEeccC
Q psy4122          31 LSHLRWILQKD--NMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSRD   80 (162)
Q Consensus        31 ~~~L~~i~~~~--~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~~   80 (162)
                      ++.|...+...  ..+..++++|++|+|||++++.+...+..+   +..+.+...
T Consensus         9 ~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    9 IERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             HHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             HHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            34444444221  234579999999999999999888666444   555666544

>KOG0481|consensus

Probab=97.83  E-value=2.7e-05  Score=70.59  Aligned_cols=93  Identities=13%  Similarity=0.239  Sum_probs=66.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeec-C-eEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVN-G-TAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~-G-~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      ||||.|+||+-||.|.+.+-...  |.-.++-....+++-|..+..-.. + .|+.+-|+++.  ..|||+-|||+|++.
T Consensus       366 NVLLLGDPgtAKSQlLKFvEkvs--PIaVYTSGKGSSAAGLTASV~RD~~tReFylEGGAMVL--ADgGVvCIDEFDKMr  441 (729)
T KOG0481|consen  366 NVLLLGDPGTAKSQLLKFVEKVS--PIAVYTSGKGSSAAGLTASVIRDPSTREFYLEGGAMVL--ADGGVVCIDEFDKMR  441 (729)
T ss_pred             eEEEecCCchhHHHHHHHHHhcC--ceEEEecCCCcccccceeeEEecCCcceEEEecceEEE--ecCCEEEeehhhccC
Confidence            79999999999999998776554  433344445556666654221111 2 34445454433  489999999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEc
Q psy4122         124 RNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~  142 (162)
                      ++=--++++.||...+.|.
T Consensus       442 e~DRVAIHEAMEQQTISIA  460 (729)
T KOG0481|consen  442 EDDRVAIHEAMEQQTISIA  460 (729)
T ss_pred             chhhhHHHHHHHhhhHHHh
Confidence            9999999999998877664

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=97.82  E-value=2.6e-05  Score=67.76  Aligned_cols=94  Identities=12%  Similarity=0.146  Sum_probs=53.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCC-ceEEEEeccCCC-h-hhhcceeEeecCeEEEeccHHHHHhhcC-cEEEEeC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQR-EVEYICLSRDTT-E-ADIKQRREIVNGTAIYYDQSAVRAAIEG-RVLILEG  118 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~-p~~~v~~~~~~~-~-~dL~g~~~~~~G~~~~~~gpl~~A~~~G-~vlllDE  118 (162)
                      ..+.++|+|++|||||.|...+.+.+.. .-.++.+|.-|- . ++|..   ..++..-.  ..+++.+.++ .+|.+||
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~---~~~~~~~l--~~va~~l~~~~~lLcfDE  135 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQ---LRGQDDPL--PQVADELAKESRLLCFDE  135 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHH---HhCCCccH--HHHHHHHHhcCCEEEEee
Confidence            4567999999999999999999887755 334566663321 1 12211   11111100  1244555555 4889999


Q ss_pred             CCC---CCccHHHHHHH-hhcCCeEEE
Q psy4122         119 IEK---AERNVLPVLNN-LLENREMHL  141 (162)
Q Consensus       119 Id~---a~~~v~~~L~~-lle~r~l~l  141 (162)
                      +.-   ++.-.+..|.+ +++.|.+.+
T Consensus       136 F~V~DiaDAmil~rLf~~l~~~gvvlV  162 (362)
T PF03969_consen  136 FQVTDIADAMILKRLFEALFKRGVVLV  162 (362)
T ss_pred             eeccchhHHHHHHHHHHHHHHCCCEEE
Confidence            955   44444554444 444444433

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=97.81  E-value=1.9e-05  Score=61.03  Aligned_cols=27  Identities=22%  Similarity=0.269  Sum_probs=24.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+++.|+||+|||++++.+|+.+|.+.
T Consensus         1 ~I~i~G~pGsGKst~a~~La~~~~~~~   27 (194)
T cd01428           1 RILLLGPPGSGKGTQAERLAKKYGLPH   27 (194)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcCCeE
Confidence            389999999999999999999998764

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=97.81  E-value=3.7e-05  Score=59.80  Aligned_cols=34  Identities=15%  Similarity=0.077  Sum_probs=26.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      |.-|.++|++|+||||+++.+++.+   |+.+..+..
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~~l~~~g~~v~~~~~   39 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKKLLQENGYDVLFTRE   39 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            5568999999999999999999887   444544433

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.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=97.81  E-value=1.9e-05  Score=62.22  Aligned_cols=26  Identities=19%  Similarity=0.377  Sum_probs=24.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+++.||||+||||+|+.+|+.++.|
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~   27 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLP   27 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCc
Confidence            58999999999999999999997776

>PHA02624 large T antigen; Provisional

Probab=97.81  E-value=0.00013  Score=67.42  Aligned_cols=98  Identities=15%  Similarity=0.209  Sum_probs=62.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA  104 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl  104 (162)
                      +.+......++.++...-.+.-++|+||||||||++++.+++.+|-....++..  ++-+...             -||+
T Consensus       412 ~~~~~~~~~lk~~l~giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsP--t~ks~Fw-------------L~pl  476 (647)
T PHA02624        412 NFDDVIYDILKLIVENVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCP--PDKLNFE-------------LGCA  476 (647)
T ss_pred             hhHHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCC--cchhHHH-------------hhhh
Confidence            345677788888888776666789999999999999999999995443334322  2222211             1344


Q ss_pred             HHHhhcCcEEEEeCCCCCCc-----------cHHHHHHHhhcCC-eEEE
Q psy4122         105 VRAAIEGRVLILEGIEKAER-----------NVLPVLNNLLENR-EMHL  141 (162)
Q Consensus       105 ~~A~~~G~vlllDEId~a~~-----------~v~~~L~~lle~r-~l~l  141 (162)
                      .    ...+++||++-...-           +=+.-|...||.. .+.|
T Consensus       477 ~----D~~~~l~dD~t~~~~~~~~Lp~G~~~dNl~~lRn~LDG~V~v~l  521 (647)
T PHA02624        477 I----DQFMVVFEDVKGQPADNKDLPSGQGMNNLDNLRDYLDGSVPVNL  521 (647)
T ss_pred             h----hceEEEeeeccccccccccCCcccccchhhHHHhhcCCCCcccc
Confidence            3    335778887743222           1135677777766 5544

>PRK06762 hypothetical protein; Provisional

Probab=97.81  E-value=2.6e-05  Score=59.31  Aligned_cols=31  Identities=19%  Similarity=0.243  Sum_probs=25.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      .-+++.|+|||||||+|+.+++.++..+..+
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l~~~~~~i   33 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERLGRGTLLV   33 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEe
Confidence            3578999999999999999999986554444

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.80  E-value=2.4e-05  Score=60.13  Aligned_cols=27  Identities=22%  Similarity=0.302  Sum_probs=24.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      -++++|||||||||+++.+|+.+|.+.
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~~~g~~~   31 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVEKYGFTH   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            578899999999999999999998763

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.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.80  E-value=1.8e-05  Score=60.05  Aligned_cols=25  Identities=20%  Similarity=0.275  Sum_probs=22.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++|+||+||||||+++.+++.++.+
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~   25 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAK   25 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCe
Confidence            4789999999999999999999855

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.79  E-value=2.1e-05  Score=58.76  Aligned_cols=25  Identities=16%  Similarity=0.268  Sum_probs=22.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++|.|+||+||||+++.+++.++.+
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~   26 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAP   26 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCE
Confidence            6899999999999999999998765

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK04132 replication factor C small subunit; Provisional

Probab=97.79  E-value=5.2e-05  Score=72.20  Aligned_cols=84  Identities=10%  Similarity=0.094  Sum_probs=54.2

Q ss_pred             cEEEEc--CCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeC
Q psy4122          46 DVFLIG--KPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEG  118 (162)
Q Consensus        46 ~vlL~G--ppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDE  118 (162)
                      +-+..|  |.+.||||+|.++|+.+     +.++..++.+.+...+++...  ++.-. .  ..|+.  -..-.+++|||
T Consensus       566 ~~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~i--Ik~~a-~--~~~~~--~~~~KVvIIDE  638 (846)
T PRK04132        566 HNFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREK--VKEFA-R--TKPIG--GASFKIIFLDE  638 (846)
T ss_pred             hhhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHH--HHHHH-h--cCCcC--CCCCEEEEEEC
Confidence            346668  99999999999999887     334555555533344444320  00000 0  00100  00125999999


Q ss_pred             CCCCCccHHHHHHHhhcC
Q psy4122         119 IEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       119 Id~a~~~v~~~L~~lle~  136 (162)
                      +|+++++.+++|+..||.
T Consensus       639 aD~Lt~~AQnALLk~lEe  656 (846)
T PRK04132        639 ADALTQDAQQALRRTMEM  656 (846)
T ss_pred             cccCCHHHHHHHHHHhhC
Confidence            999999999999999995

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.78  E-value=0.00022  Score=61.69  Aligned_cols=25  Identities=28%  Similarity=0.263  Sum_probs=23.7

Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .|+|||+.++++.+..++|+..||+
T Consensus       134 kV~iI~~ae~m~~~AaNaLLKtLEE  158 (342)
T PRK06964        134 RVVVLYPAEALNVAAANALLKTLEE  158 (342)
T ss_pred             eEEEEechhhcCHHHHHHHHHHhcC
Confidence            5999999999999999999999994

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=97.78  E-value=2.2e-05  Score=61.25  Aligned_cols=28  Identities=25%  Similarity=0.372  Sum_probs=25.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      |+.+.|+||+||||||+++.++...+.+
T Consensus         2 g~~i~l~G~sGsGKsTl~~~l~~~~~~~   29 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAALRQREQTQ   29 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCCCe
Confidence            6789999999999999999999887754

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.77  E-value=2.7e-05  Score=60.45  Aligned_cols=30  Identities=17%  Similarity=0.349  Sum_probs=26.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++++|+|++|+|||++++.+|+.+|.++.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~v   33 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFY   33 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEE
Confidence            357999999999999999999999998853

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=97.77  E-value=0.00031  Score=52.85  Aligned_cols=90  Identities=11%  Similarity=0.124  Sum_probs=54.1

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcc-eeEeecCeEEEeccHHHHHh-hcCcEEEEeC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQ-RREIVNGTAIYYDQSAVRAA-IEGRVLILEG  118 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g-~~~~~~G~~~~~~gpl~~A~-~~G~vlllDE  118 (162)
                      ...|+.+.|.||.|+|||+|.+.++......-=.+.++..    .-++ .+.+.+|..  +.-.+++|+ .+..++++||
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~----~~i~~~~~lS~G~~--~rv~laral~~~p~illlDE   96 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGST----VKIGYFEQLSGGEK--MRLALAKLLLENPNLLLLDE   96 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCe----EEEEEEccCCHHHH--HHHHHHHHHhcCCCEEEEeC
Confidence            4468899999999999999999998765322112222211    0011 001222221  111356665 5568999999


Q ss_pred             CC-CCCccHHHHHHHhhcC
Q psy4122         119 IE-KAERNVLPVLNNLLEN  136 (162)
Q Consensus       119 Id-~a~~~v~~~L~~lle~  136 (162)
                      -. ..+++....+..++.+
T Consensus        97 P~~~LD~~~~~~l~~~l~~  115 (144)
T cd03221          97 PTNHLDLESIEALEEALKE  115 (144)
T ss_pred             CccCCCHHHHHHHHHHHHH
Confidence            94 4677777777777753

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.77  E-value=5.3e-05  Score=59.12  Aligned_cols=74  Identities=14%  Similarity=0.204  Sum_probs=44.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcce----eEeecCeEEEecc--HHHHHh----hcCcEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQR----REIVNGTAIYYDQ--SAVRAA----IEGRVLI  115 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~----~~~~~G~~~~~~g--pl~~A~----~~G~vll  115 (162)
                      .+++.|+||+|||++|+.++...+.++.++.... ....+...+    ..-++..+.-.+.  .+.+++    ..+.+++
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~~-~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~~~~Vl   81 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATAQ-PFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAPGRCVL   81 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCCC-CChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCCCCEEE
Confidence            5899999999999999999998887766554432 222232211    1112222221222  344444    3367899


Q ss_pred             EeCCC
Q psy4122         116 LEGIE  120 (162)
Q Consensus       116 lDEId  120 (162)
                      +|-+.
T Consensus        82 ID~Lt   86 (170)
T PRK05800         82 VDCLT   86 (170)
T ss_pred             ehhHH
Confidence            99873

>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=97.77  E-value=2.3e-05  Score=56.10  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=20.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |+|.|+||+||||+|+.+++.+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999987

...

>PLN02165 adenylate isopentenyltransferase

Probab=97.76  E-value=2.1e-05  Score=67.69  Aligned_cols=29  Identities=21%  Similarity=0.280  Sum_probs=26.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .++.++|+||+|||||+|+..+|..++.+
T Consensus        42 ~g~iivIiGPTGSGKStLA~~LA~~l~~e   70 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSVDLATRFPSE   70 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHcCCc
Confidence            45579999999999999999999999865

>PRK02496 adk adenylate kinase; Provisional

Probab=97.75  E-value=2.9e-05  Score=60.18  Aligned_cols=28  Identities=18%  Similarity=0.259  Sum_probs=25.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+++.||||||||++++.+|+.+|.+..
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~~~~~i   30 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHLHIPHI   30 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            5899999999999999999999987643

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.75  E-value=6.2e-05  Score=66.06  Aligned_cols=91  Identities=12%  Similarity=0.199  Sum_probs=51.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh-------CCceEEEEeccCC--ChhhhcceeEeecCeEEE--eccHHHHH---hhc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT-------QREVEYICLSRDT--TEADIKQRREIVNGTAIY--YDQSAVRA---AIE  110 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l-------g~p~~~v~~~~~~--~~~dL~g~~~~~~G~~~~--~~gpl~~A---~~~  110 (162)
                      ..++|+||+|+||||.+..+|+.+       |..+..+.+...-  ....|...-.+-+=.+.-  ....+.++   +..
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~~~  254 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQSKD  254 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHhCC
Confidence            468999999999999999999754       3455555553210  111221100000101111  11223332   244


Q ss_pred             CcEEEEeCCCCCCccH--HHHHHHhhc
Q psy4122         111 GRVLILEGIEKAERNV--LPVLNNLLE  135 (162)
Q Consensus       111 G~vlllDEId~a~~~v--~~~L~~lle  135 (162)
                      -.++++|+..+.+.+.  +..|..+++
T Consensus       255 ~DlVLIDTaGr~~~~~~~l~el~~~l~  281 (388)
T PRK12723        255 FDLVLVDTIGKSPKDFMKLAEMKELLN  281 (388)
T ss_pred             CCEEEEcCCCCCccCHHHHHHHHHHHH
Confidence            5799999999988763  456666666

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.74  E-value=5.4e-05  Score=64.11  Aligned_cols=48  Identities=17%  Similarity=0.096  Sum_probs=38.7

Q ss_pred             CCHHHHHHHHHHHHhc-------CCCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          26 LTQDWLSHLRWILQKD-------NMSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~-------~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ++|+-.+.+..|++.+       ..+.+++|+|.+|||||++++.+|+.+|.++.
T Consensus       108 l~~~~~~~~~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~i  162 (309)
T PRK08154        108 ASPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVPFV  162 (309)
T ss_pred             CCHHHHHHHHHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            5666666666666642       24557999999999999999999999999966

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=97.74  E-value=9.9e-05  Score=55.34  Aligned_cols=26  Identities=23%  Similarity=0.229  Sum_probs=22.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+.|+||+|+|||+|++.+++.....
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~~~~   26 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFDPN   26 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcCCcc
Confidence            37899999999999999999876544

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.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=97.73  E-value=0.00026  Score=59.98  Aligned_cols=99  Identities=14%  Similarity=0.175  Sum_probs=60.6

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe-------ccCCChhhhcceeEeecCe--EEEec
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL-------SRDTTEADIKQRREIVNGT--AIYYD  101 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~-------~~~~~~~dL~g~~~~~~G~--~~~~~  101 (162)
                      -+.|+..+......+..|++||.|+||+.+|..+|..+-..-..-.|       |+|     +.--  ..+|.  ..-.+
T Consensus         6 ~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD-----~~~i--~p~~~~~~I~id   78 (290)
T PRK05917          6 WEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPD-----IHEF--SPQGKGRLHSIE   78 (290)
T ss_pred             HHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCC-----EEEE--ecCCCCCcCcHH
Confidence            35566666666666678899999999999999999876432100011       222     1100  01111  11111


Q ss_pred             cH--HHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QS--AVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gp--l~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..  +.+.+    -+|  .|++||++++++.+..++|+..||+
T Consensus        79 qiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEE  121 (290)
T PRK05917         79 TPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLED  121 (290)
T ss_pred             HHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHHHhhc
Confidence            11  11111    122  5899999999999999999999995

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.73  E-value=0.00019  Score=67.42  Aligned_cols=111  Identities=16%  Similarity=0.161  Sum_probs=59.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEeccCCChhhhc----cee--EeecCe
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSRDTTEADIK----QRR--EIVNGT   96 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~~~~~~dL~----g~~--~~~~G~   96 (162)
                      +++.-.+.++.+.    ..+.++|.|+||||||++++.+.+.+...   ...+-+.+.-.+++-+    |..  ++. .-
T Consensus       324 l~~~Q~~Ai~~~~----~~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~g~~a~Tih-~l  398 (720)
T TIGR01448       324 LSEEQKQALDTAI----QHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVTGLTASTIH-RL  398 (720)
T ss_pred             CCHHHHHHHHHHH----hCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhcCCccccHH-HH
Confidence            4444444444443    24578999999999999999887655321   2222222221122211    110  000 00


Q ss_pred             EEEeccHH----HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC-eEEE
Q psy4122          97 AIYYDQSA----VRAAIEGRVLILEGIEKAERNVLPVLNNLLENR-EMHL  141 (162)
Q Consensus        97 ~~~~~gpl----~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r-~l~l  141 (162)
                      ..|..+..    ........+|++||...++......|.+.+..+ ++.+
T Consensus       399 L~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~~~~~~Ll~~~~~~~rlil  448 (720)
T TIGR01448       399 LGYGPDTFRHNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLL  448 (720)
T ss_pred             hhccCCccchhhhhccccCCEEEEeccccCCHHHHHHHHHhCCCCCEEEE
Confidence            00111000    011134579999999999999888888877643 5555

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.

>KOG0744|consensus

Probab=97.73  E-value=2e-05  Score=67.99  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=21.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      -+||.||||||||+|++++|..+.
T Consensus       179 liLlhGPPGTGKTSLCKaLaQkLS  202 (423)
T KOG0744|consen  179 LILLHGPPGTGKTSLCKALAQKLS  202 (423)
T ss_pred             EEEEeCCCCCChhHHHHHHHHhhe
Confidence            379999999999999999998774

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.72  E-value=0.0002  Score=61.41  Aligned_cols=103  Identities=15%  Similarity=0.157  Sum_probs=57.4

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC--CceEEEEeccCCChhhhcc----eeEee-cCeEE
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ--REVEYICLSRDTTEADIKQ----RREIV-NGTAI   98 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg--~p~~~v~~~~~~~~~dL~g----~~~~~-~G~~~   98 (162)
                      +++...+.|+.++.   .++++++.|+||+||||+.++++....  .|-.++..-+|..  +|..    ...+. .+...
T Consensus       129 ~~~~~~~~L~~~v~---~~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~--El~~~~~n~v~l~~~~~~~  203 (323)
T PRK13833        129 MTEAQASVIRSAID---SRLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTA--EIQCAAENAVALHTSDTVD  203 (323)
T ss_pred             CCHHHHHHHHHHHH---cCCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCc--ccccCCCCEEEeccCCCcC
Confidence            34555566666555   467999999999999999999987763  2223332223322  2221    00111 12122


Q ss_pred             EeccHHHHHhhcC-cEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          99 YYDQSAVRAAIEG-RVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        99 ~~~gpl~~A~~~G-~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      +. ..+..|+|.. .++++.||.-  ++....|.. +..|
T Consensus       204 ~~-~lv~~aLR~~PD~IivGEiRg--~ea~~~l~a-~~tG  239 (323)
T PRK13833        204 MA-RLLKSTMRLRPDRIIVGEVRD--GAALTLLKA-WNTG  239 (323)
T ss_pred             HH-HHHHHHhCCCCCEEEEeecCC--HHHHHHHHH-HcCC
Confidence            21 1223455554 7999999974  355555444 4444

>PRK14528 adenylate kinase; Provisional

Probab=97.72  E-value=3.4e-05  Score=60.54  Aligned_cols=28  Identities=18%  Similarity=0.292  Sum_probs=25.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +.+++.||||+|||++++.+|+.+|.+.
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~~~~~   29 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERLSIPQ   29 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            3689999999999999999999999874

>KOG0740|consensus

Probab=97.72  E-value=2.5e-05  Score=69.23  Aligned_cols=63  Identities=19%  Similarity=0.396  Sum_probs=42.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh------hcCcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA------IEGRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~------~~G~vlllDEI  119 (162)
                      .+||.||||+|||.|++++|...+.-+  +++    +++.|...+.   |..    .-++.|+      ...+|+++|||
T Consensus       188 glLLfGPpgtGKtmL~~aiAsE~~atf--f~i----SassLtsK~~---Ge~----eK~vralf~vAr~~qPsvifidEi  254 (428)
T KOG0740|consen  188 GLLLFGPPGTGKTMLAKAIATESGATF--FNI----SASSLTSKYV---GES----EKLVRALFKVARSLQPSVIFIDEI  254 (428)
T ss_pred             hhheecCCCCchHHHHHHHHhhhcceE--eec----cHHHhhhhcc---ChH----HHHHHHHHHHHHhcCCeEEEechh
Confidence            589999999999999999999888654  333    3455543211   110    1344443      35689999999


Q ss_pred             CC
Q psy4122         120 EK  121 (162)
Q Consensus       120 d~  121 (162)
                      |+
T Consensus       255 ds  256 (428)
T KOG0740|consen  255 DS  256 (428)
T ss_pred             HH
Confidence            75

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=97.71  E-value=0.00026  Score=54.48  Aligned_cols=96  Identities=19%  Similarity=0.200  Sum_probs=53.5

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEecc-C---CChhhhcceeEee--cCe----EEE---------e
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSR-D---TTEADIKQRREIV--NGT----AIY---------Y  100 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~-~---~~~~dL~g~~~~~--~G~----~~~---------~  100 (162)
                      .+..|+.+.|.||.|+|||+|.+.++......-=.+.++. +   ....++.......  +..    +.+         +
T Consensus        24 ~i~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~lLS~G~~q  103 (173)
T cd03246          24 SIEPGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLDGADISQWDPNELGDHVGYLPQDDELFSGSIAENILSGGQRQ  103 (173)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHHhccCCCCCeEEECCEEcccCCHHHHHhheEEECCCCccccCcHHHHCcCHHHHH
Confidence            3446888999999999999999999987642211233331 1   1122221111111  100    111         0


Q ss_pred             ccHHHHHh-hcCcEEEEeCCC-CCCccHHHHHHHhhc
Q psy4122         101 DQSAVRAA-IEGRVLILEGIE-KAERNVLPVLNNLLE  135 (162)
Q Consensus       101 ~gpl~~A~-~~G~vlllDEId-~a~~~v~~~L~~lle  135 (162)
                      .-.+++|+ .+..++++||-. ..++.....+.+++.
T Consensus       104 rv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~  140 (173)
T cd03246         104 RLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIA  140 (173)
T ss_pred             HHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHH
Confidence            11244554 456899999994 466666666666654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PLN02199 shikimate kinase

Probab=97.71  E-value=9.3e-05  Score=62.97  Aligned_cols=43  Identities=12%  Similarity=0.069  Sum_probs=35.2

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ++....-+...+.+.+++|+|.+|||||++++.+|+.+|+++.
T Consensus        89 Lk~~a~~i~~~l~~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fI  131 (303)
T PLN02199         89 LKRKAEEVKPYLNGRSMYLVGMMGSGKTTVGKLMSKVLGYTFF  131 (303)
T ss_pred             HHHHHHHHHHHcCCCEEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            4444444455666889999999999999999999999999975

>KOG0990|consensus

Probab=97.71  E-value=3.2e-06  Score=72.45  Aligned_cols=120  Identities=12%  Similarity=0.123  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee----Eee-----cCeEE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR----EIV-----NGTAI   98 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~----~~~-----~G~~~   98 (162)
                      ....+.+.+........ |+|++||||+|||+.+-..|..+-.|.-+-++...+..+|=.|.-    .+.     .+-..
T Consensus        47 ~ei~st~~~~~~~~~lP-h~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~  125 (360)
T KOG0990|consen   47 EPIWSTENRYSGMPGLP-HLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASDDRGIDPVRQQIHLFASTQQPTT  125 (360)
T ss_pred             CchhhHHHHhccCCCCC-cccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccCccCCcchHHHHHHHHhhcccee
Confidence            34444555553333333 899999999999999999998876542221111111122212100    000     01011


Q ss_pred             EeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC-----eEEEcC-CcEEecCcchH
Q psy4122          99 YYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENR-----EMHLED-GRFLVSASTYD  154 (162)
Q Consensus        99 ~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r-----~l~l~~-g~~i~~~~~f~  154 (162)
                      |.-      -..=..++|||.|.+..+.+++|.+++++-     -..+.+ -..++|+-.++
T Consensus       126 fst------~~~fKlvILDEADaMT~~AQnALRRviek~t~n~rF~ii~n~~~ki~pa~qsR  181 (360)
T KOG0990|consen  126 YST------HAAFKLVILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSR  181 (360)
T ss_pred             ccc------cCceeEEEecchhHhhHHHHHHHHHHHHHhccceEEEEeccChhhcCchhhcc
Confidence            110      001158999999999999999999999843     223333 44555555444

>PF13245 AAA_19: Part of AAA domain

Probab=97.71  E-value=5.4e-05  Score=51.69  Aligned_cols=25  Identities=32%  Similarity=0.531  Sum_probs=17.9

Q ss_pred             CCcEEE-EcCCCchHH-HHHHHHHHHh
Q psy4122          44 SQDVFL-IGKPGSLRR-SLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL-~GppG~GKT-~La~~lA~~l   68 (162)
                      +.++++ .|||||||| +++..+++..
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            345554 999999999 5555666665

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=97.71  E-value=0.00038  Score=58.89  Aligned_cols=90  Identities=13%  Similarity=0.175  Sum_probs=49.8

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcc--eeEee-----cCeEEEecc-HHHHHhhc-Cc
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQ--RREIV-----NGTAIYYDQ-SAVRAAIE-GR  112 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g--~~~~~-----~G~~~~~~g-pl~~A~~~-G~  112 (162)
                      ..++++++.||+|+||||+++.++..+......+.+ ++...-.+..  ...+.     .+....... .+..+++. ..
T Consensus       142 ~~~~~ili~G~tGsGKTTll~al~~~~~~~~~iv~i-ed~~El~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~Lr~~pd  220 (308)
T TIGR02788       142 ASRKNIIISGGTGSGKTTFLKSLVDEIPKDERIITI-EDTREIFLPHPNYVHLFYSKGGQGLAKVTPKDLLQSCLRMRPD  220 (308)
T ss_pred             hCCCEEEEECCCCCCHHHHHHHHHccCCccccEEEE-cCccccCCCCCCEEEEEecCCCCCcCccCHHHHHHHHhcCCCC
Confidence            357899999999999999999999877543333444 2211111111  00110     111011111 22334544 47


Q ss_pred             EEEEeCCCCCCccHHHHHHHhh
Q psy4122         113 VLILEGIEKAERNVLPVLNNLL  134 (162)
Q Consensus       113 vlllDEId~a~~~v~~~L~~ll  134 (162)
                      ++++||+--  .++.+.|..+.
T Consensus       221 ~ii~gE~r~--~e~~~~l~a~~  240 (308)
T TIGR02788       221 RIILGELRG--DEAFDFIRAVN  240 (308)
T ss_pred             eEEEeccCC--HHHHHHHHHHh
Confidence            999999984  55666555443

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.

>TIGR00767 rho transcription termination factor Rho

Probab=97.69  E-value=6.7e-05  Score=66.27  Aligned_cols=36  Identities=11%  Similarity=0.109  Sum_probs=29.6

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++....-.|+.++++||||||||+|++.+++.....
T Consensus       160 d~~~pig~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n  195 (415)
T TIGR00767       160 DLFAPIGKGQRGLIVAPPKAGKTVLLQKIAQAITRN  195 (415)
T ss_pred             eeEEEeCCCCEEEEECCCCCChhHHHHHHHHhhccc
Confidence            455556678899999999999999999999876443

Members of this family differ in the specificity of RNA binding.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=97.68  E-value=0.0002  Score=67.59  Aligned_cols=89  Identities=12%  Similarity=0.218  Sum_probs=53.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC---Cce-----EEEEeccCCChhhhcceeEeecCeEE--Eecc--HHHHHhhc--C
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ---REV-----EYICLSRDTTEADIKQRREIVNGTAI--YYDQ--SAVRAAIE--G  111 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg---~p~-----~~v~~~~~~~~~dL~g~~~~~~G~~~--~~~g--pl~~A~~~--G  111 (162)
                      |-+|+|+||+|||.+++-+|...-   .|-     ..+++    +...|+.     +.+..  |++.  .+.+.+++  .
T Consensus       193 NPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sL----D~g~LvA-----GakyRGeFEeRlk~vl~ev~~~~~  263 (786)
T COG0542         193 NPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSL----DLGSLVA-----GAKYRGEFEERLKAVLKEVEKSKN  263 (786)
T ss_pred             CCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEe----cHHHHhc-----cccccCcHHHHHHHHHHHHhcCCC
Confidence            789999999999999999996652   111     11111    1222321     11111  1111  12222322  3


Q ss_pred             cEEEEeCCCC---C------CccHHHHHHHhhcCCeEEEcC
Q psy4122         112 RVLILEGIEK---A------ERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       112 ~vlllDEId~---a------~~~v~~~L~~lle~r~l~l~~  143 (162)
                      -+|||||||.   |      .-|..+.|.+.|.+|++...+
T Consensus       264 vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLARGeL~~IG  304 (786)
T COG0542         264 VILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIG  304 (786)
T ss_pred             eEEEEechhhhcCCCcccccccchhhhhHHHHhcCCeEEEE
Confidence            5789999976   1      245899999999999996643

>PRK13948 shikimate kinase; Provisional

Probab=97.68  E-value=4.7e-05  Score=60.17  Aligned_cols=30  Identities=13%  Similarity=-0.021  Sum_probs=27.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..+++|+|.+|||||++++.+|+.+|+++.
T Consensus        10 ~~~I~LiG~~GsGKSTvg~~La~~lg~~~i   39 (182)
T PRK13948         10 VTWVALAGFMGTGKSRIGWELSRALMLHFI   39 (182)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            457999999999999999999999999865

>PRK04182 cytidylate kinase; Provisional

Probab=97.68  E-value=4.4e-05  Score=58.13  Aligned_cols=28  Identities=21%  Similarity=0.164  Sum_probs=25.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|.|++|||||++++.+|+.+|.++.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~i   29 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHV   29 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEe
Confidence            4789999999999999999999998854

>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=97.67  E-value=7.4e-05  Score=57.30  Aligned_cols=32  Identities=25%  Similarity=0.468  Sum_probs=26.5

Q ss_pred             EEEEcCCCchHHHHHHHHHH---HhCCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE---LTQREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~   78 (162)
                      +++.||||||||+++.+++.   ..|.++.++++.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~e   36 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLE   36 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEECC
Confidence            68999999999999999875   347788888763

A related protein is found in archaea.

>TIGR01351 adk adenylate kinases

Probab=97.67  E-value=4.5e-05  Score=60.65  Aligned_cols=27  Identities=26%  Similarity=0.229  Sum_probs=24.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++.||||+|||++++.+|+.+|.+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~i   28 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHI   28 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCee
Confidence            789999999999999999999987643

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.67  E-value=4.3e-05  Score=62.39  Aligned_cols=29  Identities=17%  Similarity=0.206  Sum_probs=25.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..++|.||||+||||+++.+|+.+|.+..
T Consensus         7 mrIvl~G~PGsGK~T~a~~La~~~g~~~i   35 (229)
T PTZ00088          7 LKIVLFGAPGVGKGTFAEILSKKENLKHI   35 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            35899999999999999999999998743

>KOG0058|consensus

Probab=97.67  E-value=0.00012  Score=68.32  Aligned_cols=37  Identities=22%  Similarity=0.202  Sum_probs=30.0

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|+++--.+..|+.+.|+||.|.||||+|..+-+..
T Consensus       482 ~Vlk~lsfti~pGe~vALVGPSGsGKSTiasLL~rfY  518 (716)
T KOG0058|consen  482 PVLKNLSFTIRPGEVVALVGPSGSGKSTIASLLLRFY  518 (716)
T ss_pred             hhhcCceeeeCCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            3455555566789999999999999999998887654

>PRK05973 replicative DNA helicase; Provisional

Probab=97.66  E-value=9.5e-05  Score=60.87  Aligned_cols=51  Identities=20%  Similarity=0.271  Sum_probs=38.1

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcc
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQ   88 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g   88 (162)
                      ++.-.+..|.-+++.|+||+|||+++.++|..   .|.++.++++  +++.+++..
T Consensus        56 ~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSl--Ees~~~i~~  109 (237)
T PRK05973         56 ELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTL--EYTEQDVRD  109 (237)
T ss_pred             HhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEE--eCCHHHHHH
Confidence            34445666777899999999999999998753   3888888877  444666653

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=97.66  E-value=0.00031  Score=60.08  Aligned_cols=103  Identities=11%  Similarity=0.082  Sum_probs=55.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcc--eeEe-ecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQ--RREI-VNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g--~~~~-~~G~~~~~  100 (162)
                      ++...+.|+..+.   .++++++.|+||+||||++++++...   ......+.+ +++..-.+..  ...+ .+....|.
T Consensus       134 ~~~~~~~L~~~v~---~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtI-Ed~~El~~~~~~~v~~~~~~~~~~~  209 (319)
T PRK13894        134 TAAQREAIIAAVR---AHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFII-EDTGEIQCAAENYVQYHTSIDVNMT  209 (319)
T ss_pred             CHHHHHHHHHHHH---cCCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEE-cCCCccccCCCCEEEEecCCCCCHH
Confidence            3444455554443   46799999999999999999998764   222222322 2221111111  0011 11222222


Q ss_pred             ccHHHHHhhcC-cEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         101 DQSAVRAAIEG-RVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       101 ~gpl~~A~~~G-~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      + .+..|+|.. .++++.|+.-.  +....| ..+..|
T Consensus       210 ~-ll~~aLR~~PD~IivGEiR~~--Ea~~~l-~A~~tG  243 (319)
T PRK13894        210 A-LLKTTLRMRPDRILVGEVRGP--EALDLL-MAWNTG  243 (319)
T ss_pred             H-HHHHHhcCCCCEEEEeccCCH--HHHHHH-HHHHcC
Confidence            1 344456554 79999999743  455544 444444

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

Probab=97.66  E-value=6.9e-05  Score=58.41  Aligned_cols=22  Identities=18%  Similarity=0.341  Sum_probs=17.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++.||||||||+++..++..+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHh
Confidence            8999999999998777666554

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=97.66  E-value=0.00022  Score=56.97  Aligned_cols=44  Identities=23%  Similarity=0.413  Sum_probs=32.1

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHH---h-CCceEEEEeccCCChhhhc
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLEL---T-QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~---l-g~p~~~v~~~~~~~~~dL~   87 (162)
                      ..|..+++.||||+|||+++.+++..   . |.++.++++.  .++++++
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~e--e~~~~l~   64 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFE--EPPEELI   64 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESS--S-HHHHH
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEec--CCHHHHH
Confidence            35667999999999999999998743   3 8999888884  3455554

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 ....

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=97.65  E-value=0.00028  Score=54.30  Aligned_cols=30  Identities=20%  Similarity=0.164  Sum_probs=25.6

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .+..|+.+.|+||.|+|||+|.+.+|....
T Consensus        22 ~i~~Ge~~~i~G~nGsGKStLl~~l~G~~~   51 (173)
T cd03230          22 TVEKGEIYGLLGPNGAGKTTLIKIILGLLK   51 (173)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCCC
Confidence            344688999999999999999999997653

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF07931 CPT: Chloramphenicol phosphotransferase-like protein; InterPro: IPR012853 The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae

Probab=97.64  E-value=0.00015  Score=57.16  Aligned_cols=91  Identities=16%  Similarity=0.092  Sum_probs=52.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcc----eeEeecCeEEEec-----cHH----------
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQ----RREIVNGTAIYYD-----QSA----------  104 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g----~~~~~~G~~~~~~-----gpl----------  104 (162)
                      |+-|+|-|++.+||||||+.+.+.+..|...+.+.      +++.    .....+....|..     ++.          
T Consensus         1 g~iI~LNG~sSSGKSsia~~Lq~~~~~p~~~l~~D------~f~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~   74 (174)
T PF07931_consen    1 GQIIILNGPSSSGKSSIARALQERLPEPWLHLSVD------TFVDMMPPGRYRPGDGLEPAGDRPDGGPLFRRLYAAMHA   74 (174)
T ss_dssp             --EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHH------HHHHHS-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHhCcCCeEEEecC------hHHhhcCcccccCCccccccccCCchhHHHHHHHHHHHH
Confidence            35689999999999999999999999886555543      2221    0011222333320     232          


Q ss_pred             -HHHh-hcCcEEEEeCCCCCCccHHHHHHHhhcCCeEE
Q psy4122         105 -VRAA-IEGRVLILEGIEKAERNVLPVLNNLLENREMH  140 (162)
Q Consensus       105 -~~A~-~~G~vlllDEId~a~~~v~~~L~~lle~r~l~  140 (162)
                       +.|+ +.|.-+|+|++-.-+....+.+..+|+...+.
T Consensus        75 ~iaa~a~aG~~VIvD~v~~~~~~l~d~l~~~L~~~~vl  112 (174)
T PF07931_consen   75 AIAAMARAGNNVIVDDVFLGPRWLQDCLRRLLAGLPVL  112 (174)
T ss_dssp             HHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHTTS-EE
T ss_pred             HHHHHHhCCCCEEEecCccCcHHHHHHHHHHhCCCceE
Confidence             1222 46778999988665555677777888766543

Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [, ]. ; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 1QHX_A 1QHN_A 1GRR_A 1QHY_A 1QHS_A 1GRQ_A.

>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=97.64  E-value=9.9e-05  Score=49.05  Aligned_cols=22  Identities=23%  Similarity=0.300  Sum_probs=20.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +.+.|+||+|||++++.+++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999987

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.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=97.64  E-value=4.8e-05  Score=57.83  Aligned_cols=26  Identities=15%  Similarity=0.221  Sum_probs=20.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      |.|+|++|||||||++.+++. |.++.
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v   27 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVV   27 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEE
Confidence            789999999999999999988 87743

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.64  E-value=9.4e-05  Score=55.89  Aligned_cols=93  Identities=17%  Similarity=0.197  Sum_probs=54.2

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccC-CC---hhhhcc----eeEeecCeEEEeccHHHHHh-hcC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRD-TT---EADIKQ----RREIVNGTAIYYDQSAVRAA-IEG  111 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~-~~---~~dL~g----~~~~~~G~~~~~~gpl~~A~-~~G  111 (162)
                      +..|+.+.|+|+.|+|||+|.+.++..+...--.+.++.. ..   ..++..    ...+.+|..  +.-.+.+|+ ...
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~--~r~~l~~~l~~~~   99 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQR--QRVALARALLLNP   99 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHH--HHHHHHHHHhcCC
Confidence            3457889999999999999999999877543334444421 11   111111    111233321  111345555 456


Q ss_pred             cEEEEeCCCC-CCccHHHHHHHhhc
Q psy4122         112 RVLILEGIEK-AERNVLPVLNNLLE  135 (162)
Q Consensus       112 ~vlllDEId~-a~~~v~~~L~~lle  135 (162)
                      .++++||... .++.....+..++.
T Consensus       100 ~i~ilDEp~~~lD~~~~~~l~~~l~  124 (157)
T cd00267         100 DLLLLDEPTSGLDPASRERLLELLR  124 (157)
T ss_pred             CEEEEeCCCcCCCHHHHHHHHHHHH
Confidence            8999999954 55555555555554

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.63  E-value=0.00011  Score=56.40  Aligned_cols=94  Identities=16%  Similarity=0.162  Sum_probs=53.4

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEecc-CC---Chhhhc----c-eeEeecCeEEEeccHHHHHhh-
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSR-DT---TEADIK----Q-RREIVNGTAIYYDQSAVRAAI-  109 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~-~~---~~~dL~----g-~~~~~~G~~~~~~gpl~~A~~-  109 (162)
                      .+..|+.+.|.||.|+|||+|.+.++......-=.+.+.. +.   +..+..    + ...+.+|..  +.-.+++|+. 
T Consensus        22 ~i~~Ge~~~l~G~nGsGKSTLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~~--qrl~laral~~   99 (163)
T cd03216          22 SVRRGEVHALLGENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSVGER--QMVEIARALAR   99 (163)
T ss_pred             EEeCCCEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCHHHH--HHHHHHHHHhc
Confidence            3446889999999999999999999976532211233321 11   111111    1 011222321  1113566664 


Q ss_pred             cCcEEEEeCCC-CCCccHHHHHHHhhc
Q psy4122         110 EGRVLILEGIE-KAERNVLPVLNNLLE  135 (162)
Q Consensus       110 ~G~vlllDEId-~a~~~v~~~L~~lle  135 (162)
                      +..++++||-. ..+++....+..++.
T Consensus       100 ~p~illlDEP~~~LD~~~~~~l~~~l~  126 (163)
T cd03216         100 NARLLILDEPTAALTPAEVERLFKVIR  126 (163)
T ss_pred             CCCEEEEECCCcCCCHHHHHHHHHHHH
Confidence            45899999994 466665555555553

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=97.63  E-value=0.00011  Score=58.97  Aligned_cols=49  Identities=10%  Similarity=0.200  Sum_probs=36.1

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEeccCCChhhh
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLSRDTTEADI   86 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~~~~~~~dL   86 (162)
                      .++..+..|.-++|.|+||+|||+++.+++...    |.++.++++  +++..++
T Consensus         5 ~~~~Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~--E~~~~~~   57 (242)
T cd00984           5 NLTGGLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL--EMSKEQL   57 (242)
T ss_pred             hhhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeC--CCCHHHH
Confidence            444556678789999999999999999887432    788877776  3344443

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.62  E-value=0.00039  Score=65.33  Aligned_cols=103  Identities=11%  Similarity=0.105  Sum_probs=59.6

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec-cCCChhhhcc----ee--Eeec----C-----e
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS-RDTTEADIKQ----RR--EIVN----G-----T   96 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~-~~~~~~dL~g----~~--~~~~----G-----~   96 (162)
                      .|...+.......-+++.||+|.|||+++.++++..+ ++..+++. .|.++..+..    ..  ...+    .     .
T Consensus        21 rl~~~l~~~~~~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~   99 (903)
T PRK04841         21 RLLAKLSGANNYRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQK   99 (903)
T ss_pred             HHHHHHhcccCCCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhcc
Confidence            3333444333344678899999999999999998777 78788886 4445443321    00  0000    0     0


Q ss_pred             EEEec-c----HHHHHhh---cCcEEEEeCCCCCCcc-HHHHHHHhhcC
Q psy4122          97 AIYYD-Q----SAVRAAI---EGRVLILEGIEKAERN-VLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~-g----pl~~A~~---~G~vlllDEId~a~~~-v~~~L~~lle~  136 (162)
                      ..+.+ .    .++.++.   ..-+||||+++.+... +...|..+++.
T Consensus       100 ~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~  148 (903)
T PRK04841        100 RQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRH  148 (903)
T ss_pred             CCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHh
Confidence            00000 0    1222222   2357899999998744 45577777763

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=97.62  E-value=0.00045  Score=62.24  Aligned_cols=109  Identities=11%  Similarity=0.184  Sum_probs=61.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce-EEEEeccCCChhhhcc--eeEeecCe--EEEe
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV-EYICLSRDTTEADIKQ--RREIVNGT--AIYY  100 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~-~~v~~~~~~~~~dL~g--~~~~~~G~--~~~~  100 (162)
                      +++..++.+++++..-  +.-++++||+|+||||+...+...++.+- ..+++ +|.-.-.+-+  +..+ +.+  ..|.
T Consensus       226 ~~~~~~~~l~~~~~~~--~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTi-EDpvE~~~~~~~q~~v-~~~~g~~f~  301 (486)
T TIGR02533       226 MSPELLSRFERLIRRP--HGIILVTGPTGSGKTTTLYAALSRLNTPERNILTV-EDPVEYQIEGIGQIQV-NPKIGLTFA  301 (486)
T ss_pred             CCHHHHHHHHHHHhcC--CCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEE-cCCeeeecCCCceEEE-ccccCccHH
Confidence            4788888888877532  22588999999999999997776665442 23333 2211111112  1111 211  1222


Q ss_pred             ccHHHHHhhcC-cEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         101 DQSAVRAAIEG-RVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       101 ~gpl~~A~~~G-~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                       ..+-.++|+. .++++.||.-  ++...........|.+++
T Consensus       302 -~~lr~~LR~dPDvI~vGEiRd--~eta~~a~~aa~tGHlvl  340 (486)
T TIGR02533       302 -AGLRAILRQDPDIIMVGEIRD--LETAQIAIQASLTGHLVL  340 (486)
T ss_pred             -HHHHHHHhcCCCEEEEeCCCC--HHHHHHHHHHHHhCCcEE
Confidence             1233445554 7999999963  334444444555777655

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.

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

Probab=97.62  E-value=0.00018  Score=59.84  Aligned_cols=91  Identities=13%  Similarity=0.105  Sum_probs=52.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh--C----CceEEEEeccCCCh-hhhcceeEeecCe--EEEeccH----HHHHhhc--
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT--Q----REVEYICLSRDTTE-ADIKQRREIVNGT--AIYYDQS----AVRAAIE--  110 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l--g----~p~~~v~~~~~~~~-~dL~g~~~~~~G~--~~~~~gp----l~~A~~~--  110 (162)
                      |.|+.|||||||||+.+-+|+.+  |    .|.....+.+..+. .-+.|.+...-|.  -+..+.|    +..|++.  
T Consensus       139 ntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaIrsm~  218 (308)
T COG3854         139 NTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIRSMS  218 (308)
T ss_pred             eeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHHHhcC
Confidence            69999999999999999999876  3    34444444322221 1233333322121  1222223    2334433  


Q ss_pred             CcEEEEeCCCCCCccHHHHHHHhhcCCe
Q psy4122         111 GRVLILEGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus       111 G~vlllDEId~a~~~v~~~L~~lle~r~  138 (162)
                      .-|+++|||-+...  ..+++..++.|.
T Consensus       219 PEViIvDEIGt~~d--~~A~~ta~~~GV  244 (308)
T COG3854         219 PEVIIVDEIGTEED--ALAILTALHAGV  244 (308)
T ss_pred             CcEEEEeccccHHH--HHHHHHHHhcCc
Confidence            56999999987433  344556667664

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.61  E-value=5.4e-05  Score=59.43  Aligned_cols=28  Identities=21%  Similarity=0.243  Sum_probs=25.3

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      +-+.|||||||||+++.+|+.+|.++..
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vs   30 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVS   30 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceee
Confidence            5678999999999999999999999753

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=97.61  E-value=0.00018  Score=55.31  Aligned_cols=95  Identities=14%  Similarity=0.118  Sum_probs=55.3

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec---------cC-----CChhhhcc---eeEeecCeEEEecc
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS---------RD-----TTEADIKQ---RREIVNGTAIYYDQ  102 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~---------~~-----~~~~dL~g---~~~~~~G~~~~~~g  102 (162)
                      .+..|+.+.++||.|+|||||++.++......-=.+.+.         .+     .+..+-+.   ...+.+|...  .=
T Consensus        23 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~~~~~LS~G~~~--rv  100 (166)
T cd03223          23 EIKPGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYPWDDVLSGGEQQ--RL  100 (166)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEECCCCccccccHHHHhhccCCCCCCHHHHH--HH
Confidence            445688999999999999999999997753211011111         11     11111110   0011222210  11


Q ss_pred             HHHHHh-hcCcEEEEeCCC-CCCccHHHHHHHhhcC
Q psy4122         103 SAVRAA-IEGRVLILEGIE-KAERNVLPVLNNLLEN  136 (162)
Q Consensus       103 pl~~A~-~~G~vlllDEId-~a~~~v~~~L~~lle~  136 (162)
                      .+++|+ .+..++++||-. ..+++....+..++.+
T Consensus       101 ~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~  136 (166)
T cd03223         101 AFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKE  136 (166)
T ss_pred             HHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHH
Confidence            345565 456899999994 4777777778777765

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.61  E-value=0.0002  Score=55.85  Aligned_cols=73  Identities=16%  Similarity=0.180  Sum_probs=44.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCCh--hhhcc-eeEeecCeEEEeccH--HHHHhh---cCcEEEEeC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTE--ADIKQ-RREIVNGTAIYYDQS--AVRAAI---EGRVLILEG  118 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~--~dL~g-~~~~~~G~~~~~~gp--l~~A~~---~G~vlllDE  118 (162)
                      +++.|++|+|||++|.+++...+.++.++......+.  .+-+. ....++..+...+.|  +.+++.   ..++++||-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLIDc   81 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLIDC   81 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEEc
Confidence            6899999999999999999887877777755433221  11111 111123333333333  445552   346899998


Q ss_pred             C
Q psy4122         119 I  119 (162)
Q Consensus       119 I  119 (162)
                      +
T Consensus        82 l   82 (169)
T cd00544          82 L   82 (169)
T ss_pred             H
Confidence            7

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.

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

Probab=97.60  E-value=0.00011  Score=60.13  Aligned_cols=52  Identities=21%  Similarity=0.297  Sum_probs=38.7

Q ss_pred             HHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhc
Q psy4122          34 LRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        34 L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~   87 (162)
                      |-.++.. +..|..++++|+||||||.++.+++..   .|.|+.+++..++  +.++.
T Consensus        12 lD~~l~GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e~--~~~l~   67 (260)
T COG0467          12 LDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEES--PEELL   67 (260)
T ss_pred             hHHHhcCCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecCC--HHHHH
Confidence            3344443 446788999999999999999999843   3889999988644  55554

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.59  E-value=0.00052  Score=51.28  Aligned_cols=40  Identities=23%  Similarity=0.162  Sum_probs=25.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHH-HHHHHHHHh
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRS-LAMSYLELT   68 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~-La~~lA~~l   68 (162)
                      +.+.=.+.+..+....   +++++.||+|+|||. ++..+.+..
T Consensus         9 ~~~~Q~~~~~~~~~~~---~~~~i~~~~GsGKT~~~~~~~~~~~   49 (201)
T smart00487        9 LRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEAL   49 (201)
T ss_pred             CCHHHHHHHHHHHcCC---CcEEEECCCCCchhHHHHHHHHHHh
Confidence            4444444555554321   799999999999999 444444443

>PRK14527 adenylate kinase; Provisional

Probab=97.59  E-value=7.2e-05  Score=58.53  Aligned_cols=30  Identities=17%  Similarity=0.210  Sum_probs=26.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++-+++.||||+|||++++.+|+.+|.+.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~~~~~   34 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQELGLKK   34 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCCCC
Confidence            355789999999999999999999998763

>PRK06696 uridine kinase; Validated

Probab=97.58  E-value=0.00021  Score=57.46  Aligned_cols=31  Identities=23%  Similarity=0.096  Sum_probs=24.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYIC   76 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~   76 (162)
                      -|.+.|++|+||||+|+.+++.+   |.++..++
T Consensus        24 iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~   57 (223)
T PRK06696         24 RVAIDGITASGKTTFADELAEEIKKRGRPVIRAS   57 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            46777999999999999999988   55554433

>PRK08233 hypothetical protein; Provisional

Probab=97.57  E-value=6.1e-05  Score=57.52  Aligned_cols=26  Identities=8%  Similarity=0.083  Sum_probs=22.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .-+.+.|+||+||||+|+.+++.++.
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l~~   29 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLKN   29 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCCC
Confidence            35778899999999999999998863

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.56  E-value=0.0001  Score=67.77  Aligned_cols=49  Identities=14%  Similarity=0.151  Sum_probs=36.6

Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC-------CcEEecCcc---hHhhhh
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLENREMHLED-------GRFLVSAST---YDKLLQ  158 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~-------g~~i~~~~~---f~~~~~  158 (162)
                      +.|++=+=|+-+++.+++-.|+.+.+++.+..++       ...|++|.|   |++|+.
T Consensus       255 NrGl~EFvEm~K~~~~~L~~LLtatQE~~i~~~~~~~~i~~D~vIiaHsNE~E~~~F~~  313 (644)
T PRK15455        255 NQGLLEFVEMFKAPIKVLHPLLTATQEGNYNGTEGIGAIPFDGIILAHSNESEWQTFRN  313 (644)
T ss_pred             cCCcEeeHHHhcCcHHHHHHhcCCCccCcccCCCCcceeccceeEEecCCHHHHHHHhc
Confidence            4466655599999999999999999999885543       357888865   455544

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.56  E-value=7.6e-05  Score=59.52  Aligned_cols=28  Identities=21%  Similarity=0.182  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+++.||||+|||++++.+|+.+|.+..
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~~~~i   29 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYGIPHI   29 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4899999999999999999999997643

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=97.56  E-value=6.6e-05  Score=58.98  Aligned_cols=92  Identities=7%  Similarity=-0.066  Sum_probs=50.0

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEG  118 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDE  118 (162)
                      ....|+.+.|+||.|+|||||.+.++......-=.+.++.. ...-+.....+.+|.-.  .-.+++|+ .+..++++||
T Consensus        21 ~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~-~i~~~~q~~~LSgGq~q--rv~laral~~~p~lllLDE   97 (177)
T cd03222          21 VVKEGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGI-TPVYKPQYIDLSGGELQ--RVAIAAALLRNATFYLFDE   97 (177)
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCE-EEEEEcccCCCCHHHHH--HHHHHHHHhcCCCEEEEEC
Confidence            34468899999999999999999999775322112222210 00000000002222210  11345565 4568999999


Q ss_pred             CC-CCCccHHHHHHHhh
Q psy4122         119 IE-KAERNVLPVLNNLL  134 (162)
Q Consensus       119 Id-~a~~~v~~~L~~ll  134 (162)
                      -. ..++.....+..++
T Consensus        98 Pts~LD~~~~~~l~~~l  114 (177)
T cd03222          98 PSAYLDIEQRLNAARAI  114 (177)
T ss_pred             CcccCCHHHHHHHHHHH
Confidence            94 45555544444444

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=97.55  E-value=0.00053  Score=52.69  Aligned_cols=97  Identities=16%  Similarity=0.183  Sum_probs=54.2

Q ss_pred             HhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEecc-CC---ChhhhcceeEe--ecC----eEEEec----c--
Q psy4122          39 QKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSR-DT---TEADIKQRREI--VNG----TAIYYD----Q--  102 (162)
Q Consensus        39 ~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~-~~---~~~dL~g~~~~--~~G----~~~~~~----g--  102 (162)
                      -.+..|+.+.|.||.|+|||+|.+.++......-=.+.++. +.   ....+.....+  .+.    .+.+++    |  
T Consensus        23 ~~i~~G~~~~l~G~nGsGKstLl~~i~G~~~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~~~~~~~~~t~~e~lLS~G~~  102 (171)
T cd03228          23 LTIKPGEKVAIVGPSGSGKSTLLKLLLRLYDPTSGEILIDGVDLRDLDLESLRKNIAYVPQDPFLFSGTIRENILSGGQR  102 (171)
T ss_pred             EEEcCCCEEEEECCCCCCHHHHHHHHHcCCCCCCCEEEECCEEhhhcCHHHHHhhEEEEcCCchhccchHHHHhhCHHHH
Confidence            34557889999999999999999999987642211233332 11   11111110111  010    011100    1  


Q ss_pred             ---HHHHHh-hcCcEEEEeCCC-CCCccHHHHHHHhhc
Q psy4122         103 ---SAVRAA-IEGRVLILEGIE-KAERNVLPVLNNLLE  135 (162)
Q Consensus       103 ---pl~~A~-~~G~vlllDEId-~a~~~v~~~L~~lle  135 (162)
                         .+++|+ .+..++++||-. -.++.....+..++.
T Consensus       103 ~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~  140 (171)
T cd03228         103 QRIAIARALLRDPPILILDEATSALDPETEALILEALR  140 (171)
T ss_pred             HHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHH
Confidence               245555 466899999984 466666666666665

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.55  E-value=0.00026  Score=59.23  Aligned_cols=26  Identities=12%  Similarity=0.230  Sum_probs=23.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +++++.||+||||||+.+.++..+..
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~~  137 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILST  137 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccCC
Confidence            58999999999999999999988754

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.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=97.55  E-value=8.6e-05  Score=56.14  Aligned_cols=27  Identities=22%  Similarity=0.276  Sum_probs=24.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +.+.|++|+|||++++.+|+.+|.|+.
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~   29 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLI   29 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCcee
Confidence            789999999999999999999998843

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.55  E-value=0.00018  Score=54.09  Aligned_cols=41  Identities=12%  Similarity=0.081  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHhcCCCCcEE--EEcCCCchHHHHHHHHHHHh
Q psy4122          28 QDWLSHLRWILQKDNMSQDVF--LIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vl--L~GppG~GKT~La~~lA~~l   68 (162)
                      +.++..++.-+..-...||+.  +.|+||||||.+++.+|+.+
T Consensus        35 ~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   35 EVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            445566666665555667776  67999999999999999875

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PLN02674 adenylate kinase

Probab=97.54  E-value=0.00015  Score=59.96  Aligned_cols=28  Identities=21%  Similarity=0.199  Sum_probs=25.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ..+++|.||||+||+|+++.+|+.+|.+
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~~~~   58 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEYCLC   58 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHcCCc
Confidence            3579999999999999999999999876

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.52  E-value=0.00033  Score=61.25  Aligned_cols=87  Identities=9%  Similarity=0.057  Sum_probs=48.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh----C-CceEEEEeccC--CChhhh------cceeEeecCeEEEeccHHHH---
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT----Q-REVEYICLSRD--TTEADI------KQRREIVNGTAIYYDQSAVR---  106 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l----g-~p~~~v~~~~~--~~~~dL------~g~~~~~~G~~~~~~gpl~~---  106 (162)
                      .+..++|+||+||||||++..+|...    | ..+..+.+...  ...+.|      .+-+...    .-..+-+.+   
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~----~~~~~~l~~~l~  211 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHA----VKDGGDLQLALA  211 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEe----cCCcccHHHHHH
Confidence            35689999999999999999999653    3 23333433211  011222      2211110    001112223   


Q ss_pred             HhhcCcEEEEeCCCCCCcc--HHHHHHHh
Q psy4122         107 AAIEGRVLILEGIEKAERN--VLPVLNNL  133 (162)
Q Consensus       107 A~~~G~vlllDEId~a~~~--v~~~L~~l  133 (162)
                      .+.+..+++||+.-+.+.+  ..+.|..+
T Consensus       212 ~l~~~DlVLIDTaG~~~~d~~l~e~La~L  240 (374)
T PRK14722        212 ELRNKHMVLIDTIGMSQRDRTVSDQIAML  240 (374)
T ss_pred             HhcCCCEEEEcCCCCCcccHHHHHHHHHH
Confidence            3456789999999876543  44444444

>smart00072 GuKc Guanylate kinase homologues

Probab=97.52  E-value=0.0002  Score=55.79  Aligned_cols=25  Identities=16%  Similarity=0.271  Sum_probs=22.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +++++|+||+|+||+++++.+....
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcC
Confidence            5689999999999999999998775

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.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=97.52  E-value=0.00016  Score=53.98  Aligned_cols=37  Identities=11%  Similarity=0.096  Sum_probs=29.0

Q ss_pred             HHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          35 RWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        35 ~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +.+.+....|.-++|.|+=|+|||++++.+++.+|..
T Consensus         6 ~~l~~~l~~g~vi~L~GdLGaGKTtf~r~l~~~lg~~   42 (123)
T PF02367_consen    6 KKLAQILKPGDVILLSGDLGAGKTTFVRGLARALGID   42 (123)
T ss_dssp             HHHHHHHSS-EEEEEEESTTSSHHHHHHHHHHHTT--
T ss_pred             HHHHHhCCCCCEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            3445555667789999999999999999999999875

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.51  E-value=0.00018  Score=58.37  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=39.4

Q ss_pred             HHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhc
Q psy4122          31 LSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        31 ~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~   87 (162)
                      +.-|-.++.. +..|..+++.||||||||+++.+++..   .|.++.++++.  .++.+++
T Consensus         7 i~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~e--e~~~~i~   65 (237)
T TIGR03877         7 IPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALE--EHPVQVR   65 (237)
T ss_pred             cHhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEee--CCHHHHH
Confidence            3445566653 446778999999999999999987743   47788888874  3455554

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.

>PRK06547 hypothetical protein; Provisional

Probab=97.51  E-value=9.9e-05  Score=57.69  Aligned_cols=28  Identities=25%  Similarity=0.275  Sum_probs=24.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+++.|++|||||++++.+++.++.++.
T Consensus        17 ~i~i~G~~GsGKTt~a~~l~~~~~~~~~   44 (172)
T PRK06547         17 TVLIDGRSGSGKTTLAGALAARTGFQLV   44 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCee
Confidence            4667799999999999999999887643

>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=97.50  E-value=0.00082  Score=51.41  Aligned_cols=32  Identities=16%  Similarity=0.244  Sum_probs=25.1

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      ++++|+||+|||+++..+|..+   |..+..+.+.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D   37 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAAD   37 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcC
Confidence            6889999999999999998764   5555555554

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.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=97.50  E-value=0.0011  Score=60.77  Aligned_cols=111  Identities=14%  Similarity=0.154  Sum_probs=63.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe-ecCe--EEEecc
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI-VNGT--AIYYDQ  102 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~-~~G~--~~~~~g  102 (162)
                      +++..++.+++++..-  ...++++||+|+||||....+.+.++.+-..+..-+|.-.-.+-+.... .+.+  ..|.+ 
T Consensus       300 ~~~~~~~~l~~~~~~~--~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~~~~~q~~v~~~~g~~~~~-  376 (564)
T TIGR02538       300 FEPDQKALFLEAIHKP--QGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINLPGINQVNVNPKIGLTFAA-  376 (564)
T ss_pred             CCHHHHHHHHHHHHhc--CCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecCCCceEEEeccccCCCHHH-
Confidence            4677777888777532  2378999999999999998877777654322222233211112221111 1211  22221 


Q ss_pred             HHHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         103 SAVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       103 pl~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .+-.++|. ..++++.||.  .++...........|.+.+
T Consensus       377 ~l~~~LR~dPDvI~vGEiR--d~eta~~a~~aa~tGHlv~  414 (564)
T TIGR02538       377 ALRSFLRQDPDIIMVGEIR--DLETAEIAIKAAQTGHLVL  414 (564)
T ss_pred             HHHHHhccCCCEEEeCCCC--CHHHHHHHHHHHHcCCcEE
Confidence            23344555 4799999997  4555554444555776655

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.

>PLN02200 adenylate kinase family protein

Probab=97.50  E-value=0.00011  Score=60.15  Aligned_cols=26  Identities=23%  Similarity=0.305  Sum_probs=23.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+++.|+||||||++++.+|+.+|.+
T Consensus        45 ii~I~G~PGSGKsT~a~~La~~~g~~   70 (234)
T PLN02200         45 ITFVLGGPGSGKGTQCEKIVETFGFK   70 (234)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCe
Confidence            47889999999999999999999876

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=97.49  E-value=0.0002  Score=61.86  Aligned_cols=89  Identities=15%  Similarity=0.213  Sum_probs=50.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee--Ee---ec--CeEEEeccHHH-HHhhc-CcE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR--EI---VN--GTAIYYDQSAV-RAAIE-GRV  113 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~--~~---~~--G~~~~~~gpl~-~A~~~-G~v  113 (162)
                      .++++++.||+|+||||++++++.........+.+ +|+..-.+-...  .+   .+  |.......-++ .++|. ..+
T Consensus       161 ~~~nilI~G~tGSGKTTll~aLl~~i~~~~rivti-Ed~~El~l~~~~~v~l~~~~~~~~~~~~t~~~ll~~~LR~~pD~  239 (344)
T PRK13851        161 GRLTMLLCGPTGSGKTTMSKTLISAIPPQERLITI-EDTLELVIPHENHVRLLYSKNGAGLGAVTAEHLLQASLRMRPDR  239 (344)
T ss_pred             cCCeEEEECCCCccHHHHHHHHHcccCCCCCEEEE-CCCccccCCCCCEEEEEeeccccCcCccCHHHHHHHHhcCCCCe
Confidence            57899999999999999999999887655444443 232211111100  00   01  11111111233 34554 478


Q ss_pred             EEEeCCCCCCccHHHHHHHhh
Q psy4122         114 LILEGIEKAERNVLPVLNNLL  134 (162)
Q Consensus       114 lllDEId~a~~~v~~~L~~ll  134 (162)
                      +++.|+.-  ++..+.|....
T Consensus       240 IivGEiR~--~ea~~~l~a~~  258 (344)
T PRK13851        240 ILLGEMRD--DAAWAYLSEVV  258 (344)
T ss_pred             EEEEeeCc--HHHHHHHHHHH
Confidence            99999973  34566555543

>PRK01184 hypothetical protein; Provisional

Probab=97.48  E-value=0.00011  Score=56.79  Aligned_cols=27  Identities=19%  Similarity=0.156  Sum_probs=22.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      -++|+|+||+||||+++ +++.+|.++.
T Consensus         3 ~i~l~G~~GsGKsT~a~-~~~~~g~~~i   29 (184)
T PRK01184          3 IIGVVGMPGSGKGEFSK-IAREMGIPVV   29 (184)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHcCCcEE
Confidence            47899999999999987 7888887753

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=97.47  E-value=0.0001  Score=55.40  Aligned_cols=23  Identities=22%  Similarity=0.245  Sum_probs=21.3

Q ss_pred             EEcCCCchHHHHHHHHHHHhCCc
Q psy4122          49 LIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        49 L~GppG~GKT~La~~lA~~lg~p   71 (162)
                      |.||||+|||++++.+|+.+|..
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~   23 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLV   23 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSE
T ss_pred             CcCCCCCChHHHHHHHHHhcCcc
Confidence            68999999999999999999865

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=97.46  E-value=0.00076  Score=52.97  Aligned_cols=35  Identities=14%  Similarity=0.159  Sum_probs=28.5

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ++.+--.+..|+.+.|.||.|+|||+|.+.+|...
T Consensus        25 l~~~~~~i~~Ge~~~l~G~nGsGKStLl~~i~Gl~   59 (194)
T cd03213          25 LKNVSGKAKPGELTAIMGPSGAGKSTLLNALAGRR   59 (194)
T ss_pred             eecceEEEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            34444445578899999999999999999999876

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=97.46  E-value=0.00017  Score=54.68  Aligned_cols=22  Identities=27%  Similarity=0.386  Sum_probs=20.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ++++|+||+|||++++.++..+
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l   23 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKL   23 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999987

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.46  E-value=0.00045  Score=57.82  Aligned_cols=35  Identities=14%  Similarity=0.154  Sum_probs=26.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh----C-CceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT----Q-REVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l----g-~p~~~v~~~   78 (162)
                      ++.++|+||+|+||||++..+|..+    | ..+..+.+.
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D  233 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTD  233 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECC
Confidence            3468999999999999999998654    3 555555553

>PF05729 NACHT: NACHT domain

Probab=97.45  E-value=0.00011  Score=54.56  Aligned_cols=23  Identities=22%  Similarity=0.380  Sum_probs=20.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++|.|+||+|||++++.++..+
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~   24 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQL   24 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHH
Confidence            58899999999999999999655

>PRK10436 hypothetical protein; Provisional

Probab=97.45  E-value=0.0015  Score=58.52  Aligned_cols=110  Identities=15%  Similarity=0.156  Sum_probs=61.3

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE-EEEeccCCChhhhcc--eeEee-cCeEEEec
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE-YICLSRDTTEADIKQ--RREIV-NGTAIYYD  101 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~-~v~~~~~~~~~dL~g--~~~~~-~G~~~~~~  101 (162)
                      +++..++.+++++..-  +.-+++.||+|+||||...++...++.+-. .+++ +|.-.-.+-+  +..+. +....|..
T Consensus       202 ~~~~~~~~l~~~~~~~--~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~Ti-EDPvE~~l~gi~Q~~v~~~~g~~f~~  278 (462)
T PRK10436        202 MTPAQLAQFRQALQQP--QGLILVTGPTGSGKTVTLYSALQTLNTAQINICSV-EDPVEIPLAGINQTQIHPKAGLTFQR  278 (462)
T ss_pred             cCHHHHHHHHHHHHhc--CCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEe-cCCccccCCCcceEeeCCccCcCHHH
Confidence            5677788888877532  337999999999999998876666655432 2333 2311111212  11121 11122321


Q ss_pred             cHHHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         102 QSAVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       102 gpl~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                       .+-.++|+ ..++++.||.-  ++...........|.+++
T Consensus       279 -~lr~~LR~dPDvI~vGEIRD--~eta~~al~AA~TGHlVl  316 (462)
T PRK10436        279 -VLRALLRQDPDVIMVGEIRD--GETAEIAIKAAQTGHLVL  316 (462)
T ss_pred             -HHHHHhcCCCCEEEECCCCC--HHHHHHHHHHHHcCCcEE
Confidence             23334554 47999999963  344443334444676655

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.45  E-value=7.6e-05  Score=58.96  Aligned_cols=27  Identities=15%  Similarity=0.127  Sum_probs=24.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++++|.|||||||+++.++ .+|.++.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~lg~~~i   28 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-ELGYKVI   28 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-HhCCcee
Confidence            47899999999999999999 8888754

>PRK14526 adenylate kinase; Provisional

Probab=97.45  E-value=0.00013  Score=58.88  Aligned_cols=27  Identities=19%  Similarity=0.240  Sum_probs=24.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +++|.|||||||||+++.+|..++.+.
T Consensus         2 ~i~l~G~pGsGKsT~a~~La~~~~~~~   28 (211)
T PRK14526          2 KLVFLGPPGSGKGTIAKILSNELNYYH   28 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCce
Confidence            488999999999999999999988763

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=97.44  E-value=0.0015  Score=55.54  Aligned_cols=104  Identities=17%  Similarity=0.252  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEee-cCeEEEecc--HHH
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIV-NGTAIYYDQ--SAV  105 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~-~G~~~~~~g--pl~  105 (162)
                      ...+.++..++.....+-.||+|+.|+||+.+++.+|..+..... -.+.++..+.++.-   +. .|...-.+.  .+.
T Consensus         3 ~~~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~-~~~~~~~~p~n~~~---~d~~g~~i~vd~Ir~l~   78 (299)
T PRK07132          3 NWIKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQI-TNLNEQELPANIIL---FDIFDKDLSKSEFLSAI   78 (299)
T ss_pred             hHHHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCC-CCCCCCCCCcceEE---eccCCCcCCHHHHHHHH
Confidence            356777877776666656679999999999999999988721100 00000111111110   10 011110000  011


Q ss_pred             H-----Hhh--cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         106 R-----AAI--EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       106 ~-----A~~--~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +     ++.  +..+++||+.++++.+..++|+..||+
T Consensus        79 ~~~~~~~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEE  116 (299)
T PRK07132         79 NKLYFSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEE  116 (299)
T ss_pred             HHhccCCcccCCceEEEEecccccCHHHHHHHHHHhhC
Confidence            1     111  336999999999999999999999996

>PRK04040 adenylate kinase; Provisional

Probab=97.44  E-value=0.00014  Score=57.50  Aligned_cols=25  Identities=24%  Similarity=0.308  Sum_probs=22.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +.++++|.|||||||+++.+++.++
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            4689999999999999999999983

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=97.43  E-value=0.00012  Score=60.66  Aligned_cols=24  Identities=21%  Similarity=0.390  Sum_probs=21.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +-+++.|+|||||||+|+.+++.+
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHC
Confidence            357889999999999999999988

>PRK13975 thymidylate kinase; Provisional

Probab=97.43  E-value=0.00013  Score=56.70  Aligned_cols=28  Identities=18%  Similarity=0.063  Sum_probs=24.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +.-+.++|++||||||+++.+|+.++..
T Consensus         2 ~~~I~ieG~~GsGKtT~~~~L~~~l~~~   29 (196)
T PRK13975          2 NKFIVFEGIDGSGKTTQAKLLAEKLNAF   29 (196)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            4568999999999999999999999853

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=97.42  E-value=0.00018  Score=51.42  Aligned_cols=20  Identities=25%  Similarity=0.398  Sum_probs=18.8

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      |++.|+||+|||||.+.+..
T Consensus         2 V~iiG~~~~GKSTlin~l~~   21 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTG   21 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999985

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.41  E-value=0.00013  Score=56.10  Aligned_cols=28  Identities=18%  Similarity=0.240  Sum_probs=24.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .+..++++|++|+||||+++.+++.++.
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~   33 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKL   33 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4668999999999999999999988864

>PRK10646 ADP-binding protein; Provisional

Probab=97.41  E-value=0.00041  Score=53.67  Aligned_cols=43  Identities=12%  Similarity=0.187  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+.+.-+.+......|.-++|.|+=|+|||++++.+++.+|.+
T Consensus        13 ~t~~l~~~la~~l~~g~vi~L~GdLGaGKTtf~rgl~~~Lg~~   55 (153)
T PRK10646         13 ATLDLGARVAKACDGATVIYLYGDLGAGKTTFSRGFLQALGHQ   55 (153)
T ss_pred             HHHHHHHHHHHhCCCCcEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            3444444555555567778999999999999999999999864

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=97.41  E-value=0.00027  Score=54.93  Aligned_cols=31  Identities=19%  Similarity=0.305  Sum_probs=26.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      +++++|+||+|+|||+|++.+.......+..
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~~~~   32 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPDKFGR   32 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTTTEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhccccccc
Confidence            5799999999999999999999887655543

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 ....

>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=97.41  E-value=0.00028  Score=54.16  Aligned_cols=27  Identities=22%  Similarity=0.174  Sum_probs=23.3

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVE   73 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~   73 (162)
                      +.|.|++||||||+++.+++.+   |..+.
T Consensus         3 I~ieG~~GsGKtT~~~~L~~~l~~~g~~v~   32 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAERLEARGYEVV   32 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEE
Confidence            6899999999999999999887   55543

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

>PRK00300 gmk guanylate kinase; Provisional

Probab=97.40  E-value=0.00014  Score=57.00  Aligned_cols=27  Identities=22%  Similarity=0.263  Sum_probs=24.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.|+||+|||||+|++.++..++
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            467899999999999999999998875

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=97.40  E-value=0.00018  Score=56.17  Aligned_cols=27  Identities=19%  Similarity=0.256  Sum_probs=24.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      |+.+.+.|++||||||+++.++..++.
T Consensus         3 ge~i~l~G~sGsGKSTl~~~la~~l~~   29 (176)
T PRK09825          3 GESYILMGVSGSGKSLIGSKIAALFSA   29 (176)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhcCC
Confidence            678999999999999999999998875

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=97.39  E-value=0.00099  Score=57.43  Aligned_cols=101  Identities=17%  Similarity=0.234  Sum_probs=57.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhc--c--eeEee------cC-
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIK--Q--RREIV------NG-   95 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~--g--~~~~~------~G-   95 (162)
                      ++...+.|+.++.   .++++++.|++|+|||++.+.++..+......+.+ ++.  .++.  .  ...+.      .| 
T Consensus       164 ~~~~~~~L~~~v~---~~~~ili~G~tGsGKTTll~al~~~i~~~~riv~i-Ed~--~El~~~~~~~~~l~~r~~~~~g~  237 (340)
T TIGR03819       164 PPGVARLLRAIVA---ARLAFLISGGTGSGKTTLLSALLALVAPDERIVLV-EDA--AELRPDHPHVVRLEARPANVEGA  237 (340)
T ss_pred             CHHHHHHHHHHHh---CCCeEEEECCCCCCHHHHHHHHHccCCCCCcEEEE-CCc--ceecCCCCCeeeEEeccccccCc
Confidence            4566666666654   35799999999999999999998776543333333 232  1121  1  00110      11 


Q ss_pred             -eEEEeccHHHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          96 -TAIYYDQSAVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        96 -~~~~~~gpl~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                       ...+.+ .+..|+|. ..++++.|+-  .+++.+.|+ .+..|
T Consensus       238 ~~~t~~~-ll~~aLR~~PD~IivGEiR--g~Ea~~~l~-a~~tG  277 (340)
T TIGR03819       238 GAVTLTD-LVRQALRMRPDRIVVGEVR--GAEVVDLLA-ALNTG  277 (340)
T ss_pred             CccCHHH-HHHHHhccCCCeEEEeCcC--cHHHHHHHH-HHHcC
Confidence             111221 23345554 4799999997  346666554 44444

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.39  E-value=0.00021  Score=58.25  Aligned_cols=23  Identities=17%  Similarity=0.342  Sum_probs=21.1

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++|+|+||+||||+|+.+++.++
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~   24 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLS   24 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999998874

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.

>PRK14529 adenylate kinase; Provisional

Probab=97.39  E-value=0.00015  Score=59.13  Aligned_cols=28  Identities=11%  Similarity=0.096  Sum_probs=25.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|.|||||||||+++.+|+.++.+..
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~~~~~i   29 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKYDLAHI   29 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCCCc
Confidence            5899999999999999999999998743

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=97.37  E-value=0.00024  Score=55.53  Aligned_cols=32  Identities=22%  Similarity=0.144  Sum_probs=25.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      +.+.|+||||||++++.+++.+   |.++..+++.
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~D   36 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLD   36 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEehh
Confidence            6789999999999999999887   4555555443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=97.37  E-value=0.00023  Score=58.79  Aligned_cols=38  Identities=5%  Similarity=0.046  Sum_probs=30.6

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEec
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLS   78 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~   78 (162)
                      +..|.-+++.|+||||||+++.++|.   ..|.++.++++.
T Consensus        33 ip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~E   73 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVE   73 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec
Confidence            34566789999999999999999875   347788888874

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=97.36  E-value=0.00048  Score=59.21  Aligned_cols=91  Identities=11%  Similarity=0.136  Sum_probs=51.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee---Ee---e--cCeEEEecc-HHHHHhhc-Cc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR---EI---V--NGTAIYYDQ-SAVRAAIE-GR  112 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~---~~---~--~G~~~~~~g-pl~~A~~~-G~  112 (162)
                      .++++++.|++|+||||+.+++.......-..+.+ +|+..-.+-..+   .+   .  .|.....-. .+-.|+|. ..
T Consensus       159 ~~~nili~G~tgSGKTTll~aL~~~ip~~~ri~ti-Ed~~El~l~~~~n~~~~~~~~~~~~~~~~~~~~ll~~~LR~~PD  237 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTFTNAALREIPAIERLITV-EDAREIVLSNHPNRVHLLASKGGQGRAKVTTQDLIEACLRLRPD  237 (332)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHhhCCCCCeEEEe-cCCCccccccCCCEEEEEecCCCCCcCcCcHHHHHHHHhccCCC
Confidence            56799999999999999999999888655444444 332111110111   11   1  111111111 23344554 47


Q ss_pred             EEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         113 VLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       113 vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ++++.|+.-  +++.+.|.. +..|
T Consensus       238 ~IivGEiR~--~ea~~~l~a-~~tG  259 (332)
T PRK13900        238 RIIVGELRG--AEAFSFLRA-INTG  259 (332)
T ss_pred             eEEEEecCC--HHHHHHHHH-HHcC
Confidence            999999974  455655444 4444

>PRK13764 ATPase; Provisional

Probab=97.36  E-value=0.00035  Score=64.45  Aligned_cols=27  Identities=19%  Similarity=0.465  Sum_probs=24.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ++++++.||||+||||++++++..+..
T Consensus       257 ~~~ILIsG~TGSGKTTll~AL~~~i~~  283 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFAQALAEFYAD  283 (602)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            568999999999999999999977754

>PRK00889 adenylylsulfate kinase; Provisional

Probab=97.35  E-value=0.00029  Score=54.15  Aligned_cols=27  Identities=19%  Similarity=0.284  Sum_probs=23.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.|+|+||+|||++++.++..+.
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~   29 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLR   29 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            356789999999999999999998873

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.34  E-value=0.00031  Score=56.12  Aligned_cols=55  Identities=15%  Similarity=0.080  Sum_probs=36.6

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADI   86 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL   86 (162)
                      ..|-+++. .+..|+-+.|+||||||||+++.++|...         +..+.++......+...+
T Consensus         6 ~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl   70 (235)
T cd01123           6 KALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL   70 (235)
T ss_pred             hhhHhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH
Confidence            34445555 34467788999999999999999998542         245566665443344433

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=97.33  E-value=0.00033  Score=54.88  Aligned_cols=23  Identities=22%  Similarity=0.268  Sum_probs=20.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +.|.||+||||||+++.++..++
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l~   24 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQLG   24 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            57899999999999999999873

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.33  E-value=0.0004  Score=54.64  Aligned_cols=44  Identities=20%  Similarity=0.229  Sum_probs=32.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~   87 (162)
                      .|.-++++||||||||+++.+++..   .|.++.++.+-. .+...+.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~-~~~~rl~   57 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG-LSPERFK   57 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC-CCHHHHH
Confidence            4667899999999999999998853   366677777743 3444443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=97.33  E-value=0.0011  Score=57.90  Aligned_cols=94  Identities=12%  Similarity=0.077  Sum_probs=52.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC--Cc-eEEEEeccCCChhhhcceeE------ee-cCe-EEEeccHHHHHhhc-C
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ--RE-VEYICLSRDTTEADIKQRRE------IV-NGT-AIYYDQSAVRAAIE-G  111 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg--~p-~~~v~~~~~~~~~dL~g~~~------~~-~G~-~~~~~gpl~~A~~~-G  111 (162)
                      +..+++.||+|+||||+.+.+....+  .+ ...+.+ +|.-.-.+.+...      .. +.+ ..|.+ .+-.|+|. .
T Consensus       149 ~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~Ivti-Edp~E~~~~~~~~~~~~~q~evg~~~~~~~~-~l~~aLR~~P  226 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTY-EDPIEYILGSPDDLLPPAQSQIGRDVDSFAN-GIRLALRRAP  226 (372)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEE-ecCchhccCCCceeecccccccCCCccCHHH-HHHHhhccCC
Confidence            34789999999999999999987663  22 233444 3321111111100      11 111 12221 23445555 4


Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .++++.|+.  .++.........+.|.+.+
T Consensus       227 D~I~vGEiR--d~et~~~al~aa~TGH~v~  254 (372)
T TIGR02525       227 KIIGVGEIR--DLETFQAAVLAGQSGHFCL  254 (372)
T ss_pred             CEEeeCCCC--CHHHHHHHHHHHhcCCcEE
Confidence            799999997  3455555556667776654

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).

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=97.33  E-value=0.00038  Score=55.63  Aligned_cols=54  Identities=17%  Similarity=0.238  Sum_probs=37.1

Q ss_pred             HHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEeccCCChhhh
Q psy4122          31 LSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLSRDTTEADI   86 (162)
Q Consensus        31 ~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~~~~~~~dL   86 (162)
                      ...|-.++. .+..|..+++.|+||+|||+++.+++.   ..|.++.+++.  +.+.+++
T Consensus         6 i~~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~--e~~~~~i   63 (229)
T TIGR03881         6 VEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTT--EESRESI   63 (229)
T ss_pred             hhhHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEc--cCCHHHH
Confidence            344555653 455778899999999999999998773   23566666665  3444444

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.

>KOG0735|consensus

Probab=97.33  E-value=0.00045  Score=64.83  Aligned_cols=74  Identities=15%  Similarity=0.250  Sum_probs=46.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCc----eEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcC-cEEE
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQRE----VEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEG-RVLI  115 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p----~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G-~vll  115 (162)
                      .....+++|.||+|||||.|+++++...-.+    ++++.|+.. ..+.+-.   +   +-.| ...+..|+.++ .+++
T Consensus       428 v~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l-~~~~~e~---i---Qk~l-~~vfse~~~~~PSiIv  499 (952)
T KOG0735|consen  428 VFRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTL-DGSSLEK---I---QKFL-NNVFSEALWYAPSIIV  499 (952)
T ss_pred             ccccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhc-cchhHHH---H---HHHH-HHHHHHHHhhCCcEEE
Confidence            3345599999999999999999999877655    345666421 1111110   0   0001 12456777776 6899


Q ss_pred             EeCCCCC
Q psy4122         116 LEGIEKA  122 (162)
Q Consensus       116 lDEId~a  122 (162)
                      ||++|..
T Consensus       500 LDdld~l  506 (952)
T KOG0735|consen  500 LDDLDCL  506 (952)
T ss_pred             Ecchhhh
Confidence            9999863

>cd01394 radB RadB

Probab=97.32  E-value=0.00035  Score=55.40  Aligned_cols=47  Identities=21%  Similarity=0.232  Sum_probs=34.5

Q ss_pred             HHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          31 LSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        31 ~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      ...|-.++. .+..|.-+++.|+||||||+++.++|...   |.++.++..
T Consensus         5 i~~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~   55 (218)
T cd01394           5 CKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDT   55 (218)
T ss_pred             hhHHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEC
Confidence            344556664 34466678999999999999999998543   567767654

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=97.31  E-value=0.00033  Score=55.39  Aligned_cols=25  Identities=20%  Similarity=0.143  Sum_probs=22.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .-+.|.|++|||||||++.++..++
T Consensus         7 ~iI~I~G~sGsGKTTl~~~l~~~l~   31 (209)
T PRK05480          7 IIIGIAGGSGSGKTTVASTIYEELG   31 (209)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688999999999999999999884

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.30  E-value=0.00054  Score=64.61  Aligned_cols=109  Identities=13%  Similarity=0.127  Sum_probs=61.7

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcce-eEeecCeE----
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQR-REIVNGTA----   97 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~-~~~~~G~~----   97 (162)
                      +++.=.+.++.++.+   ++-++|.|+||||||++++.+...+   |+.+..+..  .-...+.+.. ..+. ..+    
T Consensus       353 Ls~~Q~~Av~~i~~s---~~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~Ap--Tg~Aa~~L~~~~g~~-a~Ti~~~  426 (744)
T TIGR02768       353 LSEEQYEAVRHVTGS---GDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAAL--SGKAAEGLQAESGIE-SRTLASL  426 (744)
T ss_pred             CCHHHHHHHHHHhcC---CCEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeC--cHHHHHHHHhccCCc-eeeHHHH
Confidence            455555555555432   3468999999999999999987544   554433322  1123233211 0010 011    


Q ss_pred             --EEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc--CCeEEEc
Q psy4122          98 --IYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE--NREMHLE  142 (162)
Q Consensus        98 --~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle--~r~l~l~  142 (162)
                        .|..+.  .-.....+||+||+..++...+..|.....  .-.+++-
T Consensus       427 ~~~~~~~~--~~~~~~~llIvDEasMv~~~~~~~Ll~~~~~~~~kliLV  473 (744)
T TIGR02768       427 EYAWANGR--DLLSDKDVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLV  473 (744)
T ss_pred             HhhhccCc--ccCCCCcEEEEECcccCCHHHHHHHHHHHHhcCCEEEEE
Confidence              121110  113456899999999999988887777443  2345443

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.

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=97.29  E-value=0.00022  Score=55.96  Aligned_cols=23  Identities=22%  Similarity=0.323  Sum_probs=21.4

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |.+.||+|+||||+|+.++..++
T Consensus         2 IgI~G~sgSGKTTla~~L~~~L~   24 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLAKRLAQILN   24 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            57899999999999999999987

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=97.29  E-value=0.0019  Score=57.01  Aligned_cols=31  Identities=26%  Similarity=0.171  Sum_probs=21.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSL   60 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~L   60 (162)
                      ++|-=.+.+..+    ..|+++++.+|+|+|||..
T Consensus        27 ~t~iQ~~ai~~~----l~g~dvi~~a~TGsGKT~a   57 (460)
T PRK11776         27 MTPIQAQSLPAI----LAGKDVIAQAKTGSGKTAA   57 (460)
T ss_pred             CCHHHHHHHHHH----hcCCCEEEECCCCCcHHHH
Confidence            444334444444    3588999999999999964

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.29  E-value=0.00054  Score=54.65  Aligned_cols=51  Identities=18%  Similarity=0.146  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEec
Q psy4122          28 QDWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLS   78 (162)
Q Consensus        28 ~~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~   78 (162)
                      ++....|-.++.. +..|.-+++.|+||+|||+++.++|.   ..|.++.++.+-
T Consensus         6 ~tGi~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361          6 PTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             cCCcHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            3445556666643 34566789999999999999999996   347777777764

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=97.29  E-value=0.00013  Score=59.71  Aligned_cols=50  Identities=14%  Similarity=-0.001  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEe
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICL   77 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~   77 (162)
                      +.....|-.++..+..|..+++.|+||+|||+++.++|...    |.++.++++
T Consensus        14 ~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~   67 (271)
T cd01122          14 WWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL   67 (271)
T ss_pred             CCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEc
Confidence            44455566666566678889999999999999999987542    777777776

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG1970|consensus

Probab=97.28  E-value=0.00037  Score=63.57  Aligned_cols=33  Identities=12%  Similarity=0.051  Sum_probs=28.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYIC   76 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~   76 (162)
                      +.-+||+||+||||||.++-+|..+|..++..+
T Consensus       110 ~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew~  142 (634)
T KOG1970|consen  110 SRILLLTGPSGCGKSTTVKVLSKELGYQLIEWS  142 (634)
T ss_pred             ceEEEEeCCCCCCchhHHHHHHHhhCceeeeec
Confidence            345788899999999999999999999876544

>TIGR00235 udk uridine kinase

Probab=97.27  E-value=0.0002  Score=56.81  Aligned_cols=27  Identities=19%  Similarity=0.119  Sum_probs=23.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      |.-+.+.||+|||||||++.++..++.
T Consensus         6 g~vi~I~G~sGsGKSTl~~~l~~~l~~   32 (207)
T TIGR00235         6 GIIIGIGGGSGSGKTTVARKIYEQLGK   32 (207)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            456889999999999999999988763

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.26  E-value=0.00099  Score=61.69  Aligned_cols=31  Identities=13%  Similarity=0.173  Sum_probs=24.8

Q ss_pred             CcEEEEeCCCCCCccHHHHHHHhhcC-CeEEE
Q psy4122         111 GRVLILEGIEKAERNVLPVLNNLLEN-REMHL  141 (162)
Q Consensus       111 G~vlllDEId~a~~~v~~~L~~lle~-r~l~l  141 (162)
                      ..++|+||....+-.....|...+.. .++++
T Consensus       266 ~dvlIvDEaSMvd~~lm~~ll~al~~~~rlIl  297 (615)
T PRK10875        266 LDVLVVDEASMVDLPMMARLIDALPPHARVIF  297 (615)
T ss_pred             CCeEEEChHhcccHHHHHHHHHhcccCCEEEE
Confidence            47999999999999888888887764 35555

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=97.25  E-value=0.0013  Score=61.12  Aligned_cols=35  Identities=23%  Similarity=0.167  Sum_probs=29.3

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ++.+--....|+.+.++||.|||||||++.++...
T Consensus       495 L~~isl~i~~Ge~vaIvG~sGsGKSTLlklL~gl~  529 (710)
T TIGR03796       495 IENFSLTLQPGQRVALVGGSGSGKSTIAKLVAGLY  529 (710)
T ss_pred             ccceeEEEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45555556679999999999999999999999765

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.25  E-value=0.00048  Score=61.74  Aligned_cols=55  Identities=11%  Similarity=0.237  Sum_probs=40.0

Q ss_pred             HHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHH---H-hCCceEEEEeccCCChhhhc
Q psy4122          31 LSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLE---L-TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        31 ~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~---~-lg~p~~~v~~~~~~~~~dL~   87 (162)
                      +.-|-.|+. .+..|..+++.||||||||+++.+++.   . .|.++.++++.  -++++++
T Consensus         7 I~gLD~il~GGlp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e--E~~~~l~   66 (484)
T TIGR02655         7 IEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE--ESPQDII   66 (484)
T ss_pred             chhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe--cCHHHHH
Confidence            344555555 344677899999999999999999853   2 26899899885  3466664

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.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.25  E-value=0.00018  Score=59.62  Aligned_cols=36  Identities=19%  Similarity=0.132  Sum_probs=28.6

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+++--....|+-+.|+||+|||||||.+.+|....
T Consensus        19 l~~i~L~v~~GEfvsilGpSGcGKSTLLriiAGL~~   54 (248)
T COG1116          19 LEDINLSVEKGEFVAILGPSGCGKSTLLRLIAGLEK   54 (248)
T ss_pred             eccceeEECCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            334444555688999999999999999999997653

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=97.24  E-value=0.0011  Score=57.47  Aligned_cols=27  Identities=22%  Similarity=0.287  Sum_probs=23.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .+..++++||+|+||||+.+.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLLAAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            356899999999999999999998763

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.

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=97.24  E-value=0.0015  Score=60.60  Aligned_cols=36  Identities=25%  Similarity=0.216  Sum_probs=29.5

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|+.+--....|+.+.++|+.|||||||++.++...
T Consensus       480 vL~~i~l~i~~G~~iaIvG~sGsGKSTLlklL~gl~  515 (694)
T TIGR03375       480 ALDNVSLTIRPGEKVAIIGRIGSGKSTLLKLLLGLY  515 (694)
T ss_pred             ceeeeeEEECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344555556679999999999999999999999765

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.24  E-value=0.0018  Score=57.45  Aligned_cols=88  Identities=17%  Similarity=0.257  Sum_probs=50.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCC--Chhhhc------ceeEeecCeEEEeccHHHHHh--
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDT--TEADIK------QRREIVNGTAIYYDQSAVRAA--  108 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~--~~~dL~------g~~~~~~G~~~~~~gpl~~A~--  108 (162)
                      ++.++|+||+||||||++..+|..+     |..+..+.+...-  ....|.      +-+..    .......+..++  
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~----~~~~~~~l~~~l~~  296 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVE----VVYDPKELAKALEQ  296 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceE----ccCCHHhHHHHHHH
Confidence            4578999999999999999888543     3455555543210  111222      11111    111122333333  


Q ss_pred             -hcCcEEEEeCCCCCCc--cHHHHHHHhhc
Q psy4122         109 -IEGRVLILEGIEKAER--NVLPVLNNLLE  135 (162)
Q Consensus       109 -~~G~vlllDEId~a~~--~v~~~L~~lle  135 (162)
                       ....++|||..-+.+.  .....|..+++
T Consensus       297 ~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~  326 (424)
T PRK05703        297 LRDCDVILIDTAGRSQRDKRLIEELKALIE  326 (424)
T ss_pred             hCCCCEEEEeCCCCCCCCHHHHHHHHHHHh
Confidence             4458999998866544  45667777777

>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=97.24  E-value=0.0012  Score=53.29  Aligned_cols=112  Identities=13%  Similarity=0.146  Sum_probs=50.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh--CCceEEEEec-cCCC-hhhhcceeEe----------
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT--QREVEYICLS-RDTT-EADIKQRREI----------   92 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l--g~p~~~v~~~-~~~~-~~dL~g~~~~----------   92 (162)
                      ++.=...+..+..    .+-+.+.||+|||||.||-+.|..+  ......+.+. +..+ .+++--.+.-          
T Consensus         6 ~~~Q~~~~~al~~----~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~   81 (205)
T PF02562_consen    6 NEEQKFALDALLN----NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLR   81 (205)
T ss_dssp             SHHHHHHHHHHHH-----SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTH
T ss_pred             CHHHHHHHHHHHh----CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHH
Confidence            3333444444542    4578999999999999999888422  3333333222 2211 1222111100          


Q ss_pred             -------------------ecCeEEEeccHHHHHh-hcCcEEEEeCCCCCCccHHHHHHHhhcC-CeEEEc
Q psy4122          93 -------------------VNGTAIYYDQSAVRAA-IEGRVLILEGIEKAERNVLPVLNNLLEN-REMHLE  142 (162)
Q Consensus        93 -------------------~~G~~~~~~gpl~~A~-~~G~vlllDEId~a~~~v~~~L~~lle~-r~l~l~  142 (162)
                                         ..|.....+-.+.+.- ....++++||...+.++.+..+..-+.+ ..+++.
T Consensus        82 p~~d~l~~~~~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR~g~~skii~~  152 (205)
T PF02562_consen   82 PIYDALEELFGKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTRIGEGSKIIIT  152 (205)
T ss_dssp             HHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEE
T ss_pred             HHHHHHHHHhChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHcccCCCcEEEEe
Confidence                               1122222211111111 1247899999999998877777666654 455553

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

>KOG1942|consensus

Probab=97.23  E-value=0.00039  Score=59.75  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          29 DWLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        29 ~~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      +..-.+-+|+++.. .|+.+||.||||+|||.||-.+++.+|..+-++
T Consensus        48 eAagiivdlik~KkmaGravLlaGppgtGKTAlAlaisqELG~kvPFc   95 (456)
T KOG1942|consen   48 EAAGIIVDLIKSKKMAGRAVLLAGPPGTGKTALALAISQELGPKVPFC   95 (456)
T ss_pred             hhhhHHHHHHHhhhccCcEEEEecCCCCchhHHHHHHHHHhCCCCCcc
Confidence            34445567776554 678999999999999999999999998654433

>PRK14738 gmk guanylate kinase; Provisional

Probab=97.23  E-value=0.00019  Score=57.23  Aligned_cols=25  Identities=16%  Similarity=0.105  Sum_probs=21.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++.++|+||+|||||||++.+.+.
T Consensus        12 ~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhc
Confidence            4557899999999999999999754

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=97.22  E-value=0.00039  Score=54.17  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=27.2

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +.|...+.+. ...+++|+||.|+|||+|++.+......
T Consensus         9 ~~l~~~l~~~-~~~~~~l~G~rg~GKTsLl~~~~~~~~~   46 (234)
T PF01637_consen    9 EKLKELLESG-PSQHILLYGPRGSGKTSLLKEFINELKE   46 (234)
T ss_dssp             HHHHHCHHH---SSEEEEEESTTSSHHHHHHHHHHHCT-
T ss_pred             HHHHHHHHhh-cCcEEEEEcCCcCCHHHHHHHHHHHhhh
Confidence            3444444432 2358999999999999999999988843

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.22  E-value=0.0011  Score=57.84  Aligned_cols=93  Identities=15%  Similarity=0.190  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcce---eEeecCeEEE-
Q psy4122          28 QDWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQR---REIVNGTAIY-   99 (162)
Q Consensus        28 ~~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~---~~~~~G~~~~-   99 (162)
                      ++....|-+++.. +..|.-+++.|+||+|||+|+.++|...   +.++.+++..  -+.+++..+   .........+ 
T Consensus        65 ~TGi~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~E--Es~~qi~~Ra~rlg~~~~~l~l~  142 (372)
T cd01121          65 PTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE--ESPEQIKLRADRLGISTENLYLL  142 (372)
T ss_pred             ccCCHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECC--cCHHHHHHHHHHcCCCcccEEEE
Confidence            4445556666653 4456678999999999999999998654   3466666653  234444321   1111112111 


Q ss_pred             ecc---HHHHHhh--cCcEEEEeCCCCC
Q psy4122         100 YDQ---SAVRAAI--EGRVLILEGIEKA  122 (162)
Q Consensus       100 ~~g---pl~~A~~--~G~vlllDEId~a  122 (162)
                      .+.   -+.+++.  +..+++||+|..+
T Consensus       143 ~e~~le~I~~~i~~~~~~lVVIDSIq~l  170 (372)
T cd01121         143 AETNLEDILASIEELKPDLVIIDSIQTV  170 (372)
T ss_pred             ccCcHHHHHHHHHhcCCcEEEEcchHHh
Confidence            111   2333333  3479999999654

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.

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

Probab=97.21  E-value=0.001  Score=58.69  Aligned_cols=89  Identities=16%  Similarity=0.206  Sum_probs=52.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC-----CceEEEEec-------cCC-ChhhhcceeEeecCeEEEeccHHH---HH
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ-----REVEYICLS-------RDT-TEADIKQRREIVNGTAIYYDQSAV---RA  107 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg-----~p~~~v~~~-------~~~-~~~dL~g~~~~~~G~~~~~~gpl~---~A  107 (162)
                      ++.+.|+||+|+||||..--+|+...     ..+-.++..       +.+ +..++++-+-.    .++..--+.   .+
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~----vv~~~~el~~ai~~  278 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLE----VVYSPKELAEAIEA  278 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceE----EecCHHHHHHHHHH
Confidence            56899999999999987777776654     122223221       111 23444443221    111212243   44


Q ss_pred             hhcCcEEEEeCCCCCCcc--HHHHHHHhhcC
Q psy4122         108 AIEGRVLILEGIEKAERN--VLPVLNNLLEN  136 (162)
Q Consensus       108 ~~~G~vlllDEId~a~~~--v~~~L~~lle~  136 (162)
                      +++..++++|-+-+-+.+  ..+-|-.+++.
T Consensus       279 l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~  309 (407)
T COG1419         279 LRDCDVILVDTAGRSQYDKEKIEELKELIDV  309 (407)
T ss_pred             hhcCCEEEEeCCCCCccCHHHHHHHHHHHhc
Confidence            678899999999775554  45556666653

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=97.21  E-value=0.001  Score=56.85  Aligned_cols=28  Identities=18%  Similarity=0.212  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      -++|+|||+||||.|+-.+|+.+|-++.
T Consensus         5 ~i~I~GPTAsGKT~lai~LAk~~~~eII   32 (308)
T COG0324           5 LIVIAGPTASGKTALAIALAKRLGGEII   32 (308)
T ss_pred             EEEEECCCCcCHHHHHHHHHHHcCCcEE
Confidence            4789999999999999999999998754

>KOG0479|consensus

Probab=97.21  E-value=0.00048  Score=63.43  Aligned_cols=94  Identities=12%  Similarity=0.209  Sum_probs=62.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |+||+|+|.+-||.|.+.+-....+.  .-+.....+-.-|...-+.  +.|....+-|+.+.  ...||+-|||+|+++
T Consensus       336 NiLlvGDPSvAKSQLLRyVLntAplA--I~TTGRGSSGVGLTAAVTtD~eTGERRLEAGAMVL--ADRGVVCIDEFDKMs  411 (818)
T KOG0479|consen  336 NILLVGDPSVAKSQLLRYVLNTAPLA--IATTGRGSSGVGLTAAVTTDQETGERRLEAGAMVL--ADRGVVCIDEFDKMS  411 (818)
T ss_pred             eEEEecCchHHHHHHHHHHHhccccc--ccccCCCCCCccceeEEeeccccchhhhhcCceEE--ccCceEEehhccccc
Confidence            69999999999999999876544322  2122222222223222121  12444444444333  366899999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEcC
Q psy4122         124 RNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~~  143 (162)
                      .-=-.+++.+||.++++|..
T Consensus       412 DiDRvAIHEVMEQqtVTIaK  431 (818)
T KOG0479|consen  412 DIDRVAIHEVMEQQTVTIAK  431 (818)
T ss_pred             chhHHHHHHHHhcceEEeEe
Confidence            98889999999999999964

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=97.20  E-value=0.00032  Score=49.78  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=19.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +++.|++|||||+|++.++....
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS-
T ss_pred             EEEECcCCCCHHHHHHHHhcCCC
Confidence            78999999999999999986553

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.20  E-value=0.00076  Score=54.81  Aligned_cols=45  Identities=11%  Similarity=0.135  Sum_probs=30.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHH-H--hCCceEEEEeccCCChhhhc
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLE-L--TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~-~--lg~p~~~v~~~~~~~~~dL~   87 (162)
                      +..|..+++.|+||||||+++.+++. .  .|.++.+++..  -+..+++
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e--~~~~~~~   68 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ--LTTTEFI   68 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCC--CCHHHHH
Confidence            33567899999999999999877664 3  25666666643  3344543

>PLN02459 probable adenylate kinase

Probab=97.20  E-value=0.00037  Score=58.22  Aligned_cols=27  Identities=19%  Similarity=0.217  Sum_probs=24.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +++|.||||+|||++++.+|+.+|.+.
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~   57 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPH   57 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            588899999999999999999998763

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=97.19  E-value=0.00081  Score=53.69  Aligned_cols=52  Identities=21%  Similarity=0.307  Sum_probs=36.9

Q ss_pred             HHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhc
Q psy4122          34 LRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        34 L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~   87 (162)
                      |-.++. .+..|..+++.|+||+|||+++.+++..   .|.++.++++.  .++.+++
T Consensus         5 LD~~l~gGi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e--~~~~~l~   60 (224)
T TIGR03880         5 LDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLE--EREERIL   60 (224)
T ss_pred             hHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC--CCHHHHH
Confidence            344443 3335667899999999999999998842   37788888774  3455554

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=97.19  E-value=0.0023  Score=59.84  Aligned_cols=27  Identities=22%  Similarity=0.120  Sum_probs=21.9

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHH
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAM   62 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~   62 (162)
                      .++..+..++++++.|++|||||+.+-
T Consensus       171 qil~~i~~gkdvIv~A~TGSGKTtqvP  197 (675)
T PHA02653        171 KIFEAWISRKPVVLTGGTGVGKTSQVP  197 (675)
T ss_pred             HHHHHHHhCCCEEEECCCCCCchhHHH
Confidence            555556668999999999999999653

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.19  E-value=0.00061  Score=59.68  Aligned_cols=60  Identities=10%  Similarity=0.129  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC--Cc---eEEEEec-cCCChhhhcc
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ--RE---VEYICLS-RDTTEADIKQ   88 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg--~p---~~~v~~~-~~~~~~dL~g   88 (162)
                      .+-...-+.+..+-.|+..+++||||||||+|++.+|+.+.  +|   +.++-+. ...+..|+..
T Consensus       118 ~~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~  183 (380)
T PRK12608        118 DLSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRR  183 (380)
T ss_pred             chhHhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHH
Confidence            34444445555555788999999999999999999998663  32   3343343 4445666653

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.19  E-value=0.0011  Score=61.03  Aligned_cols=32  Identities=16%  Similarity=0.173  Sum_probs=25.1

Q ss_pred             CcEEEEeCCCCCCccHHHHHHHhhcC-CeEEEc
Q psy4122         111 GRVLILEGIEKAERNVLPVLNNLLEN-REMHLE  142 (162)
Q Consensus       111 G~vlllDEId~a~~~v~~~L~~lle~-r~l~l~  142 (162)
                      ..+||+||....+...+..|...+.. .++++-
T Consensus       260 ~dvlIiDEaSMvd~~l~~~ll~al~~~~rlIlv  292 (586)
T TIGR01447       260 LDVLVVDEASMVDLPLMAKLLKALPPNTKLILL  292 (586)
T ss_pred             ccEEEEcccccCCHHHHHHHHHhcCCCCEEEEE
Confidence            47999999999999988888887753 455553

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.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.18  E-value=0.00028  Score=57.80  Aligned_cols=26  Identities=27%  Similarity=0.473  Sum_probs=22.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ++|+|+||+|||++|+.+|+.+...-
T Consensus         4 iIlTGyPgsGKTtfakeLak~L~~~i   29 (261)
T COG4088           4 IILTGYPGSGKTTFAKELAKELRQEI   29 (261)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHhh
Confidence            68899999999999999999886543

>PRK04328 hypothetical protein; Provisional

Probab=97.18  E-value=0.00077  Score=55.31  Aligned_cols=54  Identities=19%  Similarity=0.243  Sum_probs=38.1

Q ss_pred             HHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEeccCCChhhh
Q psy4122          31 LSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLSRDTTEADI   86 (162)
Q Consensus        31 ~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~~~~~~~dL   86 (162)
                      ..-|-+++.. +..|..+++.||||||||+++.+++.   ..|.++.++++.+  ++.++
T Consensus         9 i~~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~ee--~~~~i   66 (249)
T PRK04328          9 IPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALEE--HPVQV   66 (249)
T ss_pred             chhHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEeeC--CHHHH
Confidence            3345556654 33577889999999999999998774   3477888888743  34444

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=97.17  E-value=0.00044  Score=53.90  Aligned_cols=39  Identities=23%  Similarity=0.355  Sum_probs=32.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++..++.|+..++    ++-++|.|++|+|||||++.+.....
T Consensus        22 ~~~g~~~l~~~l~----~k~~vl~G~SGvGKSSLiN~L~~~~~   60 (161)
T PF03193_consen   22 TGEGIEELKELLK----GKTSVLLGQSGVGKSSLINALLPEAK   60 (161)
T ss_dssp             TTTTHHHHHHHHT----TSEEEEECSTTSSHHHHHHHHHTSS-
T ss_pred             CCcCHHHHHHHhc----CCEEEEECCCCCCHHHHHHHHHhhcc
Confidence            5677788888776    57899999999999999999886543

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>COG0802 Predicted ATPase or kinase [General function prediction only]

Probab=97.17  E-value=0.001  Score=51.29  Aligned_cols=43  Identities=14%  Similarity=0.057  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+.+.=+.+......|.-|+|.|+=|+|||++++.+++.+|..
T Consensus        10 ~t~~lg~~l~~~l~~g~Vv~L~GdLGAGKTtf~rgi~~~Lg~~   52 (149)
T COG0802          10 ATLALGERLAEALKAGDVVLLSGDLGAGKTTLVRGIAKGLGVD   52 (149)
T ss_pred             HHHHHHHHHHhhCCCCCEEEEEcCCcCChHHHHHHHHHHcCCC
Confidence            3444444555566688899999999999999999999999853

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=97.17  E-value=0.00045  Score=55.17  Aligned_cols=27  Identities=19%  Similarity=0.156  Sum_probs=24.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .-+++.|.||+|||++++.+|..+|.+
T Consensus         4 ~~i~i~G~~G~GKst~a~~l~~~~~~~   30 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARHRAID   30 (197)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCe
Confidence            358899999999999999999998865

>TIGR00750 lao LAO/AO transport system ATPase

Probab=97.17  E-value=0.00099  Score=56.09  Aligned_cols=49  Identities=18%  Similarity=0.137  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      ....++.+......++.+.++|+||+|||+++..++..+   |..+..+.+.
T Consensus        20 ~~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~~~~~~~v~~i~~D   71 (300)
T TIGR00750        20 AKQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELRRRGLKVAVIAVD   71 (300)
T ss_pred             HHHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            444455554444456678999999999999999988755   5666666665

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.17  E-value=0.0028  Score=63.00  Aligned_cols=37  Identities=19%  Similarity=0.038  Sum_probs=28.3

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ...|+.++..++.++++|+|||||||.+-++....|+
T Consensus        72 ~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~~~  108 (1283)
T TIGR01967        72 REDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGR  108 (1283)
T ss_pred             HHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHcCC
Confidence            3455555555678999999999999999988866654

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.

>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.16  E-value=0.00039  Score=56.69  Aligned_cols=47  Identities=17%  Similarity=0.068  Sum_probs=35.3

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      ...++++--.+..|+-+.+.||.|||||||.+.+|......-=.+++
T Consensus        18 ~~~le~vsL~ia~ge~vv~lGpSGcGKTTLLnl~AGf~~P~~G~i~l   64 (259)
T COG4525          18 RSALEDVSLTIASGELVVVLGPSGCGKTTLLNLIAGFVTPSRGSIQL   64 (259)
T ss_pred             hhhhhccceeecCCCEEEEEcCCCccHHHHHHHHhcCcCcccceEEE
Confidence            55666666667789999999999999999999999766433223433

>KOG0060|consensus

Probab=97.15  E-value=0.00041  Score=63.61  Aligned_cols=56  Identities=14%  Similarity=0.129  Sum_probs=39.0

Q ss_pred             CccceeceeeeecccCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122           7 SQEYVRFTLIYLFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus         7 ~~~y~~~~~~~~~~~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|-++.|++..+..++-   .+..+   +++.-....|+++|++||.|||||+|-+.+|.+.
T Consensus       430 ~Dn~i~~e~v~l~tPt~---g~~li---e~Ls~~V~~g~~LLItG~sG~GKtSLlRvlggLW  485 (659)
T KOG0060|consen  430 ADNAIEFEEVSLSTPTN---GDLLI---ENLSLEVPSGQNLLITGPSGCGKTSLLRVLGGLW  485 (659)
T ss_pred             ccceEEeeeeeecCCCC---Cceee---eeeeeEecCCCeEEEECCCCCchhHHHHHHhccc
Confidence            34677888887766552   11111   1122234468999999999999999999999765

>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=97.13  E-value=0.00051  Score=56.33  Aligned_cols=34  Identities=24%  Similarity=0.337  Sum_probs=23.4

Q ss_pred             EEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCC
Q psy4122          49 LIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTT   82 (162)
Q Consensus        49 L~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~   82 (162)
                      ++||+|+||||+++.+.+.   .|+++..+++.+..+
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~vNLDPa~~   37 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNGRDVYIVNLDPAVE   37 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT-S-EEEEE--TT-S
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCceEEEcchHhc
Confidence            4799999999999988865   478888888875443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.13  E-value=0.00055  Score=60.49  Aligned_cols=34  Identities=9%  Similarity=0.059  Sum_probs=27.9

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +++..+-.|+..+++||||||||+|++.++....
T Consensus       161 D~l~PIGkGQR~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        161 DLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             eeecccccCceEEEeCCCCCChhHHHHHHHHHHH
Confidence            4444555788999999999999999999997664

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=97.13  E-value=0.00045  Score=62.88  Aligned_cols=30  Identities=10%  Similarity=0.167  Sum_probs=27.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      ++++|+|.+||||||+.+.+|+.+|+++..
T Consensus         7 ~~i~LiG~~GaGKttvg~~LA~~L~~~fiD   36 (542)
T PRK14021          7 PQAVIIGMMGAGKTRVGKEVAQMMRLPFAD   36 (542)
T ss_pred             ccEEEECCCCCCHHHHHHHHHHHhCCCEEE
Confidence            479999999999999999999999999763

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=97.13  E-value=0.00079  Score=54.30  Aligned_cols=26  Identities=31%  Similarity=0.296  Sum_probs=22.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .-+.|.||+|+|||||++.++..+..
T Consensus        34 ~iigi~G~~GsGKTTl~~~L~~~l~~   59 (229)
T PRK09270         34 TIVGIAGPPGAGKSTLAEFLEALLQQ   59 (229)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            35788899999999999999988754

>PRK14974 cell division protein FtsY; Provisional

Probab=97.12  E-value=0.0013  Score=56.65  Aligned_cols=23  Identities=9%  Similarity=0.135  Sum_probs=20.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      -++++|+||+||||++..+|..+
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l  164 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYL  164 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            58899999999999998888765

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.12  E-value=0.0016  Score=57.78  Aligned_cols=91  Identities=13%  Similarity=0.156  Sum_probs=51.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCC--ChhhhcceeEeecCeE--EEeccHHHHHh---h---cC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDT--TEADIKQRREIVNGTA--IYYDQSAVRAA---I---EG  111 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~--~~~dL~g~~~~~~G~~--~~~~gpl~~A~---~---~G  111 (162)
                      +.++|+||+||||||++..+|..+   |..+-.+.+...-  ..++|.......+=..  ...+..+.+++   +   .-
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~  321 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARV  321 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCC
Confidence            468999999999999999999655   3444444443111  1233332101111011  11223344444   3   24


Q ss_pred             cEEEEeCCCCCCcc--HHHHHHHhhc
Q psy4122         112 RVLILEGIEKAERN--VLPVLNNLLE  135 (162)
Q Consensus       112 ~vlllDEId~a~~~--v~~~L~~lle  135 (162)
                      .++|+|-.-+.+.+  .+..|..+++
T Consensus       322 DvVLIDTaGRs~kd~~lm~EL~~~lk  347 (436)
T PRK11889        322 DYILIDTAGKNYRASETVEEMIETMG  347 (436)
T ss_pred             CEEEEeCccccCcCHHHHHHHHHHHh
Confidence            79999999887654  4666666665

>PRK08356 hypothetical protein; Provisional

Probab=97.12  E-value=0.00049  Score=54.10  Aligned_cols=25  Identities=20%  Similarity=0.089  Sum_probs=21.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .++|.||||+||||+|+.+++ .|.+
T Consensus         7 ~i~~~G~~gsGK~t~a~~l~~-~g~~   31 (195)
T PRK08356          7 IVGVVGKIAAGKTTVAKFFEE-KGFC   31 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCc
Confidence            578999999999999999964 6665

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=97.11  E-value=0.00052  Score=53.35  Aligned_cols=25  Identities=28%  Similarity=0.175  Sum_probs=22.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +.|+|++||||||+++.+++ +|.++
T Consensus         2 i~itG~~gsGKst~~~~l~~-~g~~~   26 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-LGIPV   26 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-CCCCE
Confidence            67999999999999999998 78764

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=97.11  E-value=0.00056  Score=55.98  Aligned_cols=29  Identities=21%  Similarity=0.288  Sum_probs=23.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEY   74 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~   74 (162)
                      -.+++||||+|||.+|-.+|+.+|.|+..
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~g~pvI~   31 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKTGAPVIS   31 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--EEEE
T ss_pred             EEEEECCCCCChhHHHHHHHHHhCCCEEE
Confidence            36889999999999999999999999753

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=97.10  E-value=0.00037  Score=53.36  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=19.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +.++|+|++|||||||++.+-.
T Consensus         2 krimliG~~g~GKTTL~q~L~~   23 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNG   23 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcC
Confidence            4689999999999999998764

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

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

Probab=97.10  E-value=0.0055  Score=53.85  Aligned_cols=90  Identities=18%  Similarity=0.247  Sum_probs=54.7

Q ss_pred             HHHHHHhcCCCC-cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh--h-
Q psy4122          34 LRWILQKDNMSQ-DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA--I-  109 (162)
Q Consensus        34 L~~i~~~~~~g~-~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~--~-  109 (162)
                      +.++........ .+++.||-+||||++++.+.........+++.. |....+...             .-..+++  . 
T Consensus        26 ~~~l~~~~~~~~~i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~-d~~~~~~~l-------------~d~~~~~~~~~   91 (398)
T COG1373          26 LPRLIKKLDLRPFIILILGPRQVGKTTLLKLLIKGLLEEIIYINFD-DLRLDRIEL-------------LDLLRAYIELK   91 (398)
T ss_pred             hHHHHhhcccCCcEEEEECCccccHHHHHHHHHhhCCcceEEEEec-chhcchhhH-------------HHHHHHHHHhh
Confidence            334444444443 689999999999999988887765543334433 211111110             0111111  1 


Q ss_pred             --cCcEEEEeCCCCCCccHHHHHHHhhcCCe
Q psy4122         110 --EGRVLILEGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus       110 --~G~vlllDEId~a~~~v~~~L~~lle~r~  138 (162)
                        +...++||||...+. -...|..+.|.+.
T Consensus        92 ~~~~~yifLDEIq~v~~-W~~~lk~l~d~~~  121 (398)
T COG1373          92 EREKSYIFLDEIQNVPD-WERALKYLYDRGN  121 (398)
T ss_pred             ccCCceEEEecccCchh-HHHHHHHHHcccc
Confidence              335899999998655 6777888888776

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=97.10  E-value=0.00068  Score=62.16  Aligned_cols=43  Identities=16%  Similarity=0.253  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          28 QDWLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      |++.+.|+....... .|..++|+|.+||||||+++.+|..++.
T Consensus       375 peV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~L~~  418 (568)
T PRK05537        375 PEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVKLME  418 (568)
T ss_pred             HHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHHhhh
Confidence            666666666665443 5567899999999999999999999885

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=97.10  E-value=0.0048  Score=54.78  Aligned_cols=113  Identities=12%  Similarity=0.075  Sum_probs=65.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC---hhhhc---cee---E-eecC
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT---EADIK---QRR---E-IVNG   95 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~---~~dL~---g~~---~-~~~G   95 (162)
                      +-+-=.+.++.+...+...+..+++-|||+|||.++..+++.++..+..+.-+.+.-   ...+.   +..   . +.++
T Consensus        37 lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~~~Lvlv~~~~L~~Qw~~~~~~~~~~~~~~g~~~~~  116 (442)
T COG1061          37 LRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLVPTKELLDQWAEALKKFLLLNDEIGIYGGG  116 (442)
T ss_pred             CcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcCCEEEEECcHHHHHHHHHHHHHhcCCccccceecCc
Confidence            445555666666665444678999999999999999999999988854443321110   01111   000   0 1111


Q ss_pred             eEEEec--------cHHHHH--hh-----cCcEEEEeCCCCCCccHHHHHHHhhcCCe
Q psy4122          96 TAIYYD--------QSAVRA--AI-----EGRVLILEGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus        96 ~~~~~~--------gpl~~A--~~-----~G~vlllDEId~a~~~v~~~L~~lle~r~  138 (162)
                      ...+.+        ..+.+.  +.     +-+.||+||+|.++.+....+...+....
T Consensus       117 ~~~~~~~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~~~~~~~  174 (442)
T COG1061         117 EKELEPAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAAY  174 (442)
T ss_pred             eeccCCCcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHHHhhhccc
Confidence            222221        122221  11     34789999999999877666666555433

>cd04163 Era Era subfamily

Probab=97.09  E-value=0.00097  Score=48.59  Aligned_cols=21  Identities=19%  Similarity=0.336  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.+.|+||+||||++++++.
T Consensus         5 ~i~~~G~~g~GKttl~~~l~~   25 (168)
T cd04163           5 FVAIVGRPNVGKSTLLNALVG   25 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999863

Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.

>PRK07667 uridine kinase; Provisional

Probab=97.09  E-value=0.0015  Score=51.51  Aligned_cols=33  Identities=9%  Similarity=-0.007  Sum_probs=25.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC---CceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~   78 (162)
                      -|.+.|++|+||||+++.+++.++   .++..+.+.
T Consensus        19 iIgI~G~~gsGKStla~~L~~~l~~~~~~~~~i~~D   54 (193)
T PRK07667         19 ILGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHID   54 (193)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEEcC
Confidence            567889999999999999998764   455555543

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=97.08  E-value=0.00038  Score=53.57  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=20.1

Q ss_pred             EcCCCchHHHHHHHHHHHhCCc
Q psy4122          50 IGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        50 ~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +|++||||||+++.++..+|.+
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~   22 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAA   22 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCe
Confidence            5999999999999999999864

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=97.08  E-value=0.00053  Score=58.63  Aligned_cols=30  Identities=10%  Similarity=0.152  Sum_probs=27.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ++.++|+|++|||||+|++.+++.+|.++.
T Consensus       162 ~~~~~~~G~~~~gkstl~~~l~~~~~~~~v  191 (325)
T TIGR01526       162 VKTVAILGGESTGKSTLVNKLAAVFNTTSA  191 (325)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCCCEE
Confidence            458999999999999999999999998863

E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=97.06  E-value=0.00057  Score=60.11  Aligned_cols=28  Identities=14%  Similarity=0.205  Sum_probs=25.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +.|.++|++|||||||++.+|+..|.+.
T Consensus       220 ~~IvI~G~~gsGKTTL~~~La~~~g~~~  247 (399)
T PRK08099        220 RTVAILGGESSGKSTLVNKLANIFNTTS  247 (399)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHhCCCe
Confidence            4799999999999999999999988874

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.06  E-value=0.0047  Score=56.52  Aligned_cols=83  Identities=8%  Similarity=0.129  Sum_probs=45.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccC-CC-hhhhcceeEeecCeEE--EeccHHHH---Hhhc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRD-TT-EADIKQRREIVNGTAI--YYDQSAVR---AAIE  110 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~-~~-~~dL~g~~~~~~G~~~--~~~gpl~~---A~~~  110 (162)
                      .|+.+.|+||+|||||+++..+|..+     +..+..+.+... .. ...+......-+=.+.  .....+..   .+.+
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~  428 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLRD  428 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhcc
Confidence            46789999999999999999998653     234444444210 01 1122111001010111  11122333   3455


Q ss_pred             CcEEEEeCCCCCCcc
Q psy4122         111 GRVLILEGIEKAERN  125 (162)
Q Consensus       111 G~vlllDEId~a~~~  125 (162)
                      ..+||||..-+.+.+
T Consensus       429 ~DLVLIDTaG~s~~D  443 (559)
T PRK12727        429 YKLVLIDTAGMGQRD  443 (559)
T ss_pred             CCEEEecCCCcchhh
Confidence            689999999876654

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.06  E-value=0.00053  Score=59.53  Aligned_cols=84  Identities=19%  Similarity=0.208  Sum_probs=49.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce-EEEEeccCCC--hhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV-EYICLSRDTT--EADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIE  120 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~-~~v~~~~~~~--~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId  120 (162)
                      +-++|+|+-|+|||.|-..+-..+..+. .++.+|.-|-  -.++..   +. |.....+ ++...+ ++-.+|.+||+.
T Consensus        66 ~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~---l~-g~~dpl~-~iA~~~~~~~~vLCfDEF~  140 (367)
T COG1485          66 RGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHT---LQ-GQTDPLP-PIADELAAETRVLCFDEFE  140 (367)
T ss_pred             ceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHH---Hc-CCCCccH-HHHHHHHhcCCEEEeeeee
Confidence            4599999999999999999988875543 4455542221  111111   11 3332111 333333 566899999995


Q ss_pred             C---CCccHHHHHHHh
Q psy4122         121 K---AERNVLPVLNNL  133 (162)
Q Consensus       121 ~---a~~~v~~~L~~l  133 (162)
                      -   ++.-.+..|.+.
T Consensus       141 VtDI~DAMiL~rL~~~  156 (367)
T COG1485         141 VTDIADAMILGRLLEA  156 (367)
T ss_pred             ecChHHHHHHHHHHHH
Confidence            5   444455555543

>KOG0732|consensus

Probab=97.06  E-value=0.0011  Score=64.43  Aligned_cols=88  Identities=15%  Similarity=0.248  Sum_probs=55.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH-------HHHHh-hcCcEEEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS-------AVRAA-IEGRVLIL  116 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp-------l~~A~-~~G~vlll  116 (162)
                      +-+|+.||||+|||..|+++|...-.--..+...-.- -+|..         ..|+.-+       +-.|- ....+++.
T Consensus       300 rgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrk-gaD~l---------skwvgEaERqlrllFeeA~k~qPSIIff  369 (1080)
T KOG0732|consen  300 RGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRK-GADCL---------SKWVGEAERQLRLLFEEAQKTQPSIIFF  369 (1080)
T ss_pred             cceeecCCCCCchhHHHHhhhhhhcccccccchhhhc-Cchhh---------ccccCcHHHHHHHHHHHHhccCceEEec
Confidence            4599999999999999999998876655555443111 11221         1222111       12232 23478999


Q ss_pred             eCCCC-----------CCccHHHHHHHhhc----CCeEEEc
Q psy4122         117 EGIEK-----------AERNVLPVLNNLLE----NREMHLE  142 (162)
Q Consensus       117 DEId~-----------a~~~v~~~L~~lle----~r~l~l~  142 (162)
                      |||+-           .+.++.+-|+.+|+    ++++++.
T Consensus       370 deIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvi  410 (1080)
T KOG0732|consen  370 DEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVI  410 (1080)
T ss_pred             cccccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEE
Confidence            99993           33467888888888    4566553

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

Probab=97.05  E-value=0.0058  Score=55.25  Aligned_cols=111  Identities=15%  Similarity=0.119  Sum_probs=66.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhc--ce-eEeecCeEEEecc
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIK--QR-REIVNGTAIYYDQ  102 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~--g~-~~~~~G~~~~~~g  102 (162)
                      .++.....++.++..- .| -+|++||+|+|||+....+...++.+..-+..-+|  +-++.  |- ..-.+.+....-.
T Consensus       242 ~~~~~~~~~~~~~~~p-~G-liLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiED--PVE~~~~gI~Q~qVN~k~gltfa  317 (500)
T COG2804         242 MSPFQLARLLRLLNRP-QG-LILVTGPTGSGKTTTLYAALSELNTPERNIITIED--PVEYQLPGINQVQVNPKIGLTFA  317 (500)
T ss_pred             CCHHHHHHHHHHHhCC-Ce-EEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeC--CeeeecCCcceeecccccCCCHH
Confidence            4677777777776521 12 57888999999999999998888877653222223  22221  10 0111222111122


Q ss_pred             HHHHHh-hc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         103 SAVRAA-IE-GRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       103 pl~~A~-~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      ..++|+ |+ ..++.+.||.  ..++....-+....|.+++.
T Consensus       318 ~~LRa~LRqDPDvImVGEIR--D~ETAeiavqAalTGHLVlS  357 (500)
T COG2804         318 RALRAILRQDPDVIMVGEIR--DLETAEIAVQAALTGHLVLS  357 (500)
T ss_pred             HHHHHHhccCCCeEEEeccC--CHHHHHHHHHHHhcCCeEee
Confidence            455665 44 5799999996  44555555566667887764

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.05  E-value=0.00047  Score=55.20  Aligned_cols=83  Identities=14%  Similarity=0.173  Sum_probs=54.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCcc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERN  125 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~  125 (162)
                      .++|+|+.|+|||+..+.++...      +.   +.    +..   .       .+.....++....++.+||++.....
T Consensus        54 ~lvl~G~QG~GKStf~~~L~~~~------~~---d~----~~~---~-------~~kd~~~~l~~~~iveldEl~~~~k~  110 (198)
T PF05272_consen   54 VLVLVGKQGIGKSTFFRKLGPEY------FS---DS----IND---F-------DDKDFLEQLQGKWIVELDELDGLSKK  110 (198)
T ss_pred             eeeEecCCcccHHHHHHHHhHHh------cc---Cc----ccc---C-------CCcHHHHHHHHhHheeHHHHhhcchh
Confidence            47889999999999999885441      10   10    000   0       01123445556667789999999998


Q ss_pred             HHHHHHHhhcCCeEEE--cCCcEEecCc
Q psy4122         126 VLPVLNNLLENREMHL--EDGRFLVSAS  151 (162)
Q Consensus       126 v~~~L~~lle~r~l~l--~~g~~i~~~~  151 (162)
                      -.+.|.+++-.....+  |-|+.....+
T Consensus       111 ~~~~lK~~iT~~~~~~R~pY~~~~~~~~  138 (198)
T PF05272_consen  111 DVEALKSFITRRTDTYRPPYGRDPEEFP  138 (198)
T ss_pred             hHHHHHHHhcccceeeecCCcCcceeec
Confidence            8999999998766544  3354444333

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.05  E-value=0.0015  Score=54.90  Aligned_cols=56  Identities=14%  Similarity=0.046  Sum_probs=37.3

Q ss_pred             HHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhh
Q psy4122          31 LSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADI   86 (162)
Q Consensus        31 ~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL   86 (162)
                      ...+..++.. +..|.-+.++||||||||+++.++|...         +..+.++......++..+
T Consensus        81 ~~~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl  146 (310)
T TIGR02236        81 SKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERI  146 (310)
T ss_pred             CHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHH
Confidence            3445555553 3356667899999999999999998653         235666666544455444

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.04  E-value=0.0011  Score=53.35  Aligned_cols=50  Identities=14%  Similarity=0.098  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec
Q psy4122          29 DWLSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS   78 (162)
Q Consensus        29 ~~~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~   78 (162)
                      +.+.-|-.++. .+..|.-+++.|+||+|||+++.+++..   .|.++.++.+.
T Consensus         9 tGi~~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e   62 (234)
T PRK06067          9 TGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE   62 (234)
T ss_pred             cCCHHHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC
Confidence            33445556664 3345667899999999999999999743   47788888774

>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=97.04  E-value=0.00045  Score=50.48  Aligned_cols=28  Identities=21%  Similarity=0.242  Sum_probs=24.3

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+.+.++|+.|||||+|.+.++....
T Consensus         9 ~~g~~~~i~G~nGsGKStLl~~l~g~~~   36 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKSTLLKALAGLLP   36 (137)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHTTSSH
T ss_pred             cCCCEEEEEccCCCccccceeeeccccc
Confidence            3578899999999999999999987654

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 ....

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=97.04  E-value=0.0029  Score=59.51  Aligned_cols=36  Identities=22%  Similarity=0.244  Sum_probs=29.4

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+++--.+..|+.+-++|+.|||||||++.+.....
T Consensus       489 L~~isL~I~~Ge~vaIvG~SGsGKSTL~KLL~gly~  524 (709)
T COG2274         489 LEDLSLEIPPGEKVAIVGRSGSGKSTLLKLLLGLYK  524 (709)
T ss_pred             hhceeEEeCCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            444444566799999999999999999999997654

>TIGR00017 cmk cytidylate kinase

Probab=97.04  E-value=0.00067  Score=54.87  Aligned_cols=28  Identities=14%  Similarity=0.059  Sum_probs=24.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+.+.||+||||||+++.+|+.++.++.
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~~~~~~~   31 (217)
T TIGR00017         4 IIAIDGPSGAGKSTVAKAVAEKLGYAYL   31 (217)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcee
Confidence            4789999999999999999999997643

This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.04  E-value=0.00048  Score=54.98  Aligned_cols=30  Identities=13%  Similarity=0.126  Sum_probs=26.0

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +...|+.+.++||.|||||+|.+++|.+..
T Consensus        25 ~v~~Ge~iaitGPSG~GKStllk~va~Lis   54 (223)
T COG4619          25 SVRAGEFIAITGPSGCGKSTLLKIVASLIS   54 (223)
T ss_pred             eecCCceEEEeCCCCccHHHHHHHHHhccC
Confidence            345688999999999999999999997764

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=97.04  E-value=0.00072  Score=57.19  Aligned_cols=26  Identities=19%  Similarity=0.409  Sum_probs=23.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ++++||||+|||+|+..+|+.++.++
T Consensus         2 i~i~G~t~~GKs~la~~l~~~~~~~i   27 (287)
T TIGR00174         2 IFIMGPTAVGKSQLAIQLAKKLNAEI   27 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCcE
Confidence            68999999999999999999988653

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=97.03  E-value=0.00069  Score=53.75  Aligned_cols=28  Identities=11%  Similarity=0.000  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+.++|++|||||++++.+++.+|.++.
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~g~~~i   30 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQKGIPIL   30 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCeEe
Confidence            4889999999999999999998888753

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

Probab=97.03  E-value=0.0064  Score=48.69  Aligned_cols=36  Identities=8%  Similarity=0.030  Sum_probs=30.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEecc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLSR   79 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~~   79 (162)
                      ...++++|++|.||||.|..+|-   ..|.++..+++-.
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlK   60 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIK   60 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEec
Confidence            45899999999999999998773   4588888888864

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.03  E-value=0.0015  Score=55.34  Aligned_cols=59  Identities=14%  Similarity=0.030  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhhc
Q psy4122          29 DWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        29 ~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL~   87 (162)
                      +....+..++.. +..|.-+.++||||||||+++.++|...         +..+.++.+....+++.|.
T Consensus        86 Tg~~~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~  154 (317)
T PRK04301         86 TGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE  154 (317)
T ss_pred             CCCHHHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH
Confidence            344556666653 4466678899999999999999998653         3356667665544454443

>KOG0927|consensus

Probab=97.03  E-value=0.0017  Score=59.34  Aligned_cols=49  Identities=14%  Similarity=0.266  Sum_probs=39.2

Q ss_pred             HhhcCcEEEEeCC-CCCCccHHHHHHHhhcCCeEEEcCCcEEecCcchHhhhhhh
Q psy4122         107 AAIEGRVLILEGI-EKAERNVLPVLNNLLENREMHLEDGRFLVSASTYDKLLQVE  160 (162)
Q Consensus       107 A~~~G~vlllDEI-d~a~~~v~~~L~~lle~r~l~l~~g~~i~~~~~f~~~~~~~  160 (162)
                      |++..++|+|||- |...-+..+.|...|.+     -+|..|..-++|+.+.|+.
T Consensus       524 ~~kqP~lLlLDEPtnhLDi~tid~laeaiNe-----~~Ggvv~vSHDfrlI~qVa  573 (614)
T KOG0927|consen  524 AVKQPHLLLLDEPTNHLDIETIDALAEAINE-----FPGGVVLVSHDFRLISQVA  573 (614)
T ss_pred             HhcCCcEEEecCCCcCCCchhHHHHHHHHhc-----cCCceeeeechhhHHHHHH
Confidence            4577899999998 77888889999988864     2466777777899999975

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.02  E-value=0.0018  Score=57.66  Aligned_cols=32  Identities=19%  Similarity=0.262  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      .++++|++|+|||+++..+|..+   |+.+..+.+
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~  131 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAA  131 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecC
Confidence            58999999999999999998765   455555544

>PRK13973 thymidylate kinase; Provisional

Probab=97.01  E-value=0.0012  Score=52.87  Aligned_cols=43  Identities=12%  Similarity=0.010  Sum_probs=31.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADI   86 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL   86 (162)
                      |.=+.+.|..||||||.++.+++.+   |.++.......++...++
T Consensus         3 g~~IviEG~dGsGKtTq~~~l~~~l~~~g~~~~~~~~p~~~~~g~~   48 (213)
T PRK13973          3 GRFITFEGGEGAGKSTQIRLLAERLRAAGYDVLVTREPGGSPGAEA   48 (213)
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEECCCCCchHHH
Confidence            4557889999999999999999988   777655544444334443

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.01  E-value=0.0005  Score=59.41  Aligned_cols=30  Identities=20%  Similarity=0.200  Sum_probs=25.2

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .+..|+-+.|.||.||||||+.+.+|.+..
T Consensus        25 ~i~~Gef~vllGPSGcGKSTlLr~IAGLe~   54 (338)
T COG3839          25 DIEDGEFVVLLGPSGCGKSTLLRMIAGLEE   54 (338)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            344578899999999999999999996643

>PRK06761 hypothetical protein; Provisional

Probab=97.00  E-value=0.00099  Score=56.22  Aligned_cols=31  Identities=13%  Similarity=0.149  Sum_probs=25.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      +-+++.|+|||||||+++.+++.++.....+
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~g~~v   34 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQNGIEV   34 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcCceEE
Confidence            4588999999999999999999887544333

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=97.00  E-value=0.0016  Score=58.57  Aligned_cols=59  Identities=12%  Similarity=0.192  Sum_probs=43.6

Q ss_pred             CHHHHHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHH--H-h-CCceEEEEeccCCChhhhc
Q psy4122          27 TQDWLSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLE--L-T-QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        27 ~~~~~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~--~-l-g~p~~~v~~~~~~~~~dL~   87 (162)
                      -++.+.-|-.++. .+..|..+++.|+||+|||+++.+++.  + . |.++.++++.  .+.++++
T Consensus        13 i~TGI~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~e--e~~~~i~   76 (509)
T PRK09302         13 LPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFE--ESPEDII   76 (509)
T ss_pred             ccCCchhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEcc--CCHHHHH
Confidence            4566777777875 455688899999999999999999874  2 2 6788888774  3455544

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.00  E-value=0.00098  Score=53.57  Aligned_cols=21  Identities=10%  Similarity=0.009  Sum_probs=19.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA   65 (162)
                      +-++|+||.|+|||++.+.++
T Consensus        30 ~~~~itGpNg~GKStlLk~i~   50 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVA   50 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            458999999999999999988

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

>PLN03130 ABC transporter C family member; Provisional

Probab=97.00  E-value=0.0031  Score=64.07  Aligned_cols=36  Identities=17%  Similarity=0.226  Sum_probs=30.5

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|+.+--....|+.+-++|++|+|||||++.+.+..
T Consensus      1254 VL~~is~~I~~GekVaIVGrSGSGKSTLl~lL~rl~ 1289 (1622)
T PLN03130       1254 VLHGLSFEISPSEKVGIVGRTGAGKSSMLNALFRIV 1289 (1622)
T ss_pred             eecceeEEEcCCCEEEEECCCCCCHHHHHHHHhCcC
Confidence            355666667789999999999999999999999765

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=96.99  E-value=0.00025  Score=59.16  Aligned_cols=30  Identities=17%  Similarity=0.112  Sum_probs=26.4

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +...|+-+.|.||.|||||||.+.++..+.
T Consensus        24 ~i~~G~i~~iiGpNG~GKSTLLk~l~g~l~   53 (258)
T COG1120          24 SIPKGEITGILGPNGSGKSTLLKCLAGLLK   53 (258)
T ss_pred             EecCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            445688999999999999999999998775

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=96.99  E-value=0.00064  Score=50.73  Aligned_cols=23  Identities=13%  Similarity=0.219  Sum_probs=20.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +++++|++|||||+|++++....
T Consensus         1 ~i~~vG~~~~GKstLi~~l~~~~   23 (167)
T cd04160           1 SVLILGLDNAGKTTFLEQLKTLF   23 (167)
T ss_pred             CEEEEecCCCCHHHHHHHHhhhc
Confidence            48899999999999999987654

Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=96.98  E-value=0.0021  Score=49.17  Aligned_cols=24  Identities=13%  Similarity=0.033  Sum_probs=20.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...+++||.|+|||++.++++-..
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i~~~~   45 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAIGLAL   45 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            378999999999999999987544

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.

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=96.98  E-value=0.0012  Score=53.84  Aligned_cols=56  Identities=18%  Similarity=0.250  Sum_probs=35.1

Q ss_pred             HHHHHHHHHhc-CCCCcEEEEcCCCchHHHHHHHHHHH--hCCce---EEEEeccCCChhhh
Q psy4122          31 LSHLRWILQKD-NMSQDVFLIGKPGSLRRSLAMSYLEL--TQREV---EYICLSRDTTEADI   86 (162)
Q Consensus        31 ~~~L~~i~~~~-~~g~~vlL~GppG~GKT~La~~lA~~--lg~p~---~~v~~~~~~~~~dL   86 (162)
                      ++.+.+.+... ...+.+.|+|++|+|||+||.++++.  ....+   ..+.+....+..++
T Consensus         5 ~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~   66 (287)
T PF00931_consen    5 IEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQL   66 (287)
T ss_dssp             HHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHH
T ss_pred             HHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccc
Confidence            44444444442 23447899999999999999999966  44433   34556554444443

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PRK06851 hypothetical protein; Provisional

Probab=96.98  E-value=0.0013  Score=57.39  Aligned_cols=49  Identities=16%  Similarity=0.262  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCC
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDT   81 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~   81 (162)
                      .+.+..++..  ..+-++|.|+||||||++++.++...   |..+.++.|..+-
T Consensus       203 ~s~~~~l~~~--~~~~~~i~G~pG~GKstl~~~i~~~a~~~G~~v~~~hC~~dP  254 (367)
T PRK06851        203 VDFVPSLTEG--VKNRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCGFDP  254 (367)
T ss_pred             HhhHHhHhcc--cceEEEEeCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCCCCC
Confidence            3344455532  23468999999999999999998765   8888888887553

>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=96.98  E-value=0.00067  Score=54.06  Aligned_cols=32  Identities=16%  Similarity=0.190  Sum_probs=23.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      .++|+||+|+||||.+-.+|+.+   ++.+..+++
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~   37 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLKGKKVALISA   37 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhccccceeecC
Confidence            57999999999999998888544   555555555

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 ....

>KOG0922|consensus

Probab=96.98  E-value=0.0029  Score=58.63  Aligned_cols=106  Identities=18%  Similarity=0.189  Sum_probs=58.5

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE-EEEecc-----CCC------------hhhhcc-eeEe
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE-YICLSR-----DTT------------EADIKQ-RREI   92 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~-~v~~~~-----~~~------------~~dL~g-~~~~   92 (162)
                      +.-..|+......+.++++|++||||||=+-++...-|..-. .+.|..     -++            ..+.+| ...+
T Consensus        54 ~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~IRF  133 (674)
T KOG0922|consen   54 KYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYTIRF  133 (674)
T ss_pred             HHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHHHHHHHHHHHHHhCCCcCceeeeEEEe
Confidence            333455555555778999999999999988887765554321 122210     001            111122 1112


Q ss_pred             ec---Ce---EEEeccHHHHHhh------cCcEEEEeCCCC--CCccHHHH-HHHhhcCC
Q psy4122          93 VN---GT---AIYYDQSAVRAAI------EGRVLILEGIEK--AERNVLPV-LNNLLENR  137 (162)
Q Consensus        93 ~~---G~---~~~~~gpl~~A~~------~G~vlllDEId~--a~~~v~~~-L~~lle~r  137 (162)
                      ++   .+   -...||-|++-+.      +=.+++|||.|.  .+.|++-. |..++.+|
T Consensus       134 ed~ts~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R  193 (674)
T KOG0922|consen  134 EDSTSKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLHTDILLGLLKKILKKR  193 (674)
T ss_pred             cccCCCceeEEEecchHHHHHHhcCCccccccEEEEechhhhhhHHHHHHHHHHHHHhcC
Confidence            11   22   2346788776543      227999999976  55565444 44455443

>KOG0736|consensus

Probab=96.98  E-value=0.00097  Score=63.02  Aligned_cols=33  Identities=18%  Similarity=0.151  Sum_probs=31.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .+||.|+||||||++++.+|..+|.++..+.|+
T Consensus       433 ~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~  465 (953)
T KOG0736|consen  433 SVLLHGPPGSGKTTVVRAVASELGLHLLEVDCY  465 (953)
T ss_pred             EEEEeCCCCCChHHHHHHHHHHhCCceEeccHH
Confidence            489999999999999999999999999988887

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.98  E-value=0.00086  Score=56.10  Aligned_cols=23  Identities=22%  Similarity=0.254  Sum_probs=18.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++|.|-||+|||++|+.++..+.
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~   26 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLE   26 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHH
Confidence            67889999999999999998753

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.96  E-value=0.0012  Score=51.26  Aligned_cols=34  Identities=21%  Similarity=0.119  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      |.-++|+|-+|+|||+||+++.+.+   |++++.+-.
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDg   38 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDG   38 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecC
Confidence            3458999999999999999999765   677665533

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.96  E-value=0.0014  Score=51.91  Aligned_cols=55  Identities=16%  Similarity=0.099  Sum_probs=36.4

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---C------CceEEEEeccCCChhhh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---Q------REVEYICLSRDTTEADI   86 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---g------~p~~~v~~~~~~~~~dL   86 (162)
                      ..|-.++. .+..|+-+.|.||||||||+++.++|...   +      ..+.++..........+
T Consensus         6 ~~lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl   70 (226)
T cd01393           6 KALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERL   70 (226)
T ss_pred             HHHHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHH
Confidence            34445554 34567789999999999999999998643   2      45555655443344343

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.

>PRK13808 adenylate kinase; Provisional

Probab=96.95  E-value=0.00078  Score=58.10  Aligned_cols=27  Identities=19%  Similarity=0.276  Sum_probs=24.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.||||+|||++++.+|..+|.+.
T Consensus         2 rIiv~GpPGSGK~T~a~~LA~~ygl~~   28 (333)
T PRK13808          2 RLILLGPPGAGKGTQAQRLVQQYGIVQ   28 (333)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCce
Confidence            489999999999999999999998764

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

Probab=96.94  E-value=0.0048  Score=47.96  Aligned_cols=34  Identities=9%  Similarity=-0.008  Sum_probs=27.2

Q ss_pred             cEEEEcCCCchHHHHHHHHH---HHhCCceEEEEecc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL---ELTQREVEYICLSR   79 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA---~~lg~p~~~v~~~~   79 (162)
                      -+.+++++|.||||+|..+|   ...|..+..+++-.
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~vQFlK   40 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGHGYRVGVVQFLK   40 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEEeC
Confidence            46778888999999999877   34588888888763

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=96.94  E-value=0.0011  Score=43.94  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=21.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |...+|.||.|+|||+|..++...+
T Consensus        23 g~~tli~G~nGsGKSTllDAi~~~L   47 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLLDAIQTVL   47 (62)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3468999999999999999988665

>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

Probab=96.94  E-value=0.00088  Score=52.06  Aligned_cols=25  Identities=24%  Similarity=0.263  Sum_probs=22.3

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +.+.|++||||||+++.+++.++..
T Consensus         2 I~ieG~~GsGKSTl~~~L~~~~~~~   26 (193)
T cd01673           2 IVVEGNIGAGKSTLAKELAEHLGYE   26 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCc
Confidence            6789999999999999999887754

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.93  E-value=0.0022  Score=62.82  Aligned_cols=111  Identities=10%  Similarity=0.129  Sum_probs=65.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChh-hhc---c--eeEeecC
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEA-DIK---Q--RREIVNG   95 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~-dL~---g--~~~~~~G   95 (162)
                      .+++.=.+.++.+.   ..+.-.+++|++|||||++.+.+.+.   .|+.+.-+..+  -... .|-   |  ..++..=
T Consensus       381 ~Ls~eQ~~Av~~i~---~~~r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApT--gkAA~~L~e~~Gi~a~TIas~  455 (1102)
T PRK13826        381 RLSDEQKTAIEHVA---GPARIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALA--GKAAEGLEKEAGIQSRTLSSW  455 (1102)
T ss_pred             CCCHHHHHHHHHHh---ccCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCc--HHHHHHHHHhhCCCeeeHHHH
Confidence            46666666666654   22456899999999999999988764   46554332221  1122 221   1  0011000


Q ss_pred             eEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC--CeEEEc
Q psy4122          96 TAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN--REMHLE  142 (162)
Q Consensus        96 ~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~--r~l~l~  142 (162)
                      ...|..+.  ..+..+.+||+||...++...+..|....+.  -.+.+-
T Consensus       456 ll~~~~~~--~~l~~~~vlVIDEAsMv~~~~m~~Ll~~~~~~garvVLV  502 (1102)
T PRK13826        456 ELRWNQGR--DQLDNKTVFVLDEAGMVASRQMALFVEAVTRAGAKLVLV  502 (1102)
T ss_pred             HhhhccCc--cCCCCCcEEEEECcccCCHHHHHHHHHHHHhcCCEEEEE
Confidence            01222221  1234567999999999999999998888863  355554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	162
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.74
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.56
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.54
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.54
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.51
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.51
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.51
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.5
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.47
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.46
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.46
3co5_A	143	Putative two-component system transcriptional RES	99.45
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.43
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.43
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.42
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.41
3f8t_A	506	Predicted ATPase involved in replication control,	99.41
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.4
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.39
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.36
3pvs_A	447	Replication-associated recombination protein A; ma	99.34
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	99.33
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	99.29
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.24
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.23
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.23
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.23
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.22
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.22
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.21
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.2
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.2
3bos_A	242	Putative DNA replication factor; P-loop containing	99.19
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.19
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.17
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.17
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.15
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.14
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.13
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.11
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.11
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.11
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.1
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.08
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.07
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.07
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.05
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.04
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.03
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.02
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.02
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.01
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.01
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.01
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.0
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.0
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.99
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.99
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.98
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.97
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.97
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.97
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.97
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.96
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.95
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.93
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.91
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.91
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.9
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.89
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.88
2qgz_A	308	Helicase loader, putative primosome component; str	98.87
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.86
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.85
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.85
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.85
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.85
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.84
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.82
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.8
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.79
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.78
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.77
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	98.72
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.66
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	98.63
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	98.63
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	98.6
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.59
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.57
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.56
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	98.55
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.48
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	98.47
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.46
2fna_A	357	Conserved hypothetical protein; structural genomic	98.45
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.33
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.29
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.25
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.2
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	98.19
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	98.17
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	98.15
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	98.15
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	98.15
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	98.12
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	98.09
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	98.08
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	98.05
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	98.05
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	98.05
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.01
1via_A	175	Shikimate kinase; structural genomics, transferase	98.01
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	98.0
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	97.99
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.97
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.95
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.93
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.93
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.92
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.92
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.91
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.91
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	97.9
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.89
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.89
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.88
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.88
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.88
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.87
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	97.87
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.86
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.86
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.85
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.85
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.84
2eyu_A	261	Twitching motility protein PILT; pilus retraction	97.84
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.81
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.81
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.8
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.8
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.8
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.79
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.79
2ewv_A	372	Twitching motility protein PILT; pilus retraction	97.78
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.78
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.78
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.76
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.76
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	97.75
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	97.75
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.74
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.74
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.73
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	97.72
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.72
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.71
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.7
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	97.7
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	97.69
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	97.69
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	97.68
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	97.68
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.68
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	97.65
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.64
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	97.62
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	97.62
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.61
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.61
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.61
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	97.6
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	97.59
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	97.59
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.58
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.58
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	97.56
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	97.55
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.55
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	97.55
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.54
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.51
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	97.51
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.51
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	97.51
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	97.51
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.51
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.5
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	97.49
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	97.47
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.47
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	97.45
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	97.45
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	97.44
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	97.43
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	97.42
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	97.41
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	97.4
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	97.4
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	97.39
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	97.39
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	97.39
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.38
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.38
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	97.38
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	97.37
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	97.36
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	97.36
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	97.35
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	97.35
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.33
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	97.32
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	97.3
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.3
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.3
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	97.3
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	97.29
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.28
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	97.27
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	97.26
1p9r_A	418	General secretion pathway protein E; bacterial typ	97.26
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	97.25
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	97.25
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	97.25
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	97.23
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	97.23
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.22
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	97.21
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	97.21
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.19
2r6a_A	454	DNAB helicase, replicative helicase; replication,	97.18
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.15
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	97.13
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	97.13
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	97.13
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	97.11
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.11
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	97.1
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.1
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.09
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	97.09
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	97.08
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	97.08
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	97.07
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	97.06
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	97.05
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	97.04
2hf9_A	226	Probable hydrogenase nickel incorporation protein	97.03
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.02
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	97.01
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.0
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	96.99
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.99
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	96.96
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.96
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	96.95
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.93
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	96.93
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	96.88
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	96.87
2ged_A	193	SR-beta, signal recognition particle receptor beta	96.87
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.87
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	96.86
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	96.86
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	96.86
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	96.85
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	96.85
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	96.85
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.85
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.84
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	96.83
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.82
3kta_A	182	Chromosome segregation protein SMC; structural mai	96.81
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.81
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	96.8
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.79
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	96.79
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	96.79
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.79
3io5_A	333	Recombination and repair protein; storage dimer, i	96.79
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	96.78
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	96.78
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	96.78
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.78
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	96.77
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	96.77
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.76
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	96.76
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.75
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.75
1b0u_A	262	Histidine permease; ABC transporter, transport pro	96.75
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	96.74
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.74
2wji_A	165	Ferrous iron transport protein B homolog; membrane	96.72
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	96.72
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	96.72
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.72
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	96.72
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.72
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.71
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.71
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.71
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	96.71
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	96.71
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	96.69
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	96.69
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	96.69
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	96.68
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	96.68
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	96.67
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	96.67
1g6h_A	257	High-affinity branched-chain amino acid transport	96.67
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	96.67
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.67
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	96.67
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	96.66
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	96.65
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	96.65
1ji0_A	240	ABC transporter; ATP binding protein, structural g	96.65
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	96.65
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	96.64
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	96.64
1nrj_B	218	SR-beta, signal recognition particle receptor beta	96.64
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	96.64
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	96.64
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	96.64
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	96.64
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	96.63
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.63
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.63
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	96.63
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.62
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	96.62
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	96.62
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.61
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	96.61
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	96.61
3h1t_A	590	Type I site-specific restriction-modification syst	96.6
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	96.6
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	96.59
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	96.59
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	96.59
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	96.58
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	96.58
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	96.58
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	96.57
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	96.57
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	96.57
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	96.57
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.56
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.56
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	96.56
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	96.56
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	96.55
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	96.55
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	96.54
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.53
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	96.53
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	96.53
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	96.53
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.52
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	96.52
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	96.52
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	96.51
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	96.51
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	96.51
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	96.51
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.5
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	96.5
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	96.5
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	96.5
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	96.49
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	96.49
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	96.49
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	96.49
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	96.49
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.48
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	96.48
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	96.48
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	96.48
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	96.47
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	96.46
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	96.46
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	96.45
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	96.45
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	96.44
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	96.43
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	96.43
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.43
2og2_A	359	Putative signal recognition particle receptor; nuc	96.43
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	96.42
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	96.42
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	96.41
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	96.41
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	96.41
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	96.4
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	96.4
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	96.4
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	96.39
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	96.39
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	96.39
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	96.39
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	96.38
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	96.38
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	96.38
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	96.38
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	96.38
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	96.38
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	96.37
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	96.37
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	96.36
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	96.36
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	96.36
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	96.36
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	96.36
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	96.36
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	96.35
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	96.35
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	96.34
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	96.34
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	96.34
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	96.34
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	96.33
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	96.33
3ice_A	422	Transcription termination factor RHO; transcriptio	96.32
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	96.32
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	96.32
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	96.32
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	96.32
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	96.32
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	96.32
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	96.32
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	96.29
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	96.29
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	96.29
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	96.29
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	96.27
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	96.25
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	96.25
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	96.25
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	96.24
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	96.24
2fh5_B	214	SR-beta, signal recognition particle receptor beta	96.24
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	96.24
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	96.24
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	96.23
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	96.21
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	96.21
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	96.21
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	96.19
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.18
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	96.18
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	96.18
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	96.18
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	96.17
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	96.17
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	96.16
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	96.15
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	96.15
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	96.15
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	96.14
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	96.13
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	96.13
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.13
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	96.12
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	96.11
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	96.11
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	96.1
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.09
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	96.09
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	96.08
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	96.08
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	96.06
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	96.06
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	96.06
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	96.06
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	96.05
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	96.02
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.02
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	96.02
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	95.99
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	95.98
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	95.98
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.97
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	95.95
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	95.95
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	95.94
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.93
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	95.92
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	95.92
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	95.89
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.88
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	95.88
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	95.88
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	95.87
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	95.86
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	95.86
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	95.86
3llu_A	196	RAS-related GTP-binding protein C; structural geno	95.86
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	95.85

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.74  E-value=8.2e-18  Score=139.14  Aligned_cols=94  Identities=11%  Similarity=0.172  Sum_probs=83.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEee--cCeEEEeccHHHHHhhcCcEEEEeCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIV--NGTAIYYDQSAVRAAIEGRVLILEGIEK  121 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~--~G~~~~~~gpl~~A~~~G~vlllDEId~  121 (162)
                      +.+++|+||||||||++|+.+|+.++.++..++++.+++.+++.|.....  .|.+.|.+|++     .+++++|||||+
T Consensus        46 ~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~~l~g~~~~~~~~~~~~~~~g~l-----~~~vl~iDEi~~  120 (331)
T 2r44_A           46 GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPSDLIGTMIYNQHKGNFEVKKGPV-----FSNFILADEVNR  120 (331)
T ss_dssp             TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHHEEEEEETTTTEEEEEECTT-----CSSEEEEETGGG
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChhhcCCceeecCCCCceEeccCcc-----cccEEEEEcccc
Confidence            67999999999999999999999999999999999999999999865543  46777888775     468999999999


Q ss_pred             CCccHHHHHHHhhcCCeEEEc
Q psy4122         122 AERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       122 a~~~v~~~L~~lle~r~l~l~  142 (162)
                      +++++++.|+++++++.+.+.
T Consensus       121 ~~~~~~~~Ll~~l~~~~~~~~  141 (331)
T 2r44_A          121 SPAKVQSALLECMQEKQVTIG  141 (331)
T ss_dssp             SCHHHHHHHHHHHHHSEEEET
T ss_pred             CCHHHHHHHHHHHhcCceeeC
Confidence            999999999999999987763

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.56  E-value=8.3e-15  Score=148.99  Aligned_cols=123  Identities=9%  Similarity=-0.005  Sum_probs=102.5

Q ss_pred             ccCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEE
Q psy4122          20 SVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIY   99 (162)
Q Consensus        20 ~~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~   99 (162)
                      +.+...+||.+.+....+..+...+.++++.||+|||||++++.+|+.+|+++.+++|+++++.+++-            
T Consensus       621 ~~~rlViTPltdr~~~tl~~Al~~~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg------------  688 (2695)
T 4akg_A          621 IPERLIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLS------------  688 (2695)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHH------------
T ss_pred             CCCcceecHHHHHHHHHHHHHHHhCCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhh------------
Confidence            34455679999999999999999999999999999999999999999999999999999999999883            


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhh-------cCCeEEEc-CCcEEecCcchHhh
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLL-------ENREMHLE-DGRFLVSASTYDKL  156 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~ll-------e~r~l~l~-~g~~i~~~~~f~~~  156 (162)
                        ..+..++..|.|+++||||+++++++++|.+.+       .++...++ +|+.+..+++|..+
T Consensus       689 --~~~~g~~~~Gaw~~~DE~nr~~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vf  751 (2695)
T 4akg_A          689 --RLLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVF  751 (2695)
T ss_dssp             --HHHHHHHHHTCEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEE
T ss_pred             --HHHHHHHhcCCEeeehhhhhcChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEE
Confidence              145667788999999999999999999994433       34443333 57777777777544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.54  E-value=2.7e-14  Score=105.82  Aligned_cols=94  Identities=19%  Similarity=0.135  Sum_probs=68.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ++.+.+..+.+......+.|++|+||||||||++|+.+++..   +.|+. ++|....+..++              .+.
T Consensus         7 s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~--------------~~~   71 (145)
T 3n70_A            7 SEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQL--------------NDF   71 (145)
T ss_dssp             SHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCH--------------HHH
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhh--------------hcH
Confidence            344444444444444567799999999999999999999876   77888 888643322111              122


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      +..  .++++|+||||++++++++..|..+++.+
T Consensus        72 ~~~--a~~g~l~ldei~~l~~~~q~~Ll~~l~~~  103 (145)
T 3n70_A           72 IAL--AQGGTLVLSHPEHLTREQQYHLVQLQSQE  103 (145)
T ss_dssp             HHH--HTTSCEEEECGGGSCHHHHHHHHHHHHSS
T ss_pred             HHH--cCCcEEEEcChHHCCHHHHHHHHHHHhhc
Confidence            322  37789999999999999999999999653

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.54  E-value=3.5e-14  Score=113.86  Aligned_cols=111  Identities=17%  Similarity=0.216  Sum_probs=75.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEeccCCC---hhhhccee-EeecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLSRDTT---EADIKQRR-EIVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~~~~~---~~dL~g~~-~~~~G~~~~   99 (162)
                      ++.+.+.++.+......+.+++|+||||||||++|+.++...+   .|+..++|+....   .+++.|.. ..-.|....
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~~~~~~~l~g~~~~~~~g~~~~   91 (265)
T 2bjv_A           12 ANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKR   91 (265)
T ss_dssp             CHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCHHHHHHHHHCCC---------C
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCChhHHHHHhcCCccccccccccc
Confidence            4444444444444444567999999999999999999998875   6788888874321   23344421 111233333


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      ..|.+..|  ++++|+||||++++++++..|..+++++.+
T Consensus        92 ~~~~l~~a--~~~~l~lDEi~~l~~~~q~~Ll~~l~~~~~  129 (265)
T 2bjv_A           92 HPGRFERA--DGGTLFLDELATAPMMVQEKLLRVIEYGEL  129 (265)
T ss_dssp             CCCHHHHT--TTSEEEEESGGGSCHHHHHHHHHHHHHCEE
T ss_pred             ccchhhhc--CCcEEEEechHhcCHHHHHHHHHHHHhCCe
Confidence            44555443  578999999999999999999999998764

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.51  E-value=7.3e-14  Score=115.32  Aligned_cols=100  Identities=13%  Similarity=0.202  Sum_probs=75.6

Q ss_pred             CHHHHHHHHHHHHhc----CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          27 TQDWLSHLRWILQKD----NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~----~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      .....+.++.++...    ....+++|+||||||||++|+++|+.++.++..+++.......++.               
T Consensus        34 ~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~~~~~~~~~~~~---------------   98 (338)
T 3pfi_A           34 QESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSANIKTTAAPMIEKSGDLA---------------   98 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEEGGGCCSHHHHH---------------
T ss_pred             hHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEecchhccchhHHH---------------
Confidence            356666666666543    2335899999999999999999999999998888876443333332               


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .......++++|+||||+.+++++++.|+.+++++.+.+
T Consensus        99 ~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~  137 (338)
T 3pfi_A           99 AILTNLSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDI  137 (338)
T ss_dssp             HHHHTCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC--
T ss_pred             HHHHhccCCCEEEEechhhcCHHHHHHHHHHHHhccchh
Confidence            223334578999999999999999999999999887544

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.51  E-value=6.5e-15  Score=132.66  Aligned_cols=93  Identities=16%  Similarity=0.288  Sum_probs=74.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEe--ecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREI--VNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~--~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      |+||+||||||||++|+++|+.++++...  .....+..++.+....  ..|...+..|++..|  +|++++|||||+++
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~~~--~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A--~~gil~IDEid~l~  404 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAVYT--TGKGSTAAGLTAAVVREKGTGEYYLEAGALVLA--DGGIAVIDEIDKMR  404 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEECC--CTTCSTTTTSEEECSSGGGTSSCSEEECHHHHH--SSSEECCTTTTCCC
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCceec--CCCccccccccceeeeccccccccccCCeeEec--CCCcEEeehhhhCC
Confidence            89999999999999999999999876432  3233455666653211  246677788888776  88999999999999


Q ss_pred             ccHHHHHHHhhcCCeEEEc
Q psy4122         124 RNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       124 ~~v~~~L~~lle~r~l~l~  142 (162)
                      +++++.|+++||++.+.+.
T Consensus       405 ~~~q~~Ll~~le~~~i~i~  423 (595)
T 3f9v_A          405 DEDRVAIHEAMEQQTVSIA  423 (595)
T ss_dssp             SHHHHHHHHHHHSSSEEEE
T ss_pred             HhHhhhhHHHHhCCEEEEe
Confidence            9999999999999998875

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.51  E-value=2.3e-14  Score=127.09  Aligned_cols=101  Identities=22%  Similarity=0.237  Sum_probs=72.9

Q ss_pred             HHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEeccCCChhhhcceeEe----ecCeE-EEeccHHHHHhh
Q psy4122          37 ILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR--EVEYICLSRDTTEADIKQRREI----VNGTA-IYYDQSAVRAAI  109 (162)
Q Consensus        37 i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~~~~~~~~dL~g~~~~----~~G~~-~~~~gpl~~A~~  109 (162)
                      +..+...+.|+||+||||||||++|+.+|..++.  ++..+.+. -+++++|+|....    ..|.+ .+..|++    .
T Consensus        34 l~~al~~~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~-~~t~~dL~G~~~~~~~~~~g~~~~~~~g~l----~  108 (500)
T 3nbx_X           34 CLLAALSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTR-FSTPEEVFGPLSIQALKDEGRYERLTSGYL----P  108 (500)
T ss_dssp             HHHHHHHTCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCT-TCCHHHHHCCBC----------CBCCTTSG----G
T ss_pred             HHHHHhcCCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHh-cCCHHHhcCcccHHHHhhchhHHhhhccCC----C
Confidence            3334445789999999999999999999998854  44444443 3478899884332    12333 2444442    2


Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      .+++|+||||+++++++++.|+.+++++.+.+.
T Consensus       109 ~~~IL~IDEI~r~~~~~q~~LL~~lee~~v~i~  141 (500)
T 3nbx_X          109 EAEIVFLDEIWKAGPAILNTLLTAINERQFRNG  141 (500)
T ss_dssp             GCSEEEEESGGGCCHHHHHHHHHHHHSSEEECS
T ss_pred             cceeeeHHhHhhhcHHHHHHHHHHHHHHhccCC
Confidence            467999999999999999999999999988763

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.50  E-value=2e-14  Score=116.86  Aligned_cols=112  Identities=14%  Similarity=0.205  Sum_probs=78.9

Q ss_pred             HHHHHHHHHHHHhcCC--------CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeEee
Q psy4122          28 QDWLSHLRWILQKDNM--------SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRREIV   93 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~--------g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~~~   93 (162)
                      ...++.+...+.....        ..+++|+||||||||++|+.+|+.+   +.++..+.|.....   .++++|..   
T Consensus        23 ~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~---   99 (311)
T 4fcw_A           23 DEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAP---   99 (311)
T ss_dssp             HHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHHHHHHCCC---
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccHHHhcCCC---
Confidence            3455555555544321        2479999999999999999999987   55678888864332   44555521   


Q ss_pred             cCeEEEec-cHHHHHhh--cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122          94 NGTAIYYD-QSAVRAAI--EGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus        94 ~G~~~~~~-gpl~~A~~--~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      .+...+.. +.+..++.  .+++++|||++++++++++.|+.+++++.+...
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~le~~~~~~~  151 (311)
T 4fcw_A          100 PGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAHPDVFNILLQMLDDGRLTDS  151 (311)
T ss_dssp             TTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSCHHHHHHHHHHHHHSEEECT
T ss_pred             CccccccccchHHHHHHhCCCeEEEEeChhhcCHHHHHHHHHHHhcCEEEcC
Confidence            22222222 46666665  457999999999999999999999999887643

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.47  E-value=5.5e-14  Score=115.83  Aligned_cols=97  Identities=16%  Similarity=0.223  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC-------ce------------------------EEEEeccCCChhhhcceeEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR-------EV------------------------EYICLSRDTTEADIKQRREI   92 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~-------p~------------------------~~v~~~~~~~~~dL~g~~~~   92 (162)
                      ..++||+||||||||++|+.+|+.++.       ++                        ..+......+.+++.|...+
T Consensus        45 ~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~  124 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDI  124 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECH
T ss_pred             CceEEEECCCCccHHHHHHHHHHhCccccccccccccccccccccchhhhhccccccCCCcccccCCCcchhhheeechh
Confidence            458999999999999999999998874       21                        12222333445566653211


Q ss_pred             ----ecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122          93 ----VNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus        93 ----~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                          .++...+.+|.+..|  ++++|+||||+++++++++.|+.+++++...+.
T Consensus       125 ~~~~~~~~~~~~~g~~~~a--~~~vl~iDEi~~l~~~~~~~Ll~~le~~~~~~~  176 (350)
T 1g8p_A          125 ERAISKGEKAFEPGLLARA--NRGYLYIDECNLLEDHIVDLLLDVAQSGENVVE  176 (350)
T ss_dssp             HHHHHHCGGGEECCHHHHH--TTEEEEETTGGGSCHHHHHHHHHHHHHSEEEEC
T ss_pred             hhhhcCCceeecCceeeec--CCCEEEEeChhhCCHHHHHHHHHHHhcCceEEE
Confidence                234455667776555  688999999999999999999999998875553

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.46  E-value=7.6e-14  Score=127.49  Aligned_cols=97  Identities=20%  Similarity=0.262  Sum_probs=75.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC---hhhhcceeEeecCeEEEec-cHHHHHhhc--CcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT---EADIKQRREIVNGTAIYYD-QSAVRAAIE--GRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~---~~dL~g~~~~~~G~~~~~~-gpl~~A~~~--G~vlllDEI  119 (162)
                      ++||+||||||||++|+.+|+.++.++.+++|+..++   .++++|.+   .|.+.+.. +.+..+++.  +++|+||||
T Consensus       490 ~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~~~l~g~~---~g~~g~~~~~~l~~~~~~~~~~vl~lDEi  566 (758)
T 1r6b_X          490 SFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAP---PGYVGFDQGGLLTDAVIKHPHAVLLLDEI  566 (758)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCC---SCSHHHHHTTHHHHHHHHCSSEEEEEETG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhHhhhcCCC---CCCcCccccchHHHHHHhCCCcEEEEeCc
Confidence            6999999999999999999999999999999985543   46666642   23222222 234555543  579999999


Q ss_pred             CCCCccHHHHHHHhhcCCeEEEcCCc
Q psy4122         120 EKAERNVLPVLNNLLENREMHLEDGR  145 (162)
Q Consensus       120 d~a~~~v~~~L~~lle~r~l~l~~g~  145 (162)
                      +++++++++.|+++||++.++...|+
T Consensus       567 ~~~~~~~~~~Ll~~le~~~~~~~~g~  592 (758)
T 1r6b_X          567 EKAHPDVFNILLQVMDNGTLTDNNGR  592 (758)
T ss_dssp             GGSCHHHHHHHHHHHHHSEEEETTTE
T ss_pred             cccCHHHHHHHHHHhcCcEEEcCCCC
Confidence            99999999999999999988765553

>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=99.46  E-value=2.2e-13  Score=111.33  Aligned_cols=101  Identities=18%  Similarity=0.218  Sum_probs=77.2

Q ss_pred             CHHHHHHHHHHHHhc----CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          27 TQDWLSHLRWILQKD----NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~----~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      .....+.++..+...    ....+++|+||||||||++|+++|+.++.++..+++.......++.+              
T Consensus        17 ~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~~l~~--------------   82 (324)
T 1hqc_A           17 QERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAA--------------   82 (324)
T ss_dssp             CHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCSHHHHHH--------------
T ss_pred             HHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCChHHHHH--------------
Confidence            345556666555432    24468999999999999999999999999988887765545555543              


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .+..++.++++|+||||+.++++.++.|..+++++.+.+
T Consensus        83 ~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~  121 (324)
T 1hqc_A           83 ILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDI  121 (324)
T ss_dssp             HHTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEE
T ss_pred             HHHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHH
Confidence            122235678899999999999999999999999887654

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.45  E-value=4e-14  Score=104.83  Aligned_cols=88  Identities=17%  Similarity=0.159  Sum_probs=62.8

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhc
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIE  110 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~  110 (162)
                      +.++..+. ....+.|++|+||||||||++|+.++...+ |+..++|...  .+++             ..+.+.  ..+
T Consensus        14 ~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~--~~~~-------------~~~~~~--~a~   75 (143)
T 3co5_A           14 QEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEY--LIDM-------------PMELLQ--KAE   75 (143)
T ss_dssp             HHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTH--HHHC-------------HHHHHH--HTT
T ss_pred             HHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhC--ChHh-------------hhhHHH--hCC
Confidence            33444433 234567999999999999999999998877 6665555311  1121             122222  235


Q ss_pred             CcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         111 GRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       111 G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      +++++||||+.++++++..|..+++++
T Consensus        76 ~~~l~lDei~~l~~~~q~~Ll~~l~~~  102 (143)
T 3co5_A           76 GGVLYVGDIAQYSRNIQTGITFIIGKA  102 (143)
T ss_dssp             TSEEEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             CCeEEEeChHHCCHHHHHHHHHHHHhC
Confidence            789999999999999999999999865

>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=99.43  E-value=5.5e-13  Score=107.69  Aligned_cols=97  Identities=13%  Similarity=0.158  Sum_probs=64.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeE--eecCeEEEeccHHHHHhhcCcEEEEeCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRRE--IVNGTAIYYDQSAVRAAIEGRVLILEGIE  120 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~--~~~G~~~~~~gpl~~A~~~G~vlllDEId  120 (162)
                      ...+++|+||||||||++|+.+|+.++.++..+++....+. .+.+...  ....-+....|.+ .....+++|+|||++
T Consensus        49 ~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~vl~iDEi~  126 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEV-GYVGKEVDSIIRDLTDSAGGAI-DAVEQNGIVFIDEID  126 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSC-CSGGGSTTHHHHHHHHTTTTCH-HHHHHHCEEEEECGG
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccC-CccCccHHHHHHHHHHHhhHHH-hhccCCCEEEEEChh
Confidence            35689999999999999999999999999888888643221 1111000  0000000000111 112346899999999


Q ss_pred             CCCccH------------HHHHHHhhcCCeEEE
Q psy4122         121 KAERNV------------LPVLNNLLENREMHL  141 (162)
Q Consensus       121 ~a~~~v------------~~~L~~lle~r~l~l  141 (162)
                      +++++.            ++.|++++|++.+..
T Consensus       127 ~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~  159 (310)
T 1ofh_A          127 KICKKGEYSGADVSREGVQRDLLPLVEGSTVST  159 (310)
T ss_dssp             GGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEE
T ss_pred             hcCccccccccchhHHHHHHHHHHHhcCCeEec
Confidence            999886            899999999876544

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.43  E-value=4.6e-13  Score=110.94  Aligned_cols=111  Identities=16%  Similarity=0.176  Sum_probs=75.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+........+++|+||||||||++|+.++...   +.|+..++|....+   .++|.|... .-.|...-
T Consensus         8 s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~~~lfg~~~g~~tg~~~~   87 (304)
T 1ojl_A            8 SPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKR   87 (304)
T ss_dssp             SHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHHHHHHHHTCCCSSCCC---CC
T ss_pred             CHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChHHHHHHhcCccccccCchhhh
Confidence            444444444444444456799999999999999999999865   67888898874322   234444210 00121112


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      ..|.+..|  ++++|+||||+.++++++..|+.+++++.+
T Consensus        88 ~~g~~~~a--~~g~L~LDEi~~l~~~~q~~Ll~~l~~~~~  125 (304)
T 1ojl_A           88 REGRFVEA--DGGTLFLDEIGDISPLMQVRLLRAIQEREV  125 (304)
T ss_dssp             CCCHHHHH--TTSEEEEESCTTCCHHHHHHHHHHHHSSBC
T ss_pred             hcCHHHhc--CCCEEEEeccccCCHHHHHHHHHHHhcCEe
Confidence            33444433  678999999999999999999999998875

>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=99.42  E-value=3.1e-13  Score=113.82  Aligned_cols=89  Identities=18%  Similarity=0.238  Sum_probs=60.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH---------hhcCcEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA---------AIEGRVL  114 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A---------~~~G~vl  114 (162)
                      ..+++|+||||||||++|+.+|+.++.|+..+++... +.+.+.|.      .   ..+.+..+         ...++++
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l~~~~~~~~~~~~-~~~~~~g~------~---~~~~~~~~~~~~~~~~~~~~~~vl  141 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSL-TEAGYVGE------D---VENILTRLLQASDWNVQKAQKGIV  141 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGC-C-----------------CTHHHHHHHHHTTTCHHHHTTSEE
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhCCCEEEecchhh-hhcCcCCc------c---HHHHHHHHHhhccchhhhcCCeEE
Confidence            4589999999999999999999999999988877632 22223221      0   01112111         1257899


Q ss_pred             EEeCCCCCCcc--------------HHHHHHHhhcCCeEEEc
Q psy4122         115 ILEGIEKAERN--------------VLPVLNNLLENREMHLE  142 (162)
Q Consensus       115 llDEId~a~~~--------------v~~~L~~lle~r~l~l~  142 (162)
                      +||||++++++              +++.|+.+||++.+.++
T Consensus       142 ~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~  183 (376)
T 1um8_A          142 FIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIP  183 (376)
T ss_dssp             EEETGGGC--------------CHHHHHHHHHHHHCCEEC--
T ss_pred             EEcCHHHHhhhcCCCceecccchHHHHHHHHHHhhccceecc
Confidence            99999999998              99999999998876554

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=99.41  E-value=1.5e-14  Score=121.49  Aligned_cols=90  Identities=20%  Similarity=0.220  Sum_probs=63.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH---------hhcCcE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA---------AIEGRV  113 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A---------~~~G~v  113 (162)
                      .+.+++|+||||||||++|+++|+.++.|+..+++..- ..+++.|..   .      .+.+..+         ...+++
T Consensus        50 ~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l-~~~~~~g~~---~------~~~~~~~~~~~~~~~~~~~~~v  119 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTL-TEAGYVGED---V------ENIIQKLLQKCDYDVQKAQRGI  119 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH-TTCHHHHHH---H------THHHHHHHHHTTTCHHHHHHCE
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHh-ccccccccc---H------HHHHHHHHHHhhhhHHhcCCcE
Confidence            45689999999999999999999999999988888632 222333310   0      0111111         135689


Q ss_pred             EEEeCCCCCCcc--------------HHHHHHHhhcCCeEEEc
Q psy4122         114 LILEGIEKAERN--------------VLPVLNNLLENREMHLE  142 (162)
Q Consensus       114 lllDEId~a~~~--------------v~~~L~~lle~r~l~l~  142 (162)
                      |+||||++++++              +++.|+++||++...++
T Consensus       120 l~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~  162 (363)
T 3hws_A          120 VYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVP  162 (363)
T ss_dssp             EEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC-----
T ss_pred             EEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeecc
Confidence            999999999988              99999999995555443

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=99.41  E-value=6.3e-13  Score=117.64  Aligned_cols=93  Identities=22%  Similarity=0.228  Sum_probs=73.8

Q ss_pred             cEEEEcCCCchHHHHHHHH-HHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSY-LELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAER  124 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~l-A~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~  124 (162)
                      |+||+|+||| ||.+++.+ +....+- .+. .....+..+|.+...-.+| +.++.|++..|  +||++++||||++++
T Consensus       241 hVLL~G~PGt-KS~Lar~i~~~i~pR~-~ft-~g~~ss~~gLt~s~r~~tG-~~~~~G~l~LA--dgGvl~lDEIn~~~~  314 (506)
T 3f8t_A          241 HVLLAGYPVV-CSEILHHVLDHLAPRG-VYV-DLRRTELTDLTAVLKEDRG-WALRAGAAVLA--DGGILAVDHLEGAPE  314 (506)
T ss_dssp             CEEEESCHHH-HHHHHHHHHHHTCSSE-EEE-EGGGCCHHHHSEEEEESSS-EEEEECHHHHT--TTSEEEEECCTTCCH
T ss_pred             eEEEECCCCh-HHHHHHHHHHHhCCCe-EEe-cCCCCCccCceEEEEcCCC-cccCCCeeEEc--CCCeeehHhhhhCCH
Confidence            8999999999 99999999 7776543 222 2223345667765111257 88999998776  899999999999999


Q ss_pred             cHHHHHHHhhcCCeEEEcCCc
Q psy4122         125 NVLPVLNNLLENREMHLEDGR  145 (162)
Q Consensus       125 ~v~~~L~~lle~r~l~l~~g~  145 (162)
                      ++++.|++.||++++++. |.
T Consensus       315 ~~qsaLlEaMEe~~VtI~-G~  334 (506)
T 3f8t_A          315 PHRWALMEAMDKGTVTVD-GI  334 (506)
T ss_dssp             HHHHHHHHHHHHSEEEET-TE
T ss_pred             HHHHHHHHHHhCCcEEEC-CE
Confidence            999999999999999887 54

>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=99.40  E-value=3.1e-13  Score=125.54  Aligned_cols=93  Identities=17%  Similarity=0.242  Sum_probs=67.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeEeecCeEEEec-cHHHHHhhc--CcEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRREIVNGTAIYYD-QSAVRAAIE--GRVLIL  116 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~~~~G~~~~~~-gpl~~A~~~--G~vlll  116 (162)
                      +++|+||||||||++|+.+|..+   +.++.+++|+.-++   .+.++|.+   .|.+.+.. |.+..+++.  +++|+|
T Consensus       590 ~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~s~l~g~~---~~~~G~~~~g~l~~~~~~~~~~vl~l  666 (854)
T 1qvr_A          590 SFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAP---PGYVGYEEGGQLTEAVRRRPYSVILF  666 (854)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC-----------------CHHHHHHHCSSEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHHHHHcCCC---CCCcCccccchHHHHHHhCCCeEEEE
Confidence            79999999999999999999988   77888888864332   34555532   34444444 567777643  679999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         117 EGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      |||+++++++++.|+++||++.+.-
T Consensus       667 DEi~~l~~~~~~~Ll~~l~~~~~~~  691 (854)
T 1qvr_A          667 DEIEKAHPDVFNILLQILDDGRLTD  691 (854)
T ss_dssp             SSGGGSCHHHHHHHHHHHTTTEECC
T ss_pred             ecccccCHHHHHHHHHHhccCceEC
Confidence            9999999999999999999998763

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.39  E-value=5.3e-13  Score=122.28  Aligned_cols=86  Identities=21%  Similarity=0.275  Sum_probs=63.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh--cCcEEEEeCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI--EGRVLILEGIE  120 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~--~G~vlllDEId  120 (162)
                      ++||+||||||||++|+++|+.+   +.++.+++|+.-++....      .       .|.+..+++  .+++|+||||+
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~------~-------~~~l~~~~~~~~~~vl~lDEi~  589 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHST------S-------GGQLTEKVRRKPYSVVLLDAIE  589 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCC------C----------CHHHHHHCSSSEEEEECGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccccccc------c-------cchhhHHHHhCCCeEEEEeCcc
Confidence            59999999999999999999987   678888888643322111      1       234555554  45799999999


Q ss_pred             CCCccHHHHHHHhhcCCeEEEcCC
Q psy4122         121 KAERNVLPVLNNLLENREMHLEDG  144 (162)
Q Consensus       121 ~a~~~v~~~L~~lle~r~l~l~~g  144 (162)
                      ++++++++.|+++||++.+...+|
T Consensus       590 ~~~~~~~~~Ll~~le~g~~~~~~g  613 (758)
T 3pxi_A          590 KAHPDVFNILLQVLEDGRLTDSKG  613 (758)
T ss_dssp             GSCHHHHHHHHHHHHHSBCC----
T ss_pred             ccCHHHHHHHHHHhccCeEEcCCC
Confidence            999999999999999988765433

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.36  E-value=1.1e-12  Score=133.58  Aligned_cols=129  Identities=12%  Similarity=0.215  Sum_probs=100.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEec-cCCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLS-RDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~-~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      ++..+..+..+.+....+++++|+||||||||++++.+|+.+    +.+.....++ ..++..+|.|.  +...+..|.|
T Consensus       906 ~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~La~al~~l~~~~~~~~~inpk~~t~~el~G~--~d~~t~eW~D  983 (2695)
T 4akg_A          906 SEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGS--MLKATLEWRD  983 (2695)
T ss_dssp             CHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEEEECTTTSCHHHHTTE--ECTTTCCEEC
T ss_pred             cHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEeCCCCCCHHHhcce--ecCCCCeEec
Confidence            344444333444444456789999999999999999999775    5555555666 45688999985  3344558999


Q ss_pred             cHHHHHhhc------------CcEEEEeCCCCCCccHHHHHHHhhcC-CeEEEcCCcEEecCcchHhhhhh
Q psy4122         102 QSAVRAAIE------------GRVLILEGIEKAERNVLPVLNNLLEN-REMHLEDGRFLVSASTYDKLLQV  159 (162)
Q Consensus       102 gpl~~A~~~------------G~vlllDEId~a~~~v~~~L~~lle~-r~l~l~~g~~i~~~~~f~~~~~~  159 (162)
                      |.++.++|+            +.|+++|  .-+++..++.||++||+ +.|.|++|++|..+++++++--+
T Consensus       984 Gils~~~R~~~~~~~~~~~~~~~WivfD--G~vD~~WIE~LNsVLDDNk~L~L~ngErI~l~~~~~llFEv 1052 (2695)
T 4akg_A          984 GLFTSILRRVNDDITGTFKNSRIWVVFD--SDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNFRILFET 1052 (2695)
T ss_dssp             CSHHHHHHHHHTCCCSSCSSEEEEEEEC--SCCCHHHHHTTHHHHSTTCEEECSSSCEEECCSSCEEEEEE
T ss_pred             ChHHHHHHHHHhccccccCCCCeEEEEC--CCCCHHHHHHHHHHhcCCCccccCCCCEEecCCCcEEEEEe
Confidence            999999875            4699999  88899999999999985 67899999999999999887433

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.34  E-value=2.7e-12  Score=112.05  Aligned_cols=94  Identities=17%  Similarity=0.300  Sum_probs=65.9

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH----
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA----  107 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A----  107 (162)
                      ..|+.++..... .+++|+||||||||++|+.+|+.++.++..+++. .....++..              .+..|    
T Consensus        39 ~~L~~~i~~~~~-~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~-~~~~~~ir~--------------~~~~a~~~~  102 (447)
T 3pvs_A           39 KPLPRAIEAGHL-HSMILWGPPGTGKTTLAEVIARYANADVERISAV-TSGVKEIRE--------------AIERARQNR  102 (447)
T ss_dssp             SHHHHHHHHTCC-CEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETT-TCCHHHHHH--------------HHHHHHHHH
T ss_pred             HHHHHHHHcCCC-cEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEec-cCCHHHHHH--------------HHHHHHHhh
Confidence            677777776544 4899999999999999999999999988777653 233444332              11111    


Q ss_pred             -hhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         108 -AIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       108 -~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                       ...+++|+||||++++.+.++.|+..+|++.+.+
T Consensus       103 ~~~~~~iLfIDEI~~l~~~~q~~LL~~le~~~v~l  137 (447)
T 3pvs_A          103 NAGRRTILFVDEVHRFNKSQQDAFLPHIEDGTITF  137 (447)
T ss_dssp             HTTCCEEEEEETTTCC------CCHHHHHTTSCEE
T ss_pred             hcCCCcEEEEeChhhhCHHHHHHHHHHHhcCceEE
Confidence             2356899999999999999999999999987654

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=99.33  E-value=4.2e-12  Score=130.57  Aligned_cols=123  Identities=13%  Similarity=0.035  Sum_probs=96.9

Q ss_pred             ecccCCCCCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeE
Q psy4122          18 LFSVNTDALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        18 ~~~~~~~~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~   97 (162)
                      +=+.+.+.+||-+-+.-.-+..++..+....+.||+|||||.+++.+|+.+|+++..++|+..++...+ |+        
T Consensus       578 lG~~~rLViTPLTdrcy~tl~~Al~~~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~-g~--------  648 (3245)
T 3vkg_A          578 LGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAM-SR--------  648 (3245)
T ss_dssp             CCSCCCCCCCHHHHHHHHHHHHHHHTTCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHH-HH--------
T ss_pred             CCCCCCCcCChHHHHHHHHHHHHHHhcCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHH-HH--------
Confidence            334445567999999999999999888889999999999999999999999999999999999888765 21        


Q ss_pred             EEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc---------CCeEEEcCCcEEecCcchH
Q psy4122          98 IYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE---------NREMHLEDGRFLVSASTYD  154 (162)
Q Consensus        98 ~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle---------~r~l~l~~g~~i~~~~~f~  154 (162)
                           -+..++..|.|..+|||||+++++++++.+.+.         .+++.+.+|+.|..+++|.
T Consensus       649 -----i~~G~~~~GaW~cfDEfNrl~~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~  709 (3245)
T 3vkg_A          649 -----IFVGLCQCGAWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMG  709 (3245)
T ss_dssp             -----HHHHHHHHTCEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCE
T ss_pred             -----HHhhHhhcCcEEEehhhhcCCHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeE
Confidence                 234466789999999999999999999888665         4455555454444444443

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=99.29  E-value=1.3e-12  Score=134.24  Aligned_cols=130  Identities=15%  Similarity=0.152  Sum_probs=94.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHH-HHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEec--c
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMS-YLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYD--Q  102 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~-lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~--g  102 (162)
                      +|..+.+....+-.....++|+||+||||||||.++.. +++..+.++..++++..|+++++.+... ......|.+  |
T Consensus      1286 PT~DTvR~~~ll~~ll~~~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta~~l~~~~e-~~~e~~~~~~~G 1364 (3245)
T 3vkg_A         1286 PTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFD-HHCEYKRTPSGE 1364 (3245)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCHHHHHHHHH-HHEEEEECTTSC
T ss_pred             cchHHHHHHHHHHHHHHCCCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCHHHHHHHHh-hcceEEeccCCC
Confidence            57777777776666666789999999999999988765 4445577788899999999988876321 112334443  5


Q ss_pred             HHHHHhhcCc--EEEEeCCCCCCcc------HHHHHHHhhcCCeEEEcCCcEEecCcchHhh
Q psy4122         103 SAVRAAIEGR--VLILEGIEKAERN------VLPVLNNLLENREMHLEDGRFLVSASTYDKL  156 (162)
Q Consensus       103 pl~~A~~~G~--vlllDEId~a~~~------v~~~L~~lle~r~l~l~~g~~i~~~~~f~~~  156 (162)
                      ++..+...|.  |+++||||.+.++      +++.|++++|.|.+..+.+...+...+|+++
T Consensus      1365 ~~~~p~~~Gk~~VlFiDDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~v 1426 (3245)
T 3vkg_A         1365 TVLRPTQLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFV 1426 (3245)
T ss_dssp             EEEEESSTTCEEEEEETTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEE
T ss_pred             cccCCCcCCceEEEEecccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEE
Confidence            5555555564  6678999998887      9999999999999988754444455666554

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.24  E-value=1e-11  Score=111.40  Aligned_cols=110  Identities=15%  Similarity=0.197  Sum_probs=73.1

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce-EE--EEec--------------------------
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV-EY--ICLS--------------------------   78 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~-~~--v~~~--------------------------   78 (162)
                      ...++.+...+.   .+++++|+||||||||++++.+|..++... ..  +.++                          
T Consensus        47 ~~~l~~l~~~i~---~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~~~~~~~~~~~~~~p~i~~~p~g~~~~~~e~~~~  123 (604)
T 3k1j_A           47 EHAVEVIKTAAN---QKRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVPACQGRRIVEKYRE  123 (604)
T ss_dssp             HHHHHHHHHHHH---TTCCEEEECCTTSSHHHHHHHHHHTSCCSSCEEEEEECCTTCTTSCEEEEEETTHHHHHHHHHHH
T ss_pred             hhhHhhcccccc---CCCEEEEEeCCCCCHHHHHHHHhccCCcccCCeEEEeCCcccccCCcEEEEecchHHHHHHHHHH
Confidence            444555554444   578999999999999999999999886442 11  1110                          


Q ss_pred             ---------------------------------------cCCChhhhcceeEee----cC-----eEEEeccHHHHHhhc
Q psy4122          79 ---------------------------------------RDTTEADIKQRREIV----NG-----TAIYYDQSAVRAAIE  110 (162)
Q Consensus        79 ---------------------------------------~~~~~~dL~g~~~~~----~G-----~~~~~~gpl~~A~~~  110 (162)
                                                             ...+..+|+|.....    +|     ......|.+..  .+
T Consensus       124 ~~~~~~~~r~~~~~~~~~~~~~nl~v~~~~~~~~~~v~~~~~~~~~L~G~~~~~~~~~g~~~~g~~~~i~~g~~~~--a~  201 (604)
T 3k1j_A          124 KAKSQESVKSSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLGTPAHERVEPGMIHR--AH  201 (604)
T ss_dssp             HHHHHTCC-----------CCCEEEECCTTCSSCCEEECTTCCHHHHHCEECCCCC----CCCCGGGGEECCHHHH--TT
T ss_pred             hhccchhhhhhcccccccccccceeeccccCCCCCEEEcCCCCHHhcCceEEechhhcCCccccccccccCceeee--cC
Confidence                                                   022233444422110    11     11134555544  37


Q ss_pred             CcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         111 GRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       111 G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      |++|+|||++++++++++.|+.+|+++.+.+.
T Consensus       202 ~gvL~LDEi~~l~~~~q~~Ll~~Le~~~~~~~  233 (604)
T 3k1j_A          202 KGVLFIDEIATLSLKMQQSLLTAMQEKKFPIT  233 (604)
T ss_dssp             TSEEEETTGGGSCHHHHHHHHHHHHHSEECCB
T ss_pred             CCEEEEechhhCCHHHHHHHHHHHHcCcEEec
Confidence            89999999999999999999999999998764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.23  E-value=7e-12  Score=101.85  Aligned_cols=85  Identities=19%  Similarity=0.280  Sum_probs=55.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCC-------ceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQR-------EVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLI  115 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~-------p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vll  115 (162)
                      .+.+++|+||||||||++|+.+|+.++.       ++..+++      +++.+..  .+.......+.+..  ..+++|+
T Consensus        66 ~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~------~~l~~~~--~g~~~~~~~~~~~~--~~~~vl~  135 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTR------DDLVGQY--IGHTAPKTKEVLKR--AMGGVLF  135 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECG------GGTCCSS--TTCHHHHHHHHHHH--HTTSEEE
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcH------HHhhhhc--ccccHHHHHHHHHh--cCCCEEE
Confidence            3457999999999999999999988743       5544443      2332210  01000001112222  2578999


Q ss_pred             EeCCCCC---------CccHHHHHHHhhcCC
Q psy4122         116 LEGIEKA---------ERNVLPVLNNLLENR  137 (162)
Q Consensus       116 lDEId~a---------~~~v~~~L~~lle~r  137 (162)
                      |||++.+         ++++++.|+.+++++
T Consensus       136 iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~  166 (309)
T 3syl_A          136 IDEAYYLYRPDNERDYGQEAIEILLQVMENN  166 (309)
T ss_dssp             EETGGGSCCCC---CCTHHHHHHHHHHHHHC
T ss_pred             EEChhhhccCCCcccccHHHHHHHHHHHhcC
Confidence            9999976         788999999999865

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=99.23  E-value=3.2e-12  Score=113.83  Aligned_cols=92  Identities=23%  Similarity=0.267  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH----HHHHhhcCcEEEEeC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS----AVRAAIEGRVLILEG  118 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp----l~~A~~~G~vlllDE  118 (162)
                      .+.+++|+||||||||++++.+|..++.++..+++....+.+++.+.....-|   ...+.    +..|...+++++|||
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g~~~~~ig---~~~~~~~~~~~~a~~~~~vl~lDE  183 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRGHRRTYVG---AMPGRIIQGMKKAGKLNPVFLLDE  183 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC-----------------------CHHHHHHTTCSSSEEEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhhHHHHHhc---cCchHHHHHHHHhhccCCEEEEhh
Confidence            46789999999999999999999999999888888765555555542111001   11222    333444677999999


Q ss_pred             CCCCCcc----HHHHHHHhhcCC
Q psy4122         119 IEKAERN----VLPVLNNLLENR  137 (162)
Q Consensus       119 Id~a~~~----v~~~L~~lle~r  137 (162)
                      |++++++    .++.|+++||..
T Consensus       184 id~l~~~~~~~~~~~LL~~ld~~  206 (543)
T 3m6a_A          184 IDKMSSDFRGDPSSAMLEVLDPE  206 (543)
T ss_dssp             SSSCC---------CCGGGTCTT
T ss_pred             hhhhhhhhccCHHHHHHHHHhhh
Confidence            9999998    568899998754

>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=99.23  E-value=4.3e-11  Score=98.24  Aligned_cols=97  Identities=11%  Similarity=0.150  Sum_probs=71.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSA  104 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl  104 (162)
                      .-.+...+.++.++........+++.||||||||++++.+|+.++.++..+++.. ....++..              .+
T Consensus        29 vg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~~-~~~~~i~~--------------~~   93 (324)
T 3u61_B           29 ILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSD-CKIDFVRG--------------PL   93 (324)
T ss_dssp             CCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETTT-CCHHHHHT--------------HH
T ss_pred             hCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEcccc-cCHHHHHH--------------HH
Confidence            3457788888888886555545677788999999999999999998887777642 22333321              01


Q ss_pred             HHHh------hcCcEEEEeCCCCCC-ccHHHHHHHhhcC
Q psy4122         105 VRAA------IEGRVLILEGIEKAE-RNVLPVLNNLLEN  136 (162)
Q Consensus       105 ~~A~------~~G~vlllDEId~a~-~~v~~~L~~lle~  136 (162)
                      ....      ....+++|||++.++ ++.++.|+.++++
T Consensus        94 ~~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~  132 (324)
T 3u61_B           94 TNFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEA  132 (324)
T ss_dssp             HHHHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHH
T ss_pred             HHHHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHh
Confidence            1111      145799999999999 9999999999985

>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=99.22  E-value=6.2e-11  Score=93.74  Aligned_cols=87  Identities=15%  Similarity=0.111  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHhc-----------CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCe
Q psy4122          28 QDWLSHLRWILQKD-----------NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGT   96 (162)
Q Consensus        28 ~~~~~~L~~i~~~~-----------~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~   96 (162)
                      ....+.++.++...           ....+++|+||||||||++|+.+|+.++.++..+++..-.+  .+.+.     +.
T Consensus        12 ~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~--~~~~~-----~~   84 (262)
T 2qz4_A           12 HEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVE--VIGGL-----GA   84 (262)
T ss_dssp             HHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSS--SSTTH-----HH
T ss_pred             HHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHh--hccCh-----hH
Confidence            45566666555422           23457999999999999999999999999988887753211  11110     00


Q ss_pred             EEEeccHHHHHhh-cCcEEEEeCCCCC
Q psy4122          97 AIYYDQSAVRAAI-EGRVLILEGIEKA  122 (162)
Q Consensus        97 ~~~~~gpl~~A~~-~G~vlllDEId~a  122 (162)
                      . -....+..|.. .+.+|+|||+|.+
T Consensus        85 ~-~~~~~~~~a~~~~~~vl~iDeid~l  110 (262)
T 2qz4_A           85 A-RVRSLFKEARARAPCIVYIDEIDAV  110 (262)
T ss_dssp             H-HHHHHHHHHHHTCSEEEEEECC---
T ss_pred             H-HHHHHHHHHHhcCCeEEEEeCcchh
Confidence            0 00112222322 2579999999998

>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=99.22  E-value=7.4e-11  Score=89.32  Aligned_cols=98  Identities=12%  Similarity=0.236  Sum_probs=64.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC-----CceEEEEeccCCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ-----REVEYICLSRDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg-----~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      .....+.++..+..... .+++|+||||||||++++.+++.+.     .++..+++........+...  +         
T Consensus        22 ~~~~~~~l~~~l~~~~~-~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~---------   89 (226)
T 2chg_A           22 QDEVIQRLKGYVERKNI-PHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHK--I---------   89 (226)
T ss_dssp             CHHHHHHHHHHHHTTCC-CCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHH--H---------
T ss_pred             cHHHHHHHHHHHhCCCC-CeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHH--H---------
Confidence            35667777777765433 3699999999999999999998752     23444444333222222110  0         


Q ss_pred             cHHHH----HhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVR----AAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~----A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..+..    ......+|+|||++.++++.++.|..++++
T Consensus        90 ~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~  128 (226)
T 2chg_A           90 KEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEM  128 (226)
T ss_dssp             HHHHTSCCSTTCSCEEEEEETGGGSCHHHHHHHHHHHHH
T ss_pred             HHHhcccCCCccCceEEEEeChhhcCHHHHHHHHHHHHh
Confidence            00000    013457999999999999999999999985

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.21  E-value=8.3e-12  Score=102.65  Aligned_cols=85  Identities=12%  Similarity=0.036  Sum_probs=53.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH-----hhcCcEEEEeCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA-----AIEGRVLILEGI  119 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A-----~~~G~vlllDEI  119 (162)
                      ..+||+||||||||++|+++|+.+|.++.+++++      ++...+.  +.........+..|     -..+.+|+||||
T Consensus        37 ~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~------~l~~~~~--g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEi  108 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVFRKMGINPIMMSAG------ELESGNA--GEPAKLIRQRYREAAEIIRKGNMCCLFINDL  108 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHH------HHHCC-----HHHHHHHHHHHHHHHHHTTSSCCCEEEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHH------HhhhccC--chhHHHHHHHHHHHHHHHhcCCCeEEEEech
Confidence            3589999999999999999999999999988875      2221100  00000000112222     124579999999


Q ss_pred             CCCCc-------------cHHHHHHHhhcCC
Q psy4122         120 EKAER-------------NVLPVLNNLLENR  137 (162)
Q Consensus       120 d~a~~-------------~v~~~L~~lle~r  137 (162)
                      |++.+             .+++.|+++||+.
T Consensus       109 D~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~  139 (293)
T 3t15_A          109 DAGAGRMGGTTQYTVNNQMVNATLMNIADNP  139 (293)
T ss_dssp             C--------------CHHHHHHHHHHHHHCC
T ss_pred             hhhcCCCCCCccccchHHHHHHHHHHHhccc
Confidence            88765             3568899998743

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.20  E-value=1.6e-11  Score=91.23  Aligned_cols=102  Identities=16%  Similarity=0.259  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~   97 (162)
                      ...++.+...+.. ....+++|+||||||||++++.+++.+          +.++..+.+.      ++...... .|. 
T Consensus        28 ~~~~~~l~~~l~~-~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~-~~~-   98 (187)
T 2p65_A           28 DTEIRRAIQILSR-RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLS------SLIAGAKY-RGD-   98 (187)
T ss_dssp             HHHHHHHHHHHTS-SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHH------HHHHHCCS-HHH-
T ss_pred             hHHHHHHHHHHhC-CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHH------HhhcCCCc-hhH-
Confidence            4445555555543 234589999999999999999999886          5554444332      22110000 000 


Q ss_pred             EEec--cHHHHHhh---cCcEEEEeCCCCCC---------ccHHHHHHHhhcCCeE
Q psy4122          98 IYYD--QSAVRAAI---EGRVLILEGIEKAE---------RNVLPVLNNLLENREM  139 (162)
Q Consensus        98 ~~~~--gpl~~A~~---~G~vlllDEId~a~---------~~v~~~L~~lle~r~l  139 (162)
                       +..  ..+...+.   .+.+|+|||++.+.         .++++.|..+++++.+
T Consensus        99 -~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~  153 (187)
T 2p65_A           99 -FEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLARGEL  153 (187)
T ss_dssp             -HHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSSCTTSCCTHHHHHHHHHTTCS
T ss_pred             -HHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccccccchHHHHHHHHHHhcCCe
Confidence             000  01112221   24699999999987         6788889898887643

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.20  E-value=4.3e-11  Score=96.28  Aligned_cols=101  Identities=17%  Similarity=0.178  Sum_probs=63.8

Q ss_pred             CHHHHHHHHHHHHh------------cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeec
Q psy4122          27 TQDWLSHLRWILQK------------DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVN   94 (162)
Q Consensus        27 ~~~~~~~L~~i~~~------------~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~   94 (162)
                      -....+.|+..+..            ...+.+++|+||||||||++|+++|..++.++..+++.....  ...+.     
T Consensus        22 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~--~~~~~-----   94 (285)
T 3h4m_A           22 LEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVK--KFIGE-----   94 (285)
T ss_dssp             CHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGGCC--CSTTH-----
T ss_pred             HHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHHHH--hccch-----
Confidence            35666666655543            245668999999999999999999999999988877642211  11110     


Q ss_pred             CeEEEeccHHHHHhh-cCcEEEEeCCCCC-----------CccHHHHHHHhhc
Q psy4122          95 GTAIYYDQSAVRAAI-EGRVLILEGIEKA-----------ERNVLPVLNNLLE  135 (162)
Q Consensus        95 G~~~~~~gpl~~A~~-~G~vlllDEId~a-----------~~~v~~~L~~lle  135 (162)
                       ........+..+.. ...+|+|||+|.+           .++.+..|..+++
T Consensus        95 -~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~  146 (285)
T 3h4m_A           95 -GASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLA  146 (285)
T ss_dssp             -HHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHH
Confidence             00000011222222 2369999999986           5566677777665

>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=99.19  E-value=7.1e-11  Score=91.28  Aligned_cols=91  Identities=14%  Similarity=0.155  Sum_probs=63.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ....++.++.+.... .+.+++|+||||||||++++.+++.++   .++.++++....  ..+.               .
T Consensus        36 ~~~~~~~l~~~~~~~-~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~--~~~~---------------~   97 (242)
T 3bos_A           36 NDELIGALKSAASGD-GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHA--SIST---------------A   97 (242)
T ss_dssp             CHHHHHHHHHHHHTC-SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGG--GSCG---------------G
T ss_pred             CHHHHHHHHHHHhCC-CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHH--HHHH---------------H
Confidence            357777787777643 456999999999999999999997764   566666654211  1110               1


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccH--HHHHHHhhc
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNV--LPVLNNLLE  135 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v--~~~L~~lle  135 (162)
                      ..+.+....+++|||++.++.+.  +..|..+++
T Consensus        98 ~~~~~~~~~vliiDe~~~~~~~~~~~~~l~~~l~  131 (242)
T 3bos_A           98 LLEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYN  131 (242)
T ss_dssp             GGTTGGGSSEEEEETGGGGTTCHHHHHHHHHHHH
T ss_pred             HHHhccCCCEEEEeccccccCCHHHHHHHHHHHH
Confidence            12234567899999999998876  676777654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.19  E-value=2.6e-11  Score=89.90  Aligned_cols=104  Identities=13%  Similarity=0.177  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~   97 (162)
                      ...++.+...+.. ....+++|+||||||||++++.+++.+          +.++..+++..........+      ...
T Consensus        28 ~~~~~~l~~~l~~-~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~  100 (195)
T 1jbk_A           28 DEEIRRTIQVLQR-RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRG------EFE  100 (195)
T ss_dssp             HHHHHHHHHHHTS-SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHH------HHH
T ss_pred             hHHHHHHHHHHhc-CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCccc------cHH
Confidence            4455555555543 234589999999999999999999886          55555554431110000000      000


Q ss_pred             EEeccHHHHHh-h--cCcEEEEeCCCCCC--------ccHHHHHHHhhcCCeE
Q psy4122          98 IYYDQSAVRAA-I--EGRVLILEGIEKAE--------RNVLPVLNNLLENREM  139 (162)
Q Consensus        98 ~~~~gpl~~A~-~--~G~vlllDEId~a~--------~~v~~~L~~lle~r~l  139 (162)
                      ... ..+...+ +  .+.+|+|||++.+.        .++.+.|+.+++++.+
T Consensus       101 ~~~-~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~~~~~~  152 (195)
T 1jbk_A          101 ERL-KGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGEL  152 (195)
T ss_dssp             HHH-HHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHTTSC
T ss_pred             HHH-HHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhhccCCe
Confidence            000 0112212 2  23489999999985        5678899999887643

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.17  E-value=6.6e-11  Score=98.26  Aligned_cols=35  Identities=20%  Similarity=0.330  Sum_probs=29.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCC--ceEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQR--EVEYICL   77 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~--p~~~v~~   77 (162)
                      .+++++|+||||||||++|+.+|+.++.  |+..+++
T Consensus        69 ~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~  105 (368)
T 3uk6_A           69 AGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAG  105 (368)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEG
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccc
Confidence            3468999999999999999999999985  5555554

>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=99.17  E-value=1.6e-10  Score=96.34  Aligned_cols=96  Identities=19%  Similarity=0.267  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHHHhc----CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKD----NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~----~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ...++.+...+...    ....+++|+||||||||||++.+|..++.++...+........++.               .
T Consensus        31 ~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~~~~~~l~---------------~   95 (334)
T 1in4_A           31 ENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMA---------------A   95 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHHHHH---------------H
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHhcCHHHHH---------------H
Confidence            55667777666542    1226899999999999999999999999876655443222222221               1


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCe
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~  138 (162)
                      +...+..+.++++||++++.+.+.+.|...++.+.
T Consensus        96 ~~~~~~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~  130 (334)
T 1in4_A           96 ILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQ  130 (334)
T ss_dssp             HHHHCCTTCEEEEETGGGCCHHHHHHHHHHHHTSC
T ss_pred             HHHHccCCCEEEEcchhhcCHHHHHHHHHHHHhcc
Confidence            12233456899999999999999999988887654

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.15  E-value=1.1e-10  Score=99.28  Aligned_cols=115  Identities=15%  Similarity=0.147  Sum_probs=80.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--eEEEEeccC---CChhhhcceeE-eecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--VEYICLSRD---TTEADIKQRRE-IVNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--~~~v~~~~~---~~~~dL~g~~~-~~~G~~~~~  100 (162)
                      ++.+.+..+.+-.......++++.|++||||+.+|+.++...++.  +..++|..-   .-.++|.|... .-.|...+.
T Consensus       135 s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~lfg~~~g~~tga~~~~  214 (368)
T 3dzd_A          135 HPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTGALTRK  214 (368)
T ss_dssp             SHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHHHHEECSCSSSSCCCCE
T ss_pred             chHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHHhcCccccccCCccccc
Confidence            344444333333333345689999999999999999999887654  777777632   22456666311 112334456


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEcC
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      .|-+..|  +||.|+||||++++++++..|+++|+++++.-.+
T Consensus       215 ~g~~~~a--~~gtlfldei~~l~~~~Q~~Ll~~l~~~~~~~~g  255 (368)
T 3dzd_A          215 KGKLELA--DQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLG  255 (368)
T ss_dssp             ECHHHHT--TTSEEEEETGGGSCHHHHHHHHHHHHHSEECCBT
T ss_pred             CChHhhc--CCCeEEecChhhCCHHHHHHHHHHHHhCCcccCC
Confidence            6666544  7899999999999999999999999999876433

>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=99.14  E-value=1.6e-10  Score=88.06  Aligned_cols=110  Identities=15%  Similarity=0.125  Sum_probs=63.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC--hhhhcc-----eeEeecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT--EADIKQ-----RREIVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~--~~dL~g-----~~~~~~G~~~~   99 (162)
                      -+..++.|+..+........++|+||||||||++++.+++.++.............  ...+..     ...........
T Consensus        28 ~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (250)
T 1njg_A           28 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTK  107 (250)
T ss_dssp             CHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEEETTCGGG
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEecCccccc
Confidence            46677778777776544457999999999999999999988764321100000000  000000     00011100000


Q ss_pred             ec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         100 YD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       100 ~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .+  ..+...+      ....+|+|||++.++++.++.|...+++
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~  152 (250)
T 1njg_A          108 VEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE  152 (250)
T ss_dssp             HHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhc
Confidence            00  0111211      1246899999999999999999999985

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.13  E-value=5.7e-11  Score=101.45  Aligned_cols=113  Identities=14%  Similarity=0.121  Sum_probs=78.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEeccCCC---hhhhcceeE-eecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLSRDTT---EADIKQRRE-IVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~~~~~---~~dL~g~~~-~~~G~~~~   99 (162)
                      ++.+.+.++.+........++++.|++||||+.+|+.++...+   .|+..++|..-..   .++|.|... .-.|....
T Consensus       143 s~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~~elfg~~~g~~tga~~~  222 (387)
T 1ny5_A          143 SPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSS  222 (387)
T ss_dssp             SHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCSC
T ss_pred             cHHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHHHHHhcCCCCCCCCCcccc
Confidence            3444333333333333556899999999999999999998764   5788888864321   345665310 01133334


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..|.+..  .+||+|+||||+.++++++..|+++|+++++.-
T Consensus       223 ~~g~~~~--a~~gtlfldei~~l~~~~q~~Ll~~l~~~~~~~  262 (387)
T 1ny5_A          223 KEGFFEL--ADGGTLFLDEIGELSLEAQAKLLRVIESGKFYR  262 (387)
T ss_dssp             BCCHHHH--TTTSEEEEESGGGCCHHHHHHHHHHHHHSEECC
T ss_pred             cCCceee--CCCcEEEEcChhhCCHHHHHHHHHHHhcCcEEe
Confidence            5565544  478999999999999999999999999988753

>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=99.11  E-value=1.1e-10  Score=96.09  Aligned_cols=99  Identities=11%  Similarity=0.085  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ......++.++..-. .+.+++|+||||||||++++.++..+   +.++.++++...  ..++.+.  +..+.    ...
T Consensus        20 ~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~--~~~~~~~--~~~~~----~~~   91 (324)
T 1l8q_A           20 RLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF--AQAMVEH--LKKGT----INE   91 (324)
T ss_dssp             HHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH--HHHHHHH--HHHTC----HHH
T ss_pred             HHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHH--HHHHHHH--HHcCc----HHH
Confidence            344556666666432 34689999999999999999999888   888888877522  2233221  11110    113


Q ss_pred             HHHHhhcCcEEEEeCCCCCCc--cHHHHHHHhh
Q psy4122         104 AVRAAIEGRVLILEGIEKAER--NVLPVLNNLL  134 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~--~v~~~L~~ll  134 (162)
                      +..++.+..+|+||||+.++.  ..+..|..++
T Consensus        92 ~~~~~~~~~vL~iDEi~~l~~~~~~~~~l~~~l  124 (324)
T 1l8q_A           92 FRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIF  124 (324)
T ss_dssp             HHHHHHTCSEEEEECGGGGTTCHHHHHHHHHHH
T ss_pred             HHHHhcCCCEEEEcCcccccCChHHHHHHHHHH
Confidence            445566789999999999886  4555555544

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.11  E-value=2.9e-11  Score=102.56  Aligned_cols=100  Identities=12%  Similarity=0.080  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHh-----------cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCe
Q psy4122          28 QDWLSHLRWILQK-----------DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGT   96 (162)
Q Consensus        28 ~~~~~~L~~i~~~-----------~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~   96 (162)
                      ....+.|+.++..           .....++||+||||||||++|+++|..++.++..+++....  ....|.      .
T Consensus       121 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l~--~~~~g~------~  192 (389)
T 3vfd_A          121 DLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT--SKYVGE------G  192 (389)
T ss_dssp             HHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC---------------C
T ss_pred             HHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHhh--ccccch------H
Confidence            5566666655521           11346899999999999999999999999998877775321  112110      0


Q ss_pred             EEEeccHHHHHhh-cCcEEEEeCCCCC-----------CccHHHHHHHhhc
Q psy4122          97 AIYYDQSAVRAAI-EGRVLILEGIEKA-----------ERNVLPVLNNLLE  135 (162)
Q Consensus        97 ~~~~~gpl~~A~~-~G~vlllDEId~a-----------~~~v~~~L~~lle  135 (162)
                      .......+..|.. ..++|+|||||.+           ...++..|...++
T Consensus       193 ~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~  243 (389)
T 3vfd_A          193 EKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFD  243 (389)
T ss_dssp             HHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhh
Confidence            0001112222322 3379999999887           3345556666665

>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=99.11  E-value=8.8e-11  Score=88.85  Aligned_cols=99  Identities=14%  Similarity=0.216  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHHhcC--CCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          29 DWLSHLRWILQKDN--MSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        29 ~~~~~L~~i~~~~~--~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      ...+.++.++.++.  .|++++|+||||||||+|++.++..+    |..+.++++..-  ...+...  ...+..    .
T Consensus        21 ~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~--~~~~~~~--~~~~~~----~   92 (180)
T 3ec2_A           21 RALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDL--IFRLKHL--MDEGKD----T   92 (180)
T ss_dssp             HHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHH--HHHHHHH--HHHTCC----S
T ss_pred             HHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHH--HHHHHHH--hcCchH----H
Confidence            45555666665543  46789999999999999999999776    666666554321  1112110  111111    1


Q ss_pred             HHHHHhhcCcEEEEeCCC--CCCccHHHHHHHhhc
Q psy4122         103 SAVRAAIEGRVLILEGIE--KAERNVLPVLNNLLE  135 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId--~a~~~v~~~L~~lle  135 (162)
                      .+...+.+..+|+|||++  ..++.....|..+++
T Consensus        93 ~~~~~~~~~~llilDE~~~~~~~~~~~~~l~~ll~  127 (180)
T 3ec2_A           93 KFLKTVLNSPVLVLDDLGSERLSDWQRELISYIIT  127 (180)
T ss_dssp             HHHHHHHTCSEEEEETCSSSCCCHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCEEEEeCCCCCcCCHHHHHHHHHHHH
Confidence            455667788999999998  455666667777665

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.10  E-value=1.6e-10  Score=95.27  Aligned_cols=108  Identities=14%  Similarity=0.107  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHhc---CCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhhccee----E
Q psy4122          28 QDWLSHLRWILQKD---NMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADIKQRR----E   91 (162)
Q Consensus        28 ~~~~~~L~~i~~~~---~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL~g~~----~   91 (162)
                      ....+.+...+...   ..+.+++|+||||||||++++.+++.+         +.++.+++|....+..++....    .
T Consensus        25 ~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~  104 (387)
T 2v1u_A           25 EAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVG  104 (387)
T ss_dssp             HHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhC
Confidence            45566666655443   345689999999999999999999887         6677778877665555443210    0


Q ss_pred             eecCeEEEecc----HHHHHhhcCc---EEEEeCCCCCCcc--HHHHHHHhhc
Q psy4122          92 IVNGTAIYYDQ----SAVRAAIEGR---VLILEGIEKAERN--VLPVLNNLLE  135 (162)
Q Consensus        92 ~~~G~~~~~~g----pl~~A~~~G~---vlllDEId~a~~~--v~~~L~~lle  135 (162)
                      .......+..+    .+..++...+   +|+|||++.+...  .++.|+.+++
T Consensus       105 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~  157 (387)
T 2v1u_A          105 VRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITR  157 (387)
T ss_dssp             CCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhh
Confidence            00000000011    2233343333   8999999998876  7777777765

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=99.08  E-value=1.1e-10  Score=96.71  Aligned_cols=101  Identities=11%  Similarity=0.078  Sum_probs=61.9

Q ss_pred             CHHHHHHHHHHHH-----------hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecC
Q psy4122          27 TQDWLSHLRWILQ-----------KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        27 ~~~~~~~L~~i~~-----------~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      -....+.|+.++.           .....+++||+||||||||++|+++|+.++.++..+++..-  .+...|.      
T Consensus        23 ~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l--~~~~~g~------   94 (322)
T 3eie_A           23 LEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDL--VSKWMGE------   94 (322)
T ss_dssp             CHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHH--HTTTGGG------
T ss_pred             hHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHH--hhcccch------
Confidence            4666777776652           11123469999999999999999999999999888876421  1111110      


Q ss_pred             eEEEeccHHHHHhh-cCcEEEEeCCCCCCcc-----------HHHHHHHhhc
Q psy4122          96 TAIYYDQSAVRAAI-EGRVLILEGIEKAERN-----------VLPVLNNLLE  135 (162)
Q Consensus        96 ~~~~~~gpl~~A~~-~G~vlllDEId~a~~~-----------v~~~L~~lle  135 (162)
                      ........+..|.. .+++|+|||||.+.+.           ++..|+..++
T Consensus        95 ~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~  146 (322)
T 3eie_A           95 SEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMN  146 (322)
T ss_dssp             HHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHG
T ss_pred             HHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhc
Confidence            00000011222222 3479999999987652           3556666665

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=99.07  E-value=4.1e-10  Score=94.76  Aligned_cols=101  Identities=12%  Similarity=0.069  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHh-----------cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCe
Q psy4122          28 QDWLSHLRWILQK-----------DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGT   96 (162)
Q Consensus        28 ~~~~~~L~~i~~~-----------~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~   96 (162)
                      ....+.|+.++..           ....+++||+||||||||++|+++|..++.++..+++.....  ...|.      .
T Consensus        90 ~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~--~~~g~------~  161 (357)
T 3d8b_A           90 EFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTS--KWVGE------G  161 (357)
T ss_dssp             HHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCC--SSTTH------H
T ss_pred             HHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhc--cccch------H
Confidence            4555566655532           123568999999999999999999999999988887753211  11110      0


Q ss_pred             EEEeccHHHHHh-hcCcEEEEeCCCCCCc-----------cHHHHHHHhhcC
Q psy4122          97 AIYYDQSAVRAA-IEGRVLILEGIEKAER-----------NVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~gpl~~A~-~~G~vlllDEId~a~~-----------~v~~~L~~lle~  136 (162)
                      .......+..|. ..+++|+|||||.+.+           .+++.|+..++.
T Consensus       162 ~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~  213 (357)
T 3d8b_A          162 EKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDG  213 (357)
T ss_dssp             HHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhc
Confidence            000011122222 2357999999987644           345556666653

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=99.07  E-value=1.8e-10  Score=92.52  Aligned_cols=85  Identities=22%  Similarity=0.193  Sum_probs=55.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEee-cCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIV-NGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~-~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..++||+||||||||++|+.+|+..+.++..+++..     ++.|..... .+.   ....+..+. ..+++|+||||+.
T Consensus        64 ~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~-----~~~g~~~~~~~~~---~~~~~~~~~~~~~~vl~iDEid~  135 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPD-----KMIGFSETAKCQA---MKKIFDDAYKSQLSCVVVDDIER  135 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGG-----GCTTCCHHHHHHH---HHHHHHHHHTSSEEEEEECCHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHH-----HhcCCchHHHHHH---HHHHHHHHHhcCCcEEEEEChhh
Confidence            347999999999999999999999999988887643     333311000 000   001122232 2357999999988


Q ss_pred             C----------CccHHHHHHHhhcC
Q psy4122         122 A----------ERNVLPVLNNLLEN  136 (162)
Q Consensus       122 a----------~~~v~~~L~~lle~  136 (162)
                      +          ...++..|..+++.
T Consensus       136 l~~~~~~~~~~~~~~l~~L~~~~~~  160 (272)
T 1d2n_A          136 LLDYVPIGPRFSNLVLQALLVLLKK  160 (272)
T ss_dssp             HTTCBTTTTBCCHHHHHHHHHHTTC
T ss_pred             hhccCCCChhHHHHHHHHHHHHhcC
Confidence            6          44566777777663

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.05  E-value=3.3e-10  Score=91.67  Aligned_cols=90  Identities=12%  Similarity=0.096  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHHHHh----------c-CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecC
Q psy4122          27 TQDWLSHLRWILQK----------D-NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        27 ~~~~~~~L~~i~~~----------~-~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      .....+.|+.++..          . ..+++++|+||||||||++|+.+|..++.++..+++.....  ...+.     +
T Consensus        26 ~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~--~~~~~-----~   98 (297)
T 3b9p_A           26 QDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTS--KYVGD-----G   98 (297)
T ss_dssp             CHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSS--SSCSC-----H
T ss_pred             hHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhh--cccch-----H
Confidence            35566666665532          1 13568999999999999999999999999988777753211  11110     0


Q ss_pred             eEEEeccHHHHHh-hcCcEEEEeCCCCCCc
Q psy4122          96 TAIYYDQSAVRAA-IEGRVLILEGIEKAER  124 (162)
Q Consensus        96 ~~~~~~gpl~~A~-~~G~vlllDEId~a~~  124 (162)
                      . ......+..+. ..+++|+|||++.+.+
T Consensus        99 ~-~~~~~~~~~~~~~~~~vl~iDEid~l~~  127 (297)
T 3b9p_A           99 E-KLVRALFAVARHMQPSIIFIDEVDSLLS  127 (297)
T ss_dssp             H-HHHHHHHHHHHHTCSEEEEEETGGGTSB
T ss_pred             H-HHHHHHHHHHHHcCCcEEEeccHHHhcc
Confidence            0 00001122222 2457999999988744

>1sxj_D Activator 1 41 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=99.04  E-value=3.3e-10  Score=93.00  Aligned_cols=109  Identities=12%  Similarity=0.162  Sum_probs=62.4

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC------ceEEEEeccCCChhhhccee-EeecCeE-EE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR------EVEYICLSRDTTEADIKQRR-EIVNGTA-IY   99 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~------p~~~v~~~~~~~~~dL~g~~-~~~~G~~-~~   99 (162)
                      ...++.++..+..... .+++|+||||||||++++.+|+.++.      .+..+++........+.... ....... ..
T Consensus        43 ~~~~~~l~~~l~~~~~-~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (353)
T 1sxj_D           43 DHAVTVLKKTLKSANL-PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKP  121 (353)
T ss_dssp             CTTHHHHHHHTTCTTC-CCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCC
T ss_pred             HHHHHHHHHHHhcCCC-CEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHHHHHHHHhhhccccc
Confidence            4455666666554333 36999999999999999999988653      23333333222222221100 0000000 00


Q ss_pred             eccHH-HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         100 YDQSA-VRAAIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       100 ~~gpl-~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ..... ........+++|||+++++++.++.|..++++.
T Consensus       122 ~~~~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~  160 (353)
T 1sxj_D          122 SKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETY  160 (353)
T ss_dssp             CTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHT
T ss_pred             chhhcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhc
Confidence            00000 000123469999999999999999999999854

>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=99.03  E-value=1.3e-09  Score=90.18  Aligned_cols=109  Identities=15%  Similarity=0.061  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHHHhc---CCCC--cEEEEcCCCchHHHHHHHHHHHh----CCceEEEEeccCCChhhhccee--Ee--ec
Q psy4122          28 QDWLSHLRWILQKD---NMSQ--DVFLIGKPGSLRRSLAMSYLELT----QREVEYICLSRDTTEADIKQRR--EI--VN   94 (162)
Q Consensus        28 ~~~~~~L~~i~~~~---~~g~--~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~~~~~~~dL~g~~--~~--~~   94 (162)
                      ...++.+...+...   ..+.  +++|+||||||||++++.++..+    +.++.+++|....+..++....  .+  ..
T Consensus        23 ~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~  102 (389)
T 1fnn_A           23 EQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPF  102 (389)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHHHHhCccC
Confidence            44555565555543   2334  79999999999999999999888    5566777776665554443210  00  00


Q ss_pred             CeEEEeccHHHH----Hhh---cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          95 GTAIYYDQSAVR----AAI---EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        95 G~~~~~~gpl~~----A~~---~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +...+....+..    .+.   ...+|+|||++.++++++..|..++++
T Consensus       103 ~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~  151 (389)
T 1fnn_A          103 PRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQE  151 (389)
T ss_dssp             CSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTC
T ss_pred             CCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHh
Confidence            000011111111    121   234899999999999999999998864

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=99.02  E-value=8.1e-10  Score=93.08  Aligned_cols=84  Identities=13%  Similarity=0.166  Sum_probs=53.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEKA  122 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~a  122 (162)
                      .+++||+||||||||++|+++|..++.++..+++.      ++...+.  +.........+..|. ..+.+|+|||||.+
T Consensus        84 ~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~------~l~~~~~--g~~~~~~~~~f~~a~~~~~~vl~iDEid~l  155 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSS------DLVSKWM--GESEKLVKQLFAMARENKPSIIFIDQVDAL  155 (355)
T ss_dssp             CCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHH------HHHSCC-----CHHHHHHHHHHHHHTSSEEEEEECGGGG
T ss_pred             CceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHH------HHhhhhc--chHHHHHHHHHHHHHHcCCeEEEEechHhh
Confidence            45799999999999999999999999998877664      3332110  000000011122222 24579999999998


Q ss_pred             Ccc-----------HHHHHHHhhc
Q psy4122         123 ERN-----------VLPVLNNLLE  135 (162)
Q Consensus       123 ~~~-----------v~~~L~~lle  135 (162)
                      .+.           +++.|+..++
T Consensus       156 ~~~r~~~~~~~~~~~~~~ll~~l~  179 (355)
T 2qp9_X          156 TGTRGEGESEASRRIKTELLVQMN  179 (355)
T ss_dssp             TC------CTHHHHHHHHHHHHHH
T ss_pred             cccCCCCcchHHHHHHHHHHHHhh
Confidence            753           4566666665

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=99.02  E-value=1.2e-09  Score=89.75  Aligned_cols=100  Identities=16%  Similarity=0.115  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHh------------cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecC
Q psy4122          28 QDWLSHLRWILQK------------DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~------------~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      ....+.|+.++..            ...+++++|+||||||||++|+.+|..++.++..+++..-  .+.+.|..   ..
T Consensus        21 ~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l--~~~~~g~~---~~   95 (301)
T 3cf0_A           21 EDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPEL--LTMWFGES---EA   95 (301)
T ss_dssp             HHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHH--HHHHHTTC---TT
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHH--HhhhcCch---HH
Confidence            4555666655542            2456789999999999999999999999988776655311  11222210   00


Q ss_pred             eEEEeccHHHHHhh-cCcEEEEeCCCCCCc--------------cHHHHHHHhhc
Q psy4122          96 TAIYYDQSAVRAAI-EGRVLILEGIEKAER--------------NVLPVLNNLLE  135 (162)
Q Consensus        96 ~~~~~~gpl~~A~~-~G~vlllDEId~a~~--------------~v~~~L~~lle  135 (162)
                      .   ..+.+..|.. ..++++||||+.+.+              .++..|+..++
T Consensus        96 ~---~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~  147 (301)
T 3cf0_A           96 N---VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMD  147 (301)
T ss_dssp             H---HHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHH
T ss_pred             H---HHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhh
Confidence            0   0112333332 347999999986432              34666777776

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.01  E-value=3.2e-10  Score=98.32  Aligned_cols=73  Identities=16%  Similarity=0.170  Sum_probs=48.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~  121 (162)
                      ..+.+||+||||||||.+|+++|..++.++..++++.-.  +..+|.     +. .-....+..|-. ...+|+|||||.
T Consensus       181 ~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~--sk~vGe-----se-~~vr~lF~~Ar~~aP~IIFiDEiDa  252 (405)
T 4b4t_J          181 QPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELV--QKYIGE-----GS-RMVRELFVMAREHAPSIIFMDEIDS  252 (405)
T ss_dssp             CCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGS--CSSTTH-----HH-HHHHHHHHHHHHTCSEEEEEESSSC
T ss_pred             CCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhh--ccccch-----HH-HHHHHHHHHHHHhCCceEeeecchh
Confidence            446799999999999999999999999998888775321  111210     00 000112333333 347899999998


Q ss_pred             CC
Q psy4122         122 AE  123 (162)
Q Consensus       122 a~  123 (162)
                      +.
T Consensus       253 i~  254 (405)
T 4b4t_J          253 IG  254 (405)
T ss_dssp             CT
T ss_pred             hc
Confidence            64

>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=99.01  E-value=5.7e-10  Score=98.31  Aligned_cols=109  Identities=10%  Similarity=0.037  Sum_probs=67.7

Q ss_pred             CHHHHHHHHHHHHhcC----------------CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee
Q psy4122          27 TQDWLSHLRWILQKDN----------------MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR   90 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~----------------~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~   90 (162)
                      .+...+.|+.++..+.                ..++++|+||||||||++|+.+|+.+|.++..+++........+....
T Consensus        44 ~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~~~i~in~s~~~~~~~~~~~i  123 (516)
T 1sxj_A           44 NKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGV  123 (516)
T ss_dssp             CHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTTSCCCHHHHHHTG
T ss_pred             CHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCCCEEEEeCCCcchHHHHHHHH
Confidence            4677777877776532                235899999999999999999999999988777775433322111000


Q ss_pred             -EeecCeEEEeccHHHH------HhhcCcEEEEeCCCCCCccH---HHHHHHhhcCC
Q psy4122          91 -EIVNGTAIYYDQSAVR------AAIEGRVLILEGIEKAERNV---LPVLNNLLENR  137 (162)
Q Consensus        91 -~~~~G~~~~~~gpl~~------A~~~G~vlllDEId~a~~~v---~~~L~~lle~r  137 (162)
                       ...+.. . ..+-+..      +...+.+|+|||++.+..+.   +..|+.++++.
T Consensus       124 ~~~~~~~-~-~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~  178 (516)
T 1sxj_A          124 KNALDNM-S-VVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT  178 (516)
T ss_dssp             GGGTTBC-C-STTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC
T ss_pred             HHHhccc-c-HHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhc
Confidence             000000 0 0000000      11345799999999987643   47788887743

>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=99.01  E-value=6.8e-10  Score=89.90  Aligned_cols=102  Identities=12%  Similarity=0.197  Sum_probs=63.5

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-----eEEEEeccCCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-----VEYICLSRDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-----~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      -+...+.|+.++...... +++|+||||||||++|+.+|+.++.+     +..+++........+...  +..  +. ..
T Consensus        30 ~~~~~~~l~~~l~~~~~~-~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~--~~-~~  103 (327)
T 1iqp_A           30 QEHIVKRLKHYVKTGSMP-HLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREK--VKE--FA-RT  103 (327)
T ss_dssp             CHHHHHHHHHHHHHTCCC-EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHH--HHH--HH-HS
T ss_pred             CHHHHHHHHHHHHcCCCC-eEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHHHHHH--HHH--HH-hh
Confidence            467778888777764333 79999999999999999999886422     223332211111111100  000  00 00


Q ss_pred             cHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .|+.  -....+++|||+++++++.++.|..++++
T Consensus       104 ~~~~--~~~~~vliiDe~~~l~~~~~~~L~~~le~  136 (327)
T 1iqp_A          104 KPIG--GASFKIIFLDEADALTQDAQQALRRTMEM  136 (327)
T ss_dssp             CCGG--GCSCEEEEEETGGGSCHHHHHHHHHHHHH
T ss_pred             CCcC--CCCCeEEEEeCCCcCCHHHHHHHHHHHHh
Confidence            0100  02357999999999999999999999985

>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=99.00  E-value=2e-09  Score=88.98  Aligned_cols=107  Identities=15%  Similarity=0.110  Sum_probs=65.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE--EEeccC--------CChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY--ICLSRD--------TTEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~--v~~~~~--------~~~~dL~g~~~~~~G~   96 (162)
                      -+...+.|+..+........++|+||+|||||++++.+|+.++.....  ..|..-        ....++.   .+....
T Consensus        21 ~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~   97 (373)
T 1jr3_A           21 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI---EIDAAS   97 (373)
T ss_dssp             CHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCSSCE---EEETTC
T ss_pred             cHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCCceE---Eecccc
Confidence            467778888887765555568999999999999999999988643210  001000        0000111   111110


Q ss_pred             EEEec--cHHHHHhh------cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          97 AIYYD--QSAVRAAI------EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        97 ~~~~~--gpl~~A~~------~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ....+  ..+...+.      ...+++|||++.++++.++.|...+++
T Consensus        98 ~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~  145 (373)
T 1jr3_A           98 RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE  145 (373)
T ss_dssp             SCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhc
Confidence            00000  01222222      236999999999999999999999986

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.00  E-value=6.1e-10  Score=85.36  Aligned_cols=98  Identities=12%  Similarity=0.128  Sum_probs=57.7

Q ss_pred             HHHHHHHHHHhcCCC---CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          30 WLSHLRWILQKDNMS---QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g---~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ..+.++.++.....+   .+++|+||||||||++++.++..+   +.++.++++...  ..++...  ...+.  +  ..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~--~~~~~--~--~~  108 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPEL--FRELKHS--LQDQT--M--NE  108 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHH--HHHHHHC-----CC--C--HH
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHH--HHHHHHH--hccch--H--HH
Confidence            455666666655322   689999999999999999999876   566666666421  1222211  11111  1  13


Q ss_pred             HHHHhhcCcEEEEeCCCC--CCccHHH-HHHHhhc
Q psy4122         104 AVRAAIEGRVLILEGIEK--AERNVLP-VLNNLLE  135 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~--a~~~v~~-~L~~lle  135 (162)
                      +...+.+..+|+|||++.  ..+..+. .|..+++
T Consensus       109 ~~~~~~~~~~lilDei~~~~~~~~~~~~ll~~~l~  143 (202)
T 2w58_A          109 KLDYIKKVPVLMLDDLGAEAMSSWVRDDVFGPILQ  143 (202)
T ss_dssp             HHHHHHHSSEEEEEEECCC---CCGGGTTHHHHHH
T ss_pred             HHHHhcCCCEEEEcCCCCCcCCHHHHHHHHHHHHH
Confidence            445556678999999965  4443333 3333443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.99  E-value=2e-09  Score=89.50  Aligned_cols=88  Identities=13%  Similarity=0.065  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHHh-----------cCCCCcEEEEcCCCchHHHHHHHHHHHh-CCceEEEEeccCCChhhhcceeEeecC
Q psy4122          28 QDWLSHLRWILQK-----------DNMSQDVFLIGKPGSLRRSLAMSYLELT-QREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~-----------~~~g~~vlL~GppG~GKT~La~~lA~~l-g~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      ....+.|+.++..           ....+++||+||||||||++|+++|..+ +.++..+++..-..  ...|.      
T Consensus        18 ~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~--~~~g~------   89 (322)
T 1xwi_A           18 EGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVS--KWLGE------   89 (322)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCC--SSCCS------
T ss_pred             HHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHh--hhhhH------
Confidence            5566666655531           1223579999999999999999999988 78877777653211  11110      


Q ss_pred             eEEEeccHHHHHh-hcCcEEEEeCCCCCC
Q psy4122          96 TAIYYDQSAVRAA-IEGRVLILEGIEKAE  123 (162)
Q Consensus        96 ~~~~~~gpl~~A~-~~G~vlllDEId~a~  123 (162)
                      .......-+..|. ....+|+|||||.+.
T Consensus        90 ~~~~~~~lf~~a~~~~~~vl~iDEid~l~  118 (322)
T 1xwi_A           90 SEKLVKNLFQLARENKPSIIFIDEIDSLC  118 (322)
T ss_dssp             CHHHHHHHHHHHHHTSSEEEEEETTTGGG
T ss_pred             HHHHHHHHHHHHHhcCCcEEEeecHHHhc
Confidence            0000001111222 234799999999873

>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=98.99  E-value=3.9e-10  Score=91.03  Aligned_cols=98  Identities=12%  Similarity=0.247  Sum_probs=62.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      .+...+.++..+...... +++|+||||||||++|+.+|+.+     +.++..+++.......++...  +         
T Consensus        22 ~~~~~~~l~~~l~~~~~~-~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~--~---------   89 (319)
T 2chq_A           22 QDEVIQRLKGYVERKNIP-HLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHK--I---------   89 (319)
T ss_dssp             CHHHHHHHHTTTTTTCCC-CEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTCTTTSSHH--H---------
T ss_pred             CHHHHHHHHHHHhCCCCC-eEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccChHHHHHH--H---------
Confidence            355666666665543222 69999999999999999999876     223444554432222111100  0         


Q ss_pred             cHHHH--Hh--hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVR--AA--IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~--A~--~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      ..+..  .+  ....+++|||++.++++.++.|..++++
T Consensus        90 ~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~  128 (319)
T 2chq_A           90 KEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEM  128 (319)
T ss_dssp             HHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSS
T ss_pred             HHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHh
Confidence            00000  01  2357999999999999999999999986

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.98  E-value=6.9e-10  Score=97.01  Aligned_cols=73  Identities=15%  Similarity=0.135  Sum_probs=47.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..+.+||+||||||||++|+++|..+|.++..++++.-.+  ...|.      +..-....+..|- ..+.+|+|||||.
T Consensus       214 ~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~s--k~~Ge------se~~ir~~F~~A~~~~P~IifiDEiDa  285 (437)
T 4b4t_L          214 PPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVD--KYIGE------SARIIREMFAYAKEHEPCIIFMDEVDA  285 (437)
T ss_dssp             CCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTCC--SSSSH------HHHHHHHHHHHHHHSCSEEEEEECCCS
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhcc--ccchH------HHHHHHHHHHHHHhcCCceeeeecccc
Confidence            3457999999999999999999999999988887753211  11110      0000011223333 2457999999997


Q ss_pred             CC
Q psy4122         122 AE  123 (162)
Q Consensus       122 a~  123 (162)
                      +.
T Consensus       286 i~  287 (437)
T 4b4t_L          286 IG  287 (437)
T ss_dssp             SS
T ss_pred             cc
Confidence            53

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=98.97  E-value=2e-10  Score=91.76  Aligned_cols=75  Identities=13%  Similarity=0.109  Sum_probs=49.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~  121 (162)
                      ..++++|+||||||||++|+.+|..++.|+..+++..-  .+.+.+.    +..  -....+..|.. ..++|+|||+|.
T Consensus        43 ~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~--~~~~~~~----~~~--~~~~~~~~a~~~~~~vl~iDEid~  114 (268)
T 2r62_A           43 IPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSF--IEMFVGL----GAS--RVRDLFETAKKQAPSIIFIDEIDA  114 (268)
T ss_dssp             CCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTT--TTSCSSS----CSS--SSSTTHHHHHHSCSCEEEESCGGG
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHH--HHhhcch----HHH--HHHHHHHHHHhcCCeEEEEeChhh
Confidence            34579999999999999999999999999876665422  1112221    000  01123444443 347999999998


Q ss_pred             CCcc
Q psy4122         122 AERN  125 (162)
Q Consensus       122 a~~~  125 (162)
                      +.++
T Consensus       115 l~~~  118 (268)
T 2r62_A          115 IGKS  118 (268)
T ss_dssp             TTC-
T ss_pred             hccc
Confidence            8664

>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=98.97  E-value=7e-10  Score=97.86  Aligned_cols=100  Identities=11%  Similarity=0.177  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHHHh------------cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecC
Q psy4122          28 QDWLSHLRWILQK------------DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~------------~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      ....+.|+.++..            .....++||+||||||||++|+++|...+.++..++|..-  .+++.|.   ..+
T Consensus       210 ~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l--~~~~~g~---~~~  284 (489)
T 3hu3_A          210 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI--MSKLAGE---SES  284 (489)
T ss_dssp             HHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHH--HTSCTTH---HHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHh--hhhhcch---hHH
Confidence            4455556555543            2345689999999999999999999999999988887522  1122220   000


Q ss_pred             eEEEeccHHHHHhhc-CcEEEEeCCCCCCc-----------cHHHHHHHhhc
Q psy4122          96 TAIYYDQSAVRAAIE-GRVLILEGIEKAER-----------NVLPVLNNLLE  135 (162)
Q Consensus        96 ~~~~~~gpl~~A~~~-G~vlllDEId~a~~-----------~v~~~L~~lle  135 (162)
                      .   ..+.+..|... .++|+|||||.+.+           .+++.|+.+++
T Consensus       285 ~---~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld  333 (489)
T 3hu3_A          285 N---LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMD  333 (489)
T ss_dssp             H---HHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHH
T ss_pred             H---HHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhh
Confidence            0   11233334322 35999999977655           56788888887

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.97  E-value=7.6e-10  Score=93.03  Aligned_cols=91  Identities=7%  Similarity=-0.030  Sum_probs=52.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC----------CceEEEEeccCCChhhhccee--EeecCeEEEecc--HHH---
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ----------REVEYICLSRDTTEADIKQRR--EIVNGTAIYYDQ--SAV---  105 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg----------~p~~~v~~~~~~~~~dL~g~~--~~~~G~~~~~~g--pl~---  105 (162)
                      .+.+++|+||||||||++++.+++.+.          ..+.+++|....+..++....  .+.+-...+...  .+-   
T Consensus        44 ~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f  123 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYI  123 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHH
Confidence            445899999999999999999998873          234456665655554432100  011101111111  111   


Q ss_pred             HHh---hc-CcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         106 RAA---IE-GRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       106 ~A~---~~-G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                      ..+   .. ..+++|||||++.  .+++|+++++
T Consensus       124 ~~~~~~~~~~~ii~lDE~d~l~--~q~~L~~l~~  155 (318)
T 3te6_A          124 TNVPKAKKRKTLILIQNPENLL--SEKILQYFEK  155 (318)
T ss_dssp             HHSCGGGSCEEEEEEECCSSSC--CTHHHHHHHH
T ss_pred             HHhhhccCCceEEEEecHHHhh--cchHHHHHHh
Confidence            111   11 2588999999998  5678888875

>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=98.97  E-value=8.9e-10  Score=95.55  Aligned_cols=99  Identities=13%  Similarity=0.073  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      ......++.++..-....+++|+||||||||+|++.+|..+     +.++.++++..-  ..++...  +..+.    ..
T Consensus       114 ~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~--~~~~~~~--~~~~~----~~  185 (440)
T 2z4s_A          114 SFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKF--LNDLVDS--MKEGK----LN  185 (440)
T ss_dssp             HHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHH--HHHHHHH--HHTTC----HH
T ss_pred             HHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH--HHHHHHH--HHccc----HH
Confidence            33455555555543224689999999999999999999887     777777766432  2233321  11111    11


Q ss_pred             HHHHHhh-cCcEEEEeCCCCCCc--cHHHHHHHhh
Q psy4122         103 SAVRAAI-EGRVLILEGIEKAER--NVLPVLNNLL  134 (162)
Q Consensus       103 pl~~A~~-~G~vlllDEId~a~~--~v~~~L~~ll  134 (162)
                      .+..+++ ...+|+|||++.+..  ..+..|..++
T Consensus       186 ~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l  220 (440)
T 2z4s_A          186 EFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTF  220 (440)
T ss_dssp             HHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHH
Confidence            3445566 778999999999886  4566665554

>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=98.96  E-value=1e-09  Score=88.71  Aligned_cols=94  Identities=15%  Similarity=0.214  Sum_probs=63.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC-----CceEEEEeccCCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ-----REVEYICLSRDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg-----~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      -+...+.|+..+...... +++|+||||+|||++|+.+|+.+.     .++..+++.......++..             
T Consensus        26 ~~~~~~~l~~~l~~~~~~-~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i~~-------------   91 (323)
T 1sxj_B           26 NKETIDRLQQIAKDGNMP-HMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRN-------------   91 (323)
T ss_dssp             CTHHHHHHHHHHHSCCCC-CEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHT-------------
T ss_pred             CHHHHHHHHHHHHcCCCC-eEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHHHH-------------
Confidence            356677788777754443 599999999999999999998763     2233333322222222221             


Q ss_pred             cHHHHH-------h-h-cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRA-------A-I-EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A-------~-~-~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                        +.+.       + . ...+++|||++.++++.++.|..++++
T Consensus        92 --~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~  133 (323)
T 1sxj_B           92 --QIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMEL  133 (323)
T ss_dssp             --HHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHH
T ss_pred             --HHHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhc
Confidence              1111       1 1 246999999999999999999999985

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.95  E-value=2e-09  Score=80.46  Aligned_cols=82  Identities=18%  Similarity=0.306  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      +......++.+     .++.++|+||+|+|||+|++.++...   |....++...      ++...              
T Consensus        24 n~~~~~~l~~~-----~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~------~~~~~--------------   78 (149)
T 2kjq_A           24 NAELVYVLRHK-----HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAA------SMPLT--------------   78 (149)
T ss_dssp             THHHHHHCCCC-----CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETT------TSCCC--------------
T ss_pred             cHHHHHHHHhc-----CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHH------HhhHH--------------
Confidence            34444444444     67899999999999999999999877   5555555442      12110              


Q ss_pred             HHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         104 AVRAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                        ..+.+..+|+|||++...+.....|..+++
T Consensus        79 --~~~~~~~lLilDE~~~~~~~~~~~l~~li~  108 (149)
T 2kjq_A           79 --DAAFEAEYLAVDQVEKLGNEEQALLFSIFN  108 (149)
T ss_dssp             --GGGGGCSEEEEESTTCCCSHHHHHHHHHHH
T ss_pred             --HHHhCCCEEEEeCccccChHHHHHHHHHHH
Confidence              113456899999999988866666666655

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=98.93  E-value=5e-09  Score=92.30  Aligned_cols=90  Identities=14%  Similarity=0.151  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHHhc-----------CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCe
Q psy4122          28 QDWLSHLRWILQKD-----------NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGT   96 (162)
Q Consensus        28 ~~~~~~L~~i~~~~-----------~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~   96 (162)
                      ....+.++.++..+           ...++++|+||||||||++|+.+|...+.|+..+++..-..  .+.|.    ++.
T Consensus        22 ~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~--~~~g~----~~~   95 (476)
T 2ce7_A           22 EEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVE--LFVGV----GAA   95 (476)
T ss_dssp             HHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTT--CCTTH----HHH
T ss_pred             HHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHH--HHhcc----cHH
Confidence            45555666555432           23457999999999999999999999999988887753221  11210    000


Q ss_pred             EEEeccHHHHHhh-cCcEEEEeCCCCCCcc
Q psy4122          97 AIYYDQSAVRAAI-EGRVLILEGIEKAERN  125 (162)
Q Consensus        97 ~~~~~gpl~~A~~-~G~vlllDEId~a~~~  125 (162)
                        -....+..|.. ...+|+|||||.+.++
T Consensus        96 --~~r~lf~~A~~~~p~ILfIDEid~l~~~  123 (476)
T 2ce7_A           96 --RVRDLFAQAKAHAPCIVFIDEIDAVGRH  123 (476)
T ss_dssp             --HHHHHHHHHHHTCSEEEEEETGGGTCCC
T ss_pred             --HHHHHHHHHHhcCCCEEEEechhhhhhh
Confidence              01112334433 3469999999987653

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.91  E-value=2.9e-09  Score=88.28  Aligned_cols=109  Identities=10%  Similarity=0.074  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHhcC---CCCcEEEEcCCCchHHHHHHHHHHHh-----------CCceEEEEeccCC-Chhhhccee--
Q psy4122          28 QDWLSHLRWILQKDN---MSQDVFLIGKPGSLRRSLAMSYLELT-----------QREVEYICLSRDT-TEADIKQRR--   90 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~---~g~~vlL~GppG~GKT~La~~lA~~l-----------g~p~~~v~~~~~~-~~~dL~g~~--   90 (162)
                      ...++.+...+..+.   ...+++|+||||||||++++.+++.+           +.++.+++|.... +..++....  
T Consensus        26 ~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~  105 (384)
T 2qby_B           26 EDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAG  105 (384)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHH
Confidence            455566665555432   23469999999999999999999887           8888888876544 433332100  


Q ss_pred             Ee---ecCeEEEeccH----HHHHhhcCc-EEEEeCCCCCCccH-HHH-HHHhhcC
Q psy4122          91 EI---VNGTAIYYDQS----AVRAAIEGR-VLILEGIEKAERNV-LPV-LNNLLEN  136 (162)
Q Consensus        91 ~~---~~G~~~~~~gp----l~~A~~~G~-vlllDEId~a~~~v-~~~-L~~lle~  136 (162)
                      .+   ..+........    +...+...+ +|+|||++.+.... .+. |..+++.
T Consensus       106 ~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~  161 (384)
T 2qby_B          106 KLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRS  161 (384)
T ss_dssp             HHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTS
T ss_pred             HhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcC
Confidence            00   00000000111    223343434 99999999876542 455 5565553

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.91  E-value=3.9e-09  Score=83.94  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=30.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .++++|+||||||||++|+.+|..++.|+..+++.
T Consensus        45 ~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~   79 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGS   79 (257)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSC
T ss_pred             CCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHH
Confidence            45799999999999999999999999998766553

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=98.90  E-value=2.5e-09  Score=92.76  Aligned_cols=89  Identities=12%  Similarity=0.052  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHHh-----------cCCCCcEEEEcCCCchHHHHHHHHHHHh-CCceEEEEeccCCChhhhcceeEeecC
Q psy4122          28 QDWLSHLRWILQK-----------DNMSQDVFLIGKPGSLRRSLAMSYLELT-QREVEYICLSRDTTEADIKQRREIVNG   95 (162)
Q Consensus        28 ~~~~~~L~~i~~~-----------~~~g~~vlL~GppG~GKT~La~~lA~~l-g~p~~~v~~~~~~~~~dL~g~~~~~~G   95 (162)
                      ....+.|+.++..           ....+++||+||||||||++|+++|..+ +.++..+++..-  .+...|.      
T Consensus       140 ~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l--~~~~~g~------  211 (444)
T 2zan_A          140 EGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDL--VSKWLGE------  211 (444)
T ss_dssp             HHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC-----------------
T ss_pred             HHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHH--Hhhhcch------
Confidence            5666677665521           1234679999999999999999999998 777766655421  1111110      


Q ss_pred             eEEEeccHHHHHh-hcCcEEEEeCCCCCCc
Q psy4122          96 TAIYYDQSAVRAA-IEGRVLILEGIEKAER  124 (162)
Q Consensus        96 ~~~~~~gpl~~A~-~~G~vlllDEId~a~~  124 (162)
                      ........+..|. ...++|+|||||.+.+
T Consensus       212 ~~~~~~~~f~~a~~~~~~vl~iDEid~l~~  241 (444)
T 2zan_A          212 SEKLVKNLFQLARENKPSIIFIDEIDSLCG  241 (444)
T ss_dssp             CCCTHHHHHHHHHHSCSEEEEESCTTTTCC
T ss_pred             HHHHHHHHHHHHHHcCCeEEEEechHhhcc
Confidence            0000011122222 2357999999998743

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.89  E-value=7.6e-10  Score=96.65  Aligned_cols=72  Identities=13%  Similarity=0.183  Sum_probs=46.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh-hcCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA-IEGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~-~~G~vlllDEId~  121 (162)
                      ..+.+||+||||||||++|+++|..+|.++..++++      ++...+  .+.+..-....+..|- ....+|++||||.
T Consensus       214 ~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s------~l~~~~--vGese~~ir~lF~~A~~~aP~IifiDEiDa  285 (434)
T 4b4t_M          214 APKGALMYGPPGTGKTLLARACAAQTNATFLKLAAP------QLVQMY--IGEGAKLVRDAFALAKEKAPTIIFIDELDA  285 (434)
T ss_dssp             CCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGG------GGCSSC--SSHHHHHHHHHHHHHHHHCSEEEEEECTHH
T ss_pred             CCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehh------hhhhcc--cchHHHHHHHHHHHHHhcCCeEEeecchhh
Confidence            345799999999999999999999999998877764      333210  0000000001122232 3457999999975


Q ss_pred             C
Q psy4122         122 A  122 (162)
Q Consensus       122 a  122 (162)
                      +
T Consensus       286 l  286 (434)
T 4b4t_M          286 I  286 (434)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=98.88  E-value=9.3e-09  Score=85.61  Aligned_cols=107  Identities=11%  Similarity=0.042  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEE--EEecc--------CCChhhhcceeEeec---
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEY--ICLSR--------DTTEADIKQRREIVN---   94 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~--v~~~~--------~~~~~dL~g~~~~~~---   94 (162)
                      +...+.|...++.....+.+||+||||+|||++|+.+|+.+..+...  ..|..        .-...|+.   .+..   
T Consensus         8 ~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~---~~~~~~~   84 (334)
T 1a5t_A            8 RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYY---TLAPEKG   84 (334)
T ss_dssp             HHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEE---EECCCTT
T ss_pred             HHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEE---EEecccc
Confidence            44556666666655555459999999999999999999987643210  00000        00001111   0100   


Q ss_pred             CeEEEec--cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          95 GTAIYYD--QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        95 G~~~~~~--gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ++..-.+  ..+.+.+      ....+++|||+|+++.+.++.|+..+|+.
T Consensus        85 ~~~~~i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep  135 (334)
T 1a5t_A           85 KNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEP  135 (334)
T ss_dssp             CSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSC
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCC
Confidence            0000000  0111111      12369999999999999999999999963

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.87  E-value=1.5e-09  Score=90.11  Aligned_cols=84  Identities=19%  Similarity=0.220  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHhcCC--CCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEeccCCChhhhcceeEeecCeEEEeccH
Q psy4122          30 WLSHLRWILQKDNM--SQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        30 ~~~~L~~i~~~~~~--g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      .++.+..++..+..  +.+++|+||||||||+|+..+|..+    |.++.++++..-  ..++...  ..+|.  +  ..
T Consensus       136 ~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l--~~~l~~~--~~~~~--~--~~  207 (308)
T 2qgz_A          136 AFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSF--AIDVKNA--ISNGS--V--KE  207 (308)
T ss_dssp             HHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHH--HHHHHCC--CC--------CC
T ss_pred             HHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHH--HHHHHHH--hccch--H--HH
Confidence            34444455555432  5799999999999999999999744    467766666421  2233321  12222  1  12


Q ss_pred             HHHHhhcCcEEEEeCCCC
Q psy4122         104 AVRAAIEGRVLILEGIEK  121 (162)
Q Consensus       104 l~~A~~~G~vlllDEId~  121 (162)
                      +...+.+..+|+||||..
T Consensus       208 ~~~~~~~~~lLiiDdig~  225 (308)
T 2qgz_A          208 EIDAVKNVPVLILDDIGA  225 (308)
T ss_dssp             TTHHHHTSSEEEEETCCC
T ss_pred             HHHHhcCCCEEEEcCCCC
Confidence            345566778999999954

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.86  E-value=1.2e-09  Score=95.52  Aligned_cols=73  Identities=19%  Similarity=0.170  Sum_probs=47.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~  121 (162)
                      ..+.+||+||||||||.+|+++|..++.++..++++      ++...+.  +.+.......+..|-. ...+|+|||||.
T Consensus       215 ~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s------~l~sk~v--Gesek~ir~lF~~Ar~~aP~IIfiDEiDa  286 (437)
T 4b4t_I          215 PPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGS------ELIQKYL--GDGPRLCRQIFKVAGENAPSIVFIDEIDA  286 (437)
T ss_dssp             CCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESG------GGCCSSS--SHHHHHHHHHHHHHHHTCSEEEEEEEESS
T ss_pred             CCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHH------HhhhccC--chHHHHHHHHHHHHHhcCCcEEEEehhhh
Confidence            345699999999999999999999999998877765      3332100  0000000011222322 357999999987


Q ss_pred             CC
Q psy4122         122 AE  123 (162)
Q Consensus       122 a~  123 (162)
                      +.
T Consensus       287 i~  288 (437)
T 4b4t_I          287 IG  288 (437)
T ss_dssp             SS
T ss_pred             hc
Confidence            53

>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=98.85  E-value=2.2e-09  Score=99.71  Aligned_cols=105  Identities=12%  Similarity=0.213  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~   97 (162)
                      ...++.+..++... ...+++|+||||||||++|+.+|..+          +.++..+.+..........       |.+
T Consensus       176 ~~~i~~l~~~l~~~-~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~-------g~~  247 (854)
T 1qvr_A          176 DEEIRRVIQILLRR-TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYR-------GEF  247 (854)
T ss_dssp             HHHHHHHHHHHHCS-SCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------------CH
T ss_pred             HHHHHHHHHHHhcC-CCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccc-------hHH
Confidence            45555555555443 23489999999999999999999887          6665555443211111111       110


Q ss_pred             EEeccHHHHHhhc---CcEEEEeCCCCCC--------ccHHHHHHHhhcCCeEE
Q psy4122          98 IYYDQSAVRAAIE---GRVLILEGIEKAE--------RNVLPVLNNLLENREMH  140 (162)
Q Consensus        98 ~~~~gpl~~A~~~---G~vlllDEId~a~--------~~v~~~L~~lle~r~l~  140 (162)
                      ...-..+...+..   ..+|+|||++.+.        .++.+.|.++++++.+.
T Consensus       248 ~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~~~~i~  301 (854)
T 1qvr_A          248 EERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELR  301 (854)
T ss_dssp             HHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTTCCC
T ss_pred             HHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHHhCCCeE
Confidence            0000112222322   3488999999987        66778899999887653

>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=98.85  E-value=9.5e-09  Score=85.20  Aligned_cols=98  Identities=12%  Similarity=0.226  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc---eEEEEecc--CCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE---VEYICLSR--DTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p---~~~v~~~~--~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      .+..++.|...+...... |++|+||||||||++++.+|..+..+   .....++.  .....++...  +         
T Consensus        30 ~~~~~~~L~~~i~~g~~~-~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~~~~~~~~ir~~--i---------   97 (340)
T 1sxj_C           30 QNEVITTVRKFVDEGKLP-HLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQ--I---------   97 (340)
T ss_dssp             CHHHHHHHHHHHHTTCCC-CEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTH--H---------
T ss_pred             cHHHHHHHHHHHhcCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCcccccHHHHHHH--H---------
Confidence            367788888777764433 49999999999999999999876432   12233321  1112111100  0         


Q ss_pred             cHHHHH---h-hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRA---A-IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A---~-~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +.+...   + ....++++||++.++.+.++.|..++|+
T Consensus        98 ~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~  136 (340)
T 1sxj_C           98 KDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIER  136 (340)
T ss_dssp             HHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhc
Confidence            000000   1 1247899999999999999999999985

>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=98.85  E-value=6.9e-09  Score=85.29  Aligned_cols=107  Identities=17%  Similarity=0.228  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHHhc---CCCCcEEEEcCCCchHHHHHHHHHHHh------CCceEEEEeccCCChhhhccee----E--e
Q psy4122          28 QDWLSHLRWILQKD---NMSQDVFLIGKPGSLRRSLAMSYLELT------QREVEYICLSRDTTEADIKQRR----E--I   92 (162)
Q Consensus        28 ~~~~~~L~~i~~~~---~~g~~vlL~GppG~GKT~La~~lA~~l------g~p~~~v~~~~~~~~~dL~g~~----~--~   92 (162)
                      ..-++.|...+...   ..+.+++|+||+|||||++++.++..+      +.++.++++....+..++....    .  .
T Consensus        26 ~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~  105 (386)
T 2qby_A           26 EDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKV  105 (386)
T ss_dssp             HHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCC
T ss_pred             HHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCC
Confidence            44555565555532   235689999999999999999999887      7888888876544443333210    0  0


Q ss_pred             -ecCeEEEe--ccHHHHHhhc---CcEEEEeCCCCCC----ccHHHHHHHhhc
Q psy4122          93 -VNGTAIYY--DQSAVRAAIE---GRVLILEGIEKAE----RNVLPVLNNLLE  135 (162)
Q Consensus        93 -~~G~~~~~--~gpl~~A~~~---G~vlllDEId~a~----~~v~~~L~~lle  135 (162)
                       ..|.. ..  ...+..++..   ..+|+|||++.+.    .+.+..|...++
T Consensus       106 ~~~~~~-~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~  157 (386)
T 2qby_A          106 PFTGLS-IAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINS  157 (386)
T ss_dssp             CSSSCC-HHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHH
T ss_pred             CCCCCC-HHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchh
Confidence             01100 00  0012223332   3589999998864    677777877774

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.85  E-value=1.3e-09  Score=95.01  Aligned_cols=71  Identities=13%  Similarity=0.102  Sum_probs=46.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEK  121 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~  121 (162)
                      ..+.+||+||||||||++|+++|..+|.++..++++.-.+  ..+|.      +..-....+..|-. ...++++||+|.
T Consensus       205 ~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~~--~~~Ge------~e~~ir~lF~~A~~~aP~IifiDEiD~  276 (428)
T 4b4t_K          205 PPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVH--KYLGE------GPRMVRDVFRLARENAPSIIFIDEVDS  276 (428)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTCC--SSCSH------HHHHHHHHHHHHHHTCSEEEEEECTHH
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhhc--cccch------hHHHHHHHHHHHHHcCCCeeechhhhh
Confidence            3445999999999999999999999999998887753211  11210      00000112233332 347899999975

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.84  E-value=1.6e-09  Score=95.34  Aligned_cols=74  Identities=16%  Similarity=0.187  Sum_probs=48.3

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIE  120 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId  120 (162)
                      ...+.+||+||||||||++|+++|..++.++..++++      +|+..+  .+.+..-....+..|-. ...+|++||||
T Consensus       241 ~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s------~L~sk~--vGesek~ir~lF~~Ar~~aP~IIfiDEiD  312 (467)
T 4b4t_H          241 DPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGS------ELVQKY--VGEGARMVRELFEMARTKKACIIFFDEID  312 (467)
T ss_dssp             CCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGG------GGCCCS--SSHHHHHHHHHHHHHHHTCSEEEEEECCT
T ss_pred             CCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhH------Hhhccc--CCHHHHHHHHHHHHHHhcCCceEeecccc
Confidence            3456799999999999999999999999998888765      333210  00000000012233332 35799999998


Q ss_pred             CCC
Q psy4122         121 KAE  123 (162)
Q Consensus       121 ~a~  123 (162)
                      .+.
T Consensus       313 ai~  315 (467)
T 4b4t_H          313 AVG  315 (467)
T ss_dssp             TTS
T ss_pred             ccc
Confidence            754

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=98.82  E-value=3.4e-09  Score=91.94  Aligned_cols=88  Identities=14%  Similarity=0.080  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHHHh----cCCCCcEEEEcCCCchHHHHHHHHHHHhC--CceEEEEeccCCChhhhcceeEeecCeEEEec
Q psy4122          28 QDWLSHLRWILQK----DNMSQDVFLIGKPGSLRRSLAMSYLELTQ--REVEYICLSRDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        28 ~~~~~~L~~i~~~----~~~g~~vlL~GppG~GKT~La~~lA~~lg--~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      ....+.++.++..    ...++++||+||||||||++|+.+|..++  .++..+++....  +...|.    .+.   ..
T Consensus        43 ~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~--~~~~~~----~~~---~~  113 (456)
T 2c9o_A           43 ENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVY--STEIKK----TEV---LM  113 (456)
T ss_dssp             HHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGC--CSSSCH----HHH---HH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHH--HHhhhh----hHH---HH
Confidence            4455544444433    23446899999999999999999999999  666655554221  111110    000   01


Q ss_pred             cHHHHH----hhcCcEEEEeCCCCCCc
Q psy4122         102 QSAVRA----AIEGRVLILEGIEKAER  124 (162)
Q Consensus       102 gpl~~A----~~~G~vlllDEId~a~~  124 (162)
                      ..+.+|    ..++.+|++||||.+.+
T Consensus       114 ~~f~~a~~~~~~~~~il~iDEid~l~~  140 (456)
T 2c9o_A          114 ENFRRAIGLRIKETKEVYEGEVTELTP  140 (456)
T ss_dssp             HHHHHTEEEEEEEEEEEEEEEEEEEEE
T ss_pred             HHHHHHHhhhhcCCcEEEEechhhccc
Confidence            122222    23457999999987654

>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=98.80  E-value=1.3e-08  Score=84.55  Aligned_cols=92  Identities=18%  Similarity=0.248  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC------CceEEEEecc-CCChhhhcceeEeecCeEEEec
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ------REVEYICLSR-DTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg------~p~~~v~~~~-~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      ...+.|+..++... ..++||+||||+|||++|+.+|+..+      ..+..++... +...+++.              
T Consensus         4 ~~~~~L~~~i~~~~-~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir--------------   68 (305)
T 2gno_A            4 DQLETLKRIIEKSE-GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIR--------------   68 (305)
T ss_dssp             CHHHHHHHHHHTCS-SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHH--------------
T ss_pred             HHHHHHHHHHHCCC-CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHH--------------
Confidence            45677888877655 44789999999999999999998531      2222222211 22222222              


Q ss_pred             cHHHHHh------hcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRAA------IEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A~------~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       .+.+.+      ....+++|||+++++.+.+++|+..||+
T Consensus        69 -~li~~~~~~p~~~~~kvviIdead~lt~~a~naLLk~LEe  108 (305)
T 2gno_A           69 -TIKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEE  108 (305)
T ss_dssp             -HHHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHS
T ss_pred             -HHHHHHhhccccCCceEEEeccHHHhCHHHHHHHHHHHhC
Confidence             111111      1236999999999999999999999997

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.79  E-value=4.4e-09  Score=91.75  Aligned_cols=97  Identities=14%  Similarity=0.215  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCeE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGTA   97 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~~   97 (162)
                      ...++.+..++... ...|+||+||||||||++|+.+|..+          +.++..+++.     ....       |.+
T Consensus       186 ~~~i~~l~~~l~r~-~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~-----~~~~-------g~~  252 (468)
T 3pxg_A          186 SKEIQRVIEVLSRR-TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-----TKYR-------GEF  252 (468)
T ss_dssp             HHHHHHHHHHHHCS-SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------------------
T ss_pred             HHHHHHHHHHHhcc-CCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCC-----cccc-------chH
Confidence            55566666666553 33489999999999999999999886          4444444433     1111       111


Q ss_pred             EEeccHHHHHhh--cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122          98 IYYDQSAVRAAI--EGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus        98 ~~~~gpl~~A~~--~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .-.-..+...+.  .+.+|+||    ...+.++.|.+.|+++.+.+
T Consensus       253 e~~~~~~~~~~~~~~~~iLfiD----~~~~a~~~L~~~L~~g~v~v  294 (468)
T 3pxg_A          253 EDRLKKVMDEIRQAGNIILFID----AAIDASNILKPSLARGELQC  294 (468)
T ss_dssp             CTTHHHHHHHHHTCCCCEEEEC----C--------CCCTTSSSCEE
T ss_pred             HHHHHHHHHHHHhcCCeEEEEe----CchhHHHHHHHhhcCCCEEE
Confidence            101112333333  35789999    56778888999999886544

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=98.78  E-value=3e-08  Score=86.79  Aligned_cols=35  Identities=14%  Similarity=0.280  Sum_probs=32.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .++++|+||||||||++|+.+|..++.++..+.++
T Consensus        50 ~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~   84 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEAT   84 (444)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHcCCCceeecch
Confidence            46899999999999999999999999999888764

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.77  E-value=3.6e-09  Score=96.55  Aligned_cols=107  Identities=11%  Similarity=0.140  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---Cc-----eEEEEeccCCChhhhcceeEeecCeEEE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---RE-----VEYICLSRDTTEADIKQRREIVNGTAIY   99 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p-----~~~v~~~~~~~~~dL~g~~~~~~G~~~~   99 (162)
                      ...++.+..++... .+.+++|+||||||||++|+.+|..+.   .|     ...+.++    ..++.... ...|.+..
T Consensus       192 ~~~i~~l~~~l~~~-~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~----~~~l~~~~-~~~g~~e~  265 (758)
T 1r6b_X          192 EKELERAIQVLCRR-RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLD----IGSLLAGT-KYRGDFEK  265 (758)
T ss_dssp             HHHHHHHHHHHTSS-SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECC----CC---CCC-CCSSCHHH
T ss_pred             HHHHHHHHHHHhcc-CCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEc----HHHHhccc-cccchHHH
Confidence            34455555555433 445899999999999999999998762   11     1112221    11121100 00111110


Q ss_pred             eccHHHHHhhc--CcEEEEeCCCCC---------CccHHHHHHHhhcCCeEE
Q psy4122         100 YDQSAVRAAIE--GRVLILEGIEKA---------ERNVLPVLNNLLENREMH  140 (162)
Q Consensus       100 ~~gpl~~A~~~--G~vlllDEId~a---------~~~v~~~L~~lle~r~l~  140 (162)
                      .-..+...+..  +.+|+|||++.+         ..++.+.|.++++++.+.
T Consensus       266 ~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~~~~~  317 (758)
T 1r6b_X          266 RFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIR  317 (758)
T ss_dssp             HHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCE
T ss_pred             HHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhCCCeE
Confidence            00112223322  579999999987         334567788888876553

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=98.72  E-value=4.7e-09  Score=97.75  Aligned_cols=72  Identities=14%  Similarity=0.199  Sum_probs=48.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeE-EEeccHHHHHhhc-CcEEEEeCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTA-IYYDQSAVRAAIE-GRVLILEGIEK  121 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~-~~~~gpl~~A~~~-G~vlllDEId~  121 (162)
                      .+.+||+||||||||+||+++|..+|.++..+++.      ++++.+   .|.. .-....+..|.++ +.+|+|||||.
T Consensus       238 p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~------~l~sk~---~gese~~lr~lF~~A~~~~PsIIfIDEiDa  308 (806)
T 3cf2_A          238 PRGILLYGPPGTGKTLIARAVANETGAFFFLINGP------EIMSKL---AGESESNLRKAFEEAEKNAPAIIFIDELDA  308 (806)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHH------HHHSSC---TTHHHHHHHHHHHHHTTSCSEEEEEESGGG
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhH------Hhhccc---chHHHHHHHHHHHHHHHcCCeEEEEehhcc
Confidence            35699999999999999999999999998877764      333210   0100 0000123344333 57999999998


Q ss_pred             CCc
Q psy4122         122 AER  124 (162)
Q Consensus       122 a~~  124 (162)
                      +.+
T Consensus       309 l~~  311 (806)
T 3cf2_A          309 IAP  311 (806)
T ss_dssp             TCC
T ss_pred             ccc
Confidence            654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.66  E-value=1.8e-08  Score=92.27  Aligned_cols=98  Identities=14%  Similarity=0.200  Sum_probs=53.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----------CCceEEEEeccCCChhhhcceeEeecCe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----------QREVEYICLSRDTTEADIKQRREIVNGT   96 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----------g~p~~~v~~~~~~~~~dL~g~~~~~~G~   96 (162)
                      -...++.+..++... ...|+||+||||||||++|+.+|..+          +.++..+++     ....       .|.
T Consensus       185 ~~~~i~~l~~~l~~~-~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~-----g~~~-------~G~  251 (758)
T 3pxi_A          185 RSKEIQRVIEVLSRR-TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM-----GTKY-------RGE  251 (758)
T ss_dssp             CHHHHHHHHHHHHCS-SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC---------------------
T ss_pred             chHHHHHHHHHHhCC-CCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc-----cccc-------cch
Confidence            355666666666543 34489999999999999999999986          444433333     0001       122


Q ss_pred             EEEeccHHHHHhh--cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122          97 AIYYDQSAVRAAI--EGRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus        97 ~~~~~gpl~~A~~--~G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      +...-..+...+.  .+.+|+||    ...+.++.|.+.++++.+.+
T Consensus       252 ~e~~l~~~~~~~~~~~~~iLfiD----~~~~~~~~L~~~l~~~~v~~  294 (758)
T 3pxi_A          252 FEDRLKKVMDEIRQAGNIILFID----AAIDASNILKPSLARGELQC  294 (758)
T ss_dssp             -CTTHHHHHHHHHTCCCCEEEEC----C--------CCCTTSSSCEE
T ss_pred             HHHHHHHHHHHHHhcCCEEEEEc----CchhHHHHHHHHHhcCCEEE
Confidence            2111122333332  35799999    66778889999999877654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=98.63  E-value=2.6e-07  Score=81.76  Aligned_cols=52  Identities=19%  Similarity=0.188  Sum_probs=39.9

Q ss_pred             CHHHHHHHHHHHHhc-----------CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          27 TQDWLSHLRWILQKD-----------NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~-----------~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .......++.+...+           ...+.++|+||||||||+|++.+|...+.++..+++.
T Consensus        36 ~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~   98 (499)
T 2dhr_A           36 AEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGS   98 (499)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             cHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehh
Confidence            356666666665432           1234699999999999999999999999888777764

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=98.60  E-value=2e-07  Score=75.86  Aligned_cols=35  Identities=20%  Similarity=0.165  Sum_probs=29.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      ..+.++|+||||||||+|++.+|...+.++..+..
T Consensus        43 ~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g   77 (274)
T 2x8a_A           43 TPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKG   77 (274)
T ss_dssp             CCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEET
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEc
Confidence            34459999999999999999999999887655554

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.59  E-value=3.5e-08  Score=78.79  Aligned_cols=92  Identities=14%  Similarity=0.292  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA  108 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~  108 (162)
                      ..++.|+.++...-....++++||||||||++|..+|..++..+  +.+. .. .+            ..|     ...+
T Consensus        43 ~f~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i--~~fa-ns-~s------------~f~-----l~~l  101 (212)
T 1tue_A           43 TFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAV--ISFV-NS-TS------------HFW-----LEPL  101 (212)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEE--CCCC-CS-SS------------CGG-----GGGG
T ss_pred             HHHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCCCe--eeEE-ec-cc------------hhh-----hccc
Confidence            44777788777532333599999999999999999999875432  1110 00 00            001     1122


Q ss_pred             hcCcEEEEeCCCCCCccH-HHHHHHhhcCCeEEE
Q psy4122         109 IEGRVLILEGIEKAERNV-LPVLNNLLENREMHL  141 (162)
Q Consensus       109 ~~G~vlllDEId~a~~~v-~~~L~~lle~r~l~l  141 (162)
                      ....+++|||++.+..+. ...+..++|.+.+.+
T Consensus       102 ~~~kIiiLDEad~~~~~~~d~~lrn~ldG~~~~i  135 (212)
T 1tue_A          102 TDTKVAMLDDATTTCWTYFDTYMRNALDGNPISI  135 (212)
T ss_dssp             TTCSSEEEEEECHHHHHHHHHHCHHHHHTCCEEE
T ss_pred             CCCCEEEEECCCchhHHHHHHHHHHHhCCCcccH
Confidence            345699999998654333 346788888876555

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.57  E-value=1.5e-07  Score=72.56  Aligned_cols=95  Identities=13%  Similarity=0.150  Sum_probs=56.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChh--hhcceeEeecCe----EEEec-cHHHHHhh-cCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEA--DIKQRREIVNGT----AIYYD-QSAVRAAI-EGR  112 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~--dL~g~~~~~~G~----~~~~~-gpl~~A~~-~G~  112 (162)
                      |+-.+++||+|+|||+++..++..   .|.++..++...|....  .+..    ..|.    ....+ ..+.+.+. ...
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d~r~~~~~i~s----~~g~~~~~~~~~~~~~~~~~~~~~~d   78 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVS----HSGNGVEAHVIERPEEMRKYIEEDTR   78 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-----CCCEECC--------CEECEEESSGGGGGGGCCTTEE
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeeccccccCcccEEe----cCCCceeeEEECCHHHHHHHhcCCCC
Confidence            556789999999999999777754   36666666555443211  1110    1110    00010 11222222 346


Q ss_pred             EEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         113 VLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       113 vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      +|+|||+..++++++..|..+.+.+.-.+-
T Consensus        79 vviIDE~Q~~~~~~~~~l~~l~~~~~~Vi~  108 (184)
T 2orw_A           79 GVFIDEVQFFNPSLFEVVKDLLDRGIDVFC  108 (184)
T ss_dssp             EEEECCGGGSCTTHHHHHHHHHHTTCEEEE
T ss_pred             EEEEECcccCCHHHHHHHHHHHHCCCCEEE
Confidence            999999999999999999999887654443

>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=98.56  E-value=1.4e-07  Score=77.64  Aligned_cols=41  Identities=20%  Similarity=0.377  Sum_probs=30.7

Q ss_pred             CHHHHHHHHHHH-HhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          27 TQDWLSHLRWIL-QKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        27 ~~~~~~~L~~i~-~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+...+.|+..+ ..... .+++|+||+|+|||++++.+|..+
T Consensus        19 ~~~~~~~l~~~~~~~~~~-~~~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E           19 NEELTNFLKSLSDQPRDL-PHLLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             CHHHHHHHHTTTTCTTCC-CCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CHHHHHHHHHHHhhCCCC-CeEEEECCCCCCHHHHHHHHHHHH
Confidence            456666666665 33223 359999999999999999999954

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=98.55  E-value=3.6e-08  Score=91.81  Aligned_cols=71  Identities=15%  Similarity=0.142  Sum_probs=45.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh-cCcEEEEeCCCCCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI-EGRVLILEGIEKAE  123 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~-~G~vlllDEId~a~  123 (162)
                      +.+||+||||||||.+|+++|...+.++..+.      .++|+..+.  +.+..-...-+..|-+ ...||+|||||.+-
T Consensus       512 ~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~------~~~l~s~~v--Gese~~vr~lF~~Ar~~~P~IifiDEiDsl~  583 (806)
T 3cf2_A          512 KGVLFYGPPGCGKTLLAKAIANECQANFISIK------GPELLTMWF--GESEANVREIFDKARQAAPCVLFFDELDSIA  583 (806)
T ss_dssp             SCCEEESSTTSSHHHHHHHHHHTTTCEEEECC------HHHHHTTTC--SSCHHHHHHHHHHHHTTCSEEEECSCGGGCC
T ss_pred             ceEEEecCCCCCchHHHHHHHHHhCCceEEec------cchhhcccc--chHHHHHHHHHHHHHHcCCceeechhhhHHh
Confidence            46999999999999999999999999876443      345543210  1000000112233322 35799999999753

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.48  E-value=3.7e-07  Score=74.06  Aligned_cols=46  Identities=17%  Similarity=0.074  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      +.-++.|...+..   +..++++||+|+|||+|++++++..+  ..++++.
T Consensus        18 ~~el~~L~~~l~~---~~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~   63 (350)
T 2qen_A           18 EEESRKLEESLEN---YPLTLLLGIRRVGKSSLLRAFLNERP--GILIDCR   63 (350)
T ss_dssp             HHHHHHHHHHHHH---CSEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHH
T ss_pred             HHHHHHHHHHHhc---CCeEEEECCCcCCHHHHHHHHHHHcC--cEEEEee
Confidence            4456666666654   46899999999999999999998875  5567765

>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=98.46  E-value=1.9e-07  Score=77.85  Aligned_cols=91  Identities=18%  Similarity=0.155  Sum_probs=52.8

Q ss_pred             CCcEEE--EcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhhccee------Eee-cCeEEEec--cH
Q psy4122          44 SQDVFL--IGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADIKQRR------EIV-NGTAIYYD--QS  103 (162)
Q Consensus        44 g~~vlL--~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL~g~~------~~~-~G~~~~~~--gp  103 (162)
                      +.+++|  +||+|+|||++++.+++.+         +.++.+++|....+..++....      ... .|.. ..+  ..
T Consensus        50 ~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~-~~~~~~~  128 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAP-ALDILKA  128 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCC-HHHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCC-HHHHHHH
Confidence            447888  9999999999999999766         4455667765555555543210      000 1110 000  01


Q ss_pred             HHHHhh---cCcEEEEeCCCCCCc------cHHHHHHHhhc
Q psy4122         104 AVRAAI---EGRVLILEGIEKAER------NVLPVLNNLLE  135 (162)
Q Consensus       104 l~~A~~---~G~vlllDEId~a~~------~v~~~L~~lle  135 (162)
                      +...+.   ...+|+|||++.+..      +++..|...++
T Consensus       129 l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~  169 (412)
T 1w5s_A          129 LVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHE  169 (412)
T ss_dssp             HHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHH
T ss_pred             HHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHH
Confidence            122222   234789999988643      56665556554

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.45  E-value=8.9e-07  Score=71.82  Aligned_cols=35  Identities=11%  Similarity=0.093  Sum_probs=30.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEecc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSR   79 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~   79 (162)
                      ..++++||+|+|||+|++++++..+.+..++++..
T Consensus        31 ~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~   65 (357)
T 2fna_A           31 PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRK   65 (357)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchh
Confidence            58999999999999999999998877777777763

>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=98.33  E-value=1.7e-06  Score=74.85  Aligned_cols=116  Identities=14%  Similarity=0.162  Sum_probs=68.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCC-cEEEEcCCCchHHHHHHHHHHHh---CC-ceEEEEeccC-------------CChhhh
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQ-DVFLIGKPGSLRRSLAMSYLELT---QR-EVEYICLSRD-------------TTEADI   86 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~-~vlL~GppG~GKT~La~~lA~~l---g~-p~~~v~~~~~-------------~~~~dL   86 (162)
                      .+++.=.+.+..++..+..++ ++++.|+||||||+++.++++.+   +. .+..+..+..             .|...+
T Consensus        25 ~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~Aa~~l~~~~~~~~~T~h~~  104 (459)
T 3upu_A           25 DLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLSGKEASTIHSI  104 (459)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHHHHHHHHHHSSCEEEHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCcHHHHHHHHhhhccchhhHHHH
Confidence            367777777777665544344 89999999999999999988655   33 2222222110             011112


Q ss_pred             cceeE-eecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC-CeEEE
Q psy4122          87 KQRRE-IVNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN-REMHL  141 (162)
Q Consensus        87 ~g~~~-~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~-r~l~l  141 (162)
                      .+... ..+....|... .........++++||+...++..+..|...+.. ..+.+
T Consensus       105 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~iiiDE~~~~~~~~~~~l~~~~~~~~~~~~  160 (459)
T 3upu_A          105 LKINPVTYEENVLFEQK-EVPDLAKCRVLICDEVSMYDRKLFKILLSTIPPWCTIIG  160 (459)
T ss_dssp             HTEEEEECSSCEEEEEC-SCCCCSSCSEEEESCGGGCCHHHHHHHHHHSCTTCEEEE
T ss_pred             hccCcccccccchhccc-ccccccCCCEEEEECchhCCHHHHHHHHHhccCCCEEEE
Confidence            22111 11122223211 011234568999999999999999999998873 44544

>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=98.29  E-value=9.5e-07  Score=74.72  Aligned_cols=75  Identities=16%  Similarity=0.196  Sum_probs=45.6

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec--cCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS--RDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEG  118 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~--~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDE  118 (162)
                      +..+..++|+||||||||+||.++|...|.++.++.+.  +..+.   .   . .+.....  .-+.+++.+..+|+|||
T Consensus       120 i~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~---~---~-~~le~~l--~~i~~~l~~~~LLVIDs  190 (331)
T 2vhj_A          120 RYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSG---Y---N-TDFNVFV--DDIARAMLQHRVIVIDS  190 (331)
T ss_dssp             EEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTT---C---B-CCHHHHH--HHHHHHHHHCSEEEEEC
T ss_pred             CCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhh---h---h-cCHHHHH--HHHHHHHhhCCEEEEec
Confidence            33455679999999999999999998777777777772  21111   0   0 0000000  01233444444999999


Q ss_pred             CCCCCc
Q psy4122         119 IEKAER  124 (162)
Q Consensus       119 Id~a~~  124 (162)
                      |+...+
T Consensus       191 I~aL~~  196 (331)
T 2vhj_A          191 LKNVIG  196 (331)
T ss_dssp             CTTTC-
T ss_pred             cccccc
Confidence            987643

>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=98.25  E-value=4.8e-06  Score=66.47  Aligned_cols=95  Identities=14%  Similarity=0.061  Sum_probs=57.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC-hhhhcceeEeecCeEEEe-ccHHHHHhhc------C
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT-EADIKQRREIVNGTAIYY-DQSAVRAAIE------G  111 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~-~~dL~g~~~~~~G~~~~~-~gpl~~A~~~------G  111 (162)
                      .|.-++++||+|+|||+++.+++...   |..+..++...+.. ...+..+..+.-....+. ...+...+++      -
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~   90 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDET   90 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTC
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCC
Confidence            45567889999999999999888554   66777776654432 111211111110111111 1123333333      4


Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      .+|+|||+.-++.+++..|..+.+.+
T Consensus        91 dvViIDEaQ~l~~~~ve~l~~L~~~g  116 (223)
T 2b8t_A           91 KVIGIDEVQFFDDRICEVANILAENG  116 (223)
T ss_dssp             CEEEECSGGGSCTHHHHHHHHHHHTT
T ss_pred             CEEEEecCccCcHHHHHHHHHHHhCC
Confidence            69999999999999888888877654

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=98.20  E-value=9.7e-06  Score=62.01  Aligned_cols=26  Identities=19%  Similarity=0.431  Sum_probs=23.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+.|+||+|||||||++.++..++..
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~i~   27 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCc
Confidence            57899999999999999999988643

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=98.19  E-value=2.3e-06  Score=67.66  Aligned_cols=34  Identities=21%  Similarity=0.213  Sum_probs=29.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      .+.++|+||||||||+|++.+|...+.++..+.+
T Consensus        49 ~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~   82 (254)
T 1ixz_A           49 PKGVLLVGPPGVGKTHLARAVAGEARVPFITASG   82 (254)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeH
Confidence            3459999999999999999999999877665554

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=98.17  E-value=1.5e-06  Score=66.69  Aligned_cols=31  Identities=16%  Similarity=0.214  Sum_probs=28.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++.++|+|++||||||+++.+|+.+|.++.
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l~~~~i   54 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKLNVPFI   54 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHTCCEE
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcCCCEE
Confidence            4678999999999999999999999998854

>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=98.15  E-value=2.2e-06  Score=63.82  Aligned_cols=33  Identities=6%  Similarity=0.030  Sum_probs=28.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYIC   76 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~   76 (162)
                      ++.++|+|+||+||||+++.+|+.++.++..+.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~   35 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFG   35 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCCeEEec
Confidence            457899999999999999999999998765443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=98.15  E-value=1.6e-06  Score=65.05  Aligned_cols=30  Identities=27%  Similarity=0.408  Sum_probs=27.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ++.++|+|+|||||||+++.+|+.+|.++.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i   34 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILY   34 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            457999999999999999999999998854

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=98.15  E-value=5.1e-06  Score=66.78  Aligned_cols=50  Identities=18%  Similarity=0.177  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHhc-----------CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          28 QDWLSHLRWILQKD-----------NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        28 ~~~~~~L~~i~~~~-----------~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      +.....++.+...+           ...+.++|+||||||||+|++.+|...+.++..+.+
T Consensus        46 ~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~  106 (278)
T 1iy2_A           46 EEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASG  106 (278)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEH
T ss_pred             HHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecH
Confidence            55666666555432           223459999999999999999999999877666554

>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=98.12  E-value=9.1e-06  Score=68.88  Aligned_cols=104  Identities=11%  Similarity=0.150  Sum_probs=59.8

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--eEEEEeccCCCh--hh---hcceeEeecCeEEEeccHHH
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--VEYICLSRDTTE--AD---IKQRREIVNGTAIYYDQSAV  105 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--~~~v~~~~~~~~--~d---L~g~~~~~~G~~~~~~gpl~  105 (162)
                      .+++++.  ..+..++++||+||||||+.+.++..++..  -..+......+.  ..   ++.+.........|. ..+.
T Consensus       114 ~l~~l~~--~~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~-~~La  190 (356)
T 3jvv_A          114 VFKRVSD--VPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFS-EALR  190 (356)
T ss_dssp             HHHHHHH--CSSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHH-HHHH
T ss_pred             HHHHHHh--CCCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccccCCHH-HHHH
Confidence            3444432  334589999999999999999998876533  223333211111  00   010111111111222 1466


Q ss_pred             HHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         106 RAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       106 ~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .|++. ..++++||+-  .++....+..+.+.|...+
T Consensus       191 ~aL~~~PdvillDEp~--d~e~~~~~~~~~~~G~~vl  225 (356)
T 3jvv_A          191 SALREDPDIILVGEMR--DLETIRLALTAAETGHLVF  225 (356)
T ss_dssp             HHTTSCCSEEEESCCC--SHHHHHHHHHHHHTTCEEE
T ss_pred             HHhhhCcCEEecCCCC--CHHHHHHHHHHHhcCCEEE
Confidence            77765 4799999997  5677777777777776544

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=98.09  E-value=2.7e-06  Score=63.01  Aligned_cols=28  Identities=18%  Similarity=0.405  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++.+.|+||+||||||+++.+|..++.+
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~~l~~~   31 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQQLNME   31 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            5689999999999999999999999875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=98.08  E-value=2.6e-06  Score=63.18  Aligned_cols=29  Identities=38%  Similarity=0.259  Sum_probs=26.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ++++|+|++||||||+++.+|+.+|.|+.
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~i   36 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVL   36 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            48999999999999999999999999864

>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=98.05  E-value=3.5e-06  Score=61.93  Aligned_cols=28  Identities=11%  Similarity=0.109  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|+|++||||||+++.+++.+|.++.
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i   30 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPII   30 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeee
Confidence            5889999999999999999999998753

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=98.05  E-value=8.3e-06  Score=68.19  Aligned_cols=90  Identities=14%  Similarity=0.187  Sum_probs=54.8

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccC--CChhhhcceeEee--cCeEEEeccHHHHHhh-cCcEEEE
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRD--TTEADIKQRREIV--NGTAIYYDQSAVRAAI-EGRVLIL  116 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~--~~~~dL~g~~~~~--~G~~~~~~gpl~~A~~-~G~vlll  116 (162)
                      ..|+.++++||+|+||||+.+.++......--.+.+...  ...........+.  +|..  ..-.+..|++ +..++++
T Consensus       169 ~~g~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~~~e~~~~~~~~~i~~~~ggg~~--~r~~la~aL~~~p~ilil  246 (330)
T 2pt7_A          169 AIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNIT--SADCLKSCLRMRPDRIIL  246 (330)
T ss_dssp             HHTCCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEESSCCCCCSSCSSEEEEECBTTBC--HHHHHHHHTTSCCSEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECCeeccccccchhEEEEEeCCChh--HHHHHHHHhhhCCCEEEE
Confidence            357899999999999999999999887644344544421  1111111111122  2221  1124566765 4579999


Q ss_pred             eCCCCCCccHHHHHHHhhc
Q psy4122         117 EGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle  135 (162)
                      ||...  .++.+.|..+-.
T Consensus       247 dE~~~--~e~~~~l~~~~~  263 (330)
T 2pt7_A          247 GELRS--SEAYDFYNVLCS  263 (330)
T ss_dssp             CCCCS--THHHHHHHHHHT
T ss_pred             cCCCh--HHHHHHHHHHhc
Confidence            99975  567777666544

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=98.05  E-value=9.4e-06  Score=62.84  Aligned_cols=25  Identities=32%  Similarity=0.499  Sum_probs=22.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |+.+.|+||+||||||+++.++..+
T Consensus         1 G~~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHHHHhhc
Confidence            4578999999999999999999876

>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=98.01  E-value=2.2e-05  Score=62.25  Aligned_cols=110  Identities=12%  Similarity=0.040  Sum_probs=61.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC---hhhhc--ce--eEeecC--
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT---EADIK--QR--REIVNG--   95 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~---~~dL~--g~--~~~~~G--   95 (162)
                      .+.+.=.+.+..++.    ++++++.||+|+|||.++..++...+.+..++.-....-   ...+.  +.  ...-.|  
T Consensus        93 ~l~~~Q~~ai~~~~~----~~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~v~~~~g~~  168 (237)
T 2fz4_A           93 SLRDYQEKALERWLV----DKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRI  168 (237)
T ss_dssp             CCCHHHHHHHHHHTT----TSEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSC
T ss_pred             CcCHHHHHHHHHHHh----CCCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCCeEEEEeCCC
Confidence            345555555555443    457999999999999999998888876655543321100   01111  10  111111  


Q ss_pred             ----e-EEEeccHHHHHh----hcCcEEEEeCCCCCCccHHHHHHHhhcCCe
Q psy4122          96 ----T-AIYYDQSAVRAA----IEGRVLILEGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus        96 ----~-~~~~~gpl~~A~----~~G~vlllDEId~a~~~v~~~L~~lle~r~  138 (162)
                          . .+-..+-+....    ..-.+||+||+++++......+...+....
T Consensus       169 ~~~~~i~v~T~~~l~~~~~~~~~~~~llIiDEaH~l~~~~~~~i~~~~~~~~  220 (237)
T 2fz4_A          169 KELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPF  220 (237)
T ss_dssp             BCCCSEEEEEHHHHHHTHHHHTTTCSEEEEECSSCCCTTTHHHHHHTCCCSE
T ss_pred             CCcCCEEEEeHHHHHhhHHHhcccCCEEEEECCccCCChHHHHHHHhccCCE
Confidence                1 111112222221    124799999999999887776666665443

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=98.01  E-value=4e-06  Score=62.61  Aligned_cols=28  Identities=21%  Similarity=0.184  Sum_probs=25.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|.|+|||||||+++.+|+.+|.++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~   33 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFL   33 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEE
Confidence            6999999999999999999999998753

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=98.00  E-value=4.9e-06  Score=62.40  Aligned_cols=29  Identities=17%  Similarity=0.257  Sum_probs=26.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..++|+|+|||||||+++.+|+.+|.++.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~i   31 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALGVGLL   31 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHTCCEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            46899999999999999999999998853

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=97.99  E-value=2.3e-05  Score=64.41  Aligned_cols=89  Identities=10%  Similarity=0.085  Sum_probs=50.1

Q ss_pred             HHHHHHHHHhcCC-CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhh
Q psy4122          31 LSHLRWILQKDNM-SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAI  109 (162)
Q Consensus        31 ~~~L~~i~~~~~~-g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~  109 (162)
                      ...++.+++.... ...++|+||||||||.+|+++|...+.- -.++.+ +   +           .+     ++. .+.
T Consensus        90 ~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~~l~-G~vn~~-~---~-----------~f-----~l~-~~~  147 (267)
T 1u0j_A           90 ASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWT-N---E-----------NF-----PFN-DCV  147 (267)
T ss_dssp             HHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTT-C---S-----------SC-----TTG-GGS
T ss_pred             HHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhhccc-ceeecc-c---c-----------cc-----ccc-ccc
Confidence            3335555544322 2259999999999999999999876431 111111 0   0           00     111 123


Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      ...+++.||.... .+....+..+++...+.+.
T Consensus       148 ~k~i~l~Ee~~~~-~d~~~~lr~i~~G~~~~id  179 (267)
T 1u0j_A          148 DKMVIWWEEGKMT-AKVVESAKAILGGSKVRVD  179 (267)
T ss_dssp             SCSEEEECSCCEE-TTTHHHHHHHHTTCCEEC-
T ss_pred             ccEEEEeccccch-hHHHHHHHHHhCCCcEEEe
Confidence            4456666666543 4566677888875555553

>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=97.97  E-value=6.2e-06  Score=61.74  Aligned_cols=29  Identities=17%  Similarity=0.306  Sum_probs=26.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ++.++|+|+|||||||+++.+|+.+|.++
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~~~~   39 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSGLKY   39 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHCCEE
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhCCeE
Confidence            56799999999999999999999998764

>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=97.95  E-value=3e-05  Score=60.32  Aligned_cols=96  Identities=7%  Similarity=0.097  Sum_probs=56.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhh--hcceeEeecCeEEEe-ccHHHHHhhc-CcEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEAD--IKQRREIVNGTAIYY-DQSAVRAAIE-GRVLI  115 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~d--L~g~~~~~~G~~~~~-~gpl~~A~~~-G~vll  115 (162)
                      .|+-.+++||.|+|||+.+..++...   |..+..++...|+...+  +..+..+.-....+. ...+...+.. -.+|+
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            35567889999999999998888654   77777776554443221  111100000001111 1123333332 37999


Q ss_pred             EeCCCCCCccHHHHHHHhhcCCe
Q psy4122         116 LEGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus       116 lDEId~a~~~v~~~L~~lle~r~  138 (162)
                      |||+..++++.++.|..+.+.+.
T Consensus        87 IDEaqfl~~~~v~~l~~l~~~~~  109 (191)
T 1xx6_A           87 IDEVQFFDDEIVEIVNKIAESGR  109 (191)
T ss_dssp             ECSGGGSCTHHHHHHHHHHHTTC
T ss_pred             EECCCCCCHHHHHHHHHHHhCCC
Confidence            99999999999998888777643

>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=97.93  E-value=6.7e-06  Score=61.64  Aligned_cols=29  Identities=10%  Similarity=0.194  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..++|+|+|||||||+++.+++.+|.++
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l~~~~   33 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGLRLPL   33 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHTCCE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCeE
Confidence            44689999999999999999999998764

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.93  E-value=4.7e-06  Score=62.38  Aligned_cols=29  Identities=21%  Similarity=0.266  Sum_probs=25.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      |..++|+|+|||||||+++.+|+.+|.++
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l~~~~   32 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQELGFKK   32 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHHTCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            45789999999999999999999998764

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=97.92  E-value=7.6e-06  Score=60.42  Aligned_cols=29  Identities=14%  Similarity=0.240  Sum_probs=26.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +.++|+|+|||||||+++.+|+.+|.++.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~i   31 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALGYEFV   31 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            46899999999999999999999998743

>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=97.92  E-value=1.5e-05  Score=71.45  Aligned_cols=108  Identities=15%  Similarity=0.138  Sum_probs=62.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcc------eeEe---
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQ------RREI---   92 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g------~~~~---   92 (162)
                      .+++.=.+.++.++.    +..+++.|+||||||+++..++..+   |.++..+..+  -...+.+.      ..++   
T Consensus       189 ~L~~~Q~~Av~~~~~----~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT--~~Aa~~L~e~~~~~a~Tih~l  262 (574)
T 3e1s_A          189 GLSEEQASVLDQLAG----HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPT--GKAARRLGEVTGRTASTVHRL  262 (574)
T ss_dssp             TCCHHHHHHHHHHTT----CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS--HHHHHHHHHHHTSCEEEHHHH
T ss_pred             CCCHHHHHHHHHHHh----CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCc--HHHHHHhHhhhcccHHHHHHH
Confidence            356655555555543    5689999999999999999888644   5554433222  11222111      0010   


Q ss_pred             --ecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC-eEEE
Q psy4122          93 --VNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENR-EMHL  141 (162)
Q Consensus        93 --~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r-~l~l  141 (162)
                        ..++ .|....  .......+||+||+..++...+..|...+..+ .+.+
T Consensus       263 l~~~~~-~~~~~~--~~~~~~dvlIIDEasml~~~~~~~Ll~~~~~~~~lil  311 (574)
T 3e1s_A          263 LGYGPQ-GFRHNH--LEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLL  311 (574)
T ss_dssp             TTEETT-EESCSS--SSCCSCSEEEECCGGGCCHHHHHHHHTTSCTTCEEEE
T ss_pred             HcCCcc-hhhhhh--cccccCCEEEEcCccCCCHHHHHHHHHhCcCCCEEEE
Confidence              0010 121110  01124579999999999999888888877643 4555

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.91  E-value=4.5e-06  Score=62.89  Aligned_cols=29  Identities=24%  Similarity=0.318  Sum_probs=25.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..+.|+|+|||||||+++.+|+.+|.++
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~   40 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTH   40 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            45799999999999999999999998653

>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=97.91  E-value=6.2e-06  Score=62.48  Aligned_cols=31  Identities=16%  Similarity=0.207  Sum_probs=26.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHH-hCCceE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLEL-TQREVE   73 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~-lg~p~~   73 (162)
                      .+..++|+|+|||||||+++.+|+. +|.++.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~l~g~~~i   40 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAELDGFQHL   40 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhcCCCEEe
Confidence            3567999999999999999999998 786643

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=97.90  E-value=1.9e-05  Score=60.62  Aligned_cols=27  Identities=15%  Similarity=0.111  Sum_probs=24.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .++.++|+||+|+||||+++.+++.++
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            477899999999999999999998874

>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=97.89  E-value=6.6e-06  Score=61.22  Aligned_cols=29  Identities=17%  Similarity=0.138  Sum_probs=25.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .++.++|+|++|+||||+++.++..+|.+
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~~g~~   35 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQLHAA   35 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHHTCE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhhCcE
Confidence            35679999999999999999999998865

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.89  E-value=8.9e-06  Score=61.11  Aligned_cols=29  Identities=17%  Similarity=0.289  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..++|+|+|||||||+++.+|+.+|.++
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~   37 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKYGYTH   37 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHCCEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            45799999999999999999999999764

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=97.88  E-value=1.1e-05  Score=61.58  Aligned_cols=29  Identities=24%  Similarity=0.311  Sum_probs=25.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..++|+|+|||||||+++.+++.+|.++
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~~~~   48 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLGIPQ   48 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCCE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            34589999999999999999999999874

>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=97.88  E-value=7.2e-06  Score=61.19  Aligned_cols=26  Identities=15%  Similarity=0.199  Sum_probs=23.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +..++|+|+|||||||+++.+++.++
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45789999999999999999999887

>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=97.88  E-value=8.6e-06  Score=59.31  Aligned_cols=27  Identities=22%  Similarity=0.294  Sum_probs=23.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|+|+|||||||+++.+ +.+|.++.
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i   29 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVI   29 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEE
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEE
Confidence            5789999999999999999 88888743

>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=97.87  E-value=7.1e-06  Score=61.64  Aligned_cols=32  Identities=25%  Similarity=0.289  Sum_probs=26.7

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ...|+.+.|+||+||||||+++.++...+.+.
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~La~~~~~g~   37 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEALANLPGVPK   37 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHHHTCSSSCE
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHhccCCCe
Confidence            34577899999999999999999998766553

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=97.87  E-value=1.1e-05  Score=65.13  Aligned_cols=41  Identities=12%  Similarity=0.096  Sum_probs=33.1

Q ss_pred             HHHHHHHhcCC---CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          33 HLRWILQKDNM---SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        33 ~L~~i~~~~~~---g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .|+.+......   |+.+.|+|++||||||+++.+|..+|.++.
T Consensus        34 ~l~~~~~~i~~~l~g~~i~l~G~~GsGKSTl~~~La~~lg~~~~   77 (250)
T 3nwj_A           34 ILKKKAEEVKPYLNGRSMYLVGMMGSGKTTVGKIMARSLGYTFF   77 (250)
T ss_dssp             HHHHHHHTTHHHHTTCCEEEECSTTSCHHHHHHHHHHHHTCEEE
T ss_pred             hhhhhhhhhhhhcCCCEEEEECCCCCCHHHHHHHHHHhcCCcEE
Confidence            34444444444   889999999999999999999999998754

>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=97.86  E-value=2.4e-05  Score=59.60  Aligned_cols=55  Identities=16%  Similarity=0.096  Sum_probs=40.6

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADI   86 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL   86 (162)
                      ..|-.++. .+..|.-++|.||||+|||+++.++|...+.++.++......+...+
T Consensus         7 ~~LD~~l~Ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~~~~~~~~   62 (220)
T 2cvh_A            7 KSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEGGFSPERL   62 (220)
T ss_dssp             HHHHHHTTSSBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSCCCCHHHH
T ss_pred             HHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCCCCCHHHH
Confidence            34555664 45577789999999999999999999866777777776543344433

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.86  E-value=7.2e-06  Score=61.08  Aligned_cols=30  Identities=17%  Similarity=0.083  Sum_probs=22.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +..++|+|+|||||||+++.+++.+|.++.
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~~~~i   34 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLPGSFV   34 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHSTTCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            346899999999999999999999998754

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.85  E-value=1.1e-05  Score=61.71  Aligned_cols=29  Identities=24%  Similarity=0.315  Sum_probs=26.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .|+.+.|+||+||||||+++.++..+|..
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~g~~   56 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADETGLE   56 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHCCE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhhCCe
Confidence            46789999999999999999999999864

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.85  E-value=9.5e-06  Score=60.57  Aligned_cols=28  Identities=21%  Similarity=0.286  Sum_probs=25.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ..++|+|+|||||||+++.+++.+|.++
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~~~~~   31 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKYGYTH   31 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            4689999999999999999999999764

>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=97.84  E-value=1.1e-05  Score=62.34  Aligned_cols=29  Identities=28%  Similarity=0.292  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..++|+|+|||||||+++.+|+.++.++
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~   32 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFHAAH   32 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCceE
Confidence            45789999999999999999999999764

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=97.84  E-value=6.1e-05  Score=60.92  Aligned_cols=35  Identities=11%  Similarity=0.152  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.  ...|+.++++||+||||||+.+.++....
T Consensus        16 vl~~i~--i~~g~~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           16 KVLELC--HRKMGLILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             HHHHGG--GCSSEEEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             HHHHHh--hCCCCEEEEECCCCccHHHHHHHHHHhCC
Confidence            344443  45677899999999999999999998764

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.81  E-value=1.5e-05  Score=58.70  Aligned_cols=28  Identities=14%  Similarity=0.068  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|+|++||||||+++.+++.+|.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i   29 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFY   29 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999998753

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.81  E-value=1.5e-05  Score=60.79  Aligned_cols=28  Identities=18%  Similarity=0.235  Sum_probs=25.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ..++|+|++|+||||+++.+++.+|.++
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~lg~~~   46 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEACGYPF   46 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHHTCCE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCEE
Confidence            4699999999999999999999998763

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.80  E-value=1.5e-05  Score=61.68  Aligned_cols=28  Identities=18%  Similarity=0.109  Sum_probs=25.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +..++|+|+|||||||+++.+|+.++.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~~~   32 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQLA   32 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCc
Confidence            4579999999999999999999999965

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.80  E-value=1.5e-05  Score=61.19  Aligned_cols=28  Identities=21%  Similarity=0.303  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|+|+|||||||+++.+|+.+|.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i   29 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYEIPHI   29 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEe
Confidence            4789999999999999999999987743

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=97.80  E-value=1.4e-05  Score=61.52  Aligned_cols=28  Identities=18%  Similarity=0.216  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|+|||||||||+++.+|+.+|.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i   29 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYGIPHI   29 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4889999999999999999999987643

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=97.79  E-value=1.5e-05  Score=59.45  Aligned_cols=28  Identities=21%  Similarity=0.256  Sum_probs=25.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ..++|+|+|||||||+++.+++.+|.++
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l~~~~   34 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDFGWVH   34 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            4689999999999999999999998764

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.79  E-value=3e-05  Score=61.57  Aligned_cols=30  Identities=13%  Similarity=0.153  Sum_probs=26.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+..++|.||||+||||+++.+++.+|.+.
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~g~~~   57 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSHCYCH   57 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHCCEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            344689999999999999999999998764

>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=97.78  E-value=2.4e-05  Score=66.43  Aligned_cols=97  Identities=11%  Similarity=0.170  Sum_probs=51.3

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCCc--eEEEEeccCCChhhhcceeE-eec-----CeEEEeccHHHHHhhcC-
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQRE--VEYICLSRDTTEADIKQRRE-IVN-----GTAIYYDQSAVRAAIEG-  111 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~p--~~~v~~~~~~~~~dL~g~~~-~~~-----G~~~~~~gpl~~A~~~G-  111 (162)
                      ...|+.++++||+|+||||+++.++......  -..+......+. .+..... +..     ....| ...+..+++.+ 
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~e~~~e~-~~~~~~~~v~Q~~~g~~~~~~-~~~l~~~L~~~p  210 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEY-VFKHKKSIVNQREVGEDTKSF-ADALRAALREDP  210 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEEESSCCS-CCCCSSSEEEEEEBTTTBSCS-HHHHHHHTTSCC
T ss_pred             hcCCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEecccHhh-hhccCceEEEeeecCCCHHHH-HHHHHHHhhhCc
Confidence            3456789999999999999999999876432  122222211111 0110000 000     11122 23455666554 


Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      .++++||+-  .++....+......+...+
T Consensus       211 d~illdE~~--d~e~~~~~l~~~~~g~~vi  238 (372)
T 2ewv_A          211 DVIFVGEMR--DLETVETALRAAETGHLVF  238 (372)
T ss_dssp             SEEEESCCC--SHHHHHHHHHHHTTTCEEE
T ss_pred             CEEEECCCC--CHHHHHHHHHHHhcCCEEE
Confidence            699999996  3443333333345555444

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.78  E-value=1.6e-05  Score=61.64  Aligned_cols=30  Identities=20%  Similarity=0.174  Sum_probs=26.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +..++|+|+|||||||+++.+|+.+|.++.
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i   34 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEYGLAHL   34 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHCCEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCceEE
Confidence            357899999999999999999999997643

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.78  E-value=1.1e-05  Score=59.57  Aligned_cols=25  Identities=24%  Similarity=0.332  Sum_probs=21.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHH-HhCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE-LTQR   70 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~-~lg~   70 (162)
                      .++|.|+||+||||+++.+++ .+|.
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~~~~~~   29 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIAKNPGF   29 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHSTTE
T ss_pred             EEEEecCCCCCHHHHHHHHHhhcCCc
Confidence            588999999999999999998 4553

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.76  E-value=1.7e-05  Score=61.81  Aligned_cols=29  Identities=14%  Similarity=0.194  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..++|+|+|||||||+++.+|+.+|.++
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~   35 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHFELKH   35 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHSSSEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCeE
Confidence            35699999999999999999999998764

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=97.76  E-value=2e-05  Score=61.73  Aligned_cols=29  Identities=17%  Similarity=0.112  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..++|+|+|||||||+++.+|+.++.++
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~   44 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFCVCH   44 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCce
Confidence            35799999999999999999999999764

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=97.75  E-value=1.9e-05  Score=59.41  Aligned_cols=27  Identities=11%  Similarity=0.244  Sum_probs=24.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+.|+|++||||||+++.+|+.++.++
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~   28 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEI   28 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcE
Confidence            478999999999999999999999754

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=97.75  E-value=2e-05  Score=60.72  Aligned_cols=29  Identities=17%  Similarity=0.164  Sum_probs=25.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..+.|+||+||||||+++.+++.+|.++.
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~   34 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLL   34 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcc
Confidence            46899999999999999999999987643

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.74  E-value=2e-05  Score=63.06  Aligned_cols=27  Identities=19%  Similarity=0.134  Sum_probs=24.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.|||||||||+++.+|+.++.++
T Consensus         3 li~I~G~~GSGKSTla~~La~~~~~~~   29 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQETGWPV   29 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCCE
T ss_pred             EEEEECCCCcCHHHHHHHHHhcCCCeE
Confidence            478999999999999999999998764

>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=97.74  E-value=2.6e-05  Score=58.34  Aligned_cols=33  Identities=18%  Similarity=0.214  Sum_probs=28.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYI   75 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v   75 (162)
                      .|..+.|+|++||||||+++.++..+   |.|+..+
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~   39 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTL   39 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEE
Confidence            35678999999999999999999987   8886544

>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=97.72  E-value=2.2e-05  Score=59.35  Aligned_cols=32  Identities=16%  Similarity=0.264  Sum_probs=27.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh-CCceEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT-QREVEYI   75 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l-g~p~~~v   75 (162)
                      +..+.|+|++||||||+++.+++.+ |.++..+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~   36 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESIPANTIKYL   36 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTSCGGGEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHCCCceEEE
Confidence            5679999999999999999999988 5765543

>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=97.72  E-value=2.3e-05  Score=60.51  Aligned_cols=27  Identities=19%  Similarity=0.178  Sum_probs=24.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|+|+|||||||+++.+|+.+|.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~g~~~   28 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKYGIPQ   28 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            489999999999999999999998764

>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=97.71  E-value=5.8e-05  Score=57.65  Aligned_cols=27  Identities=19%  Similarity=0.278  Sum_probs=24.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|..+.|+||+||||||+++.+|..+
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            356789999999999999999999988

>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=97.70  E-value=5.6e-05  Score=67.94  Aligned_cols=32  Identities=13%  Similarity=0.196  Sum_probs=23.7

Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcC-CeEEE
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLEN-REMHL  141 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~-r~l~l  141 (162)
                      +..++|+||.+.++...+..|...+.. .++.+
T Consensus       262 ~~d~lIIDEAsml~~~~~~~Ll~~l~~~~~liL  294 (608)
T 1w36_D          262 HLDVLVVDEASMIDLPMMSRLIDALPDHARVIF  294 (608)
T ss_dssp             SCSEEEECSGGGCBHHHHHHHHHTCCTTCEEEE
T ss_pred             CCCEEEEechhhCCHHHHHHHHHhCCCCCEEEE
Confidence            457999999999988777777776653 45555

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=97.70  E-value=1.6e-05  Score=59.23  Aligned_cols=24  Identities=17%  Similarity=0.213  Sum_probs=22.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .++|+|+|||||||+++.+++.++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            588999999999999999999876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=97.69  E-value=3.5e-05  Score=57.49  Aligned_cols=29  Identities=21%  Similarity=0.083  Sum_probs=25.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEY   74 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~   74 (162)
                      .+.|+|++||||||+++.+++.+   |.++..
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~   33 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSL   33 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence            47899999999999999999987   887553

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=97.69  E-value=5.7e-05  Score=58.98  Aligned_cols=33  Identities=18%  Similarity=0.271  Sum_probs=24.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH--------hC-CceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL--------TQ-REVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~--------lg-~p~~~v~~~   78 (162)
                      -.+++|+||+|||++|..++..        .| +++.+.++.
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~   48 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIK   48 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCC
Confidence            5789999999999999886533        34 776656554

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=97.68  E-value=2.7e-05  Score=61.11  Aligned_cols=27  Identities=15%  Similarity=0.143  Sum_probs=24.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.||||+||+|.|+.+|+.+|.+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g~~~   28 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKGFVH   28 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCeE
Confidence            478999999999999999999999873

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=97.68  E-value=2.3e-05  Score=59.30  Aligned_cols=28  Identities=18%  Similarity=0.074  Sum_probs=24.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +..++|.|+|||||||+++.+++.++..
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            4468999999999999999999988764

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.68  E-value=2.6e-05  Score=59.23  Aligned_cols=27  Identities=15%  Similarity=0.231  Sum_probs=24.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|+|+|||||||+++.+++.+|.++
T Consensus        17 ~I~l~G~~GsGKsT~~~~L~~~~g~~~   43 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQCEKLVKDYSFVH   43 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCceE
Confidence            588999999999999999999998753

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=97.65  E-value=3.5e-05  Score=60.16  Aligned_cols=27  Identities=11%  Similarity=0.124  Sum_probs=24.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|+|+|||||||+++.+++.+|.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~lg~~~   28 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKYSLAH   28 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            478999999999999999999998653

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.64  E-value=0.00054  Score=55.00  Aligned_cols=91  Identities=10%  Similarity=0.093  Sum_probs=51.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCC--hhhhc-ceeEe------ecCeEEEeccHHHHHh-hcCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTT--EADIK-QRREI------VNGTAIYYDQSAVRAA-IEGR  112 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~--~~dL~-g~~~~------~~G~~~~~~gpl~~A~-~~G~  112 (162)
                      ++++.|+||||||+++-.+|..   .|..+..+-+.+.-.  ..++. +....      ..|... .+..+-.++ +...
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D~q~~~~~~al~~gl~~~~~~~~~~~~~~~-~e~~l~~~L~~~pd   86 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVETHGRAETEALLNGLPQQPLLRTEYRGMTL-EEMDLDALLKAAPS   86 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCTTCHHHHHHHTTSCBCCCEEEEETTEEE-EECCHHHHHHHCCS
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeCCCCChhHHHHhcCccccCcceeecCCccc-ccccHHHHHhcCCC
Confidence            6999999999999999988855   377766555543212  22332 21111      112211 223333323 4568


Q ss_pred             EEEEeCCCCCCc------cHHHHHHHhhcCC
Q psy4122         113 VLILEGIEKAER------NVLPVLNNLLENR  137 (162)
Q Consensus       113 vlllDEId~a~~------~v~~~L~~lle~r  137 (162)
                      ++++||+-..+.      .....+..+++.+
T Consensus        87 lvIVDElG~~~~~~~r~~~~~qDV~~~l~sg  117 (228)
T 2r8r_A           87 LVLVDELAHTNAPGSRHTKRWQDIQELLAAG  117 (228)
T ss_dssp             EEEESCTTCBCCTTCSSSBHHHHHHHHHHTT
T ss_pred             EEEEeCCCCCCcccchhHHHHHHHHHHHcCC
Confidence            999999965422      2344444455555

>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=97.62  E-value=4e-05  Score=58.23  Aligned_cols=26  Identities=23%  Similarity=0.235  Sum_probs=23.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+.|+|++||||||+++.+|. +|.++
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~   28 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYV   28 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEE
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEE
Confidence            588999999999999999999 88664

>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=97.62  E-value=4.7e-05  Score=60.02  Aligned_cols=29  Identities=14%  Similarity=0.177  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +..+.|+||+||||||+++.+|+.+|...
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~   55 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQH   55 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            45799999999999999999999988753

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.61  E-value=3.9e-05  Score=57.87  Aligned_cols=27  Identities=22%  Similarity=0.391  Sum_probs=24.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.|+||+|||||||++.++....
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            467899999999999999999998764

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.61  E-value=3.8e-05  Score=60.92  Aligned_cols=28  Identities=18%  Similarity=0.324  Sum_probs=24.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +-++|.||||+||+|.|+.+|+.+|.+.
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~~g~~h   57 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQKFHFNH   57 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHHCCEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHCCce
Confidence            4578899999999999999999999763

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.61  E-value=3.3e-05  Score=61.51  Aligned_cols=29  Identities=14%  Similarity=0.151  Sum_probs=24.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..++|.|+|||||||+++.+++.++.+..
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l~~~~~   61 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEFQGNIV   61 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHTTTCCE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCcE
Confidence            35899999999999999999999885443

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=97.60  E-value=5.2e-05  Score=57.33  Aligned_cols=28  Identities=18%  Similarity=-0.046  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+.|.|++||||||+++.+|+.+|.++.
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg~~~~   31 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALGVPYL   31 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCcee
Confidence            5889999999999999999999998754

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=97.59  E-value=4.2e-05  Score=59.78  Aligned_cols=37  Identities=16%  Similarity=-0.018  Sum_probs=24.6

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +.|+.+--....|+.+.|+||+|||||||++.++...
T Consensus        11 ~~l~~isl~i~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           11 SSGLVPRGSMNNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             -----------CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             ccccCCceecCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3455555556678899999999999999999999877

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=97.59  E-value=2.6e-05  Score=59.34  Aligned_cols=29  Identities=10%  Similarity=0.070  Sum_probs=25.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .+..+.|+|++||||||+++.+++.++.+
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~~l~~~   37 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVEYLKNN   37 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            35679999999999999999999887644

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.58  E-value=7.6e-05  Score=60.96  Aligned_cols=25  Identities=40%  Similarity=0.474  Sum_probs=22.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .++|.|||||||||+++.+++.++.
T Consensus        35 livl~G~sGsGKSTla~~L~~~~~~   59 (287)
T 1gvn_B           35 AFLLGGQPGSGKTSLRSAIFEETQG   59 (287)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4889999999999999999998743

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.58  E-value=3.8e-05  Score=67.26  Aligned_cols=94  Identities=13%  Similarity=0.070  Sum_probs=57.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhccee------EeecCeEEEeccHHHHHhh----cCcEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRR------EIVNGTAIYYDQSAVRAAI----EGRVLI  115 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~------~~~~G~~~~~~gpl~~A~~----~G~vll  115 (162)
                      -.++.|+||||||+++..++..  .+...+..+.. ...++..+-      ........-.++.+.+...    +..+++
T Consensus       163 v~~I~G~aGsGKTt~I~~~~~~--~~~lVlTpT~~-aa~~l~~kl~~~~~~~~~~~~V~T~dsfL~~~~~~~~~~~d~li  239 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEILSRVNF--EEDLILVPGRQ-AAEMIRRRANASGIIVATKDNVRTVDSFLMNYGKGARCQFKRLF  239 (446)
T ss_dssp             EEEEEECTTSCHHHHHHHHCCT--TTCEEEESCHH-HHHHHHHHHTTTSCCCCCTTTEEEHHHHHHTTTSSCCCCCSEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHhcc--CCeEEEeCCHH-HHHHHHHHhhhcCccccccceEEEeHHhhcCCCCCCCCcCCEEE
Confidence            4678899999999999887743  33333333311 133333211      0011123323344444332    268999


Q ss_pred             EeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         116 LEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       116 lDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      +||+-.+++..+..|..++....+.+-
T Consensus       240 iDE~sm~~~~~l~~l~~~~~~~~vilv  266 (446)
T 3vkw_A          240 IDEGLMLHTGCVNFLVEMSLCDIAYVY  266 (446)
T ss_dssp             EETGGGSCHHHHHHHHHHTTCSEEEEE
T ss_pred             EeCcccCCHHHHHHHHHhCCCCEEEEe
Confidence            999999999999988888877776663

>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=97.56  E-value=4.2e-05  Score=58.34  Aligned_cols=26  Identities=23%  Similarity=0.175  Sum_probs=23.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+.|+|++||||||+++.+|. +|.++
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~   29 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPL   29 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcc
Confidence            478999999999999999998 78774

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=97.55  E-value=5.3e-05  Score=60.41  Aligned_cols=31  Identities=13%  Similarity=0.153  Sum_probs=27.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+..+.|+||+||||||+++.+|+.+|.++.
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~Lg~~~~   56 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESLNWRLL   56 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHTTCEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhcCCCcC
Confidence            3567999999999999999999999998643

>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=97.55  E-value=9.5e-05  Score=57.10  Aligned_cols=36  Identities=11%  Similarity=0.041  Sum_probs=28.3

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ..|-+++. .+..|.-+.|.||||+|||+|+.++|..
T Consensus        11 ~~LD~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~   47 (243)
T 1n0w_A           11 KELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVT   47 (243)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hHHHHhhcCCCcCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            44555553 3446778999999999999999999984

>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=97.55  E-value=5.8e-05  Score=59.68  Aligned_cols=27  Identities=19%  Similarity=0.116  Sum_probs=24.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|.-+.|.|++||||||+++.+++.++
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~   51 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLV   51 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            456789999999999999999999886

>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=97.54  E-value=0.0003  Score=55.97  Aligned_cols=95  Identities=7%  Similarity=0.028  Sum_probs=53.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhh--hcceeEeecCeEEEec-cHHHHHhh-cCcEEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEAD--IKQRREIVNGTAIYYD-QSAVRAAI-EGRVLIL  116 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~d--L~g~~~~~~G~~~~~~-gpl~~A~~-~G~vlll  116 (162)
                      |+-.+++||.|+|||+.+...+..   .|..+..++...|....+  +..+..+.-......+ ..+...+. +-.+|+|
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvViI  107 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAI  107 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEEEE
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEEEE
Confidence            444568999999999999888754   477777777655543221  2211111000011111 11111122 2369999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCe
Q psy4122         117 EGIEKAERNVLPVLNNLLENRE  138 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~  138 (162)
                      ||+.-++++.++.|..+.+.+.
T Consensus       108 DEaQF~~~~~V~~l~~l~~~~~  129 (214)
T 2j9r_A          108 DEVQFFDGDIVEVVQVLANRGY  129 (214)
T ss_dssp             CCGGGSCTTHHHHHHHHHHTTC
T ss_pred             ECcccCCHHHHHHHHHHhhCCC
Confidence            9999999998888888776553

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.51  E-value=0.00027  Score=55.49  Aligned_cols=96  Identities=10%  Similarity=0.043  Sum_probs=58.5

Q ss_pred             CCCcEEEEcCCCchHH-HHHHHHHH--HhCCceEEEEeccCCCh-hhhcceeEee-cCeEEEeccHHHHHhhcCcEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRR-SLAMSYLE--LTQREVEYICLSRDTTE-ADIKQRREIV-NGTAIYYDQSAVRAAIEGRVLILE  117 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT-~La~~lA~--~lg~p~~~v~~~~~~~~-~dL~g~~~~~-~G~~~~~~gpl~~A~~~G~vlllD  117 (162)
                      .++=.+++||.|+||| +|.+.+.+  ..+..+.++.-..|+.. .++..+.... +....-....+....+.-.+|+||
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlID   98 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGID   98 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEES
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEE
Confidence            4566789999999999 77777664  34667777765545442 2222110000 000000111233345556899999


Q ss_pred             CCCCCCccHHHHHHHhhcCCeE
Q psy4122         118 GIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       118 EId~a~~~v~~~L~~lle~r~l  139 (162)
                      |+.-+ +++.+.++.+.+.+.-
T Consensus        99 EaQFf-k~~ve~~~~L~~~gk~  119 (195)
T 1w4r_A           99 EGQFF-PDIVEFCEAMANAGKT  119 (195)
T ss_dssp             SGGGC-TTHHHHHHHHHHTTCE
T ss_pred             chhhh-HHHHHHHHHHHHCCCe
Confidence            99999 8899999888876543

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=97.51  E-value=5.5e-05  Score=57.18  Aligned_cols=26  Identities=12%  Similarity=0.141  Sum_probs=23.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|+-+.|+||+||||||+++.++...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            46789999999999999999999886

>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=97.51  E-value=6.8e-05  Score=59.98  Aligned_cols=29  Identities=17%  Similarity=0.316  Sum_probs=24.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHH---hCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLEL---TQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~---lg~p~~   73 (162)
                      ..++|+|+|||||||+++.+++.   .|.++.
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i   36 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVI   36 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEE
Confidence            35899999999999999999987   677654

>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=97.51  E-value=4.5e-05  Score=58.00  Aligned_cols=27  Identities=11%  Similarity=0.032  Sum_probs=23.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +..++|+|++||||||+++.+++.++.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            557999999999999999999987643

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=97.51  E-value=5.3e-05  Score=57.28  Aligned_cols=26  Identities=15%  Similarity=0.133  Sum_probs=23.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|+.+.|+||+||||||+++.++..+
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            46789999999999999999999876

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.51  E-value=4.8e-05  Score=58.00  Aligned_cols=46  Identities=13%  Similarity=0.221  Sum_probs=33.8

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      ..|..++. .+..|+.++|.||+|+|||+|+++++...   +.++.++..
T Consensus        10 ~~Ld~~~~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~   59 (235)
T 2w0m_A           10 LDFDKLIQGGIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTT   59 (235)
T ss_dssp             HHHHGGGTTSEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEES
T ss_pred             hHHHHHhcCCCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEc
Confidence            34555554 45567889999999999999999999543   556655554

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=97.50  E-value=0.00015  Score=61.95  Aligned_cols=40  Identities=20%  Similarity=0.201  Sum_probs=31.8

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ..++.+......|+.++|+||+||||||+++.++...+..
T Consensus       157 ~~l~~~~~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~  196 (377)
T 1svm_A          157 DFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGK  196 (377)
T ss_dssp             HHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCE
T ss_pred             HHHHhcccccCCCCEEEEECCCCCCHHHHHHHHHhhcCCc
Confidence            4444554556677789999999999999999999887654

>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=97.49  E-value=4.5e-05  Score=57.40  Aligned_cols=26  Identities=8%  Similarity=0.074  Sum_probs=22.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+.+.|+||+|+||||+++.++...+
T Consensus         2 g~ii~l~G~~GaGKSTl~~~L~~~~~   27 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTTCKRLAAQLD   27 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CeEEEEECCCCCcHHHHHHHHhcccC
Confidence            44678999999999999999998554

>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=97.47  E-value=7.4e-05  Score=56.27  Aligned_cols=27  Identities=19%  Similarity=0.070  Sum_probs=23.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+.|+|++||||||+++.+|+. |.++.
T Consensus        10 ~I~i~G~~GsGKST~~~~La~~-g~~~i   36 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVAALLRSW-GYPVL   36 (203)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHT-TCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHC-CCEEE
Confidence            5889999999999999999998 87643

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=97.47  E-value=0.00012  Score=62.81  Aligned_cols=27  Identities=19%  Similarity=0.205  Sum_probs=23.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .-++|+|+|||||||+++.+++.++..
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~~~~~~  285 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLVSAGYV  285 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTGGGTCE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhcCcE
Confidence            458889999999999999999988764

>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=97.45  E-value=7e-05  Score=57.83  Aligned_cols=27  Identities=11%  Similarity=0.119  Sum_probs=24.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+-+.|+||+|+||||+++.++..+.
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            466799999999999999999998874

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=97.45  E-value=0.0001  Score=57.82  Aligned_cols=32  Identities=9%  Similarity=-0.090  Sum_probs=27.8

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..+..+.|+|++||||||+++.+|+.+|.++.
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~~lg~~~~   45 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAKDFGFTYL   45 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHHHHCCEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHcCCcee
Confidence            34667999999999999999999999997643

>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=97.44  E-value=7.9e-05  Score=57.28  Aligned_cols=30  Identities=13%  Similarity=0.106  Sum_probs=25.0

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ....|+.+.|+||.|||||||++.++..+.
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            455688899999999999999999998874

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=97.43  E-value=8.8e-05  Score=57.08  Aligned_cols=36  Identities=25%  Similarity=0.219  Sum_probs=28.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEec
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLS   78 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~   78 (162)
                      .|+-+.|+||+|+|||||++.++..+.   ...-.+...
T Consensus        21 ~g~~v~I~G~sGsGKSTl~~~l~~~~~~~g~~~g~v~~d   59 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLSNPLAAALSAQGLPAEVVPMD   59 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHHHHTTCCEEEEESG
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEecC
Confidence            456789999999999999999998875   234455543

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=97.42  E-value=6.3e-05  Score=56.54  Aligned_cols=26  Identities=35%  Similarity=0.485  Sum_probs=23.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +..++|+|++||||||+++.+|..++
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~   38 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQ   38 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            45689999999999999999998764

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=97.40  E-value=0.0001  Score=59.11  Aligned_cols=28  Identities=14%  Similarity=0.065  Sum_probs=25.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ..+.|.||+||||||+++.+|+.+|.++
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~~lg~~~   37 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLARALGARY   37 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCc
Confidence            4689999999999999999999999764

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=97.40  E-value=0.00011  Score=56.96  Aligned_cols=28  Identities=14%  Similarity=0.058  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+.|+|++||||||+++.+++.+|.++.
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vi   41 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVV   41 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEE
Confidence            4789999999999999999999898754

>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=97.39  E-value=0.00012  Score=59.09  Aligned_cols=45  Identities=7%  Similarity=-0.041  Sum_probs=35.2

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEe
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICL   77 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~   77 (162)
                      .|..+.-.+..|+-++|.||||+|||+|++++|...    |.++.++..
T Consensus        24 ~Ld~i~~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           24 GINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             THHHHHCSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             HHHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            466677667788899999999999999999998654    445655544

>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=97.39  E-value=0.00055  Score=51.60  Aligned_cols=33  Identities=12%  Similarity=0.088  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAM   62 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~   62 (162)
                      +++.=.+.+..++    .++++++.+|+|+|||..+.
T Consensus        26 ~~~~Q~~~i~~~~----~~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A           26 PSPIQEESIPIAL----SGRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             CCHHHHHHHHHHH----TTCCEEEECCSSSTTHHHHH
T ss_pred             CCHHHHHHHHHHc----cCCCEEEECCCCCchHHHHH
Confidence            4444444444444    46899999999999996544

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=97.39  E-value=0.0001  Score=56.60  Aligned_cols=27  Identities=19%  Similarity=0.241  Sum_probs=22.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.|+||+|+|||||++.++....
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            367899999999999999999998763

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.38  E-value=9.7e-05  Score=62.09  Aligned_cols=31  Identities=26%  Similarity=0.434  Sum_probs=26.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      +.++|+||+|||||+++..+|+.++.+  .+++
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~~~--iis~   36 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALPCE--LISV   36 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEE--EEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCc--EEec
Confidence            468999999999999999999999854  4444

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.38  E-value=0.00011  Score=62.58  Aligned_cols=27  Identities=26%  Similarity=0.470  Sum_probs=25.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +++|+|++|||||++++.+|..++.++
T Consensus        26 ~i~l~G~~G~GKTTl~~~la~~l~~~f   52 (359)
T 2ga8_A           26 CVILVGSPGSGKSTIAEELCQIINEKY   52 (359)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhCCCe
Confidence            499999999999999999999998876

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=97.38  E-value=0.00014  Score=55.78  Aligned_cols=29  Identities=10%  Similarity=-0.009  Sum_probs=25.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..+.|+|++|||||++++.+|+.+|.++.
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~   32 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYV   32 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcee
Confidence            46899999999999999999999997743

>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=97.37  E-value=0.00012  Score=56.42  Aligned_cols=27  Identities=26%  Similarity=0.244  Sum_probs=23.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ..+.|+|++||||||+++.+++ +|.++
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~   31 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINV   31 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEE
Confidence            3588999999999999999998 88764

>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=97.36  E-value=0.00013  Score=56.04  Aligned_cols=29  Identities=17%  Similarity=0.217  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|..++|+|++||||||+++.++..++
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34566899999999999999999998764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=97.36  E-value=0.00025  Score=54.69  Aligned_cols=46  Identities=15%  Similarity=0.261  Sum_probs=33.7

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHH----HhCCceEEEEeccCCChhhhc
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLE----LTQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~----~lg~p~~~v~~~~~~~~~dL~   87 (162)
                      .+..|.-+++.|+||+|||+++.++|.    ..+.++.++++  +++..++.
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~--E~~~~~~~   75 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTL--EERARDLR   75 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEES--SSCHHHHH
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecc--cCCHHHHH
Confidence            344677899999999999999999873    23677777765  45555553

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=97.35  E-value=0.0002  Score=59.57  Aligned_cols=37  Identities=19%  Similarity=0.239  Sum_probs=32.2

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|+.+......|+.+.|+||+|||||||++.++..+
T Consensus       114 ~vL~~vsl~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          114 NALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             HHHHHHHHTCTTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             hhhccceEEecCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            3566777777788899999999999999999999887

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=97.35  E-value=0.00033  Score=57.75  Aligned_cols=57  Identities=11%  Similarity=0.096  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhc
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~   87 (162)
                      +....|-.++-.+..|.-++|.|+||+|||+++.++|...   |.++.++++  +++..++.
T Consensus        53 TG~~~LD~~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~sl--E~s~~~l~  112 (315)
T 3bh0_A           53 SGFTELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL--EMGKKENI  112 (315)
T ss_dssp             CSCHHHHHHHSSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEES--SSCHHHHH
T ss_pred             CChHHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEEC--CCCHHHHH
Confidence            3455566666556677789999999999999999998532   456666665  45555443

>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=97.33  E-value=0.00012  Score=55.93  Aligned_cols=37  Identities=19%  Similarity=0.126  Sum_probs=28.6

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|-+++. .+..|+-+.|+||+|||||||++.++...
T Consensus        12 ~~LD~~l~ggi~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           12 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             HHHHHHTTSSEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             hhHHhHhcCCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            44545553 34467789999999999999999999754

>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=97.32  E-value=0.00019  Score=55.53  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=22.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +|++|+||+|+|||||++.+.+...
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            5899999999999999999987764

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=97.30  E-value=0.00013  Score=57.90  Aligned_cols=26  Identities=15%  Similarity=0.144  Sum_probs=24.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .|.|.|++||||||+++.+++.+|.+
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~lg~~   49 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLLGQN   49 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            48899999999999999999999876

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.30  E-value=0.00033  Score=70.73  Aligned_cols=49  Identities=16%  Similarity=0.141  Sum_probs=35.7

Q ss_pred             HHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEecc
Q psy4122          31 LSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSR   79 (162)
Q Consensus        31 ~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~   79 (162)
                      ...|-.++-  .+..+++++|+||||||||+||.+++..   .|..+.++.+..
T Consensus      1412 ~~~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~ 1465 (2050)
T 3cmu_A         1412 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH 1465 (2050)
T ss_dssp             CHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTS
T ss_pred             CHHHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEccc
Confidence            334555554  3446789999999999999999998754   466676666643

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=97.30  E-value=0.0015  Score=53.61  Aligned_cols=81  Identities=14%  Similarity=0.067  Sum_probs=54.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh---C-CceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHH-hhcCcEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT---Q-REVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRA-AIEGRVLILE  117 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l---g-~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A-~~~G~vlllD  117 (162)
                      .....+|+||+|.||++.++.+++.+   + .++..+...++.+..++...             .-... +....++++|
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-------------~~~~plf~~~kvvii~   83 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSL-------------CQAMSLFASRQTLLLL   83 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCTTCCHHHHHHH-------------HHHHHHCCSCEEEEEE
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecCCCCHHHHHHH-------------hcCcCCccCCeEEEEE
Confidence            34467888999999999999998765   3 23333444433344444310             00111 1234699999


Q ss_pred             CCCC-CCccHHHHHHHhhcC
Q psy4122         118 GIEK-AERNVLPVLNNLLEN  136 (162)
Q Consensus       118 EId~-a~~~v~~~L~~lle~  136 (162)
                      |.+. ++.+..+.|...+|+
T Consensus        84 ~~~~kl~~~~~~aLl~~le~  103 (343)
T 1jr3_D           84 LPENGPNAAINEQLLTLTGL  103 (343)
T ss_dssp             CCSSCCCTTHHHHHHHHHTT
T ss_pred             CCCCCCChHHHHHHHHHHhc
Confidence            9999 999999999999996

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=97.29  E-value=0.00011  Score=55.98  Aligned_cols=27  Identities=15%  Similarity=0.044  Sum_probs=24.1

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .+.-+.|+||+||||||+++.++..++
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            355688999999999999999999887

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.28  E-value=0.00026  Score=54.57  Aligned_cols=38  Identities=21%  Similarity=0.247  Sum_probs=29.5

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS   78 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~   78 (162)
                      +..|.-++|.||||+|||+++.++|..   .+.++.++...
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            446778999999999999999988753   36677666653

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=97.27  E-value=0.00017  Score=56.53  Aligned_cols=27  Identities=22%  Similarity=0.298  Sum_probs=24.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.|+||+|||||||++.+++...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            577899999999999999999998764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=97.26  E-value=0.00035  Score=61.77  Aligned_cols=49  Identities=8%  Similarity=0.182  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      +++..++.+...+.   .|+.++++||+||||||+.+.++..+......+.+
T Consensus       245 ~~~~~l~~l~~~v~---~g~~i~I~GptGSGKTTlL~aL~~~i~~~~giiti  293 (511)
T 2oap_1          245 VPSGVLAYLWLAIE---HKFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSI  293 (511)
T ss_dssp             SCHHHHHHHHHHHH---TTCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEE
T ss_pred             CCHHHHHHHHHHHh---CCCEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEE
Confidence            34555555554443   57889999999999999999999888544344444

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=97.26  E-value=0.00052  Score=59.27  Aligned_cols=44  Identities=14%  Similarity=0.186  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .++.....|+.++.  ..+..++++||+|+||||+.+.++..++..
T Consensus       151 ~~~~~~~~L~~l~~--~~ggii~I~GpnGSGKTTlL~allg~l~~~  194 (418)
T 1p9r_A          151 MTAHNHDNFRRLIK--RPHGIILVTGPTGSGKSTTLYAGLQELNSS  194 (418)
T ss_dssp             CCHHHHHHHHHHHT--SSSEEEEEECSTTSCHHHHHHHHHHHHCCT
T ss_pred             CCHHHHHHHHHHHH--hcCCeEEEECCCCCCHHHHHHHHHhhcCCC
Confidence            45666677777742  455679999999999999999999888654

>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=97.25  E-value=0.00026  Score=53.14  Aligned_cols=29  Identities=21%  Similarity=0.253  Sum_probs=25.9

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ....|+-+.|.||.|+|||||++.++..+
T Consensus        29 ~i~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           29 HTEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CCSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            34567789999999999999999999988

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=97.25  E-value=0.00046  Score=58.19  Aligned_cols=59  Identities=17%  Similarity=0.144  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcc
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQ   88 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g   88 (162)
                      ++....|-.++..+..|.-++|.|+||+|||+++.++|..   .|.++.++++  +++..++..
T Consensus        30 ~TG~~~LD~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl--Ems~~ql~~   91 (338)
T 4a1f_A           30 PTGFVQLDNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL--EMSAEQLAL   91 (338)
T ss_dssp             CCSCHHHHHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES--SSCHHHHHH
T ss_pred             cCCChHHHHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC--CCCHHHHHH
Confidence            4455667777777778888999999999999999999854   4777777766  677777654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=97.25  E-value=0.0001  Score=62.44  Aligned_cols=28  Identities=18%  Similarity=0.268  Sum_probs=24.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++.++|+||+|||||+|+..+|+.++.+
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l~~e   67 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHFPLE   67 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTSCEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHCCCc
Confidence            3468999999999999999999998754

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=97.23  E-value=0.00012  Score=55.88  Aligned_cols=26  Identities=15%  Similarity=0.029  Sum_probs=23.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+.-+.|+|++||||||+++.++..+
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            45568899999999999999999877

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=97.23  E-value=0.00017  Score=58.08  Aligned_cols=25  Identities=24%  Similarity=0.349  Sum_probs=21.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh-CC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT-QR   70 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l-g~   70 (162)
                      .++|.|+|||||||+++.+++.+ |.
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~~~~~~   29 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIAKNPGF   29 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHSTTE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCCCc
Confidence            58899999999999999999863 54

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.22  E-value=0.00087  Score=51.20  Aligned_cols=32  Identities=16%  Similarity=-0.048  Sum_probs=25.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYI   75 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v   75 (162)
                      +.-+.|.|++||||||+++.++..+   +.++...
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            3458899999999999999999875   5555444

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=97.21  E-value=0.00025  Score=54.95  Aligned_cols=28  Identities=14%  Similarity=-0.092  Sum_probs=26.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      -|.|.|++|||||++++.+|+.+|.++.
T Consensus         8 iI~i~g~~GsGk~ti~~~la~~lg~~~~   35 (201)
T 3fdi_A            8 IIAIGREFGSGGHLVAKKLAEHYNIPLY   35 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTCCEE
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHhCcCEE
Confidence            5888999999999999999999999965

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=97.21  E-value=0.00019  Score=56.61  Aligned_cols=38  Identities=11%  Similarity=0.034  Sum_probs=25.9

Q ss_pred             HHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          34 LRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        34 L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      |..+--....|.-+-|.||.|+||||+++.++..+|..
T Consensus        15 l~~isl~i~~g~iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           15 TENLYFQSMRPFLIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             --------CCSEEEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             ecceeccCCCCEEEEEECCCCCCHHHHHHHHHHHhchh
Confidence            33333344455668999999999999999999988754

>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=97.19  E-value=0.00041  Score=57.26  Aligned_cols=55  Identities=16%  Similarity=0.042  Sum_probs=36.6

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADI   86 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL   86 (162)
                      ..|-.++. .+..|.-+++.||||+|||+++.++|...         +.++.++......++..+
T Consensus        94 ~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l  158 (324)
T 2z43_A           94 QALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERI  158 (324)
T ss_dssp             HHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHH
T ss_pred             hhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHH
Confidence            33444443 34456678999999999999999999764         455666665433334444

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=97.18  E-value=0.00063  Score=58.69  Aligned_cols=55  Identities=13%  Similarity=0.212  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH----hCCceEEEEeccCCChhhh
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL----TQREVEYICLSRDTTEADI   86 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~----lg~p~~~v~~~~~~~~~dL   86 (162)
                      ....|-.++..+..|.-++|.|+||+|||+++.++|..    .|.++.++++  +++..++
T Consensus       189 G~~~LD~~~gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~--E~s~~~l  247 (454)
T 2r6a_A          189 GFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL--EMSAQQL  247 (454)
T ss_dssp             SCHHHHHHHSSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES--SSCHHHH
T ss_pred             CcHHHHhhcCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC--CCCHHHH
Confidence            44556667656667888999999999999999998853    2567777765  4444444

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.15  E-value=0.00082  Score=53.68  Aligned_cols=100  Identities=7%  Similarity=0.013  Sum_probs=54.7

Q ss_pred             CCCCcEEEEcCCCchHHH-HHHHHHH--HhCCceEEEEeccCCChh--hhcceeEeecCeEEEe-ccHHHHHh-hcCcEE
Q psy4122          42 NMSQDVFLIGKPGSLRRS-LAMSYLE--LTQREVEYICLSRDTTEA--DIKQRREIVNGTAIYY-DQSAVRAA-IEGRVL  114 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~-La~~lA~--~lg~p~~~v~~~~~~~~~--dL~g~~~~~~G~~~~~-~gpl~~A~-~~G~vl  114 (162)
                      ..|.-.+++||-|+|||+ |.+.+-+  ..|..+..++...|+..+  .+..+..+.-...... ...+...+ ..-.+|
T Consensus        26 ~~G~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D~R~~~~~I~Sr~G~~~~a~~v~~~~di~~~i~~~~dvV  105 (219)
T 3e2i_A           26 HSGWIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVI  105 (219)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC-----------CBTTBCCEEEEESSGGGGGGSCCTTCSEE
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEEeccCCcchhhhHHHhcCCceeeEEeCCHHHHHHHHhcCCCEE
Confidence            345567889999999999 4444332  236676666665554332  1221100100011111 11222222 234699


Q ss_pred             EEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         115 ILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       115 llDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ++||+.-+++++.+.|..+.+.+.-++
T Consensus       106 ~IDEaQFf~~~~v~~l~~la~~gi~Vi  132 (219)
T 3e2i_A          106 GIDEVQFFDDEIVSIVEKLSADGHRVI  132 (219)
T ss_dssp             EECCGGGSCTHHHHHHHHHHHTTCEEE
T ss_pred             EEechhcCCHHHHHHHHHHHHCCCEEE
Confidence            999999999999999999987665444

>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=97.13  E-value=0.0022  Score=49.24  Aligned_cols=20  Identities=10%  Similarity=0.245  Sum_probs=17.2

Q ss_pred             CCCcEEEEcCCCchHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAM   62 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~   62 (162)
                      .|+++++.+|+|+|||..+.
T Consensus        56 ~~~~~l~~apTGsGKT~~~~   75 (228)
T 3iuy_A           56 QGIDLIVVAQTGTGKTLSYL   75 (228)
T ss_dssp             TTCCEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEECCCCChHHHHHH
Confidence            47899999999999997543

>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=97.13  E-value=0.00014  Score=55.30  Aligned_cols=24  Identities=17%  Similarity=0.151  Sum_probs=21.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      -+.++|++||||||+++.+++.++
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999998875

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=97.13  E-value=0.00075  Score=58.07  Aligned_cols=57  Identities=11%  Similarity=0.119  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH----hCCceEEEEeccCCChhhhc
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL----TQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~----lg~p~~~v~~~~~~~~~dL~   87 (162)
                      +....|-.++..+..|.-++|.|+||+|||+++.++|..    .|.++.++++  +++..++.
T Consensus       185 tG~~~LD~~lgGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~sl--E~~~~~l~  245 (444)
T 2q6t_A          185 TGFKELDQLIGTLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSL--EMPAAQLT  245 (444)
T ss_dssp             CSCHHHHHHHCCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEES--SSCHHHHH
T ss_pred             CCCHhhhhhcCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEC--CCCHHHHH
Confidence            345567777756667878999999999999999998853    2567777666  45554443

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=97.11  E-value=0.0002  Score=53.66  Aligned_cols=21  Identities=33%  Similarity=0.354  Sum_probs=18.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMS   63 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~   63 (162)
                      .|+-+.|+||+|||||||++.
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            466789999999999999994

>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=97.11  E-value=0.0027  Score=49.78  Aligned_cols=37  Identities=8%  Similarity=0.077  Sum_probs=30.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEeccC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLSRD   80 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~~~   80 (162)
                      ...+++++++|.||||.|-.+|-   -.|..+..+++-..
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg   67 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKG   67 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCC
Confidence            34899999999999999998773   45888888988643

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=97.10  E-value=0.001  Score=50.66  Aligned_cols=43  Identities=19%  Similarity=0.145  Sum_probs=31.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .....+.++..+..... ..+.++|++|+|||||+.+++..+..
T Consensus        14 ~~~~~~~~~~~~~~~~~-~~i~i~G~~g~GKTTl~~~l~~~~~~   56 (221)
T 2wsm_A           14 NKRLAEKNREALRESGT-VAVNIMGAIGSGKTLLIERTIERIGN   56 (221)
T ss_dssp             HHHHHHHHHHHHHHHTC-EEEEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHhhcccCc-eEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            35566677766643322 36899999999999999999977543

>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=97.10  E-value=0.00052  Score=68.43  Aligned_cols=37  Identities=16%  Similarity=0.243  Sum_probs=29.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEecc
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSR   79 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~   79 (162)
                      .|+.++++||||||||.||.++|..   .|-|..++.+.+
T Consensus      1081 ~g~~~l~~G~~g~GKT~la~~~~~~~~~~g~~~~fi~~~~ 1120 (1706)
T 3cmw_A         1081 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH 1120 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTS
T ss_pred             CCCEEEEEcCCCCChHHHHHHHHHHhhhcCCceeEEEccc
Confidence            3456999999999999999999853   367777777643

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.09  E-value=0.00066  Score=56.60  Aligned_cols=55  Identities=7%  Similarity=-0.011  Sum_probs=36.3

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCChhhh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTTEADI   86 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~~~dL   86 (162)
                      ..|-.++. .+..|.-++|.||||+|||+++.++|...         +.++.++......++..+
T Consensus       109 ~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l  173 (343)
T 1v5w_A          109 QEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRL  173 (343)
T ss_dssp             HHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHH
T ss_pred             hhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHH
Confidence            33444443 34456678999999999999999999752         455666666433344444

>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=97.09  E-value=0.0026  Score=54.06  Aligned_cols=112  Identities=11%  Similarity=0.005  Sum_probs=63.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC---hhhhc--c-e-eEee-cC-
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT---EADIK--Q-R-REIV-NG-   95 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~---~~dL~--g-~-~~~~-~G-   95 (162)
                      .+.|.=.+.+..++.    +.+++|.+|+|+|||..+-..+...+.+...+.-.....   ...+.  + . ...- ++ 
T Consensus        93 ~l~~~Q~~ai~~i~~----~~~~ll~~~TGsGKT~~~l~~i~~~~~~~Lvl~P~~~L~~Q~~~~~~~~~~~~v~~~~g~~  168 (472)
T 2fwr_A           93 SLRDYQEKALERWLV----DKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRI  168 (472)
T ss_dssp             CBCHHHHHHHHHHTT----TTEEEEECCTTSCHHHHHHHHHHHHCSCEEEEESSHHHHHHHHHHGGGGCGGGEEEBSSSC
T ss_pred             CcCHHHHHHHHHHHh----cCCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEECCHHHHHHHHHHHHhCCCcceEEECCCc
Confidence            456666666666554    457999999999999999888887777665443321110   11111  1 1 1111 11 


Q ss_pred             ----e-EEEeccHHHHHh----hcCcEEEEeCCCCCCccHHHHHHHhhcCCeEE
Q psy4122          96 ----T-AIYYDQSAVRAA----IEGRVLILEGIEKAERNVLPVLNNLLENREMH  140 (162)
Q Consensus        96 ----~-~~~~~gpl~~A~----~~G~vlllDEId~a~~~v~~~L~~lle~r~l~  140 (162)
                          . .+-.++.+...+    ..=+++|+||.|++.......+...+....+.
T Consensus       169 ~~~~~Ivv~T~~~l~~~~~~~~~~~~liIvDEaH~~~~~~~~~~~~~~~~~~~l  222 (472)
T 2fwr_A          169 KELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRL  222 (472)
T ss_dssp             BCCCSEEEEEHHHHHHTHHHHTTTCSEEEEETGGGTTSTTTHHHHHTCCCSEEE
T ss_pred             CCcCCEEEEEcHHHHHHHHHhcCCCCEEEEECCcCCCChHHHHHHHhcCCCeEE
Confidence                1 122222332222    12379999999998766555555555544443

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=97.08  E-value=0.00032  Score=56.89  Aligned_cols=26  Identities=23%  Similarity=0.085  Sum_probs=22.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .+.|+|++||||||+++.++ .+|.++
T Consensus        77 iI~I~G~~GSGKSTva~~La-~lg~~~  102 (281)
T 2f6r_A           77 VLGLTGISGSGKSSVAQRLK-NLGAYI  102 (281)
T ss_dssp             EEEEEECTTSCHHHHHHHHH-HHTCEE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HCCCcE
Confidence            48999999999999999999 578764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=97.08  E-value=0.0004  Score=58.45  Aligned_cols=44  Identities=11%  Similarity=0.258  Sum_probs=32.8

Q ss_pred             HHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          35 RWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        35 ~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      +.+-.....|+.++|+||+|+||||+++.++......--.+.+.
T Consensus       166 ~~l~~~i~~G~~i~ivG~sGsGKSTll~~l~~~~~~~~g~I~ie  209 (361)
T 2gza_A          166 SFLRRAVQLERVIVVAGETGSGKTTLMKALMQEIPFDQRLITIE  209 (361)
T ss_dssp             HHHHHHHHTTCCEEEEESSSSCHHHHHHHHHTTSCTTSCEEEEE
T ss_pred             HHHHHHHhcCCEEEEECCCCCCHHHHHHHHHhcCCCCceEEEEC
Confidence            33433445688999999999999999999998876444445443

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=97.07  E-value=0.00019  Score=55.79  Aligned_cols=26  Identities=15%  Similarity=0.170  Sum_probs=17.3

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHH-HHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYL-ELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA-~~l   68 (162)
                      .|+-+.|+||+||||||+++.++ ...
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCCEEEEECSCC----CHHHHHHC---
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            46778999999999999999999 775

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=97.06  E-value=0.00067  Score=58.82  Aligned_cols=56  Identities=11%  Similarity=0.095  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhc
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~   87 (162)
                      ....|-.++..+..|.-+++.|+||+|||+++.++|...   |.++.++++  +++..++.
T Consensus       183 G~~~LD~~lgGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSl--Ems~~ql~  241 (444)
T 3bgw_A          183 GFTELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL--EMGKKENI  241 (444)
T ss_dssp             SCHHHHHHHSSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECS--SSCTTHHH
T ss_pred             CcHHHHhhcCCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEEC--CCCHHHHH
Confidence            344556666566677789999999999999999988533   667666655  45555443

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=97.05  E-value=0.00037  Score=54.87  Aligned_cols=27  Identities=15%  Similarity=0.133  Sum_probs=24.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+.+.|+||.|+|||||.+.++....
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            477899999999999999999998774

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=97.04  E-value=0.00052  Score=58.00  Aligned_cols=31  Identities=16%  Similarity=0.156  Sum_probs=25.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      ..+.|.||+|+|||+++..+|..++.  ..+++
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~--~iis~   38 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNG--EIISG   38 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTE--EEEEC
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCC--ceecc
Confidence            35889999999999999999999983  34544

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=97.03  E-value=0.0012  Score=50.47  Aligned_cols=41  Identities=17%  Similarity=0.163  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +...+.++.+..... ...+.++|++|+|||+|+.+++....
T Consensus        23 ~~~a~~~r~~~~~~~-~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           23 KRLADKNRKLLNKHG-VVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             HHHHHHHHHHHHHTT-CEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCC-CeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            456677777665432 23688999999999999999997653

>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=97.02  E-value=0.00038  Score=55.78  Aligned_cols=29  Identities=14%  Similarity=0.031  Sum_probs=24.3

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+..|.-++|+||+|+|||+|+.+++...
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34467789999999999999999998543

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=97.01  E-value=0.00087  Score=58.35  Aligned_cols=54  Identities=6%  Similarity=0.011  Sum_probs=38.6

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEeccCCChhhhc
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~~~~~~~dL~   87 (162)
                      ..|-.++..+..|.-++|.|+||+|||+++.++|...    |.++.++++  +++..++.
T Consensus       230 ~~LD~~lgGl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~--E~s~~~l~  287 (503)
T 1q57_A          230 TGINDKTLGARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAML--EESVEETA  287 (503)
T ss_dssp             TTHHHHHCCCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEES--SSCHHHHH
T ss_pred             hhhhHhhcccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEec--cCCHHHHH
Confidence            3444555556677778999999999999999998543    567766665  55555543

>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=97.00  E-value=0.0043  Score=49.94  Aligned_cols=94  Identities=11%  Similarity=0.046  Sum_probs=52.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEeccCCChh-hhcceeEee-cCeEEEeccHHHHHhhcCcEEEEe
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLSRDTTEA-DIKQRREIV-NGTAIYYDQSAVRAAIEGRVLILE  117 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~~~~~~~-dL~g~~~~~-~G~~~~~~gpl~~A~~~G~vlllD  117 (162)
                      .|+-.+++||.|+|||+.+-..+.   ..|+.+..++...|+... .+..+..+. .....+....+...+.+-.+|+||
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViID   97 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGID   97 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC-----------CEEEEESSGGGGHHHHTTCSEEEES
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCCccchHHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEE
Confidence            466678899999999977776653   346777777766555432 111111110 011123322333334445799999


Q ss_pred             CCCCCCccHHHHHHHhhcCC
Q psy4122         118 GIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       118 EId~a~~~v~~~L~~lle~r  137 (162)
                      |+.-+.. +.+.+..+.+.+
T Consensus        98 EaQF~~~-v~el~~~l~~~g  116 (234)
T 2orv_A           98 EGQFFPD-IVEFCEAMANAG  116 (234)
T ss_dssp             SGGGCTT-HHHHHHHHHHTT
T ss_pred             chhhhhh-HHHHHHHHHhCC
Confidence            9999975 655555554433

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=96.99  E-value=0.00066  Score=54.00  Aligned_cols=33  Identities=12%  Similarity=0.066  Sum_probs=23.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh-------CCceEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT-------QREVEYI   75 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l-------g~p~~~v   75 (162)
                      .|.-+.+.|++||||||+++.+++.+       |.++...
T Consensus        24 ~g~~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~   63 (227)
T 3v9p_A           24 RGKFITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVT   63 (227)
T ss_dssp             CCCEEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhccccceeeeee
Confidence            46678999999999999999999876       6665433

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=96.99  E-value=0.0012  Score=55.12  Aligned_cols=33  Identities=15%  Similarity=0.135  Sum_probs=27.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      .+.++|+||+||||++..++..+   |..+..+.+.
T Consensus        81 ~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~~D  116 (355)
T 3p32_A           81 RVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVD  116 (355)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEecC
Confidence            58999999999999999998765   6666666554

>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=96.96  E-value=0.00042  Score=58.17  Aligned_cols=31  Identities=26%  Similarity=0.460  Sum_probs=25.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      +.+++.||+|||||+|+..+|+.++.+  .+++
T Consensus        11 ~~i~i~GptgsGKt~la~~La~~~~~~--iis~   41 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIELRKILPVE--LISV   41 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEE--EEEC
T ss_pred             cEEEEECCCccCHHHHHHHHHHhCCCc--EEec
Confidence            357889999999999999999998754  4444

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=96.96  E-value=0.0032  Score=61.31  Aligned_cols=31  Identities=23%  Similarity=0.297  Sum_probs=26.0

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ....|+.+.++||+|||||||++.+......
T Consensus       440 ~i~~G~~vaivG~sGsGKSTll~ll~~~~~~  470 (1321)
T 4f4c_A          440 RVNAGQTVALVGSSGCGKSTIISLLLRYYDV  470 (1321)
T ss_dssp             EECTTCEEEEEECSSSCHHHHHHHHTTSSCC
T ss_pred             eecCCcEEEEEecCCCcHHHHHHHhcccccc
Confidence            3446889999999999999999999876643

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=96.95  E-value=0.00031  Score=54.95  Aligned_cols=25  Identities=32%  Similarity=0.290  Sum_probs=23.0

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|+-+.|+||.|||||||.+.++..
T Consensus        21 ~Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           21 TNTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             HCSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4888999999999999999999976

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.93  E-value=0.00089  Score=55.98  Aligned_cols=24  Identities=8%  Similarity=-0.025  Sum_probs=21.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      -+.|.||+||||||+++.++..++
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            378899999999999999999886

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=96.93  E-value=0.0006  Score=52.73  Aligned_cols=31  Identities=23%  Similarity=0.251  Sum_probs=26.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      ++++|++|+|||++|+++|.. +.|+.++...
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~   32 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATS   32 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecC
Confidence            689999999999999999977 8887766553

>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=96.88  E-value=0.00049  Score=57.88  Aligned_cols=26  Identities=8%  Similarity=0.060  Sum_probs=22.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +.+++.||+|||||+|+..+|+.++.
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~   29 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNG   29 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTE
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCcc
Confidence            35788999999999999999998864

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=96.87  E-value=0.00071  Score=53.59  Aligned_cols=28  Identities=14%  Similarity=-0.065  Sum_probs=25.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      -+.+.|++|||||++++.+|+.+|.++.
T Consensus        16 iI~i~g~~gsGk~~i~~~la~~lg~~~~   43 (223)
T 3hdt_A           16 IITIEREYGSGGRIVGKKLAEELGIHFY   43 (223)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTCEEE
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHcCCcEE
Confidence            4788899999999999999999999865

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=96.87  E-value=0.00089  Score=49.61  Aligned_cols=42  Identities=14%  Similarity=0.152  Sum_probs=27.8

Q ss_pred             CHHHHHHHHHHHHhcCC-----CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          27 TQDWLSHLRWILQKDNM-----SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~-----g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      -....+.++.++.....     ...++++|++|+|||+|+..++...
T Consensus        26 ~~~l~~~l~~~~~~~~~~~~~~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           26 ISQWREWIDEKLGGGSGGGGSYQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CHHHHHHHHHHC--------CCCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35556666655543321     1268999999999999999998653

>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=96.87  E-value=0.0011  Score=56.26  Aligned_cols=51  Identities=12%  Similarity=0.005  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec
Q psy4122          28 QDWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS   78 (162)
Q Consensus        28 ~~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~   78 (162)
                      ++....|-.++-  .+..|.-++|.||||||||+|+.++|..   .+.++.++...
T Consensus        43 ~TG~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E   98 (356)
T 3hr8_A           43 PTGSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAE   98 (356)
T ss_dssp             CCSCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCCCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecc
Confidence            444566667765  4556778999999999999999999865   36667666554

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=96.86  E-value=0.00066  Score=60.22  Aligned_cols=44  Identities=14%  Similarity=0.042  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          27 TQDWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        27 ~~~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .|+..+.++..... ...+..++|+|.+||||||+++.+|+.++.
T Consensus       377 rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          377 YPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             CHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             ChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            46677777765532 224557999999999999999999999985

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=96.86  E-value=0.00062  Score=60.82  Aligned_cols=42  Identities=19%  Similarity=0.253  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          28 QDWLSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        28 ~~~~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +...+.++.-.. ....|..+.|+|++|||||||++.+|..++
T Consensus       352 peV~~vLR~~~~~~~~~G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          352 PEVLAELHRQTPPRERQGFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             HHHHHHHHHHSCCGGGSCEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhhcccccccceEEEEECCCCChHHHHHHHHHHhhc
Confidence            455555554332 233577899999999999999999999885

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=96.86  E-value=0.00082  Score=53.87  Aligned_cols=28  Identities=21%  Similarity=0.166  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+-|.|+||+||||+++.+|+.+|.+..
T Consensus        10 ~~~~~G~pGsGKsT~a~~L~~~~g~~~i   37 (230)
T 3gmt_A           10 RLILLGAPGAGKGTQANFIKEKFGIPQI   37 (230)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCCEE
T ss_pred             ceeeECCCCCCHHHHHHHHHHHhCCCee
Confidence            4678999999999999999999998743

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=96.85  E-value=0.00043  Score=54.80  Aligned_cols=26  Identities=15%  Similarity=0.302  Sum_probs=23.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++-++|.||+|+|||++|..+++..+
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~   59 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH   59 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC
Confidence            45689999999999999999998765

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=96.85  E-value=0.0016  Score=56.45  Aligned_cols=47  Identities=15%  Similarity=0.073  Sum_probs=37.7

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      ...|..+ -.+..|+-+.|+||.|||||||.+.+|.......-.+.+.
T Consensus       145 ~~vld~v-l~i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~~~G~i~~~  191 (438)
T 2dpy_A          145 VRAINAL-LTVGRGQRMGLFAGSGVGKSVLLGMMARYTRADVIVVGLI  191 (438)
T ss_dssp             CHHHHHH-SCCBTTCEEEEEECTTSSHHHHHHHHHHHSCCSEEEEEEE
T ss_pred             ceEEeee-EEecCCCEEEEECCCCCCHHHHHHHHhcccCCCeEEEEEe
Confidence            3466677 6677889999999999999999999999986555455554

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=96.85  E-value=0.00059  Score=57.04  Aligned_cols=28  Identities=14%  Similarity=0.178  Sum_probs=25.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      ++.+.|+||+|||||||++.++..+...
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            6689999999999999999999987643

>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=96.85  E-value=0.0014  Score=55.13  Aligned_cols=51  Identities=12%  Similarity=-0.000  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec
Q psy4122          28 QDWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS   78 (162)
Q Consensus        28 ~~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~   78 (162)
                      ++....|-.++.  .+..|.-++|.||||+|||+|+.++|..   .|.++.++...
T Consensus        43 ~TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E   98 (349)
T 2zr9_A           43 PTGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAE   98 (349)
T ss_dssp             CCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             ccCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            344555666665  4556778999999999999999999854   36677777664

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.84  E-value=0.0008  Score=60.46  Aligned_cols=43  Identities=14%  Similarity=0.251  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHH-HHHHhCCc
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMS-YLELTQRE   71 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~-lA~~lg~p   71 (162)
                      ++++=.+.++.++.   .....++.||||||||+.+-+ ++.++...
T Consensus       190 LN~~Q~~AV~~al~---~~~~~lI~GPPGTGKT~ti~~~I~~l~~~~  233 (646)
T 4b3f_X          190 LDTSQKEAVLFALS---QKELAIIHGPPGTGKTTTVVEIILQAVKQG  233 (646)
T ss_dssp             CCHHHHHHHHHHHH---CSSEEEEECCTTSCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHhc---CCCceEEECCCCCCHHHHHHHHHHHHHhCC
Confidence            56666666766654   233578889999999975544 44444333

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=96.83  E-value=0.00067  Score=48.39  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|+++++..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999854

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=96.82  E-value=0.00094  Score=54.75  Aligned_cols=27  Identities=11%  Similarity=0.044  Sum_probs=23.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|.-+.|+||+||||||+++.++..++
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            445689999999999999999999876

>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=96.81  E-value=0.00078  Score=50.05  Aligned_cols=25  Identities=16%  Similarity=0.155  Sum_probs=22.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      -.+|+||.|||||+|+++++..++.
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~~   52 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLGG   52 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHcC
Confidence            5789999999999999999988753

>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=96.81  E-value=0.0007  Score=55.98  Aligned_cols=26  Identities=15%  Similarity=0.164  Sum_probs=23.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++.+.|+||.||||||+++.+|..+.
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            56789999999999999999997763

>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=96.80  E-value=0.00087  Score=53.15  Aligned_cols=28  Identities=18%  Similarity=0.146  Sum_probs=24.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.++....
T Consensus        29 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~~   56 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKSTMLNIIGCLDK   56 (235)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            3588899999999999999999997654

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=96.79  E-value=0.00093  Score=60.72  Aligned_cols=32  Identities=19%  Similarity=0.238  Sum_probs=27.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYI   75 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v   75 (162)
                      +..++|+|.+||||||+++.+++.+   |.++..+
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~l   86 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTL   86 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            3458999999999999999999998   8886543

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=96.79  E-value=0.00099  Score=55.58  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=31.7

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      .++.+......+..+.|+||||+|||||.+.++..+   +..+.....
T Consensus        44 ~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g~~~~~~g~v~i~~~   91 (337)
T 2qm8_A           44 LIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAV   91 (337)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHhCCcccCCCeEEEEECCCCCCHHHHHHHHHHhhhhCCCEEEEEEE
Confidence            344444444566679999999999999999999765   444444433

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=96.79  E-value=0.00072  Score=50.81  Aligned_cols=23  Identities=26%  Similarity=0.384  Sum_probs=20.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+.|+|++|||||||++.++...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999998754

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.79  E-value=0.0014  Score=53.71  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=21.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      -+.+.|++||||||+++.++..++
T Consensus        33 ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           33 FIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            478899999999999999998875

>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=96.79  E-value=0.0032  Score=53.17  Aligned_cols=48  Identities=8%  Similarity=0.077  Sum_probs=32.9

Q ss_pred             HHHHHHHH-----hcCCCCcEEEEcCCCchHHHHHHHHHHHh-----CCceEEEEeccC
Q psy4122          32 SHLRWILQ-----KDNMSQDVFLIGKPGSLRRSLAMSYLELT-----QREVEYICLSRD   80 (162)
Q Consensus        32 ~~L~~i~~-----~~~~g~~vlL~GppG~GKT~La~~lA~~l-----g~p~~~v~~~~~   80 (162)
                      ..|-.++-     .+..| -+++.||||+|||+|+-+++...     |..+.++..-..
T Consensus        12 ~~LD~~LGg~~~GGl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s   69 (333)
T 3io5_A           12 PMMNIALSGEITGGMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFG   69 (333)
T ss_dssp             HHHHHHHHSSTTCCBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCC
T ss_pred             HHHHHHhCCCCCCCCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccch
Confidence            34445554     24456 68999999999999999887543     556666665433

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=96.78  E-value=0.00073  Score=47.96  Aligned_cols=22  Identities=14%  Similarity=0.388  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.++..
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999854

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=96.78  E-value=0.00074  Score=48.37  Aligned_cols=22  Identities=14%  Similarity=0.253  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999999998853

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=96.78  E-value=0.00077  Score=48.01  Aligned_cols=22  Identities=18%  Similarity=0.415  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6899999999999999998753

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=96.78  E-value=0.0024  Score=62.10  Aligned_cols=30  Identities=13%  Similarity=0.177  Sum_probs=25.9

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ....|+.+-|+|++|||||||++.+.+...
T Consensus      1101 ~I~~Ge~vaIVG~SGsGKSTL~~lL~rl~~ 1130 (1321)
T 4f4c_A         1101 SVEPGQTLALVGPSGCGKSTVVALLERFYD 1130 (1321)
T ss_dssp             EECTTCEEEEECSTTSSTTSHHHHHTTSSC
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHhcCcc
Confidence            455689999999999999999999987653

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=96.77  E-value=0.00075  Score=50.76  Aligned_cols=23  Identities=26%  Similarity=0.384  Sum_probs=20.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+.|+|++|+|||+|++.++...
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999998653

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=96.77  E-value=0.00098  Score=52.41  Aligned_cols=28  Identities=25%  Similarity=0.202  Sum_probs=24.4

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.++....
T Consensus        28 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~~   55 (224)
T 2pcj_A           28 KKGEFVSIIGASGSGKSTLLYILGLLDA   55 (224)
T ss_dssp             ETTCEEEEEECTTSCHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3577899999999999999999997664

>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=96.76  E-value=0.0014  Score=55.44  Aligned_cols=51  Identities=16%  Similarity=0.107  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec
Q psy4122          28 QDWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS   78 (162)
Q Consensus        28 ~~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~   78 (162)
                      ++....|-.++.  .+..|.-+++.|+||+|||+||.++|..   .|.++.++...
T Consensus        45 ~TG~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E  100 (356)
T 1u94_A           45 STGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE  100 (356)
T ss_dssp             CCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            344555666664  4556778999999999999999998854   36777777764

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=96.76  E-value=0.00077  Score=48.72  Aligned_cols=21  Identities=38%  Similarity=0.582  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCccHHHHHHHHhc
Confidence            589999999999999998863

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.75  E-value=0.0012  Score=54.07  Aligned_cols=37  Identities=16%  Similarity=-0.024  Sum_probs=27.8

Q ss_pred             HHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          31 LSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        31 ~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ...|-.++. .+..|.-+++.||||+|||+++.++|..
T Consensus        84 ~~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           84 SSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             CHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             ChhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            344555553 3445667899999999999999999964

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=96.75  E-value=0.0014  Score=54.92  Aligned_cols=37  Identities=19%  Similarity=0.126  Sum_probs=28.4

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|-.++. .+..|.-+.|+||+|||||+|+.+++...
T Consensus       118 ~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          118 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             HHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34444543 33466678999999999999999999876

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=96.75  E-value=0.001  Score=53.67  Aligned_cols=29  Identities=17%  Similarity=0.201  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        29 i~~Ge~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           29 ARAGDVISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34578899999999999999999997764

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=96.74  E-value=0.00064  Score=50.53  Aligned_cols=21  Identities=19%  Similarity=0.504  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++.++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999875

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=96.74  E-value=0.00073  Score=55.99  Aligned_cols=27  Identities=11%  Similarity=-0.024  Sum_probs=23.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|.-+.|.||+|||||||++.++..+.
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            455689999999999999999998774

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=96.72  E-value=0.00083  Score=49.02  Aligned_cols=21  Identities=19%  Similarity=0.363  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.|+|++|+|||+|.+.++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999975

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=96.72  E-value=0.013  Score=56.35  Aligned_cols=41  Identities=20%  Similarity=0.158  Sum_probs=31.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCCC--cEEEEcCCCchHHHHHHHHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQ--DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~--~vlL~GppG~GKT~La~~lA   65 (162)
                      .++|.=.+.+..++.....++  ++++.||+|+|||..+...|
T Consensus       603 ~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa  645 (1151)
T 2eyq_A          603 ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAA  645 (1151)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHH
Confidence            357777777777777655565  79999999999998876444

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=96.72  E-value=0.00088  Score=47.74  Aligned_cols=22  Identities=18%  Similarity=0.448  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         6 ~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            6899999999999999998853

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.72  E-value=0.00088  Score=47.95  Aligned_cols=22  Identities=14%  Similarity=0.406  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999998754

>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=96.72  E-value=0.0015  Score=51.19  Aligned_cols=30  Identities=23%  Similarity=0.061  Sum_probs=24.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~   73 (162)
                      |.-+.+.|++||||||+++.+++.+   |.++.
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~   38 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQ   38 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTTTCCEE
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHcCCCcc
Confidence            5578899999999999999999876   45554

>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=96.72  E-value=0.0031  Score=62.92  Aligned_cols=52  Identities=15%  Similarity=0.106  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccC
Q psy4122          29 DWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRD   80 (162)
Q Consensus        29 ~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~   80 (162)
                      +.+..|-.++.  .+..|..++|+||||||||+||.+++..   .|.++.++.+...
T Consensus        17 TGi~~LD~lL~~GGi~~G~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~te~~   73 (1706)
T 3cmw_A           17 TGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHA   73 (1706)
T ss_dssp             CSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSC
T ss_pred             cCcHHHHHHhhcCCcCCCeEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEecCc
Confidence            34455666664  4557789999999999999999998853   4777888877543

>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=96.71  E-value=0.026  Score=49.17  Aligned_cols=33  Identities=15%  Similarity=0.271  Sum_probs=25.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      .++++|++|+||||++..+|..+   |..+..+.+.
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D  137 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSD  137 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            57899999999999999998655   5665555553

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=96.71  E-value=0.0007  Score=53.75  Aligned_cols=28  Identities=21%  Similarity=0.144  Sum_probs=24.5

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...|+-+.|+||.|||||||.+.++...
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           28 IPEGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3458889999999999999999998765

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=96.71  E-value=0.00093  Score=47.95  Aligned_cols=23  Identities=26%  Similarity=0.463  Sum_probs=20.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++++|++|+|||+|++.+....
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            68999999999999999987543

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=96.71  E-value=0.0022  Score=53.97  Aligned_cols=46  Identities=9%  Similarity=0.086  Sum_probs=36.4

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      ...+..+ ..+..|+-+.|+||.|||||||.+.++.......-.+.+
T Consensus        59 ~~ald~l-l~i~~Gq~~gIiG~nGaGKTTLl~~I~g~~~~~~g~i~~  104 (347)
T 2obl_A           59 VRAIDGL-LTCGIGQRIGIFAGSGVGKSTLLGMICNGASADIIVLAL  104 (347)
T ss_dssp             CHHHHHH-SCEETTCEEEEEECTTSSHHHHHHHHHHHSCCSEEEEEE
T ss_pred             CEEEEee-eeecCCCEEEEECCCCCCHHHHHHHHhcCCCCCEEEEEE
Confidence            4566666 666788999999999999999999999998755444444

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=96.71  E-value=0.0008  Score=55.50  Aligned_cols=25  Identities=8%  Similarity=0.102  Sum_probs=22.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |+.+.|+||.||||||+++.+|..+
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4568999999999999999999876

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=96.69  E-value=0.00095  Score=47.99  Aligned_cols=22  Identities=32%  Similarity=0.424  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999999998854

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=96.69  E-value=0.00096  Score=48.41  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999998753

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=96.69  E-value=0.0015  Score=50.78  Aligned_cols=30  Identities=17%  Similarity=0.101  Sum_probs=24.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh--CCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT--QREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l--g~p~~   73 (162)
                      |+-+.+.|+.||||||.++.+++.+  |.++.
T Consensus         2 ~kFI~~EG~dGsGKsTq~~~L~~~L~~~~~v~   33 (205)
T 4hlc_A            2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVI   33 (205)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHTTTSCEE
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHHHCCCCEE
Confidence            4568899999999999999999887  44544

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=96.68  E-value=0.0015  Score=57.72  Aligned_cols=26  Identities=8%  Similarity=0.151  Sum_probs=23.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      -++|+|.||+||||+++.+|+.++.+
T Consensus        37 lIvlvGlpGSGKSTia~~La~~L~~~   62 (520)
T 2axn_A           37 VIVMVGLPARGKTYISKKLTRYLNWI   62 (520)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            58899999999999999999988543

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=96.68  E-value=0.00095  Score=47.88  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5899999999999999998843

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=96.67  E-value=0.00095  Score=47.87  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            689999999999999999874

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=96.67  E-value=0.001  Score=48.29  Aligned_cols=22  Identities=27%  Similarity=0.489  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        10 ~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A           10 KVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            6899999999999999998753

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=96.67  E-value=0.0013  Score=52.83  Aligned_cols=28  Identities=21%  Similarity=0.269  Sum_probs=24.7

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.++....
T Consensus        31 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~~   58 (257)
T 1g6h_A           31 NKGDVTLIIGPNGSGKSTLINVITGFLK   58 (257)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            3578899999999999999999997764

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=96.67  E-value=0.002  Score=50.85  Aligned_cols=33  Identities=6%  Similarity=0.050  Sum_probs=27.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      .|.-+.+.|++|+||||+++.+++.++.+...+
T Consensus         4 ~g~~i~~eG~~g~GKst~~~~l~~~l~~~~~~~   36 (216)
T 3tmk_A            4 RGKLILIEGLDRTGKTTQCNILYKKLQPNCKLL   36 (216)
T ss_dssp             CCCEEEEEECSSSSHHHHHHHHHHHHCSSEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcccceEE
Confidence            367799999999999999999999998754333

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=96.67  E-value=0.0014  Score=51.47  Aligned_cols=28  Identities=14%  Similarity=0.091  Sum_probs=24.6

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.++....
T Consensus        33 ~~Ge~~~iiG~NGsGKSTLlk~l~Gl~~   60 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTLLKTISTYLK   60 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3588899999999999999999997653

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.67  E-value=0.001  Score=48.63  Aligned_cols=32  Identities=9%  Similarity=0.165  Sum_probs=23.8

Q ss_pred             HHHHHHhcCC---CCcEEEEcCCCchHHHHHHHHH
Q psy4122          34 LRWILQKDNM---SQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        34 L~~i~~~~~~---g~~vlL~GppG~GKT~La~~lA   65 (162)
                      ++.++..+..   ...++++|++|+|||+|++.+.
T Consensus         5 ~~~~~~~~~~~~~~~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A            5 FSSMFDKLWGSNKELRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             HHHHHGGGTTCSSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             HHHHHHHhcCCCCccEEEEECCCCCCHHHHHHHHh
Confidence            4455554433   2369999999999999998775

>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=96.66  E-value=0.0095  Score=49.21  Aligned_cols=24  Identities=13%  Similarity=0.061  Sum_probs=19.1

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHH
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMS   63 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~   63 (162)
                      .+..++++++.+|+|+|||..+..
T Consensus        70 ~i~~~~~~lv~a~TGsGKT~~~~~   93 (410)
T 2j0s_A           70 QIIKGRDVIAQSQSGTGKTATFSI   93 (410)
T ss_dssp             HHHTTCCEEEECCTTSSHHHHHHH
T ss_pred             HHhCCCCEEEECCCCCCchHHHHH
Confidence            344578999999999999976654

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=96.65  E-value=0.00089  Score=50.74  Aligned_cols=38  Identities=16%  Similarity=0.197  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +++.++|+.+.... ..-.++++|++|+|||+|++.+..
T Consensus        15 ~~~~~~m~~~~~~~-~~~ki~vvG~~~~GKSsLi~~l~~   52 (204)
T 4gzl_A           15 VPRGSHMENLYFQG-QAIKCVVVGDGAVGKTCLLISYTT   52 (204)
T ss_dssp             ----------------CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ccchhHHHhHhhcC-CeEEEEEECcCCCCHHHHHHHHHh
Confidence            55666666655432 223799999999999999998885

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=96.65  E-value=0.00096  Score=58.57  Aligned_cols=46  Identities=7%  Similarity=0.184  Sum_probs=33.8

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHH--HHHh--CCceEEEEe
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSY--LELT--QREVEYICL   77 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~l--A~~l--g~p~~~v~~   77 (162)
                      ..|..+.- .+..|+.++|+||+|||||||++++  +...  +....++..
T Consensus        26 ~~Ld~i~~G~i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g   76 (525)
T 1tf7_A           26 EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   76 (525)
T ss_dssp             TTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             hhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            34666666 6667889999999999999999994  4544  444455554

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=96.65  E-value=0.0013  Score=52.14  Aligned_cols=28  Identities=25%  Similarity=0.222  Sum_probs=24.6

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.++....
T Consensus        30 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   57 (240)
T 1ji0_A           30 PRGQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            3578899999999999999999997654

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=96.65  E-value=0.00097  Score=52.19  Aligned_cols=25  Identities=4%  Similarity=-0.007  Sum_probs=22.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..+.+.|++||||||+++.+++.++
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            4588999999999999999999884

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=96.64  E-value=0.0037  Score=51.96  Aligned_cols=38  Identities=16%  Similarity=0.218  Sum_probs=28.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEecc
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSR   79 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~   79 (162)
                      ..+..+.++|+||+||||+++.++..+   +..+..+....
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~~~~~~~v~v~~~d~   94 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDP   94 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEeecC
Confidence            345578999999999999999998654   55555555443

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=96.64  E-value=0.0011  Score=47.47  Aligned_cols=22  Identities=18%  Similarity=0.419  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999853

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.64  E-value=0.001  Score=50.43  Aligned_cols=24  Identities=17%  Similarity=0.159  Sum_probs=21.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..++++|++|+|||+|+.+++...
T Consensus        13 ~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           13 PSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            369999999999999999998654

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=96.64  E-value=0.0013  Score=53.33  Aligned_cols=30  Identities=23%  Similarity=0.170  Sum_probs=25.7

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ....|+.+.|+||.|||||||.+.++....
T Consensus        41 ~i~~Ge~~~i~G~nGsGKSTLlk~l~Gl~~   70 (271)
T 2ixe_A           41 TLYPGKVTALVGPNGSGKSTVAALLQNLYQ   70 (271)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            344688899999999999999999997764

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=96.64  E-value=0.0014  Score=52.43  Aligned_cols=28  Identities=14%  Similarity=0.220  Sum_probs=24.7

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.++....
T Consensus        33 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   60 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTLTKLIQRFYI   60 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3578899999999999999999997764

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=96.64  E-value=0.001  Score=47.84  Aligned_cols=21  Identities=29%  Similarity=0.482  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999999863

>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=96.64  E-value=0.001  Score=53.71  Aligned_cols=28  Identities=14%  Similarity=0.135  Sum_probs=24.5

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...|+-+.|+||.|||||||.+.++...
T Consensus        43 i~~Ge~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           43 VHPGEVHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTCT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4458889999999999999999999863

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=96.63  E-value=0.0011  Score=47.40  Aligned_cols=21  Identities=14%  Similarity=0.507  Sum_probs=19.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus         5 ki~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999985

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.63  E-value=0.0015  Score=51.58  Aligned_cols=29  Identities=21%  Similarity=0.168  Sum_probs=25.1

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+.+.|+||.|||||||.+.++....
T Consensus        31 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           31 IERGQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            34588899999999999999999997764

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.63  E-value=0.0026  Score=54.55  Aligned_cols=35  Identities=14%  Similarity=0.045  Sum_probs=25.8

Q ss_pred             HHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          33 HLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        33 ~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|-+++. .+..|.-+.|.||||||||+|+.++|..
T Consensus       166 ~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la~~  201 (400)
T 3lda_A          166 NLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVT  201 (400)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHHHH
Confidence            3444442 3345677999999999999999988744

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=96.63  E-value=0.0011  Score=48.54  Aligned_cols=22  Identities=18%  Similarity=0.350  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        13 ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           13 KFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6899999999999999999853

>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=96.62  E-value=0.0025  Score=54.08  Aligned_cols=51  Identities=12%  Similarity=0.034  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHH---hCCceEEEEec
Q psy4122          28 QDWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLS   78 (162)
Q Consensus        28 ~~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~   78 (162)
                      ++....|-.++.  .+..|.-+++.||||+|||+|+.++|..   .|.++.++.+.
T Consensus        56 ~TG~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E  111 (366)
T 1xp8_A           56 STGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAE  111 (366)
T ss_dssp             CCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCCCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECC
Confidence            444556666665  4556778999999999999999998854   36777777774

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=96.62  E-value=0.0011  Score=48.86  Aligned_cols=21  Identities=19%  Similarity=0.363  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.|+|++|+|||+|++.++.
T Consensus         9 ~i~lvG~~gvGKStL~~~l~~   29 (188)
T 2wjg_A            9 EIALIGNPNVGKSTIFNALTG   29 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999875

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=96.62  E-value=0.0011  Score=47.39  Aligned_cols=22  Identities=5%  Similarity=0.122  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999754

>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=96.61  E-value=0.0012  Score=54.32  Aligned_cols=36  Identities=14%  Similarity=0.352  Sum_probs=27.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh----CCceEEEEec
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT----QREVEYICLS   78 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l----g~p~~~v~~~   78 (162)
                      .++.++++||+|+||||++..+|..+    |..+..+.+.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D  143 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTD  143 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            35578999999999999999999654    5555555543

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=96.61  E-value=0.00091  Score=50.81  Aligned_cols=25  Identities=12%  Similarity=0.215  Sum_probs=22.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +.+.++|++|||||||++.++..+.
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3588999999999999999998764

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=96.61  E-value=0.0014  Score=53.00  Aligned_cols=29  Identities=21%  Similarity=0.186  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        47 i~~Gei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           47 IREGEVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            34578899999999999999999997764

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=96.60  E-value=0.016  Score=50.82  Aligned_cols=44  Identities=7%  Similarity=-0.093  Sum_probs=33.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCC-CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          25 ALTQDWLSHLRWILQKDNMS-QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g-~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+.+.=.+.+++++..+..+ +++++.+|+|+|||..+-.++..+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l  222 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKL  222 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHH
Confidence            46677777777777765545 469999999999999987777543

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=96.60  E-value=0.00097  Score=49.26  Aligned_cols=24  Identities=21%  Similarity=0.302  Sum_probs=21.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      +..+.|+|++|+|||+|.+.++..
T Consensus         4 ~~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            4 GMKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            456999999999999999999853

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=96.59  E-value=0.0011  Score=47.65  Aligned_cols=20  Identities=35%  Similarity=0.582  Sum_probs=18.4

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|+|||+|++.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~   23 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFG   23 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            58999999999999999885

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=96.59  E-value=0.0012  Score=53.60  Aligned_cols=24  Identities=13%  Similarity=0.382  Sum_probs=21.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++.|+||+|+|||||.+.++....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~   27 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQV   27 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            588999999999999999997763

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=96.59  E-value=0.0012  Score=52.71  Aligned_cols=26  Identities=15%  Similarity=0.089  Sum_probs=23.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ..|+.+.|+||.|||||||.+.++..
T Consensus        27 ~~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            35788999999999999999999986

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=96.58  E-value=0.0014  Score=52.66  Aligned_cols=29  Identities=17%  Similarity=0.248  Sum_probs=25.2

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+.+.|+||.|+|||||.+.++....
T Consensus        23 i~~Ge~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           23 VRAGEILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34678899999999999999999997764

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=96.58  E-value=0.0016  Score=53.16  Aligned_cols=29  Identities=10%  Similarity=0.157  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        31 i~~Ge~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           31 IKRGEVTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcCCC
Confidence            34578899999999999999999997764

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=96.58  E-value=0.0012  Score=47.68  Aligned_cols=21  Identities=14%  Similarity=0.352  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus        16 ~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999884

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=96.57  E-value=0.0013  Score=47.70  Aligned_cols=22  Identities=14%  Similarity=0.468  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        11 ~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           11 KLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            6899999999999999998864

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=96.57  E-value=0.0013  Score=47.59  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        17 ~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           17 KYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6999999999999999999854

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=96.57  E-value=0.0012  Score=47.90  Aligned_cols=21  Identities=19%  Similarity=0.422  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus         8 ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            8 KIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHG
T ss_pred             EEEEECcCCCCHHHHHHHHHh
Confidence            589999999999999999874

>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=96.57  E-value=0.0024  Score=49.81  Aligned_cols=23  Identities=13%  Similarity=0.274  Sum_probs=19.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .|+.+++.||+|||||++...+.
T Consensus        75 ~g~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           75 QNSVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             HCSEEEEECCTTSSHHHHHHHHH
T ss_pred             cCCEEEEEeCCCCCcHHhHHHHH
Confidence            47889999999999998766544

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=96.56  E-value=0.00085  Score=53.35  Aligned_cols=29  Identities=10%  Similarity=0.091  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+.+.|+||.|||||||.+.++....
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   53 (243)
T 1mv5_A           25 AQPNSIIAFAGPSGGGKSTIFSLLERFYQ   53 (243)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34578899999999999999999997653

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.56  E-value=0.001  Score=53.57  Aligned_cols=30  Identities=17%  Similarity=0.164  Sum_probs=25.8

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ....|+.+.|+||.|||||||.+.++....
T Consensus        42 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           42 FIPSGTTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            344688899999999999999999998764

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=96.56  E-value=0.0018  Score=55.02  Aligned_cols=29  Identities=21%  Similarity=0.305  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|.||.|||||||.+.+|....
T Consensus        27 i~~Ge~~~llGpsGsGKSTLLr~iaGl~~   55 (359)
T 3fvq_A           27 LDPGEILFIIGASGCGKTTLLRCLAGFEQ   55 (359)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEECCCCchHHHHHHHHhcCCC
Confidence            33578899999999999999999997653

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=96.56  E-value=0.0016  Score=52.40  Aligned_cols=29  Identities=17%  Similarity=0.056  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        38 i~~Gei~~l~G~NGsGKSTLlk~l~Gl~~   66 (256)
T 1vpl_A           38 IEEGEIFGLIGPNGAGKTTTLRIISTLIK   66 (256)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34578899999999999999999997764

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=96.55  E-value=0.0013  Score=47.25  Aligned_cols=21  Identities=10%  Similarity=0.306  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus         9 ~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            9 RILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            699999999999999999874

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=96.55  E-value=0.0016  Score=52.49  Aligned_cols=29  Identities=21%  Similarity=0.227  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        30 i~~Ge~~~liG~nGsGKSTLl~~i~Gl~~   58 (266)
T 2yz2_A           30 INEGECLLVAGNTGSGKSTLLQIVAGLIE   58 (266)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34578899999999999999999997653

>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=96.54  E-value=0.0013  Score=56.97  Aligned_cols=30  Identities=17%  Similarity=0.216  Sum_probs=25.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      .+++.||+|+|||+|+..+|+.++.+  .+++
T Consensus         4 ~i~i~GptgsGKttla~~La~~~~~~--iis~   33 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKFNGE--VINS   33 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHTEE--EEEC
T ss_pred             EEEEECcchhhHHHHHHHHHHHCCCe--Eeec
Confidence            47889999999999999999998754  4554

>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=96.53  E-value=0.0012  Score=55.16  Aligned_cols=25  Identities=12%  Similarity=0.154  Sum_probs=22.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |.-+.|+||+||||||+++.+|..+
T Consensus       129 g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568999999999999999999765

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=96.53  E-value=0.0014  Score=48.43  Aligned_cols=22  Identities=14%  Similarity=0.388  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999999999854

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=96.53  E-value=0.0019  Score=54.56  Aligned_cols=29  Identities=7%  Similarity=0.068  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|.||.|||||||.+.+|....
T Consensus        23 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           23 VESGEYFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             ECTTCEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEECCCCccHHHHHHHHHcCCC
Confidence            34578899999999999999999997754

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=96.53  E-value=0.0012  Score=48.51  Aligned_cols=21  Identities=10%  Similarity=0.235  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~   23 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTG   23 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999874

>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=96.52  E-value=0.0013  Score=54.53  Aligned_cols=33  Identities=9%  Similarity=0.136  Sum_probs=25.3

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      +-++++||+||||||++..+|..+   |..+..+.+
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~  140 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA  140 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            358899999999999999999765   444444443

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=96.52  E-value=0.0014  Score=47.48  Aligned_cols=22  Identities=14%  Similarity=0.104  Sum_probs=19.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ..++++|++|+|||+|++.+..
T Consensus         9 ~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            9 PVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4699999999999999999874

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=96.52  E-value=0.0012  Score=48.09  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus         9 ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            9 RLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999998863

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=96.51  E-value=0.0014  Score=47.64  Aligned_cols=22  Identities=18%  Similarity=0.448  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        20 ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           20 KVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            6999999999999999998853

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=96.51  E-value=0.0015  Score=47.87  Aligned_cols=22  Identities=14%  Similarity=0.255  Sum_probs=20.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999864

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=96.51  E-value=0.0015  Score=47.76  Aligned_cols=22  Identities=14%  Similarity=0.401  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999853

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=96.51  E-value=0.0014  Score=47.95  Aligned_cols=22  Identities=23%  Similarity=0.508  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        12 ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           12 KFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6899999999999999998754

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=96.50  E-value=0.0029  Score=56.76  Aligned_cols=38  Identities=16%  Similarity=0.237  Sum_probs=28.3

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ++++-.+.+..++.    +...++.||||||||+++..++..
T Consensus       181 ln~~Q~~av~~~l~----~~~~li~GppGTGKT~~~~~~i~~  218 (624)
T 2gk6_A          181 LNHSQVYAVKTVLQ----RPLSLIQGPPGTGKTVTSATIVYH  218 (624)
T ss_dssp             CCHHHHHHHHHHHT----CSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhc----CCCeEEECCCCCCHHHHHHHHHHH
Confidence            56666666666653    447889999999999988776654

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=96.50  E-value=0.0019  Score=52.65  Aligned_cols=29  Identities=14%  Similarity=0.053  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        44 i~~Ge~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           44 IAKGDKWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34578899999999999999999997764

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=96.50  E-value=0.0012  Score=53.40  Aligned_cols=28  Identities=18%  Similarity=0.115  Sum_probs=24.5

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...|+-+.|+||.|||||||.+.++...
T Consensus        34 i~~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           34 IASGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             EETTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            3458889999999999999999999765

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=96.50  E-value=0.0032  Score=54.97  Aligned_cols=33  Identities=15%  Similarity=0.151  Sum_probs=27.4

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .+-.....|+-+.|+||.|||||||++.++...
T Consensus       130 ~vsl~i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          130 KIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             HHHHHSSSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             cCceEeCCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            344455678899999999999999999999764

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=96.49  E-value=0.00055  Score=51.55  Aligned_cols=24  Identities=13%  Similarity=0.153  Sum_probs=20.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+..+.|+|++|+|||||++.++.
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g   48 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTN   48 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            456799999999999999998764

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=96.49  E-value=0.0015  Score=47.46  Aligned_cols=22  Identities=23%  Similarity=0.505  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5899999999999999998853

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=96.49  E-value=0.0015  Score=48.45  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           27 KVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999998863

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=96.49  E-value=0.0015  Score=47.43  Aligned_cols=22  Identities=23%  Similarity=0.446  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            6899999999999999998754

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=96.49  E-value=0.0015  Score=48.21  Aligned_cols=22  Identities=9%  Similarity=0.244  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus         9 ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            9 KIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999864

>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=96.48  E-value=0.0033  Score=47.96  Aligned_cols=32  Identities=13%  Similarity=0.051  Sum_probs=25.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      -+.+.|++|+|||++++.++..+   |..+..+..
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            47899999999999999998764   556655554

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=96.48  E-value=0.0014  Score=47.53  Aligned_cols=20  Identities=25%  Similarity=0.564  Sum_probs=18.6

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|+|||+|++.+.
T Consensus        11 ~i~v~G~~~~GKssl~~~l~   30 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFA   30 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            68999999999999999876

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=96.48  E-value=0.0032  Score=50.22  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.|+|+||||||||.+++..
T Consensus         5 ~i~lvG~~g~GKTTL~n~l~g   25 (271)
T 3k53_A            5 TVALVGNPNVGKTTIFNALTG   25 (271)
T ss_dssp             EEEEEECSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            689999999999999999864

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=96.48  E-value=0.0022  Score=54.37  Aligned_cols=28  Identities=18%  Similarity=0.241  Sum_probs=24.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|.||.|||||||.+.+|....
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           27 KDGEFMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CCCCEEEEECCCCchHHHHHHHHhcCCC
Confidence            3577899999999999999999997754

>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=96.47  E-value=0.015  Score=55.76  Aligned_cols=37  Identities=11%  Similarity=0.081  Sum_probs=27.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .++|.=.+.+..+    ..++++++.||||+|||..+...+
T Consensus       184 ~ltp~Q~~AI~~i----~~g~dvLV~ApTGSGKTlva~l~i  220 (1108)
T 3l9o_A          184 TLDPFQDTAISCI----DRGESVLVSAHTSAGKTVVAEYAI  220 (1108)
T ss_dssp             CCCHHHHHHHHHH----TTTCCEEEECCSSSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHH----HcCCCEEEECCCCCChHHHHHHHH
Confidence            3555555555554    457899999999999998876544

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=96.46  E-value=0.0023  Score=54.29  Aligned_cols=28  Identities=14%  Similarity=0.184  Sum_probs=24.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|.||.|||||||.+.+|....
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (359)
T 2yyz_A           27 KDGEFVALLGPSGCGKTTTLLMLAGIYK   54 (359)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             cCCCEEEEEcCCCchHHHHHHHHHCCCC
Confidence            3577899999999999999999997653

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=96.46  E-value=0.0023  Score=54.78  Aligned_cols=28  Identities=18%  Similarity=0.228  Sum_probs=24.7

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|+||.|||||||.+.+|....
T Consensus        27 ~~Ge~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           27 HEGEFVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CCCCEEEEEcCCCchHHHHHHHHHcCCC
Confidence            4578899999999999999999997764

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=96.45  E-value=0.0016  Score=47.60  Aligned_cols=22  Identities=14%  Similarity=0.480  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        20 ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           20 KLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            6899999999999999998853

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=96.45  E-value=0.0017  Score=47.38  Aligned_cols=21  Identities=19%  Similarity=0.360  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~   27 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTT   27 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999875

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=96.44  E-value=0.0013  Score=56.87  Aligned_cols=26  Identities=8%  Similarity=0.116  Sum_probs=23.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .++|+|.||+||||+++.+|+.++.+
T Consensus        41 ~IvlvGlpGsGKSTia~~La~~l~~~   66 (469)
T 1bif_A           41 LIVMVGLPARGKTYISKKLTRYLNFI   66 (469)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            58999999999999999999887543

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=96.43  E-value=0.0028  Score=50.63  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.|+|+||||||||.+++..
T Consensus         3 kI~lvG~~n~GKSTL~n~L~g   23 (256)
T 3iby_A            3 HALLIGNPNCGKTTLFNALTN   23 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            689999999999999998864

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=96.43  E-value=0.0014  Score=48.41  Aligned_cols=22  Identities=18%  Similarity=0.317  Sum_probs=19.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ..++++|++|+|||+|++++..
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~   45 (195)
T 1svi_A           24 PEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3699999999999999999874

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=96.43  E-value=0.009  Score=44.72  Aligned_cols=39  Identities=13%  Similarity=0.088  Sum_probs=30.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .+.+.=.+.+..++.    ++++++.+|+|+|||.++...+..
T Consensus        33 ~l~~~Q~~~i~~~~~----~~~~li~~~tGsGKT~~~~~~~~~   71 (216)
T 3b6e_A           33 QLRPYQMEVAQPALE----GKNIIICLPTGSGKTRVAVYIAKD   71 (216)
T ss_dssp             CCCHHHHHHHHHHHT----TCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHhc----CCCEEEEcCCCCCHHHHHHHHHHH
Confidence            456666666666664    679999999999999998876643

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=96.43  E-value=0.0015  Score=55.39  Aligned_cols=25  Identities=8%  Similarity=0.102  Sum_probs=22.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |+.+.|+||.||||||+++.+|..+
T Consensus       157 g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHhhc
Confidence            4468999999999999999999876

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=96.42  E-value=0.0025  Score=54.02  Aligned_cols=29  Identities=21%  Similarity=0.162  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|.||.|||||||.+.+|....
T Consensus        38 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           38 IREGEMVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            33578899999999999999999997653

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=96.42  E-value=0.0025  Score=54.22  Aligned_cols=29  Identities=14%  Similarity=0.121  Sum_probs=24.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|.||.|||||||.+.+|....
T Consensus        34 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   62 (372)
T 1v43_A           34 IKDGEFLVLLGPSGCGKTTTLRMIAGLEE   62 (372)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            33578899999999999999999997653

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=96.41  E-value=0.0026  Score=50.71  Aligned_cols=25  Identities=12%  Similarity=0.191  Sum_probs=22.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +.+.|+||.|||||||.+.++....
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~   49 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCC
Confidence            6789999999999999999997764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=96.41  E-value=0.0015  Score=52.40  Aligned_cols=29  Identities=17%  Similarity=0.213  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+.+.|+||.|+|||||.+.++....
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           28 LNKGDILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             EETTCEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            33578899999999999999999997753

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=96.41  E-value=0.0018  Score=47.94  Aligned_cols=22  Identities=23%  Similarity=0.415  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        24 ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           24 KLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6999999999999999998854

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=96.40  E-value=0.0021  Score=53.25  Aligned_cols=30  Identities=13%  Similarity=0.193  Sum_probs=25.7

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ....|+.+.|+||.|||||||++.++....
T Consensus        76 ~i~~Ge~vaivG~sGsGKSTLl~ll~gl~~  105 (306)
T 3nh6_A           76 TVMPGQTLALVGPSGAGKSTILRLLFRFYD  105 (306)
T ss_dssp             EECTTCEEEEESSSCHHHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCchHHHHHHHHHcCCC
Confidence            344688899999999999999999987664

>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=96.40  E-value=0.00071  Score=53.73  Aligned_cols=26  Identities=8%  Similarity=0.124  Sum_probs=22.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +.-+.|.|++||||||+++.+++.++
T Consensus        24 ~~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           24 IKKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            34688999999999999999999883

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=96.40  E-value=0.0019  Score=46.95  Aligned_cols=23  Identities=17%  Similarity=0.218  Sum_probs=20.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      -.++++|++|+|||+|++.+...
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            36999999999999999998853

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=96.39  E-value=0.002  Score=54.40  Aligned_cols=29  Identities=10%  Similarity=0.100  Sum_probs=24.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|.||.|||||||.+.+|....
T Consensus        28 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   56 (353)
T 1oxx_K           28 IENGERFGILGPSGAGKTTFMRIIAGLDV   56 (353)
T ss_dssp             ECTTCEEEEECSCHHHHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34578899999999999999999997653

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=96.39  E-value=0.002  Score=48.03  Aligned_cols=22  Identities=18%  Similarity=0.543  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            6999999999999999998854

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=96.39  E-value=0.0016  Score=47.77  Aligned_cols=22  Identities=18%  Similarity=0.315  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        25 ~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           25 EVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6999999999999999988643

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=96.39  E-value=0.0019  Score=48.17  Aligned_cols=23  Identities=17%  Similarity=0.423  Sum_probs=20.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ..++++|++|+|||+|++.+...
T Consensus        29 ~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           29 VKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            36999999999999999998864

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=96.38  E-value=0.0019  Score=47.76  Aligned_cols=22  Identities=14%  Similarity=0.288  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        22 ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6999999999999999998753

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=96.38  E-value=0.0026  Score=54.04  Aligned_cols=28  Identities=14%  Similarity=0.178  Sum_probs=24.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+.|.||.|||||||.+.+|....
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (372)
T 1g29_1           27 KDGEFMILLGPSGCGKTTTLRMIAGLEE   54 (372)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             cCCCEEEEECCCCcHHHHHHHHHHcCCC
Confidence            3577899999999999999999997654

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=96.38  E-value=0.00074  Score=55.23  Aligned_cols=24  Identities=8%  Similarity=0.220  Sum_probs=18.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      -+.|.||+||||||+++.+++.+|
T Consensus         7 iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            478899999999999999998776

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=96.38  E-value=0.002  Score=48.06  Aligned_cols=22  Identities=27%  Similarity=0.326  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|||||+|++.+...
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6999999999999999988753

>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=96.38  E-value=0.0035  Score=55.61  Aligned_cols=25  Identities=8%  Similarity=0.069  Sum_probs=22.2

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |.-+.|+|+.||||||+++.+|..+
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHh
Confidence            4468999999999999999999876

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=96.38  E-value=0.0019  Score=48.28  Aligned_cols=21  Identities=10%  Similarity=0.207  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus        25 ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           25 KLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            799999999999999999985

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=96.37  E-value=0.0021  Score=57.56  Aligned_cols=31  Identities=23%  Similarity=0.273  Sum_probs=25.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC----CceEEE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ----REVEYI   75 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg----~p~~~v   75 (162)
                      ..++|+|.+|+||||+++.+++.++    +++..+
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~l  431 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLL  431 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEE
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEE
Confidence            3588999999999999999999876    665444

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=96.37  E-value=0.0018  Score=47.30  Aligned_cols=21  Identities=19%  Similarity=0.445  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus         8 ki~~~G~~~~GKSsli~~l~~   28 (181)
T 3t5g_A            8 KIAILGYRSVGKSSLTIQFVE   28 (181)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHHc
Confidence            689999999999999999884

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=96.36  E-value=0.002  Score=48.05  Aligned_cols=22  Identities=23%  Similarity=0.446  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            6999999999999999999753

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=96.36  E-value=0.002  Score=47.97  Aligned_cols=22  Identities=18%  Similarity=0.448  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            6899999999999999998753

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=96.36  E-value=0.0019  Score=48.60  Aligned_cols=22  Identities=32%  Similarity=0.475  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++|+|+||+|||+|.++++..
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999854

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=96.36  E-value=0.002  Score=47.39  Aligned_cols=22  Identities=23%  Similarity=0.522  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6899999999999999999754

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=96.36  E-value=0.0029  Score=53.71  Aligned_cols=27  Identities=22%  Similarity=0.282  Sum_probs=23.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+-+.|+||+|+|||||++.++....
T Consensus       214 ~G~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          214 TGRISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHhcccc
Confidence            367899999999999999999986554

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=96.36  E-value=0.002  Score=47.54  Aligned_cols=22  Identities=23%  Similarity=0.480  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999999998853

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=96.35  E-value=0.0022  Score=52.51  Aligned_cols=26  Identities=15%  Similarity=0.059  Sum_probs=22.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .|+-+.|+||+|+|||||++.++ ...
T Consensus       164 ~G~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          164 EGFICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             cCcEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            36678999999999999999999 543

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=96.35  E-value=0.0024  Score=55.54  Aligned_cols=34  Identities=9%  Similarity=0.122  Sum_probs=28.1

Q ss_pred             HHHHHHhcCCCCc--EEEEcCCCchHHHHHHHHHHH
Q psy4122          34 LRWILQKDNMSQD--VFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        34 L~~i~~~~~~g~~--vlL~GppG~GKT~La~~lA~~   67 (162)
                      +..+-.....|..  +.|+||+|+|||||++.++..
T Consensus        30 L~~vsl~i~~Gei~~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           30 DQLVNKSVSQGFCFNILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             HHHHHHSCC-CCEEEEEEECSTTSSSHHHHHHHHTS
T ss_pred             cCCCceEecCCCeeEEEEECCCCCCHHHHHHHHhCc
Confidence            5666667777887  999999999999999999865

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=96.34  E-value=0.0021  Score=47.22  Aligned_cols=23  Identities=9%  Similarity=-0.094  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++++|++|+|||+|++.+....
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            58999999999999998776544

>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=96.34  E-value=0.0048  Score=48.16  Aligned_cols=33  Identities=24%  Similarity=0.389  Sum_probs=26.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh--CCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT--QREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l--g~p~~~v~~~   78 (162)
                      .+++.|.+|+||||++..+|..+  |..+..+.+.
T Consensus        16 i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd~D   50 (262)
T 1yrb_A           16 IVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLD   50 (262)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEECC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            47888999999999999999765  6665555554

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=96.34  E-value=0.0019  Score=55.37  Aligned_cols=29  Identities=31%  Similarity=0.405  Sum_probs=25.1

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ....|+-+.|+||.|||||||.+.+|...
T Consensus        43 ~i~~Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           43 SISPGQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             EECTTCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            34468889999999999999999999765

>3i8s_A Ferrous iron transport protein B; GTPase, GPCR, iron uptake, FEO, cell inner membrane, cell ME GTP-binding, ION transport, membrane; 1.80A {Escherichia coli} PDB: 3i8x_A* 3i92_A* 3hyr_A 3hyt_A* 2wic_A* 2wib_A* 2wia_A*

Probab=96.34  E-value=0.0049  Score=49.50  Aligned_cols=21  Identities=29%  Similarity=0.330  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.|+|+||||||||.+++..
T Consensus         5 ~I~lvG~~n~GKSTLin~l~g   25 (274)
T 3i8s_A            5 TIGLIGNPNSGKTTLFNQLTG   25 (274)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            689999999999999999864

>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=96.33  E-value=0.0024  Score=48.68  Aligned_cols=33  Identities=9%  Similarity=-0.032  Sum_probs=25.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      .-+.+.|++|+||||+++.++..+   |..+-.+..
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l~~~g~~v~~i~~   42 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIKH   42 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhccccCCceeEEee
Confidence            357899999999999999988753   445544444

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=96.33  E-value=0.0021  Score=47.68  Aligned_cols=22  Identities=14%  Similarity=0.067  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999853

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.32  E-value=0.0031  Score=54.70  Aligned_cols=33  Identities=9%  Similarity=0.026  Sum_probs=28.0

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +++..+-.|+.++|+||+|||||+|+..+|+..
T Consensus       166 D~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          166 DLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             HHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             eeeeeecCCcEEEEecCCCCChhHHHHHHHHHH
Confidence            444556678999999999999999999999765

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=96.32  E-value=0.0022  Score=47.87  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A           10 KVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            6899999999999999998754

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=96.32  E-value=0.002  Score=48.14  Aligned_cols=21  Identities=19%  Similarity=0.499  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus        10 ki~v~G~~~~GKSsli~~l~~   30 (203)
T 1zbd_A           10 KILIIGNSSVGKTSFLFRYAD   30 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            689999999999999998874

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=96.32  E-value=0.0022  Score=47.68  Aligned_cols=22  Identities=18%  Similarity=0.431  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999998853

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=96.32  E-value=0.0022  Score=47.47  Aligned_cols=21  Identities=24%  Similarity=0.498  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus        10 ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A           10 RVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHc
Confidence            699999999999999999986

>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=96.32  E-value=0.0024  Score=51.01  Aligned_cols=25  Identities=12%  Similarity=0.141  Sum_probs=22.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |.-+.+.|++|+||||+++.+++.+
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5678999999999999999999766

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=96.32  E-value=0.0022  Score=47.63  Aligned_cols=23  Identities=22%  Similarity=0.416  Sum_probs=20.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++++|++|+|||+|++.+....
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            59999999999999999998654

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=96.32  E-value=0.002  Score=51.33  Aligned_cols=41  Identities=20%  Similarity=0.181  Sum_probs=27.1

Q ss_pred             CCHHHHHHHHHHHHhcC----CCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDN----MSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~----~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ++....+.+..++....    ..-.++++|++|+|||+|++.+..
T Consensus        17 l~~~~~~~l~~~~~~~~~~~~~~~~I~vvG~~g~GKSSLin~l~~   61 (270)
T 1h65_A           17 FAPATQTKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIG   61 (270)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHHhhcCCCCeEEEEECCCCCCHHHHHHHHhC
Confidence            34444445444443222    123689999999999999999874

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=96.29  E-value=0.0023  Score=47.99  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        30 ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           30 KIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            6999999999999999998753

>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=96.29  E-value=0.0066  Score=51.56  Aligned_cols=36  Identities=11%  Similarity=0.107  Sum_probs=25.3

Q ss_pred             CCHHHHHHHHHH------------HHhcCCCCcEEEEcCCCchHHHHH
Q psy4122          26 LTQDWLSHLRWI------------LQKDNMSQDVFLIGKPGSLRRSLA   61 (162)
Q Consensus        26 ~~~~~~~~L~~i------------~~~~~~g~~vlL~GppG~GKT~La   61 (162)
                      +++..++.|+.+            +.....|+++++.+|+|+|||...
T Consensus        63 l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~  110 (434)
T 2db3_A           63 LRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAF  110 (434)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHH
Confidence            456666666432            233446889999999999999743

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=96.29  E-value=0.0023  Score=47.55  Aligned_cols=22  Identities=9%  Similarity=0.279  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            6999999999999999998864

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=96.29  E-value=0.0022  Score=48.08  Aligned_cols=22  Identities=23%  Similarity=0.471  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y           10 KLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6899999999999999998753

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=96.27  E-value=0.0019  Score=52.33  Aligned_cols=28  Identities=25%  Similarity=0.353  Sum_probs=24.9

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ... |+.+.|+||.|||||||.+.++...
T Consensus        27 ~i~-Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           27 EVN-GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             EEC-SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEC-CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            345 7889999999999999999999876

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=96.25  E-value=0.0022  Score=47.54  Aligned_cols=21  Identities=14%  Similarity=0.273  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus        18 ki~ivG~~~vGKSsL~~~l~~   38 (181)
T 1fzq_A           18 RILLLGLDNAGKTTLLKQLAS   38 (181)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            699999999999999998864

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=96.25  E-value=0.0024  Score=47.92  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        26 ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           26 KVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            6999999999999999998854

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=96.25  E-value=0.0022  Score=47.17  Aligned_cols=22  Identities=5%  Similarity=0.214  Sum_probs=19.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ..++++|++|+|||+|++++..
T Consensus        19 ~~i~v~G~~~~GKssl~~~l~~   40 (186)
T 1ksh_A           19 LRLLMLGLDNAGKTTILKKFNG   40 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            3699999999999999998874

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=96.24  E-value=0.0019  Score=52.99  Aligned_cols=27  Identities=22%  Similarity=0.206  Sum_probs=23.7

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|+.+.|+||.|||||||.+.++...
T Consensus        62 ~~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           62 ERGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            356778999999999999999998765

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=96.24  E-value=0.0033  Score=54.23  Aligned_cols=22  Identities=23%  Similarity=0.332  Sum_probs=20.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .+.|+||+|+|||||.+.++..
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            7899999999999999999974

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=96.24  E-value=0.0026  Score=48.01  Aligned_cols=24  Identities=21%  Similarity=0.196  Sum_probs=21.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..++++|++|+|||+|+.++....
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            369999999999999999998643

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=96.24  E-value=0.0042  Score=50.70  Aligned_cols=21  Identities=19%  Similarity=0.350  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+.|+|+||+|||||.+++..
T Consensus        10 ~VaIvG~~nvGKSTLln~L~g   30 (301)
T 1ega_A           10 FIAIVGRPNVGKSTLLNKLLG   30 (301)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            689999999999999999874

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.24  E-value=0.0026  Score=47.64  Aligned_cols=21  Identities=29%  Similarity=0.629  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|++|+|||+|++.+..
T Consensus        22 ~i~v~G~~~~GKSsli~~l~~   42 (213)
T 3cph_A           22 KILLIGDSGVGKSCLLVRFVE   42 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            689999999999999999884

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=96.23  E-value=0.0024  Score=47.19  Aligned_cols=22  Identities=9%  Similarity=0.297  Sum_probs=19.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      -.++++|++|+|||+|++++..
T Consensus        17 ~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           17 HKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3699999999999999999873

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=96.21  E-value=0.0031  Score=49.48  Aligned_cols=25  Identities=16%  Similarity=0.165  Sum_probs=22.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |.-+.++|++|+||||.++.+++.+
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5678999999999999999999766

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=96.21  E-value=0.0027  Score=48.43  Aligned_cols=23  Identities=9%  Similarity=0.199  Sum_probs=20.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ..++++|++|+|||+|++.++..
T Consensus        29 ~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           29 CKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            36999999999999999999864

>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=96.21  E-value=0.0029  Score=51.73  Aligned_cols=27  Identities=15%  Similarity=-0.012  Sum_probs=23.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ++-+.|+||+|||||||.+.++.....
T Consensus       169 geiv~l~G~sG~GKSTll~~l~g~~~~  195 (301)
T 1u0l_A          169 GKISTMAGLSGVGKSSLLNAINPGLKL  195 (301)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHSTTCCC
T ss_pred             CCeEEEECCCCCcHHHHHHHhcccccc
Confidence            567899999999999999999876543

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=96.19  E-value=0.0028  Score=47.00  Aligned_cols=22  Identities=23%  Similarity=0.327  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        20 ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6899999999999999999864

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=96.18  E-value=0.0054  Score=47.24  Aligned_cols=39  Identities=13%  Similarity=0.067  Sum_probs=28.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEAD   85 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~d   85 (162)
                      +.+.|+-||||||.++.+++.+   |.++....-...+...+
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~treP~~t~~~~   44 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVILKREPGGTETGE   44 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCSSHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEECCCCCcHHH
Confidence            5688999999999999999765   67765554444443333

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=96.18  E-value=0.0028  Score=48.24  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++++...
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            6899999999999999998854

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=96.18  E-value=0.002  Score=48.55  Aligned_cols=20  Identities=30%  Similarity=0.519  Sum_probs=18.5

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|||||+|++.++
T Consensus        25 ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           25 KVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            58999999999999999885

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=96.18  E-value=0.0036  Score=54.75  Aligned_cols=39  Identities=18%  Similarity=0.140  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHhcC-CCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          28 QDWLSHLRWILQKDN-MSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~-~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +.-++.|...+.... ....+.++|++|+|||+||.++++
T Consensus       130 ~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~  169 (591)
T 1z6t_A          130 KKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVR  169 (591)
T ss_dssp             HHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHh
Confidence            455666666654321 234689999999999999999874

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=96.17  E-value=0.0025  Score=50.56  Aligned_cols=31  Identities=16%  Similarity=0.005  Sum_probs=25.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC----CceEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ----REVEY   74 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg----~p~~~   74 (162)
                      |.-+.+.|++||||||+++.+++.++    .++..
T Consensus        21 ~~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~   55 (223)
T 3ld9_A           21 SMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVV   55 (223)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhccCceeeE
Confidence            45688889999999999999997654    46554

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=96.17  E-value=0.0015  Score=47.84  Aligned_cols=21  Identities=24%  Similarity=0.512  Sum_probs=9.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus        10 ki~v~G~~~~GKssl~~~l~~   30 (183)
T 2fu5_C           10 KLLLIGDSGVGKTCVLFRFSE   30 (183)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999998874

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=96.16  E-value=0.0022  Score=47.18  Aligned_cols=21  Identities=10%  Similarity=0.292  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus        23 ~i~v~G~~~~GKSsli~~l~~   43 (181)
T 2h17_A           23 KVIIVGLDNAGKTTILYQFSM   43 (181)
T ss_dssp             EEEEEEETTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            699999999999999999874

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=96.15  E-value=0.0027  Score=47.78  Aligned_cols=21  Identities=24%  Similarity=0.554  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++++..
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           27 KFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHh
Confidence            699999999999999998873

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=96.15  E-value=0.0028  Score=47.27  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=19.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      -.++++|++|+|||+|++.+..
T Consensus        21 ~ki~~~G~~~~GKssl~~~l~~   42 (201)
T 2q3h_A           21 VKCVLVGDGAVGKTSLVVSYTT   42 (201)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3699999999999999998873

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=96.15  E-value=0.0083  Score=51.22  Aligned_cols=18  Identities=17%  Similarity=0.097  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCchHHHHH
Q psy4122          44 SQDVFLIGKPGSLRRSLA   61 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La   61 (162)
                      |+++++.||+|+|||..+
T Consensus         2 g~~~lv~a~TGsGKT~~~   19 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRV   19 (431)
T ss_dssp             CCEEEEECCTTSCTTTTH
T ss_pred             CCEEEEEcCCCCCHHHHH
Confidence            679999999999999876

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=96.14  E-value=0.003  Score=47.69  Aligned_cols=22  Identities=9%  Similarity=0.246  Sum_probs=20.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           27 KLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            6999999999999999998853

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=96.13  E-value=0.0028  Score=49.25  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|+|+|++|+|||+|++.+...
T Consensus        31 ~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           31 RIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            6899999999999999998753

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=96.13  E-value=0.0031  Score=55.29  Aligned_cols=45  Identities=11%  Similarity=0.093  Sum_probs=32.2

Q ss_pred             HHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          33 HLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        33 ~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      .+.+++. .+..|.-++|.||+|||||+|+++++...   |.++.++..
T Consensus       269 ~ld~vL~g~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~~  317 (525)
T 1tf7_A          269 RLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY  317 (525)
T ss_dssp             HHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             HHHHHhCCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            3455544 34477789999999999999999999654   445544544

>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=96.13  E-value=0.0043  Score=53.92  Aligned_cols=34  Identities=18%  Similarity=0.162  Sum_probs=26.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      ..++++||+|+||||++..+|..+   |..+..+.+.
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D  134 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAAD  134 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecC
Confidence            357889999999999999998655   6666655553

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=96.12  E-value=0.0029  Score=46.79  Aligned_cols=21  Identities=14%  Similarity=0.118  Sum_probs=19.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA   65 (162)
                      ..|+++|++|||||+|++++.
T Consensus        18 ~ki~v~G~~~~GKSsl~~~l~   38 (199)
T 4bas_A           18 LQVVMCGLDNSGKTTIINQVK   38 (199)
T ss_dssp             EEEEEECCTTSCHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            369999999999999999876

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=96.11  E-value=0.003  Score=47.76  Aligned_cols=21  Identities=14%  Similarity=0.449  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|++|+|||+|++.+..
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~   47 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTD   47 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhc
Confidence            699999999999999998874

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=96.11  E-value=0.0031  Score=47.35  Aligned_cols=22  Identities=9%  Similarity=0.261  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           27 KLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            6999999999999999998853

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=96.10  E-value=0.0024  Score=48.20  Aligned_cols=20  Identities=10%  Similarity=0.170  Sum_probs=18.7

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|+|||+|++++.
T Consensus        27 ki~lvG~~~vGKSsLi~~l~   46 (198)
T 1f6b_A           27 KLVFLGLDNAGKTTLLHMLK   46 (198)
T ss_dssp             EEEEEEETTSSHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            69999999999999999886

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=96.09  E-value=0.0062  Score=56.55  Aligned_cols=38  Identities=16%  Similarity=0.237  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ++++-.+.+..++.    +...++.||||||||+++..++..
T Consensus       357 Ln~~Q~~Av~~~l~----~~~~lI~GppGTGKT~ti~~~i~~  394 (800)
T 2wjy_A          357 LNHSQVYAVKTVLQ----RPLSLIQGPPGTGKTVTSATIVYH  394 (800)
T ss_dssp             CCHHHHHHHHHHHT----SSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhcc----CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            56666666666553    446899999999999988776654

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=96.09  E-value=0.0029  Score=47.21  Aligned_cols=21  Identities=29%  Similarity=0.499  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~   48 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTD   48 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            599999999999999998863

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=96.08  E-value=0.0035  Score=47.28  Aligned_cols=21  Identities=10%  Similarity=0.289  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus        31 ki~vvG~~~vGKSsli~~l~~   51 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKT   51 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHhh
Confidence            599999999999999999874

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=96.08  E-value=0.0032  Score=51.53  Aligned_cols=20  Identities=30%  Similarity=0.436  Sum_probs=18.4

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      -|.++|.||+|||||.+++.
T Consensus        12 ~v~ivG~~nvGKSTLin~l~   31 (308)
T 3iev_A           12 YVAIVGKPNVGKSTLLNNLL   31 (308)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHh
Confidence            58999999999999999876

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=96.06  E-value=0.0025  Score=49.72  Aligned_cols=29  Identities=14%  Similarity=0.266  Sum_probs=23.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .|.-+.|+|+.|+||||+++.++.. +..+
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~-~g~v   47 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY-KNDI   47 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG-TTTE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc-cCCe
Confidence            3556899999999999999999987 4443

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=96.06  E-value=0.0032  Score=47.96  Aligned_cols=21  Identities=33%  Similarity=0.577  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|+|||+|++.+..
T Consensus        36 ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           36 KVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHc
Confidence            699999999999999999873

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=96.06  E-value=0.0044  Score=48.85  Aligned_cols=27  Identities=19%  Similarity=0.170  Sum_probs=24.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .+-|+|..||||||+++.+++ +|.|+.
T Consensus        11 ~iglTGgigsGKStv~~~l~~-~g~~vi   37 (210)
T 4i1u_A           11 AIGLTGGIGSGKTTVADLFAA-RGASLV   37 (210)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-TTCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcEE
Confidence            478999999999999999998 898854

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=96.06  E-value=0.0031  Score=47.22  Aligned_cols=20  Identities=5%  Similarity=0.253  Sum_probs=18.7

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|+|||+|++.+.
T Consensus        31 ki~v~G~~~vGKSsLi~~l~   50 (192)
T 2b6h_A           31 RILMVGLDAAGKTTILYKLK   50 (192)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            69999999999999999885

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=96.05  E-value=0.0036  Score=47.13  Aligned_cols=22  Identities=9%  Similarity=0.206  Sum_probs=19.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        11 ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           11 KCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999998853

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=96.02  E-value=0.0026  Score=47.07  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=20.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++++|++|+|||+|++.+....
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            69999999999999999887543

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.02  E-value=0.0038  Score=54.98  Aligned_cols=33  Identities=15%  Similarity=0.074  Sum_probs=26.9

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +.+..+..|+.++|+||+|+|||+|++.++...
T Consensus       143 D~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          143 DLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             HHHSCEETTCEEEEECCSSSCHHHHHHHHHHHH
T ss_pred             HHHhhhccCCEEEEECCCCCCccHHHHHHHhhh
Confidence            334556678899999999999999999887554

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=96.02  E-value=0.0014  Score=54.43  Aligned_cols=26  Identities=15%  Similarity=0.143  Sum_probs=21.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|+.+.|+||+|+|||||++.++...
T Consensus       172 ~G~~~~lvG~sG~GKSTLln~L~g~~  197 (307)
T 1t9h_A          172 QDKTTVFAGQSGVGKSSLLNAISPEL  197 (307)
T ss_dssp             TTSEEEEEESHHHHHHHHHHHHCC--
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcccc
Confidence            56789999999999999999987554

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=95.99  E-value=0.0038  Score=48.43  Aligned_cols=21  Identities=33%  Similarity=0.469  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+|+|++|+|||+|++++..
T Consensus        39 kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           39 RVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999998873

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=95.98  E-value=0.0041  Score=52.01  Aligned_cols=24  Identities=21%  Similarity=0.267  Sum_probs=21.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..+.|+|+||+|||||.+.++..+
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            368899999999999999999754

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=95.98  E-value=0.0037  Score=55.59  Aligned_cols=42  Identities=17%  Similarity=0.109  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHhc-CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          28 QDWLSHLRWILQKD-NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        28 ~~~~~~L~~i~~~~-~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +++.+.++.-.... ..+..++|+|++||||||+++.+++.++
T Consensus       355 ~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~  397 (546)
T 2gks_A          355 PEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQ  397 (546)
T ss_dssp             HHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhh
Confidence            55666666554211 2345689999999999999999998764

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=95.97  E-value=0.0038  Score=53.15  Aligned_cols=29  Identities=21%  Similarity=0.098  Sum_probs=24.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++....
T Consensus        51 i~~Gei~~IiGpnGaGKSTLlr~i~GL~~   79 (366)
T 3tui_C           51 VPAGQIYGVIGASGAGKSTLIRCVNLLER   79 (366)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEEcCCCchHHHHHHHHhcCCC
Confidence            34578899999999999999999997654

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=95.95  E-value=0.0045  Score=45.55  Aligned_cols=23  Identities=30%  Similarity=0.229  Sum_probs=20.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      -.+++||.|+|||++.+++...+
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999998766

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=95.95  E-value=0.03  Score=53.09  Aligned_cols=35  Identities=14%  Similarity=0.091  Sum_probs=25.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMS   63 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~   63 (162)
                      ++++.=.+.+..++.    |+++++.+|||+|||..+..
T Consensus        39 ~l~~~Q~~aI~~il~----g~~vlv~apTGsGKTlv~~~   73 (997)
T 4a4z_A           39 ELDTFQKEAVYHLEQ----GDSVFVAAHTSAGKTVVAEY   73 (997)
T ss_dssp             CCCHHHHHHHHHHHT----TCEEEEECCTTSCSHHHHHH
T ss_pred             CCCHHHHHHHHHHHc----CCCEEEEECCCCcHHHHHHH
Confidence            356655555655554    78999999999999976543

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=95.94  E-value=0.0032  Score=48.38  Aligned_cols=21  Identities=19%  Similarity=0.229  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|++|+|||+|++.+..
T Consensus        31 kI~vvG~~~vGKSsLin~l~~   51 (228)
T 2qu8_A           31 TIILSGAPNVGKSSFMNIVSR   51 (228)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            699999999999999998863

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.93  E-value=0.0075  Score=53.32  Aligned_cols=33  Identities=15%  Similarity=0.225  Sum_probs=27.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      .++++|+||+||||++..+|..+   |..+..+.+.
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~D  138 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICAD  138 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEecc
Confidence            58899999999999999999655   6776666663

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=95.92  E-value=0.0038  Score=49.00  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=19.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ..|+|+|++|+|||+|++.+..
T Consensus        23 ~~I~lvG~~g~GKStl~n~l~~   44 (260)
T 2xtp_A           23 LRIILVGKTGTGKSAAGNSILR   44 (260)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhC
Confidence            3699999999999999999874

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=95.92  E-value=0.0044  Score=47.38  Aligned_cols=22  Identities=23%  Similarity=0.410  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|+|||+|++.+...
T Consensus        15 ki~v~G~~~vGKSsli~~l~~~   36 (223)
T 3cpj_B           15 KIVLIGDSGVGKSNLLSRFTKN   36 (223)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            6899999999999999998753

>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=95.89  E-value=0.0039  Score=53.99  Aligned_cols=34  Identities=18%  Similarity=0.215  Sum_probs=26.6

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      ..++++|++|+||||++..+|..+   |..+..+.+.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D  136 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAAD  136 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecc
Confidence            368999999999999999999755   4565555543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.88  E-value=0.0042  Score=51.60  Aligned_cols=31  Identities=13%  Similarity=0.093  Sum_probs=24.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYIC   76 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~   76 (162)
                      -++++|++|+||||++..+|..+   |..+..+.
T Consensus       107 vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid  140 (320)
T 1zu4_A          107 IFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAA  140 (320)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            58899999999999999999655   45544443

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=95.88  E-value=0.0048  Score=47.13  Aligned_cols=23  Identities=9%  Similarity=0.094  Sum_probs=20.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      -.++++|++|||||+|++.+...
T Consensus        28 ~ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           28 CKLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            36999999999999999998753

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=95.88  E-value=0.0027  Score=46.87  Aligned_cols=21  Identities=14%  Similarity=0.219  Sum_probs=18.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA   65 (162)
                      -.++++|++|+|||+|++++.
T Consensus        23 ~~i~v~G~~~~GKssli~~l~   43 (189)
T 2x77_A           23 IRVLMLGLDNAGKTSILYRLH   43 (189)
T ss_dssp             EEEEEEEETTSSHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            379999999999999999874

>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=95.87  E-value=0.018  Score=51.84  Aligned_cols=23  Identities=9%  Similarity=-0.062  Sum_probs=19.3

Q ss_pred             HHhcCCCCcEEEEcCCCchHHHH
Q psy4122          38 LQKDNMSQDVFLIGKPGSLRRSL   60 (162)
Q Consensus        38 ~~~~~~g~~vlL~GppG~GKT~L   60 (162)
                      +..+..++++++.+|||+|||..
T Consensus       180 i~~l~~g~dvlv~a~TGSGKT~~  202 (618)
T 2whx_A          180 EDIFRKKRLTIMDLHPGAGKTKR  202 (618)
T ss_dssp             GGGGSTTCEEEECCCTTSSTTTT
T ss_pred             HHHHhcCCeEEEEcCCCCCHHHH
Confidence            44555689999999999999985

>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=95.86  E-value=0.033  Score=50.97  Aligned_cols=36  Identities=6%  Similarity=0.026  Sum_probs=25.6

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      ++|-=.+.+..++    .++++++.+|+|+|||..+-..+
T Consensus       249 l~~~Q~~~i~~~l----~~~~~ll~~~TGsGKTl~~~~~i  284 (797)
T 4a2q_A          249 ARSYQIELAQPAI----NGKNALICAPTGSGKTFVSILIC  284 (797)
T ss_dssp             CCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH----hCCCEEEEeCCCChHHHHHHHHH
Confidence            4444445555554    36899999999999998766555

>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A

Probab=95.86  E-value=0.0045  Score=49.47  Aligned_cols=21  Identities=29%  Similarity=0.230  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++|+|+||||||+|.+++..
T Consensus         7 kI~lvG~~nvGKTsL~n~l~g   27 (258)
T 3a1s_A            7 KVALAGCPNVGKTSLFNALTG   27 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            589999999999999999863

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=95.86  E-value=0.0089  Score=47.50  Aligned_cols=22  Identities=9%  Similarity=0.261  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|.++|.||+|||||++++...
T Consensus        28 ~i~vvG~~~~GKSSLln~l~g~   49 (299)
T 2aka_B           28 QIAVVGGQSAGKSSVLENFVGR   49 (299)
T ss_dssp             EEEEEEBTTSCHHHHHHHHHTS
T ss_pred             eEEEEeCCCCCHHHHHHHHHCC
Confidence            4899999999999999998743

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=95.86  E-value=0.0046  Score=46.24  Aligned_cols=22  Identities=18%  Similarity=0.270  Sum_probs=19.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      -.++++|++|+|||+|++.+..
T Consensus        21 ~ki~~vG~~~vGKTsLi~~l~~   42 (196)
T 3llu_A           21 PRILLMGLRRSGKSSIQKVVFH   42 (196)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3699999999999999986654

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=95.85  E-value=0.0049  Score=48.08  Aligned_cols=21  Identities=14%  Similarity=0.352  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -|+|+|++|||||+|+.++..
T Consensus        15 KivlvGd~~VGKTsLi~r~~~   35 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMY   35 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCcCHHHHHHHHHh
Confidence            389999999999999999874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	162
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.68
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.57
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.53
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.52
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.51
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.5
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.33
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.22
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.19
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.13
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.12
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.11
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.09
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.07
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.06
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.03
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.02
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	98.99
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.89
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.88
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.88
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.87
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.86
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.77
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.73
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.72
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.71
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.71
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.66
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.65
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	98.64
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.62
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.57
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.52
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	98.5
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.49
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	98.44
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	98.42
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	98.36
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	98.33
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	98.32
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	98.31
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	98.3
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	98.24
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	98.2
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	98.19
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	98.19
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	98.13
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.13
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	98.13
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	98.12
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	98.11
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	98.11
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	98.1
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	98.09
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	98.03
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	98.02
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	98.01
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.99
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.99
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.98
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.95
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.94
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	97.91
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.91
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.89
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.88
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.81
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.8
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.8
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.77
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	97.71
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.71
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	97.7
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	97.69
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	97.68
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.67
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	97.63
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.61
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.58
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.5
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.49
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	97.49
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	97.49
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	97.46
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.3
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	97.28
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	97.23
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	97.23
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	97.2
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	97.2
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	97.17
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.13
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	97.09
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	97.08
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	97.06
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	97.05
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.02
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.01
d1okkd2	207	GTPase domain of the signal recognition particle r	97.01
d2fh5b1	207	Signal recognition particle receptor beta-subunit	97.0
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	96.99
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.98
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.98
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	96.95
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	96.95
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.94
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	96.94
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.92
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.91
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	96.91
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.9
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.89
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.86
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.86
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	96.85
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	96.85
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	96.85
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.85
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	96.83
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	96.83
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	96.83
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.82
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	96.82
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	96.82
d1nrjb_	209	Signal recognition particle receptor beta-subunit	96.82
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	96.81
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.8
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.8
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	96.79
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	96.78
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	96.78
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	96.77
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	96.76
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	96.76
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.75
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	96.74
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	96.73
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	96.73
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	96.71
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.7
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	96.69
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.69
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	96.68
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.68
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	96.68
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	96.67
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	96.67
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.67
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.67
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.66
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.66
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.66
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	96.65
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	96.65
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	96.65
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.65
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.63
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.62
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	96.61
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	96.6
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	96.59
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	96.59
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.58
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.58
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	96.58
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.56
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	96.56
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.55
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.55
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.54
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.52
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	96.52
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	96.5
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	96.5
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	96.48
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	96.47
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.46
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	96.44
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	96.44
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	96.44
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	96.4
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.4
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	96.39
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.39
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	96.39
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	96.38
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	96.35
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	96.34
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	96.32
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	96.31
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.29
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.28
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	96.26
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.24
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	96.23
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	96.21
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	96.2
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.19
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	96.18
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	96.17
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	96.13
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.12
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	96.08
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	96.08
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.08
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	96.06
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	96.04
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	96.03
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	96.03
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	96.01
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	95.99
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	95.97
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	95.96
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.95
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	95.93
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	95.92
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	95.91
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.85
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.84
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	95.83
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	95.82
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.8
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	95.79
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	95.73
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	95.66
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.63
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	95.62
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	95.54
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	95.5
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	95.4
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.33
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	95.3
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	95.25
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	95.2
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.19
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.12
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	95.04
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	95.02
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	94.99
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	94.65
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	94.54
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	94.45
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	94.43
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	94.36
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	94.18
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	94.11
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.97
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	93.95
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	93.75
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	93.74
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	93.69
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	93.45
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	93.33
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	93.22
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	93.13
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	92.97
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	92.29
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	92.28
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	92.19
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	92.15
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	91.82
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	91.68
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	91.43
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	91.31
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	91.07
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	90.89
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	90.63
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	90.49
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	89.7
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	89.39
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	88.77
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	88.7
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	88.59
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	88.56
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	88.34
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	87.21
d1r5ba3	245	Eukaryotic peptide chain release factor ERF2, G do	86.92
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	86.58
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	86.54
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	86.5
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	86.12
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	85.6
d1vcha1	174	Putative phosphoribosyltransferase TTHA1613 {Therm	85.52
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	85.32
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	84.95
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	84.93
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	84.77
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	84.67
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	84.03
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	83.95
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	83.56
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.44
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	83.11
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	82.98
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	82.74
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	82.62
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	82.15
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	81.59
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	80.46
d1o5za2	296	Folylpolyglutamate synthetase {Thermotoga maritima	80.28

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

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: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=99.68  E-value=6.6e-18  Score=138.76  Aligned_cols=110  Identities=15%  Similarity=0.207  Sum_probs=86.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCC-------------------------------ceEEEEeccCCChhhhcceeE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQR-------------------------------EVEYICLSRDTTEADIKQRRE   91 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~-------------------------------p~~~v~~~~~~~~~dL~g~~~   91 (162)
                      .++|+||+||||||||++|+.+|.++..                               |...+..+..++.++++|...
T Consensus        27 ~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~d  106 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALD  106 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEEC
T ss_pred             CCCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCccccccchhhccccCcccccCceeeccCCCCcccccCcch
Confidence            3468999999999999999999988720                               112345566778888887443


Q ss_pred             e----ecCeEEEeccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEEEc-CCcEEecCcchH
Q psy4122          92 I----VNGTAIYYDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMHLE-DGRFLVSASTYD  154 (162)
Q Consensus        92 ~----~~G~~~~~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~l~-~g~~i~~~~~f~  154 (162)
                      .    .+|...++.|++.+|  +++++++|||+++++++++.|.+.||++++.+. +|..+.-+.+|.
T Consensus       107 ~~~~~~~g~~~~~~G~l~~A--~~gvl~iDEi~~~~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~  172 (333)
T d1g8pa_         107 IERAISKGEKAFEPGLLARA--NRGYLYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFV  172 (333)
T ss_dssp             HHHHHHHCGGGEECCHHHHH--TTEEEEETTGGGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEE
T ss_pred             hhhccccCcceeeccccccc--cccEeecccHHHHHHHHHHHHhhhhcCCeEEecccCceecCCCCEE
Confidence            2    357888899999887  899999999999999999999999999999996 354444444443

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {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: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.57  E-value=1.7e-15  Score=124.71  Aligned_cols=99  Identities=19%  Similarity=0.241  Sum_probs=76.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC---hhhhcceeEeecCeEEEec-cHHHHHhhc--CcEEEEeCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT---EADIKQRREIVNGTAIYYD-QSAVRAAIE--GRVLILEGI  119 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~---~~dL~g~~~~~~G~~~~~~-gpl~~A~~~--G~vlllDEI  119 (162)
                      ++||+||||||||.||+.+|+.++.|+.++.|+.-++   .+.|+|.+   .|...+.+ |.+...+++  .+++++|||
T Consensus        54 ~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~l~g~~---~gy~g~~~~~~l~~~~~~~~~~vvl~Dei  130 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAP---PGYVGFDQGGLLTDAVIKHPHAVLLLDEI  130 (315)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCC---SCSHHHHHTTHHHHHHHHCSSEEEEEETG
T ss_pred             EEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhhhcccC---CCccccccCChhhHHHHhCccchhhhccc
Confidence            5899999999999999999999999999999885433   45667632   22222222 234444443  369999999


Q ss_pred             CCCCccHHHHHHHhhcCCeEEEcCCcEE
Q psy4122         120 EKAERNVLPVLNNLLENREMHLEDGRFL  147 (162)
Q Consensus       120 d~a~~~v~~~L~~lle~r~l~l~~g~~i  147 (162)
                      ++++++|++.|++++|+|.++...|+.+
T Consensus       131 eKa~~~V~~~lLqild~G~ltd~~Gr~v  158 (315)
T d1r6bx3         131 EKAHPDVFNILLQVMDNGTLTDNNGRKA  158 (315)
T ss_dssp             GGSCHHHHHHHHHHHHHSEEEETTTEEE
T ss_pred             ccccchHhhhhHHhhccceecCCCCCcc
Confidence            9999999999999999999988777654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

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: Thermus thermophilus [TaxId: 274]

Probab=99.53  E-value=2.2e-14  Score=111.53  Aligned_cols=99  Identities=18%  Similarity=0.217  Sum_probs=75.2

Q ss_pred             CHHHHHHHHHHHHhcCC----CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          27 TQDWLSHLRWILQKDNM----SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~----g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      .+++.+.|+.++.....    -.++||+||||||||++|+.+|+.++.++..++.+.........              .
T Consensus        14 q~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~~~~--------------~   79 (239)
T d1ixsb2          14 QERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLA--------------A   79 (239)
T ss_dssp             CHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHHHHH--------------H
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccchhhH--------------H
Confidence            46788888877765432    24899999999999999999999999998777655332222221              1


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                      -+.+...++.++++||+++++++.++.|...+++..+
T Consensus        80 ~~~~~~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~  116 (239)
T d1ixsb2          80 ILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVM  116 (239)
T ss_dssp             HHHTTCCTTCEEEEETGGGCCHHHHHHHHHHHHHSEE
T ss_pred             HHHhhccCCCeeeeecccccchhHHHhhhhhhhhhhh
Confidence            2333456678999999999999999999999987654

>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=99.52  E-value=1.6e-15  Score=124.32  Aligned_cols=98  Identities=14%  Similarity=0.189  Sum_probs=64.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKA  122 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a  122 (162)
                      ..+++||+||||||||.||+++|+.++.++..+.+++-++.+.+.+.....-+......+-...+....+++++||||++
T Consensus        48 ~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki  127 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKI  127 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGG
T ss_pred             CCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhh
Confidence            45689999999999999999999999999999988765544444331100000000000111122223479999999999


Q ss_pred             Ccc------------HHHHHHHhhcCCeEE
Q psy4122         123 ERN------------VLPVLNNLLENREMH  140 (162)
Q Consensus       123 ~~~------------v~~~L~~lle~r~l~  140 (162)
                      ++.            +++.|+.++|.+...
T Consensus       128 ~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~  157 (309)
T d1ofha_         128 CKKGEYSGADVSREGVQRDLLPLVEGSTVS  157 (309)
T ss_dssp             SCCSSCCSSHHHHHHHHHHHHHHHHCCEEE
T ss_pred             hhhccCcccchhhhHHHHHhhHHhcCCEEe
Confidence            875            566677888876553

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.51  E-value=8e-15  Score=120.92  Aligned_cols=99  Identities=18%  Similarity=0.269  Sum_probs=70.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCC---hhhhcceeEeecCeEEEe-ccHHHHHhhcC--cEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTT---EADIKQRREIVNGTAIYY-DQSAVRAAIEG--RVLIL  116 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~---~~dL~g~~~~~~G~~~~~-~gpl~~A~~~G--~vlll  116 (162)
                      .++|+||||||||.+|+.+|+.+   +.++.++.++.-++   .+.|+|.+.   |...+. .|.+.+++++.  +|+++
T Consensus        55 ~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~~L~g~~~---gyvG~~~~~~l~~~~~~~p~~Vvl~  131 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPP---GYVGYEEGGQLTEAVRRRPYSVILF  131 (315)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC-----------------CHHHHHHHCSSEEEEE
T ss_pred             EEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhhhhhcCCCC---CCcCcccCChHHHHHHhCCCcEEEE
Confidence            36888999999999999999987   66777777764443   355666432   222222 25677887654  79999


Q ss_pred             eCCCCCCccHHHHHHHhhcCCeEEEcCCcEE
Q psy4122         117 EGIEKAERNVLPVLNNLLENREMHLEDGRFL  147 (162)
Q Consensus       117 DEId~a~~~v~~~L~~lle~r~l~l~~g~~i  147 (162)
                      |||+++++++++.|.+++|+|.++..+|+.+
T Consensus       132 DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v  162 (315)
T d1qvra3         132 DEIEKAHPDVFNILLQILDDGRLTDSHGRTV  162 (315)
T ss_dssp             SSGGGSCHHHHHHHHHHHTTTEECCSSSCCE
T ss_pred             ehHhhcCHHHHHHHHHHhccCceeCCCCcEe
Confidence            9999999999999999999999876656544

>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=99.50  E-value=4.1e-14  Score=109.77  Aligned_cols=98  Identities=18%  Similarity=0.266  Sum_probs=76.0

Q ss_pred             CHHHHHHHHHHHHhcC----CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          27 TQDWLSHLRWILQKDN----MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~----~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      .++..+.|+.++....    ...++||+||||||||++|+.+|+.++.++..++.+......++..              
T Consensus        14 qe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~~~~~~~--------------   79 (238)
T d1in4a2          14 QENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAA--------------   79 (238)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHH--------------
T ss_pred             hHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccccHHHHHH--------------
Confidence            4677888887765432    2247999999999999999999999999988777665545555431              


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeE
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREM  139 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l  139 (162)
                       ......++.++++||++++.+.+.+.|...++.+.+
T Consensus        80 -~~~~~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~  115 (238)
T d1in4a2          80 -ILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQI  115 (238)
T ss_dssp             -HHHHCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC
T ss_pred             -HHHhhccCCchHHHHHHHhhhHHHhhcccceeeeee
Confidence             223345678999999999999999999999997654

>d1um8a_ c.37.1.20 (A:) ClpX {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: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=99.33  E-value=1.5e-12  Score=109.14  Aligned_cols=91  Identities=14%  Similarity=0.179  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHH---------HhhcCcE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVR---------AAIEGRV  113 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~---------A~~~G~v  113 (162)
                      ...++|++||+|||||.||+++|+.++.|+.++.++.-++. ...|.   .-+      +.+.+         .....++
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~~~~~~~ir~D~s~~~e~-gyvg~---dv~------~~i~~l~~~~~~~v~~~~~~i  136 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEA-GYVGE---DVE------NILTRLLQASDWNVQKAQKGI  136 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGCC------------CT------HHHHHHHHHTTTCHHHHTTSE
T ss_pred             CCcceeeeCCCCccHHHHHHHHHhhcccceeehhhhhcccc-hhhHh---hhc------cchhhhhhhchhHHHHhhccc
Confidence            34589999999999999999999999999998888755442 22221   001      11111         1234689


Q ss_pred             EEEeCCCC--------------CCccHHHHHHHhhcCCeEEEcC
Q psy4122         114 LILEGIEK--------------AERNVLPVLNNLLENREMHLED  143 (162)
Q Consensus       114 lllDEId~--------------a~~~v~~~L~~lle~r~l~l~~  143 (162)
                      +++|||++              ++++|++.|++++|.+.+.+++
T Consensus       137 v~lDEieK~~~~s~~~~~~~d~a~~~V~~~lLqild~~~~~~~~  180 (364)
T d1um8a_         137 VFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIPP  180 (364)
T ss_dssp             EEEETGGGC--------------CHHHHHHHHHHHHCCEEC---
T ss_pred             chhhhhhhhccccccccccccccchHHHHhhhhhhcCceeccCC
Confidence            99999999              8889999999999998887754

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

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: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.22  E-value=9.7e-12  Score=98.63  Aligned_cols=83  Identities=22%  Similarity=0.199  Sum_probs=54.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCe-EEEeccHHHHHhhcC-cEEEEeCCCCC-
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGT-AIYYDQSAVRAAIEG-RVLILEGIEKA-  122 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~-~~~~~gpl~~A~~~G-~vlllDEId~a-  122 (162)
                      .+||+||||||||++|+++|..+|.|+..+++...     +.|.   .++. .......+..|.+.. .+|+|||||++ 
T Consensus        42 ~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~-----~~g~---~~~~~~~~i~~if~~A~~~~p~il~iDEid~l~  113 (246)
T d1d2na_          42 SVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK-----MIGF---SETAKCQAMKKIFDDAYKSQLSCVVVDDIERLL  113 (246)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGG-----CTTC---CHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHT
T ss_pred             EEEEECcCCCCHHHHHHHHhhcccccccccccccc-----cccc---cccchhhhhhhhhhhhhhcccceeehhhhhhHh
Confidence            59999999999999999999999999887776422     1121   0000 000111234455444 69999999763 


Q ss_pred             ---------CccHHHHHHHhhcC
Q psy4122         123 ---------ERNVLPVLNNLLEN  136 (162)
Q Consensus       123 ---------~~~v~~~L~~lle~  136 (162)
                               ...++..|..+++.
T Consensus       114 ~~~~~~~~~~~~~~~~ll~~l~~  136 (246)
T d1d2na_         114 DYVPIGPRFSNLVLQALLVLLKK  136 (246)
T ss_dssp             TCBTTTTBCCHHHHHHHHHHTTC
T ss_pred             hhcccccchhHHHHHHHHHHhcC
Confidence                     22356677777764

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {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: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.19  E-value=2.6e-11  Score=96.26  Aligned_cols=112  Identities=15%  Similarity=0.133  Sum_probs=77.6

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---CceEEEEeccCCC---hhhhccee-EeecCeEEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---REVEYICLSRDTT---EADIKQRR-EIVNGTAIY   99 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p~~~v~~~~~~~---~~dL~g~~-~~~~G~~~~   99 (162)
                      ++.+.+.++.+-.....+.||+|.|++|||||.+|+.++....   .++..+.|.....   .+.|.|.. ....+....
T Consensus         6 S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~lfg~~~~~~~~~~~~   85 (247)
T d1ny5a2           6 SPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSS   85 (247)
T ss_dssp             SHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCSC
T ss_pred             CHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHHhcCcccCCcCCcccc
Confidence            4566666666666666778999999999999999999987653   3455566643221   23344421 001122333


Q ss_pred             eccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCCeEE
Q psy4122         100 YDQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENREMH  140 (162)
Q Consensus       100 ~~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r~l~  140 (162)
                      ..|.+.+|  +||.|+||||+.++++.+..|..++++++..
T Consensus        86 ~~g~l~~a--~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~  124 (247)
T d1ny5a2          86 KEGFFELA--DGGTLFLDEIGELSLEAQAKLLRVIESGKFY  124 (247)
T ss_dssp             BCCHHHHT--TTSEEEEESGGGCCHHHHHHHHHHHHHSEEC
T ss_pred             cCCHHHcc--CCCEEEEeChHhCCHHHHHHHHHHHHhCCEE
Confidence            45555444  8899999999999999999999999987754

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {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: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.13  E-value=4.7e-11  Score=91.85  Aligned_cols=102  Identities=11%  Similarity=0.172  Sum_probs=67.6

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-----ceEEEEeccCCChhhhcceeEeecCeEEEe
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-----EVEYICLSRDTTEADIKQRREIVNGTAIYY  100 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-----p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~  100 (162)
                      -.....+.|+.+++..... ++||+||||||||++|+.+|+.++.     ++..+++.......++...  .       .
T Consensus        28 g~~~~~~~l~~~i~~~~~~-~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~~~~~~~~~~--~-------~   97 (231)
T d1iqpa2          28 GQEHIVKRLKHYVKTGSMP-HLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREK--V-------K   97 (231)
T ss_dssp             SCHHHHHHHHHHHHHTCCC-EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHH--H-------H
T ss_pred             CcHHHHHHHHHHHHcCCCC-eEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcccchhHHHHH--H-------H
Confidence            3588899999998877554 8999999999999999999987643     3333333211111111100  0       0


Q ss_pred             ccHH--HHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         101 DQSA--VRAAIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       101 ~gpl--~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      +...  ........++++||++.+..+.+..|..+++.+
T Consensus        98 ~~~~~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~  136 (231)
T d1iqpa2          98 EFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMF  136 (231)
T ss_dssp             HHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHT
T ss_pred             HHHhhhhccCCCceEEeehhhhhcchhHHHHHhhhcccC
Confidence            0000  001235679999999999999999999998843

>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=99.12  E-value=1.4e-10  Score=90.48  Aligned_cols=109  Identities=17%  Similarity=0.179  Sum_probs=65.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEecc-CCC--hhhhcc-----eeEeecCeEE
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSR-DTT--EADIKQ-----RREIVNGTAI   98 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~-~~~--~~dL~g-----~~~~~~G~~~   98 (162)
                      .++..+.|+..+......+.+||+||||+|||++|+.+++.++.+... .... ...  ...+..     ...+..++..
T Consensus        17 ~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~-~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~   95 (239)
T d1njfa_          17 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI-TATPCGVCDNCREIEQGRFVDLIEIDAASRT   95 (239)
T ss_dssp             CHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCS-CSSCCSCSHHHHHHHHTCCTTEEEEETTCSS
T ss_pred             hHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCcccc-ccCccccchHHHHHHcCCCCeEEEecchhcC
Confidence            588889999888876665569999999999999999999887654210 0000 000  000000     0001110000


Q ss_pred             Eec--cHHHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          99 YYD--QSAVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        99 ~~~--gpl~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      -.+  ..+.+-+    .+|  .++||||+|+++++.++.|+..+|+
T Consensus        96 ~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~  141 (239)
T d1njfa_          96 KVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE  141 (239)
T ss_dssp             SHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhc
Confidence            000  0011111    122  4899999999999999999999986

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {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 C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.11  E-value=5.8e-11  Score=91.21  Aligned_cols=102  Identities=14%  Similarity=0.168  Sum_probs=66.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc-----eEEEEeccCCChhhhcceeE-eecCeEEEe
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE-----VEYICLSRDTTEADIKQRRE-IVNGTAIYY  100 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p-----~~~v~~~~~~~~~dL~g~~~-~~~G~~~~~  100 (162)
                      .+..++.|+.++...... ++||+||||||||++|+.+|+.++..     +..++.+......++..... ...-..  .
T Consensus        20 ~~~~~~~L~~~~~~~~~~-~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~--~   96 (224)
T d1sxjb2          20 NKETIDRLQQIAKDGNMP-HMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKL--H   96 (224)
T ss_dssp             CTHHHHHHHHHHHSCCCC-CEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCC--C
T ss_pred             CHHHHHHHHHHHHcCCCC-eEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHHHHhhc--c
Confidence            467889999988876654 79999999999999999999887643     23333333322332221000 000000  0


Q ss_pred             ccHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         101 DQSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       101 ~gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                           .......++++||+|.++.+.+..|...++.
T Consensus        97 -----~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~  127 (224)
T d1sxjb2          97 -----LPPGKHKIVILDEADSMTAGAQQALRRTMEL  127 (224)
T ss_dssp             -----CCTTCCEEEEEESGGGSCHHHHHTTHHHHHH
T ss_pred             -----CCCcceEEEEEecccccchhHHHHHhhhccc
Confidence                 0012346999999999999999999988884

>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=99.09  E-value=2.8e-11  Score=93.75  Aligned_cols=112  Identities=11%  Similarity=0.009  Sum_probs=69.8

Q ss_pred             CCCCHHHHHHHHHHHHhcC----------------CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhc
Q psy4122          24 DALTQDWLSHLRWILQKDN----------------MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIK   87 (162)
Q Consensus        24 ~~~~~~~~~~L~~i~~~~~----------------~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~   87 (162)
                      ....+...+.|+.++..+.                ...+++|+||||||||++|+.+|+.++.++..++++...+...+.
T Consensus        16 lig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~~~~~~~~~~~~   95 (253)
T d1sxja2          16 VCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLN   95 (253)
T ss_dssp             CCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTTSCCCHHHHH
T ss_pred             hcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhhhccccccchhhHHHH
Confidence            3457888888888776421                124799999999999999999999999998877776554444432


Q ss_pred             ceeEeecCeEEE----ec-cHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122          88 QRREIVNGTAIY----YD-QSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus        88 g~~~~~~G~~~~----~~-gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                      ....-.-+...+    .. ......-....++++||++....+....+..+++
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~  148 (253)
T d1sxja2          96 AGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQ  148 (253)
T ss_dssp             HTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHH
T ss_pred             HHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccchhhhhHHHhh
Confidence            210000000000    00 0000011233589999999988887666666554

>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=99.07  E-value=2.4e-10  Score=87.35  Aligned_cols=102  Identities=11%  Similarity=0.169  Sum_probs=64.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCce---EEEEec--cCCChhhhcceeEeecCeEEEec
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREV---EYICLS--RDTTEADIKQRREIVNGTAIYYD  101 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~---~~v~~~--~~~~~~dL~g~~~~~~G~~~~~~  101 (162)
                      .+...+.|+.++...... ++||+||||||||++|+.+|+.++...   ..+.++  .............. ...  +. 
T Consensus        19 ~~~~~~~L~~~i~~~~~~-~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~-~~~--~~-   93 (227)
T d1sxjc2          19 QNEVITTVRKFVDEGKLP-HLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKD-FAS--TR-   93 (227)
T ss_dssp             CHHHHHHHHHHHHTTCCC-CEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHH-HHH--BC-
T ss_pred             cHHHHHHHHHHHHcCCCC-eEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhh-ccc--cc-
Confidence            478889999888876554 799999999999999999998764321   122222  11111111100000 000  00 


Q ss_pred             cHHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         102 QSAVRAAIEGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       102 gpl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                       .  .......++++||++.++++.+..|...++.
T Consensus        94 -~--~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~  125 (227)
T d1sxjc2          94 -Q--IFSKGFKLIILDEADAMTNAAQNALRRVIER  125 (227)
T ss_dssp             -C--SSSCSCEEEEETTGGGSCHHHHHHHHHHHHH
T ss_pred             -c--ccCCCeEEEEEeccccchhhHHHHHHHHhhh
Confidence             0  0001224999999999999999999999984

>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=99.06  E-value=2.1e-10  Score=91.50  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=31.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .+.+||+||||||||++|+.+|+.++.|+..+.++
T Consensus        45 ~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~   79 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGS   79 (256)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSC
T ss_pred             CCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhH
Confidence            35699999999999999999999999998877775

>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=99.03  E-value=7.3e-11  Score=90.31  Aligned_cols=108  Identities=12%  Similarity=0.194  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh------CCceEEEEeccCCChhhhccee-EeecCeEEEe
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT------QREVEYICLSRDTTEADIKQRR-EIVNGTAIYY  100 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l------g~p~~~v~~~~~~~~~dL~g~~-~~~~G~~~~~  100 (162)
                      +...+.|+.++...... +++|+||||||||++++.+|+.+      +.....++.+............ ..........
T Consensus        18 ~~~~~~l~~~i~~~~~~-~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (237)
T d1sxjd2          18 DHAVTVLKKTLKSANLP-HMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKP   96 (237)
T ss_dssp             CTTHHHHHHHTTCTTCC-CEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCC
T ss_pred             HHHHHHHHHHHHcCCCC-eEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhhhhhhhh
Confidence            56677888777655443 79999999999999999999875      3333333333332222221100 0000000001


Q ss_pred             ccHHHHHhh--cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         101 DQSAVRAAI--EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       101 ~gpl~~A~~--~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      .........  ...+++|||++.++.+..+.|..+++.
T Consensus        97 ~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~  134 (237)
T d1sxjd2          97 SKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMET  134 (237)
T ss_dssp             CTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHH
T ss_pred             hHHHHhhccccCceEEEEecccccCHHHHHHHhhcccc
Confidence            111122222  235899999999999999999998873

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

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: Thermus thermophilus [TaxId: 274]

Probab=99.02  E-value=1.9e-10  Score=91.23  Aligned_cols=34  Identities=24%  Similarity=0.230  Sum_probs=31.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      +.+||+||||||||++|+++|+.+|.++..++++
T Consensus        43 ~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~   76 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAGEARVPFITASGS   76 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             ceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhH
Confidence            4699999999999999999999999998887764

>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=98.99  E-value=1.9e-10  Score=94.93  Aligned_cols=70  Identities=14%  Similarity=0.190  Sum_probs=43.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC--CceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ--REVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg--~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      ++||+||||||||.||+.+|..++  .++..+....-  .+..+|.     +..  .=..+.+..++..+||+||||.+.
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~--~~~~~G~-----~e~--~~~~~f~~a~~~~ilf~DEid~~~  195 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEP--LSGYNTD-----FNV--FVDDIARAMLQHRVIVIDSLKNVI  195 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCS--STTCBCC-----HHH--HHHHHHHHHHHCSEEEEECCTTTC
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHh--hhcccch-----HHH--HHHHHHHHHhhccEEEeehhhhhc
Confidence            456689999999999999999987  45554444321  1122220     000  001233444668899999999976


Q ss_pred             c
Q psy4122         124 R  124 (162)
Q Consensus       124 ~  124 (162)
                      +
T Consensus       196 ~  196 (321)
T d1w44a_         196 G  196 (321)
T ss_dssp             -
T ss_pred             c
Confidence            5

>d1r7ra3 c.37.1.20 (A:471-735) 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=98.89  E-value=1.1e-09  Score=87.32  Aligned_cols=73  Identities=18%  Similarity=0.155  Sum_probs=47.5

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEE-eccHHHHHhhc-CcEEEEeCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIY-YDQSAVRAAIE-GRVLILEGIE  120 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~-~~gpl~~A~~~-G~vlllDEId  120 (162)
                      ..+.+||+||||||||++|+++|..+|.|+..+.++      ++.+.+   .|.... ....+..|... ..+++|||+|
T Consensus        40 ~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~------~l~~~~---~~~~~~~l~~~f~~A~~~~p~il~ideid  110 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGP------ELLTMW---FGESEANVREIFDKARQAAPCVLFFDELD  110 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHH------HHHTSC---TTTHHHHHHHHHHHHHHTCSEEEEESSGG
T ss_pred             CCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHH------Hhhhcc---ccchHHHHHHHHHHHHhcCCcceeHHhhh
Confidence            345799999999999999999999999998766553      333210   010000 00123334433 3689999999


Q ss_pred             CCCc
Q psy4122         121 KAER  124 (162)
Q Consensus       121 ~a~~  124 (162)
                      .+-.
T Consensus       111 ~l~~  114 (265)
T d1r7ra3         111 SIAK  114 (265)
T ss_dssp             GTCC
T ss_pred             hccc
Confidence            7654

>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=98.88  E-value=1.5e-09  Score=85.92  Aligned_cols=72  Identities=14%  Similarity=0.192  Sum_probs=46.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEE-eccHHHHHhhc-CcEEEEeCCCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIY-YDQSAVRAAIE-GRVLILEGIEK  121 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~-~~gpl~~A~~~-G~vlllDEId~  121 (162)
                      .+.+||+||||||||++++++|...+.++..+.++      ++...+   -|.... ...-+..|-.. ..+|+|||+|.
T Consensus        38 ~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~------~l~~~~---~g~~~~~l~~~f~~A~~~~p~il~iDeid~  108 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIARAVANETGAFFFLINGP------EIMSKL---AGESESNLRKAFEEAEKNAPAIIFIDELDA  108 (258)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHH------HHTTSC---TTHHHHHHHHHHHHHHHTCSEEEEESSGGG
T ss_pred             CceeEEecCCCCCchHHHHHHHHHhCCeEEEEEch------hhcccc---cccHHHHHHHHHHHHHhcCCeEEEehhhhh
Confidence            35699999999999999999999999998877664      222110   000000 00112333333 46899999998


Q ss_pred             CCc
Q psy4122         122 AER  124 (162)
Q Consensus       122 a~~  124 (162)
                      +-+
T Consensus       109 l~~  111 (258)
T d1e32a2         109 IAP  111 (258)
T ss_dssp             TCC
T ss_pred             hcc
Confidence            753

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.88  E-value=4.5e-10  Score=86.84  Aligned_cols=106  Identities=15%  Similarity=0.261  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhC---Cc-----eEEEEeccCCChhhhcceeEeecCeEEE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQ---RE-----VEYICLSRDTTEADIKQRREIVNGTAIY   99 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg---~p-----~~~v~~~~~~~~~dL~g~~~~~~G~~~~   99 (162)
                      +.-++.|..++.... ..|++|+||||+|||++++.+|...-   .|     ...++++    .+.|+.....   ...|
T Consensus        28 d~Ei~~l~~iL~r~~-k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld----~~~LiAg~~~---rG~~   99 (195)
T d1jbka_          28 DEEIRRTIQVLQRRT-KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALD----MGALVAGAKY---RGEF   99 (195)
T ss_dssp             HHHHHHHHHHHTSSS-SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEEC----HHHHHTTTCS---HHHH
T ss_pred             HHHHHHHHHHHhccC-CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEee----HHHHhccCCc---cHHH
Confidence            444556666665433 23899999999999999999997541   11     1233332    3344311000   0112


Q ss_pred             ecc--HHHHH-hh-cCc-EEEEeCCCCC--------CccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQ--SAVRA-AI-EGR-VLILEGIEKA--------ERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~g--pl~~A-~~-~G~-vlllDEId~a--------~~~v~~~L~~lle~r~l~l  141 (162)
                      +..  .+.+. .. +|. +|+|||++.+        ..++.+.|.+.|++|++.+
T Consensus       100 E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~  154 (195)
T d1jbka_         100 EERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHC  154 (195)
T ss_dssp             HHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHTTSCCE
T ss_pred             HHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhCCCceE
Confidence            221  12322 23 344 7899999775        2357799999999998865

>d1a5ta2 c.37.1.20 (A:1-207) 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=98.87  E-value=6.4e-09  Score=79.68  Aligned_cols=108  Identities=9%  Similarity=-0.012  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE--EEEeccCCChhhhc-c----eeEe---ecCeEE
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE--YICLSRDTTEADIK-Q----RREI---VNGTAI   98 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~--~v~~~~~~~~~dL~-g----~~~~---~~G~~~   98 (162)
                      ...+.|...+......+.+||+||||+|||++|+.+|+.+...-.  .-.+....+...+. +    ...+   .++...
T Consensus         9 ~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i   88 (207)
T d1a5ta2           9 PDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTL   88 (207)
T ss_dssp             HHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSB
T ss_pred             HHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhccccc
Confidence            456777777776666656999999999999999999987632110  00000000000000 0    0001   011110


Q ss_pred             Eecc--HHHHHhh------cCcEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122          99 YYDQ--SAVRAAI------EGRVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus        99 ~~~g--pl~~A~~------~G~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      -.+.  .+.+.+.      ...++++||+|+++.+.+++|+..||+
T Consensus        89 ~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEe  134 (207)
T d1a5ta2          89 GVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEE  134 (207)
T ss_dssp             CHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTS
T ss_pred             ccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHh
Confidence            0110  0122111      125899999999999999999999996

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {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 C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.86  E-value=2.2e-09  Score=82.55  Aligned_cols=42  Identities=17%  Similarity=0.290  Sum_probs=32.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .....+.|+.++.......+++|+||||||||++|+++|+.+
T Consensus        16 ~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2          16 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             CHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            456666666665544344579999999999999999999876

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {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: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.77  E-value=1.7e-09  Score=87.03  Aligned_cols=106  Identities=10%  Similarity=0.181  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC---c-----eEEEEeccCCChhhhcceeEeecCeEEE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR---E-----VEYICLSRDTTEADIKQRREIVNGTAIY   99 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~---p-----~~~v~~~~~~~~~dL~g~~~~~~G~~~~   99 (162)
                      ..-+++|..++.... ..|++|+||||||||++++.+|...-.   |     ...+.++    .+.|+...   .....|
T Consensus        24 d~Ei~~l~~iL~r~~-k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~----~~~liag~---~~~g~~   95 (268)
T d1r6bx2          24 EKELERAIQVLCRRR-KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLD----IGSLLAGT---KYRGDF   95 (268)
T ss_dssp             HHHHHHHHHHHTSSS-SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECC----CC---CCC---CCSSCH
T ss_pred             HHHHHHHHHHHhcCc-cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEee----echHhccC---ccchhH
Confidence            334555555554332 348999999999999999999975411   1     1223332    22333100   011123


Q ss_pred             ecc--HHHH-HhhcCc-EEEEeCCCCC----C-----ccHHHHHHHhhcCCeEEE
Q psy4122         100 YDQ--SAVR-AAIEGR-VLILEGIEKA----E-----RNVLPVLNNLLENREMHL  141 (162)
Q Consensus       100 ~~g--pl~~-A~~~G~-vlllDEId~a----~-----~~v~~~L~~lle~r~l~l  141 (162)
                      +.-  .+.. +..+|. ++++||++.+    .     .++.+.|.+.|.+|++.+
T Consensus        96 e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~v  150 (268)
T d1r6bx2          96 EKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRV  150 (268)
T ss_dssp             HHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEE
T ss_pred             HHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeE
Confidence            321  1222 224454 6779999775    1     257889999999998866

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

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: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=98.73  E-value=3.8e-10  Score=94.22  Aligned_cols=50  Identities=20%  Similarity=0.188  Sum_probs=39.0

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccC
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRD   80 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~   80 (162)
                      .+.++.++...-.+..++|+||||||||++|+.+|..+|.++..++++..
T Consensus       141 ~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~  190 (362)
T d1svma_         141 YDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLD  190 (362)
T ss_dssp             HHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTT
T ss_pred             HHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcch
Confidence            34556666655555679999999999999999999999999776665533

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.72  E-value=6.8e-09  Score=79.99  Aligned_cols=48  Identities=29%  Similarity=0.270  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHhcCCC---CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          30 WLSHLRWILQKDNMS---QDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g---~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      ..+.++++......+   +.+||+||||||||++|+.+|..++.++..++.
T Consensus        15 ~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~   65 (273)
T d1gvnb_          15 LNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   65 (273)
T ss_dssp             HHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             HHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEec
Confidence            344555555544332   249999999999999999999999998777655

>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=98.71  E-value=4.2e-09  Score=74.30  Aligned_cols=30  Identities=17%  Similarity=0.349  Sum_probs=27.6

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++++|+|||||||||+|+.+|+.+|.|+.
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L~~~~i   31 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFY   31 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCeE
Confidence            468999999999999999999999999864

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

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: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.71  E-value=6.8e-09  Score=79.32  Aligned_cols=107  Identities=16%  Similarity=0.033  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHhcC-----CCCcEEEEcCCCchHHHHHHHHHHHhCC----ceEEEEeccCCChhhhcceeEeec----C
Q psy4122          29 DWLSHLRWILQKDN-----MSQDVFLIGKPGSLRRSLAMSYLELTQR----EVEYICLSRDTTEADIKQRREIVN----G   95 (162)
Q Consensus        29 ~~~~~L~~i~~~~~-----~g~~vlL~GppG~GKT~La~~lA~~lg~----p~~~v~~~~~~~~~dL~g~~~~~~----G   95 (162)
                      .-++.+..++.++.     ...+++|+||||||||++++.+++.++.    .+..+++........+........    +
T Consensus        23 ~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (276)
T d1fnna2          23 QQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFP  102 (276)
T ss_dssp             HHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhhhhhhhhhHHhhhhhhh
Confidence            33555555555432     2248999999999999999999998753    333445544545444432111000    0


Q ss_pred             eEEEec----cHHHHHh---hcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122          96 TAIYYD----QSAVRAA---IEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus        96 ~~~~~~----gpl~~A~---~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                      ......    ..+.+..   ......++|+++.........+..+++
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~  149 (276)
T d1fnna2         103 RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQ  149 (276)
T ss_dssp             SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTT
T ss_pred             hhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHh
Confidence            000000    1122222   224577899999999988887777665

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.66  E-value=1.4e-08  Score=85.35  Aligned_cols=107  Identities=13%  Similarity=0.255  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh--C-Cc-----eEEEEeccCCChhhhcceeEeecCeEEE
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT--Q-RE-----VEYICLSRDTTEADIKQRREIVNGTAIY   99 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l--g-~p-----~~~v~~~~~~~~~dL~g~~~~~~G~~~~   99 (162)
                      ..-++++..++.... ..|++|+||||||||++++.+|...  | .|     ...+.++    .+.|+.....   ...|
T Consensus        28 ~~ei~~~~~~L~r~~-k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld----~~~l~ag~~~---~g~~   99 (387)
T d1qvra2          28 DEEIRRVIQILLRRT-KNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQ----MGSLLAGAKY---RGEF   99 (387)
T ss_dssp             HHHHHHHHHHHHCSS-CCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEEC----C--------------CH
T ss_pred             HHHHHHHHHHHhcCC-CCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEee----HhhhhcccCc---chhH
Confidence            344555555555332 2379999999999999999999653  2 11     1233332    2223311001   1123


Q ss_pred             ecc--HHHHHh-h-cCc-EEEEeCCCCC--------CccHHHHHHHhhcCCeEEEc
Q psy4122         100 YDQ--SAVRAA-I-EGR-VLILEGIEKA--------ERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       100 ~~g--pl~~A~-~-~G~-vlllDEId~a--------~~~v~~~L~~lle~r~l~l~  142 (162)
                      +..  .+...+ . +|. +|+|||++.+        ..++.+.|.+.|.+|++.+-
T Consensus       100 e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I  155 (387)
T d1qvra2         100 EERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLI  155 (387)
T ss_dssp             HHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTTCCCEE
T ss_pred             HHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCccee
Confidence            322  122222 2 343 6899999875        34778999999999988653

>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=98.65  E-value=4.4e-08  Score=75.48  Aligned_cols=107  Identities=13%  Similarity=0.116  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHHHhcCCC-CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcceeEeecCeEEEecc
Q psy4122          27 TQDWLSHLRWILQKDNMS-QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQRREIVNGTAIYYDQ  102 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g-~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~g  102 (162)
                      +....+.++.+++..... .+++|+||+|||||||+.++|..+   +..+.+++...-  ...+..  .+..+.    ..
T Consensus        18 N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~--~~~~~~--~~~~~~----~~   89 (213)
T d1l8qa2          18 NRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF--AQAMVE--HLKKGT----IN   89 (213)
T ss_dssp             THHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH--HHHHHH--HHHHTC----HH
T ss_pred             HHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHH--HHHHHH--HHHccc----hh
Confidence            455666677776643322 369999999999999999999765   344444444311  111110  011111    11


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCc--cH----HHHHHHhhcCC-eEEE
Q psy4122         103 SAVRAAIEGRVLILEGIEKAER--NV----LPVLNNLLENR-EMHL  141 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~--~v----~~~L~~lle~r-~l~l  141 (162)
                      .+...++...+|+||+|+....  +.    ...++.+.+.+ .+.+
T Consensus        90 ~~~~~~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iii  135 (213)
T d1l8qa2          90 EFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIIL  135 (213)
T ss_dssp             HHHHHHHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEE
T ss_pred             hHHHHHhhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEE
Confidence            3445567789999999998753  33    44555555544 4444

>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=98.64  E-value=4e-08  Score=75.07  Aligned_cols=90  Identities=18%  Similarity=0.203  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC-----c-eEEEEecc-CCChhhhcceeEeecCeEEEeccH
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR-----E-VEYICLSR-DTTEADIKQRREIVNGTAIYYDQS  103 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~-----p-~~~v~~~~-~~~~~dL~g~~~~~~G~~~~~~gp  103 (162)
                      ++.|+.+++.. .+.+++|+||||+|||++|..+|.....     | +..+...+ ....+++..               
T Consensus         3 ~~~l~~~i~~~-~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~---------------   66 (198)
T d2gnoa2           3 LETLKRIIEKS-EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRT---------------   66 (198)
T ss_dssp             HHHHHHHHHTC-SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHH---------------
T ss_pred             HHHHHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHH---------------
Confidence            56788888865 3569999999999999999999986532     2 22222111 112222221               


Q ss_pred             HHHHh----hcC--cEEEEeCCCCCCccHHHHHHHhhcC
Q psy4122         104 AVRAA----IEG--RVLILEGIEKAERNVLPVLNNLLEN  136 (162)
Q Consensus       104 l~~A~----~~G--~vlllDEId~a~~~v~~~L~~lle~  136 (162)
                      +.+-+    -+|  .|++|||+|+++.+.+++|+..||+
T Consensus        67 i~~~~~~~~~~~~~KviIId~ad~l~~~aqNaLLK~LEE  105 (198)
T d2gnoa2          67 IKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEE  105 (198)
T ss_dssp             HHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHS
T ss_pred             HHHHHhhCcccCCCEEEEEeCccccchhhhhHHHHHHhC
Confidence            11111    112  5999999999999999999999994

>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=98.62  E-value=2.5e-08  Score=72.45  Aligned_cols=33  Identities=15%  Similarity=0.262  Sum_probs=27.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .++|+||||||||||++.++..++.+.-.+.++
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~~~g~~~~~   34 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGKRAIGFWTE   34 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGGEEEEEEE
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCCCcceEEEC
Confidence            489999999999999999999998776555444

>d1g41a_ 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=98.57  E-value=2.2e-08  Score=85.36  Aligned_cols=40  Identities=15%  Similarity=0.245  Sum_probs=35.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTT   82 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~   82 (162)
                      ..+|+||+||||||||.||+.+|+.++.|+..+.++.-|.
T Consensus        48 ~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fTe   87 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE   87 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC-
T ss_pred             ccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceeee
Confidence            3569999999999999999999999999999998875554

>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=98.52  E-value=2.4e-08  Score=71.67  Aligned_cols=31  Identities=13%  Similarity=0.168  Sum_probs=27.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      ..+.|+++|||||||||||+.+|+.+|.++.
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~~~~~~i   36 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAVFNTTSA   36 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHHTTCEEE
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHhCCCeE
Confidence            3468999999999999999999999998754

>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=98.50  E-value=3.8e-08  Score=72.15  Aligned_cols=30  Identities=13%  Similarity=0.248  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++++|+|+|||||||+++.+|+.+|.|+.
T Consensus         2 ~~~Iil~G~~GsGKSTia~~LA~~Lg~~~i   31 (170)
T d1e6ca_           2 TEPIFMVGARGCGMTTVGRELARALGYEFV   31 (170)
T ss_dssp             CCCEEEESCTTSSHHHHHHHHHHHHTCEEE
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            478999999999999999999999999955

>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=98.49  E-value=3.7e-08  Score=70.61  Aligned_cols=28  Identities=18%  Similarity=0.312  Sum_probs=26.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|+|||||||||+|+.+|+.+|.++.
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i   33 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYI   33 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEE
Confidence            6899999999999999999999999864

>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=98.44  E-value=6.1e-08  Score=70.84  Aligned_cols=29  Identities=21%  Similarity=0.195  Sum_probs=27.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      |+++|+|+|||||||+++.+|+.+|.|+.
T Consensus         1 k~I~liG~~GsGKsTi~k~La~~l~~~~~   29 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARALAKDLDLVFL   29 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHTCEEE
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            57999999999999999999999999965

>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=98.42  E-value=5.4e-08  Score=70.06  Aligned_cols=33  Identities=21%  Similarity=0.232  Sum_probs=28.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      .|+-++|.|||||||||+|+.+|+.+|.++..+
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~lg~~~~~~   35 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLPGVPKVHF   35 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEe
Confidence            466789999999999999999999999886533

>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=98.36  E-value=1.1e-07  Score=68.10  Aligned_cols=24  Identities=33%  Similarity=0.505  Sum_probs=22.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ++|+|+||||||||+|++++++.+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            689999999999999999999776

>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=98.33  E-value=1.7e-07  Score=68.24  Aligned_cols=28  Identities=18%  Similarity=0.268  Sum_probs=26.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|+|+|||||||+++.+|+.+|+|+.
T Consensus         3 ~IvliG~~G~GKSTig~~La~~l~~~fi   30 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRRLAKALGVGLL   30 (165)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHTCCEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCeE
Confidence            5888999999999999999999999965

>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=98.32  E-value=1.3e-07  Score=67.21  Aligned_cols=28  Identities=7%  Similarity=0.075  Sum_probs=25.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +-++|.|||||||||+|+.+|+.++.+.
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~~~~   30 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLDNSA   30 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCE
Confidence            4589999999999999999999998753

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {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: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.31  E-value=2.3e-07  Score=68.84  Aligned_cols=62  Identities=13%  Similarity=0.097  Sum_probs=39.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcCcEEEEeCCCCCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEGRVLILEGIEKAE  123 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G~vlllDEId~a~  123 (162)
                      -++|+|+|||||||+|+.++...+..  +++.....+...+.              ..+..++..|..+|+|..+...
T Consensus        16 liil~G~pGsGKST~a~~l~~~~~~~--~i~~D~~~~~~~~~--------------~~~~~~l~~g~~vIiD~t~~~~   77 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFIQEHLVSAGYV--HVNRDTLGSWQRCV--------------SSCQAALRQGKRVVIDNTNPDV   77 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHTGGGTCE--EEEHHHHCSHHHHH--------------HHHHHHHHTTCCEEEESCCCSH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCE--EEchHHHHHHHHHH--------------HHHHHHHHCCCCceeeCcCCCH
Confidence            58899999999999999998887754  33332111111111              1234456677777777666433

>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=98.30  E-value=2.8e-07  Score=65.87  Aligned_cols=32  Identities=6%  Similarity=0.051  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYI   75 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v   75 (162)
                      .+-|+|.|+||+||||+|+.+|+.++.+...+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~   34 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAF   34 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEe
Confidence            45788999999999999999999999876544

>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=98.24  E-value=1.8e-07  Score=66.88  Aligned_cols=28  Identities=18%  Similarity=0.178  Sum_probs=24.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .|.-|+|+|+|||||||+|+.+|+.++.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4567899999999999999999998854

>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=98.20  E-value=4.8e-07  Score=64.86  Aligned_cols=27  Identities=19%  Similarity=0.327  Sum_probs=24.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +.+++|.|||||||||+++.+|+.++.
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            346999999999999999999999875

>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=98.19  E-value=4.7e-07  Score=65.91  Aligned_cols=28  Identities=18%  Similarity=0.210  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|.|||||||||+|+.+|+.+|.+..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~~~~~i   29 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAYGIPHI   29 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcee
Confidence            4899999999999999999999998743

>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=98.19  E-value=5.1e-07  Score=64.69  Aligned_cols=29  Identities=17%  Similarity=0.173  Sum_probs=25.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ++-++|.|||||||||+++.+|+.+|.+.
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~   34 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAF   34 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            34578899999999999999999998764

>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=98.13  E-value=2.3e-07  Score=67.81  Aligned_cols=29  Identities=21%  Similarity=0.252  Sum_probs=24.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      |.-|+|+|+|||||||+|+.+|+.++.+.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~~~   47 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVCHG   47 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            34678999999999999999999987654

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

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: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.13  E-value=1.7e-06  Score=65.42  Aligned_cols=36  Identities=11%  Similarity=0.060  Sum_probs=32.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      .+++++++||+|||||+|+++++...+.+..++.+.
T Consensus        28 ~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~   63 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLR   63 (283)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGG
T ss_pred             cCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEec
Confidence            356899999999999999999999999998888775

>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=98.13  E-value=8e-07  Score=65.63  Aligned_cols=29  Identities=17%  Similarity=0.112  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      |-.++|.|||||||||+|+.+|+.+|.+.
T Consensus         3 ~~riil~G~pGSGKsT~a~~La~~~g~~~   31 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLAKNFCVCH   31 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEE
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            45788999999999999999999999763

>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=98.12  E-value=9.3e-07  Score=64.95  Aligned_cols=28  Identities=21%  Similarity=0.268  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .++|.|||||||||+|+.+|+.+|.+..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g~~~i   29 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYGTPHI   29 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcee
Confidence            4889999999999999999999998743

>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=98.11  E-value=7.4e-07  Score=65.87  Aligned_cols=27  Identities=19%  Similarity=0.103  Sum_probs=25.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.|||||||||+|+.+|+.+|.+.
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~~~~~~   31 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTKYQLAH   31 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcE
Confidence            589999999999999999999999874

>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=98.11  E-value=6.6e-07  Score=66.52  Aligned_cols=29  Identities=21%  Similarity=0.306  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ++-++|.|||||||||+|+.+|+.+|.+.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~   36 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTH   36 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCee
Confidence            56789999999999999999999999763

>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=98.10  E-value=8.4e-07  Score=65.60  Aligned_cols=27  Identities=22%  Similarity=0.257  Sum_probs=24.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      -++|+|||||||||+|+.+|+.+|.+.
T Consensus         8 iI~i~G~pGSGKsT~a~~La~~~g~~~   34 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANIVRDFGWVH   34 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCce
Confidence            378899999999999999999999763

>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=98.09  E-value=1e-06  Score=64.54  Aligned_cols=28  Identities=25%  Similarity=0.304  Sum_probs=25.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +++|.|||||||||+|+.+|+.+|.+..
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g~~~i   29 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLGIPQI   29 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            5899999999999999999999998743

>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=98.03  E-value=1.4e-06  Score=64.58  Aligned_cols=27  Identities=15%  Similarity=0.231  Sum_probs=24.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      -++|.|||||||||+|+.+|+.+|.+.
T Consensus        10 iI~i~GppGSGKsT~a~~La~~~g~~~   36 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCEKLVKDYSFVH   36 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            478889999999999999999999863

>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=98.02  E-value=1.8e-06  Score=63.02  Aligned_cols=27  Identities=19%  Similarity=0.178  Sum_probs=24.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.|||||||||+++.+|+.+|.+.
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~~~~   28 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYGIPQ   28 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCce
Confidence            478999999999999999999999774

>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=98.01  E-value=1.7e-06  Score=63.64  Aligned_cols=27  Identities=26%  Similarity=0.310  Sum_probs=24.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.|||||||||+++.+|+.+|.+.
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~g~~~   30 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERFHAAH   30 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCce
Confidence            588999999999999999999999763

>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=97.99  E-value=1.8e-06  Score=64.60  Aligned_cols=27  Identities=15%  Similarity=0.240  Sum_probs=25.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .++|.|||||||||+++.+|+.+|.+.
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~g~~~   34 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHFELKH   34 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHBCCEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHCCeE
Confidence            689999999999999999999999764

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

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: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.99  E-value=1.8e-06  Score=65.69  Aligned_cols=22  Identities=23%  Similarity=0.132  Sum_probs=19.8

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ++|+||||||||++++.+++.+
T Consensus        49 l~l~GppGtGKT~l~~~l~~~l   70 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKFTVKRV   70 (287)
T ss_dssp             EECTTCCSSSHHHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHHHH
Confidence            5678999999999999999876

>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=97.98  E-value=2.1e-06  Score=63.27  Aligned_cols=27  Identities=22%  Similarity=0.316  Sum_probs=24.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      -|+|.||||+||||+|+.+|+.+|.+.
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~g~~~   29 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKYGYTH   29 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCce
Confidence            378999999999999999999999763

>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=97.95  E-value=5.3e-06  Score=58.06  Aligned_cols=90  Identities=10%  Similarity=0.025  Sum_probs=50.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhh-------hccee-E-eecCe-------EEEec-cHHH--
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEAD-------IKQRR-E-IVNGT-------AIYYD-QSAV--  105 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~d-------L~g~~-~-~~~G~-------~~~~~-gpl~--  105 (162)
                      +..+|.+|+|+|||.++..++...|..+..+.-... -..+       ..+.. . ...|.       ..+.- +-..  
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVA-ATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLAD   87 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESCHH-HHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEHHHHHHT
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcChHH-HHHHHHHHHHHHhhccccccccccccccccceEEEeeeeeccc
Confidence            468999999999999998777777766543332211 1111       11100 1 11111       12211 1111  


Q ss_pred             --HHhhcCcEEEEeCCCCCCccHHHHHHHhhc
Q psy4122         106 --RAAIEGRVLILEGIEKAERNVLPVLNNLLE  135 (162)
Q Consensus       106 --~A~~~G~vlllDEId~a~~~v~~~L~~lle  135 (162)
                        ..+.+-+++|+||++.++.+....+..+++
T Consensus        88 ~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~l~  119 (136)
T d1a1va1          88 GGCSGGAYDIIICDECHSTDATSILGIGTVLD  119 (136)
T ss_dssp             TGGGGCCCSEEEEETTTCCSHHHHHHHHHHHH
T ss_pred             cchhhhcCCEEEEecccccCHHHHHHHHHHHH
Confidence              112334799999999999887666655554

>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=97.94  E-value=2e-06  Score=60.52  Aligned_cols=24  Identities=25%  Similarity=0.443  Sum_probs=20.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +-++|.|+||+||||+|+.+++..
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            457889999999999999987654

>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=97.91  E-value=1.9e-05  Score=64.17  Aligned_cols=102  Identities=19%  Similarity=0.217  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcc---eeEee-cCeEEEeccH
Q psy4122          28 QDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQ---RREIV-NGTAIYYDQS  103 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g---~~~~~-~G~~~~~~gp  103 (162)
                      +...+.|+.++..   ++++++.|++|+||||+.++++.........+.+ +|+..-.+-.   ..... ++...+.+ .
T Consensus       153 ~~~~~~l~~~v~~---~~nili~G~tgSGKTT~l~al~~~i~~~~rivti-Ed~~El~l~~~~~~~~~~~~~~~~~~~-l  227 (323)
T d1g6oa_         153 EQAISAIKDGIAI---GKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISI-EDTEEIVFKHHKNYTQLFFGGNITSAD-C  227 (323)
T ss_dssp             HHHHHHHHHHHHH---TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEE-ESSCCCCCSSCSSEEEEECBTTBCHHH-H
T ss_pred             HHHHHHHHHHHHh---CCCEEEEeeccccchHHHHHHhhhcccccceeec-cchhhhhcccccccceeccccchhHHH-H
Confidence            4555666666553   6799999999999999999999888765555555 3322212211   11111 22222221 2


Q ss_pred             HHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         104 AVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       104 l~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      +-.|+|. ...+++.|+.  .+++.+.|+. +..|
T Consensus       228 l~~~lR~~pd~iivgEiR--~~ea~~~l~a-~~tG  259 (323)
T d1g6oa_         228 LKSCLRMRPDRIILGELR--SSEAYDFYNV-LCSG  259 (323)
T ss_dssp             HHHHTTSCCSEEEESCCC--STHHHHHHHH-HHTT
T ss_pred             HHHHhccCCCcccCCccC--chhHHHHHHH-HHhc
Confidence            3345554 4799999997  4577776654 4544

>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=97.91  E-value=2.5e-06  Score=60.98  Aligned_cols=26  Identities=15%  Similarity=0.222  Sum_probs=23.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +-|++.|+|||||||+++.+++.++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~   27 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRK   27 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            56899999999999999999988754

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

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 protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=97.89  E-value=4.4e-06  Score=64.42  Aligned_cols=93  Identities=14%  Similarity=0.330  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHh
Q psy4122          29 DWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAA  108 (162)
Q Consensus        29 ~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~  108 (162)
                      .-+..|+.+++..-...-++|+|||+||||.++..+++.++-.+  ++...+  -+.             |.    +..+
T Consensus        38 ~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~v--is~~N~--~s~-------------F~----Lq~l   96 (205)
T d1tuea_          38 TFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAV--ISFVNS--TSH-------------FW----LEPL   96 (205)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEE--CCCCCS--SSC-------------GG----GGGG
T ss_pred             HHHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhCCEE--EeccCC--CCC-------------cc----cccc
Confidence            45566777776554444589999999999999999999986432  121110  001             11    1123


Q ss_pred             hcCcEEEEeCCCCCCccHHHH-HHHhhcCCeEEEc
Q psy4122         109 IEGRVLILEGIEKAERNVLPV-LNNLLENREMHLE  142 (162)
Q Consensus       109 ~~G~vlllDEId~a~~~v~~~-L~~lle~r~l~l~  142 (162)
                      ....++++||+.....+..+. |..+++...+.+.
T Consensus        97 ~~~kv~l~dD~t~~~~~~~d~~lK~ll~G~~vsvd  131 (205)
T d1tuea_          97 TDTKVAMLDDATTTCWTYFDTYMRNALDGNPISID  131 (205)
T ss_dssp             TTCSSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC
T ss_pred             cCCeEEEEeccccchHHHHHHHHHhccCCCeeeee
Confidence            455788999987766666665 6778887777664

>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=97.88  E-value=4.1e-06  Score=62.08  Aligned_cols=27  Identities=22%  Similarity=0.283  Sum_probs=23.4

Q ss_pred             cEE-EEcCCCchHHHHHHHHHHHhCCce
Q psy4122          46 DVF-LIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        46 ~vl-L~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      ||+ +.|||||||+|+|+.+|+.+|.+.
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~gl~~   31 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEALQWHL   31 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            444 459999999999999999999874

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

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: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.81  E-value=5.8e-06  Score=61.74  Aligned_cols=26  Identities=12%  Similarity=-0.036  Sum_probs=23.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +.+.|||||||||+|+.+|+.+|.+.
T Consensus         6 IaIdGp~GsGKgT~ak~La~~lg~~~   31 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDFGFTY   31 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            45669999999999999999999883

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {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: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.80  E-value=7.6e-05  Score=58.55  Aligned_cols=31  Identities=23%  Similarity=0.267  Sum_probs=26.2

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .+..|+.+.|+||.|||||||++.++.....
T Consensus        37 ~i~~Ge~iaivG~sGsGKSTLl~ll~gl~~p   67 (253)
T d3b60a1          37 KIPAGKTVALVGRSGSGKSTIASLITRFYDI   67 (253)
T ss_dssp             EECTTCEEEEEECTTSSHHHHHHHHTTTTCC
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhcccCC
Confidence            3446889999999999999999999876643

>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=97.80  E-value=4.2e-06  Score=61.48  Aligned_cols=23  Identities=9%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++|+|.||+||||+|+++|+.++
T Consensus         5 i~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            68899999999999999998764

>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=97.77  E-value=6.7e-06  Score=58.28  Aligned_cols=30  Identities=10%  Similarity=0.019  Sum_probs=23.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYI   75 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v   75 (162)
                      .+.++|++|||||||++++++.+   |..+..+
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~   36 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLI   36 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEe
Confidence            46889999999999999999764   5544433

>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=97.71  E-value=1.1e-05  Score=59.63  Aligned_cols=26  Identities=12%  Similarity=0.225  Sum_probs=23.5

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +||+|+||+|+|||+|++.+++....
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~   27 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPD   27 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCc
Confidence            58999999999999999999988653

>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=97.71  E-value=2e-05  Score=56.88  Aligned_cols=32  Identities=13%  Similarity=-0.010  Sum_probs=24.1

Q ss_pred             HhcCCCCc--EEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          39 QKDNMSQD--VFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        39 ~~~~~g~~--vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      .+...+.+  |-+.||+||||||+|+++++.++.
T Consensus        15 ~~~~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          15 LAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             HTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HhccCCCCEEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            34444445  347899999999999999987653

>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=97.70  E-value=5.4e-05  Score=62.82  Aligned_cols=110  Identities=11%  Similarity=0.138  Sum_probs=67.6

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceE-EEEeccCCChhhhcceeE--eec-CeEEEec
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVE-YICLSRDTTEADIKQRRE--IVN-GTAIYYD  101 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~-~v~~~~~~~~~dL~g~~~--~~~-G~~~~~~  101 (162)
                      .++...+.+++++..- .| -+++.||+|+||||....+...++.+.. .+++ +|--.-.+-+...  +.. ....|. 
T Consensus       142 ~~~~~~~~l~~l~~~~-~G-liLvtGpTGSGKSTTl~~~l~~~~~~~~~i~ti-EdPiE~~~~~~~q~~v~~~~~~~~~-  217 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRP-HG-IILVTGPTGSGKSTTLYAGLQELNSSERNILTV-EDPIEFDIDGIGQTQVNPRVDMTFA-  217 (401)
T ss_dssp             CCHHHHHHHHHHHTSS-SE-EEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEE-ESSCCSCCSSSEEEECBGGGTBCHH-
T ss_pred             ccHHHHHHHHHHHhhh-hc-eEEEEcCCCCCccHHHHHHhhhhcCCCceEEEe-ccCcccccCCCCeeeecCCcCCCHH-
Confidence            5788888999887522 22 5899999999999999998887765532 2333 3322222223222  111 112233 


Q ss_pred             cHHHHHhhc-CcEEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         102 QSAVRAAIE-GRVLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       102 gpl~~A~~~-G~vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ..+..++|+ ..++++.||.  ++++.......-..|.+++
T Consensus       218 ~~l~~~lR~dPDvi~igEiR--d~~ta~~a~~aa~tGhlV~  256 (401)
T d1p9ra_         218 RGLRAILRQDPDVVMVGEIR--DLETAQIAVQASLTGHLVM  256 (401)
T ss_dssp             HHHHHHGGGCCSEEEESCCC--SHHHHHHHHHHHHTTCEEE
T ss_pred             HHHHHHHhhcCCEEEecCcC--ChHHHHHHHHHHhcCCeEE
Confidence            134445665 4799999997  4455555556667787766

>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=97.69  E-value=8.5e-06  Score=58.42  Aligned_cols=26  Identities=15%  Similarity=0.222  Sum_probs=22.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      -+++.|+||+||||+++.+|+.++..
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            36789999999999999999988543

>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=97.68  E-value=1.3e-05  Score=59.68  Aligned_cols=28  Identities=18%  Similarity=0.236  Sum_probs=24.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +||.|+||+|+|||+|++.+++..+.-+
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            4899999999999999999998876443

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

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 multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.67  E-value=6.9e-05  Score=58.99  Aligned_cols=30  Identities=13%  Similarity=0.153  Sum_probs=25.6

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ....|+-+.|+||.|||||||++.++....
T Consensus        40 ~i~~Ge~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          40 SIEKGETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHHhcCC
Confidence            445688999999999999999999887654

>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=97.63  E-value=1.3e-05  Score=59.58  Aligned_cols=54  Identities=13%  Similarity=0.010  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh---------CCceEEEEeccCCC
Q psy4122          29 DWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT---------QREVEYICLSRDTT   82 (162)
Q Consensus        29 ~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l---------g~p~~~v~~~~~~~   82 (162)
                      +.+..|-.++.. +..|.-++|.||||||||+++.++|...         +.++.++.......
T Consensus        18 TGi~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~   81 (251)
T d1szpa2          18 TGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFR   81 (251)
T ss_dssp             CSCHHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCC
T ss_pred             CCCHHHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHH
Confidence            344455566655 4567789999999999999999998542         34555665554433

>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=97.61  E-value=0.00014  Score=54.45  Aligned_cols=35  Identities=11%  Similarity=0.097  Sum_probs=28.4

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEE
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYIC   76 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~   76 (162)
                      ..+++.++..|+|+|||.++-.++..++.+...+.
T Consensus        83 ~~~~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~  117 (206)
T d2fz4a1          83 LVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVV  117 (206)
T ss_dssp             TTTSEEEEEESSSTTHHHHHHHHHHHSCSCEEEEE
T ss_pred             HhCCCcEEEeCCCCCceehHHhHHHHhcCceeEEE
Confidence            34567899999999999999988888888765443

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=97.58  E-value=0.00013  Score=57.60  Aligned_cols=87  Identities=10%  Similarity=0.130  Sum_probs=54.7

Q ss_pred             HHHHHHHhcCCCC-cEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCCChhhhcceeEeecCeEEEeccHHHHHhhcC
Q psy4122          33 HLRWILQKDNMSQ-DVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDTTEADIKQRREIVNGTAIYYDQSAVRAAIEG  111 (162)
Q Consensus        33 ~L~~i~~~~~~g~-~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~~~~dL~g~~~~~~G~~~~~~gpl~~A~~~G  111 (162)
                      .|..++......+ -++|+|||++|||++++.+++.+|.-   .+.+..-+             .+     + +..+...
T Consensus        92 ~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~---~~~~~~~~-------------~f-----~-l~~l~~k  149 (267)
T d1u0ja_          92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFY---GCVNWTNE-------------NF-----P-FNDCVDK  149 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSSCE---EECCTTCS-------------SC-----T-TGGGSSC
T ss_pred             HHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHhcch---hhccccCC-------------Cc-----c-ccccCCC
Confidence            4444443332223 47889999999999999999999753   22221100             00     1 1234455


Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcCCeEEEc
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLENREMHLE  142 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~r~l~l~  142 (162)
                      .++++||.+... ...+.+.+++....+.+.
T Consensus       150 ~~~~~~e~~~~~-~~~~~~K~l~gGd~i~v~  179 (267)
T d1u0ja_         150 MVIWWEEGKMTA-KVVESAKAILGGSKVRVD  179 (267)
T ss_dssp             SEEEECSCCEET-TTHHHHHHHHTTCCEEC-
T ss_pred             EEEEEeCCCccc-cHHHHHHHhcCCCceEee
Confidence            788999987654 455678999987777664

>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=97.50  E-value=0.00013  Score=59.74  Aligned_cols=33  Identities=12%  Similarity=0.162  Sum_probs=24.5

Q ss_pred             cCcEEEEeCCCCCCccHHHHHHHhhcC-CeEEEc
Q psy4122         110 EGRVLILEGIEKAERNVLPVLNNLLEN-REMHLE  142 (162)
Q Consensus       110 ~G~vlllDEId~a~~~v~~~L~~lle~-r~l~l~  142 (162)
                      ...++++||...++......+...+.. .++++-
T Consensus       261 ~~d~lIIDEaSmv~~~l~~~ll~~~~~~~~lILv  294 (359)
T d1w36d1         261 HLDVLVVDEASMIDLPMMSRLIDALPDHARVIFL  294 (359)
T ss_dssp             SCSEEEECSGGGCBHHHHHHHHHTCCTTCEEEEE
T ss_pred             ccceeeehhhhccCHHHHHHHHHHhcCCCEEEEE
Confidence            357999999999988877777776654 355553

>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=97.49  E-value=6.1e-05  Score=56.59  Aligned_cols=54  Identities=11%  Similarity=0.124  Sum_probs=37.4

Q ss_pred             HHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhc
Q psy4122          32 SHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIK   87 (162)
Q Consensus        32 ~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~   87 (162)
                      ..|-.++.. +..|.-+++.||||||||+++.++|...   +.++.++++  +.+..++.
T Consensus        13 ~~LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~--e~~~~~~~   70 (242)
T d1tf7a2          13 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY--EESRAQLL   70 (242)
T ss_dssp             HHHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES--SSCHHHHH
T ss_pred             HHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec--cCCHHHHH
Confidence            345555553 3466678999999999999999999654   556666655  44455543

>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=97.49  E-value=3.1e-05  Score=56.64  Aligned_cols=26  Identities=15%  Similarity=0.116  Sum_probs=23.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+-++|+||+|+|||||++.+.+...
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhCC
Confidence            77899999999999999999988763

>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=97.49  E-value=1.9e-05  Score=56.60  Aligned_cols=37  Identities=11%  Similarity=0.036  Sum_probs=28.6

Q ss_pred             HHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          32 SHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        32 ~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..|-.++. .+..|.-+++.||||+|||+++.++|...
T Consensus        10 ~~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          10 KELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34455555 34467789999999999999999999654

>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=97.46  E-value=3.8e-05  Score=57.62  Aligned_cols=41  Identities=17%  Similarity=0.067  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          28 QDWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        28 ~~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ++.+..|=.++.. +-.|.-+++.||||||||+++.++|...
T Consensus        19 ~TGi~~LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          19 STGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             CCSCHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCHHHHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3444455566665 4467789999999999999999998654

>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=97.30  E-value=9.1e-05  Score=56.08  Aligned_cols=26  Identities=19%  Similarity=0.224  Sum_probs=22.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|.-++|+|.||+||||||+.+++.+
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~~l   48 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEHQL   48 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45579999999999999999999765

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=97.28  E-value=6.9e-05  Score=52.12  Aligned_cols=22  Identities=5%  Similarity=0.122  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|+|+|+||||||+|+++++..
T Consensus         2 kivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3789999999999999998743

>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=97.23  E-value=9.6e-05  Score=54.52  Aligned_cols=27  Identities=22%  Similarity=0.391  Sum_probs=23.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +.++++|+||+|+|||+|++.+.+...
T Consensus         2 m~k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           2 MRKTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHhCC
Confidence            467999999999999999999987653

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {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: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=8.3e-05  Score=55.28  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=21.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      |-+.|++||||||+++.+++.++.+
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~~~   29 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLGQN   29 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhchh
Confidence            4577999999999999999998754

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {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: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.20  E-value=8.7e-05  Score=55.33  Aligned_cols=40  Identities=8%  Similarity=-0.105  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          28 QDWLSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        28 ~~~~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      ++....|-.++.. +..|.-+++.||||||||+++.++|..
T Consensus        20 ~TGi~~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          20 TTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             CCSCHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             cCCCHHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4445555566653 336667999999999999999999853

>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=97.20  E-value=0.00015  Score=53.93  Aligned_cols=32  Identities=25%  Similarity=0.441  Sum_probs=24.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh--CCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT--QREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l--g~p~~~v~~~   78 (162)
                      +++.|++|+|||||++++.+.+  ++....++..
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn~d   36 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLD   36 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTTSCEEEEECC
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEecC
Confidence            6899999999999999998755  3444455543

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {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: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=97.17  E-value=0.00026  Score=52.03  Aligned_cols=28  Identities=21%  Similarity=0.277  Sum_probs=25.1

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      |.-++|.|+=|+|||++++.+++.+|.+
T Consensus        33 g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          33 AIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            3458999999999999999999999875

>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=97.13  E-value=5.2e-05  Score=55.82  Aligned_cols=48  Identities=8%  Similarity=0.213  Sum_probs=33.3

Q ss_pred             HHHHHHHHHH-hcCCCCcEEEEcCCCchHHHHHHHHHH--H--hCCceEEEEe
Q psy4122          30 WLSHLRWILQ-KDNMSQDVFLIGKPGSLRRSLAMSYLE--L--TQREVEYICL   77 (162)
Q Consensus        30 ~~~~L~~i~~-~~~~g~~vlL~GppG~GKT~La~~lA~--~--lg~p~~~v~~   77 (162)
                      .++.|-.++. .+..|.-++|.|+||+|||+++.++|.  .  .+.++.++..
T Consensus        11 Gi~~LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~   63 (242)
T d1tf7a1          11 MIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   63 (242)
T ss_dssp             CCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CcHHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccc
Confidence            3444556665 345777899999999999999988763  2  2456655544

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {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: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.09  E-value=0.00014  Score=50.15  Aligned_cols=21  Identities=10%  Similarity=0.207  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+|+||||||+|++.+..
T Consensus         2 KI~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            488999999999999999875

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=97.08  E-value=0.00014  Score=50.65  Aligned_cols=21  Identities=10%  Similarity=0.306  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++|+|+||||||||++++..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999874

>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=97.06  E-value=0.00015  Score=53.33  Aligned_cols=38  Identities=16%  Similarity=-0.034  Sum_probs=28.7

Q ss_pred             HHHHHHHHHh-cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          31 LSHLRWILQK-DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        31 ~~~L~~i~~~-~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...|-+++.. +..|.-++|.|+||+|||+++.++|...
T Consensus        20 ~~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          20 SSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             CHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CHHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3445555554 4467778999999999999999999644

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {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: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=97.05  E-value=0.00023  Score=50.86  Aligned_cols=20  Identities=20%  Similarity=0.497  Sum_probs=18.2

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      |.++|+||+|||||++++..
T Consensus         3 V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999998863

>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=97.02  E-value=0.00035  Score=53.49  Aligned_cols=33  Identities=9%  Similarity=0.168  Sum_probs=24.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      .++|+||+|+||||.+-.+|+.+   |.++-.+++.
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~D   48 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAAD   48 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeec
Confidence            37889999999999887777543   5666666663

>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=97.01  E-value=0.0002  Score=51.16  Aligned_cols=30  Identities=13%  Similarity=0.108  Sum_probs=23.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYIC   76 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~   76 (162)
                      +-++|++|+|||||+++++..+   |..+-.+-
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            4589999999999999998654   55555443

>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=97.01  E-value=0.00019  Score=54.76  Aligned_cols=34  Identities=12%  Similarity=0.142  Sum_probs=24.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      ++.++|+||+|+||||.+-.+|+.+   |..+-.+++
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~   42 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAG   42 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEe
Confidence            4568999999999999888777544   455444444

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {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: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.00  E-value=0.00018  Score=52.99  Aligned_cols=22  Identities=23%  Similarity=0.280  Sum_probs=20.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ++|+|+|+||+|||+|.+++..
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            5799999999999999999875

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=96.99  E-value=0.00013  Score=51.62  Aligned_cols=20  Identities=10%  Similarity=0.170  Sum_probs=18.3

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++|+|++|||||||.+++.
T Consensus        15 kI~lvG~~~vGKTsLl~~l~   34 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLK   34 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            59999999999999999874

>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=96.98  E-value=0.00029  Score=53.85  Aligned_cols=32  Identities=16%  Similarity=0.151  Sum_probs=20.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      -++|+||+|+||||.+-.+|+.+   |..+-.+++
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            37889999999999877777544   556555555

>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=96.98  E-value=0.00038  Score=52.97  Aligned_cols=32  Identities=22%  Similarity=0.176  Sum_probs=23.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      -++|+||+|+||||.+-.+|..+   |..+-.+++
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~   46 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA   46 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEec
Confidence            36789999999999888888554   555554544

>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=96.95  E-value=0.00063  Score=52.06  Aligned_cols=54  Identities=6%  Similarity=0.011  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH----hCCceEEEEeccCCChhhh
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL----TQREVEYICLSRDTTEADI   86 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~----lg~p~~~v~~~~~~~~~dL   86 (162)
                      ...|-+++..+..|+-+++.|+||+|||+++.++|..    .|.++.++++  +++..++
T Consensus        22 ~~~lD~~~~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~--E~~~~~~   79 (277)
T d1cr2a_          22 CTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML--EESVEET   79 (277)
T ss_dssp             CTTHHHHHCSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES--SSCHHHH
T ss_pred             chhHHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee--ccchhhH
Confidence            3344555555667888899999999999999988842    3667666655  4555443

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {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: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.95  E-value=0.00021  Score=51.30  Aligned_cols=21  Identities=19%  Similarity=0.485  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            388999999999999998874

>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=96.94  E-value=0.00071  Score=54.67  Aligned_cols=36  Identities=17%  Similarity=0.266  Sum_probs=27.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDT   81 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~   81 (162)
                      .|-++||||+|||||+..++..+   |..+-.+...+.+
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss   94 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSS   94 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCce
Confidence            48899999999999999998543   5666666665443

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {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: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.94  E-value=0.00022  Score=50.67  Aligned_cols=21  Identities=14%  Similarity=0.335  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+|+|+||||||+|+.++..
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998875

>d1kaoa_ c.37.1.8 (A:) Rap2a {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: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.92  E-value=0.00024  Score=50.59  Aligned_cols=21  Identities=19%  Similarity=0.504  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+|++|||||+|++++..
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999875

>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=96.91  E-value=0.00035  Score=53.46  Aligned_cols=32  Identities=9%  Similarity=0.063  Sum_probs=23.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      -++|+||+|+||||.+-.+|+.+   |..+..+++
T Consensus        11 vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~   45 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAG   45 (211)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEec
Confidence            37889999999999888888654   454444444

>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=96.91  E-value=0.00029  Score=53.13  Aligned_cols=26  Identities=15%  Similarity=0.151  Sum_probs=23.3

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+-++|+||+|+|||+|.+.+.+...
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhCC
Confidence            66789999999999999999998764

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=96.90  E-value=0.00023  Score=50.54  Aligned_cols=21  Identities=10%  Similarity=0.292  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|.||||||+|+.++..
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            699999999999999998764

>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=96.89  E-value=6.1e-05  Score=57.75  Aligned_cols=32  Identities=16%  Similarity=0.149  Sum_probs=26.2

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      |++..+..|.-.+|.|+||+|||+++.++|..
T Consensus        21 ~li~G~~pg~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          21 YVLPNMVAGTVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             EEETTEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHhCCccCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            44455666778899999999999999998864

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=96.86  E-value=0.00025  Score=50.21  Aligned_cols=20  Identities=5%  Similarity=0.275  Sum_probs=18.5

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|||||+|++++.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~   23 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFN   23 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            58999999999999999875

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {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: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.86  E-value=0.0027  Score=47.03  Aligned_cols=22  Identities=18%  Similarity=0.234  Sum_probs=18.2

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .|+++++.+|+|+||| +|..+.
T Consensus        37 ~g~dvi~~a~tGsGKT-lay~lp   58 (206)
T d1s2ma1          37 TGRDILARAKNGTGKT-AAFVIP   58 (206)
T ss_dssp             HTCCEEEECCTTSCHH-HHHHHH
T ss_pred             cCCCEEEecCCcchhh-hhhccc
Confidence            4889999999999998 555554

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {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: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.85  E-value=0.00029  Score=50.42  Aligned_cols=21  Identities=19%  Similarity=0.520  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+|++|||||+|++++..
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999886

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {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: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.85  E-value=0.00029  Score=50.19  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++|+|++|||||+|++++..
T Consensus         5 KivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999874

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.85  E-value=0.00027  Score=50.87  Aligned_cols=21  Identities=29%  Similarity=0.376  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|.|+|.||+|||+|++++..
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~   27 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLG   27 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            599999999999999999864

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {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: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.85  E-value=0.00029  Score=50.13  Aligned_cols=21  Identities=24%  Similarity=0.354  Sum_probs=19.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~   67 (162)
                      ++|+|++|||||+|++++...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998753

>d1r2qa_ c.37.1.8 (A:) Rab5a {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: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.83  E-value=0.00031  Score=50.22  Aligned_cols=21  Identities=19%  Similarity=0.509  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++++|++|||||+|+.++..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999884

>d1wmsa_ c.37.1.8 (A:) Rab9a {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: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.83  E-value=0.00037  Score=49.98  Aligned_cols=20  Identities=35%  Similarity=0.551  Sum_probs=18.7

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|+.++..
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999999875

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=96.83  E-value=0.00049  Score=53.30  Aligned_cols=40  Identities=20%  Similarity=0.192  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHHHHhcC----CCCcEEEEcCCCchHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDN----MSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~----~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      +++.+.+.|..++....    ..-+++|+|.||+||||+++.+.
T Consensus        10 ~~~~~~~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~il   53 (257)
T d1h65a_          10 FAPATQTKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSII   53 (257)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHh
Confidence            44444555544443322    23479999999999999999876

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {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: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.82  E-value=0.00031  Score=50.22  Aligned_cols=21  Identities=14%  Similarity=0.510  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+|++|||||+|++++..
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999875

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {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: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.82  E-value=0.00029  Score=50.95  Aligned_cols=21  Identities=14%  Similarity=0.449  Sum_probs=18.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            389999999999999998873

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G 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: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=96.82  E-value=0.00027  Score=49.56  Aligned_cols=21  Identities=24%  Similarity=0.389  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|+||+|||||.+++..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999998863

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {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: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.82  E-value=0.00031  Score=51.16  Aligned_cols=22  Identities=18%  Similarity=0.153  Sum_probs=19.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|+|+|+||||||||.+++...
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999854

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {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: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.00032  Score=49.94  Aligned_cols=21  Identities=14%  Similarity=0.453  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus         5 Ki~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999999875

>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=96.80  E-value=0.00038  Score=51.59  Aligned_cols=25  Identities=16%  Similarity=0.165  Sum_probs=22.5

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |+-+.+.|+.||||||+++.+++.+
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            5678899999999999999999766

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, 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: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.80  E-value=0.00054  Score=53.07  Aligned_cols=30  Identities=17%  Similarity=0.144  Sum_probs=25.5

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ...|+-+.|+||.|||||||.+.++.....
T Consensus        23 i~~Gei~~liGpsGsGKSTLl~~i~Gl~~p   52 (232)
T d2awna2          23 IHEGEFVVFVGPSGCGKSTLLRMIAGLETI   52 (232)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhcCCCC
Confidence            345788999999999999999999977643

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {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: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.79  E-value=0.00035  Score=49.35  Aligned_cols=22  Identities=14%  Similarity=0.288  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|+++|++|||||+|++++..-
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3899999999999999998753

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {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: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.78  E-value=0.00035  Score=49.97  Aligned_cols=21  Identities=24%  Similarity=0.491  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+|++|||||+|++++..
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999985

>d3raba_ c.37.1.8 (A:) Rab3a {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: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.78  E-value=0.00035  Score=49.91  Aligned_cols=21  Identities=19%  Similarity=0.428  Sum_probs=19.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~   67 (162)
                      ++++|++|||||+|++++...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            899999999999999998753

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal 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: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.77  E-value=0.00036  Score=53.98  Aligned_cols=41  Identities=17%  Similarity=0.037  Sum_probs=31.3

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      +...++.|+..++    ++-..|+|++|+|||||++++.......
T Consensus        82 ~~~g~~~L~~~l~----~kt~~~~G~SGVGKSTLiN~L~~~~~~~  122 (225)
T d1u0la2          82 TGMGIEELKEYLK----GKISTMAGLSGVGKSSLLNAINPGLKLR  122 (225)
T ss_dssp             TCTTHHHHHHHHS----SSEEEEECSTTSSHHHHHHHHSTTCCCC
T ss_pred             cchhHhhHHHHhc----CCeEEEECCCCCCHHHHHHhhcchhhhh
Confidence            4455677777664    7889999999999999999886544433

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {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: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.76  E-value=0.00038  Score=49.65  Aligned_cols=20  Identities=30%  Similarity=0.595  Sum_probs=18.6

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|++++..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            89999999999999999875

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {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: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.00037  Score=50.05  Aligned_cols=21  Identities=14%  Similarity=0.523  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|++|||||+|++++..
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999874

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {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: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.75  E-value=0.00036  Score=49.67  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=18.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            388999999999999998874

>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=96.74  E-value=0.00077  Score=49.21  Aligned_cols=31  Identities=19%  Similarity=0.259  Sum_probs=24.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      |.+.|..||||||+++.+++.+   |.++..+..
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~~   36 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAF   36 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEec
Confidence            6788999999999999999765   667655443

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {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: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.73  E-value=0.0004  Score=49.12  Aligned_cols=20  Identities=15%  Similarity=0.361  Sum_probs=18.5

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      |+++|++|||||+|++++..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999874

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {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: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.73  E-value=0.0004  Score=49.89  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998864

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {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: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.71  E-value=0.00042  Score=49.19  Aligned_cols=20  Identities=30%  Similarity=0.652  Sum_probs=18.6

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|++++..
T Consensus         5 i~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999875

>d1vg8a_ c.37.1.8 (A:) Rab7 {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: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.70  E-value=0.00044  Score=49.97  Aligned_cols=20  Identities=30%  Similarity=0.587  Sum_probs=18.7

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      |+++|.+|||||+|++++..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999875

>d1c1ya_ c.37.1.8 (A:) Rap1A {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: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.69  E-value=0.00045  Score=49.15  Aligned_cols=22  Identities=14%  Similarity=0.418  Sum_probs=19.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|||||+|++++..-
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999998753

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=96.69  E-value=0.00046  Score=48.96  Aligned_cols=21  Identities=14%  Similarity=0.140  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+++.|++|||||+|+.++..
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            588999999999999999874

>d1kmqa_ c.37.1.8 (A:) RhoA {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: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.00045  Score=49.63  Aligned_cols=23  Identities=9%  Similarity=0.177  Sum_probs=19.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      +-++++|++|||||+|+.++..-
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            35899999999999999998753

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

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: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.68  E-value=0.00036  Score=54.03  Aligned_cols=29  Identities=17%  Similarity=0.098  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+.+-|+||.|||||||.+.++.+..
T Consensus        28 i~~Ge~~~iiG~sGsGKSTLl~~i~gl~~   56 (230)
T d1l2ta_          28 IKEGEFVSIMGPSGSGKSTMLNIIGCLDK   56 (230)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCcchhhHhccCCCC
Confidence            34588999999999999999999987654

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {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: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.00046  Score=49.35  Aligned_cols=20  Identities=25%  Similarity=0.585  Sum_probs=18.6

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|++++..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999874

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.67  E-value=0.00039  Score=49.67  Aligned_cols=21  Identities=10%  Similarity=0.235  Sum_probs=18.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+|+|+||+|||||.+++..
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999863

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {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: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.00047  Score=48.98  Aligned_cols=21  Identities=19%  Similarity=0.445  Sum_probs=19.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|+++|++|||||+|++++..
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999999874

>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=96.67  E-value=0.00034  Score=52.67  Aligned_cols=29  Identities=14%  Similarity=0.045  Sum_probs=24.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||.+.++..+.
T Consensus        24 i~~Gei~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          24 IEKGNVVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             EETTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhcccc
Confidence            34588899999999999999999997653

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

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: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=96.67  E-value=0.00064  Score=49.37  Aligned_cols=25  Identities=20%  Similarity=0.096  Sum_probs=20.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +-++|++|+||||+|+.+. ..|.++
T Consensus         6 IgitG~~gSGKstva~~l~-~~g~~~   30 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALLR-SWGYPV   30 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHH-HTTCCE
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeE
Confidence            3467999999999999985 578764

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=96.66  E-value=0.00028  Score=50.58  Aligned_cols=20  Identities=5%  Similarity=0.248  Sum_probs=18.6

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|+||+|||+|++++.
T Consensus        14 kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            69999999999999999875

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=96.66  E-value=0.00024  Score=51.74  Aligned_cols=24  Identities=17%  Similarity=0.267  Sum_probs=21.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      |.+.|+.||||||+++.+++.++.
T Consensus        12 I~ieG~~GsGKTTl~~~L~~~l~~   35 (197)
T d2vp4a1          12 VLIEGNIGSGKTTYLNHFEKYKND   35 (197)
T ss_dssp             EEEECSTTSCHHHHHHTTGGGTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            678899999999999999998865

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=96.66  E-value=0.00042  Score=49.37  Aligned_cols=20  Identities=15%  Similarity=0.283  Sum_probs=18.2

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|||||+|++++.
T Consensus        18 kI~vvG~~~vGKSsLi~~l~   37 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLA   37 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            59999999999999999774

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

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: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=96.65  E-value=0.0007  Score=52.37  Aligned_cols=30  Identities=7%  Similarity=0.056  Sum_probs=25.9

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ...|+-+.|+||.|||||||.+.++.....
T Consensus        23 i~~Ge~~~liGpsGaGKSTll~~l~Gl~~p   52 (229)
T d3d31a2          23 VESGEYFVILGPTGAGKTLFLELIAGFHVP   52 (229)
T ss_dssp             ECTTCEEEEECCCTHHHHHHHHHHHTSSCC
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHhcCcCC
Confidence            345788999999999999999999987654

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {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: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.65  E-value=0.00051  Score=48.83  Aligned_cols=21  Identities=29%  Similarity=0.547  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|.+|||||+|++++..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999874

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, 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: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.65  E-value=0.00089  Score=47.49  Aligned_cols=21  Identities=19%  Similarity=0.350  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|.|+|.||+|||||++++..
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999863

>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=96.65  E-value=0.0013  Score=52.92  Aligned_cols=36  Identities=17%  Similarity=0.224  Sum_probs=28.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDT   81 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~   81 (162)
                      -+-++||||+|||||+..++..   .|..+-.+...+.+
T Consensus        53 ~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss   91 (323)
T d2qm8a1          53 RVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSS   91 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGG
T ss_pred             EEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeeccccc
Confidence            4889999999999999999965   37777777776443

>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=96.63  E-value=0.0015  Score=50.05  Aligned_cols=18  Identities=11%  Similarity=0.117  Sum_probs=16.0

Q ss_pred             CCCCcEEEEcCCCchHHH
Q psy4122          42 NMSQDVFLIGKPGSLRRS   59 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~   59 (162)
                      ..++++++.+|||+|||.
T Consensus         7 ~~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             STTCEEEECCCTTSSTTT
T ss_pred             hcCCcEEEEECCCCCHHH
Confidence            467899999999999995

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

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: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.62  E-value=0.00043  Score=53.96  Aligned_cols=28  Identities=14%  Similarity=0.178  Sum_probs=24.6

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+-|+||.|||||||++.++....
T Consensus        27 ~~Ge~~~liG~sGaGKSTll~~i~gl~~   54 (240)
T d1g2912          27 KDGEFMILLGPSGCGKTTTLRMIAGLEE   54 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcCCC
Confidence            3578899999999999999999997764

>d1ek0a_ c.37.1.8 (A:) Ypt51 {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: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.61  E-value=0.00055  Score=48.72  Aligned_cols=21  Identities=14%  Similarity=0.472  Sum_probs=18.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|+.++..
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999998874

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {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: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.60  E-value=0.00057  Score=48.71  Aligned_cols=20  Identities=25%  Similarity=0.556  Sum_probs=18.7

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|++++..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998875

>d1mh1a_ c.37.1.8 (A:) Rac {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: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.59  E-value=0.00057  Score=49.39  Aligned_cols=21  Identities=19%  Similarity=0.360  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++++|++|||||+|++++..
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999999875

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

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: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=96.59  E-value=0.0013  Score=51.12  Aligned_cols=42  Identities=19%  Similarity=0.227  Sum_probs=28.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh----CCc---eEEEEeccCCChhhh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT----QRE---VEYICLSRDTTEADI   86 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l----g~p---~~~v~~~~~~~~~dL   86 (162)
                      ..|.|+|..|+|||+||+++.+..    +..   +..++.....+..++
T Consensus        45 ~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l   93 (277)
T d2a5yb3          45 FFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTF   93 (277)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHH
Confidence            367899999999999999987652    222   233555554444444

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

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: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.58  E-value=0.00089  Score=52.06  Aligned_cols=30  Identities=13%  Similarity=0.107  Sum_probs=25.5

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ...|+-+-|+||.|||||||.+.++.+...
T Consensus        29 v~~Ge~~~liGpsGaGKSTLl~~i~Gl~~p   58 (239)
T d1v43a3          29 IKDGEFLVLLGPSGCGKTTTLRMIAGLEEP   58 (239)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCCCC
Confidence            345788999999999999999999977643

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=96.58  E-value=0.00059  Score=48.80  Aligned_cols=21  Identities=19%  Similarity=0.532  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++++|++|||||+|++++..
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999874

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {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: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.58  E-value=0.00057  Score=49.08  Aligned_cols=21  Identities=33%  Similarity=0.469  Sum_probs=18.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -|+|+|++|||||+|++++..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998874

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC 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: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.56  E-value=0.00038  Score=54.33  Aligned_cols=30  Identities=23%  Similarity=0.191  Sum_probs=25.7

Q ss_pred             hcCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          40 KDNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        40 ~~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .+..|+.+.|+||.|||||||++.++....
T Consensus        36 ~i~~Ge~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          36 TLRPGEVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhcccC
Confidence            445688999999999999999999987664

>d2gjsa1 c.37.1.8 (A:91-258) Rad {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: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.56  E-value=0.0006  Score=48.69  Aligned_cols=20  Identities=35%  Similarity=0.561  Sum_probs=18.2

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|++++..
T Consensus         4 i~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCcCHHHHHHHHhC
Confidence            78999999999999998864

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {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: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.55  E-value=0.00049  Score=54.52  Aligned_cols=29  Identities=24%  Similarity=0.203  Sum_probs=24.6

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||++.++..+.
T Consensus        59 i~~Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          59 IEKGEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhCCCc
Confidence            34567789999999999999999997664

>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=96.55  E-value=0.0015  Score=48.85  Aligned_cols=33  Identities=12%  Similarity=0.100  Sum_probs=25.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEE
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELT---QREVEYIC   76 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~   76 (162)
                      |.=+.+.|+.|+||||+++.+++.+   |.++..+.
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            4456777999999999999999865   66665443

>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=96.54  E-value=0.00071  Score=52.50  Aligned_cols=30  Identities=10%  Similarity=0.290  Sum_probs=21.9

Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcC-CeEEE
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLEN-REMHL  141 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~-r~l~l  141 (162)
                      .++++||..-.++-.+..+..+... +.+.+
T Consensus       218 ~~i~iDE~QD~s~~q~~~~~~l~~~~~~~~~  248 (318)
T d1pjra1         218 QYIHIDEYQDTNRAQYTLVKKLAERFQNICA  248 (318)
T ss_dssp             SEEEESSGGGCCHHHHHHHHHHHTTTCCEEE
T ss_pred             chhhhHHHHHHHHHHHHHHHHHHHhhcceee
Confidence            5888999988888877777776554 33444

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=96.52  E-value=0.00085  Score=52.06  Aligned_cols=30  Identities=13%  Similarity=0.153  Sum_probs=25.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ...|+.+.++||.|+|||||++.++..+..
T Consensus        26 i~~Ge~vaIvG~sGsGKSTLl~ll~gl~~p   55 (241)
T d2pmka1          26 IKQGEVIGIVGRSGSGKSTLTKLIQRFYIP   55 (241)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            345889999999999999999999987653

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {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: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.52  E-value=0.00066  Score=49.19  Aligned_cols=22  Identities=9%  Similarity=0.244  Sum_probs=19.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      -++|+|++|||||+|++++..-
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4799999999999999988753

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=96.50  E-value=0.00085  Score=48.19  Aligned_cols=20  Identities=10%  Similarity=0.353  Sum_probs=18.2

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++|++|+|||+|++++.
T Consensus        19 KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            69999999999999999763

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {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: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.50  E-value=0.00072  Score=48.57  Aligned_cols=21  Identities=24%  Similarity=0.610  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999875

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

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: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=96.48  E-value=0.00039  Score=54.02  Aligned_cols=29  Identities=10%  Similarity=0.091  Sum_probs=25.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+.|+||.|||||||++.++....
T Consensus        25 i~~Ge~vaivG~sGsGKSTLl~ll~gl~~   53 (242)
T d1mv5a_          25 AQPNSIIAFAGPSGGGKSTIFSLLERFYQ   53 (242)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHHhhC
Confidence            34588899999999999999999987663

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {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: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.47  E-value=0.00076  Score=48.94  Aligned_cols=21  Identities=24%  Similarity=0.406  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|++|||||+|++++..
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            389999999999999999875

>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=96.46  E-value=0.00086  Score=49.33  Aligned_cols=23  Identities=13%  Similarity=0.007  Sum_probs=19.0

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHH
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMS   63 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~   63 (162)
                      +..|+++++.+|+|+|||..+..
T Consensus        37 l~~~~~~il~apTGsGKT~~a~l   59 (202)
T d2p6ra3          37 VFSGKNLLLAMPTAAGKTLLAEM   59 (202)
T ss_dssp             HTTCSCEEEECSSHHHHHHHHHH
T ss_pred             HHcCCCEEEEcCCCCchhHHHHH
Confidence            34588999999999999988743

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {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: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.44  E-value=0.00084  Score=48.01  Aligned_cols=21  Identities=14%  Similarity=0.536  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++|+|++|||||+|++++..
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999885

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

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: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=96.44  E-value=0.00057  Score=53.30  Aligned_cols=28  Identities=11%  Similarity=0.121  Sum_probs=24.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...|+-+.|+||.|||||||.+.++.+.
T Consensus        28 i~~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          28 IENGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             ECTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            4458899999999999999999999765

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {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: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=96.44  E-value=0.00061  Score=53.04  Aligned_cols=29  Identities=21%  Similarity=0.098  Sum_probs=25.1

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+-|+||.|||||||++.++.+..
T Consensus        28 i~~Ge~~~iiG~sGsGKSTLl~~i~Gl~~   56 (240)
T d3dhwc1          28 VPAGQIYGVIGASGAGKSTLIRCVNLLER   56 (240)
T ss_dssp             ECSSCEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHcCCcc
Confidence            34588899999999999999999997764

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {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: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.40  E-value=0.00085  Score=49.05  Aligned_cols=20  Identities=25%  Similarity=0.576  Sum_probs=18.6

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++|++|||||+|++++..
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            89999999999999999874

>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=96.40  E-value=0.0008  Score=51.51  Aligned_cols=30  Identities=10%  Similarity=0.290  Sum_probs=24.1

Q ss_pred             cEEEEeCCCCCCccHHHHHHHhhcC-CeEEE
Q psy4122         112 RVLILEGIEKAERNVLPVLNNLLEN-REMHL  141 (162)
Q Consensus       112 ~vlllDEId~a~~~v~~~L~~lle~-r~l~l  141 (162)
                      .++++||.--.++-....+..+..+ ..+.+
T Consensus       208 ~~i~vDE~QD~~~~~~~~l~~~~~~~~~~~~  238 (306)
T d1uaaa1         208 RYLLVDEYQDTNTSQYELVKLLVGSRARFTV  238 (306)
T ss_dssp             SEEEESCGGGCBHHHHHHHHHHHTTTCCEEE
T ss_pred             hHHHHHHHHHhhHHHHhhhhhcccCCCcceE
Confidence            6999999999999999998888765 33443

>d2ngra_ c.37.1.8 (A:) CDC42 {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: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.39  E-value=0.00087  Score=48.79  Aligned_cols=21  Identities=19%  Similarity=0.360  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -|+|+|++|||||+|+.++..
T Consensus         5 KvvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999998875

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase 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: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.39  E-value=0.0019  Score=50.70  Aligned_cols=43  Identities=19%  Similarity=0.051  Sum_probs=34.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCC--cEEEEcCCCchHHHHHHHHH
Q psy4122          23 TDALTQDWLSHLRWILQKDNMSQ--DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        23 ~~~~~~~~~~~L~~i~~~~~~g~--~vlL~GppG~GKT~La~~lA   65 (162)
                      |..+|++=.+.++.|......++  +-||.|++|||||.++-..+
T Consensus        81 PFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~  125 (264)
T d1gm5a3          81 PFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAI  125 (264)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHH
T ss_pred             cccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHH
Confidence            34688888888888888776555  46999999999999987655

>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=96.39  E-value=0.0022  Score=48.01  Aligned_cols=35  Identities=6%  Similarity=0.060  Sum_probs=29.4

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      |+-|.+.|+-||||||+++.+++.+......+...
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L~~~~~~~~~p   37 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFP   37 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHTTTSEEEEESS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHhCCEEEEEC
Confidence            56788999999999999999999997766655544

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase 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: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.38  E-value=0.0004  Score=48.62  Aligned_cols=22  Identities=23%  Similarity=0.398  Sum_probs=19.5

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .+.|+|.||+|||||++++...
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999998754

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=96.35  E-value=0.00082  Score=48.83  Aligned_cols=21  Identities=19%  Similarity=0.335  Sum_probs=19.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|.|+|+||+|||||++.+..
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            489999999999999999863

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine 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: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.34  E-value=0.0011  Score=49.63  Aligned_cols=26  Identities=4%  Similarity=-0.001  Sum_probs=23.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +-+.+.|+-||||||+++.+++.++.
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            34789999999999999999998864

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=96.32  E-value=0.0011  Score=49.41  Aligned_cols=30  Identities=13%  Similarity=0.248  Sum_probs=24.8

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .|+-++|.|++|+|||++|-.+.+. |+.+.
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~~~-g~~lv   42 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELVQR-GHRLI   42 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHHT-TCEEE
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            4667999999999999999888764 87653

>d1i2ma_ c.37.1.8 (A:) Ran {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: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.31  E-value=0.00061  Score=48.83  Aligned_cols=21  Identities=19%  Similarity=0.396  Sum_probs=18.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++++|++|||||+|++++..
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998764

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {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: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.29  E-value=0.0018  Score=51.89  Aligned_cols=23  Identities=13%  Similarity=0.089  Sum_probs=20.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |.+.|++|+||||+|+.++..+.
T Consensus        83 IGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEeCCCCCCCcHHHHHHHHHHh
Confidence            56789999999999999999874

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {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: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.28  E-value=0.0016  Score=50.57  Aligned_cols=25  Identities=12%  Similarity=0.191  Sum_probs=21.7

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .-+.|+||.|||||||.+.++..+.
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~~   49 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEECCCCChHHHHHHHHHcCCC
Confidence            4567899999999999999998764

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {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: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.26  E-value=0.0006  Score=48.82  Aligned_cols=20  Identities=25%  Similarity=0.529  Sum_probs=8.6

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~   66 (162)
                      |+++|.+|||||+|++++..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998764

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, 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: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=96.24  E-value=0.0029  Score=50.42  Aligned_cols=36  Identities=8%  Similarity=0.026  Sum_probs=30.8

Q ss_pred             HHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          33 HLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        33 ~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ..-+.+..+-.|+.++|.|++|||||+|+..++...
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            455666777789999999999999999999999744

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine 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: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.23  E-value=0.00048  Score=51.23  Aligned_cols=25  Identities=8%  Similarity=0.153  Sum_probs=22.4

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      +-+.+.|+-||||||+++.+++.+.
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4588999999999999999998874

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {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: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=96.21  E-value=0.0021  Score=45.85  Aligned_cols=21  Identities=24%  Similarity=0.449  Sum_probs=19.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .|.++|.+|+|||||++++..
T Consensus        10 kV~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            589999999999999998864

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {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: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.20  E-value=0.0011  Score=47.65  Aligned_cols=21  Identities=14%  Similarity=0.200  Sum_probs=18.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+|++|+|||+|+.++..
T Consensus         4 KivllG~~~vGKTsll~r~~f   24 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQMRI   24 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999999953

>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=96.19  E-value=0.0031  Score=48.63  Aligned_cols=44  Identities=18%  Similarity=0.085  Sum_probs=34.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCC--cEEEEcCCCchHHHHHHHHHH
Q psy4122          23 TDALTQDWLSHLRWILQKDNMSQ--DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        23 ~~~~~~~~~~~L~~i~~~~~~g~--~vlL~GppG~GKT~La~~lA~   66 (162)
                      |..+|++-...+..+......++  +.||.|++|+|||.++-..+.
T Consensus        53 P~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~   98 (233)
T d2eyqa3          53 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAF   98 (233)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHH
T ss_pred             ccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHH
Confidence            45678777788888877666555  579999999999999987664

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {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: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.18  E-value=0.0013  Score=49.29  Aligned_cols=26  Identities=19%  Similarity=0.050  Sum_probs=23.0

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      -+-|+|+.||||||+|+.+++.+|.+
T Consensus         3 iIgiTG~igSGKsTva~~l~e~~g~~   28 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMSNYSAV   28 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHSCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCCCe
Confidence            36799999999999999999988865

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {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: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.13  E-value=0.0012  Score=51.56  Aligned_cols=29  Identities=17%  Similarity=0.201  Sum_probs=24.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ...|+-+-|+||.|||||||++.++.+..
T Consensus        25 i~~GEi~~iiG~sGsGKSTLl~~i~Gl~~   53 (258)
T d1b0ua_          25 ARAGDVISIIGSSGSGKSTFLRCINFLEK   53 (258)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHHcCcc
Confidence            34578899999999999999999987653

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.12  E-value=0.0045  Score=49.06  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=18.8

Q ss_pred             CcEE--EEcCCCchHHHHHHHHHHHh
Q psy4122          45 QDVF--LIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        45 ~~vl--L~GppG~GKT~La~~lA~~l   68 (162)
                      +|++  |.|++||||||++..+...+
T Consensus        26 ~P~iIGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_          26 CPLFIFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEeECCCCCCHHHHHHHHHHHH
Confidence            3544  57999999999998886554

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [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: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=96.08  E-value=0.0021  Score=49.65  Aligned_cols=28  Identities=25%  Similarity=0.222  Sum_probs=24.7

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+-|+||.|+|||||.+.++..+.
T Consensus        30 ~~Gei~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          30 PRGQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            3578899999999999999999997764

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.08  E-value=0.0072  Score=47.58  Aligned_cols=26  Identities=12%  Similarity=0.089  Sum_probs=23.1

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +|+.++|+.|+|||||++++....|.
T Consensus         7 Rni~i~gh~~~GKTtL~e~ll~~~g~   32 (276)
T d2bv3a2           7 RNIGIAAHIDAGKTTTTERILYYTGR   32 (276)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTS
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhcCc
Confidence            38999999999999999999877664

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.08  E-value=0.0042  Score=47.23  Aligned_cols=44  Identities=14%  Similarity=0.165  Sum_probs=34.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEeccCCChhhhcc
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELT---QREVEYICLSRDTTEADIKQ   88 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~~~~~~~dL~g   88 (162)
                      +-+++.|.-|+||||++-.+|..+   |+++..+.+.+..+.++++|
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~Dp~~~l~~~lg   55 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTDPASNVGQVFS   55 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHTT
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCCCCCCHHHHhC
Confidence            457888999999999999888554   88887787776666777765

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.06  E-value=0.0013  Score=47.14  Aligned_cols=20  Identities=35%  Similarity=0.428  Sum_probs=18.2

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      +|.|+|.||+|||||++++.
T Consensus         3 ~VaivG~~nvGKSTLin~L~   22 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMT   22 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            58999999999999999875

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.04  E-value=0.00081  Score=52.12  Aligned_cols=29  Identities=14%  Similarity=0.086  Sum_probs=21.8

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ++.++-.+|+|++|+|||||++++.....
T Consensus        94 ~l~~~~~vl~G~SGVGKSSLiN~L~~~~~  122 (231)
T d1t9ha2          94 HFQDKTTVFAGQSGVGKSSLLNAISPELG  122 (231)
T ss_dssp             GGTTSEEEEEESHHHHHHHHHHHHCC---
T ss_pred             hhccceEEEECCCCccHHHHHHhhccHhH
Confidence            33566789999999999999998874443

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=96.03  E-value=0.0021  Score=47.54  Aligned_cols=26  Identities=23%  Similarity=0.114  Sum_probs=21.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      +-|+|++||||||+++.+. ..|.++.
T Consensus         5 IgITG~igSGKStv~~~l~-~~G~~vi   30 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT-DLGVPLV   30 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH-TTTCCEE
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeEE
Confidence            5689999999999999886 5787743

>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=96.03  E-value=0.00058  Score=48.01  Aligned_cols=23  Identities=13%  Similarity=0.186  Sum_probs=20.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      .+|+||.|+|||++..++...++
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            46889999999999999997764

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {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: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=96.01  E-value=0.00086  Score=47.35  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=18.3

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .|.|+|+|++|||||.+++.
T Consensus        18 ~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          18 EVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             EEEEEECTTSSHHHHHTTTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            59999999999999999874

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA 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: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=95.99  E-value=0.0023  Score=47.45  Aligned_cols=25  Identities=28%  Similarity=0.247  Sum_probs=21.1

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      +-|+|.+|+||||+++.+. .+|.++
T Consensus         6 IgitG~igSGKStv~~~l~-~~G~~v   30 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA-DLGINV   30 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HTTCEE
T ss_pred             EEEECCCcCCHHHHHHHHH-HCCCcE
Confidence            5689999999999999886 678763

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {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: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.97  E-value=0.002  Score=46.05  Aligned_cols=23  Identities=13%  Similarity=0.213  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++|.|..|||||+|+.++..-.
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48999999999999999997553

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=95.96  E-value=0.002  Score=47.52  Aligned_cols=29  Identities=14%  Similarity=0.286  Sum_probs=23.9

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCce
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREV   72 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~   72 (162)
                      .|+-+++.|++|+|||+++-.+.+. |+.+
T Consensus        14 ~g~gvli~G~sg~GKS~la~~l~~~-g~~l   42 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETALELIKR-GHRL   42 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHT-TCEE
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc-CCeE
Confidence            4667999999999999999877755 7654

>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=95.95  E-value=0.026  Score=39.69  Aligned_cols=95  Identities=16%  Similarity=0.099  Sum_probs=54.2

Q ss_pred             EEEEcCCCchHHH-HHHHHH--HHhCCceEEEEeccCCChh-hhcceeEeecCeEEEecc-HHHHHh------hcCcEEE
Q psy4122          47 VFLIGKPGSLRRS-LAMSYL--ELTQREVEYICLSRDTTEA-DIKQRREIVNGTAIYYDQ-SAVRAA------IEGRVLI  115 (162)
Q Consensus        47 vlL~GppG~GKT~-La~~lA--~~lg~p~~~v~~~~~~~~~-dL~g~~~~~~G~~~~~~g-pl~~A~------~~G~vll  115 (162)
                      -+++||=.+|||+ |.+.+-  ...|.++..+.-..|+... ++.-+....-........ .+...+      ..-.+++
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~   84 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   84 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             EEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEE
Confidence            4678999999999 666653  4568887777776565432 221111011011222222 222222      1346999


Q ss_pred             EeCCCCCCccHHHHHHHhhcCC-eEEE
Q psy4122         116 LEGIEKAERNVLPVLNNLLENR-EMHL  141 (162)
Q Consensus       116 lDEId~a~~~v~~~L~~lle~r-~l~l  141 (162)
                      +||+.-++..+...+..+.+.+ .+.+
T Consensus        85 IDE~QFf~d~i~~~~~~~~~~g~~Viv  111 (139)
T d2b8ta1          85 IDEVQFFDDRICEVANILAENGFVVII  111 (139)
T ss_dssp             ECSGGGSCTHHHHHHHHHHHTTCEEEE
T ss_pred             echhhhcchhHHHHHHHHHhcCceEEE
Confidence            9999999865666666666655 4444

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=95.93  E-value=0.0014  Score=46.96  Aligned_cols=20  Identities=30%  Similarity=0.287  Sum_probs=18.0

Q ss_pred             cEEEEcCCCchHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA   65 (162)
                      .|-|+|+|++|||||.+++.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~   22 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVS   22 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSE
T ss_pred             eEEEECCCCCCHHHHHHHHh
Confidence            48899999999999999874

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=95.92  E-value=0.0017  Score=48.29  Aligned_cols=30  Identities=17%  Similarity=0.300  Sum_probs=24.4

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHhCCceE
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELTQREVE   73 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~lg~p~~   73 (162)
                      .|+-++|.|++|+|||++|-.+.+ .|+.+.
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~-~G~~lv   43 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLIN-KNHLFV   43 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHT-TTCEEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH-cCCcee
Confidence            466799999999999999988875 477643

>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=95.91  E-value=0.001  Score=44.76  Aligned_cols=20  Identities=15%  Similarity=0.089  Sum_probs=17.2

Q ss_pred             CCCcEEEEcCCCchHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAM   62 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~   62 (162)
                      .|++++|.+|||+|||..+.
T Consensus         6 ~~~~~il~~~tGsGKT~~~~   25 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFL   25 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHH
T ss_pred             cCCcEEEEcCCCCChhHHHH
Confidence            47899999999999996653

>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=95.84  E-value=0.0095  Score=45.49  Aligned_cols=75  Identities=11%  Similarity=0.170  Sum_probs=38.8

Q ss_pred             CcEEEEcCCCchHHHHHHHHHH-----HhCCce--EEEEeccCCChhhhcce----eEeecCeEEEecc-----HHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLE-----LTQREV--EYICLSRDTTEADIKQR----REIVNGTAIYYDQ-----SAVRAA  108 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~-----~lg~p~--~~v~~~~~~~~~dL~g~----~~~~~G~~~~~~g-----pl~~A~  108 (162)
                      +.++|+||..+|||++.+++|-     ..|.++  ....+..   ...+..+    ..+..|...|.-.     -+.+..
T Consensus        42 ~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~---~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~  118 (234)
T d1wb9a2          42 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGP---IDRIFTRVGAADDLASGRSTFMVEMTETANILHNA  118 (234)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECC---CCEEEEEEC-----------CHHHHHHHHHHHHHC
T ss_pred             eEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceeccc---chhheeEEccCcccccchhHHHHHHHHHHHHHHhc
Confidence            4588999999999999999883     345432  2333321   1112211    1122343333221     122233


Q ss_pred             hcCcEEEEeCCCCC
Q psy4122         109 IEGRVLILEGIEKA  122 (162)
Q Consensus       109 ~~G~vlllDEId~a  122 (162)
                      .+..++++||+-+-
T Consensus       119 ~~~sLvliDE~~~g  132 (234)
T d1wb9a2         119 TEYSLVLMDEIGRG  132 (234)
T ss_dssp             CTTEEEEEESCCCC
T ss_pred             ccccEEeecccccC
Confidence            45679999999773

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G 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: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.83  E-value=0.0026  Score=46.00  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=19.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++++|++|||||+|+.++...
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999988753

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {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: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=95.82  E-value=0.0018  Score=49.65  Aligned_cols=28  Identities=18%  Similarity=0.254  Sum_probs=24.4

Q ss_pred             cCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          41 DNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        41 ~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      ...|+-+-|+||.|+|||||.+.++...
T Consensus        22 I~~Gei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          22 VRAGEILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             EETTCEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3468889999999999999999999754

>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=95.80  E-value=0.0064  Score=47.37  Aligned_cols=50  Identities=16%  Similarity=0.113  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          28 QDWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        28 ~~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      |+....|-.++-  .+..|+-+.+.||||||||+++-++|...   |..+.++..
T Consensus        36 sTG~~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidt   90 (263)
T d1u94a1          36 STGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   90 (263)
T ss_dssp             CCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             ccCCHHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcc
Confidence            444455666653  33466778999999999999999888543   455555544

>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=95.79  E-value=0.0017  Score=48.81  Aligned_cols=24  Identities=8%  Similarity=0.052  Sum_probs=19.6

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      +.|+++++++|||+|||..+...+
T Consensus        56 l~g~~~~i~apTGsGKT~~~~~~~   79 (237)
T d1gkub1          56 LRKESFAATAPTGVGKTSFGLAMS   79 (237)
T ss_dssp             HTTCCEECCCCBTSCSHHHHHHHH
T ss_pred             HCCCCEEEEecCCChHHHHHHHHH
Confidence            358999999999999997665444

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

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: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.73  E-value=0.0023  Score=49.71  Aligned_cols=28  Identities=21%  Similarity=0.269  Sum_probs=24.6

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+-|+||.|+|||||++.++....
T Consensus        28 ~~Gei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          28 NKGDVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHHCCCc
Confidence            3578899999999999999999997764

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {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: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.66  E-value=0.0028  Score=45.03  Aligned_cols=22  Identities=14%  Similarity=0.247  Sum_probs=19.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .++|+|..|||||+|++++..-
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4899999999999999998643

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {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: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=95.63  E-value=0.0026  Score=49.05  Aligned_cols=28  Identities=18%  Similarity=0.103  Sum_probs=24.5

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      ..|+-+-|+||.|+|||||.+.++....
T Consensus        26 ~~Gei~glvG~nGaGKSTLl~~l~G~~~   53 (238)
T d1vpla_          26 EEGEIFGLIGPNGAGKTTTLRIISTLIK   53 (238)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            4577889999999999999999997764

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.62  E-value=0.0028  Score=47.44  Aligned_cols=22  Identities=18%  Similarity=0.252  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~   67 (162)
                      .|+|.|+.|+|||+|++++...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999998643

>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=95.54  E-value=0.0049  Score=44.46  Aligned_cols=23  Identities=17%  Similarity=0.229  Sum_probs=18.7

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHH
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ++++++++|+|+|||.++..++.
T Consensus        23 ~~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          23 ETNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             GSCEEEECCTTSCHHHHHHHHHH
T ss_pred             cCCeEEEeCCCCcHHHHHHHHHH
Confidence            46899999999999986665553

>d1w1wa_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.50  E-value=0.0037  Score=49.51  Aligned_cols=24  Identities=17%  Similarity=0.112  Sum_probs=21.4

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      -+++||.|+|||++..+++..+|.
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~lg~   51 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVLGV   51 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            479999999999999999987764

>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=95.40  E-value=0.0026  Score=48.87  Aligned_cols=24  Identities=13%  Similarity=0.120  Sum_probs=21.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      -+|+||.|||||++.++++..+|.
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~lg~   50 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVFGE   50 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTSCC
T ss_pred             EEEECCCCCcHHHHHHHHHHHhCC
Confidence            589999999999999999887653

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase 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: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=95.30  E-value=0.0074  Score=44.00  Aligned_cols=23  Identities=9%  Similarity=0.007  Sum_probs=18.7

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHH
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .|+++++.-|||+|||.......
T Consensus        39 ~g~~vlv~apTGsGKT~~~~~~~   61 (206)
T d1oywa2          39 SGRDCLVVMPTGGGKSLCYQIPA   61 (206)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHH
T ss_pred             cCCCEEEEcCCCCCCcchhhhhh
Confidence            47899999999999987764433

>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=95.25  E-value=0.0049  Score=49.68  Aligned_cols=22  Identities=14%  Similarity=0.255  Sum_probs=18.9

Q ss_pred             CCcEEEEcCCCchHHHHHHHHH
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .+|++++|+||+|||++++.+.
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li   71 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELA   71 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHH
T ss_pred             cceEEEEeCCCCcHHHHHHHHH
Confidence            3589999999999999987655

>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=95.20  E-value=0.008  Score=43.21  Aligned_cols=31  Identities=10%  Similarity=0.094  Sum_probs=24.6

Q ss_pred             CcEEEEcC-CCchHHHHHHHHHHHh---CCceEEE
Q psy4122          45 QDVFLIGK-PGSLRRSLAMSYLELT---QREVEYI   75 (162)
Q Consensus        45 ~~vlL~Gp-pG~GKT~La~~lA~~l---g~p~~~v   75 (162)
                      |.+++.|- +|||||+++-.+|..+   |+.+..+
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEE
Confidence            46889998 6999999999999655   6665544

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.19  E-value=0.02  Score=43.24  Aligned_cols=43  Identities=14%  Similarity=0.092  Sum_probs=26.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQ   88 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g   88 (162)
                      -+++.|.-|+||||++-.+|..   .|+.+..+-+......++++|
T Consensus        22 iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~Dp~~~l~~~lg   67 (279)
T d1ihua2          22 LIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLN   67 (279)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESCCC--------
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCCCChHHHhC
Confidence            4677799999999998887754   477776666654444444443

>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=95.12  E-value=0.012  Score=44.62  Aligned_cols=21  Identities=10%  Similarity=-0.009  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      -++|+||..+|||++.++++-
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHH
T ss_pred             EEEEECCCccccchhhhhhHH
Confidence            479999999999999998883

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) 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: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.04  E-value=0.025  Score=45.59  Aligned_cols=106  Identities=15%  Similarity=0.190  Sum_probs=61.1

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEec---cCCChhhhc-c------------------
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLS---RDTTEADIK-Q------------------   88 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~---~~~~~~dL~-g------------------   88 (162)
                      .+.|+.|......=+|+.++|+.++|||||+.++....|.--..-...   -|+...+.. |                  
T Consensus         4 ~~~~~~lm~~~~~IRNI~iiGhvd~GKTTL~d~Ll~~~g~i~~~~~~~~~~~D~~~~E~eRgiTi~~~~~~l~~~~~~~~   83 (341)
T d1n0ua2           4 VDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDED   83 (341)
T ss_dssp             HHHHHHHHHCGGGEEEEEEECCGGGTHHHHHHHHHHHHBCCBC------------------CCCBCCCEEEEEEECCHHH
T ss_pred             HHHHHHHhcCcccCcEEEEEeCCCCcHHHHHHHHHHHCCCccccccccccccccchhHHhcCceEeCCEEEEEeccCccc
Confidence            466777776533335899999999999999999986665321111000   011111110 0                  


Q ss_pred             -----------e--eEe--ecCeEEEeccHHHHHh--hcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122          89 -----------R--REI--VNGTAIYYDQSAVRAA--IEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus        89 -----------~--~~~--~~G~~~~~~gpl~~A~--~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                                 .  ..+  .+|+..|... ...|+  ..|.+|++|=++-..+.....+..+.+.+
T Consensus        84 ~~~~~~~~~~~~~~inliDtPGh~dF~~e-v~~al~~~D~allVVda~eGv~~qT~~~~~~a~~~~  148 (341)
T d1n0ua2          84 VKEIKQKTDGNSFLINLIDSPGHVDFSSE-VTAALRVTDGALVVVDTIEGVCVQTETVLRQALGER  148 (341)
T ss_dssp             HHHCSSCCCSSEEEEEEECCCCCCSSCHH-HHHHHHTCSEEEEEEETTTBSCHHHHHHHHHHHHTT
T ss_pred             ccchhccccccceEEEEEcCCCcHHHHHH-HHHHHhhcCceEEEEecccCcchhHHHHHHHHHHcC
Confidence                       0  011  1243333321 23343  46788999999988888888888887765

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {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: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.02  E-value=0.0083  Score=49.13  Aligned_cols=21  Identities=24%  Similarity=0.290  Sum_probs=19.2

Q ss_pred             CcEEEEcCCCchHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA   65 (162)
                      -+|.++|.||+|||||++++.
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~   77 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLR   77 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999999885

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

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: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=94.99  E-value=0.0074  Score=48.68  Aligned_cols=26  Identities=12%  Similarity=0.097  Sum_probs=22.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .|.+.|+-||||||+++.+++.++..
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~~~   33 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAASGG   33 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGGCS
T ss_pred             EEEEECCccCCHHHHHHHHHHHhccC
Confidence            47899999999999999999987644

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

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: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=94.65  E-value=0.0037  Score=49.73  Aligned_cols=23  Identities=9%  Similarity=0.284  Sum_probs=17.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |-+.|++||||||+++.+++.++
T Consensus         7 IgIaG~SGSGKTTva~~l~~i~~   29 (288)
T d1a7ja_           7 ISVTGSSGAGTSTVKHTFDQIFR   29 (288)
T ss_dssp             EEEESCC---CCTHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHHh
Confidence            56779999999999999998774

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=94.54  E-value=0.0092  Score=46.62  Aligned_cols=26  Identities=31%  Similarity=0.378  Sum_probs=22.9

Q ss_pred             CcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      +|+.++|+.|+|||||++++....|.
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~g~   28 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKTGA   28 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTS
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHcCC
Confidence            38999999999999999999877664

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {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: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.45  E-value=0.013  Score=46.13  Aligned_cols=33  Identities=18%  Similarity=0.164  Sum_probs=27.4

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      +.+..+-.|+.+++.|++|||||+|+..++...
T Consensus        60 D~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          60 DLLAPYAKGGKIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             HHHSCEETTCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eeeccccCCCEEEeeCCCCCCHHHHHHHHHHHH
Confidence            444456678899999999999999999998663

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=94.43  E-value=0.01  Score=42.47  Aligned_cols=21  Identities=14%  Similarity=0.188  Sum_probs=19.3

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      +|-++|.|++|||||.+++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            688999999999999999874

>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=94.36  E-value=0.24  Score=34.14  Aligned_cols=94  Identities=10%  Similarity=0.031  Sum_probs=52.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHH---hCCceEEEEeccCCChhhhcc-eeEee-cCeEEEeccHHHHHhhcCcEEEEeCCCC
Q psy4122          47 VFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSRDTTEADIKQ-RREIV-NGTAIYYDQSAVRAAIEGRVLILEGIEK  121 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~~~~~~dL~g-~~~~~-~G~~~~~~gpl~~A~~~G~vlllDEId~  121 (162)
                      -+++||=.+|||+-.-+.+..   .|..+..+.-..|+..++-.. +.... ..-..-......+-+.+-.++++||+.-
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~ikp~~D~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~I~IDEaQF   84 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQF   84 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCC--------------CEEESSGGGGHHHHHTCSEEEESSGGG
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHcCCcEEEEecccccCCcceeeecCCCcceeeeeechhhhhhhhcccceEEeehhHH
Confidence            467899999999866655533   477777777666664432221 10000 0111111112234455678999999999


Q ss_pred             CCccHHHHHHHhhcCCeEEE
Q psy4122         122 AERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       122 a~~~v~~~L~~lle~r~l~l  141 (162)
                      ++ ++......+.+.+.-++
T Consensus        85 f~-dl~~~~~~~~~~~~~Vi  103 (133)
T d1xbta1          85 FP-DIVEFCEAMANAGKTVI  103 (133)
T ss_dssp             CT-THHHHHHHHHHTTCEEE
T ss_pred             HH-HHHHHHHHHHhcCCcEE
Confidence            96 67777777776654433

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {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: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.18  E-value=0.022  Score=41.45  Aligned_cols=36  Identities=11%  Similarity=-0.033  Sum_probs=24.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .++|-=.+.+..++.    |+++++..|+|+|||. |-.+.
T Consensus        23 ~pt~iQ~~aip~~l~----G~dvii~a~TGSGKTl-ayllp   58 (209)
T d1q0ua_          23 KPTEIQERIIPGALR----GESMVGQSQTGTGKTH-AYLLP   58 (209)
T ss_dssp             SCCHHHHHHHHHHHH----TCCEEEECCSSHHHHH-HHHHH
T ss_pred             CCCHHHHHHHHHHHC----CCCeEeecccccccce-eeeee
Confidence            345544555555555    8999999999999986 43333

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

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: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=94.11  E-value=0.01  Score=47.74  Aligned_cols=26  Identities=19%  Similarity=0.229  Sum_probs=22.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .|.+.|+-|+||||+++.+++.++..
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~~   32 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAIT   32 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            47899999999999999999987653

>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=93.97  E-value=0.019  Score=43.02  Aligned_cols=22  Identities=23%  Similarity=0.244  Sum_probs=19.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .++.|.-|+|||||.+++.+..
T Consensus         6 ~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           6 TLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEESSSSSCHHHHHHHHHSC
T ss_pred             EEEeeCCCCCHHHHHHHHHhcC
Confidence            4778999999999999988753

>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=93.95  E-value=0.019  Score=44.80  Aligned_cols=49  Identities=12%  Similarity=0.001  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          29 DWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        29 ~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      +....|-.++-  .+..|.-..+.||+|||||+++-+++...   |..+.++-.
T Consensus        43 TG~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDt   96 (269)
T d1mo6a1          43 TGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDA   96 (269)
T ss_dssp             CSCHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             cCCHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEEC
Confidence            33445555553  44467778999999999999998877533   444444443

>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=93.75  E-value=0.02  Score=44.57  Aligned_cols=50  Identities=12%  Similarity=0.034  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHH--hcCCCCcEEEEcCCCchHHHHHHHHHHHh---CCceEEEEe
Q psy4122          28 QDWLSHLRWILQ--KDNMSQDVFLIGKPGSLRRSLAMSYLELT---QREVEYICL   77 (162)
Q Consensus        28 ~~~~~~L~~i~~--~~~~g~~vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~   77 (162)
                      ++....|-.++-  .+..|+-..+.||+|||||+++-+++...   |..+.++-.
T Consensus        39 ~TGs~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDt   93 (268)
T d1xp8a1          39 STGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDA   93 (268)
T ss_dssp             CCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             cCCCHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEEC
Confidence            333445555553  23356678999999999999999888543   445555433

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.74  E-value=0.016  Score=43.01  Aligned_cols=24  Identities=17%  Similarity=0.158  Sum_probs=20.6

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+.++|.+++|||||+.++....|
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~~~g   28 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTYVAA   28 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHhh
Confidence            688999999999999999865543

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

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: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=93.69  E-value=0.013  Score=47.20  Aligned_cols=26  Identities=19%  Similarity=0.327  Sum_probs=19.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCCc
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQRE   71 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~p   71 (162)
                      .|.+.|+-|+||||+++.+++.++..
T Consensus         6 rI~IEG~iGsGKTTl~~~La~~l~~~   31 (329)
T d1e2ka_           6 RVYIDGPHGMGKTTTTQLLVALGSRD   31 (329)
T ss_dssp             EEEECSCTTSSHHHHHHHHTC----C
T ss_pred             EEEEECCcCCCHHHHHHHHHHHhCCC
Confidence            37889999999999999999876543

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.45  E-value=0.024  Score=42.22  Aligned_cols=22  Identities=14%  Similarity=0.070  Sum_probs=19.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |.++|.|.+|||||++++....
T Consensus         8 IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           8 VSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCccHHHHHHHHHhhc
Confidence            8899999999999999987654

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.33  E-value=0.027  Score=44.40  Aligned_cols=32  Identities=19%  Similarity=0.105  Sum_probs=26.5

Q ss_pred             HHHHhcCCCCcEEEEcCCCchHHHHHHHHHHH
Q psy4122          36 WILQKDNMSQDVFLIGKPGSLRRSLAMSYLEL   67 (162)
Q Consensus        36 ~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~   67 (162)
                      +.+..+-.|+.+++.|++|+|||+++..++..
T Consensus        60 D~l~pig~GQr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          60 DSLVPIGRGQRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             HHHSCCBTTCBCEEEESTTSSHHHHHHHHHHH
T ss_pred             ecccCccCCCEEEeecCCCCChHHHHHHHHHh
Confidence            44556667899999999999999999887754

>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=93.22  E-value=0.19  Score=35.18  Aligned_cols=94  Identities=9%  Similarity=0.157  Sum_probs=54.8

Q ss_pred             CCcEEEEcCCCchHHHHHHHHHH---HhCCceEEEEeccCCChh--hhcceeEeecCe----EEEec-cHHHHHh-hcCc
Q psy4122          44 SQDVFLIGKPGSLRRSLAMSYLE---LTQREVEYICLSRDTTEA--DIKQRREIVNGT----AIYYD-QSAVRAA-IEGR  112 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~~lA~---~lg~p~~~v~~~~~~~~~--dL~g~~~~~~G~----~~~~~-gpl~~A~-~~G~  112 (162)
                      |.=-+++||=.+|||+-.-+.++   ..|..+..+.-..|+..+  .+.    ...|.    ..... ..+.... .+-.
T Consensus         7 G~l~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~~~~D~Ry~~~~i~----sh~g~~~~a~~~~~~~~~~~~~~~~~d   82 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVV----SHMGEKEQAVAIKNSREILKYFEEDTE   82 (141)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEE----CTTSCEEECEEESSSTHHHHHCCTTCS
T ss_pred             eeEEEEEeccccHHHHHHHHHHHHhhhcCCcEEEEEeccccccccceee----ecccceEEEEEecchhhhhhhhccccc
Confidence            43347789999999987666553   458887777776665322  222    11221    11111 1122222 3458


Q ss_pred             EEEEeCCCCCCccHHHHHHHhhcCCeEEE
Q psy4122         113 VLILEGIEKAERNVLPVLNNLLENREMHL  141 (162)
Q Consensus       113 vlllDEId~a~~~v~~~L~~lle~r~l~l  141 (162)
                      ++++||+.-++......+..+.+.+.-++
T Consensus        83 vI~IDE~QFf~d~~~~~~~~l~~~g~~Vi  111 (141)
T d1xx6a1          83 VIAIDEVQFFDDEIVEIVNKIAESGRRVI  111 (141)
T ss_dssp             EEEECSGGGSCTHHHHHHHHHHHTTCEEE
T ss_pred             EEEEeehhhccccHHHHHHhheeCCcEEE
Confidence            99999999999888888888877654333

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {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: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.13  E-value=0.04  Score=40.55  Aligned_cols=35  Identities=11%  Similarity=0.101  Sum_probs=23.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      ++|-=...+..++    .|+++++..|+|+|||. |-.+.
T Consensus        24 pt~iQ~~aip~il----~g~dvl~~A~TGsGKTl-a~~lp   58 (207)
T d1t6na_          24 PSEVQHECIPQAI----LGMDVLCQAKSGMGKTA-VFVLA   58 (207)
T ss_dssp             CCHHHHHHHHHHH----TTCCEEEECCTTSCHHH-HHHHH
T ss_pred             CCHHHHHHHHHHH----cCCCeEEEecccccccc-ccccc
Confidence            4444444444444    48999999999999964 44444

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

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 DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.97  E-value=0.053  Score=39.78  Aligned_cols=21  Identities=14%  Similarity=0.096  Sum_probs=17.0

Q ss_pred             CcEEEEcCCCchHHHHHHHHH
Q psy4122          45 QDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La~~lA   65 (162)
                      .++++..|+|+|||......+
T Consensus        43 ~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1          43 YNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             SEEEEECCSSSSHHHHHHHHH
T ss_pred             CCeeeechhcccccceeeccc
Confidence            489999999999998765433

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=92.29  E-value=0.06  Score=44.35  Aligned_cols=47  Identities=13%  Similarity=0.078  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHhcCCC-CcEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          28 QDWLSHLRWILQKDNMS-QDVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g-~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      |..++.|..-+   ..| ++.+|.|-+|+|||.++..+++.+++|...+.-
T Consensus        17 P~aI~~l~~~l---~~g~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~   64 (413)
T d1t5la1          17 PQAIAKLVDGL---RRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAH   64 (413)
T ss_dssp             HHHHHHHHHHH---HHTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECS
T ss_pred             HHHHHHHHHHH---hcCCCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeC
Confidence            44444444333   334 579999999999999999999999999764443

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {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: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.28  E-value=0.062  Score=39.44  Aligned_cols=36  Identities=14%  Similarity=0.012  Sum_probs=23.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          25 ALTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        25 ~~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .++|-=...+..++    .|+++++..|+|+||| +|..+.
T Consensus        25 ~pt~iQ~~aip~il----~g~dvl~~a~TGsGKT-layllP   60 (206)
T d1veca_          25 KPSPIQEESIPIAL----SGRDILARAKNGTGKS-GAYLIP   60 (206)
T ss_dssp             SCCHHHHHHHHHHH----TTCCEEEECCSSSTTH-HHHHHH
T ss_pred             CCCHHHHHHHHHHH----cCCCEEeeccCccccc-cccccc
Confidence            34444444444444    5899999999999997 444444

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

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 VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=92.15  E-value=0.086  Score=39.59  Aligned_cols=30  Identities=20%  Similarity=0.161  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRS   59 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~   59 (162)
                      ++|-=...+..++    .|+++++..|+|+|||.
T Consensus        44 pt~iQ~~~ip~il----~g~dvvi~a~TGsGKTl   73 (238)
T d1wrba1          44 PTPIQKNAIPAIL----EHRDIMACAQTGSGKTA   73 (238)
T ss_dssp             CCHHHHHHHHHHH----TTCCEEEECCTTSSHHH
T ss_pred             CCHHHHHHhhhhh----CCCCEEEECCCCCCcce
Confidence            4554455555555    48999999999999986

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {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: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.82  E-value=0.08  Score=39.09  Aligned_cols=37  Identities=14%  Similarity=0.093  Sum_probs=26.8

Q ss_pred             CCCHHHHHHHHHH------------HHhcCCCCcEEEEcCCCchHHHHH
Q psy4122          25 ALTQDWLSHLRWI------------LQKDNMSQDVFLIGKPGSLRRSLA   61 (162)
Q Consensus        25 ~~~~~~~~~L~~i------------~~~~~~g~~vlL~GppG~GKT~La   61 (162)
                      .+++..++.|+++            +.....|+++++..|+|+|||...
T Consensus        16 ~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~   64 (212)
T d1qdea_          16 ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTF   64 (212)
T ss_dssp             TCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhh
Confidence            3567777777532            334556899999999999998644

>d2akab1 c.37.1.8 (B:6-304) Dynamin G 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: G proteins
domain: Dynamin G domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.68  E-value=0.1  Score=39.73  Aligned_cols=37  Identities=11%  Similarity=0.212  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhcCCCCc-----EEEEcCCCchHHHHHHHHHH
Q psy4122          30 WLSHLRWILQKDNMSQD-----VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~-----vlL~GppG~GKT~La~~lA~   66 (162)
                      .+..|.+.+.++-....     +.++|.-++|||||++++..
T Consensus         7 ~~~~l~d~l~~lg~~~~~~~P~ivvvG~~SsGKSsliNaLlg   48 (299)
T d2akab1           7 LVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVG   48 (299)
T ss_dssp             HHHHHHHHHTTSCCCTTCCCCEEEEEEBTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCCCCCCCeEEEEcCCCCCHHHHHHHHhC
Confidence            45566666666543333     68999999999999999974

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

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: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=91.43  E-value=0.14  Score=38.26  Aligned_cols=32  Identities=13%  Similarity=0.105  Sum_probs=25.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      |-++|.=||||||++-.+|..+   |+.+..+=+.
T Consensus         4 Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~D   38 (269)
T d1cp2a_           4 VAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             EEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEecC
Confidence            5578999999999999888554   7776666555

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {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: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.31  E-value=0.099  Score=38.76  Aligned_cols=23  Identities=13%  Similarity=0.073  Sum_probs=18.0

Q ss_pred             CCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          42 NMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        42 ~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      ..|+++++..|+|+|||... .+.
T Consensus        47 l~g~dvl~~a~TGsGKTlay-llp   69 (218)
T d2g9na1          47 IKGYDVIAQAQSGTGKTATF-AIS   69 (218)
T ss_dssp             HHTCCEEEECCTTSSHHHHH-HHH
T ss_pred             HcCCCEEEEcccchhhhhhh-hhh
Confidence            35889999999999997544 444

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

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: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=91.07  E-value=0.26  Score=40.16  Aligned_cols=46  Identities=13%  Similarity=0.106  Sum_probs=35.9

Q ss_pred             HHHHHHHHhcCCCC-cEEEEcCCCchHHHHHHHHHHHhCCceEEEEe
Q psy4122          32 SHLRWILQKDNMSQ-DVFLIGKPGSLRRSLAMSYLELTQREVEYICL   77 (162)
Q Consensus        32 ~~L~~i~~~~~~g~-~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~   77 (162)
                      +.++.+++.+..|+ .++|.|-+|++|+.++-.+++.+++|+..+.-
T Consensus        15 ~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~   61 (408)
T d1c4oa1          15 KAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAP   61 (408)
T ss_dssp             HHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEEES
T ss_pred             HHHHHHHHHHhcCCCcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeC
Confidence            44555555555554 57999999999999999999999999876543

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=90.89  E-value=0.046  Score=42.80  Aligned_cols=32  Identities=16%  Similarity=0.104  Sum_probs=25.0

Q ss_pred             HhcCCCCcEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          39 QKDNMSQDVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        39 ~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ..+-.|+.+++.|++|+|||+|+..++...+.
T Consensus        62 ~pig~GQr~~Ifg~~g~GKt~l~~~~~~~~~~   93 (276)
T d1fx0a3          62 IPVGRGQRELIIGDRQTGKTAVATDTILNQQG   93 (276)
T ss_dssp             SCCBTTCBCBEEESSSSSHHHHHHHHHHTCCT
T ss_pred             ccccCCceEeeccCCCCChHHHHHHHHhhhcc
Confidence            34456889999999999999999876654433

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.63  E-value=0.079  Score=38.28  Aligned_cols=34  Identities=15%  Similarity=0.161  Sum_probs=24.1

Q ss_pred             CCcEEEE-cCCCchHHHHHHHHHHH---hCCceEEEEe
Q psy4122          44 SQDVFLI-GKPGSLRRSLAMSYLEL---TQREVEYICL   77 (162)
Q Consensus        44 g~~vlL~-GppG~GKT~La~~lA~~---lg~p~~~v~~   77 (162)
                      ++-|-++ +..|||||+++-.+|..   .|.++..+-+
T Consensus         2 ~~vIav~~~kGGvGKTtia~nLA~~la~~g~~VlliD~   39 (237)
T d1g3qa_           2 GRIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVDG   39 (237)
T ss_dssp             CEEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CeEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEeC
Confidence            3445455 77899999999998854   4677655544

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {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: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.49  E-value=0.11  Score=38.82  Aligned_cols=40  Identities=18%  Similarity=0.199  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHHHH------------HHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          25 ALTQDWLSHLRWI------------LQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        25 ~~~~~~~~~L~~i------------~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .+++..++.|+.+            +...+.|++++...|+|+||| +|..+.
T Consensus        23 ~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKT-layllP   74 (222)
T d2j0sa1          23 GLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKT-ATFSIS   74 (222)
T ss_dssp             CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHH-HHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhh-hhhccc
Confidence            3566777766643            234456899999999999997 444444

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.70  E-value=0.11  Score=37.51  Aligned_cols=31  Identities=13%  Similarity=0.130  Sum_probs=22.5

Q ss_pred             EEEcCCCchHHHHHHHHHHHh---CCceEEEEec
Q psy4122          48 FLIGKPGSLRRSLAMSYLELT---QREVEYICLS   78 (162)
Q Consensus        48 lL~GppG~GKT~La~~lA~~l---g~p~~~v~~~   78 (162)
                      +..|..|+|||+++..+|..+   |..+..+=++
T Consensus         6 v~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D   39 (232)
T d1hyqa_           6 VASGKGGTGKTTITANLGVALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            445889999999999988654   6665555443

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

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: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=89.39  E-value=0.26  Score=37.16  Aligned_cols=33  Identities=12%  Similarity=0.147  Sum_probs=24.4

Q ss_pred             EEEEcCCCchHHHHHHHHHHH---hCCceEEEEecc
Q psy4122          47 VFLIGKPGSLRRSLAMSYLEL---TQREVEYICLSR   79 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~---lg~p~~~v~~~~   79 (162)
                      +.+.|.=||||||++-.+|..   .|+.+..+=+.+
T Consensus         5 IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID~Dp   40 (289)
T d2afhe1           5 CAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDP   40 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEECS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEecCC
Confidence            456899999999998888754   477766665543

>d1wxqa1 c.37.1.8 (A:1-319) GTP-binding protein PH0525 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein PH0525
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.77  E-value=0.12  Score=39.95  Aligned_cols=29  Identities=14%  Similarity=0.188  Sum_probs=17.8

Q ss_pred             EEEEcCCCchHHHHHHHHHH----HhCCceEEE
Q psy4122          47 VFLIGKPGSLRRSLAMSYLE----LTQREVEYI   75 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~----~lg~p~~~v   75 (162)
                      |=|+|-|.||||||-+++..    .-++|+.++
T Consensus         3 v~lvG~pn~GKStlfn~lt~~~~~v~nypftT~   35 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATLVDVEIANYPFTTI   35 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC-------------
T ss_pred             EeEECCCCCCHHHHHHHHHCCCCchhcCCCCcc
Confidence            66999999999999999863    335676554

>d1jnya3 c.37.1.8 (A:4-227) Elongation factor eEF-1alpha, N-terminal (G) domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=88.70  E-value=0.13  Score=38.03  Aligned_cols=24  Identities=17%  Similarity=0.181  Sum_probs=20.2

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+.+.|..+.|||||+.++...+|
T Consensus         5 Ni~viGHVd~GKTTL~~~Ll~~~g   28 (224)
T d1jnya3           5 NLIVIGHVDHGKSTLVGRLLMDRG   28 (224)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHB
T ss_pred             EEEEEecCCCCHHHHHHHHHHHcC
Confidence            689999999999999998864443

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {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: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.59  E-value=0.22  Score=36.36  Aligned_cols=31  Identities=23%  Similarity=0.251  Sum_probs=23.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhCCceEEEEec
Q psy4122          47 VFLIGKPGSLRRSLAMSYLELTQREVEYICLS   78 (162)
Q Consensus        47 vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~   78 (162)
                      +|++|+..+|||..|++++.. +.++.++...
T Consensus         2 iLVtGGarSGKS~~AE~l~~~-~~~~~YiAT~   32 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALIGD-APQVLYIATS   32 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECC
T ss_pred             EEEECCCCccHHHHHHHHHhc-CCCcEEEEcc
Confidence            688999999999999999754 4455555543

>d1zunb3 c.37.1.8 (B:16-237) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=88.56  E-value=0.15  Score=38.02  Aligned_cols=25  Identities=12%  Similarity=0.088  Sum_probs=21.7

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      ++..+|...+|||||+.++....|.
T Consensus        11 ~i~viGHVd~GKSTL~~~Ll~~~g~   35 (222)
T d1zunb3          11 RFLTCGNVDDGKSTLIGRLLHDSKM   35 (222)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            4788999999999999999876664

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=88.34  E-value=0.12  Score=37.81  Aligned_cols=23  Identities=17%  Similarity=0.200  Sum_probs=20.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHh
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      |+.++|.+..|||||+.++...+
T Consensus         5 ni~iiGHvd~GKSTL~~~l~~~~   27 (196)
T d1d2ea3           5 NVGTIGHVDHGKTTLTAAITKIL   27 (196)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHH
Confidence            58899999999999999887643

>d1f60a3 c.37.1.8 (A:2-240) Elongation factor eEF-1alpha, N-terminal (G) 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: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.21  E-value=0.2  Score=37.80  Aligned_cols=25  Identities=16%  Similarity=0.134  Sum_probs=21.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhCC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQR   70 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg~   70 (162)
                      |+.++|..+.|||||+.++...+|.
T Consensus         8 Ni~iiGHvD~GKsTl~~~ll~~~g~   32 (239)
T d1f60a3           8 NVVVIGHVDSGKSTTTGHLIYKCGG   32 (239)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHSC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHcCC
Confidence            7899999999999999999866553

>d1r5ba3 c.37.1.8 (A:215-459) Eukaryotic peptide chain release factor ERF2, G domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Eukaryotic peptide chain release factor ERF2, G domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=86.92  E-value=0.18  Score=38.07  Aligned_cols=24  Identities=25%  Similarity=0.340  Sum_probs=20.8

Q ss_pred             cEEEEcCCCchHHHHHHHHHHHhC
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLELTQ   69 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~lg   69 (162)
                      |+.+.|..+.|||||+.++....|
T Consensus        26 Ni~iiGHVD~GKSTL~~~Ll~~~g   49 (245)
T d1r5ba3          26 NIVFIGHVDAGKSTLGGNILFLTG   49 (245)
T ss_dssp             EEEEEECGGGTHHHHHHHHHHHTT
T ss_pred             EEEEEeeCCCCHHHHHHHHHHHcC
Confidence            688999999999999999965554

>d1jwyb_ c.37.1.8 (B:) Dynamin G domain {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: G proteins
domain: Dynamin G domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=86.58  E-value=0.37  Score=36.66  Aligned_cols=36  Identities=11%  Similarity=0.211  Sum_probs=25.1

Q ss_pred             HHHHHHHHHhcCCC---C-cEEEEcCCCchHHHHHHHHHH
Q psy4122          31 LSHLRWILQKDNMS---Q-DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        31 ~~~L~~i~~~~~~g---~-~vlL~GppG~GKT~La~~lA~   66 (162)
                      ...|++.+..+...   - -+.++|..++||||+++++..
T Consensus         7 ~n~l~d~~~~~~~~~~~lP~ivVvG~~ssGKSSliNaLlG   46 (306)
T d1jwyb_           7 INKLQDVFNTLGSDPLDLPQIVVVGSQSSGKSSVLENIVG   46 (306)
T ss_dssp             HHHHHHHTTTSSSCTTCCCEEEEEECSSSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCcCCCCCCeEEEEeCCCCCHHHHHHHHhC
Confidence            44555555543211   1 278999999999999999874

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=86.54  E-value=0.19  Score=38.28  Aligned_cols=21  Identities=19%  Similarity=0.327  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      .++++|-|.||||||++.+..
T Consensus       114 ~v~vvG~PNvGKSsliN~L~~  134 (273)
T d1puja_         114 RALIIGIPNVGKSTLINRLAK  134 (273)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEEecCccchhhhhhhhhc
Confidence            489999999999999998874

>d1kk1a3 c.37.1.8 (A:6-200) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Archaeon 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: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=86.50  E-value=0.18  Score=35.98  Aligned_cols=21  Identities=10%  Similarity=0.210  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      |+-+.|.+..|||||+.++..
T Consensus         7 nIaiiGhvd~GKSTL~~~L~g   27 (195)
T d1kk1a3           7 NIGMVGHVDHGKTTLTKALTG   27 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEEeccCCcHHHHHHHHHh
Confidence            678999999999999999863

>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=86.12  E-value=0.3  Score=37.47  Aligned_cols=37  Identities=8%  Similarity=-0.222  Sum_probs=25.7

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          26 LTQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        26 ~~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +-+-=.+.+..+++    .++.++.-|+|+|||-++..++.
T Consensus       114 ~rdyQ~~av~~~l~----~~~~il~~pTGsGKT~i~~~i~~  150 (282)
T d1rifa_         114 PHWYQKDAVFEGLV----NRRRILNLPTSAGRSLIQALLAR  150 (282)
T ss_dssp             CCHHHHHHHHHHHH----HSEEEECCCTTSCHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHh----cCCceeEEEcccCccHHHHHHHH
Confidence            33444445555554    35789999999999988877764

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=85.60  E-value=0.23  Score=35.83  Aligned_cols=21  Identities=10%  Similarity=0.181  Sum_probs=18.9

Q ss_pred             cEEEEcCCCchHHHHHHHHHH
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~   66 (162)
                      |+.++|....|||||+.++..
T Consensus        10 ni~iiGhVd~GKSTL~~~L~~   30 (205)
T d2qn6a3          10 NIGVVGHVDHGKTTLVQAITG   30 (205)
T ss_dssp             EEEEECSTTSSHHHHHHHHHS
T ss_pred             EEEEEEccCCcHHHHHHHHHh
Confidence            588999999999999999864

>d1vcha1 c.61.1.1 (A:2-175) Putative phosphoribosyltransferase TTHA1613 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PRTase-like
superfamily: PRTase-like
family: Phosphoribosyltransferases (PRTases)
domain: Putative phosphoribosyltransferase TTHA1613
species: Thermus thermophilus [TaxId: 274]

Probab=85.52  E-value=3.4  Score=28.87  Aligned_cols=110  Identities=12%  Similarity=0.080  Sum_probs=65.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHHHhCCceEEEEeccCC-Chhhhcc-eeEe--ecCeEEEecc
Q psy4122          27 TQDWLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLELTQREVEYICLSRDT-TEADIKQ-RREI--VNGTAIYYDQ  102 (162)
Q Consensus        27 ~~~~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~~lg~p~~~v~~~~~~-~~~dL~g-~~~~--~~G~~~~~~g  102 (162)
                      .|...+.+-..+......++=.++|++= |-=-+|..+|..+|.|+..+.-.... ....+.. ....  ..+...+.+.
T Consensus        33 dp~~~~~~~~~la~~~~~~~D~Ivgi~~-~Gi~~A~~lA~~L~~p~~~~rk~~k~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (174)
T d1vcha1          33 DPEFTRAAAEALRPLVPKEAEILFTTET-SPIPLTHVLAEALGLPYVVARRRRRPYMEDPIIQEVQTLTLGVGEVLWLDR  111 (174)
T ss_dssp             CHHHHHHHHHHHGGGSCTTCCEEEEESS-THHHHHHHHHHHHTCCEEEEBSSCCTTCCSCEEEECCC------CEEEECH
T ss_pred             CHHHHHHHHHHHHHHcCCCCCEEEecCC-CcchHhHHHHHHcCCCEEEEEEeccCCCCCCeEEEEEEEEeccceeEEEee
Confidence            6888888888877666555557778874 45578999999999998655333221 1111221 1111  2234444444


Q ss_pred             HHHHHhhcCcEEEEeCCCCCCccHHHHHHHhhcCC
Q psy4122         103 SAVRAAIEGRVLILEGIEKAERNVLPVLNNLLENR  137 (162)
Q Consensus       103 pl~~A~~~G~vlllDEId~a~~~v~~~L~~lle~r  137 (162)
                      ....-.+...++++|++=.-...+.++..-+-+.|
T Consensus       112 ~~~~~~~g~rVlIVDDvi~TG~Tl~a~~~~l~~~G  146 (174)
T d1vcha1         112 RFAEKLLNQRVVLVSDVVASGETMRAMEKMVLRAG  146 (174)
T ss_dssp             HHHHHHTTCEEEEEEEEESSSHHHHHHHHHHHHTT
T ss_pred             ccccccCCCEEEEEeceecccHHHHHHHHHHHHCC
Confidence            43333344579999999776666666555555544

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.32  E-value=0.24  Score=38.64  Aligned_cols=29  Identities=14%  Similarity=0.145  Sum_probs=21.3

Q ss_pred             HHHHHHHhcCCCCc--EEEEcCCCchHHHHH
Q psy4122          33 HLRWILQKDNMSQD--VFLIGKPGSLRRSLA   61 (162)
Q Consensus        33 ~L~~i~~~~~~g~~--vlL~GppG~GKT~La   61 (162)
                      ..+.++.+...|.+  ++-+|++|+|||+..
T Consensus        63 ~~~~lv~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          63 CAKKIVKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HTHHHHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHHHcCCCcceeeecccCCCCceec
Confidence            34456666566664  677899999999976

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal 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: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.95  E-value=0.32  Score=33.51  Aligned_cols=26  Identities=15%  Similarity=0.114  Sum_probs=21.6

Q ss_pred             CCCcEEEEcCCCchHHHHHHHHHHHh
Q psy4122          43 MSQDVFLIGKPGSLRRSLAMSYLELT   68 (162)
Q Consensus        43 ~g~~vlL~GppG~GKT~La~~lA~~l   68 (162)
                      .|--++|.|-.|+||++||+++...+
T Consensus         5 qgf~i~~tg~~~~gk~~ia~al~~~l   30 (122)
T d1g8fa3           5 QGFSIVLGNSLTVSREQLSIALLSTF   30 (122)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHH
T ss_pred             cceEEEEeCCCCCCHHHHHHHHHHHH
Confidence            34578999999999999999986544

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), 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: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.93  E-value=0.11  Score=40.31  Aligned_cols=37  Identities=19%  Similarity=0.069  Sum_probs=27.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCc---EEEEcCCCchHHHHHHHHHH
Q psy4122          24 DALTQDWLSHLRWILQKDNMSQD---VFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        24 ~~~~~~~~~~L~~i~~~~~~g~~---vlL~GppG~GKT~La~~lA~   66 (162)
                      ..++++.++.|+.+      .+|   |-++||.++|||+|...++.
T Consensus        15 l~~~~e~l~~l~~~------~~~v~vvsi~G~~~sGKS~llN~l~~   54 (277)
T d1f5na2          15 LMANPEALKILSAI------TQPMVVVAIVGLYRTGKSYLMNKLAG   54 (277)
T ss_dssp             EEECHHHHHHHHTC------CSBEEEEEEEEBTTSSHHHHHHHHTT
T ss_pred             EEECHHHHHHHHcC------CCCEEEEEEECCCCCCHHHHHHHHcC
Confidence            35688888766554      224   56679999999999998874

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=84.77  E-value=0.32  Score=38.39  Aligned_cols=30  Identities=13%  Similarity=0.120  Sum_probs=22.9

Q ss_pred             HHHHHHHHhcCCCCc--EEEEcCCCchHHHHH
Q psy4122          32 SHLRWILQKDNMSQD--VFLIGKPGSLRRSLA   61 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~--vlL~GppG~GKT~La   61 (162)
                      +..+.++.+...|.+  ++-+|.+|+|||+..
T Consensus        66 ~~~~plv~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          66 FSIKPTVDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHTHHHHHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHHhhccCceeEEecccCCCCcceee
Confidence            345777777777776  666799999999764

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=84.67  E-value=0.49  Score=40.91  Aligned_cols=34  Identities=18%  Similarity=0.252  Sum_probs=25.1

Q ss_pred             HHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          32 SHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      ...+.|.... ..+.|++.|..|+|||+-++.+-+
T Consensus        75 ~Ay~~l~~~~-~~QsIiisGeSGsGKTe~~k~il~  108 (684)
T d1lkxa_          75 DAYRSMRQSQ-ENQCVIISGESGAGKTEASKKIMQ  108 (684)
T ss_dssp             HHHHHHHHHC-CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCeEEEEEcCCCCCHHHHHHHHHH
Confidence            4455555543 345899999999999999987654

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {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: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=84.03  E-value=0.54  Score=40.92  Aligned_cols=36  Identities=14%  Similarity=0.214  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +.+..+.|+... ..+.+++.|..|+|||.-++.+-+
T Consensus       112 A~~Ay~~m~~~~-~nQsIiisGeSGaGKTe~~k~il~  147 (712)
T d1d0xa2         112 SDVAYRSMLDDR-QNQSLLITGESGAGKTENTKKVIQ  147 (712)
T ss_dssp             HHHHHHHHHHHT-CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCceEEEeCCCCCCHHHHHHHHHH
Confidence            334555666543 346899999999999998886643

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal 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: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=83.95  E-value=0.24  Score=37.66  Aligned_cols=31  Identities=13%  Similarity=0.075  Sum_probs=22.1

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH----hCCceEEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL----TQREVEYIC   76 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~----lg~p~~~v~   76 (162)
                      .+=|+|-|.+|||||-.++...    -++|+.++.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~~~~~~~ypf~ti~   38 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKAGIEAANYPFCTIE   38 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTC------CCCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHCCCCccccCCCCCCC
Confidence            4679999999999999988843    356665443

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=83.56  E-value=0.28  Score=37.63  Aligned_cols=30  Identities=10%  Similarity=0.104  Sum_probs=23.4

Q ss_pred             cEEEEcCCCchHHHHHHHHHHH-----hCCceEEE
Q psy4122          46 DVFLIGKPGSLRRSLAMSYLEL-----TQREVEYI   75 (162)
Q Consensus        46 ~vlL~GppG~GKT~La~~lA~~-----lg~p~~~v   75 (162)
                      -+=|+|-|.||||||-.++...     -++|+.++
T Consensus        12 kiGivG~Pn~GKSTlfnalT~~~~~~~anypftTi   46 (296)
T d1ni3a1          12 KTGIVGMPNVGKSTFFRAITKSVLGNPANYPYATI   46 (296)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHSTTTSTTCCSSCCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCCCCcCCCCccCc
Confidence            3789999999999999998743     35676543

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=83.44  E-value=0.56  Score=36.71  Aligned_cols=34  Identities=18%  Similarity=0.222  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHhcCCCCc--EEEEcCCCchHHHHH
Q psy4122          28 QDWLSHLRWILQKDNMSQD--VFLIGKPGSLRRSLA   61 (162)
Q Consensus        28 ~~~~~~L~~i~~~~~~g~~--vlL~GppG~GKT~La   61 (162)
                      ...-+.+..++.....|.+  ++-+|.+|+|||+..
T Consensus        65 ~~vy~~v~~~v~~~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          65 VDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             HHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHHHhhhhhcchhcccccceeeeeccCCcccccc
Confidence            4455566677787777775  556799999999865

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=83.11  E-value=0.62  Score=40.39  Aligned_cols=35  Identities=17%  Similarity=0.250  Sum_probs=25.3

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      .+..+.|.... ..+.|++.|..|+|||+-++.+-+
T Consensus        79 ~~Ay~~m~~~~-~~Q~IiisGeSGaGKTe~~k~il~  113 (710)
T d1br2a2          79 DTAYRSMLQDR-EDQSILCTGESGAGKTENTKKVIQ  113 (710)
T ss_dssp             HHHHHHHHHHT-CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCcEEEEEeCCCCCHHHHHHHHHH
Confidence            34455555543 346899999999999998886653

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=82.98  E-value=0.64  Score=40.38  Aligned_cols=36  Identities=11%  Similarity=0.155  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +.+..+.|.... ..+.+++.|..|+|||.-++.+-+
T Consensus        81 A~~Ay~~l~~~~-~~Q~IiisGeSGsGKTe~~k~il~  116 (730)
T d1w7ja2          81 AEEAYKQMARDE-RNQSIIVSGESGAGKTVSAKYAMR  116 (730)
T ss_dssp             HHHHHHHHHHHT-CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCeEEEEEeCCCCCHHHHHHHHHH
Confidence            344455555543 456899999999999998886654

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=82.74  E-value=0.4  Score=37.61  Aligned_cols=30  Identities=23%  Similarity=0.248  Sum_probs=22.1

Q ss_pred             HHHHHHHHhcCCCCc--EEEEcCCCchHHHHH
Q psy4122          32 SHLRWILQKDNMSQD--VFLIGKPGSLRRSLA   61 (162)
Q Consensus        32 ~~L~~i~~~~~~g~~--vlL~GppG~GKT~La   61 (162)
                      +..+.++.....|.+  ++-+|.+|+|||+..
T Consensus        67 ~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          67 SVVCPILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHHHhHHHHhccCCceEEeeeeccccceEEe
Confidence            445667777777775  567799999999653

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=82.62  E-value=0.65  Score=40.84  Aligned_cols=34  Identities=12%  Similarity=0.276  Sum_probs=24.3

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHH
Q psy4122          31 LSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYL   65 (162)
Q Consensus        31 ~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA   65 (162)
                      .+..+.|.... ..+.+++.|..|+|||.-++.+-
T Consensus       111 ~~Ay~~m~~~~-~~QsIiisGeSGaGKTe~~K~il  144 (794)
T d2mysa2         111 DNAYQFMLTDR-ENQSILITGESGAGKTVNTKRVI  144 (794)
T ss_dssp             HHHHHHHHHHT-CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcC-CCcEEEEEcCCCCCHHHHHHHHH
Confidence            34456666543 34689999999999997777443

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=82.15  E-value=0.59  Score=41.08  Aligned_cols=36  Identities=8%  Similarity=0.108  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEcCCCchHHHHHHHHHH
Q psy4122          30 WLSHLRWILQKDNMSQDVFLIGKPGSLRRSLAMSYLE   66 (162)
Q Consensus        30 ~~~~L~~i~~~~~~g~~vlL~GppG~GKT~La~~lA~   66 (162)
                      +.+..+.|.... ..+.+++.|..|+|||.-++.+-+
T Consensus       108 A~~Ay~~m~~~~-~nQ~IiisGESGaGKTe~~K~il~  143 (789)
T d1kk8a2         108 ADNAYQNMVTDR-ENQSCLITGESGAGKTENTKKVIM  143 (789)
T ss_dssp             HHHHHHHHHHHT-SEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcEEEEEeCCCCCHHHHHHHHHH
Confidence            445666666543 346899999999999998775543

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=81.59  E-value=0.32  Score=38.65  Aligned_cols=19  Identities=16%  Similarity=0.330  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCchHHHHHH
Q psy4122          44 SQDVFLIGKPGSLRRSLAM   62 (162)
Q Consensus        44 g~~vlL~GppG~GKT~La~   62 (162)
                      |...++.|..|||||||..
T Consensus        14 ~~valffGLSGTGKTTLs~   32 (318)
T d1j3ba1          14 GDVAVFFGLSGTGKTTLST   32 (318)
T ss_dssp             CCEEEEEECTTSCHHHHTC
T ss_pred             CCEEEEEccCCCCcccccc
Confidence            4567999999999999763

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), 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: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.46  E-value=0.49  Score=37.14  Aligned_cols=24  Identities=17%  Similarity=0.225  Sum_probs=19.1

Q ss_pred             CcEEEEcCCCchHHHHH-HHHHHHh
Q psy4122          45 QDVFLIGKPGSLRRSLA-MSYLELT   68 (162)
Q Consensus        45 ~~vlL~GppG~GKT~La-~~lA~~l   68 (162)
                      .++|+.+.+|||||+.+ ..++.++
T Consensus        17 g~~lv~A~AGsGKT~~l~~r~~~ll   41 (485)
T d1w36b1          17 GERLIEASAGTGKTFTIAALYLRLL   41 (485)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEcCchHHHHHHHHHHHHHH
Confidence            37899999999999764 4566665