Citrus Sinensis ID: 048347

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-
Protein Sequence
MTAESMIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIYPIGI
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEccccHHHHHHHHHcccccccEEEEEcccccHHHHHHHHHcccccccccccEEEEEEEcccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHccccEEEEEEEccccccHHHHHHccccccccccEEEEEccHHHHHHccccccccEEEEccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHcccEEEEEcccccccccccccccccccccEEEEccccccccEEEEcccccccccEEEEcccccccEEEEEccccccccEEEEccccccccccccccccccccEEEcccccHHHHHHHHccccccEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEccccEEcccccHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHccHHHHccEcEEEEEEEcccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHccccccccccEEEEEEccHHHHHHHcccccccEEEEEccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHccHHHHHcHHHHcccccHHHHcccccHHHEEcHcccccHccHEEEccccccccccHHHHHHHHHHHHHccccccccEEEEcccHHHcccccHHHHHHHccEEEEccccHHHHHHccccccccEEEEEEEcccc
Coil and Loop (DISEMBL)
MTAESMidnfrglswdnkvdLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEalpdhqngsRILTALIHIVGlsscrlendekirldlvppkgklRARQLYQLWIAEafipdncesTAEEYLKELIDRGFIQvnkkdleleddpmpapeklphlkVLKLKrssysgrklvcghggfprqEILHLKSMLWLEEWKMETGAMQKLKslivnpcaylrKFPEELWRIKALRKLeswwprpelrqslhkfeeidrldmqiypigi
Flexible Loop (DISEMBL)
mtaesmidnfrglswdnkvDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSscrlendekirldlvppkgkLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLeleddpmpapeklphlkvlKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRkleswwprpelrqslhkfeeidrldmqiypigi
Low Complexity Region (SEG)
MTAESMIDNFRGLSWDNKVdldledkmeelldllieRQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIYPIGI
Disordered region (IsUnstruct)
********NFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNK******************LKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIY****
Disordered Region (DISOPRED)
********NFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKS****************MKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPEL**********DRLDMQIYPIGI
Disordered Region (DISEMBL)
MTAESMIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIYPIGI
Disordered Region (DISPRO)
*****MIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIYPIGI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTAESMIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIYPIGI
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	351	2.2.26 [Sep-21-2011]
Q9FJB5	901	Disease resistance RPP8-l	yes	no	0.247	0.096	0.413	4e-15
Q8W4J9	908	Disease resistance protei	no	no	0.247	0.095	0.391	7e-14
P0DI18	1049	Probable disease resistan	no	no	0.222	0.074	0.444	5e-13
P0DI17	1049	Probable disease resistan	no	no	0.222	0.074	0.444	5e-13
Q9FJK8	908	Probable disease resistan	no	no	0.247	0.095	0.391	8e-13
P0C8S1	906	Probable disease resistan	no	no	0.245	0.094	0.380	1e-12
Q9XIF0	906	Putative disease resistan	no	no	0.242	0.093	0.428	4e-12
Q8W474	907	Probable disease resistan	no	no	0.242	0.093	0.431	5e-12
P59584	910	Disease resistance protei	no	no	0.247	0.095	0.369	8e-12
P0DI16	1017	Probable disease resistan	no	no	0.276	0.095	0.39	3e-11

>sp|Q9FJB5|RP8L3_ARATH Disease resistance RPP8-like protein 3 OS=Arabidopsis thaliana GN=RPP8L3 PE=2 SV=1

 Score = 82.4 bits (202), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/92 (41%), Positives = 61/92 (66%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           +E+DPMP  EKL HLK ++L+R ++ GR++VC  GGFP+   L +     LEEW +E G+
Sbjct: 773 MEEDPMPILEKLLHLKSVELRRKAFIGRRMVCSKGGFPQLRALQISEQSELEEWIVEEGS 832

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLE 321
           M  L+ LI++ C  L + P+ L  + +L++L+
Sbjct: 833 MPCLRDLIIHSCEKLEELPDGLKYVTSLKELK 864

Disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8W4J9|RPP8_ARATH Disease resistance protein RPP8 OS=Arabidopsis thaliana GN=RPP8 PE=1 SV=2

 Score = 78.6 bits (192), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 61/92 (66%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           +E+DPMP  EKL HLK ++L R ++ G ++VC  GGFP+  ++ +     LEEW +E G+
Sbjct: 782 MEEDPMPILEKLLHLKSVRLARKAFLGSRMVCSKGGFPQLCVIEISKESELEEWIVEEGS 841

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLE 321
           M  L++L ++ C  L++ P+ L  I +L++L+
Sbjct: 842 MPCLRTLTIDDCKKLKELPDGLKYITSLKELK 873

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. The interaction with TIP (TCV-interacting protein) may be essential for the recognition of the avirulence proteins, and the triggering of the defense response.

Arabidopsis thaliana (taxid: 3702)

>sp|P0DI18|DRL45_ARATH Probable disease resistance protein RDL6 OS=Arabidopsis thaliana GN=RDL6 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 36/81 (44%), Positives = 55/81 (67%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           LE+DPMP  EKL  LK L+L+R S+SG+++VC  GGFP+ + L +K +   E+WK+E  +
Sbjct: 789 LEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESS 848

Query: 290 MQKLKSLIVNPCAYLRKFPEE 310
           M  L +L +  C  L++ P+E
Sbjct: 849 MPVLHTLDIRDCRKLKQLPDE 869

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P0DI17|DRL11_ARATH Probable disease resistance protein RF9 OS=Arabidopsis thaliana GN=RF9 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 36/81 (44%), Positives = 55/81 (67%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           LE+DPMP  EKL  LK L+L+R S+SG+++VC  GGFP+ + L +K +   E+WK+E  +
Sbjct: 789 LEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESS 848

Query: 290 MQKLKSLIVNPCAYLRKFPEE 310
           M  L +L +  C  L++ P+E
Sbjct: 849 MPVLHTLDIRDCRKLKQLPDE 869

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJK8|RP8L4_ARATH Probable disease resistance RPP8-like protein 4 OS=Arabidopsis thaliana GN=RPP8L4 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 59/92 (64%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           +++DPMP  EKL HLK + L   ++ GR++VC  GGFP+   L +     LEEW +E G+
Sbjct: 782 MKEDPMPILEKLLHLKSVALSYGAFIGRRVVCSKGGFPQLCALGISGESELEEWIVEEGS 841

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLE 321
           M  L++L ++ C  L++ P+ L  I +L++L+
Sbjct: 842 MPCLRTLTIHDCEKLKELPDGLKYITSLKELK 873

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8S1|RP8L2_ARATH Probable disease resistance RPP8-like protein 2 OS=Arabidopsis thaliana GN=RPP8L2 PE=1 SV=1

 Score = 74.7 bits (182), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 58/92 (63%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           +E+DPMP  EKL HLK + L   ++ GR++VC  GGFP+   L +     L EW++E G+
Sbjct: 780 MEEDPMPILEKLLHLKSVYLSSGAFLGRRMVCSKGGFPQLLALKMSYKKELVEWRVEEGS 839

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLE 321
           M  L++L ++ C  L++ P+ L  +  L++L+
Sbjct: 840 MPCLRTLTIDNCKKLKQLPDGLKYVTCLKELK 871

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XIF0|DRL13_ARATH Putative disease resistance protein At1g59780 OS=Arabidopsis thaliana GN=At1g59780 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 39/91 (42%), Positives = 57/91 (62%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           LE+DPMP  EKL  LKV+ L  ++Y GR++VC  GGFP    L +  +  LEEW +E G+
Sbjct: 765 LEEDPMPTLEKLLQLKVVSLWYNAYVGRRMVCTGGGFPPLHRLEIWGLDALEEWIVEEGS 824

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKL 320
           M  L +L +  C  L++ P+ L  I +L++L
Sbjct: 825 MPLLHTLHIVDCKKLKEIPDGLRFISSLKEL 855

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W474|DRL7_ARATH Probable disease resistance protein At1g58390 OS=Arabidopsis thaliana GN=At1g58390 PE=2 SV=4

 Score = 72.4 bits (176), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 56/88 (63%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           LE+DPMP  EKL HLK + L + SY GR++VC  GGFP+ + L +  +   EEW +E G+
Sbjct: 783 LEEDPMPILEKLLHLKGVILLKGSYCGRRMVCSGGGFPQLKKLEIVGLNKWEEWLVEEGS 842

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKAL 317
           M  L++L +  C  L++ P+ L  I +L
Sbjct: 843 MPLLETLSILDCEELKEIPDGLRFIYSL 870

Possible disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P59584|RP8HA_ARATH Disease resistance protein RPH8A OS=Arabidopsis thaliana GN=RPH8A PE=3 SV=1

 Score = 71.6 bits (174), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 59/92 (64%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           +E+DPMP  EKL HLK ++L+  ++ GR++VC   GF +   L +     LE+W +E G+
Sbjct: 784 MEEDPMPILEKLHHLKSVQLRYKAFVGRRMVCSKDGFTQLCALDISKQSELEDWIVEEGS 843

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLE 321
           M  L++L ++ C  L++ P+ L  I +L++L+
Sbjct: 844 MPCLRTLTIHDCEKLKELPDGLKYITSLKELK 875

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to RPP8, it does not specifically recognize the Emco5 avirulence protein from Hyaloperonospora parasitica.

Arabidopsis thaliana (taxid: 3702)

>sp|P0DI16|DRL44_ARATH Probable disease resistance protein RDL5 OS=Arabidopsis thaliana GN=RDL5 PE=1 SV=1

 Score = 69.7 bits (169), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 59/100 (59%), Gaps = 3/100 (3%)

Query: 230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
           LE DP+P   +L +LK L+L   ++SGR +VC  GGFP+ + L +  +   EEW +E G+
Sbjct: 877 LEKDPLPTLGRLVYLKELQLGFRTFSGRIMVCSGGGFPQLQKLSIYRLEEWEEWIVEQGS 936

Query: 290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKL---ESWWPR 326
           M  L +L ++ C  L+K P+ L  I +L+ L   E W  R
Sbjct: 937 MPFLHTLYIDDCPKLKKLPDGLQFIYSLKNLKISERWKER 976

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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	351
255582949	514	conserved hypothetical protein [Ricinus	0.811	0.554	0.255	2e-18
297744817	543	unnamed protein product [Vitis vinifera]	0.857	0.554	0.260	5e-18
297745275	1136	unnamed protein product [Vitis vinifera]	0.361	0.111	0.340	2e-14
115486357	528	Os11g0633500 [Oryza sativa Japonica Grou	0.378	0.251	0.326	2e-14
125555508	773	hypothetical protein OsI_23143 [Oryza sa	0.378	0.172	0.326	3e-14
125576117	773	hypothetical protein OsJ_32864 [Oryza sa	0.378	0.172	0.326	3e-14
224064832	920	cc-nbs-lrr resistance protein [Populus t	0.376	0.143	0.312	3e-14
359480122	934	PREDICTED: disease resistance protein RP	0.396	0.148	0.333	5e-14
255566474	942	Disease resistance protein RPP8, putativ	0.367	0.136	0.355	8e-14
225454212	936	PREDICTED: putative disease resistance p	0.253	0.095	0.489	9e-14

>gi|255582949|ref|XP_002532245.1| conserved hypothetical protein [Ricinus communis] gi|223528063|gb|EEF30139.1| conserved hypothetical protein [Ricinus communis]

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/305 (25%), Positives = 136/305 (44%), Gaps = 20/305 (6%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ 80
           + +E    EL   L+E   +++ ++++   G  +T    + Y+S  V  +FDC AW+   
Sbjct: 166 VGIESPKSELTSRLVEGASEIAAISLVGMGGLGKTTLAKKVYDSKIVTAHFDCKAWITVS 225

Query: 81  LS------LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG 134
            S      L  M+  + +  M L A    + N+  +    L  YLK KRY+++  DVW  
Sbjct: 226 QSYKEEELLRTMIRKLQRENM-LPAFGINMINELSLIPE-LREYLKEKRYMVIFDDVWGI 283

Query: 135 DIWDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIRLDLVPPKGKLRARQLYQLW 194
           D W+++  ALPD+     +    +        R            P + +  +  + +  
Sbjct: 284 DFWEYIMTALPDNDFNLCLKEKPMSSSAKKVFRSNGGN------CPSQLEQLSHAIEKKC 337

Query: 195 IAEAFIPDN----CESTAEEYLKELIDRGFIQVNKKDLELEDDPMPAPEKLPHLKVLKLK 250
            AE FI        E  AEEY  EL++R  +QV K  +   +D M   + LP+L+ L+  
Sbjct: 338 EAEGFIKKTYGRIAEEVAEEYFNELVNRSLVQVEKFSVH-GNDAMQVLQALPNLQELRF- 395

Query: 251 RSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEE 310
              Y+G +L      F    IL+L  +  L +  +E GA+  ++ LI+  C  L++ P  
Sbjct: 396 YEGYNGEQLHFRKRCFSVLRILYLHILTQLNKLIIEKGALPAIEELIIGGCPELKELPTG 455

Query: 311 LWRIK 315
           +  I+
Sbjct: 456 MASIR 460

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744817|emb|CBI38085.3| unnamed protein product [Vitis vinifera]

 Score = 98.2 bits (243), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 93/357 (26%), Positives = 156/357 (43%), Gaps = 56/357 (15%)

Query: 34  LIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY----YQLSLDMMLDA 89
           L+  + + ++V+I+   G  +T    + YN + V+  FDC AW+Y    Y +   ++  A
Sbjct: 170 LLNGEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVRQCFDCHAWIYVSQEYTIRELLLGVA 229

Query: 90  IMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQN 149
           +   ++     S++ ++D     N+L +YL  ++YLIV+ D+WR + WD L    PD  N
Sbjct: 230 VCVRILSEEERSKMNESDL---GNSLRDYLTTRKYLIVMDDMWRNEAWDRLGLYFPDSVN 286

Query: 150 GSRIL-TALIHIVGL---------------------------------SSCR-------- 167
           GSR+L T+    +GL                                 ++CR        
Sbjct: 287 GSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANACRNGPLSVGH 346

Query: 168 LENDEKIRLDL---VPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVN 224
           L N + + L        +G  +  +L +L IA   I         E +K+L     + + 
Sbjct: 347 LTNLQSLGLRAGSWCCGEGLGKLIELRELTIAWTEIAQTKNQGFSESVKKLTALQSLCLY 406

Query: 225 KKDLELEDDPMPAPEKLPHL----KVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWL 280
            +  E  +   P     PHL    K L+L   S   +K+VC  GGF + E L L ++  L
Sbjct: 407 PRIGENFNHAAPHAFLRPHLPLPSKFLRLFHCSSMLKKMVCTSGGFQQLETLKLWNLKEL 466

Query: 281 EEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFE 337
           +E   E GAM  LK L+++ C  +++    L + K L+ L  +   PEL   L + E
Sbjct: 467 KELIAEEGAMPDLKDLVIDTCPKMKRLSHGLLQRKNLQNLSLYDLSPELMDELSRIE 523

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745275|emb|CBI40355.3| unnamed protein product [Vitis vinifera]

 Score = 86.7 bits (213), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 48/141 (34%), Positives = 82/141 (58%), Gaps = 14/141 (9%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ 80
           + +ED +EE+  +L++ + + S+V+I+   G  +T F  + YN   V+ +FDC AWVY  
Sbjct: 169 VGIEDGIEEVKQMLMKEETRRSVVSIVGMGGLGKTTFAKKVYNQRDVQQHFDCKAWVYVS 228

Query: 81  LSL---DMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH----NYLKNKRYLIVIQDVWR 133
                 +++LD I    M LS      + + EM+++ L      YLK K+YLIV+ DVW 
Sbjct: 229 QEFRAREILLD-IANHFMSLS------EKEKEMRESELGEKLCEYLKEKKYLIVMDDVWS 281

Query: 134 GDIWDFLKEALPDHQNGSRIL 154
            ++W  L+  LP+ ++GS++L
Sbjct: 282 SEVWSRLRSHLPEAKDGSKVL 302

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115486357|ref|NP_001068322.1| Os11g0633500 [Oryza sativa Japonica Group] gi|108864604|gb|ABA94849.2| NB-ARC domain containing protein, expressed [Oryza sativa Japonica Group] gi|108864605|gb|ABG22560.1| NB-ARC domain containing protein, expressed [Oryza sativa Japonica Group] gi|113645544|dbj|BAF28685.1| Os11g0633500 [Oryza sativa Japonica Group] gi|215694679|dbj|BAG89870.1| unnamed protein product [Oryza sativa Japonica Group]

 Score = 86.7 bits (213), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 83/141 (58%), Gaps = 8/141 (5%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ 80
           +  +++  E+++ L+E++ +LS+V+I+   G  +T    + YNS+ ++N+FD  AWV   
Sbjct: 170 VGFDNEYNEIVEKLVEQENELSVVSIVAMGGAGKTTLARKIYNSTRIRNHFDTTAWVTVS 229

Query: 81  L---SLDMMLDAIMKSLMPLSALSEILDNDFEMK-KNTLHNYLKNKRYLIVIQDVWRGDI 136
                +D++ D IM+ +MP    S  +D   E++    +H +L NKRY++V+ DVW  D 
Sbjct: 230 QKFKGIDLLKD-IMRQIMPNKLESREIDQMQELEVGKKIHEFLLNKRYVVVLDDVWATDT 288

Query: 137 WDFLK---EALPDHQNGSRIL 154
           W+ +    +  PD  NGSR+L
Sbjct: 289 WNQINRVGKVFPDANNGSRVL 309

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125555508|gb|EAZ01114.1| hypothetical protein OsI_23143 [Oryza sativa Indica Group]

 Score = 85.9 bits (211), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 83/141 (58%), Gaps = 8/141 (5%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ 80
           +  +++  E+++ L+E++ +LS+V+I+   G  +T    + YNS+ ++N+FD  AWV   
Sbjct: 170 VGFDNEYNEIVEKLVEQENELSVVSIVAMGGAGKTTLARKIYNSTRIRNHFDTTAWVTVS 229

Query: 81  L---SLDMMLDAIMKSLMPLSALSEILDNDFEMK-KNTLHNYLKNKRYLIVIQDVWRGDI 136
                +D++ D IM+ +MP    S  +D   E++    +H +L NKRY++V+ DVW  D 
Sbjct: 230 QKFKGIDLLKD-IMRQIMPNKLESREIDQMQELEVGKKIHEFLLNKRYVVVLDDVWATDT 288

Query: 137 WDFLK---EALPDHQNGSRIL 154
           W+ +    +  PD  NGSR+L
Sbjct: 289 WNQINRVGKVFPDANNGSRVL 309

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125576117|gb|EAZ17339.1| hypothetical protein OsJ_32864 [Oryza sativa Japonica Group]

 Score = 85.9 bits (211), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 83/141 (58%), Gaps = 8/141 (5%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ 80
           +  +++  E+++ L+E++ +LS+V+I+   G  +T    + YNS+ ++N+FD  AWV   
Sbjct: 170 VGFDNEYNEIVEKLVEQENELSVVSIVAMGGAGKTTLARKIYNSTRIRNHFDTTAWVTVS 229

Query: 81  L---SLDMMLDAIMKSLMPLSALSEILDNDFEMK-KNTLHNYLKNKRYLIVIQDVWRGDI 136
                +D++ D IM+ +MP    S  +D   E++    +H +L NKRY++V+ DVW  D 
Sbjct: 230 QKFKGIDLLKD-IMRQIMPNKLESREIDQMQELEVGKKIHEFLLNKRYVVVLDDVWATDT 288

Query: 137 WDFLK---EALPDHQNGSRIL 154
           W+ +    +  PD  NGSR+L
Sbjct: 289 WNQINRVGKVFPDANNGSRVL 309

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224064832|ref|XP_002301573.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222843299|gb|EEE80846.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/141 (31%), Positives = 79/141 (56%), Gaps = 9/141 (6%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ 80
           + +E+  E+LL  L+E +P+ ++++I+   G  +T  +   YN+  +K  FDC AW+   
Sbjct: 167 VGMEESTEQLLGWLMEDEPRRTVISIVGMGGLGKTTLVTRVYNNHIIKRGFDCWAWISVS 226

Query: 81  LSLDM--MLDAIMKSLMPLSALSEILDN-----DFEMKKNTLHNYLKNKRYLIVIQDVWR 133
            +     +L +I+K L    A S ++ N     ++      L +YL  KRY+IV+ DVW 
Sbjct: 227 QTCGTGELLRSIIKEL--FGATSVVIPNNVGSMNYRQLVGMLIDYLHQKRYVIVLDDVWS 284

Query: 134 GDIWDFLKEALPDHQNGSRIL 154
            D+W  ++ A P+++ GSRI+
Sbjct: 285 IDLWSIIRTAFPNNRYGSRII 305

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480122|ref|XP_002265617.2| PREDICTED: disease resistance protein RPM1-like [Vitis vinifera] gi|147771833|emb|CAN60254.1| hypothetical protein VITISV_025805 [Vitis vinifera]

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 48/144 (33%), Positives = 77/144 (53%), Gaps = 5/144 (3%)

Query: 29  ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDM--M 86
           EL+  L+E  P+ ++++++   G  +T F  + Y++  V  +FDC AWV    S  M  +
Sbjct: 179 ELISRLVEGNPKRTVISVVGMGGLGKTTFAKKVYDNQRVVGHFDCNAWVTVSQSFKMEEL 238

Query: 87  LDAIMKSLMP--LSALSEILDNDFEMKKNTL-HNYLKNKRYLIVIQDVWRGDIWDFLKEA 143
           L  + K        A+ E +D   EM    L   YL++KRY++V  DVW+ D W F+K  
Sbjct: 239 LRNMTKKFYQGRKEAVPEGIDTIDEMSLIALIRQYLQDKRYVVVFDDVWKLDFWGFIKYV 298

Query: 144 LPDHQNGSRILTALIHIVGLSSCR 167
           LP++  GSRI+    +    SSC+
Sbjct: 299 LPENGKGSRIIITTRNDEVASSCK 322

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255566474|ref|XP_002524222.1| Disease resistance protein RPP8, putative [Ricinus communis] gi|223536499|gb|EEF38146.1| Disease resistance protein RPP8, putative [Ricinus communis]

 Score = 84.3 bits (207), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 48/135 (35%), Positives = 76/135 (56%), Gaps = 6/135 (4%)

Query: 22  DLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYY-- 79
            L+   ++++  L++ + QL +V+I+   G  +T    + YN   VK +FDCC+W +   
Sbjct: 164 SLDSTTKDVMAQLMKEEDQLRVVSIVGMGGLGKTTLAKKVYNYIDVKQHFDCCSWAFISQ 223

Query: 80  QLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDF 139
           Q S   +L  I+  + P +  S I D   E+ + TL N LK KRYL+V+ D+W    WD 
Sbjct: 224 QYSPRDVLLGILMEVSPSAERSMIED---ELVR-TLKNVLKEKRYLLVLDDIWNEQAWDS 279

Query: 140 LKEALPDHQNGSRIL 154
           LK+A P  + GSR+L
Sbjct: 280 LKQAFPKGKKGSRVL 294

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454212|ref|XP_002274233.1| PREDICTED: putative disease resistance protein At1g50180-like [Vitis vinifera]

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 45/92 (48%), Positives = 59/92 (64%)

Query: 229 ELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETG 288
           ELEDDPM   EKLP L++L L R SY G+K+VC  GGF + E L L  +  LEE  +E G
Sbjct: 813 ELEDDPMLILEKLPTLRILGLLRGSYVGKKMVCSCGGFLQLESLELNGLNELEELTVEEG 872

Query: 289 AMQKLKSLIVNPCAYLRKFPEELWRIKALRKL 320
           AM  L++L +  C  ++KFP  L ++K L KL
Sbjct: 873 AMCNLRTLQILSCDKMKKFPHGLLQMKKLEKL 904

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	351
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.336	0.130	0.347	5.2e-29
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.296	0.114	0.365	8.5e-24
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.296	0.114	0.365	8.9e-24
TAIR|locus:504956182	1049	AT1G58848 [Arabidopsis thalian	0.230	0.077	0.444	5.7e-20
TAIR|locus:2826978	1049	AT1G59218 [Arabidopsis thalian	0.230	0.077	0.444	5.7e-20
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.270	0.104	0.410	5.9e-20
TAIR|locus:504956184	1017	AT1G58807 "AT1G58807" [Arabido	0.227	0.078	0.463	1.1e-18
TAIR|locus:2827038	1017	AT1G59124 "AT1G59124" [Arabido	0.227	0.078	0.463	1.1e-18
TAIR|locus:2037623	899	AT1G58410 [Arabidopsis thalian	0.310	0.121	0.403	1.2e-18
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.339	0.131	0.375	7.7e-18

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 209 (78.6 bits), Expect = 5.2e-29, Sum P(3) = 5.2e-29
 Identities = 42/121 (34%), Positives = 74/121 (61%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             +E+DPMP  EKL HLK ++L+R ++ GR++VC  GGFP+   L +     LEEW +E G+
Sbjct:   773 MEEDPMPILEKLLHLKSVELRRKAFIGRRMVCSKGGFPQLRALQISEQSELEEWIVEEGS 832

Query:   290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSL--HKFEEIDRL-DMQI 346
             M  L+ LI++ C  L + P+ L  + +L++L+    + E ++ L    + ++  + D+Q 
Sbjct:   833 MPCLRDLIIHSCEKLEELPDGLKYVTSLKELKIEGMKREWKEKLVGEDYYKVQHIPDVQF 892

Query:   347 Y 347
             +
Sbjct:   893 F 893

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2176486 RPP8 "RECOGNITION OF PERONOSPORA PARASITICA 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 195 (73.7 bits), Expect = 8.5e-24, Sum P(3) = 8.5e-24
 Identities = 38/104 (36%), Positives = 66/104 (63%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             +E+DPMP  EKL HLK ++L R ++ G ++VC  GGFP+  ++ +     LEEW +E G+
Sbjct:   782 MEEDPMPILEKLLHLKSVRLARKAFLGSRMVCSKGGFPQLCVIEISKESELEEWIVEEGS 841

Query:   290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSL 333
             M  L++L ++ C  L++ P+ L  I +L++L+    + E ++ L
Sbjct:   842 MPCLRTLTIDDCKKLKELPDGLKYITSLKELKIEGMKREWKEKL 885

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0051707 "response to other organism" evidence=IMP

TAIR|locus:2152536 AT5G48620 [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 8.9e-24, Sum P(3) = 8.9e-24
 Identities = 38/104 (36%), Positives = 64/104 (61%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             +++DPMP  EKL HLK + L   ++ GR++VC  GGFP+   L +     LEEW +E G+
Sbjct:   782 MKEDPMPILEKLLHLKSVALSYGAFIGRRVVCSKGGFPQLCALGISGESELEEWIVEEGS 841

Query:   290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSL 333
             M  L++L ++ C  L++ P+ L  I +L++L+    + E ++ L
Sbjct:   842 MPCLRTLTIHDCEKLKELPDGLKYITSLKELKIREMKREWKEKL 885

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:504956182 AT1G58848 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 5.7e-20, Sum P(2) = 5.7e-20
 Identities = 36/81 (44%), Positives = 55/81 (67%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             LE+DPMP  EKL  LK L+L+R S+SG+++VC  GGFP+ + L +K +   E+WK+E  +
Sbjct:   789 LEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESS 848

Query:   290 MQKLKSLIVNPCAYLRKFPEE 310
             M  L +L +  C  L++ P+E
Sbjct:   849 MPVLHTLDIRDCRKLKQLPDE 869

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2826978 AT1G59218 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 5.7e-20, Sum P(2) = 5.7e-20
 Identities = 36/81 (44%), Positives = 55/81 (67%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             LE+DPMP  EKL  LK L+L+R S+SG+++VC  GGFP+ + L +K +   E+WK+E  +
Sbjct:   789 LEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESS 848

Query:   290 MQKLKSLIVNPCAYLRKFPEE 310
             M  L +L +  C  L++ P+E
Sbjct:   849 MPVLHTLDIRDCRKLKQLPDE 869

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 5.9e-20, Sum P(3) = 5.9e-20
 Identities = 39/95 (41%), Positives = 58/95 (61%)

Query:   223 VNKKDLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEE 282
             V   +  LE+DPMP  EKL HLK + L + SY GR++VC  GGFP+ + L +  +   EE
Sbjct:   776 VKLSECGLEEDPMPILEKLLHLKGVILLKGSYCGRRMVCSGGGFPQLKKLEIVGLNKWEE 835

Query:   283 WKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL 317
             W +E G+M  L++L +  C  L++ P+ L  I +L
Sbjct:   836 WLVEEGSMPLLETLSILDCEELKEIPDGLRFIYSL 870

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:504956184 AT1G58807 "AT1G58807" [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 1.1e-18, Sum P(2) = 1.1e-18
 Identities = 38/82 (46%), Positives = 54/82 (65%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPR-QEILHLKSMLWLEEWKMETG 288
             LE+DPMP  EKL  LK L+L   S+SG+K+VC  GGFP+ Q +  LK   W E+WK+E  
Sbjct:   781 LEEDPMPILEKLLQLKELELGFESFSGKKMVCSSGGFPQLQRLSLLKLEEW-EDWKVEES 839

Query:   289 AMQKLKSLIVNPCAYLRKFPEE 310
             +M  L++L +  C  L++ P+E
Sbjct:   840 SMPLLRTLDIQVCRKLKQLPDE 861

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2827038 AT1G59124 "AT1G59124" [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 1.1e-18, Sum P(2) = 1.1e-18
 Identities = 38/82 (46%), Positives = 54/82 (65%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPR-QEILHLKSMLWLEEWKMETG 288
             LE+DPMP  EKL  LK L+L   S+SG+K+VC  GGFP+ Q +  LK   W E+WK+E  
Sbjct:   781 LEEDPMPILEKLLQLKELELGFESFSGKKMVCSSGGFPQLQRLSLLKLEEW-EDWKVEES 839

Query:   289 AMQKLKSLIVNPCAYLRKFPEE 310
             +M  L++L +  C  L++ P+E
Sbjct:   840 SMPLLRTLDIQVCRKLKQLPDE 861

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037623 AT1G58410 [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 1.2e-18, Sum P(2) = 1.2e-18
 Identities = 46/114 (40%), Positives = 64/114 (56%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             LE+DPMP  EKL  LK L L   S+SGRK+VC  GGFP+   L L      EEW +E G+
Sbjct:   780 LEEDPMPILEKLLELKDLSLDYLSFSGRKMVCSAGGFPQLRKLALDEQEEWEEWIVEEGS 839

Query:   290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKL---ESWWPR-PELRQSLHKFEEI 339
             M +L +L +     L++ P+ L  I +L+ L   +SW  R  E  +  +K + I
Sbjct:   840 MSRLHTLSIWSST-LKELPDGLRFIYSLKNLIMGKSWMERLSERGEEFYKVQNI 892

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2025916 AT1G59780 "AT1G59780" [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 7.7e-18, Sum P(2) = 7.7e-18
 Identities = 45/120 (37%), Positives = 67/120 (55%)

Query:   230 LEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGA 289
             LE+DPMP  EKL  LKV+ L  ++Y GR++VC  GGFP    L +  +  LEEW +E G+
Sbjct:   765 LEEDPMPTLEKLLQLKVVSLWYNAYVGRRMVCTGGGFPPLHRLEIWGLDALEEWIVEEGS 824

Query:   290 MQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHKFEEIDRLDMQIYPI 349
             M  L +L +  C  L++ P+ L  I +L++L         ++ + K  E D   MQ  P+
Sbjct:   825 MPLLHTLHIVDCKKLKEIPDGLRFISSLKELAIRTNEKVFQKKVSKGGE-DYYKMQHVPL 883

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: 4350972 disease resistance RPP8-like protein 3, putative, expressed (528 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	351
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-15

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 75.4 bits (186), Expect = 2e-15
 Identities = 38/133 (28%), Positives = 63/133 (47%), Gaps = 4/133 (3%)

Query: 24  EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSL 83
           ED +E L++ L+E    L +V I+   G  +T    + YN   V  +FD  AWV   +S 
Sbjct: 2   EDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWV--VVSK 59

Query: 84  DMMLDAIMKSL--MPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLK 141
                 + K +        S+ ++ +       +   L  KR+L+V+ DVW  + WD + 
Sbjct: 60  TYTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKIG 119

Query: 142 EALPDHQNGSRIL 154
              PD +NGSR++
Sbjct: 120 VPFPDGENGSRVI 132

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	351
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.97
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.94
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.96
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.84
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.76
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.75
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.63
cd01128	249	rho_factor Transcription termination factor rho is	98.6
PF05729	166	NACHT: NACHT domain	98.54
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.51
PTZ00202	550	tuzin; Provisional	98.5
PRK09376	416	rho transcription termination factor Rho; Provisio	98.47
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.43
KOG0617	264	consensus Ras suppressor protein (contains leucine	98.43
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.39
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.38
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.33
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.31
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	98.3
KOG0617	264	consensus Ras suppressor protein (contains leucine	98.29
PF13173	128	AAA_14: AAA domain	98.27
TIGR00767	415	rho transcription termination factor Rho. Members	98.25
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	98.24
PRK04841	903	transcriptional regulator MalT; Provisional	98.12
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.11
PRK13342	413	recombination factor protein RarA; Reviewed	98.08
KOG2028	554	consensus ATPase related to the helicase subunit o	98.04
PLN03150	623	hypothetical protein; Provisional	98.02
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.02
PLN03150	623	hypothetical protein; Provisional	98.01
KOG0472	565	consensus Leucine-rich repeat protein [Function un	98.0
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.99
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.97
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.94
PRK12402	337	replication factor C small subunit 2; Reviewed	97.94
PRK04195	482	replication factor C large subunit; Provisional	97.92
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.89
PRK06893	229	DNA replication initiation factor; Validated	97.87
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	97.87
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.87
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.85
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	97.84
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.82
PLN03025	319	replication factor C subunit; Provisional	97.8
PRK13341	725	recombination factor protein RarA/unknown domain f	97.79
PRK15386	426	type III secretion protein GogB; Provisional	97.78
PRK08118	167	topology modulation protein; Reviewed	97.78
PHA02544	316	44 clamp loader, small subunit; Provisional	97.76
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.75
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.72
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.72
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.72
smart00382	148	AAA ATPases associated with a variety of cellular	97.72
KOG0472	565	consensus Leucine-rich repeat protein [Function un	97.71
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.71
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.7
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.7
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.69
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.68
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.67
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.64
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.64
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.61
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	97.61
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.58
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.58
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.56
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.55
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	97.55
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.54
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.53
PRK08116	268	hypothetical protein; Validated	97.53
PRK10536	262	hypothetical protein; Provisional	97.51
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.5
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.5
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.49
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.49
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.49
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.48
PRK07261	171	topology modulation protein; Provisional	97.47
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	97.43
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.43
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.41
CHL00095	821	clpC Clp protease ATP binding subunit	97.41
PRK12608	380	transcription termination factor Rho; Provisional	97.4
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.4
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	97.39
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.38
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.35
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.35
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.34
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.34
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.31
PRK08727	233	hypothetical protein; Validated	97.31
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.3
PRK12377	248	putative replication protein; Provisional	97.29
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.29
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.29
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.27
PRK10865	857	protein disaggregation chaperone; Provisional	97.27
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.26
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.25
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.25
PRK06696	223	uridine kinase; Validated	97.24
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.24
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.24
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.23
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.23
PF00004	132	AAA: ATPase family associated with various cellula	97.23
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.22
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.2
PRK07952	244	DNA replication protein DnaC; Validated	97.2
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.2
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.19
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.18
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.16
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.14
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	97.14
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.12
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	97.11
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.1
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.1
PRK07667	193	uridine kinase; Provisional	97.09
CHL00181	287	cbbX CbbX; Provisional	97.08
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.07
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.06
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.05
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.04
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.04
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.04
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.02
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.02
PRK05541	176	adenylylsulfate kinase; Provisional	97.02
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	97.0
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.0
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.98
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.98
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.98
CHL00176	638	ftsH cell division protein; Validated	96.98
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.97
PRK10865	857	protein disaggregation chaperone; Provisional	96.96
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.95
PHA00729	226	NTP-binding motif containing protein	96.92
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.91
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.91
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.91
CHL00095	821	clpC Clp protease ATP binding subunit	96.9
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.88
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.88
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.87
PTZ00301	210	uridine kinase; Provisional	96.87
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.86
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.85
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.85
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.84
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.84
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.84
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.82
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.81
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.81
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.8
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.79
PRK06526	254	transposase; Provisional	96.78
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.78
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.76
PRK08181	269	transposase; Validated	96.75
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.75
COG3899	849	Predicted ATPase [General function prediction only	96.75
PRK09087	226	hypothetical protein; Validated	96.75
PRK15455	644	PrkA family serine protein kinase; Provisional	96.74
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.74
PRK08084	235	DNA replication initiation factor; Provisional	96.72
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.72
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.7
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.7
PRK08233	182	hypothetical protein; Provisional	96.7
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.69
PRK09183	259	transposase/IS protein; Provisional	96.69
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.68
PRK06620	214	hypothetical protein; Validated	96.67
PRK14974	336	cell division protein FtsY; Provisional	96.67
PRK06835	329	DNA replication protein DnaC; Validated	96.66
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	96.65
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.64
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.61
PRK08939	306	primosomal protein DnaI; Reviewed	96.61
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.6
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.6
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.6
PRK05480	209	uridine/cytidine kinase; Provisional	96.59
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.57
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	96.57
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.57
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.56
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.56
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.55
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.55
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.53
PRK15386	426	type III secretion protein GogB; Provisional	96.53
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.52
PRK05642	234	DNA replication initiation factor; Validated	96.52
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.51
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.51
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.5
PF14516	331	AAA_35: AAA-like domain	96.49
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.46
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.46
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.45
PRK06067	234	flagellar accessory protein FlaH; Validated	96.44
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	96.43
PRK15453	290	phosphoribulokinase; Provisional	96.41
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.4
PRK10867	433	signal recognition particle protein; Provisional	96.4
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.4
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.38
PRK09354	349	recA recombinase A; Provisional	96.38
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.38
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.37
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.36
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.35
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.35
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.35
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.34
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.32
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.3
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.3
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.27
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	96.27
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.26
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.26
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.24
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	96.24
PRK12422	445	chromosomal replication initiation protein; Provis	96.24
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	96.23
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.22
PRK06547	172	hypothetical protein; Provisional	96.22
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.2
PRK06762	166	hypothetical protein; Provisional	96.2
PRK06921	266	hypothetical protein; Provisional	96.2
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.18
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	96.18
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.17
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.17
TIGR00959	428	ffh signal recognition particle protein. This mode	96.16
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.16
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	96.15
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.15
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.14
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.13
PRK05439	311	pantothenate kinase; Provisional	96.13
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.13
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.12
PRK03839	180	putative kinase; Provisional	96.12
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.1
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.08
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.08
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.08
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.07
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	96.07
PRK13531	498	regulatory ATPase RavA; Provisional	96.07
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.06
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.04
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.04
PRK14738	206	gmk guanylate kinase; Provisional	96.03
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.03
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.03
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	96.02
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.01
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	96.01
PRK04296	190	thymidine kinase; Provisional	96.0
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.99
PRK08149	428	ATP synthase SpaL; Validated	95.98
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	95.95
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.95
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	95.95
PRK10416	318	signal recognition particle-docking protein FtsY;	95.95
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.95
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.93
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.9
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.89
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	95.89
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.89
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.88
PLN02318	656	phosphoribulokinase/uridine kinase	95.88
PRK04040	188	adenylate kinase; Provisional	95.88
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.88
KOG1969	877	consensus DNA replication checkpoint protein CHL12	95.87
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.87
PRK00279	215	adk adenylate kinase; Reviewed	95.87
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.83
PRK06217	183	hypothetical protein; Validated	95.83
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	95.82
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	95.82
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.82
cd03246	173	ABCC_Protease_Secretion This family represents the	95.82
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.82
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.81
PRK00625	173	shikimate kinase; Provisional	95.81
PRK11823	446	DNA repair protein RadA; Provisional	95.81
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	95.8
PRK00131	175	aroK shikimate kinase; Reviewed	95.79
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	95.79
PRK13765	637	ATP-dependent protease Lon; Provisional	95.79
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	95.78
PRK04301	317	radA DNA repair and recombination protein RadA; Va	95.78
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	95.77
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.76
PRK00889	175	adenylylsulfate kinase; Provisional	95.76
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	95.75
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.73
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.73
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.73
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.71
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.69
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.68
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.66
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.66
PTZ00035	337	Rad51 protein; Provisional	95.64
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.63
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.63
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.62
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.62
PRK13947	171	shikimate kinase; Provisional	95.61
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	95.6
cd03216	163	ABC_Carb_Monos_I This family represents the domain	95.6
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	95.59
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.59
COG3903	414	Predicted ATPase [General function prediction only	95.59
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	95.55
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	95.55
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	95.55
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.54
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.54
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	95.54
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.54
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.54
PRK00300	205	gmk guanylate kinase; Provisional	95.54
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	95.52
PRK13949	169	shikimate kinase; Provisional	95.49
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	95.49
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.49
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	95.48
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.48
PRK03846	198	adenylylsulfate kinase; Provisional	95.47
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.47
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.47
PRK13975	196	thymidylate kinase; Provisional	95.47
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.47
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	95.46
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.46
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.45
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.45
PLN02348	395	phosphoribulokinase	95.43
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	95.39
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.39
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.37
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	95.34
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.33
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.32
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.31
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.31
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.31
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.3
PRK06936	439	type III secretion system ATPase; Provisional	95.29
COG1100	219	GTPase SAR1 and related small G proteins [General	95.28
PRK05057	172	aroK shikimate kinase I; Reviewed	95.27
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	95.27
PRK13948	182	shikimate kinase; Provisional	95.24
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.24
PRK12678	672	transcription termination factor Rho; Provisional	95.21
PRK14737	186	gmk guanylate kinase; Provisional	95.21
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	95.2
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.2
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.2
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.19
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.19
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	95.19
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	95.19
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.17
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.15
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	95.14
PF00154	322	RecA: recA bacterial DNA recombination protein; In	95.12
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.1
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.1
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.1
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	95.06
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.05
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.05
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.04
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.03
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.03
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	95.02
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	95.02
TIGR00991	313	3a0901s02IAP34 GTP-binding protein (Chloroplast En	95.02
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.02
PRK14530	215	adenylate kinase; Provisional	95.01
PRK13946	184	shikimate kinase; Provisional	95.0
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	94.99
PF00005	137	ABC_tran: ABC transporter This structure is on hol	94.99
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	94.98
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	94.97
COG0488	530	Uup ATPase components of ABC transporters with dup	94.97
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	94.96
PRK13768	253	GTPase; Provisional	94.94
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	94.94
PRK04182	180	cytidylate kinase; Provisional	94.94
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	94.94
PF07726	131	AAA_3: ATPase family associated with various cellu	94.93
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	94.92
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	94.92
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	94.9
PRK09519	790	recA DNA recombination protein RecA; Reviewed	94.9
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	94.89
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	94.89
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.88
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.87
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	94.86
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	94.86
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	94.83
PRK09099	441	type III secretion system ATPase; Provisional	94.81
PRK14527	191	adenylate kinase; Provisional	94.81
PRK09825	176	idnK D-gluconate kinase; Provisional	94.8
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	94.77
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	94.77
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.76
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	94.73
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	94.73
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.73
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	94.71
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	94.71
TIGR01287	275	nifH nitrogenase iron protein. This model describe	94.71
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	94.7
KOG0736	953	consensus Peroxisome assembly factor 2 containing	94.7
PRK00698	205	tmk thymidylate kinase; Validated	94.69
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	94.69
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	94.67
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	94.67
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	94.67
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	94.66
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	94.64
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	94.63
PLN02796	347	D-glycerate 3-kinase	94.63
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	94.62
PRK09302	509	circadian clock protein KaiC; Reviewed	94.62
cd03116	159	MobB Molybdenum is an essential trace element in t	94.62
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	94.61
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	94.6
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	94.59
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	94.59
CHL00195	489	ycf46 Ycf46; Provisional	94.58
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	94.58
PRK05922	434	type III secretion system ATPase; Validated	94.56
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	94.56
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	94.55
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.55
PRK03731	171	aroL shikimate kinase II; Reviewed	94.55
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	94.55
PRK08356	195	hypothetical protein; Provisional	94.54
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	94.53
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.53
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	94.53
PRK08099	399	bifunctional DNA-binding transcriptional repressor	94.52
PRK13230	279	nitrogenase reductase-like protein; Reviewed	94.52
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	94.52
PRK04328	249	hypothetical protein; Provisional	94.51
cd02117	212	NifH_like This family contains the NifH (iron prot	94.51
PTZ00185	574	ATPase alpha subunit; Provisional	94.5
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	94.5
cd02040	270	NifH NifH gene encodes component II (iron protein)	94.5
PRK13232	273	nifH nitrogenase reductase; Reviewed	94.5
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	94.49
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	94.47
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	94.47
PRK13236	296	nitrogenase reductase; Reviewed	94.46
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	94.46
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	94.45
PLN02200	234	adenylate kinase family protein	94.45
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	94.44
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	94.44
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	94.44
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	94.43
cd03114	148	ArgK-like The function of this protein family is u	94.43
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	94.43
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	94.43
PRK05973	237	replicative DNA helicase; Provisional	94.42
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	94.42
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	94.41
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	94.4
PRK06761	282	hypothetical protein; Provisional	94.39
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	94.39
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	94.38
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	94.38
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	94.38
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	94.37
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.37
PRK13695	174	putative NTPase; Provisional	94.37
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	94.35
) 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	94.35
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	94.34

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=3.1e-45  Score=374.53  Aligned_cols=301  Identities=24%  Similarity=0.371  Sum_probs=245.4

Q ss_pred             ccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcc-cccCCCeeEEEEEe--CCHHHHHHHHHHHhCCC
Q 048347           21 LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSY-VKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~   97 (351)
                      ||.|+.++++.+.|..++.  .++||+||||+||||||++++|+.. ++.+|+.++||+||  |+..+++++|+..++..
T Consensus       161 VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~  238 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLL  238 (889)
T ss_pred             ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccC
Confidence            9999999999999998864  8999999999999999999999987 99999999999999  99999999999999885


Q ss_pred             CCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccchhh------------
Q 048347           98 SALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIVGLS------------  164 (351)
Q Consensus        98 ~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v~lL------------  164 (351)
                      ....  .....++++..+.+.|++|||++||||||+..+|+.+..++|....||+|++ ||++.|+..            
T Consensus       239 ~~~~--~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~  316 (889)
T KOG4658|consen  239 DEEW--EDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVEC  316 (889)
T ss_pred             Cccc--chhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccc
Confidence            4411  2223478899999999999999999999999999999999999888999999 999999111            


Q ss_pred             --------------------------------------------------c-------cc---------cCCCC-----c
Q 048347          165 --------------------------------------------------S-------CR---------LENDE-----K  173 (351)
Q Consensus       165 --------------------------------------------------~-------w~---------l~~~~-----~  173 (351)
                                                                        +       |+         +..+-     .
T Consensus       317 L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~  396 (889)
T KOG4658|consen  317 LTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEES  396 (889)
T ss_pred             cCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhh
Confidence                                                              1       32         11111     0


Q ss_pred             --------------------eEEccCCCCeEEeccchHHHHHHcCCCC-----CCHHHHHHHHHHHHHHCCCceeeccc-
Q 048347          174 --------------------IRLDLVPPKGKLRARQLYQLWIAEAFIP-----DNCESTAEEYLKELIDRGFIQVNKKD-  227 (351)
Q Consensus       174 --------------------iy~~~fp~~~~~~~~~l~~~w~~eg~i~-----~~~~~~~~~~~~~L~~~~~l~~~~~~-  227 (351)
                                          .|||+||+||.|++++++.+|+||||++     ..+++.|.+|+++|+.+++++..... 
T Consensus       397 i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~~  476 (889)
T KOG4658|consen  397 ILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDEG  476 (889)
T ss_pred             hHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhccccc
Confidence                                1999999999999999999999999997     67789999999999999999987631 


Q ss_pred             ---------------c---------------c------------------------cCCCCCCCCCCCCCceEEEEeccc
Q 048347          228 ---------------L---------------E------------------------LEDDPMPAPEKLPHLKVLKLKRSS  253 (351)
Q Consensus       228 ---------------l---------------~------------------------l~~~~~~~l~~l~~L~~L~l~~~~  253 (351)
                                     +               .                        ..-..++.-...+.|++|-+..+.
T Consensus       477 ~~~~~kmHDvvRe~al~ias~~~~~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~~~~~~~~~~~~~~~~L~tLll~~n~  556 (889)
T KOG4658|consen  477 RKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLSEIPQVKSWNSVRRMSLMNNKIEHIAGSSENPKLRTLLLQRNS  556 (889)
T ss_pred             ceeEEEeeHHHHHHHHHHhccccccccceEEECCcCccccccccchhheeEEEEeccchhhccCCCCCCccceEEEeecc
Confidence                           0               0                        000011222345567777774333


Q ss_pred             ccCceeee-CCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          254 YSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       254 ~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      .....++. .+..++.|++|||++|..+.++|.+||.|-+||+|++++ +.+..+|.++++|++|.+|++..+.
T Consensus       557 ~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~-t~I~~LP~~l~~Lk~L~~Lnl~~~~  629 (889)
T KOG4658|consen  557 DWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSD-TGISHLPSGLGNLKKLIYLNLEVTG  629 (889)
T ss_pred             hhhhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccC-CCccccchHHHHHHhhheecccccc
Confidence            21323333 266788999999999888889999999999999999997 7889999999999999999988765

>PLN03210 Resistant to P

Probab=99.97  E-value=3.8e-29  Score=267.33  Aligned_cols=141  Identities=18%  Similarity=0.235  Sum_probs=111.9

Q ss_pred             ccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--------CC-
Q 048347           12 GLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--------LS-   82 (351)
Q Consensus        12 ~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--------~~-   82 (351)
                      .++.+.+++|||+++++++.++|..+.+++++|+||||||+||||||+++|++  +..+|+..+|+...        +. 
T Consensus       178 ~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~--l~~~F~g~vfv~~~~v~~~~~~~~~  255 (1153)
T PLN03210        178 TPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSR--LSRQFQSSVFIDRAFISKSMEIYSS  255 (1153)
T ss_pred             ccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHH--HhhcCCeEEEeeccccccchhhccc
Confidence            34556678999999999999999777778999999999999999999999998  88999998887531        10 


Q ss_pred             --------HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEE
Q 048347           83 --------LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRIL  154 (351)
Q Consensus        83 --------~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Ii  154 (351)
                              ...++.+++.++......   ....    ...+++.+++||+|+||||||+.++|+.+.....+.++||+||
T Consensus       256 ~~~~~~~~~~~l~~~~l~~il~~~~~---~~~~----~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrII  328 (1153)
T PLN03210        256 ANPDDYNMKLHLQRAFLSEILDKKDI---KIYH----LGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRII  328 (1153)
T ss_pred             ccccccchhHHHHHHHHHHHhCCCCc---ccCC----HHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEE
Confidence                    123455566665443321   1111    2457788999999999999999999999998777788899999


Q ss_pred             E-Eeeccc
Q 048347          155 T-ALIHIV  161 (351)
Q Consensus       155 v-TR~~~v  161 (351)
                      | ||++++
T Consensus       329 iTTrd~~v  336 (1153)
T PLN03210        329 VITKDKHF  336 (1153)
T ss_pred             EEeCcHHH
Confidence            9 999877

syringae 6; Provisional

>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=99.94  E-value=1.8e-27  Score=218.42  Aligned_cols=138  Identities=30%  Similarity=0.485  Sum_probs=115.0

Q ss_pred             chhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC
Q 048347           23 LEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL  100 (351)
Q Consensus        23 r~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~  100 (351)
                      ||.++++|.+.|....++.++|+|+||||+||||||.+++++..++.+|+.++|+.++  .+..++++.|+.++......
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            7899999999999866789999999999999999999999998899999999999999  77899999999999987431


Q ss_pred             ccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccc
Q 048347          101 SEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIV  161 (351)
Q Consensus       101 ~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v  161 (351)
                      . ....+..+....+++.|+++++|+||||||+...|+.+...++....|++||+ ||+..+
T Consensus        81 ~-~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v  141 (287)
T PF00931_consen   81 I-SDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSV  141 (287)
T ss_dssp             S-SCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGG
T ss_pred             c-ccccccccccccchhhhccccceeeeeeeccccccccccccccccccccccccccccccc
Confidence            1 14567888999999999999999999999999999999888888778999999 999987

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.96  E-value=1.1e-08  Score=98.25  Aligned_cols=118  Identities=14%  Similarity=0.168  Sum_probs=85.2

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMM   86 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~   86 (351)
                      +...++.++||++++++|...+...  +.....+.|+|+.|+|||++++.++++  .........|+++.    .+...+
T Consensus        25 ~~~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~--l~~~~~~~~~v~in~~~~~~~~~~  102 (394)
T PRK00411         25 PDYVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEE--LEEIAVKVVYVYINCQIDRTRYAI  102 (394)
T ss_pred             CCCcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEECCcCCCHHHH
Confidence            4556788999999999999998543  223345679999999999999999998  44433334455555    667789


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG  134 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~  134 (351)
                      +..|+.++......  ....+..++.+.+.+.+.  ++..+||||+++..
T Consensus       103 ~~~i~~~l~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l  150 (394)
T PRK00411        103 FSEIARQLFGHPPP--SSGLSFDELFDKIAEYLDERDRVLIVALDDINYL  150 (394)
T ss_pred             HHHHHHHhcCCCCC--CCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHh
Confidence            99999998763211  123356667777777775  45689999999764

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.84  E-value=2.9e-08  Score=94.29  Aligned_cols=118  Identities=16%  Similarity=0.091  Sum_probs=81.6

Q ss_pred             ccCCCCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC------eeEEEEEe--C
Q 048347           12 GLSWDNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD------CCAWVYYQ--L   81 (351)
Q Consensus        12 ~~~~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~------~~~wv~~~--~   81 (351)
                      .+....+.++||++++++|...+...  +.....+.|+|++|+|||++++.+++.  .....+      ..+|++..  .
T Consensus         9 ~~~~~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~--l~~~~~~~~~~~~~v~in~~~~~   86 (365)
T TIGR02928         9 EPDYVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKE--LEEAAEDRDVRVVTVYVNCQILD   86 (365)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHhhccCCceEEEEEECCCCC
Confidence            35556678999999999999998641  233456789999999999999999987  322211      12344433  5


Q ss_pred             CHHHHHHHHHHHhCC---CCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh
Q 048347           82 SLDMMLDAIMKSLMP---LSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG  134 (351)
Q Consensus        82 ~~~~~~~~i~~~~~~---~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~  134 (351)
                      +..+++..|+.++..   +..   ....+..+..+.+.+.+.  ++++++|||+++..
T Consensus        87 ~~~~~~~~i~~~l~~~~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        87 TLYQVLVELANQLRGSGEEVP---TTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             CHHHHHHHHHHHHhhcCCCCC---CCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence            677899999999942   211   122344555666666663  56789999999766

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.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.76  E-value=2.5e-08  Score=85.03  Aligned_cols=74  Identities=14%  Similarity=0.156  Sum_probs=42.0

Q ss_pred             ccccchhhHHHHHHHHHc-cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CC------HHHHHH
Q 048347           19 VDLDLEDKMEELLDLLIE-RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LS------LDMMLD   88 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~------~~~~~~   88 (351)
                      .+|||+++++++...+.. .+...+.+.|+|.+|+|||+|.++++..  +.... .. |+...   ..      ...+++
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~--~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~   76 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDR--LAERG-GY-VISINCDDSERNPYSPFRSALR   76 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHH--HHHHT----EEEEEEETTTS-HHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHH--HHhcC-CE-EEEEEEeccccchhhHHHHHHH
Confidence            479999999999999942 2345688999999999999999999998  44442 22 44444   31      255555


Q ss_pred             HHHHHhCC
Q 048347           89 AIMKSLMP   96 (351)
Q Consensus        89 ~i~~~~~~   96 (351)
                      +++.++..
T Consensus        77 ~l~~~~~~   84 (185)
T PF13191_consen   77 QLIDQLLD   84 (185)
T ss_dssp             HHS-----
T ss_pred             HHHHHhhc
Confidence            55555443

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

Probab=98.75  E-value=3.5e-08  Score=79.26  Aligned_cols=108  Identities=15%  Similarity=0.187  Sum_probs=74.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccC-----CCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-----FDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKK  112 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-----F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~  112 (351)
                      +.+.+.|+|.+|+|||++++++...  ....     -..++|+...  .+...+...|+.++.....    ...+...+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~l~   76 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLK----SRQTSDELR   76 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSS----STS-HHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCcccc----ccCCHHHHH
Confidence            3568889999999999999999887  3321     2345688777  7799999999999998876    345777788


Q ss_pred             HHHHHhcCCce-EEEEEeCCCCh---hhHHHHHhhcCCCCCCcEEEE
Q 048347          113 NTLHNYLKNKR-YLIVIQDVWRG---DIWDFLKEALPDHQNGSRILT  155 (351)
Q Consensus       113 ~~l~~~L~~k~-~LlVLDdv~~~---~~~~~l~~~l~~~~~gs~Iiv  155 (351)
                      +.+.+.+...+ .++|+|++...   +.++.++....  ..+.++|+
T Consensus        77 ~~~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl  121 (131)
T PF13401_consen   77 SLLIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVL  121 (131)
T ss_dssp             HHHHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEE
T ss_pred             HHHHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEE
Confidence            88888886554 59999999654   23444444333  44666666

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

Probab=98.63  E-value=9.1e-07  Score=80.28  Aligned_cols=95  Identities=14%  Similarity=0.158  Sum_probs=63.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH---
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH---  116 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~---  116 (351)
                      ..++.|+|+.|+||||+++.+++.... ..+ ..+|+... .+..++++.|+..++.+..     ..+.......+.   
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~-~~~-~~~~~~~~~~~~~~~l~~i~~~lG~~~~-----~~~~~~~~~~l~~~l  115 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQ-ERV-VAAKLVNTRVDAEDLLRMVAADFGLETE-----GRDKAALLRELEDFL  115 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCC-CCe-EEeeeeCCCCCHHHHHHHHHHHcCCCCC-----CCCHHHHHHHHHHHH
Confidence            458889999999999999999988331 111 22344334 7788999999988876533     122233333333   


Q ss_pred             -Hhc-CCceEEEEEeCCCCh--hhHHHHHh
Q 048347          117 -NYL-KNKRYLIVIQDVWRG--DIWDFLKE  142 (351)
Q Consensus       117 -~~L-~~k~~LlVLDdv~~~--~~~~~l~~  142 (351)
                       ... .+++.++|+||++..  +.++.++.
T Consensus       116 ~~~~~~~~~~vliiDe~~~l~~~~~~~l~~  145 (269)
T TIGR03015       116 IEQFAAGKRALLVVDEAQNLTPELLEELRM  145 (269)
T ss_pred             HHHHhCCCCeEEEEECcccCCHHHHHHHHH
Confidence             322 678899999999876  35565553

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.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.60  E-value=8.5e-08  Score=85.69  Aligned_cols=92  Identities=11%  Similarity=-0.000  Sum_probs=60.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHhCCCCCCcc--CCCCCHHHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSALSE--ILDNDFEMKKNT  114 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~~~~--~~~~~~~~~~~~  114 (351)
                      -..++|.|++|+|||||++.+|++.... +|+.++|+.+.    +++.++++.+...+........  ....-...+.+.
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~   94 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEK   94 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHH
Confidence            3578899999999999999999995544 89999999977    7999999999333322211000  000011112222


Q ss_pred             HHHh-cCCceEEEEEeCCCC
Q 048347          115 LHNY-LKNKRYLIVIQDVWR  133 (351)
Q Consensus       115 l~~~-L~~k~~LlVLDdv~~  133 (351)
                      .... -.+++.++++|++..
T Consensus        95 a~~~~~~G~~vll~iDei~r  114 (249)
T cd01128          95 AKRLVEHGKDVVILLDSITR  114 (249)
T ss_pred             HHHHHHCCCCEEEEEECHHH
Confidence            2222 247999999999953

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.

>PF05729 NACHT: NACHT domain

Probab=98.54  E-value=4.2e-07  Score=75.80  Aligned_cols=111  Identities=15%  Similarity=0.132  Sum_probs=64.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccC----CCeeEEEEEe-CCH----HHHHHHHHHHhCCCCCCccCCCCCHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNY----FDCCAWVYYQ-LSL----DMMLDAIMKSLMPLSALSEILDNDFEMKK  112 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~~-~~~----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~  112 (351)
                      +++.|.|.+|+||||++++++.+..-...    +...+|+... ...    ..+...|..+......       ......
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~-------~~~~~~   73 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIA-------PIEELL   73 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchh-------hhHHHH
Confidence            47889999999999999999887333332    3445566655 221    1344444444333222       111111


Q ss_pred             HHHHHhcCCceEEEEEeCCCChhh---------HHH-HHhhcCC-CCCCcEEEE-Eeeccc
Q 048347          113 NTLHNYLKNKRYLIVIQDVWRGDI---------WDF-LKEALPD-HQNGSRILT-ALIHIV  161 (351)
Q Consensus       113 ~~l~~~L~~k~~LlVLDdv~~~~~---------~~~-l~~~l~~-~~~gs~Iiv-TR~~~v  161 (351)
                      ..  -.-+.+++++|+|++++...         +.. +...++. ...+.++++ +|....
T Consensus        74 ~~--~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~  132 (166)
T PF05729_consen   74 QE--LLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAF  132 (166)
T ss_pred             HH--HHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChH
Confidence            11  11257899999999976532         222 2333343 356889999 887755

>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=98.51  E-value=1.6e-06  Score=70.20  Aligned_cols=56  Identities=13%  Similarity=0.046  Sum_probs=41.1

Q ss_pred             ccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           21 LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      +|+++.++.+...+....  .+.+.|+|..|+|||++|+++++.  ....-..++++...
T Consensus         1 ~~~~~~~~~i~~~~~~~~--~~~v~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~~   56 (151)
T cd00009           1 VGQEEAIEALREALELPP--PKNLLLYGPPGTGKTTLARAIANE--LFRPGAPFLYLNAS   56 (151)
T ss_pred             CchHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHH--hhcCCCCeEEEehh
Confidence            478888899988886542  457779999999999999999998  43222334555444

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.

>PTZ00202 tuzin; Provisional

Probab=98.50  E-value=2.3e-06  Score=80.99  Aligned_cols=106  Identities=10%  Similarity=0.048  Sum_probs=75.5

Q ss_pred             cccCCCCCccccchhhHHHHHHHHHccC-CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHH
Q 048347           11 RGLSWDNKVDLDLEDKMEELLDLLIERQ-PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDA   89 (351)
Q Consensus        11 ~~~~~~~~~~vGr~~~~~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~   89 (351)
                      .+.+.+...++||+++...+...|...+ ...+++.|.|++|+|||||++.+.....    +. ..+++. .+..++++.
T Consensus       255 ~~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~~-qL~vNp-rg~eElLr~  328 (550)
T PTZ00202        255 QSAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----MP-AVFVDV-RGTEDTLRS  328 (550)
T ss_pred             cCCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----ce-EEEECC-CCHHHHHHH
Confidence            4577788999999999999999986532 2346889999999999999999997732    11 122221 688999999


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhc-----C-CceEEEEE
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYL-----K-NKRYLIVI  128 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L-----~-~k~~LlVL  128 (351)
                      |+.+++.+..      ....++.+.+.+.+     . +++.++|+
T Consensus       329 LL~ALGV~p~------~~k~dLLrqIqeaLl~~~~e~GrtPVLII  367 (550)
T PTZ00202        329 VVKALGVPNV------EACGDLLDFISEACRRAKKMNGETPLLVL  367 (550)
T ss_pred             HHHHcCCCCc------ccHHHHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            9999997433      23345555555444     2 55666666

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.47  E-value=2e-07  Score=87.32  Aligned_cols=88  Identities=10%  Similarity=0.010  Sum_probs=59.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--C--CHHHHHHHHHHHhCCCCCCccCCCCCHHH------H
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--L--SLDMMLDAIMKSLMPLSALSEILDNDFEM------K  111 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~--~~~~~~~~i~~~~~~~~~~~~~~~~~~~~------~  111 (351)
                      ...+|+|++|+||||||+++|++...+ +|+.++||.++  +  ++.++++.|...+.....    +......      .
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~----d~~~~~~~~~a~~~  244 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTF----DEPAERHVQVAEMV  244 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECC----CCCHHHHHHHHHHH
Confidence            467899999999999999999994444 89999999998  5  778888888643222221    1111111      1


Q ss_pred             HHHHHHh-cCCceEEEEEeCCCCh
Q 048347          112 KNTLHNY-LKNKRYLIVIQDVWRG  134 (351)
Q Consensus       112 ~~~l~~~-L~~k~~LlVLDdv~~~  134 (351)
                      .+.-... -.+++.++++|++...
T Consensus       245 ie~Ae~~~e~G~dVlL~iDsItR~  268 (416)
T PRK09376        245 IEKAKRLVEHGKDVVILLDSITRL  268 (416)
T ss_pred             HHHHHHHHHcCCCEEEEEEChHHH
Confidence            1111111 2579999999999543

>PLN03210 Resistant to P

Probab=98.43  E-value=3.4e-07  Score=99.14  Aligned_cols=84  Identities=23%  Similarity=0.229  Sum_probs=49.5

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+++|+.|+| .++...+.+|. ++.+++|++|+|++|..+..+|.++++|.+|+.|++++|..++.+|.++ ++++|+.
T Consensus       632 ~l~~Lk~L~L-s~~~~l~~ip~-ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i-~l~sL~~  708 (1153)
T PLN03210        632 SLTGLRNIDL-RGSKNLKEIPD-LSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGI-NLKSLYR  708 (1153)
T ss_pred             cCCCCCEEEC-CCCCCcCcCCc-cccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcC-CCCCCCE
Confidence            3455555555 23333344443 4555666666666665566666666666666666666666666666654 5666666


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |++++|.
T Consensus       709 L~Lsgc~  715 (1153)
T PLN03210        709 LNLSGCS  715 (1153)
T ss_pred             EeCCCCC
Confidence            6666653

syringae 6; Provisional

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=98.43  E-value=1.6e-08  Score=83.26  Aligned_cols=87  Identities=22%  Similarity=0.258  Sum_probs=53.2

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccc--cccccccccCCccEEeecCCccccccChhh
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLE--EWKMETGAMQKLKSLIVNPCAYLRKFPEEL  311 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~--~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i  311 (351)
                      ..+++++++.|+.|++  +...+..+|..+++|+-|++|+|.+| ++.  .+|..+..|.-|+.|.|+. ...+.+|.++
T Consensus        71 lp~~issl~klr~lnv--gmnrl~~lprgfgs~p~levldltyn-nl~e~~lpgnff~m~tlralyl~d-ndfe~lp~dv  146 (264)
T KOG0617|consen   71 LPTSISSLPKLRILNV--GMNRLNILPRGFGSFPALEVLDLTYN-NLNENSLPGNFFYMTTLRALYLGD-NDFEILPPDV  146 (264)
T ss_pred             cChhhhhchhhhheec--chhhhhcCccccCCCchhhhhhcccc-ccccccCCcchhHHHHHHHHHhcC-CCcccCChhh
Confidence            3456677777777777  34444456777777777777777776 332  4555555555555555555 3455566666


Q ss_pred             hcCCCCCEEEecC
Q 048347          312 WRIKALRKLESWW  324 (351)
Q Consensus       312 ~~L~~L~~L~l~~  324 (351)
                      ++|++|+-|.+++
T Consensus       147 g~lt~lqil~lrd  159 (264)
T KOG0617|consen  147 GKLTNLQILSLRD  159 (264)
T ss_pred             hhhcceeEEeecc
Confidence            6666666555554

>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=98.39  E-value=3.1e-07  Score=80.96  Aligned_cols=43  Identities=21%  Similarity=0.268  Sum_probs=35.5

Q ss_pred             cccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           20 DLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++||++++++|.+++..+.  ...+.|+|+.|+|||+|++++.+.
T Consensus         1 F~gR~~el~~l~~~l~~~~--~~~~~l~G~rg~GKTsLl~~~~~~   43 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGP--SQHILLYGPRGSGKTSLLKEFINE   43 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhc--CcEEEEEcCCcCCHHHHHHHHHHH
Confidence            6899999999999987653  467889999999999999999887

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.38  E-value=5.8e-06  Score=84.10  Aligned_cols=119  Identities=13%  Similarity=0.015  Sum_probs=79.9

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCCccc---ccCCCeeEEEEEe----CC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNSSYV---KNYFDCCAWVYYQ----LS   82 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~---~~~F~~~~wv~~~----~~   82 (351)
                      +...++.++|||+++++|...|...   .....++-|+|+.|.|||+.++.|....+-   +.......++++.    .+
T Consensus       750 ~DYVPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lst  829 (1164)
T PTZ00112        750 LDVVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVH  829 (1164)
T ss_pred             cccCCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCC
Confidence            5556788999999999999988642   223357779999999999999999876221   1122323345554    56


Q ss_pred             HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC---CceEEEEEeCCCCh
Q 048347           83 LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK---NKRYLIVIQDVWRG  134 (351)
Q Consensus        83 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~---~k~~LlVLDdv~~~  134 (351)
                      ...++..|+.++.....   ....+.....+.+.+.+.   +...+||||+++..
T Consensus       830 p~sIYqvI~qqL~g~~P---~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L  881 (1164)
T PTZ00112        830 PNAAYQVLYKQLFNKKP---PNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYL  881 (1164)
T ss_pred             HHHHHHHHHHHHcCCCC---CccccHHHHHHHHHhhhhcccccceEEEeehHhhh
Confidence            88899999999955432   122334445555555542   23458999999754

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

Probab=98.33  E-value=4.5e-06  Score=78.80  Aligned_cols=116  Identities=13%  Similarity=0.105  Sum_probs=86.7

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe--eEEEEEe--CCHHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC--CAWVYYQ--LSLDMM   86 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~~~--~~~~~~   86 (351)
                      +..-++.+.+||++++++...|..-  +....-+.|+|..|.|||+.++.|+..  ++.....  .+.|+.-  .+..++
T Consensus        12 ~~~iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~--l~~~~~~~~~~yINc~~~~t~~~i   89 (366)
T COG1474          12 EDYIPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEE--LEESSANVEVVYINCLELRTPYQV   89 (366)
T ss_pred             CCCCcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHH--HHhhhccCceEEEeeeeCCCHHHH
Confidence            4445566999999999999988642  212222778999999999999999998  5555333  3555544  899999


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG  134 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~  134 (351)
                      +..|++++.....    ..++..+..+.+.+.+.  ++.+++|||++...
T Consensus        90 ~~~i~~~~~~~p~----~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L  135 (366)
T COG1474          90 LSKILNKLGKVPL----TGDSSLEILKRLYDNLSKKGKTVIVILDEVDAL  135 (366)
T ss_pred             HHHHHHHcCCCCC----CCCchHHHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence            9999999974322    35667777788887774  58899999999755

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.31  E-value=2.2e-07  Score=96.76  Aligned_cols=87  Identities=25%  Similarity=0.264  Sum_probs=78.1

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+|.|++|+| +.+..+.++|.+++.+.+||||+++++ .+.++|..+++|..|.+|++..+..+..+|..+..|++|
T Consensus       567 f~~m~~LrVLDL-s~~~~l~~LP~~I~~Li~LryL~L~~t-~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~L  644 (889)
T KOG4658|consen  567 FRSLPLLRVLDL-SGNSSLSKLPSSIGELVHLRYLDLSDT-GISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSL  644 (889)
T ss_pred             HhhCcceEEEEC-CCCCccCcCChHHhhhhhhhcccccCC-CccccchHHHHHHhhheeccccccccccccchhhhcccc
Confidence            667999999999 568888899999999999999999998 799999999999999999999877777777766779999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|.+....
T Consensus       645 r~L~l~~s~  653 (889)
T KOG4658|consen  645 RVLRLPRSA  653 (889)
T ss_pred             cEEEeeccc
Confidence            999997653

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=98.30  E-value=7.4e-07  Score=95.29  Aligned_cols=86  Identities=20%  Similarity=0.130  Sum_probs=40.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      ++++++|++|+++ ++.....+|..++.+++|++|++++|...+.+|..++++++|++|++++|.....+|..++++++|
T Consensus       184 ~~~l~~L~~L~L~-~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L  262 (968)
T PLN00113        184 LTNLTSLEFLTLA-SNQLVGQIPRELGQMKSLKWIYLGYNNLSGEIPYEIGGLTSLNHLDLVYNNLTGPIPSSLGNLKNL  262 (968)
T ss_pred             hhhCcCCCeeecc-CCCCcCcCChHHcCcCCccEEECcCCccCCcCChhHhcCCCCCEEECcCceeccccChhHhCCCCC
Confidence            3444445555552 222222344444455555555555543333445455555555555555544334455555555555


Q ss_pred             CEEEecC
Q 048347          318 RKLESWW  324 (351)
Q Consensus       318 ~~L~l~~  324 (351)
                      ++|++++
T Consensus       263 ~~L~L~~  269 (968)
T PLN00113        263 QYLFLYQ  269 (968)
T ss_pred             CEEECcC
Confidence            5555544

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=98.29  E-value=5.6e-08  Score=80.02  Aligned_cols=95  Identities=22%  Similarity=0.202  Sum_probs=83.0

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhc
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ....++.+|.|.+|+|.+++.+-..+|-.+-.+..|+-|.|.+| ..+-+|..+|+|.+|+.|.++. ..+-++|..++.
T Consensus        94 lprgfgs~p~levldltynnl~e~~lpgnff~m~tlralyl~dn-dfe~lp~dvg~lt~lqil~lrd-ndll~lpkeig~  171 (264)
T KOG0617|consen   94 LPRGFGSFPALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGDN-DFEILPPDVGKLTNLQILSLRD-NDLLSLPKEIGD  171 (264)
T ss_pred             CccccCCCchhhhhhccccccccccCCcchhHHHHHHHHHhcCC-CcccCChhhhhhcceeEEeecc-CchhhCcHHHHH
Confidence            34567899999999998888888788987778888999999999 7999999999999999999999 568889999999


Q ss_pred             CCCCCEEEecCC-----ChhHH
Q 048347          314 IKALRKLESWWP-----RPELR  330 (351)
Q Consensus       314 L~~L~~L~l~~~-----~~~~~  330 (351)
                      |+.|++|.+.|.     |||+.
T Consensus       172 lt~lrelhiqgnrl~vlppel~  193 (264)
T KOG0617|consen  172 LTRLRELHIQGNRLTVLPPELA  193 (264)
T ss_pred             HHHHHHHhcccceeeecChhhh
Confidence            999999998773     46654

>PF13173 AAA_14: AAA domain

Probab=98.27  E-value=1.4e-06  Score=69.96  Aligned_cols=97  Identities=10%  Similarity=0.128  Sum_probs=62.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      .+++.|.|+-|+||||++++++.+  .. .-..+++++.. +... ...                ...+ ..+.+.+...
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~--~~-~~~~~~yi~~~-~~~~-~~~----------------~~~~-~~~~~~~~~~   59 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKD--LL-PPENILYINFD-DPRD-RRL----------------ADPD-LLEYFLELIK   59 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--hc-ccccceeeccC-CHHH-HHH----------------hhhh-hHHHHHHhhc
Confidence            368889999999999999999987  32 22334555443 1111 000                0000 2344444444


Q ss_pred             CceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347          121 NKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus       121 ~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      .++.+++||++....+|......+.+.....+|++ +.+.
T Consensus        60 ~~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~   99 (128)
T PF13173_consen   60 PGKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSS   99 (128)
T ss_pred             cCCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccch
Confidence            57788999999988889888877776555677777 4433

>TIGR00767 rho transcription termination factor Rho

Probab=98.25  E-value=3.7e-06  Score=79.20  Aligned_cols=92  Identities=10%  Similarity=-0.017  Sum_probs=61.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHhCCCCCCccC-C-CCCHHHHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSALSEI-L-DNDFEMKKNTL  115 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~~~~~-~-~~~~~~~~~~l  115 (351)
                      ..++|+|++|+|||||++.+++....+ +|+.++||.+.    .++.++++.+...+......... . ..-...+.+..
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~A  247 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKA  247 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHH
Confidence            568899999999999999999984333 69999999988    78999999996544433221000 0 00001111111


Q ss_pred             HHh-cCCceEEEEEeCCCCh
Q 048347          116 HNY-LKNKRYLIVIQDVWRG  134 (351)
Q Consensus       116 ~~~-L~~k~~LlVLDdv~~~  134 (351)
                      ... -.+++.++++|++...
T Consensus       248 e~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       248 KRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHcCCCeEEEEEChhHH
Confidence            122 2589999999999543

Members of this family differ in the specificity of RNA binding.

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=98.24  E-value=1.1e-06  Score=94.06  Aligned_cols=90  Identities=21%  Similarity=0.208  Sum_probs=68.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      ..++.+++|++|+++ ++.....+|..++++++|++|++++|...+.+|..++++.+|++|++++|.....+|..+++++
T Consensus       158 ~~~~~l~~L~~L~L~-~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~  236 (968)
T PLN00113        158 NDIGSFSSLKVLDLG-GNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNNLSGEIPYEIGGLT  236 (968)
T ss_pred             hHHhcCCCCCEEECc-cCcccccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCccCCcCChhHhcCC
Confidence            446778888888884 3333346777778888888888888855567788888888888888888766667888888888


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|+++++.
T Consensus       237 ~L~~L~L~~n~  247 (968)
T PLN00113        237 SLNHLDLVYNN  247 (968)
T ss_pred             CCCEEECcCce
Confidence            88888887654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.12  E-value=3.2e-05  Score=82.14  Aligned_cols=136  Identities=12%  Similarity=0.072  Sum_probs=83.2

Q ss_pred             cCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDA   89 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~   89 (351)
                      ++-....+|-|..-.    ..|.. ....+++.|.|++|.||||++.++...  .    +.++|+++.   -+...+...
T Consensus         9 ~p~~~~~~~~R~rl~----~~l~~-~~~~~~~~v~apaG~GKTtl~~~~~~~--~----~~~~w~~l~~~d~~~~~f~~~   77 (903)
T PRK04841          9 RPVRLHNTVVRERLL----AKLSG-ANNYRLVLVTSPAGYGKTTLISQWAAG--K----NNLGWYSLDESDNQPERFASY   77 (903)
T ss_pred             CCCCccccCcchHHH----HHHhc-ccCCCeEEEECCCCCCHHHHHHHHHHh--C----CCeEEEecCcccCCHHHHHHH
Confidence            333455667765444    44432 235789999999999999999998854  2    268899987   466667777


Q ss_pred             HHHHhCCCCCC--c-------cCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCChh--h-HHHHHhhcCCCCCCcEEEE
Q 048347           90 IMKSLMPLSAL--S-------EILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRGD--I-WDFLKEALPDHQNGSRILT  155 (351)
Q Consensus        90 i~~~~~~~~~~--~-------~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~~--~-~~~l~~~l~~~~~gs~Iiv  155 (351)
                      ++..+......  .       .....+...+...+...+.  +.+++|||||+...+  . .+.+...+.....+..+|+
T Consensus        78 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~  157 (903)
T PRK04841         78 LIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVV  157 (903)
T ss_pred             HHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEE
Confidence            77777432111  0       0011223333444433443  678999999997652  2 2334444444555667778


Q ss_pred             -Eeec
Q 048347          156 -ALIH  159 (351)
Q Consensus       156 -TR~~  159 (351)
                       ||..
T Consensus       158 ~sR~~  162 (903)
T PRK04841        158 LSRNL  162 (903)
T ss_pred             EeCCC
Confidence             9874

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.11  E-value=5e-06  Score=57.40  Aligned_cols=58  Identities=22%  Similarity=0.244  Sum_probs=41.2

Q ss_pred             CcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccCh-hhhcCCCCCEEEecCCC
Q 048347          267 PRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPE-ELWRIKALRKLESWWPR  326 (351)
Q Consensus       267 ~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~  326 (351)
                      ++|++|++++| .+..+|.. +..+++|++|++++ ..+..+|+ .+.++++|++|++++++
T Consensus         1 p~L~~L~l~~n-~l~~i~~~~f~~l~~L~~L~l~~-N~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    1 PNLESLDLSNN-KLTEIPPDSFSNLPNLETLDLSN-NNLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TTESEEEETSS-TESEECTTTTTTGTTESEEEETS-SSESEEETTTTTTSTTESEEEETSSS
T ss_pred             CcCcEEECCCC-CCCccCHHHHcCCCCCCEeEccC-CccCccCHHHHcCCCCCCEEeCcCCc
Confidence            46777888877 67777754 67778888888886 45666665 44777888888877653

...

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.08  E-value=1.1e-05  Score=78.06  Aligned_cols=104  Identities=13%  Similarity=0.134  Sum_probs=63.0

Q ss_pred             CccccchhhHHH---HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHH
Q 048347           18 KVDLDLEDKMEE---LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIM   91 (351)
Q Consensus        18 ~~~vGr~~~~~~---l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~   91 (351)
                      +++||.+..+..   +.+++..+  ...-+.++|++|+||||+|+.+++.  ....     |+.++   ....+ .+.+ 
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~--~~~~ilL~GppGtGKTtLA~~ia~~--~~~~-----~~~l~a~~~~~~~-ir~i-   80 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAG--RLSSMILWGPPGTGKTTLARIIAGA--TDAP-----FEALSAVTSGVKD-LREV-   80 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcC--CCceEEEECCCCCCHHHHHHHHHHH--hCCC-----EEEEecccccHHH-HHHH-
Confidence            458888877665   77777554  3456778999999999999999887  4333     33333   11111 1111 


Q ss_pred             HHhCCCCCCccCCCCCHHHHHHHHHHh-cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE
Q 048347           92 KSLMPLSALSEILDNDFEMKKNTLHNY-LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT  155 (351)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~l~~~-L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv  155 (351)
                                          .+..... ..+++.++++|+++..  .+.+.+...+.   .|..+++
T Consensus        81 --------------------i~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le---~~~iilI  124 (413)
T PRK13342         81 --------------------IEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVE---DGTITLI  124 (413)
T ss_pred             --------------------HHHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhh---cCcEEEE
Confidence                                1111111 1357889999999865  34555555443   2555555

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=98.04  E-value=1.9e-05  Score=72.48  Aligned_cols=90  Identities=16%  Similarity=0.177  Sum_probs=59.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHN  117 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~  117 (351)
                      ++.-+.+||++|+||||||+.+.+.  .+.+-  ..||+.+  -.-..-.++|.++....                   .
T Consensus       161 ~ipSmIlWGppG~GKTtlArlia~t--sk~~S--yrfvelSAt~a~t~dvR~ife~aq~~-------------------~  217 (554)
T KOG2028|consen  161 RIPSMILWGPPGTGKTTLARLIAST--SKKHS--YRFVELSATNAKTNDVRDIFEQAQNE-------------------K  217 (554)
T ss_pred             CCCceEEecCCCCchHHHHHHHHhh--cCCCc--eEEEEEeccccchHHHHHHHHHHHHH-------------------H
Confidence            5777889999999999999999998  33432  6788887  22222233443332221                   2


Q ss_pred             hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE
Q 048347          118 YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT  155 (351)
Q Consensus       118 ~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv  155 (351)
                      .+.++|..+++|.|...  .+.+   ..+|.-.+|+.++|
T Consensus       218 ~l~krkTilFiDEiHRFNksQQD---~fLP~VE~G~I~lI  254 (554)
T KOG2028|consen  218 SLTKRKTILFIDEIHRFNKSQQD---TFLPHVENGDITLI  254 (554)
T ss_pred             hhhcceeEEEeHHhhhhhhhhhh---cccceeccCceEEE
Confidence            24578889999999543  2222   24677788998888

>PLN03150 hypothetical protein; Provisional

Probab=98.02  E-value=6e-06  Score=83.81  Aligned_cols=81  Identities=15%  Similarity=0.091  Sum_probs=58.1

Q ss_pred             ceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEec
Q 048347          244 LKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESW  323 (351)
Q Consensus       244 L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~  323 (351)
                      +..|+|+ ++.....+|..++.+++|+.|+|++|...+.+|..++.+++|+.|+|++|...+.+|+.+++|++|+.|+++
T Consensus       420 v~~L~L~-~n~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls  498 (623)
T PLN03150        420 IDGLGLD-NQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNLN  498 (623)
T ss_pred             EEEEECC-CCCccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEECc
Confidence            6667773 333333667777778888888888874445777778888888888888766666778888888888888877


Q ss_pred             CC
Q 048347          324 WP  325 (351)
Q Consensus       324 ~~  325 (351)
                      +.
T Consensus       499 ~N  500 (623)
T PLN03150        499 GN  500 (623)
T ss_pred             CC
Confidence            64

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.02  E-value=7.7e-05  Score=69.37  Aligned_cols=121  Identities=12%  Similarity=0.139  Sum_probs=76.9

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC----cccccCCCeeEEEEEe---CCHHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS----SYVKNYFDCCAWVYYQ---LSLDMMLDAI   90 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~----~~~~~~F~~~~wv~~~---~~~~~~~~~i   90 (351)
                      ++++|-+.-++.+.+.+..+. -.+..-++|+.|+||||+|+.++..    .....|.|...|....   ..+++ .+++
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~-~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-ir~~   81 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR-FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-IRNI   81 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-HHHH
Confidence            467898888999999886553 3456678999999999999888763    1123455554453311   22222 2222


Q ss_pred             HHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC--ChhhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347           91 MKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW--RGDIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~--~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      ...+...                    -..+++-++|+|+++  +.++++.+...+.+...++.+|+ |.+.+
T Consensus        82 ~~~~~~~--------------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~  134 (313)
T PRK05564         82 IEEVNKK--------------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLE  134 (313)
T ss_pred             HHHHhcC--------------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChH
Confidence            2222111                    112445566666664  44789999999998888898888 86543

>PLN03150 hypothetical protein; Provisional

Probab=98.01  E-value=6.5e-06  Score=83.55  Aligned_cols=92  Identities=17%  Similarity=0.108  Sum_probs=75.7

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhc
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ..+.++.+++|+.|+|+.+.. ...+|..++.+++|++|+|++|...+.+|..++.|++|++|+|++|...+.+|..++.
T Consensus       434 ip~~i~~L~~L~~L~Ls~N~l-~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls~N~l~g~iP~~l~~  512 (623)
T PLN03150        434 IPNDISKLRHLQSINLSGNSI-RGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNLNGNSLSGRVPAALGG  512 (623)
T ss_pred             CCHHHhCCCCCCEEECCCCcc-cCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEECcCCcccccCChHHhh
Confidence            334567899999999954443 3478888999999999999999655689999999999999999998888899999886


Q ss_pred             C-CCCCEEEecCCC
Q 048347          314 I-KALRKLESWWPR  326 (351)
Q Consensus       314 L-~~L~~L~l~~~~  326 (351)
                      + .++..+++.+.+
T Consensus       513 ~~~~~~~l~~~~N~  526 (623)
T PLN03150        513 RLLHRASFNFTDNA  526 (623)
T ss_pred             ccccCceEEecCCc
Confidence            4 467788877643

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=98.00  E-value=2.5e-06  Score=79.02  Aligned_cols=87  Identities=22%  Similarity=0.175  Sum_probs=72.5

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCC----------------------cccccccc-ccccCCc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSML----------------------WLEEWKME-TGAMQKL  293 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~----------------------~l~~lp~~-i~~L~~L  293 (351)
                      .++++++|..|+| +++ .+..+|...+.+..|+.|+++.|.                      .++++|.+ +++|.+|
T Consensus       430 ~l~~l~kLt~L~L-~NN-~Ln~LP~e~~~lv~Lq~LnlS~NrFr~lP~~~y~lq~lEtllas~nqi~~vd~~~l~nm~nL  507 (565)
T KOG0472|consen  430 ELSQLQKLTFLDL-SNN-LLNDLPEEMGSLVRLQTLNLSFNRFRMLPECLYELQTLETLLASNNQIGSVDPSGLKNMRNL  507 (565)
T ss_pred             HHHhhhcceeeec-ccc-hhhhcchhhhhhhhhheecccccccccchHHHhhHHHHHHHHhccccccccChHHhhhhhhc
Confidence            4578899999999 343 455899999999999999999873                      33445555 8889999


Q ss_pred             cEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          294 KSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       294 ~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      .+|||.+ ..+..+|+.+|++++|++|++.|-+
T Consensus       508 ~tLDL~n-Ndlq~IPp~LgnmtnL~hLeL~gNp  539 (565)
T KOG0472|consen  508 TTLDLQN-NDLQQIPPILGNMTNLRHLELDGNP  539 (565)
T ss_pred             ceeccCC-CchhhCChhhccccceeEEEecCCc
Confidence            9999998 6799999999999999999999866

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.99  E-value=4.8e-05  Score=70.37  Aligned_cols=118  Identities=13%  Similarity=0.109  Sum_probs=81.1

Q ss_pred             CCCccccchhhHHHHHHHHHccCCC-eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHH
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQ-LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMK   92 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~-~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~   92 (351)
                      -+..+.+|+..++.+.+++...+.. ...|-|+|-+|.|||.+.+++++...  .   ..+|++..  |+.+.++..|+.
T Consensus         4 l~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n--~---~~vw~n~~ecft~~~lle~IL~   78 (438)
T KOG2543|consen    4 LEPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLN--L---ENVWLNCVECFTYAILLEKILN   78 (438)
T ss_pred             cccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcC--C---cceeeehHHhccHHHHHHHHHH
Confidence            4567889999999999999766543 34457899999999999999999942  2   34899877  999999999999


Q ss_pred             HhCC-CCCCccCCC--CCHHHHHHHHHH--hc--CCceEEEEEeCCCChhhHH
Q 048347           93 SLMP-LSALSEILD--NDFEMKKNTLHN--YL--KNKRYLIVIQDVWRGDIWD  138 (351)
Q Consensus        93 ~~~~-~~~~~~~~~--~~~~~~~~~l~~--~L--~~k~~LlVLDdv~~~~~~~  138 (351)
                      +... .....+.+.  ....+....+.+  ..  +++.+++|||+++...+.+
T Consensus        79 ~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~  131 (438)
T KOG2543|consen   79 KSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMD  131 (438)
T ss_pred             HhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccc
Confidence            9952 222111111  111122222222  11  2468999999997665443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.97  E-value=7.8e-06  Score=80.48  Aligned_cols=133  Identities=11%  Similarity=-0.012  Sum_probs=75.3

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~   96 (351)
                      ++++|-+.-.+.|..++..+. -...+.++|+.|+||||+|+.+++.....+.+...||.+.+ ..+......-...+..
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~   92 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDA   92 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecc
Confidence            458999988888988887653 23556789999999999999998773333333334454433 1111000000000000


Q ss_pred             CCCCccCCCCCHHHHH---HHHHH-hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347           97 LSALSEILDNDFEMKK---NTLHN-YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus        97 ~~~~~~~~~~~~~~~~---~~l~~-~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                      .      .....+++.   +.+.. -+.+++-++|+|+++..  +.++.+...+........+|+ +.
T Consensus        93 ~------~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~  154 (504)
T PRK14963         93 A------SNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATT  154 (504)
T ss_pred             c------ccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcC
Confidence            0      112222222   22221 12356668999999855  567888887776555566665 54

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

Probab=97.94  E-value=4e-05  Score=73.42  Aligned_cols=117  Identities=13%  Similarity=0.114  Sum_probs=74.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLM   95 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~   95 (351)
                      +++++.++..+.+...|...    +-+.++|++|+|||++|+++++.......|+.+.||+++  ++..+++..+.    
T Consensus       175 ~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~r----  246 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYR----  246 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccC----
Confidence            45788899999999988753    366679999999999999999884444567788899988  66666654321    


Q ss_pred             CCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCChh---hHHHHHhhcC
Q 048347           96 PLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRGD---IWDFLKEALP  145 (351)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~~---~~~~l~~~l~  145 (351)
                      ...........   -..+.+.+.-.  ++++.+|+|++....   .+..+...+.
T Consensus       247 P~~vgy~~~~G---~f~~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~lLE  298 (459)
T PRK11331        247 PNGVGFRRKDG---IFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLME  298 (459)
T ss_pred             CCCCCeEecCc---hHHHHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhcc
Confidence            11000000011   11222333322  467999999997552   3445544443

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.94  E-value=6e-05  Score=70.63  Aligned_cols=45  Identities=16%  Similarity=0.115  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+++.++.+.+++..+.  .+.+-++|+.|+||||+|+.+.+.
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSPN--LPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            568899999999999886543  345679999999999999998776

>PRK04195 replication factor C large subunit; Provisional

Probab=97.92  E-value=5.3e-05  Score=74.70  Aligned_cols=48  Identities=13%  Similarity=0.069  Sum_probs=40.3

Q ss_pred             CCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|.++.++.+.+|+..-  +...+.+-|+|+.|+||||+|+.+++.
T Consensus        13 l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~e   62 (482)
T PRK04195         13 LSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAND   62 (482)
T ss_pred             HHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            356899999999999999642  222567889999999999999999998

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.89  E-value=9.6e-05  Score=74.79  Aligned_cols=137  Identities=8%  Similarity=-0.008  Sum_probs=74.1

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      +++||.+.-++.|.+++..+. -...+-++|..|+||||+|+.+.+.......++..-     ...=...+.|...-...
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~P-----CG~C~sCr~I~~G~h~D   89 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQP-----CGVCRACREIDEGRFVD   89 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCC-----CcccHHHHHHhcCCCce
Confidence            578999999999999987653 234556899999999999987766522111111000     00000011111000000


Q ss_pred             C-CCccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347           98 S-ALSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus        98 ~-~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      . ..........+++.+.+...    ..++.-++|||+++..  ..++.+...+.......++|+ |++.+
T Consensus        90 viEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~  160 (830)
T PRK07003         90 YVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQ  160 (830)
T ss_pred             EEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChh
Confidence            0 00000112233333333221    1345568889999866  468888888776666777777 66543

>PRK06893 DNA replication initiation factor; Validated

Probab=97.87  E-value=3.4e-05  Score=68.41  Aligned_cols=37  Identities=5%  Similarity=-0.016  Sum_probs=27.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEE
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYY   79 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~   79 (351)
                      .+.+.+||+.|+|||+||+.+++.  .........|+++
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~   75 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPL   75 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeH
Confidence            356789999999999999999988  4333334455543

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=97.87  E-value=2.5e-05  Score=53.82  Aligned_cols=58  Identities=19%  Similarity=0.241  Sum_probs=48.6

Q ss_pred             CCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCc
Q 048347          242 PHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCA  302 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~  302 (351)
                      |+|++|++ .++ .+..+|. .+..+++|++|++++| .+..+|.. +..+++|++|++++|.
T Consensus         1 p~L~~L~l-~~n-~l~~i~~~~f~~l~~L~~L~l~~N-~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    1 PNLESLDL-SNN-KLTEIPPDSFSNLPNLETLDLSNN-NLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TTESEEEE-TSS-TESEECTTTTTTGTTESEEEETSS-SESEEETTTTTTSTTESEEEETSSS
T ss_pred             CcCcEEEC-CCC-CCCccCHHHHcCCCCCCEeEccCC-ccCccCHHHHcCCCCCCEEeCcCCc
Confidence            67999999 344 5667875 5789999999999998 68888875 7999999999999864

...

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.87  E-value=0.00014  Score=67.64  Aligned_cols=45  Identities=13%  Similarity=0.104  Sum_probs=38.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+++.++.+..++..+.  .+.+.++|..|+||||+|+.+.+.
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~--~~~~ll~G~~G~GKt~~~~~l~~~   61 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKN--MPHLLFAGPPGTGKTTAALALARE   61 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999987643  344689999999999999999877

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

Probab=97.85  E-value=4.3e-05  Score=71.18  Aligned_cols=87  Identities=18%  Similarity=0.234  Sum_probs=53.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHH-HHh
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTL-HNY  118 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l-~~~  118 (351)
                      ++.-...||++|+||||||+.+...  ....|...-=+.  ..++++-.                      +.+.- ...
T Consensus        47 ~l~SmIl~GPPG~GKTTlA~liA~~--~~~~f~~~sAv~--~gvkdlr~----------------------i~e~a~~~~  100 (436)
T COG2256          47 HLHSMILWGPPGTGKTTLARLIAGT--TNAAFEALSAVT--SGVKDLRE----------------------IIEEARKNR  100 (436)
T ss_pred             CCceeEEECCCCCCHHHHHHHHHHh--hCCceEEecccc--ccHHHHHH----------------------HHHHHHHHH
Confidence            3555558999999999999999987  555553311111  22222222                      22222 222


Q ss_pred             cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE
Q 048347          119 LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT  155 (351)
Q Consensus       119 L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv  155 (351)
                      ..+++.+|++|.|...  .+.+.   .+|.-.+|..++|
T Consensus       101 ~~gr~tiLflDEIHRfnK~QQD~---lLp~vE~G~iilI  136 (436)
T COG2256         101 LLGRRTILFLDEIHRFNKAQQDA---LLPHVENGTIILI  136 (436)
T ss_pred             hcCCceEEEEehhhhcChhhhhh---hhhhhcCCeEEEE
Confidence            3478999999999754  23333   3566677888888

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=97.84  E-value=5.1e-06  Score=81.01  Aligned_cols=93  Identities=16%  Similarity=0.071  Sum_probs=78.9

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhh
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELW  312 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~  312 (351)
                      .++.+..+..|..|+||.|  .+.+.|..+..-+++-+|+|++| +++.+|.+ +-+|..|-+|||++ ++++.+|+.+.
T Consensus        95 iP~diF~l~dLt~lDLShN--qL~EvP~~LE~AKn~iVLNLS~N-~IetIPn~lfinLtDLLfLDLS~-NrLe~LPPQ~R  170 (1255)
T KOG0444|consen   95 IPTDIFRLKDLTILDLSHN--QLREVPTNLEYAKNSIVLNLSYN-NIETIPNSLFINLTDLLFLDLSN-NRLEMLPPQIR  170 (1255)
T ss_pred             CCchhcccccceeeecchh--hhhhcchhhhhhcCcEEEEcccC-ccccCCchHHHhhHhHhhhcccc-chhhhcCHHHH
Confidence            4456778899999999543  45678888888899999999998 79999988 45899999999998 68999999999


Q ss_pred             cCCCCCEEEecCCChhHH
Q 048347          313 RIKALRKLESWWPRPELR  330 (351)
Q Consensus       313 ~L~~L~~L~l~~~~~~~~  330 (351)
                      .|.+|++|++++.|-+..
T Consensus       171 RL~~LqtL~Ls~NPL~hf  188 (1255)
T KOG0444|consen  171 RLSMLQTLKLSNNPLNHF  188 (1255)
T ss_pred             HHhhhhhhhcCCChhhHH
Confidence            999999999999885553

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.82  E-value=0.00021  Score=67.82  Aligned_cols=54  Identities=11%  Similarity=-0.005  Sum_probs=41.4

Q ss_pred             ccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347            8 DNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus         8 ~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+++..  -++++|-+.-++.+.+.+..+. -...+-++|+.|+||||+|+.+...
T Consensus         8 ~kyrP~~--~~~iiGq~~~~~~l~~~~~~~~-~~h~~L~~Gp~G~GKTtla~~la~~   61 (363)
T PRK14961          8 RKWRPQY--FRDIIGQKHIVTAISNGLSLGR-IHHAWLLSGTRGVGKTTIARLLAKS   61 (363)
T ss_pred             HHhCCCc--hhhccChHHHHHHHHHHHHcCC-CCeEEEEecCCCCCHHHHHHHHHHH
Confidence            3344433  3568999999999999887643 3456678999999999999998776

>PLN03025 replication factor C subunit; Provisional

Probab=97.80  E-value=0.00013  Score=68.05  Aligned_cols=45  Identities=13%  Similarity=0.069  Sum_probs=35.9

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.++-++.|.+++..+.  ..-+-++|+.|+||||+|..+++.
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~G~GKTtla~~la~~   57 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDGN--MPNLILSGPPGTGKTTSILALAHE   57 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            457898888888888776543  334568999999999999998776

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

Probab=97.79  E-value=7.4e-05  Score=76.54  Aligned_cols=50  Identities=10%  Similarity=0.111  Sum_probs=37.2

Q ss_pred             CccccchhhHH---HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           18 KVDLDLEDKME---ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        18 ~~~vGr~~~~~---~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      ++++|.+..+.   .+.+.+..+  +..-+.++|++|+||||+|+.+++.  ...+|
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~--~~~slLL~GPpGtGKTTLA~aIA~~--~~~~f   80 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKAD--RVGSLILYGPPGVGKTTLARIIANH--TRAHF   80 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHH--hcCcc
Confidence            56889888774   455655543  3556678999999999999999987  54444

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.78  E-value=5.6e-05  Score=71.68  Aligned_cols=101  Identities=17%  Similarity=0.159  Sum_probs=69.3

Q ss_pred             cccCCCCCCCCCCCC-CceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeec--CCccc
Q 048347          228 LELEDDPMPAPEKLP-HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVN--PCAYL  304 (351)
Q Consensus       228 l~l~~~~~~~l~~l~-~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~--~c~~l  304 (351)
                      |.+....+..++.+| +|+.|.+ .++..+..+|..+  .++|++|++++|..+..+|.+      |+.|++.  .|..+
T Consensus        57 L~Is~c~L~sLP~LP~sLtsL~L-snc~nLtsLP~~L--P~nLe~L~Ls~Cs~L~sLP~s------Le~L~L~~n~~~~L  127 (426)
T PRK15386         57 LYIKDCDIESLPVLPNELTEITI-ENCNNLTTLPGSI--PEGLEKLTVCHCPEISGLPES------VRSLEIKGSATDSI  127 (426)
T ss_pred             EEeCCCCCcccCCCCCCCcEEEc-cCCCCcccCCchh--hhhhhheEccCcccccccccc------cceEEeCCCCCccc
Confidence            444454566666666 6999999 6777777777543  258999999999778888865      4444454  34567


Q ss_pred             cccChhhhcCC------------------CCCEEEecCCCh-----hHHhhccccc
Q 048347          305 RKFPEELWRIK------------------ALRKLESWWPRP-----ELRQSLHKFE  337 (351)
Q Consensus       305 ~~lP~~i~~L~------------------~L~~L~l~~~~~-----~~~~~l~~~~  337 (351)
                      ..+|.++..|.                  +|++|++++|..     .+..++..+.
T Consensus       128 ~~LPssLk~L~I~~~n~~~~~~lp~~LPsSLk~L~Is~c~~i~LP~~LP~SLk~L~  183 (426)
T PRK15386        128 KNVPNGLTSLSINSYNPENQARIDNLISPSLKTLSLTGCSNIILPEKLPESLQSIT  183 (426)
T ss_pred             ccCcchHhheeccccccccccccccccCCcccEEEecCCCcccCcccccccCcEEE
Confidence            88888887663                  788999988762     2444555555

>PRK08118 topology modulation protein; Reviewed

Probab=97.78  E-value=1.1e-05  Score=67.96  Aligned_cols=35  Identities=11%  Similarity=0.261  Sum_probs=27.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccc-cCCCeeEE
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVK-NYFDCCAW   76 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~w   76 (351)
                      +.|.|+|++|+||||||+.+++...+. -+|+..+|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            357899999999999999999985544 45666664

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.76  E-value=0.00015  Score=67.35  Aligned_cols=47  Identities=9%  Similarity=0.012  Sum_probs=39.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|.++..+.+..++..+. -..++-++|+.|+|||++|+.+++.
T Consensus        20 ~~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l~~~   66 (316)
T PHA02544         20 IDECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKALCNE   66 (316)
T ss_pred             HHHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHHHHH
Confidence            3678999999999999987542 3467777999999999999999887

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.75  E-value=6.5e-05  Score=69.53  Aligned_cols=47  Identities=17%  Similarity=0.133  Sum_probs=38.5

Q ss_pred             CccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++||+++.++++..++...   ......+.++|+.|+|||+||+.+.+.
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~   53 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANE   53 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999888632   223445778999999999999999987

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.72  E-value=0.00053  Score=62.34  Aligned_cols=141  Identities=10%  Similarity=0.011  Sum_probs=88.8

Q ss_pred             CCCCccccchh---hHHHHHHHHHcc-CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC------eeEEEEEe--CC
Q 048347           15 WDNKVDLDLED---KMEELLDLLIER-QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD------CCAWVYYQ--LS   82 (351)
Q Consensus        15 ~~~~~~vGr~~---~~~~l~~~L~~~-~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~------~~~wv~~~--~~   82 (351)
                      +..+.+||-..   -++.+..++... ..+..=+.|+|-+|.|||+++++.+...  ...++      .++.|...  ++
T Consensus        31 i~~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~h--p~~~d~~~~~~PVv~vq~P~~p~  108 (302)
T PF05621_consen   31 IRADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLH--PPQSDEDAERIPVVYVQMPPEPD  108 (302)
T ss_pred             HhcCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHC--CCCCCCCCccccEEEEecCCCCC
Confidence            34566777433   334445545433 2345568899999999999999998652  22221      24445554  99


Q ss_pred             HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC-ceEEEEEeCCCCh-----hhHHH---HHhhcCCCCCCcEE
Q 048347           83 LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN-KRYLIVIQDVWRG-----DIWDF---LKEALPDHQNGSRI  153 (351)
Q Consensus        83 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~~~-----~~~~~---l~~~l~~~~~gs~I  153 (351)
                      ...+...|+.+++.+..    ...+...+...+...++. +--++|+|++.+.     .+...   ....+.+...=+-|
T Consensus       109 ~~~~Y~~IL~~lgaP~~----~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV  184 (302)
T PF05621_consen  109 ERRFYSAILEALGAPYR----PRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIV  184 (302)
T ss_pred             hHHHHHHHHHHhCcccC----CCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeE
Confidence            99999999999999876    344555555555566654 4457899999764     22222   23344444445666


Q ss_pred             EE-Eeeccc
Q 048347          154 LT-ALIHIV  161 (351)
Q Consensus       154 iv-TR~~~v  161 (351)
                      .+ |++.--
T Consensus       185 ~vGt~~A~~  193 (302)
T PF05621_consen  185 GVGTREAYR  193 (302)
T ss_pred             EeccHHHHH
Confidence            66 765543

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.72  E-value=0.0003  Score=69.70  Aligned_cols=129  Identities=11%  Similarity=0.034  Sum_probs=75.1

Q ss_pred             ccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc------C-----------
Q 048347            8 DNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN------Y-----------   70 (351)
Q Consensus         8 ~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~------~-----------   70 (351)
                      +.+|...+  ++++|-+.-++.|...+..+. -...+-++|+.|+||||+|+.++.......      +           
T Consensus         8 ~KyRP~~f--~diiGq~~~v~~L~~~i~~~r-l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~   84 (546)
T PRK14957          8 RKYRPQSF--AEVAGQQHALNSLVHALETQK-VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINN   84 (546)
T ss_pred             HHHCcCcH--HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhc
Confidence            34444433  468999999999999886542 335567899999999999999876411100      0           


Q ss_pred             --CCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHH-hcCCceEEEEEeCCCCh--hhHHHHHhhcC
Q 048347           71 --FDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHN-YLKNKRYLIVIQDVWRG--DIWDFLKEALP  145 (351)
Q Consensus        71 --F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVLDdv~~~--~~~~~l~~~l~  145 (351)
                        |....++...                 ..   ....+..++.+.+.. -..+++-++|+|++...  ..++.+...+.
T Consensus        85 ~~~~dlieidaa-----------------s~---~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LE  144 (546)
T PRK14957         85 NSFIDLIEIDAA-----------------SR---TGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLE  144 (546)
T ss_pred             CCCCceEEeecc-----------------cc---cCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHh
Confidence              1111111110                 00   011111222222221 12356678999999755  56788888887


Q ss_pred             CCCCCcEEEE-Eeec
Q 048347          146 DHQNGSRILT-ALIH  159 (351)
Q Consensus       146 ~~~~gs~Iiv-TR~~  159 (351)
                      ......++|. |.+.
T Consensus       145 epp~~v~fIL~Ttd~  159 (546)
T PRK14957        145 EPPEYVKFILATTDY  159 (546)
T ss_pred             cCCCCceEEEEECCh
Confidence            7666677766 6443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.72  E-value=0.00027  Score=70.60  Aligned_cols=134  Identities=10%  Similarity=0.035  Sum_probs=74.3

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc---C----CCeeEEEEEeCCHHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN---Y----FDCCAWVYYQLSLDMMLDAI   90 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~---~----F~~~~wv~~~~~~~~~~~~i   90 (351)
                      +++||-+.-++.|.+.+..+. -.+.+-++|..|+||||+|+.+.+......   .    .+.|       ..-..-+.|
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PC-------G~C~sC~~I   87 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPC-------GQCRACTEI   87 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCC-------cccHHHHHH
Confidence            578999999999999987653 345567899999999999988865421100   0    0000       000001111


Q ss_pred             HHHhCCCC-CCccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           91 MKSLMPLS-ALSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        91 ~~~~~~~~-~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ...-.... ..........+++.+.+...    ..++.-++|||+++..  ..++.+...+.....+.++|+ |.+.
T Consensus        88 ~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep  164 (700)
T PRK12323         88 DAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDP  164 (700)
T ss_pred             HcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCCh
Confidence            00000000 00000112334443333322    1456678999999865  578888888877666677776 6544

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.72  E-value=0.00029  Score=56.17  Aligned_cols=87  Identities=5%  Similarity=0.028  Sum_probs=48.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      ..+.|+|+.|+||||+|+.+...  .......++.+... ..................     ...........+....+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~   75 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARE--LGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKK-----ASGSGELRLRLALALAR   75 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhc--cCCCCCCEEEECCEEccccCHHHHHhhhhhccC-----CCCCHHHHHHHHHHHHH
Confidence            46789999999999999999988  44443334555444 111111111111111111     12223333334444444


Q ss_pred             Cce-EEEEEeCCCChh
Q 048347          121 NKR-YLIVIQDVWRGD  135 (351)
Q Consensus       121 ~k~-~LlVLDdv~~~~  135 (351)
                      ..+ .++++|++....
T Consensus        76 ~~~~~viiiDei~~~~   91 (148)
T smart00382       76 KLKPDVLILDEITSLL   91 (148)
T ss_pred             hcCCCEEEEECCcccC
Confidence            443 899999998764

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.

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=97.71  E-value=4.3e-06  Score=77.52  Aligned_cols=88  Identities=19%  Similarity=0.114  Sum_probs=73.1

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCC-CCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhh
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHG-GFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELW  312 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~-~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~  312 (351)
                      ..|.++.+..|..|.+  +.-+++-+|...+ .++++.+|||++| +++++|.++..|++|++||+++ ..+..+|.++|
T Consensus       220 ~lPef~gcs~L~Elh~--g~N~i~~lpae~~~~L~~l~vLDLRdN-klke~Pde~clLrsL~rLDlSN-N~is~Lp~sLg  295 (565)
T KOG0472|consen  220 FLPEFPGCSLLKELHV--GENQIEMLPAEHLKHLNSLLVLDLRDN-KLKEVPDEICLLRSLERLDLSN-NDISSLPYSLG  295 (565)
T ss_pred             cCCCCCccHHHHHHHh--cccHHHhhHHHHhcccccceeeecccc-ccccCchHHHHhhhhhhhcccC-CccccCCcccc
Confidence            3456667777777777  3345556777654 8999999999999 7999999999999999999998 56999999999


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      +| +|+.|-+.|-|
T Consensus       296 nl-hL~~L~leGNP  308 (565)
T KOG0472|consen  296 NL-HLKFLALEGNP  308 (565)
T ss_pred             cc-eeeehhhcCCc
Confidence            99 89999998866

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00022  Score=73.49  Aligned_cols=147  Identities=10%  Similarity=0.030  Sum_probs=77.6

Q ss_pred             cccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe-eEEEEEe-CCHH
Q 048347            7 IDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC-CAWVYYQ-LSLD   84 (351)
Q Consensus         7 ~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~~-~~~~   84 (351)
                      .+.+|...+  +++||-+.-++.|.+++..+. -...+-++|+.|+||||+|+.+++.......... -|-.+-+ ..+.
T Consensus         7 aeKyRP~tF--ddIIGQe~Iv~~LknaI~~~r-l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~   83 (944)
T PRK14949          7 ARKWRPATF--EQMVGQSHVLHALTNALTQQR-LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIA   83 (944)
T ss_pred             HHHhCCCCH--HHhcCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHh
Confidence            334554433  568999999999999887642 2345578999999999999999877322111110 0000000 0000


Q ss_pred             HHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHH-hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           85 MMLDAIMKSLMPLSALSEILDNDFEMKKNTLHN-YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        85 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~-~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      +.....+-.+.....   ....+..++.+.+.. -..+++-++|||++...  +.++.+...+.......++|+ |.+.
T Consensus        84 ~g~~~DviEidAas~---~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~  159 (944)
T PRK14949         84 QGRFVDLIEVDAASR---TKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDP  159 (944)
T ss_pred             cCCCceEEEeccccc---cCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCc
Confidence            000000000000000   011111222222221 12467779999999765  678888888877666777777 5443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.70  E-value=0.00023  Score=72.08  Aligned_cols=135  Identities=13%  Similarity=0.082  Sum_probs=82.5

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC---eeEEEEEe-----CCHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD---CCAWVYYQ-----LSLDMMLDA   89 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~---~~~wv~~~-----~~~~~~~~~   89 (351)
                      ++++|.+.....+.+.+...  ....+.|+|+.|+||||+|+.+++..+....+.   ..-|+.+.     .+...+...
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~--~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~  231 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASP--FPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNP  231 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcC--CCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHH
Confidence            46899999999888877543  345688999999999999999988743333332   23466655     122222211


Q ss_pred             HH---------------HHhCCCCC--------------CccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHH
Q 048347           90 IM---------------KSLMPLSA--------------LSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWD  138 (351)
Q Consensus        90 i~---------------~~~~~~~~--------------~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~  138 (351)
                      ++               ...+....              ..+.+..+. ..+..+.+.+++++++++-|+.|..  ..|+
T Consensus       232 llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~-~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~  310 (615)
T TIGR02903       232 LLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDP-LLQNKLLKVLEDKRVEFSSSYYDPDDPNVPK  310 (615)
T ss_pred             hcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCH-HHHHHHHHHHhhCeEEeecceeccCCcccch
Confidence            11               11111000              011222332 2467788888888888887776654  4578


Q ss_pred             HHHhhcCCCCCCcEEEE
Q 048347          139 FLKEALPDHQNGSRILT  155 (351)
Q Consensus       139 ~l~~~l~~~~~gs~Iiv  155 (351)
                      .++..+....+...+++
T Consensus       311 ~ik~~~~~~~~~~~VLI  327 (615)
T TIGR02903       311 YIKKLFEEGAPADFVLI  327 (615)
T ss_pred             hhhhhcccCccceEEEE
Confidence            88777766655555665

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.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.0003  Score=70.40  Aligned_cols=136  Identities=10%  Similarity=0.022  Sum_probs=73.9

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      +++||.+.-.+.|.+++..+. -...+-++|+.|+||||+|+.+.+........+...     ...-..-+.|...-...
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~p-----Cg~C~sC~~I~~g~hpD   88 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTP-----CEVCATCKAVNEGRFID   88 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCC-----CccCHHHHHHhcCCCCc
Confidence            578999999999999997653 245667899999999999998866522111110000     00000001110000000


Q ss_pred             C-CCccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           98 S-ALSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        98 ~-~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      . ....-.....+++.+.+...    ..++.-++|+|++...  ...+.+...+.....+.++|+ |.+.
T Consensus        89 viEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~  158 (702)
T PRK14960         89 LIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDP  158 (702)
T ss_pred             eEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECCh
Confidence            0 00000112233333322211    2356678999999865  567778877776555667777 6553

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.69  E-value=9.7e-05  Score=65.10  Aligned_cols=53  Identities=8%  Similarity=0.076  Sum_probs=36.6

Q ss_pred             chhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEE
Q 048347           23 LEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYY   79 (351)
Q Consensus        23 r~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~   79 (351)
                      -+..++.+.+++..  .....+.|+|..|+|||+||+.+++.  ........++++.
T Consensus        22 ~~~~~~~l~~~~~~--~~~~~lll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~   74 (226)
T TIGR03420        22 NAELLAALRQLAAG--KGDRFLYLWGESGSGKSHLLQAACAA--AEERGKSAIYLPL   74 (226)
T ss_pred             cHHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeH
Confidence            45566777777543  23567889999999999999999987  4333333444443

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.68  E-value=0.00048  Score=69.86  Aligned_cols=139  Identities=15%  Similarity=0.143  Sum_probs=91.3

Q ss_pred             CCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHH
Q 048347           15 WDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIM   91 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~   91 (351)
                      ......|-|    ..+.+.|... .+.+++.|..++|.|||||+.+....  ..+ =..+.|++..   -++..+..-++
T Consensus        16 ~~~~~~v~R----~rL~~~L~~~-~~~RL~li~APAGfGKttl~aq~~~~--~~~-~~~v~Wlslde~dndp~rF~~yLi   87 (894)
T COG2909          16 VRPDNYVVR----PRLLDRLRRA-NDYRLILISAPAGFGKTTLLAQWREL--AAD-GAAVAWLSLDESDNDPARFLSYLI   87 (894)
T ss_pred             CCccccccc----HHHHHHHhcC-CCceEEEEeCCCCCcHHHHHHHHHHh--cCc-ccceeEeecCCccCCHHHHHHHHH
Confidence            334555554    4555555544 35789999999999999999999753  222 2347999988   88888988888


Q ss_pred             HHhCCCCCC--c-------cCCCCCHHHHHHHHHHhcCC--ceEEEEEeCCCChh---hHHHHHhhcCCCCCCcEEEE-E
Q 048347           92 KSLMPLSAL--S-------EILDNDFEMKKNTLHNYLKN--KRYLIVIQDVWRGD---IWDFLKEALPDHQNGSRILT-A  156 (351)
Q Consensus        92 ~~~~~~~~~--~-------~~~~~~~~~~~~~l~~~L~~--k~~LlVLDdv~~~~---~~~~l~~~l~~~~~gs~Iiv-T  156 (351)
                      ..+..-...  +       .....+...+...+..-+.+  +++.+||||..-..   --..+.-.+.+...+-.+|+ |
T Consensus        88 ~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~S  167 (894)
T COG2909          88 AALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTS  167 (894)
T ss_pred             HHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEe
Confidence            888742220  0       02334445566666665544  58999999997542   22333344455556778888 9


Q ss_pred             eeccc
Q 048347          157 LIHIV  161 (351)
Q Consensus       157 R~~~v  161 (351)
                      |+..-
T Consensus       168 R~rP~  172 (894)
T COG2909         168 RSRPQ  172 (894)
T ss_pred             ccCCC
Confidence            98764

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.67  E-value=6.1e-05  Score=48.22  Aligned_cols=40  Identities=15%  Similarity=0.171  Sum_probs=29.1

Q ss_pred             CcccEEEEecCCccccccccccccCCccEEeecCCccccccC
Q 048347          267 PRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFP  308 (351)
Q Consensus       267 ~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP  308 (351)
                      ++|++|++++| .+.++|..+++|++|++|++++| .+..+|
T Consensus         1 ~~L~~L~l~~N-~i~~l~~~l~~l~~L~~L~l~~N-~i~~i~   40 (44)
T PF12799_consen    1 KNLEELDLSNN-QITDLPPELSNLPNLETLNLSNN-PISDIS   40 (44)
T ss_dssp             TT-SEEEETSS-S-SSHGGHGTTCTTSSEEEETSS-CCSBEG
T ss_pred             CcceEEEccCC-CCcccCchHhCCCCCCEEEecCC-CCCCCc
Confidence            46788888888 68888877888888888888885 465554

...

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.64  E-value=0.00064  Score=67.59  Aligned_cols=134  Identities=10%  Similarity=0.067  Sum_probs=71.7

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC--CeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF--DCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      ++++|-+.-++.+.+++..+. -.+.+-++|+.|+||||+|+.+..........  ..|-. +      ..-..+...-.
T Consensus        16 ~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~-C------~~C~~i~~~~~   87 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGV-C------SACLEIDSGRF   87 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCC-C------HHHHHHhcCCC
Confidence            568999999999999887643 23455689999999999999886552111100  00000 0      00000000000


Q ss_pred             CCC-CCccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           96 PLS-ALSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        96 ~~~-~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ... ..........+++.+.+...    ..+++-++|+|+++..  +..+.+...+.......++|. |.+.
T Consensus        88 ~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~  159 (527)
T PRK14969         88 VDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDP  159 (527)
T ss_pred             CceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCCh
Confidence            000 00000112223332222211    1356678999999865  467778888877655677777 7544

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.64  E-value=0.00021  Score=67.92  Aligned_cols=57  Identities=12%  Similarity=0.064  Sum_probs=42.7

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc--C---------CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER--Q---------PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~--~---------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      +.+..+++.|+++.++++.+.+...  .         ...+-+.++|+.|+|||++|+++++.  ....|
T Consensus       117 p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~--l~~~~  184 (364)
T TIGR01242       117 PNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE--TNATF  184 (364)
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh--CCCCE
Confidence            4445567899999999999887421  0         12345789999999999999999998  44443

Many proteins may score above the trusted cutoff because an internal

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.61  E-value=0.00018  Score=69.80  Aligned_cols=143  Identities=10%  Similarity=0.056  Sum_probs=75.1

Q ss_pred             cccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC--CCeeEEEEEeCCHH
Q 048347            7 IDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY--FDCCAWVYYQLSLD   84 (351)
Q Consensus         7 ~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~~~~~~~   84 (351)
                      .+.+|.-.+  +++||-+.-+..|..++..+. -...+-++|+.|+||||+|+.+.........  +.. |..+  ....
T Consensus         9 ~~KyRP~~f--~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~p-Cg~C--~sC~   82 (484)
T PRK14956          9 SRKYRPQFF--RDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEP-CNEC--TSCL   82 (484)
T ss_pred             HHHhCCCCH--HHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccc-cCCC--cHHH
Confidence            334444433  568999999999999887653 2345678999999999999999776221110  110 1111  0111


Q ss_pred             HHHHHHHHHhCCCCCCccCCCCCHHHH---HHHHHHh-cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347           85 MMLDAIMKSLMPLSALSEILDNDFEMK---KNTLHNY-LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus        85 ~~~~~i~~~~~~~~~~~~~~~~~~~~~---~~~l~~~-L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                      ++...+...+..-..   ......+++   .+.+... ..++.-++|+|++...  ++++.+...+........+|. |.
T Consensus        83 ~i~~g~~~dviEIda---as~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTt  159 (484)
T PRK14956         83 EITKGISSDVLEIDA---ASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATT  159 (484)
T ss_pred             HHHccCCccceeech---hhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecC
Confidence            111111000000000   011112222   2222211 2456668999999755  578888877765544555555 54


Q ss_pred             e
Q 048347          158 I  158 (351)
Q Consensus       158 ~  158 (351)
                      +
T Consensus       160 e  160 (484)
T PRK14956        160 E  160 (484)
T ss_pred             C
Confidence            3

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=97.61  E-value=8.3e-05  Score=62.77  Aligned_cols=86  Identities=23%  Similarity=0.245  Sum_probs=36.7

Q ss_pred             CCCC-CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccc-cccCCccEEeecCCccccccC--hhh
Q 048347          236 PAPE-KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMET-GAMQKLKSLIVNPCAYLRKFP--EEL  311 (351)
Q Consensus       236 ~~l~-~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i-~~L~~L~~L~l~~c~~l~~lP--~~i  311 (351)
                      +.++ .+.+|+.|+++.+  .+..++ .+..++.|++|++++| .+.+++..+ ..+++|+.|+++++ ++..+-  ..+
T Consensus        35 e~L~~~l~~L~~L~Ls~N--~I~~l~-~l~~L~~L~~L~L~~N-~I~~i~~~l~~~lp~L~~L~L~~N-~I~~l~~l~~L  109 (175)
T PF14580_consen   35 ENLGATLDKLEVLDLSNN--QITKLE-GLPGLPRLKTLDLSNN-RISSISEGLDKNLPNLQELYLSNN-KISDLNELEPL  109 (175)
T ss_dssp             -S--TT-TT--EEE-TTS----S--T-T----TT--EEE--SS----S-CHHHHHH-TT--EEE-TTS----SCCCCGGG
T ss_pred             cchhhhhcCCCEEECCCC--CCcccc-CccChhhhhhcccCCC-CCCccccchHHhCCcCCEEECcCC-cCCChHHhHHH
Confidence            3444 4678999999333  344454 4667899999999999 688886555 46899999999984 555443  345


Q ss_pred             hcCCCCCEEEecCCC
Q 048347          312 WRIKALRKLESWWPR  326 (351)
Q Consensus       312 ~~L~~L~~L~l~~~~  326 (351)
                      ..+++|+.|++.+.|
T Consensus       110 ~~l~~L~~L~L~~NP  124 (175)
T PF14580_consen  110 SSLPKLRVLSLEGNP  124 (175)
T ss_dssp             GG-TT--EEE-TT-G
T ss_pred             HcCCCcceeeccCCc
Confidence            678899999999866

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.58  E-value=0.00027  Score=66.14  Aligned_cols=49  Identities=18%  Similarity=0.143  Sum_probs=40.0

Q ss_pred             CCCccccchhhHHHHHHHHHc---cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIE---RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.+++|+++.++.+..++..   .+.....+.++|+.|+|||+||+.+++.
T Consensus        23 ~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~   74 (328)
T PRK00080         23 SLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANE   74 (328)
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHH
Confidence            446799999999999888864   1233456779999999999999999998

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=97.58  E-value=0.00042  Score=65.86  Aligned_cols=113  Identities=11%  Similarity=0.063  Sum_probs=78.4

Q ss_pred             CCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe--eEEEE-Ee-CCHHHHHHH
Q 048347           16 DNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC--CAWVY-YQ-LSLDMMLDA   89 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~-~~-~~~~~~~~~   89 (351)
                      ..+.++||+.+...+.+++...  .+...-+-|.|-.|.|||.+...++.+  .......  ++.+. .+ ....+++..
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~--~~~~~~~~~~v~inc~sl~~~~aiF~k  225 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDS--LSKSSKSPVTVYINCTSLTEASAIFKK  225 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHh--hhhhcccceeEEEeeccccchHHHHHH
Confidence            4577999999999999999753  355677788899999999999999998  4333332  23322 22 677889999


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC--ceEEEEEeCCCCh
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYLKN--KRYLIVIQDVWRG  134 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~--k~~LlVLDdv~~~  134 (351)
                      |...+.....    ......+..+.+.+....  +.+++|+|.++..
T Consensus       226 I~~~~~q~~~----s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L  268 (529)
T KOG2227|consen  226 IFSSLLQDLV----SPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHL  268 (529)
T ss_pred             HHHHHHHHhc----CCchhHHHHHHHHHHHhcccceEEEEechhhHH
Confidence            9988844333    222334555555555544  3688899988544

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.56  E-value=0.00067  Score=68.48  Aligned_cols=46  Identities=17%  Similarity=0.078  Sum_probs=38.1

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++||.+.-++.|.+++..+. -.+-+-++|+.|+||||+|+.+...
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk~   61 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAKS   61 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            578999999999999987653 2356678999999999999988665

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.55  E-value=0.00076  Score=66.44  Aligned_cols=132  Identities=8%  Similarity=0.001  Sum_probs=72.7

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC------CCeeEEEEEeCCHHHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY------FDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~------F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      .+++|-+.-+..|...+..+. -..-+-++|+.|+||||+|+.+++.......      +.. |-.+-      --..+.
T Consensus        21 ~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~-C~~C~------~C~~i~   92 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKT-CEQCT------NCISFN   92 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCC-CCCCh------HHHHHh
Confidence            568999998888888776542 2345678999999999999999766221111      110 00000      000110


Q ss_pred             HHhCCCCC-CccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347           92 KSLMPLSA-LSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus        92 ~~~~~~~~-~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                      ........ ...-.....+++.+.+...    +.+++-++|+|+++..  .+++.+...+......+++|. |.
T Consensus        93 ~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTt  166 (507)
T PRK06645         93 NHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATT  166 (507)
T ss_pred             cCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeC
Confidence            00000000 0000112333333333221    2456778999999865  578888888877666667666 53

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=97.55  E-value=1.2e-05  Score=78.51  Aligned_cols=112  Identities=15%  Similarity=0.167  Sum_probs=91.7

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhh-hc
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEEL-WR  313 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i-~~  313 (351)
                      ...++.+|.||.+.+..|......+|..+-.+..|.+|+|+.| .+.+.|.++.+-.++-+|+|++ +.++.+|.++ .|
T Consensus        71 hGELs~Lp~LRsv~~R~N~LKnsGiP~diF~l~dLt~lDLShN-qL~EvP~~LE~AKn~iVLNLS~-N~IetIPn~lfin  148 (1255)
T KOG0444|consen   71 HGELSDLPRLRSVIVRDNNLKNSGIPTDIFRLKDLTILDLSHN-QLREVPTNLEYAKNSIVLNLSY-NNIETIPNSLFIN  148 (1255)
T ss_pred             hhhhccchhhHHHhhhccccccCCCCchhcccccceeeecchh-hhhhcchhhhhhcCcEEEEccc-CccccCCchHHHh
Confidence            3566789999999997777777779999999999999999999 7999999999999999999998 6899999887 59


Q ss_pred             CCCCCEEEecCCChhH-HhhccccccCceeeEEecC
Q 048347          314 IKALRKLESWWPRPEL-RQSLHKFEEIDRLDMQIYP  348 (351)
Q Consensus       314 L~~L~~L~l~~~~~~~-~~~l~~~~~~~~~~~~~~P  348 (351)
                      |+-|-.||+++..-++ .++++++..++..++.+=|
T Consensus       149 LtDLLfLDLS~NrLe~LPPQ~RRL~~LqtL~Ls~NP  184 (1255)
T KOG0444|consen  149 LTDLLFLDLSNNRLEMLPPQIRRLSMLQTLKLSNNP  184 (1255)
T ss_pred             hHhHhhhccccchhhhcCHHHHHHhhhhhhhcCCCh
Confidence            9999999999876444 4455555555555555544

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.54  E-value=0.00021  Score=63.20  Aligned_cols=34  Identities=21%  Similarity=0.273  Sum_probs=29.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY   78 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~   78 (351)
                      .++|+|..|.|||||+..+...  ....|..+.+++
T Consensus        15 r~viIG~sGSGKT~li~~lL~~--~~~~f~~I~l~t   48 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYY--LRHKFDHIFLIT   48 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHh--hcccCCEEEEEe
Confidence            5668899999999999999988  888997766554

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.53  E-value=0.00088  Score=64.40  Aligned_cols=47  Identities=9%  Similarity=-0.156  Sum_probs=37.1

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|-+.-++.|.+++..+. -..-+-++|+.|+||||+|..+.+.
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~   61 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKA   61 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHH
Confidence            3578999988888988886542 2344668999999999999887665

>PRK08116 hypothetical protein; Validated

Probab=97.53  E-value=0.00026  Score=64.25  Aligned_cols=74  Identities=15%  Similarity=0.144  Sum_probs=46.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      .-+.++|..|+|||.||.++++.  +......+++++    ..+++..+.........      .+..    .+.+.+.+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~----~~~ll~~i~~~~~~~~~------~~~~----~~~~~l~~  178 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVN----FPQLLNRIKSTYKSSGK------EDEN----EIIRSLVN  178 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEE----HHHHHHHHHHHHhcccc------ccHH----HHHHHhcC
Confidence            34779999999999999999998  544433444543    45666666554433211      1222    23344444


Q ss_pred             ceEEEEEeCCC
Q 048347          122 KRYLIVIQDVW  132 (351)
Q Consensus       122 k~~LlVLDdv~  132 (351)
                      -. ||||||+-
T Consensus       179 ~d-lLviDDlg  188 (268)
T PRK08116        179 AD-LLILDDLG  188 (268)
T ss_pred             CC-EEEEeccc
Confidence            44 88999993

>PRK10536 hypothetical protein; Provisional

Probab=97.51  E-value=0.00064  Score=60.59  Aligned_cols=43  Identities=12%  Similarity=0.098  Sum_probs=35.9

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+.++......+..++...    .+|.+.|.+|.|||+||.++..+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~----~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESK----QLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcC----CeEEEECCCCCCHHHHHHHHHHH
Confidence            44677999999999988653    48889999999999999998774

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.50  E-value=0.001  Score=65.81  Aligned_cols=145  Identities=12%  Similarity=0.059  Sum_probs=76.3

Q ss_pred             cccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347            7 IDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus         7 ~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      .+.||.-.+  +++||-+.-++.|.+++..+. -...+-++|+.|+||||+|+.+.........+...-     ...=..
T Consensus         7 ~~kyRP~~f--~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~p-----Cg~C~~   78 (509)
T PRK14958          7 ARKWRPRCF--QEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANP-----CNDCEN   78 (509)
T ss_pred             HHHHCCCCH--HHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCccc-----CCCCHH
Confidence            344555433  468999999999999997653 234566899999999999988866522111111000     000000


Q ss_pred             HHHHHHHhCCCC-CCccCCCCCHHHHHHHHHH----hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eee
Q 048347           87 LDAIMKSLMPLS-ALSEILDNDFEMKKNTLHN----YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALI  158 (351)
Q Consensus        87 ~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~----~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~  158 (351)
                      -+.|...-..+. ..........+++.+.+..    -..++.-++|+|+++..  +..+.+...+.......++|. |.+
T Consensus        79 C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd  158 (509)
T PRK14958         79 CREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTD  158 (509)
T ss_pred             HHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECC
Confidence            000000000000 0000011223333222211    11356668889999865  577888888777666777777 644


Q ss_pred             c
Q 048347          159 H  159 (351)
Q Consensus       159 ~  159 (351)
                      .
T Consensus       159 ~  159 (509)
T PRK14958        159 H  159 (509)
T ss_pred             h
Confidence            3

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.50  E-value=0.001  Score=66.91  Aligned_cols=138  Identities=9%  Similarity=0.016  Sum_probs=71.1

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC--CCeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY--FDCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      +++||-+.-++.|.+++..+. -...+-++|..|+||||+|+.+.........  ......-.  ...-..-+.|...-.
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~p--Cg~C~~C~~i~~g~h   92 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATP--CGVCQACRDIDSGRF   92 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCC--CCccHHHHHHHcCCC
Confidence            568898888888888887653 3456678999999999999888443111000  00000000  000001111100000


Q ss_pred             CCC-CCccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eee
Q 048347           96 PLS-ALSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALI  158 (351)
Q Consensus        96 ~~~-~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~  158 (351)
                      ... ....-.....+++.+.+...    ..++.-++|||+++..  +.++.+...+.......++|+ |.+
T Consensus        93 ~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd  163 (618)
T PRK14951         93 VDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTD  163 (618)
T ss_pred             CceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECC
Confidence            000 00000112233333333221    1245568899999865  577888888877665667776 644

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.49  E-value=0.00084  Score=59.20  Aligned_cols=106  Identities=11%  Similarity=0.110  Sum_probs=65.9

Q ss_pred             CCCCCccccchhhHHHHHHHHHc--cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIE--RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      .+.-++++|.|+.++.|++-...  .+....-+-+||..|.|||++++++.+...-++    .--|.+.           
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~G----LRlIev~-----------   87 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQG----LRLIEVS-----------   87 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC----ceEEEEC-----------
Confidence            45567799999999988664422  122344555799999999999999988722222    1223322           


Q ss_pred             HHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC---ChhhHHHHHhhcCC
Q 048347           92 KSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW---RGDIWDFLKEALPD  146 (351)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~---~~~~~~~l~~~l~~  146 (351)
                            .    .+..+...+.+.++.  +..||+|.+||+.   +...+..++..+..
T Consensus        88 ------k----~~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeG  133 (249)
T PF05673_consen   88 ------K----EDLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEG  133 (249)
T ss_pred             ------H----HHhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcC
Confidence                  0    022334444444442  3579999999995   22467777776653

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.49  E-value=0.001  Score=65.19  Aligned_cols=46  Identities=9%  Similarity=0.010  Sum_probs=36.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++||.+.-.+.|...+..+. -...+-++|+.|+||||+|+.+.+.
T Consensus        14 ~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            569999888787877776542 2345678999999999999999765

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.49  E-value=0.0013  Score=62.04  Aligned_cols=46  Identities=9%  Similarity=0.020  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|.++.++.+.+++..+. -...+-++|+.|+||||+|+.+...
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~   59 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKA   59 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            467999999999999887643 3456778999999999999887654

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.48  E-value=0.00066  Score=68.48  Aligned_cols=133  Identities=12%  Similarity=0.030  Sum_probs=73.7

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      +++||-+.-++.|...+..+. -...+-++|..|+||||+|+.+.........+...     ...    .....+++...
T Consensus        16 ~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~-----pCg----~C~~C~~i~~g   85 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLNCETGITAT-----PCG----ECDNCREIEQG   85 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCC-----CCC----CCHHHHHHHcC
Confidence            568999999999988887653 23456789999999999999987662221110000     000    00111112111


Q ss_pred             CCC--ccC---CCCCHHHHHHHHHH----hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347           98 SAL--SEI---LDNDFEMKKNTLHN----YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus        98 ~~~--~~~---~~~~~~~~~~~l~~----~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      ...  .++   .....+++.+.+..    -..+++-++|||++...  ..++.+...+.......++|. |.+.+
T Consensus        86 ~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~  160 (647)
T PRK07994         86 RFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ  160 (647)
T ss_pred             CCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCcc
Confidence            000  000   01122333222211    12466778999999755  578888887776655666666 54433

>PRK07261 topology modulation protein; Provisional

Probab=97.47  E-value=0.00025  Score=59.92  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|+|++|+||||||+++...
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~   23 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQH   23 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            5789999999999999999766

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=97.43  E-value=1.3e-05  Score=77.36  Aligned_cols=111  Identities=23%  Similarity=0.211  Sum_probs=80.5

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhc
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ..+.+.++..|.+|+|+.+  .+..+|..++.++ |++|-+++| +++.+|.++|.+..|..|+.+. ..+..+|..+++
T Consensus       113 ip~~i~~L~~lt~l~ls~N--qlS~lp~~lC~lp-Lkvli~sNN-kl~~lp~~ig~~~tl~~ld~s~-nei~slpsql~~  187 (722)
T KOG0532|consen  113 IPEAICNLEALTFLDLSSN--QLSHLPDGLCDLP-LKVLIVSNN-KLTSLPEEIGLLPTLAHLDVSK-NEIQSLPSQLGY  187 (722)
T ss_pred             cchhhhhhhHHHHhhhccc--hhhcCChhhhcCc-ceeEEEecC-ccccCCcccccchhHHHhhhhh-hhhhhchHHhhh
Confidence            4456678888888888433  4446777777777 888888888 7888998888888888888886 468888888888


Q ss_pred             CCCCCEEEecC-----CChhHHhhccccccC-ceeeEEecCCC
Q 048347          314 IKALRKLESWW-----PRPELRQSLHKFEEI-DRLDMQIYPIG  350 (351)
Q Consensus       314 L~~L~~L~l~~-----~~~~~~~~l~~~~~~-~~~~~~~~P~~  350 (351)
                      |.+|+.|+++.     .++|+. .|.-.+.. -|+++..||..
T Consensus       188 l~slr~l~vrRn~l~~lp~El~-~LpLi~lDfScNkis~iPv~  229 (722)
T KOG0532|consen  188 LTSLRDLNVRRNHLEDLPEELC-SLPLIRLDFSCNKISYLPVD  229 (722)
T ss_pred             HHHHHHHHHhhhhhhhCCHHHh-CCceeeeecccCceeecchh
Confidence            88888888754     556665 33322211 26777777753

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.43  E-value=0.0013  Score=64.33  Aligned_cols=131  Identities=14%  Similarity=0.083  Sum_probs=69.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc--CCCeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN--YFDCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~--~F~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      +++||-+.-++.|.+.+..+. -..-+-++|+.|+||||+|+.+........  ..+.|       ..-..-+.|.....
T Consensus        13 ~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pC-------g~C~~C~~i~~~~~   84 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPC-------GTCHNCISIKNSNH   84 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCc-------cccHHHHHHhccCC
Confidence            568999988888888776542 233566899999999999988865310000  00000       00000011110000


Q ss_pred             CCCC-CccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-E
Q 048347           96 PLSA-LSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-A  156 (351)
Q Consensus        96 ~~~~-~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-T  156 (351)
                      .+.. ...-+....+++.+.+...    +.++.-++|+|++...  ++++.+...+.+.....++|. |
T Consensus        85 ~Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964         85 PDVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             CCEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEe
Confidence            0000 0000112223322222111    1356668999999754  567888888877666777777 5

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.41  E-value=0.00098  Score=66.48  Aligned_cols=56  Identities=11%  Similarity=0.124  Sum_probs=42.0

Q ss_pred             ccccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347            6 MIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus         6 ~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+.+|+..+  .+++|.+.-++.+.+.+..+. -.+-+-++|+.|+||||+|+.+...
T Consensus         6 ~~~KyRP~~F--~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk~   61 (605)
T PRK05896          6 FYRKYRPHNF--KQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAKA   61 (605)
T ss_pred             HHHHhCCCCH--HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHH
Confidence            3344555433  578999999999999886643 2355668999999999999998665

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.41  E-value=0.00052  Score=72.02  Aligned_cols=45  Identities=18%  Similarity=0.251  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++||+++++.+++.|.....+ .+ .++|.+|+|||++|+.++..
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~-n~-lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKN-NP-ILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccC-Ce-EEECCCCCCHHHHHHHHHHH
Confidence            56899999999999999765433 23 48999999999999998776

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.40  E-value=0.00047  Score=64.70  Aligned_cols=102  Identities=9%  Similarity=0.004  Sum_probs=63.0

Q ss_pred             HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC-Ce-eEEEEEe---CCHHHHHHHHHHHhCCCCCCcc
Q 048347           28 EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF-DC-CAWVYYQ---LSLDMMLDAIMKSLMPLSALSE  102 (351)
Q Consensus        28 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~-~~wv~~~---~~~~~~~~~i~~~~~~~~~~~~  102 (351)
                      .++++.+..=+ +-..+.|+|..|+|||||++.+.+.  +.... +. ++|+.+.   -++.++.+.+...+........
T Consensus       121 ~RvID~l~PiG-kGQR~LIvG~pGtGKTTLl~~la~~--i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~  197 (380)
T PRK12608        121 MRVVDLVAPIG-KGQRGLIVAPPRAGKTVLLQQIAAA--VAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRP  197 (380)
T ss_pred             HhhhhheeecC-CCceEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCC
Confidence            34566555322 2245689999999999999998887  44433 33 4676777   8889999999887765433110


Q ss_pred             C-CCCCHHHHHHHHHHhc--CCceEEEEEeCCC
Q 048347          103 I-LDNDFEMKKNTLHNYL--KNKRYLIVIQDVW  132 (351)
Q Consensus       103 ~-~~~~~~~~~~~l~~~L--~~k~~LlVLDdv~  132 (351)
                      . .............+.+  .+++.++|+|++-
T Consensus       198 ~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        198 PDEHIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence            0 0001111111222222  5899999999994

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.40  E-value=0.0019  Score=61.45  Aligned_cols=47  Identities=9%  Similarity=0.014  Sum_probs=38.9

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      =++++|.+.-.+.+.+.+..+. -.+.+-++|+.|+||||+|+.+.+.
T Consensus        16 ~~~iig~~~~~~~l~~~i~~~~-~~~~~L~~G~~G~GKt~~a~~la~~   62 (367)
T PRK14970         16 FDDVVGQSHITNTLLNAIENNH-LAQALLFCGPRGVGKTTCARILARK   62 (367)
T ss_pred             HHhcCCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3567999999999999997652 3457779999999999999998766

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=97.39  E-value=0.00017  Score=60.84  Aligned_cols=83  Identities=17%  Similarity=0.184  Sum_probs=29.6

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCC-CCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhh-cCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHG-GFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELW-RIK  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~-~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~-~L~  315 (351)
                      +.+...++.|+|  .+..+..+. .++ .+.+|+.|++++| .+..++ .+..|++|+.|++++ ..+..+++++. +++
T Consensus        15 ~~n~~~~~~L~L--~~n~I~~Ie-~L~~~l~~L~~L~Ls~N-~I~~l~-~l~~L~~L~~L~L~~-N~I~~i~~~l~~~lp   88 (175)
T PF14580_consen   15 YNNPVKLRELNL--RGNQISTIE-NLGATLDKLEVLDLSNN-QITKLE-GLPGLPRLKTLDLSN-NRISSISEGLDKNLP   88 (175)
T ss_dssp             ------------------------S--TT-TT--EEE-TTS---S--T-T----TT--EEE--S-S---S-CHHHHHH-T
T ss_pred             cccccccccccc--ccccccccc-chhhhhcCCCEEECCCC-CCcccc-CccChhhhhhcccCC-CCCCccccchHHhCC
Confidence            344556899999  333443443 354 6789999999999 799887 588899999999998 57888987774 699


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|++++-.
T Consensus        89 ~L~~L~L~~N~   99 (175)
T PF14580_consen   89 NLQELYLSNNK   99 (175)
T ss_dssp             T--EEE-TTS-
T ss_pred             cCCEEECcCCc
Confidence            99999998765

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.38  E-value=0.002  Score=64.62  Aligned_cols=132  Identities=9%  Similarity=-0.014  Sum_probs=72.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC--CeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF--DCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      +++||-+.-++.|.+++..+. -...+-++|+.|+||||+|+.+..........  ..|- .|      ..-+.|...-.
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg-~C------~~C~~i~~~~~   84 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR-INHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCG-VC------ESCVALAPNGP   84 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCccc-cc------HHHHHhhcccC
Confidence            578999999999999987653 34456789999999999999887652211111  0000 00      00111110000


Q ss_pred             CCCCCccC---CCCCHHHHH---HHHHHh-cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347           96 PLSALSEI---LDNDFEMKK---NTLHNY-LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus        96 ~~~~~~~~---~~~~~~~~~---~~l~~~-L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                      .....-++   .....+++.   +.+... ..+++-++|+|++...  +..+.+...+.......++|+ |.
T Consensus        85 ~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tt  156 (584)
T PRK14952         85 GSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATT  156 (584)
T ss_pred             CCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeC
Confidence            00000000   111223222   222111 1345668899999754  678888888887666777776 63

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

Probab=97.35  E-value=0.00074  Score=70.03  Aligned_cols=45  Identities=18%  Similarity=0.248  Sum_probs=37.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++||+++++.+++.|...... . +.++|.+|+|||++|+.++..
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~~-n-~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKKN-N-PLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCCC-c-eEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999988765422 2 347899999999999999877

>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=97.35  E-value=0.0004  Score=59.94  Aligned_cols=54  Identities=13%  Similarity=0.066  Sum_probs=40.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~   97 (351)
                      +|+.++|+.|+||||.+.+++...+.  .-..+..++..   ....+-++..++.+..+
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~--~~~~v~lis~D~~R~ga~eQL~~~a~~l~vp   58 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKL--KGKKVALISADTYRIGAVEQLKTYAEILGVP   58 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHH--TT--EEEEEESTSSTHHHHHHHHHHHHHTEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhh--ccccceeecCCCCCccHHHHHHHHHHHhccc
Confidence            68999999999999999888877433  33346677776   45566777788888765

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 ....

>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=97.34  E-value=0.00074  Score=59.39  Aligned_cols=120  Identities=10%  Similarity=0.133  Sum_probs=66.4

Q ss_pred             Cccccc-hhhHHHHHHHHHcc-CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe--eEEEEEeCCHHHHHHHHHHH
Q 048347           18 KVDLDL-EDKMEELLDLLIER-QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC--CAWVYYQLSLDMMLDAIMKS   93 (351)
Q Consensus        18 ~~~vGr-~~~~~~l~~~L~~~-~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~~~~~~~~~~~~i~~~   93 (351)
                      +.++|- .+..-...+.+... +.....+-|+|..|+|||.|.+++++.  .......  ++++    +..++...+...
T Consensus         9 nfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~--~~~~~~~~~v~y~----~~~~f~~~~~~~   82 (219)
T PF00308_consen    9 NFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANE--AQKQHPGKRVVYL----SAEEFIREFADA   82 (219)
T ss_dssp             CS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHH--HHHHCTTS-EEEE----EHHHHHHHHHHH
T ss_pred             cCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHH--HHhccccccceee----cHHHHHHHHHHH
Confidence            344563 23333344444443 333456789999999999999999998  4443322  3343    345666666655


Q ss_pred             hCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh---hhHHH-HHhhcCC-CCCCcEEEE-Ee
Q 048347           94 LMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG---DIWDF-LKEALPD-HQNGSRILT-AL  157 (351)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~---~~~~~-l~~~l~~-~~~gs~Iiv-TR  157 (351)
                      +... .            ...+++.+++-. ++++||+...   ..|+. +...+.. ...|.++|+ ++
T Consensus        83 ~~~~-~------------~~~~~~~~~~~D-lL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~  138 (219)
T PF00308_consen   83 LRDG-E------------IEEFKDRLRSAD-LLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSD  138 (219)
T ss_dssp             HHTT-S------------HHHHHHHHCTSS-EEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEES
T ss_pred             HHcc-c------------chhhhhhhhcCC-EEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeC
Confidence            5442 1            244555665544 5788999754   22322 2222221 233567777 54

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.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.34  E-value=0.0023  Score=61.19  Aligned_cols=46  Identities=11%  Similarity=-0.065  Sum_probs=36.3

Q ss_pred             CccccchhhHHHHHHHHHccCC--------CeEEEEEEcCCCChHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQP--------QLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~--------~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      ++++|-+.-++.|.+.+..+..        -.+-+-++|+.|+|||++|+.+..
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~   58 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAA   58 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            4688999999999999876421        235577899999999999988754

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.31  E-value=0.00021  Score=66.75  Aligned_cols=49  Identities=6%  Similarity=0.221  Sum_probs=42.0

Q ss_pred             CCccccchhhHHHHHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           17 NKVDLDLEDKMEELLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      +++++|.++.++++++++...    +.+.+++.++|+.|+||||||+.+.+..
T Consensus        50 ~~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       50 DHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             chhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            337999999999999999763    2356899999999999999999998883

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

>PRK08727 hypothetical protein; Validated

Probab=97.31  E-value=0.00076  Score=59.93  Aligned_cols=35  Identities=9%  Similarity=0.044  Sum_probs=26.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY   78 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~   78 (351)
                      ..+.|+|..|+|||.||+.+++.  .........+++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEe
Confidence            46889999999999999999887  444433445554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.30  E-value=0.00074  Score=64.72  Aligned_cols=51  Identities=12%  Similarity=0.020  Sum_probs=39.3

Q ss_pred             CCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.-+++.|+++.++++.+.+...           -...+-|.++|++|+|||++|+++++.
T Consensus       127 ~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            344456789999999999877421           123455778999999999999999987

>PRK12377 putative replication protein; Provisional

Probab=97.29  E-value=0.0011  Score=59.37  Aligned_cols=73  Identities=12%  Similarity=0.011  Sum_probs=45.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      ..-+.++|..|+|||.||.++.+.  +......+.++++    .+++..+.......        ....    .+.+.+ 
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~----~~l~~~l~~~~~~~--------~~~~----~~l~~l-  161 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTV----PDVMSRLHESYDNG--------QSGE----KFLQEL-  161 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEH----HHHHHHHHHHHhcc--------chHH----HHHHHh-
Confidence            357889999999999999999998  5554444555543    45555554443211        1112    222333 


Q ss_pred             CceEEEEEeCCC
Q 048347          121 NKRYLIVIQDVW  132 (351)
Q Consensus       121 ~k~~LlVLDdv~  132 (351)
                      .+--||||||+-
T Consensus       162 ~~~dLLiIDDlg  173 (248)
T PRK12377        162 CKVDLLVLDEIG  173 (248)
T ss_pred             cCCCEEEEcCCC
Confidence            355689999993

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.29  E-value=0.002  Score=67.07  Aligned_cols=134  Identities=9%  Similarity=-0.059  Sum_probs=73.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe-eEEEEEeCCHHHHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC-CAWVYYQLSLDMMLDAIMKSLMP   96 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~~i~~~~~~   96 (351)
                      .++||.+.-++.|...+..+. -.+.+-++|+.|+||||+|+.+.+.......... -|=.|-      --+.|...-..
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~------sC~~~~~g~~~   87 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECD------SCVALAPGGPG   87 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccH------HHHHHHcCCCC
Confidence            468999999999999887653 3356678999999999999988655221111100 000000      00000000000


Q ss_pred             CCCCccC---CCCCHHHHHHHHH----HhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eee
Q 048347           97 LSALSEI---LDNDFEMKKNTLH----NYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALI  158 (351)
Q Consensus        97 ~~~~~~~---~~~~~~~~~~~l~----~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~  158 (351)
                      ......+   .....+++.+...    .-..++.-++|||+++..  +.++.|...+.+....+++|+ |.+
T Consensus        88 ~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~  159 (824)
T PRK07764         88 SLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTE  159 (824)
T ss_pred             CCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCC
Confidence            0000000   1112333332111    113456667889999866  677888888887666777776 643

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.29  E-value=0.0025  Score=64.41  Aligned_cols=146  Identities=10%  Similarity=0.043  Sum_probs=78.6

Q ss_pred             CcccccccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc---CCCeeEEEE
Q 048347            2 TAESMIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN---YFDCCAWVY   78 (351)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~---~F~~~~wv~   78 (351)
                      +-+...+.+|...+  +++||-+.-++.|..++..+. -...+-++|..|+||||+|+.+........   .+..     
T Consensus         2 ~~~~l~~kyRP~~~--~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~-----   73 (585)
T PRK14950          2 TVQVLYRKWRSQTF--AELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRP-----   73 (585)
T ss_pred             ccHHHHHHhCCCCH--HHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCC-----
Confidence            33344455555544  478999999999988887542 235567899999999999999876521111   1111     


Q ss_pred             EeCCHHHHHHHHHHHhCCCCC-CccCCCCCHHHHHHHH---HH-hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCc
Q 048347           79 YQLSLDMMLDAIMKSLMPLSA-LSEILDNDFEMKKNTL---HN-YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGS  151 (351)
Q Consensus        79 ~~~~~~~~~~~i~~~~~~~~~-~~~~~~~~~~~~~~~l---~~-~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs  151 (351)
                        ++.-+..+.|......... .........+++.+.+   .. -..+++-++|+|++...  +..+.+...+.+....+
T Consensus        74 --c~~c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~t  151 (585)
T PRK14950         74 --CGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHA  151 (585)
T ss_pred             --CccCHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCe
Confidence              0111222333221111000 0000112233332222   11 12345678999999744  56777877776655566


Q ss_pred             EEEE-Ee
Q 048347          152 RILT-AL  157 (351)
Q Consensus       152 ~Iiv-TR  157 (351)
                      .+|+ +.
T Consensus       152 v~Il~t~  158 (585)
T PRK14950        152 IFILATT  158 (585)
T ss_pred             EEEEEeC
Confidence            6666 53

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.27  E-value=0.0021  Score=56.61  Aligned_cols=100  Identities=11%  Similarity=0.038  Sum_probs=57.2

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC------CeeEEEEEe--CCHHHHHHHHHHHhCCCCC--
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF------DCCAWVYYQ--LSLDMMLDAIMKSLMPLSA--   99 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F------~~~~wv~~~--~~~~~~~~~i~~~~~~~~~--   99 (351)
                      |-.+|..+-+.-.++.|.|.+|+|||+||.++...  ....-      ..++|++..  ++...+ ..++........  
T Consensus         8 lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~--~~~~~~~~g~~~~v~yi~~e~~~~~~rl-~~~~~~~~~~~~~~   84 (226)
T cd01393           8 LDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVE--AQLPGELGGLEGKVVYIDTEGAFRPERL-VQLAVRFGLDPEEV   84 (226)
T ss_pred             HHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHH--hhcccccCCCcceEEEEecCCCCCHHHH-HHHHHHhccchhhh
Confidence            33444334356689999999999999999998765  22222      446777766  555443 344443322110  


Q ss_pred             ---CccCCCCCHHHHHHHHHHhcC----CceEEEEEeCCC
Q 048347          100 ---LSEILDNDFEMKKNTLHNYLK----NKRYLIVIQDVW  132 (351)
Q Consensus       100 ---~~~~~~~~~~~~~~~l~~~L~----~k~~LlVLDdv~  132 (351)
                         ..-....+.+++...+.+..+    .+--++|+|.+.
T Consensus        85 ~~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis  124 (226)
T cd01393          85 LDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVVVDSVA  124 (226)
T ss_pred             hccEEEEeCCCHHHHHHHHHHHHHHhhcCCeeEEEEcCcc
Confidence               000123445555555555543    344578888874

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.27  E-value=0.00083  Score=70.62  Aligned_cols=45  Identities=13%  Similarity=0.236  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++||+.++..+++.|......  -+.++|.+|+|||++|+.+...
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~~~--n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRTKN--NPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCCcC--ceEEECCCCCCHHHHHHHHHHH
Confidence            56899999999999988776432  3447899999999999998877

>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=97.26  E-value=0.00019  Score=56.54  Aligned_cols=22  Identities=14%  Similarity=0.211  Sum_probs=20.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ||+|.|++|+||||+|+.+.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999887

...

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=97.25  E-value=0.00047  Score=62.22  Aligned_cols=99  Identities=11%  Similarity=0.133  Sum_probs=57.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeE-EEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHHH----
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCA-WVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFEM----  110 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~-wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~~----  110 (351)
                      ..++|.|..|+||||||+.+++.  ++.+|+..+ ++-+.   -.+.++..++...=..+...   ...+......    
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~~--i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~  147 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELINN--IAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVA  147 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            56889999999999999999999  666676544 33343   56666666665431111000   0001111111    


Q ss_pred             -HHHHHHHhc---CCceEEEEEeCCCCh-hhHHHHHh
Q 048347          111 -KKNTLHNYL---KNKRYLIVIQDVWRG-DIWDFLKE  142 (351)
Q Consensus       111 -~~~~l~~~L---~~k~~LlVLDdv~~~-~~~~~l~~  142 (351)
                       ..-.+.+++   ++++.|+++||+-.. +++..+..
T Consensus       148 ~~a~~~AEyfr~~~g~~Vl~~~Dsltr~a~A~reis~  184 (274)
T cd01133         148 LTGLTMAEYFRDEEGQDVLLFIDNIFRFTQAGSEVSA  184 (274)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEeChhHHHHHHHHHHH
Confidence             122334444   389999999999543 34444443

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.25  E-value=0.0025  Score=64.33  Aligned_cols=46  Identities=9%  Similarity=-0.132  Sum_probs=36.4

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++||-+.-++.|.+.+..+. -..-+-++|+.|+||||+|+.+.+.
T Consensus        16 ~eivGQe~i~~~L~~~i~~~r-i~ha~Lf~Gp~GvGKttlA~~lAk~   61 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDR-VGHGYIFSGLRGVGKTTAARVFAKA   61 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999988886542 2344668999999999999887654

>PRK06696 uridine kinase; Validated

Probab=97.24  E-value=0.00041  Score=61.19  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=35.5

Q ss_pred             chhhHHHHHHHHHc-cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           23 LEDKMEELLDLLIE-RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        23 r~~~~~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |++-+++|.+.+.. ...+..+|+|.|.+|+||||||+.+...
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            56777888888865 3456889999999999999999999987

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.24  E-value=0.00096  Score=70.02  Aligned_cols=46  Identities=17%  Similarity=0.294  Sum_probs=37.8

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+.++||++++.++++.|......  -+.++|.+|+||||+|+.+..+
T Consensus       186 ld~~iGr~~ei~~~i~~l~r~~~~--n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       186 IDPVLGRDDEIRQMIDILLRRRQN--NPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CCcccCCHHHHHHHHHHHhcCCcC--ceeEECCCCCCHHHHHHHHHHH
Confidence            357899999999999988765422  2347999999999999999887

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.24  E-value=0.0055  Score=52.39  Aligned_cols=38  Identities=16%  Similarity=0.175  Sum_probs=27.2

Q ss_pred             CceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eee
Q 048347          121 NKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALI  158 (351)
Q Consensus       121 ~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~  158 (351)
                      +.+-++|+|++...  ++++.+...+......+.+|+ |++
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~  135 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPS  135 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence            56678999999755  457778888876665666666 653

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.23  E-value=0.00097  Score=58.82  Aligned_cols=56  Identities=14%  Similarity=0.025  Sum_probs=39.2

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHH
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMM   86 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~   86 (351)
                      .|-++|..+=+.-.++.|+|.+|+|||++|.+++..  ....-..++|++.. ++.+.+
T Consensus        11 ~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e~~~~~r~   67 (225)
T PRK09361         11 MLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTEGLSPERF   67 (225)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECCCCCHHHH
Confidence            344444444356689999999999999999998876  43444567888766 555443

>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=97.23  E-value=0.00036  Score=60.71  Aligned_cols=54  Identities=17%  Similarity=0.108  Sum_probs=36.7

Q ss_pred             CCCccccchhhHHHHHHHHHc---cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIE---RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      .-+++||-+.-++.+.-++..   ..+...-+-.||++|.||||||..+.+.  ....|
T Consensus        22 ~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e--~~~~~   78 (233)
T PF05496_consen   22 SLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANE--LGVNF   78 (233)
T ss_dssp             SCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHH--CT--E
T ss_pred             CHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhc--cCCCe
Confidence            457899988888887665542   2344666778999999999999999999  44444

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.

>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=97.23  E-value=0.00017  Score=57.55  Aligned_cols=21  Identities=10%  Similarity=0.101  Sum_probs=19.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |-|+|+.|+|||++|+.+++.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            468999999999999999999

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 ....

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.22  E-value=0.0027  Score=57.40  Aligned_cols=46  Identities=9%  Similarity=-0.002  Sum_probs=32.9

Q ss_pred             ccccchhhHHHHHHHHHc---------c----CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIE---------R----QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~---------~----~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.+.-++++.+....         .    .+...-+.++|++|+||||+|+.++..
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~   65 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKL   65 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHH
Confidence            478988777776544321         1    234455778999999999999999765

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.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.20  E-value=0.0034  Score=62.55  Aligned_cols=136  Identities=15%  Similarity=0.077  Sum_probs=94.2

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc--C-CCeEEEEEEcCCCChHHHHHHHHhCCcc---cccCCCeeEEEEEe----CC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER--Q-PQLSLVAIIDTMGFDRTAFIGEAYNSSY---VKNYFDCCAWVYYQ----LS   82 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~--~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~---~~~~F~~~~wv~~~----~~   82 (351)
                      .+.....+-+||.+..+|...+..-  + ...+.+-|.|-.|.|||..+..|.+..+   -++.-....+|.+.    ..
T Consensus       391 ls~vp~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~  470 (767)
T KOG1514|consen  391 LSAVPESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLAS  470 (767)
T ss_pred             HhhccccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecC
Confidence            3445677889999999998888542  2 2344788999999999999999988633   22233334455555    78


Q ss_pred             HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC-----CceEEEEEeCCCCh--hhHHHHHhhcCC-CCCCcEEE
Q 048347           83 LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK-----NKRYLIVIQDVWRG--DIWDFLKEALPD-HQNGSRIL  154 (351)
Q Consensus        83 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~-----~k~~LlVLDdv~~~--~~~~~l~~~l~~-~~~gs~Ii  154 (351)
                      +.+++..|..++.....       ......+.+..++.     .+.+++++|+++..  ...+-+...|.| ...+||++
T Consensus       471 ~~~~Y~~I~~~lsg~~~-------~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLv  543 (767)
T KOG1514|consen  471 PREIYEKIWEALSGERV-------TWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLV  543 (767)
T ss_pred             HHHHHHHHHHhcccCcc-------cHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceE
Confidence            99999999999988655       45556666666664     46788889988544  123344444554 55688877


Q ss_pred             E
Q 048347          155 T  155 (351)
Q Consensus       155 v  155 (351)
                      |
T Consensus       544 v  544 (767)
T KOG1514|consen  544 V  544 (767)
T ss_pred             E
Confidence            6

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.20  E-value=0.0015  Score=58.25  Aligned_cols=93  Identities=13%  Similarity=0.114  Sum_probs=52.2

Q ss_pred             HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCC
Q 048347           28 EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDND  107 (351)
Q Consensus        28 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  107 (351)
                      ..+.+.......+...+.++|.+|+|||+||.++++.  ....-..+++++    +.++...+.......       ..+
T Consensus        86 ~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~--l~~~g~~v~~it----~~~l~~~l~~~~~~~-------~~~  152 (244)
T PRK07952         86 SKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNE--LLLRGKSVLIIT----VADIMSAMKDTFSNS-------ETS  152 (244)
T ss_pred             HHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEE----HHHHHHHHHHHHhhc-------ccc
Confidence            3344444322223456789999999999999999998  444433445553    445555554433211       112


Q ss_pred             HHHHHHHHHHhcCCceEEEEEeCCCCh--hhHH
Q 048347          108 FEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWD  138 (351)
Q Consensus       108 ~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~  138 (351)
                      ...    +.+.+.+ .=+|||||+...  .+|.
T Consensus       153 ~~~----~l~~l~~-~dlLvIDDig~~~~s~~~  180 (244)
T PRK07952        153 EEQ----LLNDLSN-VDLLVIDEIGVQTESRYE  180 (244)
T ss_pred             HHH----HHHHhcc-CCEEEEeCCCCCCCCHHH
Confidence            222    3333443 347888999544  3454

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.20  E-value=0.0004  Score=44.39  Aligned_cols=35  Identities=20%  Similarity=0.240  Sum_probs=30.3

Q ss_pred             CCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          291 QKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       291 ~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      ++|++|++++ ..+..+|..+++|++|+.|++++.+
T Consensus         1 ~~L~~L~l~~-N~i~~l~~~l~~l~~L~~L~l~~N~   35 (44)
T PF12799_consen    1 KNLEELDLSN-NQITDLPPELSNLPNLETLNLSNNP   35 (44)
T ss_dssp             TT-SEEEETS-SS-SSHGGHGTTCTTSSEEEETSSC
T ss_pred             CcceEEEccC-CCCcccCchHhCCCCCCEEEecCCC
Confidence            4799999999 5799999999999999999999987

...

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.19  E-value=0.00077  Score=67.95  Aligned_cols=49  Identities=14%  Similarity=0.099  Sum_probs=40.5

Q ss_pred             CCCccccchhhHHHHHHHHHccC---CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQ---PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~---~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|-++.++++..++....   ...+++.++|+.|+||||+++.++..
T Consensus        82 ~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        82 TQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             CHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34668999999999999987542   23467999999999999999999877

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

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.18  E-value=0.0037  Score=62.95  Aligned_cols=47  Identities=9%  Similarity=-0.006  Sum_probs=38.2

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|.+.-++.|.+.+..+. -..-+-++|+.|+||||+|+.+.+.
T Consensus        23 f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~   69 (598)
T PRK09111         23 FDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARA   69 (598)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHh
Confidence            3568999999999999887653 2345668999999999999998765

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.16  E-value=0.0011  Score=69.90  Aligned_cols=45  Identities=13%  Similarity=0.237  Sum_probs=37.4

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++||+.++..++..|.....+  -+.++|.+|+|||++|+.+..+
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~--n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKN--NPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCC--ceEEEcCCCCCHHHHHHHHHHH
Confidence            56899999999999998765433  3336899999999999998877

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.14  E-value=0.0012  Score=57.51  Aligned_cols=48  Identities=10%  Similarity=0.002  Sum_probs=36.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLD   88 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~   88 (351)
                      ++-+++.|+|.+|+|||++|.++...  .......++|++.. +....+.+
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~~~~~rl~~   58 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEGLSPERFKQ   58 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCCCCHHHHHH
Confidence            56789999999999999999998877  44445677888876 55555443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=97.14  E-value=7.3e-05  Score=76.09  Aligned_cols=91  Identities=24%  Similarity=0.284  Sum_probs=59.1

Q ss_pred             ccCCCCCCCCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccccc
Q 048347          229 ELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKF  307 (351)
Q Consensus       229 ~l~~~~~~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~l  307 (351)
                      ++.+...|-+-.+++|++|+|++|.  +..+|.+ ..+|..|+.|+|+|| .+..+|.++-++..|++|...+ ..+..+
T Consensus       370 ~Ltd~c~p~l~~~~hLKVLhLsyNr--L~~fpas~~~kle~LeeL~LSGN-kL~~Lp~tva~~~~L~tL~ahs-N~l~~f  445 (1081)
T KOG0618|consen  370 HLTDSCFPVLVNFKHLKVLHLSYNR--LNSFPASKLRKLEELEELNLSGN-KLTTLPDTVANLGRLHTLRAHS-NQLLSF  445 (1081)
T ss_pred             cccccchhhhccccceeeeeecccc--cccCCHHHHhchHHhHHHhcccc-hhhhhhHHHHhhhhhHHHhhcC-Cceeec
Confidence            4566677888899999999995542  2245543 567777777788887 5777776666666666666555 345556


Q ss_pred             ChhhhcCCCCCEEEecC
Q 048347          308 PEELWRIKALRKLESWW  324 (351)
Q Consensus       308 P~~i~~L~~L~~L~l~~  324 (351)
                      | .+.+|+.|+.+|++.
T Consensus       446 P-e~~~l~qL~~lDlS~  461 (1081)
T KOG0618|consen  446 P-ELAQLPQLKVLDLSC  461 (1081)
T ss_pred             h-hhhhcCcceEEeccc
Confidence            6 455555555555543

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=97.12  E-value=0.0022  Score=55.18  Aligned_cols=82  Identities=12%  Similarity=0.046  Sum_probs=45.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccC-CC---eeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHH
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNY-FD---CCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHN  117 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~---~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~  117 (351)
                      ||+|.|.+|+||||+|+++...  +... ..   ....++.. +....-................+...+.+.+.+.++.
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~--L~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~a~d~~~l~~~l~~   78 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQI--LNKRGIPAMEMDIILSLDDFYDDYHLRDRKGRGENRYNFDHPDAFDFDLLKEDLKA   78 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH--HTTCTTTCCCSEEEEEGGGGBHHHHHHHHHHHCTTTSSTTSGGGBSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH--hCccCcCccceeEEEeecccccccchhhHhhccccccCCCCccccCHHHHHHHHHH
Confidence            7999999999999999999877  4322 22   12333322 2222211111111111111112356777888888877


Q ss_pred             hcCCceEEE
Q 048347          118 YLKNKRYLI  126 (351)
Q Consensus       118 ~L~~k~~Ll  126 (351)
                      ...++..-+
T Consensus        79 L~~g~~i~~   87 (194)
T PF00485_consen   79 LKNGGSIEI   87 (194)
T ss_dssp             HHTTSCEEE
T ss_pred             HhCCCcccc
Confidence            666666544

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 ....

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=97.11  E-value=9.3e-05  Score=75.35  Aligned_cols=85  Identities=19%  Similarity=0.207  Sum_probs=71.1

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +.+.+.-+|++|++ ++...+ ..|..++.+.+|+.|+++.| .+.++|.+.+++.+|++|.|.. +.+..+|.++..++
T Consensus        39 ~~~~~~v~L~~l~l-snn~~~-~fp~~it~l~~L~~ln~s~n-~i~~vp~s~~~~~~l~~lnL~~-n~l~~lP~~~~~lk  114 (1081)
T KOG0618|consen   39 EFVEKRVKLKSLDL-SNNQIS-SFPIQITLLSHLRQLNLSRN-YIRSVPSSCSNMRNLQYLNLKN-NRLQSLPASISELK  114 (1081)
T ss_pred             HHhhheeeeEEeec-cccccc-cCCchhhhHHHHhhcccchh-hHhhCchhhhhhhcchhheecc-chhhcCchhHHhhh
Confidence            33333445999999 344443 67888999999999999998 6999999999999999999994 88999999999999


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|+.|+++.
T Consensus       115 nl~~LdlS~  123 (1081)
T KOG0618|consen  115 NLQYLDLSF  123 (1081)
T ss_pred             cccccccch
Confidence            999999986

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.10  E-value=0.004  Score=65.73  Aligned_cols=119  Identities=8%  Similarity=0.103  Sum_probs=67.9

Q ss_pred             CCccccchhhHHHHHHHHHcc------C-CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHH
Q 048347           17 NKVDLDLEDKMEELLDLLIER------Q-PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLD   88 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~------~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~   88 (351)
                      ...++|.++-++.+...+...      . ....++.+.|+.|+|||++|+.+...  ....-...+.+..+ +.......
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~--l~~~~~~~i~~d~s~~~~~~~~~  641 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEF--LFDDEDAMVRIDMSEYMEKHSVA  641 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhhcccchHH
Confidence            356899999999998888642      1 22457789999999999999999876  33222233444444 32222211


Q ss_pred             HHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcC
Q 048347           89 AIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALP  145 (351)
Q Consensus        89 ~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~  145 (351)
                      .+   ++.+..  .........+.+.++.   ....+++||++...  +.++.+...+.
T Consensus       642 ~l---~g~~~g--~~g~~~~g~l~~~v~~---~p~~vlllDeieka~~~v~~~Ll~~l~  692 (852)
T TIGR03346       642 RL---IGAPPG--YVGYEEGGQLTEAVRR---KPYSVVLFDEVEKAHPDVFNVLLQVLD  692 (852)
T ss_pred             Hh---cCCCCC--ccCcccccHHHHHHHc---CCCcEEEEeccccCCHHHHHHHHHHHh
Confidence            11   121110  0111122233333332   23358999999755  56666666554

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.10  E-value=0.0014  Score=64.42  Aligned_cols=47  Identities=17%  Similarity=0.077  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++.|.+..++++.+.+...           -...+-+-++|+.|.|||++|+++++.
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            55778999999998887421           012344778999999999999999998

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.

>PRK07667 uridine kinase; Provisional

Probab=97.09  E-value=0.00072  Score=58.25  Aligned_cols=39  Identities=13%  Similarity=0.256  Sum_probs=32.7

Q ss_pred             hHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           26 KMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        26 ~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+++.+.+.....+..+|+|-|.+|+||||+|+.+...
T Consensus         2 ~~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~   40 (193)
T PRK07667          2 STNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKEN   40 (193)
T ss_pred             CHHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            356777777666566799999999999999999999887

>CHL00181 cbbX CbbX; Provisional

Probab=97.08  E-value=0.0066  Score=55.65  Aligned_cols=47  Identities=6%  Similarity=-0.028  Sum_probs=32.7

Q ss_pred             CccccchhhHHHHHHHHH---cc----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLI---ER----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~---~~----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|.+.-++++.++..   -.          ......+.++|.+|+||||+|+.++..
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~   82 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADI   82 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            468898877776655532   11          112234678999999999999999765

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.07  E-value=0.00023  Score=72.67  Aligned_cols=84  Identities=17%  Similarity=0.295  Sum_probs=54.3

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccC--hhhhcCCCC
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFP--EELWRIKAL  317 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP--~~i~~L~~L  317 (351)
                      .||.|++|.+.+..+....+..--.+|++|+.||++++ ++..+ ..+++|.+|+.|.+++. .++.-+  ..+.+|++|
T Consensus       146 ~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~T-nI~nl-~GIS~LknLq~L~mrnL-e~e~~~~l~~LF~L~~L  222 (699)
T KOG3665|consen  146 MLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGT-NISNL-SGISRLKNLQVLSMRNL-EFESYQDLIDLFNLKKL  222 (699)
T ss_pred             hCcccceEEecCceecchhHHHHhhccCccceeecCCC-CccCc-HHHhccccHHHHhccCC-CCCchhhHHHHhcccCC
Confidence            47888888884333333333334557888888888887 67777 46778888887777752 233222  356677777


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      +.||+|...
T Consensus       223 ~vLDIS~~~  231 (699)
T KOG3665|consen  223 RVLDISRDK  231 (699)
T ss_pred             Ceeeccccc
Confidence            777777643

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.06  E-value=0.0023  Score=67.29  Aligned_cols=118  Identities=5%  Similarity=0.058  Sum_probs=65.0

Q ss_pred             CccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDA   89 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~   89 (351)
                      ..++|-++-++.+.+.+...       .....++.++|+.|+|||.||+.+...  +-......+-+.++ |....-   
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~--l~~~~~~~~~~dmse~~~~~~---  640 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAEL--LYGGEQNLITINMSEFQEAHT---  640 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHH--HhCCCcceEEEeHHHhhhhhh---
Confidence            56889999999998888531       233567889999999999999888665  32222222222222 221111   


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcC
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALP  145 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~  145 (351)
                      +.+-++.+.  ..........+.+.+++   +...+|+||++...  +.++.+...+.
T Consensus       641 ~~~l~g~~~--gyvg~~~~g~L~~~v~~---~p~svvllDEieka~~~v~~~Llq~ld  693 (852)
T TIGR03345       641 VSRLKGSPP--GYVGYGEGGVLTEAVRR---KPYSVVLLDEVEKAHPDVLELFYQVFD  693 (852)
T ss_pred             hccccCCCC--CcccccccchHHHHHHh---CCCcEEEEechhhcCHHHHHHHHHHhh
Confidence            111111110  01112222234444443   45579999999755  45555555443

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.05  E-value=0.0043  Score=62.28  Aligned_cols=59  Identities=14%  Similarity=0.052  Sum_probs=42.5

Q ss_pred             cccccccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347            3 AESMIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+....+|...+  ++++|-+.-++.|.+.+..+. -...+-++|+.|+||||+|+.+.+.
T Consensus         3 ~~~la~KyRP~sf--~dIiGQe~v~~~L~~ai~~~r-i~ha~Lf~GPpG~GKTtiArilAk~   61 (624)
T PRK14959          3 HASLTARYRPQTF--AEVAGQETVKAILSRAAQENR-VAPAYLFSGTRGVGKTTIARIFAKA   61 (624)
T ss_pred             cchHHHHhCCCCH--HHhcCCHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHh
Confidence            3444455555544  467898888888888886542 2456668999999999999988776

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.04  E-value=0.0025  Score=62.36  Aligned_cols=75  Identities=12%  Similarity=0.175  Sum_probs=45.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      ..-+.|+|..|+|||+||+.+.+.  +...+.....+++  +..++...+...+...         ..    +.+.+.++
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~v~yi--~~~~~~~~~~~~~~~~---------~~----~~~~~~~~  210 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNY--ILEKNPNAKVVYV--TSEKFTNDFVNALRNN---------TM----EEFKEKYR  210 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEE--EHHHHHHHHHHHHHcC---------cH----HHHHHHHh
Confidence            345789999999999999999998  6555432222222  3344555555444321         11    23334444


Q ss_pred             CceEEEEEeCCCC
Q 048347          121 NKRYLIVIQDVWR  133 (351)
Q Consensus       121 ~k~~LlVLDdv~~  133 (351)
                      + .-+|+|||+..
T Consensus       211 ~-~dlLiiDDi~~  222 (450)
T PRK00149        211 S-VDVLLIDDIQF  222 (450)
T ss_pred             c-CCEEEEehhhh
Confidence            3 34788999964

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.04  E-value=0.0067  Score=55.57  Aligned_cols=47  Identities=6%  Similarity=0.001  Sum_probs=31.7

Q ss_pred             CccccchhhHHHHHHHHHc---c------C----CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIE---R------Q----PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~---~------~----~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|.++-++++.++...   .      +    ....-+.++|..|.|||++|+.+...
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~   81 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQI   81 (284)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            3688988888777664321   1      0    11224668999999999999776554

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.04  E-value=0.0082  Score=59.13  Aligned_cols=46  Identities=11%  Similarity=-0.034  Sum_probs=37.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|-+.-.+.+.+++..+. -....-++|+.|+||||+|+.+...
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk~   61 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAKV   61 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999997653 2345667999999999999987665

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

Probab=97.02  E-value=0.0073  Score=56.08  Aligned_cols=119  Identities=10%  Similarity=0.028  Sum_probs=71.9

Q ss_pred             ccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC-------------------CCeeEEEEE
Q 048347           19 VDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-------------------FDCCAWVYY   79 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~wv~~   79 (351)
                      +++|-++...++..+......-..-+-++|+.|+||||+|.++....--...                   ++....+.-
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~   81 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNP   81 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecc
Confidence            5778888899999999865433344778999999999999888765211110                   111222222


Q ss_pred             e--CC---HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcE
Q 048347           80 Q--LS---LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSR  152 (351)
Q Consensus        80 ~--~~---~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~  152 (351)
                      +  ..   ..+..+++.+.......                    .++.-++++|+++..  ++-..+...+......++
T Consensus        82 s~~~~~~i~~~~vr~~~~~~~~~~~--------------------~~~~kviiidead~mt~~A~nallk~lEep~~~~~  141 (325)
T COG0470          82 SDLRKIDIIVEQVRELAEFLSESPL--------------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTR  141 (325)
T ss_pred             cccCCCcchHHHHHHHHHHhccCCC--------------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeE
Confidence            2  11   12222222222211110                    256778999999766  566777777777777778


Q ss_pred             EEE-Ee
Q 048347          153 ILT-AL  157 (351)
Q Consensus       153 Iiv-TR  157 (351)
                      +|+ |.
T Consensus       142 ~il~~n  147 (325)
T COG0470         142 FILITN  147 (325)
T ss_pred             EEEEcC
Confidence            777 65

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.02  E-value=0.0091  Score=59.13  Aligned_cols=134  Identities=7%  Similarity=-0.049  Sum_probs=71.7

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccc--ccCCCeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYV--KNYFDCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      ++++|-+.-.+.|...+..+. -....-++|+.|+||||+|+.+....--  ...+.. |-++-      --+.+.....
T Consensus        14 deiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~p-C~~C~------~C~~~~~~~h   85 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTP-CDTCI------QCQSALENRH   85 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCC-CcccH------HHHHHhhcCC
Confidence            568999999999999886553 3456678999999999999876554110  011100 00000      0000000000


Q ss_pred             CCCC-CccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           96 PLSA-LSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        96 ~~~~-~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ...- .........+++.+.+...    ..+++-++|+|++...  ++.+.+...+......+++|+ |.+.
T Consensus        86 ~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~  157 (535)
T PRK08451         86 IDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDP  157 (535)
T ss_pred             CeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECCh
Confidence            0000 0000111233333333221    1245668899999755  567788887776666677777 7553

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.02  E-value=0.001  Score=56.31  Aligned_cols=36  Identities=14%  Similarity=0.206  Sum_probs=29.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEE
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWV   77 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv   77 (351)
                      +..+|.+.|+.|+||||+|+.++..  ....+...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~--l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYER--LKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH--HHHcCCcEEEE
Confidence            4568999999999999999999988  66566555554

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=97.00  E-value=0.0014  Score=56.79  Aligned_cols=81  Identities=9%  Similarity=-0.010  Sum_probs=47.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHh
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNY  118 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~  118 (351)
                      +++.+|||-|.+|+||||+|+.+++.  ++.++-..  ++.. +.-.-....-........-..+...+.+-+.+.|...
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~--~~~~~~~~--I~~D-~YYk~~~~~~~~~~~~~n~d~p~A~D~dLl~~~L~~L   80 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQ--LGVEKVVV--ISLD-DYYKDQSHLPFEERNKINYDHPEAFDLDLLIEHLKDL   80 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHH--hCcCcceE--eecc-ccccchhhcCHhhcCCcCccChhhhcHHHHHHHHHHH
Confidence            46789999999999999999999998  55442111  1111 0000111111111111111123567777788888888


Q ss_pred             cCCceE
Q 048347          119 LKNKRY  124 (351)
Q Consensus       119 L~~k~~  124 (351)
                      +.++..
T Consensus        81 ~~g~~v   86 (218)
T COG0572          81 KQGKPV   86 (218)
T ss_pred             HcCCcc
Confidence            888774

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

Probab=97.00  E-value=0.0058  Score=63.47  Aligned_cols=116  Identities=5%  Similarity=0.115  Sum_probs=66.6

Q ss_pred             CCccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHH
Q 048347           17 NKVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLD   88 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~   88 (351)
                      ...++|-++.++.+.+.+...       .....++-++|+.|+|||+||+.++..  ..   ...+.++.+ +.-..   
T Consensus       453 ~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~--l~---~~~~~~d~se~~~~~---  524 (731)
T TIGR02639       453 KAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEA--LG---VHLERFDMSEYMEKH---  524 (731)
T ss_pred             hcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHH--hc---CCeEEEeCchhhhcc---
Confidence            356789999999988887632       123456789999999999999999887  32   223444444 22211   


Q ss_pred             HHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcC
Q 048347           89 AIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALP  145 (351)
Q Consensus        89 ~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~  145 (351)
                      .+.+-++....  .........+.+.++.   ....+++||+++..  +.++.+...+.
T Consensus       525 ~~~~lig~~~g--yvg~~~~~~l~~~~~~---~p~~VvllDEieka~~~~~~~Ll~~ld  578 (731)
T TIGR02639       525 TVSRLIGAPPG--YVGFEQGGLLTEAVRK---HPHCVLLLDEIEKAHPDIYNILLQVMD  578 (731)
T ss_pred             cHHHHhcCCCC--CcccchhhHHHHHHHh---CCCeEEEEechhhcCHHHHHHHHHhhc
Confidence            11122222111  0122222333443332   34469999999755  45666665544

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.98  E-value=0.0083  Score=60.77  Aligned_cols=46  Identities=9%  Similarity=0.014  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|-+.-++.|...+..+. -...+-++|+.|+||||+|+.+...
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk~   62 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAKT   62 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999987653 3455778999999999999876554

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.98  E-value=0.011  Score=59.44  Aligned_cols=57  Identities=9%  Similarity=0.056  Sum_probs=42.7

Q ss_pred             cccccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347            5 SMIDNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus         5 ~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+.||.-.+  ++++|.+.-.+.+.+++..+. -.+.+-++|+.|+||||+|+.+...
T Consensus         5 al~~k~rP~~f--~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAka   61 (559)
T PRK05563          5 ALYRKWRPQTF--EDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAKA   61 (559)
T ss_pred             HHHHHhCCCcH--HhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34455555433  579999999999999997653 3455667999999999999887544

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.98  E-value=0.0038  Score=55.24  Aligned_cols=42  Identities=12%  Similarity=0.190  Sum_probs=31.1

Q ss_pred             chhhHHHHHHHHHc-------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           23 LEDKMEELLDLLIE-------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        23 r~~~~~~l~~~L~~-------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ||++.+.+.+-|..       ...+..+++|.|..|+|||||++.+...
T Consensus         8 ~~~~~~~~~~~l~~~~~~~~~~~~~~~iigi~G~~GsGKTTl~~~L~~~   56 (229)
T PRK09270          8 RDEEIEAVHKPLLRRLAALQAEPQRRTIVGIAGPPGAGKSTLAEFLEAL   56 (229)
T ss_pred             ChHhHHHHHHHHHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45555554444422       2356899999999999999999999877

>CHL00176 ftsH cell division protein; Validated

Probab=96.98  E-value=0.0035  Score=63.63  Aligned_cols=94  Identities=9%  Similarity=0.092  Sum_probs=55.6

Q ss_pred             CccccchhhHHHHHHHHH---ccC-------CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLI---ERQ-------PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMML   87 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~---~~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~   87 (351)
                      +++.|.++..+++.+.+.   ...       ...+-+.++|+.|.|||+||+.++..  ....     |++++  ..++.
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e--~~~p-----~i~is--~s~f~  253 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE--AEVP-----FFSIS--GSEFV  253 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH--hCCC-----eeecc--HHHHH
Confidence            457898888777766552   111       12345778999999999999999887  3222     33333  11111


Q ss_pred             HHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           88 DAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        88 ~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                      ...    ..         .....+...+.....+..++++||+++.
T Consensus       254 ~~~----~g---------~~~~~vr~lF~~A~~~~P~ILfIDEID~  286 (638)
T CHL00176        254 EMF----VG---------VGAARVRDLFKKAKENSPCIVFIDEIDA  286 (638)
T ss_pred             HHh----hh---------hhHHHHHHHHHHHhcCCCcEEEEecchh
Confidence            100    00         0122334445555567889999999953

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.97  E-value=0.0028  Score=61.89  Aligned_cols=100  Identities=15%  Similarity=0.164  Sum_probs=56.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      .-+.|+|..|+|||.|++++.+.  +.......-.+++  +..++...+...+....           ...+.+++.+++
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~--l~~~~~~~~v~yv--~~~~f~~~~~~~l~~~~-----------~~~~~~~~~~~~  206 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNY--IESNFSDLKVSYM--SGDEFARKAVDILQKTH-----------KEIEQFKNEICQ  206 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHH--HHHhCCCCeEEEE--EHHHHHHHHHHHHHHhh-----------hHHHHHHHHhcc
Confidence            45779999999999999999986  4332222122222  44667777776654321           112344444543


Q ss_pred             ceEEEEEeCCCCh---hh-HHHHHhhcCC-CCCCcEEEEEe
Q 048347          122 KRYLIVIQDVWRG---DI-WDFLKEALPD-HQNGSRILTAL  157 (351)
Q Consensus       122 k~~LlVLDdv~~~---~~-~~~l~~~l~~-~~~gs~IivTR  157 (351)
                       .-+|||||+...   +. .+.+...+.. ...|..||+|.
T Consensus       207 -~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIlts  246 (450)
T PRK14087        207 -NDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSS  246 (450)
T ss_pred             -CCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEEC
Confidence             337888999543   22 2344444432 22344565543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.96  E-value=0.0051  Score=64.82  Aligned_cols=118  Identities=9%  Similarity=0.133  Sum_probs=64.5

Q ss_pred             CccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDA   89 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~   89 (351)
                      ..++|.+.-++.+...+...       +....++.++|+.|+|||++|+.+++.  ....-...+.+..+ +.-...   
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~--l~~~~~~~i~id~se~~~~~~---  642 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANF--MFDSDDAMVRIDMSEFMEKHS---  642 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHH--hhcCCCcEEEEEhHHhhhhhh---
Confidence            45789999988888887532       122357889999999999999999876  32222233334433 322211   


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcC
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALP  145 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~  145 (351)
                       ...+..... ..........+.+.++   ....-+++||++...  +.+..+...+.
T Consensus       643 -~~~LiG~~p-gy~g~~~~g~l~~~v~---~~p~~vLllDEieka~~~v~~~Ll~ile  695 (857)
T PRK10865        643 -VSRLVGAPP-GYVGYEEGGYLTEAVR---RRPYSVILLDEVEKAHPDVFNILLQVLD  695 (857)
T ss_pred             -HHHHhCCCC-cccccchhHHHHHHHH---hCCCCeEEEeehhhCCHHHHHHHHHHHh
Confidence             222221111 0011111122222222   122358999999744  56666666554

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.95  E-value=0.0059  Score=54.10  Aligned_cols=62  Identities=11%  Similarity=0.072  Sum_probs=39.4

Q ss_pred             HHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC----CCeeEEEEEe--CCHHHHHHHHHHHh
Q 048347           32 DLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY----FDCCAWVYYQ--LSLDMMLDAIMKSL   94 (351)
Q Consensus        32 ~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~~--~~~~~~~~~i~~~~   94 (351)
                      ++|..+-+.-.++.|+|.+|+|||+||.+++-.......    -..++|++..  ++...+ .++++..
T Consensus        10 ~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl-~~~~~~~   77 (235)
T cd01123          10 ELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL-VQIAERF   77 (235)
T ss_pred             hhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH-HHHHHHh
Confidence            333333355689999999999999999999754222221    2567888766  554443 3344443

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 .

>PHA00729 NTP-binding motif containing protein

Probab=96.92  E-value=0.0027  Score=55.60  Aligned_cols=24  Identities=13%  Similarity=0.180  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..-|.|.|.+|+||||||..+.+.
T Consensus        17 f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         17 FVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHH
Confidence            456889999999999999999886

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

Probab=96.91  E-value=0.0022  Score=57.64  Aligned_cols=76  Identities=13%  Similarity=0.084  Sum_probs=48.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      +..=+.++|..|+|||.||.++.+.  +...--.+.++    +..++++++.......            .....+.+.+
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~--l~~~g~sv~f~----~~~el~~~Lk~~~~~~------------~~~~~l~~~l  165 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNE--LLKAGISVLFI----TAPDLLSKLKAAFDEG------------RLEEKLLREL  165 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEE----EHHHHHHHHHHHHhcC------------chHHHHHHHh
Confidence            4556778999999999999999999  54332234455    4457777776554431            1233344434


Q ss_pred             CCceEEEEEeCCCCh
Q 048347          120 KNKRYLIVIQDVWRG  134 (351)
Q Consensus       120 ~~k~~LlVLDdv~~~  134 (351)
                      ++ -=||||||+-..
T Consensus       166 ~~-~dlLIiDDlG~~  179 (254)
T COG1484         166 KK-VDLLIIDDIGYE  179 (254)
T ss_pred             hc-CCEEEEecccCc
Confidence            33 347899999643

>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=96.91  E-value=0.0047  Score=50.01  Aligned_cols=22  Identities=9%  Similarity=0.187  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ||.+.|+.|+||||+|+.+...
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~   22 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKR   22 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5778999999999999999866

...

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.91  E-value=0.0052  Score=55.87  Aligned_cols=40  Identities=13%  Similarity=0.118  Sum_probs=29.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      .+.+++.++|++|+||||++..+...  ....-..+..++..
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~--l~~~g~~V~li~~D  109 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANK--LKKQGKSVLLAAGD  109 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHH--HHhcCCEEEEEeCC
Confidence            34689999999999999999988766  33333345666655

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

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.90  E-value=0.0071  Score=63.64  Aligned_cols=118  Identities=10%  Similarity=0.094  Sum_probs=65.1

Q ss_pred             CccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDA   89 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~   89 (351)
                      ..++|-++-++.+.+.+...       ......+-++|+.|+|||+||+.+.+.  +-..-...+-+..+ |.-..-   
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~--l~~~~~~~~~~d~s~~~~~~~---  583 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASY--FFGSEDAMIRLDMSEYMEKHT---  583 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHH--hcCCccceEEEEchhcccccc---
Confidence            66889999999998887531       122455668999999999999998765  32211223333344 221111   


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCce-EEEEEeCCCCh--hhHHHHHhhcCC
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKR-YLIVIQDVWRG--DIWDFLKEALPD  146 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~-~LlVLDdv~~~--~~~~~l~~~l~~  146 (351)
                      +.+-++.+.  ..........+    .+.++.++ .+++||+++..  +.++.+...+..
T Consensus       584 ~~~l~g~~~--gyvg~~~~~~l----~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~  637 (821)
T CHL00095        584 VSKLIGSPP--GYVGYNEGGQL----TEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDD  637 (821)
T ss_pred             HHHhcCCCC--cccCcCccchH----HHHHHhCCCeEEEECChhhCCHHHHHHHHHHhcc
Confidence            111122110  01112222233    33444444 58889999755  556666665543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.88  E-value=0.01  Score=59.86  Aligned_cols=54  Identities=9%  Similarity=0.038  Sum_probs=40.8

Q ss_pred             ccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347            8 DNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus         8 ~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.||.-.+  ++++|.+.-++.|.+.+..+. -.+.+-++|+.|+||||+|+.+.+.
T Consensus         8 ~k~RP~~f--~~iiGq~~v~~~L~~~i~~~~-~~hayLf~Gp~G~GKtt~A~~lak~   61 (576)
T PRK14965          8 RKYRPQTF--SDLTGQEHVSRTLQNAIDTGR-VAHAFLFTGARGVGKTSTARILAKA   61 (576)
T ss_pred             HHhCCCCH--HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            44554433  578999999999999887652 2355678999999999999888665

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.88  E-value=0.0073  Score=56.95  Aligned_cols=142  Identities=7%  Similarity=-0.039  Sum_probs=77.5

Q ss_pred             cCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC----CCeeEEEEEeCCHHHHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY----FDCCAWVYYQLSLDMMLD   88 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~~~~~~~~~~   88 (351)
                      ++-+...++|-++-.+.+...+..+. -..-+-|+|+.|+||||+|..+...  +-.+    +..... ......-...+
T Consensus        18 ~P~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~~--Llc~~~~~~~~~~~-~~~~~~c~~c~   93 (351)
T PRK09112         18 SPSENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLANH--ILSHPDPAEAPETL-ADPDPASPVWR   93 (351)
T ss_pred             CCCchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHHH--HcCCCccccCcccc-CCCCCCCHHHH
Confidence            44456779999999999999887653 3345778999999999999887665  2110    111000 00000111223


Q ss_pred             HHHHHhC-------CCCCCcc---CCCCCHHHHHHHHHHhc-----CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCc
Q 048347           89 AIMKSLM-------PLSALSE---ILDNDFEMKKNTLHNYL-----KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGS  151 (351)
Q Consensus        89 ~i~~~~~-------~~~~~~~---~~~~~~~~~~~~l~~~L-----~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs  151 (351)
                      .|...-.       .+.....   ......+++. .+.+.+     .+++-++|+|+++..  ...+.+...+.....+.
T Consensus        94 ~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR-~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~  172 (351)
T PRK09112         94 QIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIR-RVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARA  172 (351)
T ss_pred             HHHcCCCCCEEEeecccccccccccccCCHHHHH-HHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCc
Confidence            3322211       0000000   0112234433 333333     356678999999755  46677777776655556


Q ss_pred             EEEE-Eeec
Q 048347          152 RILT-ALIH  159 (351)
Q Consensus       152 ~Iiv-TR~~  159 (351)
                      .+|+ |...
T Consensus       173 ~fiLit~~~  181 (351)
T PRK09112        173 LFILISHSS  181 (351)
T ss_pred             eEEEEECCh
Confidence            6555 6443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.87  E-value=0.0093  Score=58.24  Aligned_cols=47  Identities=11%  Similarity=-0.042  Sum_probs=37.6

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      =++++|.+.-++.+.+++..+. -...+-++|+.|+||||+|+.+...
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk~   62 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAKA   62 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999999887642 2355678999999999999888654

>PTZ00301 uridine kinase; Provisional

Probab=96.87  E-value=0.0016  Score=56.81  Aligned_cols=25  Identities=8%  Similarity=0.203  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+|||.|.+|+||||||+.+...
T Consensus         2 ~~~iIgIaG~SgSGKTTla~~l~~~   26 (210)
T PTZ00301          2 PCTVIGISGASGSGKSSLSTNIVSE   26 (210)
T ss_pred             CCEEEEEECCCcCCHHHHHHHHHHH
Confidence            3679999999999999999998776

>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=96.86  E-value=0.0074  Score=50.80  Aligned_cols=22  Identities=9%  Similarity=0.160  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+.|++|+||||++..+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~   23 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALY   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6788999999999999998876

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.85  E-value=0.0041  Score=60.56  Aligned_cols=73  Identities=15%  Similarity=0.205  Sum_probs=46.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCe--eEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC--CAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      .-+.|+|..|+|||+||+++++.  +......  ++|++    ..++..++...+...         ..+    .+++.+
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~--l~~~~~~~~v~yi~----~~~f~~~~~~~~~~~---------~~~----~f~~~~  191 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYIT----SEKFLNDLVDSMKEG---------KLN----EFREKY  191 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEE----HHHHHHHHHHHHhcc---------cHH----HHHHHH
Confidence            34889999999999999999998  5544322  34443    445666665555322         112    233333


Q ss_pred             CCceEEEEEeCCCC
Q 048347          120 KNKRYLIVIQDVWR  133 (351)
Q Consensus       120 ~~k~~LlVLDdv~~  133 (351)
                      +.+.-+|++||+..
T Consensus       192 ~~~~dvLlIDDi~~  205 (440)
T PRK14088        192 RKKVDVLLIDDVQF  205 (440)
T ss_pred             HhcCCEEEEechhh
Confidence            33455889999964

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=96.85  E-value=0.015  Score=54.11  Aligned_cols=46  Identities=9%  Similarity=0.194  Sum_probs=36.8

Q ss_pred             chhhHHHHHHHHHccC-CCeEEEEEEcCCCChHHHHHHHHhCCcccccC
Q 048347           23 LEDKMEELLDLLIERQ-PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY   70 (351)
Q Consensus        23 r~~~~~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~   70 (351)
                      |+...+.+.+.+.... +...+|+|.|.=|+|||++.+.+.+.  .+..
T Consensus         1 ~~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~--L~~~   47 (325)
T PF07693_consen    1 RKPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEE--LKED   47 (325)
T ss_pred             ChHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHH--Hhcc
Confidence            3455677888887653 57899999999999999999999888  4444

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.84  E-value=0.0098  Score=60.73  Aligned_cols=46  Identities=9%  Similarity=0.036  Sum_probs=37.3

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|-+.-++.|...+..+. -.+.+-++|+.|+||||+|+.+...
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk~   63 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFANA   63 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            568999999999999997653 3455668999999999999888654

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.84  E-value=0.016  Score=54.97  Aligned_cols=48  Identities=10%  Similarity=0.014  Sum_probs=37.4

Q ss_pred             CCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      -...+++|.++-.+.+.+.+..+. -..-+-++|+.|+||+|+|..+..
T Consensus        16 ~~~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~   63 (365)
T PRK07471         16 RETTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMAR   63 (365)
T ss_pred             CchhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            345679999999999999887653 234566899999999999977644

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.84  E-value=0.0051  Score=56.29  Aligned_cols=85  Identities=16%  Similarity=0.146  Sum_probs=46.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CC--HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LS--LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      +.++++++|++|+||||++..+......+..-..+..|+.. +.  ..+-+..-.+.+..+..    ...+..++.+.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~----~~~~~~~l~~~l~  268 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVK----VARDPKELRKALD  268 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCcee----ccCCHHHHHHHHH
Confidence            45799999999999999999988763222111244555554 22  22333333333333322    2234445555554


Q ss_pred             HhcCCceEEEEEeC
Q 048347          117 NYLKNKRYLIVIQD  130 (351)
Q Consensus       117 ~~L~~k~~LlVLDd  130 (351)
                      +. .+. =++++|.
T Consensus       269 ~~-~~~-d~vliDt  280 (282)
T TIGR03499       269 RL-RDK-DLILIDT  280 (282)
T ss_pred             Hc-cCC-CEEEEeC
Confidence            43 343 3666664

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.82  E-value=0.004  Score=58.91  Aligned_cols=87  Identities=15%  Similarity=0.049  Sum_probs=51.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      +-.++.++|+.|+||||++.++......+.....+..++..   ....+-++..++.++.+..    ...+..++...+.
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~----~~~~~~~l~~~l~  211 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVH----AVKDGGDLQLALA  211 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceE----ecCCcccHHHHHH
Confidence            35799999999999999999998773222222345566655   3444555666666655433    2223333333333


Q ss_pred             HhcCCceEEEEEeCCC
Q 048347          117 NYLKNKRYLIVIQDVW  132 (351)
Q Consensus       117 ~~L~~k~~LlVLDdv~  132 (351)
                       .+.++ -++++|..-
T Consensus       212 -~l~~~-DlVLIDTaG  225 (374)
T PRK14722        212 -ELRNK-HMVLIDTIG  225 (374)
T ss_pred             -HhcCC-CEEEEcCCC
Confidence             34454 455688774

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.81  E-value=0.0048  Score=59.50  Aligned_cols=72  Identities=14%  Similarity=0.205  Sum_probs=44.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCe--eEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC--CAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      ..+.|+|..|+|||.||+++++.  +......  +++++    ..++...+...+...         ..+    .+.+.+
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~--l~~~~~~~~v~yi~----~~~~~~~~~~~~~~~---------~~~----~~~~~~  197 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNE--ILENNPNAKVVYVS----SEKFTNDFVNALRNN---------KME----EFKEKY  197 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH--HHHhCCCCcEEEEE----HHHHHHHHHHHHHcC---------CHH----HHHHHH
Confidence            45789999999999999999998  5444322  33433    344555555554322         122    233333


Q ss_pred             CCceEEEEEeCCCC
Q 048347          120 KNKRYLIVIQDVWR  133 (351)
Q Consensus       120 ~~k~~LlVLDdv~~  133 (351)
                      ++ .-+|+|||+..
T Consensus       198 ~~-~dlLiiDDi~~  210 (405)
T TIGR00362       198 RS-VDLLLIDDIQF  210 (405)
T ss_pred             Hh-CCEEEEehhhh
Confidence            33 23788999964

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).

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.81  E-value=0.014  Score=58.60  Aligned_cols=131  Identities=8%  Similarity=-0.009  Sum_probs=71.9

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC---CCeeEEEEEeCCHHHHHHHHHHHh
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY---FDCCAWVYYQLSLDMMLDAIMKSL   94 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~---F~~~~wv~~~~~~~~~~~~i~~~~   94 (351)
                      .+++|-+.-++.|..++..+. -.+.+-++|+.|+||||+|+.+.........   +.|-.  +  .+    -+.|...-
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~-i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~--C--~~----C~~i~~~~   86 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK-IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGE--C--SS----CKSIDNDN   86 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCcc--c--hH----HHHHHcCC
Confidence            578999999999999997653 3456778999999999999998776221111   11100  0  00    01111000


Q ss_pred             CCCCC-CccCCCCCHHHHHHHHHH----hcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347           95 MPLSA-LSEILDNDFEMKKNTLHN----YLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus        95 ~~~~~-~~~~~~~~~~~~~~~l~~----~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                      ..... .........+++.+...+    -..+++-++|+|++...  .+++.+...+........+|. |.
T Consensus        87 ~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tt  157 (563)
T PRK06647         87 SLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATT  157 (563)
T ss_pred             CCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecC
Confidence            00000 000011233333332211    12356668899999755  467788877776555666665 53

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

Probab=96.80  E-value=0.0086  Score=57.52  Aligned_cols=91  Identities=10%  Similarity=0.124  Sum_probs=58.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      ++.|.|+-++||||+++.+...  ..+.   .+++...   .+..++                      .+....+.+.-
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~~~~d~~~~~~~l----------------------~d~~~~~~~~~   91 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKG--LLEE---IIYINFDDLRLDRIEL----------------------LDLLRAYIELK   91 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhh--CCcc---eEEEEecchhcchhhH----------------------HHHHHHHHHhh
Confidence            9999999999999999777766  3333   3444332   111111                      11111111111


Q ss_pred             CCceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccc
Q 048347          120 KNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIV  161 (351)
Q Consensus       120 ~~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v  161 (351)
                      ..++..++||.|.....|......+.+.+.. ++++ +-+..+
T Consensus        92 ~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~l  133 (398)
T COG1373          92 EREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSL  133 (398)
T ss_pred             ccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhh
Confidence            2277899999999999999999988877666 7777 544433

>cd01394 radB RadB

Probab=96.79  E-value=0.0052  Score=53.83  Aligned_cols=50  Identities=12%  Similarity=0.008  Sum_probs=34.3

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      .|-.+|..+=+.-.++.|.|.+|+||||||.+++..  ....-..++|++..
T Consensus         7 ~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e   56 (218)
T cd01394           7 GLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTE   56 (218)
T ss_pred             HHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECC
Confidence            344444333355689999999999999999998876  33333456677654

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK06526 transposase; Provisional

Probab=96.78  E-value=0.0024  Score=57.47  Aligned_cols=23  Identities=13%  Similarity=-0.013  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-+.++|++|+|||+||..+...
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHH
Confidence            45789999999999999999776

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

Probab=96.78  E-value=0.0074  Score=61.74  Aligned_cols=134  Identities=11%  Similarity=0.152  Sum_probs=80.5

Q ss_pred             CccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDA   89 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~   89 (351)
                      ..++|-|+-++.+.+.+...       ...+...-..|+.|+|||-||+++..-  +-+.=+..+-+.+| |.-+.-...
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~--Lfg~e~aliR~DMSEy~EkHsVSr  568 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA--LFGDEQALIRIDMSEYMEKHSVSR  568 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHH--hcCCCccceeechHHHHHHHHHHH
Confidence            55799999999998888532       234667778899999999999998766  32222344555555 443333332


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceE-EEEEeCCCCh--hhHHHHHhhcCCC----CCCc------EEEE-
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRY-LIVIQDVWRG--DIWDFLKEALPDH----QNGS------RILT-  155 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~-LlVLDdv~~~--~~~~~l~~~l~~~----~~gs------~Iiv-  155 (351)
                      +   ++.+  +..+.......    |-+.++++.| .+.||++...  +-++-+...+.++    +.|-      .||| 
T Consensus       569 L---IGaP--PGYVGyeeGG~----LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIIm  639 (786)
T COG0542         569 L---IGAP--PGYVGYEEGGQ----LTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIM  639 (786)
T ss_pred             H---hCCC--CCCceeccccc----hhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEE
Confidence            2   2222  11122333333    4445557777 7777999754  5666666665542    2333      4677 


Q ss_pred             Eeeccch
Q 048347          156 ALIHIVG  162 (351)
Q Consensus       156 TR~~~v~  162 (351)
                      |.|-...
T Consensus       640 TSN~Gs~  646 (786)
T COG0542         640 TSNAGSE  646 (786)
T ss_pred             ecccchH
Confidence            8776653

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

Probab=96.76  E-value=0.0058  Score=58.63  Aligned_cols=52  Identities=10%  Similarity=-0.065  Sum_probs=39.0

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.+.-.++.|.+..++++.+.+...           -...+-+.++|+.|.|||++|+.+++.
T Consensus       140 p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            3334455789999999988876421           023456779999999999999999988

>PRK08181 transposase; Validated

Probab=96.75  E-value=0.0035  Score=56.80  Aligned_cols=73  Identities=8%  Similarity=0.003  Sum_probs=43.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      .-+.++|+.|+|||.||..+.+.  .......+.|+    +..+++..+.....         ..+.....+    .+. 
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~----~~~~L~~~l~~a~~---------~~~~~~~l~----~l~-  166 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFT----RTTDLVQKLQVARR---------ELQLESAIA----KLD-  166 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHH--HHHcCCceeee----eHHHHHHHHHHHHh---------CCcHHHHHH----HHh-
Confidence            34789999999999999999876  43333334444    34566665543211         112222222    222 


Q ss_pred             ceEEEEEeCCCCh
Q 048347          122 KRYLIVIQDVWRG  134 (351)
Q Consensus       122 k~~LlVLDdv~~~  134 (351)
                      +--||||||+...
T Consensus       167 ~~dLLIIDDlg~~  179 (269)
T PRK08181        167 KFDLLILDDLAYV  179 (269)
T ss_pred             cCCEEEEeccccc
Confidence            3348999999533

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.75  E-value=0.0088  Score=57.93  Aligned_cols=88  Identities=9%  Similarity=-0.048  Sum_probs=50.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CC--HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LS--LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      +..+|.++|..|+||||+|..++..  .+..-..+.-|+.. +.  ..+.++.++.++..+..... ...+...+.....
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~--L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~-~~~d~~~i~~~al  170 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARY--FKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDP-DNKDAVEIAKEGL  170 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCCcEEecC-CccCHHHHHHHHH
Confidence            4678999999999999999999876  43332234445554 33  34556667777655422110 1122223233333


Q ss_pred             HhcCCceEEEEEeCC
Q 048347          117 NYLKNKRYLIVIQDV  131 (351)
Q Consensus       117 ~~L~~k~~LlVLDdv  131 (351)
                      +.+++. -++|+|-.
T Consensus       171 ~~~~~~-DvVIIDTA  184 (437)
T PRK00771        171 EKFKKA-DVIIVDTA  184 (437)
T ss_pred             HHhhcC-CEEEEECC
Confidence            333344 45777776

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.75  E-value=0.0059  Score=64.20  Aligned_cols=75  Identities=13%  Similarity=0.197  Sum_probs=52.0

Q ss_pred             ccccchhhHHHHHHHHHcc-CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeE---EEEEe-----CCHHHHHHH
Q 048347           19 VDLDLEDKMEELLDLLIER-QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCA---WVYYQ-----LSLDMMLDA   89 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~-~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~---wv~~~-----~~~~~~~~~   89 (351)
                      .++||+.+.+.|...+..- ..+-.++.|.|..|||||+++++|...  +...+...+   +-...     ....+.+++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~--i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~   78 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKP--ITQQRGYFIKGKFDQFERNIPLSPLVQAFRD   78 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHH--HhccceeeeHhhcccccCCCchHHHHHHHHH
Confidence            3789999999998888653 234569999999999999999999988  544422111   11111     445567777


Q ss_pred             HHHHhC
Q 048347           90 IMKSLM   95 (351)
Q Consensus        90 i~~~~~   95 (351)
                      ++.++.
T Consensus        79 l~~~ll   84 (849)
T COG3899          79 LMGQLL   84 (849)
T ss_pred             HHHHHh
Confidence            777773

>PRK09087 hypothetical protein; Validated

Probab=96.75  E-value=0.0072  Score=53.41  Aligned_cols=24  Identities=13%  Similarity=0.144  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.+.|||..|+|||+|++.++..
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            456899999999999999998877

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.74  E-value=0.0016  Score=64.23  Aligned_cols=46  Identities=7%  Similarity=0.196  Sum_probs=39.8

Q ss_pred             ccccchhhHHHHHHHHHc----cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIE----RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++|.++.++++++.+..    -+.+-+++.++|+.|+|||+||+.+..-
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~  126 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSL  126 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHH
Confidence            489999999999998833    2456689999999999999999999876

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.74  E-value=0.0043  Score=61.03  Aligned_cols=95  Identities=14%  Similarity=0.102  Sum_probs=63.5

Q ss_pred             CccccchhhHHHHHHHHHcc---C-------CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER---Q-------PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMML   87 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~---~-------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~   87 (351)
                      .++=|.|..+.++.+++..-   +       ...+=|-++|+.|.|||.||+++.+...  -.|     +.++  ..   
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~--vPf-----~~is--Ap---  257 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELG--VPF-----LSIS--AP---  257 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcC--Cce-----Eeec--ch---
Confidence            34557999999988887531   1       1223466899999999999999999943  333     2222  11   


Q ss_pred             HHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh
Q 048347           88 DAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus        88 ~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                       +|.         .++...+++.+.+.+.+.-..-.|++++|+++-.
T Consensus       258 -eiv---------SGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI  294 (802)
T KOG0733|consen  258 -EIV---------SGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAI  294 (802)
T ss_pred             -hhh---------cccCcccHHHHHHHHHHHhccCCeEEEeeccccc
Confidence             111         1123446667777777777888999999999643

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.72  E-value=0.0031  Score=56.12  Aligned_cols=59  Identities=12%  Similarity=0.113  Sum_probs=35.5

Q ss_pred             CCccccchh-hHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEE
Q 048347           17 NKVDLDLED-KMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYY   79 (351)
Q Consensus        17 ~~~~vGr~~-~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~   79 (351)
                      ++.++|-.. -...+.++....  ....+.|+|+.|+|||+||+.+++.  ....-..+.++++
T Consensus        22 d~f~~~~n~~a~~~l~~~~~~~--~~~~l~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~   81 (235)
T PRK08084         22 ASFYPGDNDSLLAALQNALRQE--HSGYIYLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPL   81 (235)
T ss_pred             cccccCccHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEH
Confidence            445557322 233333433322  3357889999999999999999987  4333333445543

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

Probab=96.72  E-value=0.0037  Score=64.61  Aligned_cols=45  Identities=16%  Similarity=0.192  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++||+++++++++.|......  -+.++|..|+|||++|+.++..
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~~--n~LLvGppGvGKT~lae~la~~  230 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRKN--NPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCCC--CeEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999988775322  2347999999999999998865

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.70  E-value=0.019  Score=58.32  Aligned_cols=138  Identities=10%  Similarity=-0.019  Sum_probs=72.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      .+++|.++-.+.|..++..+. -..-+-++|..|+||||+|+.+..............   .+...-+..+.+.......
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~---~~Cg~C~~C~~i~~g~h~D   91 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTP---EPCGKCELCRAIAAGNALD   91 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCC---CCCcccHHHHHHhcCCCcc
Confidence            568999999999999887652 224556899999999999999876622111000000   0000001112221111110


Q ss_pred             CC-CccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           98 SA-LSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        98 ~~-~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      .. .........+++.+.+...    ..+++-++|+|+++..  ++++.+...+........+|. |.+.
T Consensus        92 ~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~  161 (620)
T PRK14948         92 VIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDP  161 (620)
T ss_pred             EEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCCh
Confidence            00 0000112233333333211    1245568899999855  567888887776554555555 6443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.70  E-value=0.007  Score=54.80  Aligned_cols=125  Identities=13%  Similarity=0.063  Sum_probs=73.3

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEE-EEEe-CCHHHHHHHHHHHh
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAW-VYYQ-LSLDMMLDAIMKSL   94 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~w-v~~~-~~~~~~~~~i~~~~   94 (351)
                      -++++|-+..++.|.+.+...  .....-.+|+.|.|||+.|.......--.+.|.+.+- .+++ ..-..+.++     
T Consensus        35 ~de~~gQe~vV~~L~~a~~~~--~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~-----  107 (346)
T KOG0989|consen   35 FDELAGQEHVVQVLKNALLRR--ILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVRE-----  107 (346)
T ss_pred             HHhhcchHHHHHHHHHHHhhc--CCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhh-----
Confidence            356889898899998888773  4677788999999999988777655333455666432 2222 000000000     


Q ss_pred             CCCCCCccCCCCCHHHHHHHHHHhc--CCce-EEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347           95 MPLSALSEILDNDFEMKKNTLHNYL--KNKR-YLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~l~~~L--~~k~-~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                               ...+...+........  -.+. -.+|||+++..  ++|..++..+.+....++.+. +.
T Consensus       108 ---------Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcn  167 (346)
T KOG0989|consen  108 ---------KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICN  167 (346)
T ss_pred             ---------hhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcC
Confidence                     0000110000000000  0122 36788999866  789999999888776777665 54

>PRK08233 hypothetical protein; Provisional

Probab=96.70  E-value=0.0014  Score=55.52  Aligned_cols=24  Identities=13%  Similarity=0.187  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|.+|+||||||+.+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            579999999999999999999877

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.69  E-value=0.0094  Score=56.51  Aligned_cols=25  Identities=16%  Similarity=0.307  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|+++|.+|+||||++..++..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~  264 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQ  264 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHH
Confidence            4579999999999999999998765

>PRK09183 transposase/IS protein; Provisional

Probab=96.69  E-value=0.0046  Score=55.83  Aligned_cols=23  Identities=9%  Similarity=0.094  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+.|+|+.|+|||+||..+...
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHH
Confidence            46779999999999999999765

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.68  E-value=0.0077  Score=50.97  Aligned_cols=58  Identities=9%  Similarity=0.091  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHHHHhcCCceEEEEEeC----CCChhhHHHHHhhcCCCCCCcEEEE-Eeeccc
Q 048347          104 LDNDFEMKKNTLHNYLKNKRYLIVIQD----VWRGDIWDFLKEALPDHQNGSRILT-ALIHIV  161 (351)
Q Consensus       104 ~~~~~~~~~~~l~~~L~~k~~LlVLDd----v~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v  161 (351)
                      +....++..-.+.+.+-++.-+++=|.    ++..-.|+-+.-.-.-+..|..|++ |.+.++
T Consensus       137 ~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~l  199 (223)
T COG2884         137 QLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLEL  199 (223)
T ss_pred             ccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHH
Confidence            445566667778888889998888874    4444566655433333556999999 998875

>PRK06620 hypothetical protein; Validated

Probab=96.67  E-value=0.0065  Score=53.22  Aligned_cols=23  Identities=13%  Similarity=-0.114  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+-|||+.|+|||+|++.+++.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhc
Confidence            56789999999999999998887

>PRK14974 cell division protein FtsY; Provisional

Probab=96.67  E-value=0.013  Score=54.72  Aligned_cols=92  Identities=9%  Similarity=-0.018  Sum_probs=47.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CC--HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LS--LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      +..++.++|+.|+||||++..++..  .+..=..++.+... +.  ..+-++..+..++.+.............+.+.+.
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~--l~~~g~~V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~  216 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYY--LKKNGFSVVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIE  216 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH--HHHcCCeEEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHH
Confidence            3689999999999999988888765  33321123344433 22  2234555666665433211111111122233333


Q ss_pred             HhcCCceEEEEEeCCCC
Q 048347          117 NYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       117 ~~L~~k~~LlVLDdv~~  133 (351)
                      ..-....-++++|-.-.
T Consensus       217 ~~~~~~~DvVLIDTaGr  233 (336)
T PRK14974        217 HAKARGIDVVLIDTAGR  233 (336)
T ss_pred             HHHhCCCCEEEEECCCc
Confidence            32222223778887743

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.66  E-value=0.0065  Score=56.70  Aligned_cols=44  Identities=7%  Similarity=0.049  Sum_probs=30.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      .-+.++|..|+|||.||.++++.  +...-..+++++    ..+++..+.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~--l~~~g~~V~y~t----~~~l~~~l~  227 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKE--LLDRGKSVIYRT----ADELIEILR  227 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH--HHHCCCeEEEEE----HHHHHHHHH
Confidence            56889999999999999999988  443333444543    344555443

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

Probab=96.65  E-value=0.0041  Score=58.19  Aligned_cols=27  Identities=7%  Similarity=0.025  Sum_probs=24.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      +....++|||+.|.|||.+|+.+++..
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~el  172 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKM  172 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHc
Confidence            456889999999999999999999993

>TIGR00235 udk uridine kinase

Probab=96.64  E-value=0.0017  Score=56.49  Aligned_cols=26  Identities=19%  Similarity=0.305  Sum_probs=23.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++..+|+|+|++|+||||||+.+...
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            45689999999999999999999876

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>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=96.61  E-value=0.023  Score=47.42  Aligned_cols=131  Identities=11%  Similarity=0.048  Sum_probs=68.0

Q ss_pred             cchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCC-
Q 048347           22 DLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSAL-  100 (351)
Q Consensus        22 Gr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~-  100 (351)
                      |-++..+.|.+.+..+. -...+-++|..|+||+++|..+....--......   .+   ..-...+.+......+... 
T Consensus         1 gq~~~~~~L~~~~~~~~-l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~---~c---~~c~~c~~~~~~~~~d~~~~   73 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR-LPHALLFHGPSGSGKKTLALAFARALLCSNPNED---PC---GECRSCRRIEEGNHPDFIII   73 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC---SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--------SSSHHHHHHHTT-CTTEEEE
T ss_pred             CcHHHHHHHHHHHHcCC-cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCC---CC---CCCHHHHHHHhccCcceEEE
Confidence            44566677777776542 2345678999999999998876543111111100   00   0000111111100000000 


Q ss_pred             -cc--CCCCCHHHHHHHHHHhc-----CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347          101 -SE--ILDNDFEMKKNTLHNYL-----KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus       101 -~~--~~~~~~~~~~~~l~~~L-----~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                       ..  ......+++. .+.+.+     .++.-.+|+|+++..  +++..+...+.....++++|+ |++.+
T Consensus        74 ~~~~~~~~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   74 KPDKKKKSIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             ETTTSSSSBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             ecccccchhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChH
Confidence             00  0022344444 333333     245668899999865  688999999988877888888 87654

...

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.61  E-value=0.0076  Score=55.73  Aligned_cols=97  Identities=11%  Similarity=0.191  Sum_probs=55.7

Q ss_pred             cchhhHHHHHHHHHccC--CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCC
Q 048347           22 DLEDKMEELLDLLIERQ--PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSA   99 (351)
Q Consensus        22 Gr~~~~~~l~~~L~~~~--~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~   99 (351)
                      ++..-.+...+++..-.  +..+-+-++|..|+|||.||.++++.  ....-..+.++++    .+++.++...+...  
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~--l~~~g~~v~~~~~----~~l~~~lk~~~~~~--  206 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANE--LAKKGVSSTLLHF----PEFIRELKNSISDG--  206 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEEEH----HHHHHHHHHHHhcC--
Confidence            34444444455554321  13456779999999999999999998  4333333455543    45666665444211  


Q ss_pred             CccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHH
Q 048347          100 LSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWD  138 (351)
Q Consensus       100 ~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~  138 (351)
                             +..   +. .+.++ +-=+|||||+-..  .+|.
T Consensus       207 -------~~~---~~-l~~l~-~~dlLiIDDiG~e~~s~~~  235 (306)
T PRK08939        207 -------SVK---EK-IDAVK-EAPVLMLDDIGAEQMSSWV  235 (306)
T ss_pred             -------cHH---HH-HHHhc-CCCEEEEecCCCccccHHH
Confidence                   112   22 22333 4558899999533  4564

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.60  E-value=0.0052  Score=60.92  Aligned_cols=95  Identities=12%  Similarity=0.097  Sum_probs=54.8

Q ss_pred             CCccccchhhHHHHHHHHH---c-------cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           17 NKVDLDLEDKMEELLDLLI---E-------RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~---~-------~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      =++++|.++.++++.+++.   .       +....+=+-++|++|.|||++|+.++..  ....     ++.++  ..++
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~--~~~~-----~~~i~--~~~~  124 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE--AGVP-----FFSIS--GSDF  124 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH--cCCC-----eeecc--HHHH
Confidence            3457898888777766553   1       1112233668999999999999999887  3222     22332  1122


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                      ....    ..         .....+.+.+.......+++|+||+++.
T Consensus       125 ~~~~----~g---------~~~~~l~~~f~~a~~~~p~Il~iDEid~  158 (495)
T TIGR01241       125 VEMF----VG---------VGASRVRDLFEQAKKNAPCIIFIDEIDA  158 (495)
T ss_pred             HHHH----hc---------ccHHHHHHHHHHHHhcCCCEEEEechhh
Confidence            1111    00         1222334444444456678999999954

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.

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

Probab=96.60  E-value=0.0032  Score=53.49  Aligned_cols=74  Identities=15%  Similarity=0.120  Sum_probs=41.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      ..-+.++|..|+|||.||..+.+.  .-.+=..+.|++    ..+++..+-.    ...     ........    +.+.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~--~~~~g~~v~f~~----~~~L~~~l~~----~~~-----~~~~~~~~----~~l~  107 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANE--AIRKGYSVLFIT----ASDLLDELKQ----SRS-----DGSYEELL----KRLK  107 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEE----HHHHHHHHHC----CHC-----CTTHCHHH----HHHH
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHH--hccCCcceeEee----cCceeccccc----ccc-----ccchhhhc----Cccc
Confidence            355889999999999999999876  333323345554    4455555532    111     11222222    2333


Q ss_pred             CceEEEEEeCCCCh
Q 048347          121 NKRYLIVIQDVWRG  134 (351)
Q Consensus       121 ~k~~LlVLDdv~~~  134 (351)
                      + -=||||||+-..
T Consensus       108 ~-~dlLilDDlG~~  120 (178)
T PF01695_consen  108 R-VDLLILDDLGYE  120 (178)
T ss_dssp             T-SSCEEEETCTSS
T ss_pred             c-ccEeccccccee
Confidence            3 346789999644

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.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.60  E-value=0.0099  Score=57.68  Aligned_cols=50  Identities=12%  Similarity=0.148  Sum_probs=34.4

Q ss_pred             CccccchhhHH---HHHHHHHccC-------CCeEEEEEEcCCCChHHHHHHHHhCCccc
Q 048347           18 KVDLDLEDKME---ELLDLLIERQ-------PQLSLVAIIDTMGFDRTAFIGEAYNSSYV   67 (351)
Q Consensus        18 ~~~vGr~~~~~---~l~~~L~~~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~   67 (351)
                      +++-|.|+.++   ++++.|.+..       +=.+=|-++|++|.|||.||++|.-...|
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~V  363 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGV  363 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCC
Confidence            34567776554   5556665432       11344668899999999999999998554

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.59  E-value=0.0019  Score=56.25  Aligned_cols=25  Identities=16%  Similarity=0.295  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|+|.|.+|+||||||+.++..
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999999999999999887

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

Probab=96.57  E-value=0.03  Score=51.95  Aligned_cols=125  Identities=10%  Similarity=0.082  Sum_probs=72.0

Q ss_pred             CccccchhhHHHHHHHHHcc---C--------CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER---Q--------PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~---~--------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      +++=|.++.+++|.+.+.-.   +        +..+=|-++|++|.|||.||++|+++  ....|     +.+.      
T Consensus       151 ~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~--T~AtF-----Irvv------  217 (406)
T COG1222         151 EDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ--TDATF-----IRVV------  217 (406)
T ss_pred             hhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhc--cCceE-----EEec------
Confidence            34557899999998887432   0        22344668999999999999999999  44443     3332      


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc-CCceEEEEEeCCCCh-------------hh---HHHHHhhcCC--C
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL-KNKRYLIVIQDVWRG-------------DI---WDFLKEALPD--H  147 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVLDdv~~~-------------~~---~~~l~~~l~~--~  147 (351)
                      -.++.+..-+..          ..+...+.+.- ++..+.+.+|.++..             +.   +-++...+..  .
T Consensus       218 gSElVqKYiGEG----------aRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~  287 (406)
T COG1222         218 GSELVQKYIGEG----------ARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDP  287 (406)
T ss_pred             cHHHHHHHhccc----------hHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCC
Confidence            111121211211          12333333333 356788999998633             11   1122333332  2


Q ss_pred             CCCcEEEE-Eeeccc---hhhc
Q 048347          148 QNGSRILT-ALIHIV---GLSS  165 (351)
Q Consensus       148 ~~gs~Iiv-TR~~~v---~lL~  165 (351)
                      ...-|||. |...++   |+|+
T Consensus       288 ~~nvKVI~ATNR~D~LDPALLR  309 (406)
T COG1222         288 RGNVKVIMATNRPDILDPALLR  309 (406)
T ss_pred             CCCeEEEEecCCccccChhhcC
Confidence            33568888 887777   6666

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=96.57  E-value=0.00083  Score=60.51  Aligned_cols=85  Identities=20%  Similarity=0.208  Sum_probs=41.8

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      .-+|.+++|++|.|.  +.. ..++..+++|..|+|++| .+.++...-.+|-+++.|.|.+ +.++.+ +++++|-+|.
T Consensus       304 KL~Pkir~L~lS~N~--i~~-v~nLa~L~~L~~LDLS~N-~Ls~~~Gwh~KLGNIKtL~La~-N~iE~L-SGL~KLYSLv  377 (490)
T KOG1259|consen  304 KLAPKLRRLILSQNR--IRT-VQNLAELPQLQLLDLSGN-LLAECVGWHLKLGNIKTLKLAQ-NKIETL-SGLRKLYSLV  377 (490)
T ss_pred             hhccceeEEeccccc--eee-ehhhhhcccceEeecccc-hhHhhhhhHhhhcCEeeeehhh-hhHhhh-hhhHhhhhhe
Confidence            345677777774332  111 223566677777777776 3444443333444444555544 233333 2444444555


Q ss_pred             EEEecCCChhH
Q 048347          319 KLESWWPRPEL  329 (351)
Q Consensus       319 ~L~l~~~~~~~  329 (351)
                      .||+++.+.+-
T Consensus       378 nLDl~~N~Ie~  388 (490)
T KOG1259|consen  378 NLDLSSNQIEE  388 (490)
T ss_pred             eccccccchhh
Confidence            55554444333

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.57  E-value=0.012  Score=56.09  Aligned_cols=87  Identities=7%  Similarity=0.036  Sum_probs=50.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccc--cCCCeeEEEEEe-CCHHH--HHHHHHHHhCCCCCCccCCCCCHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVK--NYFDCCAWVYYQ-LSLDM--MLDAIMKSLMPLSALSEILDNDFEMKKNT  114 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~~~-~~~~~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  114 (351)
                      +..+|.++|..|+||||.+..+.......  .+-..+..++.. +....  -++..++.++.+..    ...+.+.+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~----~~~~~~~l~~~  248 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVK----AIESFKDLKEE  248 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceE----eeCcHHHHHHH
Confidence            35799999999999999999887763222  122345566666 43333  34444544444322    22344555555


Q ss_pred             HHHhcCCceEEEEEeCCC
Q 048347          115 LHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus       115 l~~~L~~k~~LlVLDdv~  132 (351)
                      +.+.  ++.-++++|-.-
T Consensus       249 L~~~--~~~DlVLIDTaG  264 (388)
T PRK12723        249 ITQS--KDFDLVLVDTIG  264 (388)
T ss_pred             HHHh--CCCCEEEEcCCC
Confidence            5443  334567778774

>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=96.56  E-value=0.0016  Score=51.60  Aligned_cols=21  Identities=19%  Similarity=0.202  Sum_probs=19.7

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+|.|+.|+||||+|+++...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999888

...

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.56  E-value=0.019  Score=48.76  Aligned_cols=117  Identities=12%  Similarity=0.020  Sum_probs=62.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE---Ee-CCHHHHHHH------HHHHhCCCCCCcc-C-CCCCH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY---YQ-LSLDMMLDA------IMKSLMPLSALSE-I-LDNDF  108 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---~~-~~~~~~~~~------i~~~~~~~~~~~~-~-~~~~~  108 (351)
                      -.+++|.|..|+|||||++.++..  ... ....+++.   +. .+.......      +++.++....... . .....
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~--~~~-~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G  101 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGL--LKP-SSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSGG  101 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--CCC-CCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHH
Confidence            468999999999999999999886  322 23333332   11 222222221      3444443221110 1 22233


Q ss_pred             HHHHHHHHHhcCCceEEEEEeCCCCh---hhHHHHHhhcCC-CCC-CcEEEE-Eeecc
Q 048347          109 EMKKNTLHNYLKNKRYLIVIQDVWRG---DIWDFLKEALPD-HQN-GSRILT-ALIHI  160 (351)
Q Consensus       109 ~~~~~~l~~~L~~k~~LlVLDdv~~~---~~~~~l~~~l~~-~~~-gs~Iiv-TR~~~  160 (351)
                      +...-.+...+....-++++|+--..   +..+.+...+.. ... |..||+ |++..
T Consensus       102 ~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~  159 (180)
T cd03214         102 ERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLN  159 (180)
T ss_pred             HHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            33444556677777888999987533   233344443332 122 556666 77654

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.55  E-value=0.0079  Score=52.91  Aligned_cols=22  Identities=5%  Similarity=0.110  Sum_probs=20.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|||.|..|+||||||+.+...
T Consensus         1 IigI~G~sGSGKTTla~~L~~~   22 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQAL   22 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHH
Confidence            5899999999999999999877

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.55  E-value=0.01  Score=61.82  Aligned_cols=48  Identities=13%  Similarity=0.034  Sum_probs=37.3

Q ss_pred             CCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+++.|.++.++++.+++...           -...+-+.++|+.|+|||+||+.+++.
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~  235 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE  235 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHH
Confidence            345789999999998887421           022345779999999999999999887

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.53  E-value=0.0078  Score=55.83  Aligned_cols=98  Identities=15%  Similarity=0.013  Sum_probs=58.5

Q ss_pred             HHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-ccC
Q 048347           28 EELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SEI  103 (351)
Q Consensus        28 ~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~~  103 (351)
                      ..|-.+|- .+=++-+++-|+|++|+||||||-+++..  ....-..++||+..  ++.     ..+++++.+... .-.
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~-----~~a~~lGvd~~~l~v~  113 (325)
T cd00983          41 LSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDP-----VYAKKLGVDLDNLLIS  113 (325)
T ss_pred             HHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHH-----HHHHHcCCCHHHheec
Confidence            34444443 23356788999999999999999998776  33444567788765  333     234444432110 001


Q ss_pred             CCCCHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          104 LDNDFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       104 ~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                      ...+.+++.+.+...++. .--++|+|.+-
T Consensus       114 ~p~~~eq~l~i~~~li~s~~~~lIVIDSva  143 (325)
T cd00983         114 QPDTGEQALEIADSLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             CCCCHHHHHHHHHHHHhccCCCEEEEcchH
Confidence            233456666666555543 45688888873

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK15386 type III secretion protein GogB; Provisional

Probab=96.53  E-value=0.0024  Score=60.87  Aligned_cols=66  Identities=15%  Similarity=0.184  Sum_probs=52.1

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCC-cccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhc
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFP-RQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~-~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      .++++..|++ +++ .+..+|.    ++ +|+.|.+++|.++..+|..+.  .+|++|++.+|..+..+|+++..
T Consensus        50 ~~~~l~~L~I-s~c-~L~sLP~----LP~sLtsL~Lsnc~nLtsLP~~LP--~nLe~L~Ls~Cs~L~sLP~sLe~  116 (426)
T PRK15386         50 EARASGRLYI-KDC-DIESLPV----LPNELTEITIENCNNLTTLPGSIP--EGLEKLTVCHCPEISGLPESVRS  116 (426)
T ss_pred             HhcCCCEEEe-CCC-CCcccCC----CCCCCcEEEccCCCCcccCCchhh--hhhhheEccCcccccccccccce
Confidence            3578999999 454 6777772    33 699999999989999996553  68999999999889999976443

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

Probab=96.52  E-value=0.0087  Score=51.64  Aligned_cols=112  Identities=6%  Similarity=0.026  Sum_probs=55.3

Q ss_pred             hhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCC
Q 048347           25 DKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEIL  104 (351)
Q Consensus        25 ~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~  104 (351)
                      ++..+.+..+....  -++..|.|.+|.||||+++.+...  ....=..++++.  ++-.. ...+......+..     
T Consensus         4 ~~Q~~a~~~~l~~~--~~~~~l~G~aGtGKT~~l~~~~~~--~~~~g~~v~~~a--pT~~A-a~~L~~~~~~~a~-----   71 (196)
T PF13604_consen    4 EEQREAVRAILTSG--DRVSVLQGPAGTGKTTLLKALAEA--LEAAGKRVIGLA--PTNKA-AKELREKTGIEAQ-----   71 (196)
T ss_dssp             HHHHHHHHHHHHCT--CSEEEEEESTTSTHHHHHHHHHHH--HHHTT--EEEEE--SSHHH-HHHHHHHHTS-EE-----
T ss_pred             HHHHHHHHHHHhcC--CeEEEEEECCCCCHHHHHHHHHHH--HHhCCCeEEEEC--CcHHH-HHHHHHhhCcchh-----
Confidence            34445555554433  356777999999999999998776  333311222222  22222 2223333332211     


Q ss_pred             CCCHHHHHHHHHHhc---------CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE
Q 048347          105 DNDFEMKKNTLHNYL---------KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT  155 (351)
Q Consensus       105 ~~~~~~~~~~l~~~L---------~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv  155 (351)
                           .+...+...-         ..++-++|+|+....  .++..+....+.  .|.++|.
T Consensus        72 -----Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klil  126 (196)
T PF13604_consen   72 -----TIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLIL  126 (196)
T ss_dssp             -----EHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEE
T ss_pred             -----hHHHHHhcCCcccccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEE
Confidence                 0011111000         123448999999765  466666666655  4667765

>PRK05642 DNA replication initiation factor; Validated

Probab=96.52  E-value=0.0076  Score=53.57  Aligned_cols=35  Identities=14%  Similarity=0.173  Sum_probs=25.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY   78 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~   78 (351)
                      ..+.|+|..|+|||.||+.+++.  ....-..++|++
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~--~~~~~~~v~y~~   80 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLR--FEQRGEPAVYLP   80 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHhCCCcEEEee
Confidence            56789999999999999999876  333323445554

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.51  E-value=0.0063  Score=53.70  Aligned_cols=44  Identities=9%  Similarity=0.067  Sum_probs=29.8

Q ss_pred             cccchhhH-HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           20 DLDLEDKM-EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        20 ~vGr~~~~-~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|..+.. ..+.++.. .......+.|+|..|+|||+||+.+++.
T Consensus        21 ~~~~~~~~~~~l~~~~~-~~~~~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         21 VAGENAELVARLRELAA-GPVADRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             ccCCcHHHHHHHHHHHh-ccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            34554444 33444443 2223456789999999999999999987

>TIGR00763 lon ATP-dependent protease La

Probab=96.51  E-value=0.006  Score=63.75  Aligned_cols=53  Identities=13%  Similarity=0.248  Sum_probs=40.1

Q ss_pred             CCccccchhhHHHHHHHHHc----cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           17 NKVDLDLEDKMEELLDLLIE----RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      +.+++|.++-++.+.+++..    ...+-.++.++|+.|+|||++|+.+.+.  ....|
T Consensus       319 ~~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~--l~~~~  375 (775)
T TIGR00763       319 DEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKA--LNRKF  375 (775)
T ss_pred             hhhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHH--hcCCe
Confidence            34578998888888886642    2223457889999999999999999988  54443

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=96.50  E-value=0.009  Score=55.39  Aligned_cols=98  Identities=13%  Similarity=0.002  Sum_probs=59.3

Q ss_pred             HHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCc-cC
Q 048347           28 EELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALS-EI  103 (351)
Q Consensus        28 ~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~-~~  103 (351)
                      ..|-.+|- .+=++-+++-|.|..|+||||||.++...  ....-..++||+..  ++.     ..+++++.+...- -.
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~-----~~a~~lGvd~~~l~v~  113 (321)
T TIGR02012        41 LSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDP-----VYARKLGVDIDNLLVS  113 (321)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHH-----HHHHHcCCCHHHeEEe
Confidence            34444443 33366789999999999999999988776  33344556787655  332     2345554321100 01


Q ss_pred             CCCCHHHHHHHHHHhcC-CceEEEEEeCCC
Q 048347          104 LDNDFEMKKNTLHNYLK-NKRYLIVIQDVW  132 (351)
Q Consensus       104 ~~~~~~~~~~~l~~~L~-~k~~LlVLDdv~  132 (351)
                      ...+.++....+...++ +.--++|+|.+-
T Consensus       114 ~p~~~eq~l~~~~~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       114 QPDTGEQALEIAETLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             cCCCHHHHHHHHHHHhhccCCcEEEEcchh
Confidence            23345566666655554 355689999884

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PF14516 AAA_35: AAA-like domain

Probab=96.49  E-value=0.023  Score=53.28  Aligned_cols=117  Identities=15%  Similarity=0.163  Sum_probs=74.4

Q ss_pred             cCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-------CCHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-------LSLDM   85 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-------~~~~~   85 (351)
                      .+.+...-|.|..--+++.+.|...+   ..+.|.|+-.+|||+|..++.+.  .+..=..++++++.       .+.++
T Consensus         6 ~~~~~~~Yi~R~~~e~~~~~~i~~~G---~~~~I~apRq~GKTSll~~l~~~--l~~~~~~~v~id~~~~~~~~~~~~~~   80 (331)
T PF14516_consen    6 LPLDSPFYIERPPAEQECYQEIVQPG---SYIRIKAPRQMGKTSLLLRLLER--LQQQGYRCVYIDLQQLGSAIFSDLEQ   80 (331)
T ss_pred             CCCCCCcccCchHHHHHHHHHHhcCC---CEEEEECcccCCHHHHHHHHHHH--HHHCCCEEEEEEeecCCCcccCCHHH
Confidence            34455566788855566666665532   48889999999999999999888  44332334577666       34666


Q ss_pred             HHHHHHHHhCCCCCCcc-------CCCCCHHHHHHHHHHhc---CCceEEEEEeCCCCh
Q 048347           86 MLDAIMKSLMPLSALSE-------ILDNDFEMKKNTLHNYL---KNKRYLIVIQDVWRG  134 (351)
Q Consensus        86 ~~~~i~~~~~~~~~~~~-------~~~~~~~~~~~~l~~~L---~~k~~LlVLDdv~~~  134 (351)
                      +++.++..+..+-....       ....+.......+.+.+   .+++.+++||+++..
T Consensus        81 f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l  139 (331)
T PF14516_consen   81 FLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRL  139 (331)
T ss_pred             HHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhh
Confidence            66666666655332110       11223444555555543   268999999999754

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.46  E-value=0.014  Score=56.27  Aligned_cols=25  Identities=8%  Similarity=0.092  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|.++|..|+||||+|..++..
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~  123 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYY  123 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3689999999999999999888765

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

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.46  E-value=0.011  Score=58.12  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|.+|+||||++.++...
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~  373 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQR  373 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999888765

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.45  E-value=0.021  Score=50.82  Aligned_cols=61  Identities=10%  Similarity=0.072  Sum_probs=41.3

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      .|-++|..+=++-+++.|.|.+|+|||+||.++.... . ..-+.++||+..-+..++.+.+.
T Consensus         9 ~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~-~-~~ge~~lyvs~ee~~~~i~~~~~   69 (237)
T TIGR03877         9 GMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNG-L-QMGEPGIYVALEEHPVQVRRNMA   69 (237)
T ss_pred             hHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHH-H-HcCCcEEEEEeeCCHHHHHHHHH
Confidence            3444454444567899999999999999998865441 2 23456788877666666666543

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.44  E-value=0.013  Score=51.87  Aligned_cols=101  Identities=14%  Similarity=0.040  Sum_probs=59.3

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCC--------
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSAL--------  100 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~--------  100 (351)
                      .|-++|..+=++-+++.|+|..|+|||+||.++.... ++ +=..++|++..-+..++.+.+ .+++-....        
T Consensus        13 ~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~-~~-~g~~~~y~~~e~~~~~~~~~~-~~~g~~~~~~~~~g~l~   89 (234)
T PRK06067         13 ELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGA-LK-QGKKVYVITTENTSKSYLKQM-ESVKIDISDFFLWGYLR   89 (234)
T ss_pred             HHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHH-Hh-CCCEEEEEEcCCCHHHHHHHH-HHCCCChhHHHhCCCce
Confidence            3444444443567889999999999999999985441 22 334677887764455555553 233221110        


Q ss_pred             ------cc--CCCCCHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          101 ------SE--ILDNDFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       101 ------~~--~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                            ..  ....+.+++.+.+.+.++. +.-++|+|.+-
T Consensus        90 i~~~~~~~~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         90 IFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             EEeccccccccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence                  00  0122345666666666653 44578888874

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=96.43  E-value=0.0021  Score=55.21  Aligned_cols=26  Identities=8%  Similarity=0.083  Sum_probs=23.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcc
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSY   66 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~   66 (351)
                      ..+|+|-||=|+||||||+.+.++.+
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhC
Confidence            57899999999999999999999944

>PRK15453 phosphoribulokinase; Provisional

Probab=96.41  E-value=0.016  Score=52.53  Aligned_cols=80  Identities=15%  Similarity=0.014  Sum_probs=46.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHhCCCCC--CccCCCCCHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSA--LSEILDNDFEMKKN  113 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~--~~~~~~~~~~~~~~  113 (351)
                      +..+|+|.|.+|+||||+|+.+...  ....=...+.++..    ++..+.-..+...-.....  ...++..+.+.+.+
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~i--f~~~~~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL~~   81 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKI--FRRENINAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDELEQ   81 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HhhcCCCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHHHH
Confidence            5679999999999999999998754  32211123444444    3444443333222221111  11146677777777


Q ss_pred             HHHHhcCC
Q 048347          114 TLHNYLKN  121 (351)
Q Consensus       114 ~l~~~L~~  121 (351)
                      .++...++
T Consensus        82 ~l~~l~~~   89 (290)
T PRK15453         82 LFREYGET   89 (290)
T ss_pred             HHHHHhcC
Confidence            77776553

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.40  E-value=0.023  Score=52.78  Aligned_cols=46  Identities=9%  Similarity=-0.078  Sum_probs=36.3

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|-++-++.+.+.+..+. -....-++|+.|+||+++|..+...
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-l~ha~Lf~G~~G~Gk~~~A~~~a~~   49 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-IAPAYLFAGPEGVGRKLAALCFIEG   49 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999887652 2367778999999999988776443

>PRK10867 signal recognition particle protein; Provisional

Probab=96.40  E-value=0.019  Score=55.60  Aligned_cols=25  Identities=12%  Similarity=0.230  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+|.++|..|+||||+|..++..
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~  123 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKY  123 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            3689999999999999988777665

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.40  E-value=0.023  Score=49.83  Aligned_cols=118  Identities=12%  Similarity=0.082  Sum_probs=71.1

Q ss_pred             CCCCccccchhhHHHHHHHHHc--cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHH
Q 048347           15 WDNKVDLDLEDKMEELLDLLIE--RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMK   92 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~   92 (351)
                      ++-..++|.|..++.+++--..  .+...-=|-+||--|.||+.|+|++.+.  +.+..-.  -|.|.  .+        
T Consensus        57 i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e--~~~~glr--LVEV~--k~--------  122 (287)
T COG2607          57 IDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNE--YADEGLR--LVEVD--KE--------  122 (287)
T ss_pred             cCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHH--HHhcCCe--EEEEc--HH--------
Confidence            4445689999888887653321  1222344668999999999999999998  6555444  23332  00        


Q ss_pred             HhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC---ChhhHHHHHhhcCCC---CCCcEEEE-Eeec
Q 048347           93 SLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW---RGDIWDFLKEALPDH---QNGSRILT-ALIH  159 (351)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~---~~~~~~~l~~~l~~~---~~gs~Iiv-TR~~  159 (351)
                                 +..+...+.+.++.  +.+||.+..||+.   ..+.+..++..+..+   .+...++. |.++
T Consensus       123 -----------dl~~Lp~l~~~Lr~--~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNR  183 (287)
T COG2607         123 -----------DLATLPDLVELLRA--RPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNR  183 (287)
T ss_pred             -----------HHhhHHHHHHHHhc--CCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCC
Confidence                       11122223333322  3589999999995   335788888877642   23334444 5544

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.38  E-value=0.0027  Score=52.11  Aligned_cols=91  Identities=10%  Similarity=0.160  Sum_probs=49.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEEEe---------CCHHHHHHH---HHHHhCC-CCCCcc--CC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVYYQ---------LSLDMMLDA---IMKSLMP-LSALSE--IL  104 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~~---------~~~~~~~~~---i~~~~~~-~~~~~~--~~  104 (351)
                      ...|+|.||.|+||||+++.+.+.  ++.. |...-+++--         |.+.++...   ++..... ......  +.
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~--L~~~g~kvgGf~t~EVR~gGkR~GF~Ivdl~tg~~~~la~~~~~~~rvGkY~V~   82 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEK--LREKGYKVGGFITPEVREGGKRIGFKIVDLATGEEGILARVGFSRPRVGKYGVN   82 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHH--HHhcCceeeeEEeeeeecCCeEeeeEEEEccCCceEEEEEcCCCCcccceEEee
Confidence            456889999999999999999988  4444 5554333211         333333210   0000000 000000  12


Q ss_pred             CCCHH-HHHHHHHHhcCCceEEEEEeCCCCh
Q 048347          105 DNDFE-MKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus       105 ~~~~~-~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                      ....+ -....+++.++. .=++|+|.+-..
T Consensus        83 v~~le~i~~~al~rA~~~-aDvIIIDEIGpM  112 (179)
T COG1618          83 VEGLEEIAIPALRRALEE-ADVIIIDEIGPM  112 (179)
T ss_pred             HHHHHHHhHHHHHHHhhc-CCEEEEecccch
Confidence            22333 445667777766 347888999655

>PRK09354 recA recombinase A; Provisional

Probab=96.38  E-value=0.012  Score=55.02  Aligned_cols=99  Identities=16%  Similarity=0.006  Sum_probs=60.9

Q ss_pred             HHHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-cc
Q 048347           27 MEELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SE  102 (351)
Q Consensus        27 ~~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~  102 (351)
                      ...|-.+|- .+=++-+++-|+|+.|+||||||-++...  ....-..++||..-  ++.     ..+++++.+... .-
T Consensus        45 i~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~--~~~~G~~~~yId~E~s~~~-----~~a~~lGvdld~lli  117 (349)
T PRK09354         45 SLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDP-----VYAKKLGVDIDNLLV  117 (349)
T ss_pred             cHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchHH-----HHHHHcCCCHHHeEE
Confidence            334445554 33366789999999999999999998776  33444567788766  333     345555443110 00


Q ss_pred             CCCCCHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          103 ILDNDFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                      ....+.++....+...++. +--++|+|.|-
T Consensus       118 ~qp~~~Eq~l~i~~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        118 SQPDTGEQALEIADTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             ecCCCHHHHHHHHHHHhhcCCCCEEEEeChh
Confidence            1233456666666655543 45689999884

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.38  E-value=0.014  Score=58.57  Aligned_cols=73  Identities=10%  Similarity=0.191  Sum_probs=44.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCC--eeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD--CCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      ..+.|+|..|.|||.|++.+++.  ....+.  .+.++    +..++..++...+...         .    .+.+++.+
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~--a~~~~~g~~V~Yi----taeef~~el~~al~~~---------~----~~~f~~~y  375 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHY--ARRLYPGTRVRYV----SSEEFTNEFINSIRDG---------K----GDSFRRRY  375 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEe----eHHHHHHHHHHHHHhc---------c----HHHHHHHh
Confidence            34789999999999999999998  444322  22343    3455555555444321         1    22333444


Q ss_pred             CCceEEEEEeCCCCh
Q 048347          120 KNKRYLIVIQDVWRG  134 (351)
Q Consensus       120 ~~k~~LlVLDdv~~~  134 (351)
                      ++- =+|+|||+...
T Consensus       376 ~~~-DLLlIDDIq~l  389 (617)
T PRK14086        376 REM-DILLVDDIQFL  389 (617)
T ss_pred             hcC-CEEEEehhccc
Confidence            433 47888999644

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.37  E-value=0.0074  Score=52.17  Aligned_cols=94  Identities=12%  Similarity=0.157  Sum_probs=52.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      .+|.|.|+.|.||||+++.+...  ...+....++.--. ..+..... ...+..+..    ...+.....+.++..++.
T Consensus         2 GlilI~GptGSGKTTll~~ll~~--~~~~~~~~i~t~e~-~~E~~~~~-~~~~i~q~~----vg~~~~~~~~~i~~aLr~   73 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY--INKNKTHHILTIED-PIEFVHES-KRSLINQRE----VGLDTLSFENALKAALRQ   73 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--hhhcCCcEEEEEcC-CccccccC-ccceeeecc----cCCCccCHHHHHHHHhcC
Confidence            36889999999999999988776  44444433332211 11111000 000000000    011223456677888877


Q ss_pred             ceEEEEEeCCCChhhHHHHHhh
Q 048347          122 KRYLIVIQDVWRGDIWDFLKEA  143 (351)
Q Consensus       122 k~~LlVLDdv~~~~~~~~l~~~  143 (351)
                      ..=.+++|++.+.+........
T Consensus        74 ~pd~ii~gEird~e~~~~~l~~   95 (198)
T cd01131          74 DPDVILVGEMRDLETIRLALTA   95 (198)
T ss_pred             CcCEEEEcCCCCHHHHHHHHHH
Confidence            7779999999877665554443

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.

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.36  E-value=0.023  Score=59.04  Aligned_cols=131  Identities=8%  Similarity=0.067  Sum_probs=77.6

Q ss_pred             CccccchhhHHHHHHHHHcc------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      +.++|-++-+..+...+...      ......+-+.|+.|+|||-||+++..-  +-+..+..+-++++    ++.. +.
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~--~Fgse~~~IriDms----e~~e-vs  634 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEY--VFGSEENFIRLDMS----EFQE-VS  634 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHH--HcCCccceEEechh----hhhh-hh
Confidence            45678788888877777542      124677888999999999999998777  54444444444443    2222 44


Q ss_pred             HHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEE-EEEeCCCCh--hhHHHHHhhcCC----C------CCCcEEEE-Ee
Q 048347           92 KSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYL-IVIQDVWRG--DIWDFLKEALPD----H------QNGSRILT-AL  157 (351)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~L-lVLDdv~~~--~~~~~l~~~l~~----~------~~gs~Iiv-TR  157 (351)
                      +-++.+..      .-..+....+.+.++.+.|- ++||||+..  +....+...+..    .      ..+..|+| |.
T Consensus       635 kligsp~g------yvG~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTs  708 (898)
T KOG1051|consen  635 KLIGSPPG------YVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTS  708 (898)
T ss_pred             hccCCCcc------cccchhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHHHHhcCccccCCCcEeeccceEEEEec
Confidence            44444321      11222344677777787764 455999765  334433343322    1      22456888 87


Q ss_pred             eccc
Q 048347          158 IHIV  161 (351)
Q Consensus       158 ~~~v  161 (351)
                      +-.-
T Consensus       709 n~~~  712 (898)
T KOG1051|consen  709 NVGS  712 (898)
T ss_pred             ccch
Confidence            6543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.35  E-value=0.019  Score=55.55  Aligned_cols=40  Identities=13%  Similarity=0.073  Sum_probs=27.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      -+++.++|++|+||||++..+.........-..+..|+..
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D  260 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLD  260 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECC
Confidence            3689999999999999988886652211222345555554

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.35  E-value=0.0055  Score=49.22  Aligned_cols=43  Identities=9%  Similarity=0.133  Sum_probs=30.8

Q ss_pred             hhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccc
Q 048347           25 DKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYV   67 (351)
Q Consensus        25 ~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~   67 (351)
                      ++.+++-+.+...-+.-.+|.+.|.-|+|||||++.+.....+
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            4445555555433233468999999999999999999887443

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.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.35  E-value=0.019  Score=47.07  Aligned_cols=36  Identities=11%  Similarity=0.107  Sum_probs=27.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      ++.|.|..|+||||+|..+...  ....-..++|++..
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e   36 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIE   36 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECC
Confidence            3678999999999999999887  44444456677665

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.016  Score=54.64  Aligned_cols=87  Identities=9%  Similarity=0.020  Sum_probs=51.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CC--HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LS--LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      +.+++.++|+.|+||||++..+...  ....-..+.+|+.. +-  ..+-++..++.+..+..    ...+..++.+.+.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~--l~~~g~~V~lItaDtyR~gAveQLk~yae~lgvpv~----~~~dp~dL~~al~  278 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQ--LLKQNRTVGFITTDTFRSGAVEQFQGYADKLDVELI----VATSPAELEEAVQ  278 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEeCCccCccHHHHHHHHhhcCCCCEE----ecCCHHHHHHHHH
Confidence            4689999999999999999998765  32222345667665 32  24445555554443322    2234555555554


Q ss_pred             Hhc-CCceEEEEEeCCC
Q 048347          117 NYL-KNKRYLIVIQDVW  132 (351)
Q Consensus       117 ~~L-~~k~~LlVLDdv~  132 (351)
                      ..- .+..=++++|-.-
T Consensus       279 ~l~~~~~~D~VLIDTAG  295 (407)
T PRK12726        279 YMTYVNCVDHILIDTVG  295 (407)
T ss_pred             HHHhcCCCCEEEEECCC
Confidence            332 1333466677664

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.32  E-value=0.021  Score=54.73  Aligned_cols=24  Identities=17%  Similarity=0.189  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++.++|++|+||||+|.++...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999999865

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

Probab=96.30  E-value=0.021  Score=59.16  Aligned_cols=115  Identities=6%  Similarity=0.096  Sum_probs=64.8

Q ss_pred             CccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDA   89 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~   89 (351)
                      ..++|-++-++.+.+.+...       ......+-++|+.|+|||++|+.+...  ....   .+.++.+ +........
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~--l~~~---~i~id~se~~~~~~~~~  532 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA--LGIE---LLRFDMSEYMERHTVSR  532 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHH--hCCC---cEEeechhhcccccHHH
Confidence            45789999999998888631       223456788999999999999999887  3222   2334444 322111111


Q ss_pred             HHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcC
Q 048347           90 IMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALP  145 (351)
Q Consensus        90 i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~  145 (351)
                      +   ++.+..  .........+.+.++   +....+++||+++..  +.++.+...+.
T Consensus       533 L---iG~~~g--yvg~~~~g~L~~~v~---~~p~sVlllDEieka~~~v~~~LLq~ld  582 (758)
T PRK11034        533 L---IGAPPG--YVGFDQGGLLTDAVI---KHPHAVLLLDEIEKAHPDVFNLLLQVMD  582 (758)
T ss_pred             H---cCCCCC--cccccccchHHHHHH---hCCCcEEEeccHhhhhHHHHHHHHHHHh
Confidence            1   222110  011111122233332   234468999999866  45666655543

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.30  E-value=0.0093  Score=56.93  Aligned_cols=76  Identities=11%  Similarity=0.150  Sum_probs=51.5

Q ss_pred             CCccccchhhHHHHHHHHHcc------------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC---CeeEEEEEe-
Q 048347           17 NKVDLDLEDKMEELLDLLIER------------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF---DCCAWVYYQ-   80 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~------------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~~~-   80 (351)
                      +.+++|.++.++.+.-.+...            +...+-|-++|+.|+|||++|+.+...  ....|   +...+...+ 
T Consensus        11 d~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~--l~~~fi~vdat~~~e~g~   88 (441)
T TIGR00390        11 DKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKL--ANAPFIKVEATKFTEVGY   88 (441)
T ss_pred             hhhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHH--hCCeEEEeecceeecCCc
Confidence            467899999999987666532            112256778999999999999999888  44444   222222222 


Q ss_pred             --CCHHHHHHHHHHHh
Q 048347           81 --LSLDMMLDAIMKSL   94 (351)
Q Consensus        81 --~~~~~~~~~i~~~~   94 (351)
                        .+.+++++.+....
T Consensus        89 vG~dvE~i~r~l~e~A  104 (441)
T TIGR00390        89 VGRDVESMVRDLTDAA  104 (441)
T ss_pred             ccCCHHHHHHHHHHHH
Confidence              46777777776655

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.

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

Probab=96.27  E-value=0.0054  Score=62.70  Aligned_cols=47  Identities=11%  Similarity=0.230  Sum_probs=37.3

Q ss_pred             CCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-+.++|||++++++++.|....++-.|+  +|.+|+|||++|.-++.+
T Consensus       168 klDPvIGRd~EI~r~iqIL~RR~KNNPvL--iGEpGVGKTAIvEGLA~r  214 (786)
T COG0542         168 KLDPVIGRDEEIRRTIQILSRRTKNNPVL--VGEPGVGKTAIVEGLAQR  214 (786)
T ss_pred             CCCCCcChHHHHHHHHHHHhccCCCCCeE--ecCCCCCHHHHHHHHHHH
Confidence            34568999999999999998876555555  699999999976655544

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=96.27  E-value=0.0089  Score=57.09  Aligned_cols=76  Identities=11%  Similarity=0.153  Sum_probs=52.5

Q ss_pred             CCccccchhhHHHHHHHHHcc--------C----CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC---CeeEEEEEe-
Q 048347           17 NKVDLDLEDKMEELLDLLIER--------Q----PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF---DCCAWVYYQ-   80 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~--------~----~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~~~-   80 (351)
                      +..++|.++.++.+...+...        .    ...+-+.++|+.|+|||++|+.+...  ....|   +...|...+ 
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~--l~~~fi~vD~t~f~e~Gy   91 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKL--ANAPFIKVEATKFTEVGY   91 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHH--hCChheeecchhhccCCc
Confidence            567999999999998888541        1    11256789999999999999999887  44444   222233222 


Q ss_pred             --CCHHHHHHHHHHHh
Q 048347           81 --LSLDMMLDAIMKSL   94 (351)
Q Consensus        81 --~~~~~~~~~i~~~~   94 (351)
                        .+.+++++.+....
T Consensus        92 vG~d~e~~ir~L~~~A  107 (443)
T PRK05201         92 VGRDVESIIRDLVEIA  107 (443)
T ss_pred             ccCCHHHHHHHHHHHH
Confidence              56677777776666

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.26  E-value=0.019  Score=59.01  Aligned_cols=56  Identities=13%  Similarity=0.031  Sum_probs=34.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CC--HHHHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LS--LDMMLDAIMKSLMP   96 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~--~~~~~~~i~~~~~~   96 (351)
                      -+|++++|+.|+||||++.++.........-..+..++.. +.  ..+-++...+.++.
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gv  243 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGV  243 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCC
Confidence            4799999999999999999988763222222244455444 22  33445555555543

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.26  E-value=0.022  Score=54.84  Aligned_cols=25  Identities=20%  Similarity=0.213  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++++|..|+||||+++.+...
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~  214 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAAR  214 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999877654

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.24  E-value=0.026  Score=51.21  Aligned_cols=89  Identities=15%  Similarity=0.077  Sum_probs=55.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHH---HH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMK---KN  113 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~---~~  113 (351)
                      ++-+++-|+|+.|.||||+|-+++-.  ....-..++|++.-  ++++.+.+ ++.....+....  ...+.++.   .+
T Consensus        58 ~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~~-l~~~~~d~l~v~--~~~~~e~q~~i~~  132 (279)
T COG0468          58 PRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAKQ-LGVDLLDNLLVS--QPDTGEQQLEIAE  132 (279)
T ss_pred             ccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHHH-HHHhhhcceeEe--cCCCHHHHHHHHH
Confidence            67799999999999999999998877  55555578899877  66665443 444421111111  22233333   33


Q ss_pred             HHHHhcCCceEEEEEeCCC
Q 048347          114 TLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus       114 ~l~~~L~~k~~LlVLDdv~  132 (351)
                      .+.+....+--|+|+|.+-
T Consensus       133 ~~~~~~~~~i~LvVVDSva  151 (279)
T COG0468         133 KLARSGAEKIDLLVVDSVA  151 (279)
T ss_pred             HHHHhccCCCCEEEEecCc
Confidence            3444434445688888873

>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=96.24  E-value=0.014  Score=49.05  Aligned_cols=69  Identities=12%  Similarity=0.072  Sum_probs=42.9

Q ss_pred             cccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHH
Q 048347           20 DLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMK   92 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~   92 (351)
                      +||.+....++++.+..-...-.-|-|+|..|+||+.+|+.+++...  ..  ..-||.+.   ++.+.+-.++..
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~--r~--~~pfi~vnc~~~~~~~~e~~LFG   72 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSP--RK--NGPFISVNCAALPEELLESELFG   72 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCST--TT--TS-EEEEETTTS-HHHHHHHHHE
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhh--cc--cCCeEEEehhhhhcchhhhhhhc
Confidence            57888888888887765322223455999999999999999999722  22  12455555   555555555543

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 ....

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.24  E-value=0.01  Score=57.80  Aligned_cols=73  Identities=10%  Similarity=0.192  Sum_probs=44.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      .-+.|+|+.|+|||+||+.+.+.  +......++++    +..++...+...+...         .    .+.++..+++
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~--l~~~~~~v~yi----~~~~f~~~~~~~l~~~---------~----~~~f~~~~~~  202 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHA--LRESGGKILYV----RSELFTEHLVSAIRSG---------E----MQRFRQFYRN  202 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHH--HHHcCCCEEEe----eHHHHHHHHHHHHhcc---------h----HHHHHHHccc
Confidence            45779999999999999999998  44332223343    3344555555444321         1    2234444444


Q ss_pred             ceEEEEEeCCCCh
Q 048347          122 KRYLIVIQDVWRG  134 (351)
Q Consensus       122 k~~LlVLDdv~~~  134 (351)
                      . -++++||+...
T Consensus       203 ~-dvLiIDDiq~l  214 (445)
T PRK12422        203 V-DALFIEDIEVF  214 (445)
T ss_pred             C-CEEEEcchhhh
Confidence            3 47888998543

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=96.23  E-value=0.0043  Score=57.30  Aligned_cols=88  Identities=22%  Similarity=0.133  Sum_probs=60.3

Q ss_pred             CCCC-CCceEEEEecccccCc---eeeeCCCCCCcccEEEEecCCccc-----cccccccccCCccEEeecCCccc----
Q 048347          238 PEKL-PHLKVLKLKRSSYSGR---KLVCGHGGFPRQEILHLKSMLWLE-----EWKMETGAMQKLKSLIVNPCAYL----  304 (351)
Q Consensus       238 l~~l-~~L~~L~l~~~~~~~~---~lp~~~~~l~~L~~L~L~~~~~l~-----~lp~~i~~L~~L~~L~l~~c~~l----  304 (351)
                      +..+ ++|+.|+++.+.....   .++..+..+++|++|++++| .+.     .++..+..+++|+.|++++|..-    
T Consensus       132 l~~~~~~L~~L~L~~n~l~~~~~~~~~~~~~~~~~L~~L~l~~n-~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~  210 (319)
T cd00116         132 LKDLPPALEKLVLGRNRLEGASCEALAKALRANRDLKELNLANN-GIGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGA  210 (319)
T ss_pred             HHhCCCCceEEEcCCCcCCchHHHHHHHHHHhCCCcCEEECcCC-CCchHHHHHHHHHHHhCCCCCEEeccCCccChHHH
Confidence            3455 8899999954443321   23444556678999999998 454     34444556679999999987421    


Q ss_pred             cccChhhhcCCCCCEEEecCCC
Q 048347          305 RKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       305 ~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      ..++..+.++++|++|++++++
T Consensus       211 ~~l~~~~~~~~~L~~L~ls~n~  232 (319)
T cd00116         211 SALAETLASLKSLEVLNLGDNN  232 (319)
T ss_pred             HHHHHHhcccCCCCEEecCCCc
Confidence            3455566778899999999876

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.22  E-value=0.0038  Score=53.12  Aligned_cols=25  Identities=8%  Similarity=0.126  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.|.|+.|+||||+|+.+...
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999866

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.

>PRK06547 hypothetical protein; Provisional

Probab=96.22  E-value=0.004  Score=52.54  Aligned_cols=26  Identities=19%  Similarity=0.151  Sum_probs=23.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|..|+||||+|+.+...
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999876

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.20  E-value=0.11  Score=47.09  Aligned_cols=128  Identities=16%  Similarity=0.068  Sum_probs=68.1

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCC--CCCC-cc
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMP--LSAL-SE  102 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~--~~~~-~~  102 (351)
                      .+.++..+... .+..-++|+|..|.|||||.+.+...  ++.. ...+++.-. ....+-.++++..+..  +... ..
T Consensus        98 ~~~~l~~l~~~-~~~~~~~i~g~~g~GKttl~~~l~~~--~~~~-~G~i~~~g~~v~~~d~~~ei~~~~~~~~q~~~~~r  173 (270)
T TIGR02858        98 ADKLLPYLVRN-NRVLNTLIISPPQCGKTTLLRDLARI--LSTG-ISQLGLRGKKVGIVDERSEIAGCVNGVPQHDVGIR  173 (270)
T ss_pred             HHHHHHHHHhC-CCeeEEEEEcCCCCCHHHHHHHHhCc--cCCC-CceEEECCEEeecchhHHHHHHHhccccccccccc
Confidence            34444445433 23567899999999999999999988  4433 223333211 1111112344433221  1110 00


Q ss_pred             CCCCCHHHHHHHHHHhcC-CceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccc
Q 048347          103 ILDNDFEMKKNTLHNYLK-NKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIV  161 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~-~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v  161 (351)
                      .+..+.....+.+...++ ...-++++|..-..+.+..+...+.   .|..+|+ |.+..+
T Consensus       174 ~~v~~~~~k~~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~  231 (270)
T TIGR02858       174 TDVLDGCPKAEGMMMLIRSMSPDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDV  231 (270)
T ss_pred             ccccccchHHHHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHH
Confidence            111111111222333333 4777899999987777777766653   3677777 876554

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.

>PRK06762 hypothetical protein; Provisional

Probab=96.20  E-value=0.0034  Score=52.45  Aligned_cols=23  Identities=17%  Similarity=0.247  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|.|+.|+||||+|+.+.+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68899999999999999999887

>PRK06921 hypothetical protein; Provisional

Probab=96.20  E-value=0.0084  Score=54.33  Aligned_cols=36  Identities=14%  Similarity=0.085  Sum_probs=27.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEE
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVY   78 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~   78 (351)
                      ..-+.++|..|+|||.||.++++.  +... -..+++++
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~  153 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFP  153 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEE
Confidence            456889999999999999999998  5443 33345554

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

Probab=96.18  E-value=0.012  Score=53.05  Aligned_cols=55  Identities=18%  Similarity=0.091  Sum_probs=44.4

Q ss_pred             ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHH
Q 048347           36 ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMK   92 (351)
Q Consensus        36 ~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~   92 (351)
                      .+=++-+++.|.|..|+|||++|.+....  ...+.+.++||+..-+.+++.....+
T Consensus        18 GG~p~g~~~lI~G~pGsGKT~f~~qfl~~--~~~~ge~vlyvs~~e~~~~l~~~~~~   72 (260)
T COG0467          18 GGLPRGSVVLITGPPGTGKTIFALQFLYE--GAREGEPVLYVSTEESPEELLENARS   72 (260)
T ss_pred             CCCcCCcEEEEEcCCCCcHHHHHHHHHHH--HHhcCCcEEEEEecCCHHHHHHHHHH
Confidence            33366789999999999999999999888  66678899999988666666666653

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=96.18  E-value=0.0064  Score=62.94  Aligned_cols=51  Identities=22%  Similarity=0.160  Sum_probs=23.9

Q ss_pred             ccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCC
Q 048347          269 QEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWP  325 (351)
Q Consensus       269 L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  325 (351)
                      |+.|+|++| .+..+|..+.  .+|+.|++++ ..+..+|..+.  .+|+.|+++++
T Consensus       243 L~~L~Ls~N-~L~~LP~~l~--s~L~~L~Ls~-N~L~~LP~~l~--~sL~~L~Ls~N  293 (754)
T PRK15370        243 IQEMELSIN-RITELPERLP--SALQSLDLFH-NKISCLPENLP--EELRYLSVYDN  293 (754)
T ss_pred             ccEEECcCC-ccCcCChhHh--CCCCEEECcC-CccCccccccC--CCCcEEECCCC
Confidence            444444444 3334443332  2455555553 34555555442  35666666554

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.17  E-value=0.011  Score=59.09  Aligned_cols=95  Identities=13%  Similarity=0.091  Sum_probs=52.4

Q ss_pred             CCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHH
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIM   91 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~   91 (351)
                      .+.+++-.-...++..+.....-.+..-|-|.|..|+|||+||+++++... ++..-.+..|+.+    ...+.+++.+ 
T Consensus       406 ~e~d~i~~~s~kke~~n~~~spv~~~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l-  483 (952)
T KOG0735|consen  406 FEHDFIQVPSYKKENANQELSPVFRHGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFL-  483 (952)
T ss_pred             CCCceeecchhhhhhhhhhcccccccccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHH-
Confidence            344444433333333332222222344577899999999999999999833 2222223344433    2222222222 


Q ss_pred             HHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347           92 KSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                                          ...+.+.+.-..-++||||++
T Consensus       484 --------------------~~vfse~~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  484 --------------------NNVFSEALWYAPSIIVLDDLD  504 (952)
T ss_pred             --------------------HHHHHHHHhhCCcEEEEcchh
Confidence                                223334445678899999995

>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=96.17  E-value=0.0035  Score=44.24  Aligned_cols=22  Identities=14%  Similarity=0.231  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|..|+||||+|+.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999998877

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.

>TIGR00959 ffh signal recognition particle protein

Probab=96.16  E-value=0.033  Score=53.85  Aligned_cols=24  Identities=13%  Similarity=0.194  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++.++|..|+||||+|..++..
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHH
Confidence            578999999999999998887766

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.16  E-value=0.054  Score=50.74  Aligned_cols=127  Identities=9%  Similarity=0.049  Sum_probs=67.3

Q ss_pred             cccc-chhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccc---cCCCe-----eEEEEEe--CCHHHHH
Q 048347           19 VDLD-LEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVK---NYFDC-----CAWVYYQ--LSLDMML   87 (351)
Q Consensus        19 ~~vG-r~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~---~~F~~-----~~wv~~~--~~~~~~~   87 (351)
                      .++| -+.-.+.+.+.+..+. -....-++|+.|+||||+|+.+....--.   ..-.|     |..+...  +++..+ 
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~-l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i-   83 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNR-LSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLV-   83 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEe-
Confidence            4566 5666677777775442 34566789999999999998874431100   10000     0000000  000000 


Q ss_pred             HHHHHHhCCCCCCccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           88 DAIMKSLMPLSALSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        88 ~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                             ... .    .....+++.+.+...    ..+.+-++|+|+++..  ++.+.+...+.+...++.+|. |.+.
T Consensus        84 -------~~~-~----~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~  150 (329)
T PRK08058         84 -------APD-G----QSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENK  150 (329)
T ss_pred             -------ccc-c----ccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCCh
Confidence                   000 0    112233333322211    2345567889998755  567788888887777777777 7544

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=96.15  E-value=0.017  Score=51.94  Aligned_cols=79  Identities=18%  Similarity=0.032  Sum_probs=45.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHhCCCCCCc--cCCCCCHHHHHHHHH
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSALS--EILDNDFEMKKNTLH  116 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~~~--~~~~~~~~~~~~~l~  116 (351)
                      +|+|.|.+|+||||+|+++...  .+..=...+.++..    ++..+.-..+...........  .++..+.+.+.+.++
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~--l~~~g~~v~vI~~D~yyr~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l~   78 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHI--FAREGIHPAVVEGDSFHRYERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELFR   78 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH--HHhcCCceEEEeccccccCCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHHH
Confidence            5899999999999999988776  33221223444433    233333333333222211111  135667777777777


Q ss_pred             HhcCCce
Q 048347          117 NYLKNKR  123 (351)
Q Consensus       117 ~~L~~k~  123 (351)
                      ..-+++.
T Consensus        79 ~L~~g~~   85 (277)
T cd02029          79 TYGETGR   85 (277)
T ss_pred             HHHcCCC
Confidence            7776654

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

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

Probab=96.15  E-value=0.019  Score=59.86  Aligned_cols=49  Identities=12%  Similarity=0.202  Sum_probs=40.4

Q ss_pred             CCCccccchhhHHHHHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+.+.+|.++-++.+++++...    ..+..++.++|+.|+||||+|+.+...
T Consensus       320 l~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~  372 (784)
T PRK10787        320 LDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKA  372 (784)
T ss_pred             hhhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3567899999999999888632    234568999999999999999999876

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.14  E-value=0.022  Score=51.01  Aligned_cols=93  Identities=5%  Similarity=-0.095  Sum_probs=58.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE--Ee----CCHHHHHHHHHHHhCCCCCCc--cC-CCCCHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY--YQ----LSLDMMLDAIMKSLMPLSALS--EI-LDNDFEM  110 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~--~~----~~~~~~~~~i~~~~~~~~~~~--~~-~~~~~~~  110 (351)
                      +-.++|++|.+|.||||+|+.+..-  .+...-.+.|--  +.    ....+...+++...+......  .+ +....+.
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L--~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQr  115 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGL--EEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQR  115 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcC--cCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhh
Confidence            4568999999999999999999887  443333333321  11    223345566666666433210  11 2333444


Q ss_pred             HHHHHHHhcCCceEEEEEeCCCCh
Q 048347          111 KKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus       111 ~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                      ..-.+.+.|.-+.-++|.|.--+.
T Consensus       116 QRi~IARALal~P~liV~DEpvSa  139 (268)
T COG4608         116 QRIGIARALALNPKLIVADEPVSA  139 (268)
T ss_pred             hhHHHHHHHhhCCcEEEecCchhh
Confidence            455678888899999999987544

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.13  E-value=0.02  Score=53.18  Aligned_cols=45  Identities=20%  Similarity=0.270  Sum_probs=34.9

Q ss_pred             CCCCcccc---chhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHH
Q 048347           15 WDNKVDLD---LEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEA   61 (351)
Q Consensus        15 ~~~~~~vG---r~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v   61 (351)
                      ..+.++.|   |..+..--..+|++++  +..|.+.|.+|.|||.||-+.
T Consensus       218 ~~~~~vwGi~prn~eQ~~ALdlLld~d--I~lV~L~G~AGtGKTlLALaA  265 (436)
T COG1875         218 HEDQEVWGIRPRNAEQRVALDLLLDDD--IDLVSLGGKAGTGKTLLALAA  265 (436)
T ss_pred             cCchhhhccCcccHHHHHHHHHhcCCC--CCeEEeeccCCccHhHHHHHH
Confidence            34556666   6667777788887764  889999999999999988553

>PRK05439 pantothenate kinase; Provisional

Probab=96.13  E-value=0.03  Score=51.68  Aligned_cols=78  Identities=12%  Similarity=0.075  Sum_probs=45.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccC--CCeeEEEEEe--CCHHHHHHHHHHHhCC-CCCCccCCCCCHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY--FDCCAWVYYQ--LSLDMMLDAIMKSLMP-LSALSEILDNDFEMKKN  113 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~~~--~~~~~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~  113 (351)
                      ...-+|||.|..|+||||+|+.+...  ....  -..+.-++..  +...+.+..  ..+.. .+.   ++.-+.+.+.+
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~--l~~~~~~~~v~vi~~DdFy~~~~~l~~--~~l~~~kg~---Pes~D~~~l~~  156 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQAL--LSRWPEHPKVELVTTDGFLYPNAVLEE--RGLMKRKGF---PESYDMRALLR  156 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHhhCCCCceEEEeccccccCHHHHhh--hhccccCCC---cccccHHHHHH
Confidence            46789999999999999999998775  3322  1223334444  222222221  11111 111   24567777777


Q ss_pred             HHHHhcCCce
Q 048347          114 TLHNYLKNKR  123 (351)
Q Consensus       114 ~l~~~L~~k~  123 (351)
                      .+.....++.
T Consensus       157 ~L~~Lk~G~~  166 (311)
T PRK05439        157 FLSDVKSGKP  166 (311)
T ss_pred             HHHHHHcCCC
Confidence            7777776664

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.13  E-value=0.031  Score=53.10  Aligned_cols=99  Identities=14%  Similarity=0.065  Sum_probs=55.0

Q ss_pred             HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCcc-CCCC
Q 048347           28 EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSE-ILDN  106 (351)
Q Consensus        28 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~-~~~~  106 (351)
                      .++-..|-.+=..-.++.|.|.+|+|||||+.+++..  ....-..++|++..-...++ +.-++.++....... ....
T Consensus        69 ~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~EEs~~qi-~~Ra~rlg~~~~~l~l~~e~  145 (372)
T cd01121          69 EELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSGEESPEQI-KLRADRLGISTENLYLLAET  145 (372)
T ss_pred             HHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCcCHHHH-HHHHHHcCCCcccEEEEccC
Confidence            3444444333244578999999999999999998876  43333456666544233332 222344443221100 1233


Q ss_pred             CHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347          107 DFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus       107 ~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      +.+.+.+.+.+   .+.-++|+|.+.
T Consensus       146 ~le~I~~~i~~---~~~~lVVIDSIq  168 (372)
T cd01121         146 NLEDILASIEE---LKPDLVIIDSIQ  168 (372)
T ss_pred             cHHHHHHHHHh---cCCcEEEEcchH
Confidence            44555554432   355678999873

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.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.12  E-value=0.016  Score=50.57  Aligned_cols=46  Identities=20%  Similarity=0.067  Sum_probs=35.2

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.++||-++..+.+.-...+++  +.=+.|.||+|+||||-+..+.+.
T Consensus        26 l~dIVGNe~tv~rl~via~~gn--mP~liisGpPG~GKTTsi~~LAr~   71 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAKEGN--MPNLIISGPPGTGKTTSILCLARE   71 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHHcCC--CCceEeeCCCCCchhhHHHHHHHH
Confidence            4578999999998887776654  556678899999999965555444

>PRK03839 putative kinase; Provisional

Probab=96.12  E-value=0.0035  Score=53.21  Aligned_cols=22  Identities=23%  Similarity=0.252  Sum_probs=20.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||+|+.+++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999988

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.10  E-value=0.0034  Score=54.17  Aligned_cols=22  Identities=18%  Similarity=0.283  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|..|+||||||+.+...
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~   22 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQ   22 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999776

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.

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=96.08  E-value=0.0012  Score=67.61  Aligned_cols=87  Identities=16%  Similarity=0.155  Sum_probs=66.5

Q ss_pred             CCCceEEEEecccccCceeeeCCC-CCCcccEEEEecCCccc-cccccccccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHG-GFPRQEILHLKSMLWLE-EWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~-~l~~L~~L~L~~~~~l~-~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      -.+|++|++++........|..++ -||+|+.|.++|-.... ++-.--.++++|..||+++ +++..+ .+|++|++|+
T Consensus       121 r~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~-TnI~nl-~GIS~LknLq  198 (699)
T KOG3665|consen  121 RQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISG-TNISNL-SGISRLKNLQ  198 (699)
T ss_pred             HHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCC-CCccCc-HHHhccccHH
Confidence            367899999655555556666555 57999999999864322 3333456899999999999 788888 8999999999


Q ss_pred             EEEecCCChhH
Q 048347          319 KLESWWPRPEL  329 (351)
Q Consensus       319 ~L~l~~~~~~~  329 (351)
                      .|.+++..-+-
T Consensus       199 ~L~mrnLe~e~  209 (699)
T KOG3665|consen  199 VLSMRNLEFES  209 (699)
T ss_pred             HHhccCCCCCc
Confidence            99999987443

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

Probab=96.08  E-value=0.0062  Score=61.06  Aligned_cols=55  Identities=16%  Similarity=0.235  Sum_probs=44.3

Q ss_pred             CCCCccccchhhHHHHHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      +-+.+-.|.++-++++++.|.-.    .-+-.+++.||++|+|||.|++.++.-  ....|
T Consensus       320 iLd~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~a--l~Rkf  378 (782)
T COG0466         320 ILDKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKA--LGRKF  378 (782)
T ss_pred             HhcccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHH--hCCCE
Confidence            34567799999999999988532    334579999999999999999999988  55554

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.08  E-value=0.077  Score=48.05  Aligned_cols=54  Identities=9%  Similarity=0.040  Sum_probs=37.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      .-.++.|.|.+|+||||+|.++...  .... =..++|++..-...++...+...+.
T Consensus        29 ~g~~~~i~g~~G~GKT~l~~~~~~~--~~~~~g~~vl~iS~E~~~~~~~~r~~~~~~   83 (271)
T cd01122          29 KGELIILTAGTGVGKTTFLREYALD--LITQHGVRVGTISLEEPVVRTARRLLGQYA   83 (271)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH--HHHhcCceEEEEEcccCHHHHHHHHHHHHh
Confidence            3457888999999999999998776  3222 3456787766555666666655543

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.07  E-value=0.011  Score=53.91  Aligned_cols=81  Identities=7%  Similarity=0.098  Sum_probs=50.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccc--CCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHh
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKN--YFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNY  118 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~--~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~  118 (351)
                      -++|-++|++|.|||+|+|+++.+..++.  .|....-+.++  -..++..=..   ..       ..-...+.+.+.+.
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEin--shsLFSKWFs---ES-------gKlV~kmF~kI~EL  244 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEIN--SHSLFSKWFS---ES-------GKLVAKMFQKIQEL  244 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEe--hhHHHHHHHh---hh-------hhHHHHHHHHHHHH
Confidence            47899999999999999999999855543  34444444443  2233322221   11       12345667777777


Q ss_pred             cCCceEE--EEEeCCCC
Q 048347          119 LKNKRYL--IVIQDVWR  133 (351)
Q Consensus       119 L~~k~~L--lVLDdv~~  133 (351)
                      ++++..|  +.+|.|..
T Consensus       245 v~d~~~lVfvLIDEVES  261 (423)
T KOG0744|consen  245 VEDRGNLVFVLIDEVES  261 (423)
T ss_pred             HhCCCcEEEEEeHHHHH
Confidence            7776654  45688843

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=96.07  E-value=0.0034  Score=58.03  Aligned_cols=84  Identities=26%  Similarity=0.177  Sum_probs=57.5

Q ss_pred             CCceEEEEecccccCc---eeeeCCCCC-CcccEEEEecCCccc-----cccccccccCCccEEeecCCccc----cccC
Q 048347          242 PHLKVLKLKRSSYSGR---KLVCGHGGF-PRQEILHLKSMLWLE-----EWKMETGAMQKLKSLIVNPCAYL----RKFP  308 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~---~lp~~~~~l-~~L~~L~L~~~~~l~-----~lp~~i~~L~~L~~L~l~~c~~l----~~lP  308 (351)
                      ++|++|+++.+.....   .+...+..+ ++|+.|++++|. +.     .++..+..+.+|++|++++|..-    ..++
T Consensus       108 ~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~-l~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~  186 (319)
T cd00116         108 SSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNR-LEGASCEALAKALRANRDLKELNLANNGIGDAGIRALA  186 (319)
T ss_pred             CcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCc-CCchHHHHHHHHHHhCCCcCEEECcCCCCchHHHHHHH
Confidence            5599999954433211   223345566 889999999994 44     34545667788999999986432    2455


Q ss_pred             hhhhcCCCCCEEEecCCC
Q 048347          309 EELWRIKALRKLESWWPR  326 (351)
Q Consensus       309 ~~i~~L~~L~~L~l~~~~  326 (351)
                      ..+..+++|++|+++++.
T Consensus       187 ~~l~~~~~L~~L~L~~n~  204 (319)
T cd00116         187 EGLKANCNLEVLDLNNNG  204 (319)
T ss_pred             HHHHhCCCCCEEeccCCc
Confidence            566677899999999875

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.07  E-value=0.0069  Score=58.89  Aligned_cols=44  Identities=9%  Similarity=0.036  Sum_probs=37.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...++|+++.++.+...+..+.    -|-+.|++|+|||++|+.+...
T Consensus        19 ~~~i~gre~vI~lll~aalag~----hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         19 EKGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             hhhccCcHHHHHHHHHHHccCC----CEEEECCCChhHHHHHHHHHHH
Confidence            4678999999999998887764    3557899999999999999886

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.06  E-value=0.019  Score=51.16  Aligned_cols=119  Identities=13%  Similarity=0.095  Sum_probs=65.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcc-----cc------cCC---CeeEEEEE----e----CCHH--------------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSY-----VK------NYF---DCCAWVYY----Q----LSLD--------------   84 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~-----~~------~~F---~~~~wv~~----~----~~~~--------------   84 (351)
                      -.+++|+|+.|+|||||.|.+..-.+     ++      ..+   ..+.||.-    .    .++.              
T Consensus        30 G~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~  109 (254)
T COG1121          30 GEITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWF  109 (254)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCccccccc
Confidence            36899999999999999999977311     11      001   12334321    0    2222              


Q ss_pred             --------HHHHHHHHHhCCCCC-CccCCCC-CHHHHHHHHHHhcCCceEEEEEeCCCCh------hhHHHHHhhcCCCC
Q 048347           85 --------MMLDAIMKSLMPLSA-LSEILDN-DFEMKKNTLHNYLKNKRYLIVIQDVWRG------DIWDFLKEALPDHQ  148 (351)
Q Consensus        85 --------~~~~~i~~~~~~~~~-~~~~~~~-~~~~~~~~l~~~L~~k~~LlVLDdv~~~------~~~~~l~~~l~~~~  148 (351)
                              +...+.++..+...- ..++... ..+...-.+.+.|..+.=|++||.=-..      .+.-.+...+... 
T Consensus       110 ~~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e-  188 (254)
T COG1121         110 RRLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE-  188 (254)
T ss_pred             ccccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC-
Confidence                    233333333333211 1123333 3444566778999999999999965322      2222233333322 


Q ss_pred             CCcEEEE-Eeeccc
Q 048347          149 NGSRILT-ALIHIV  161 (351)
Q Consensus       149 ~gs~Iiv-TR~~~v  161 (351)
                       |..|++ |.|-+.
T Consensus       189 -g~tIl~vtHDL~~  201 (254)
T COG1121         189 -GKTVLMVTHDLGL  201 (254)
T ss_pred             -CCEEEEEeCCcHH
Confidence             778888 887654

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.04  E-value=0.0067  Score=49.84  Aligned_cols=44  Identities=16%  Similarity=0.089  Sum_probs=33.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      +|.|-|.+|.||||+|+.+.++...+.       |    +.-.++++|+++.+-.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~~-------v----saG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLKL-------V----SAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCce-------e----eccHHHHHHHHHcCCC
Confidence            688999999999999999999833221       1    2337888888877664

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

Probab=96.04  E-value=0.006  Score=54.71  Aligned_cols=51  Identities=16%  Similarity=0.072  Sum_probs=39.2

Q ss_pred             CCCccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCCcc
Q 048347           16 DNKVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNSSY   66 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~~~   66 (351)
                      .-.++||-++-++++.-.+...   +...-=+-++|++|.||||||.-+.+...
T Consensus        24 ~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emg   77 (332)
T COG2255          24 TLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELG   77 (332)
T ss_pred             cHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhc
Confidence            3467899888888887766542   23345577899999999999999999843

>PRK14738 gmk guanylate kinase; Provisional

Probab=96.03  E-value=0.0056  Score=53.26  Aligned_cols=31  Identities=19%  Similarity=0.305  Sum_probs=25.6

Q ss_pred             HHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           34 LIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        34 L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+..+.+++.|+|++|+|||||++.+...
T Consensus         6 ~~~~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          6 LFNKPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             ccCCCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            3444556788999999999999999999765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.03  E-value=0.053  Score=56.50  Aligned_cols=95  Identities=11%  Similarity=0.025  Sum_probs=56.8

Q ss_pred             CCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHH
Q 048347           16 DNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLD   84 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~   84 (351)
                      .-.++.|.+.-+++|.+.+...           -...+-+-++|+.|.|||++|+++.+.  ....|     +.+.  ..
T Consensus       451 ~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e--~~~~f-----i~v~--~~  521 (733)
T TIGR01243       451 RWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE--SGANF-----IAVR--GP  521 (733)
T ss_pred             chhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh--cCCCE-----EEEe--hH
Confidence            3455778888888887776421           112334678999999999999999998  43333     3332  11


Q ss_pred             HHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347           85 MMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus        85 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      +++    ....         ..++..+.+.+...-....+++++|+++
T Consensus       522 ~l~----~~~v---------Gese~~i~~~f~~A~~~~p~iifiDEid  556 (733)
T TIGR01243       522 EIL----SKWV---------GESEKAIREIFRKARQAAPAIIFFDEID  556 (733)
T ss_pred             HHh----hccc---------CcHHHHHHHHHHHHHhcCCEEEEEEChh
Confidence            111    1111         1122333444444445677999999985

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.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.03  E-value=0.057  Score=47.61  Aligned_cols=57  Identities=21%  Similarity=0.081  Sum_probs=36.1

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHH
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLD   88 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~   88 (351)
                      |-++|..+=++-.++.|.|.+|+||||||.++...  .-..-+.++|++..-..+++..
T Consensus         9 LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~--~~~~g~~~~~is~e~~~~~i~~   65 (229)
T TIGR03881         9 LDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYK--GLRDGDPVIYVTTEESRESIIR   65 (229)
T ss_pred             HHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHH--HHhcCCeEEEEEccCCHHHHHH
Confidence            33444333345689999999999999999987654  2123345677765544444443

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.

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=96.02  E-value=0.014  Score=60.46  Aligned_cols=75  Identities=16%  Similarity=0.157  Sum_probs=59.1

Q ss_pred             CCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEE
Q 048347          242 PHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLE  321 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~  321 (351)
                      ++|+.|+++.+  .+..+|..+  +.+|++|++++| .+..+|..+.  .+|+.|+|++| .+..+|.++.  ++|+.|+
T Consensus       199 ~~L~~L~Ls~N--~LtsLP~~l--~~nL~~L~Ls~N-~LtsLP~~l~--~~L~~L~Ls~N-~L~~LP~~l~--s~L~~L~  268 (754)
T PRK15370        199 EQITTLILDNN--ELKSLPENL--QGNIKTLYANSN-QLTSIPATLP--DTIQEMELSIN-RITELPERLP--SALQSLD  268 (754)
T ss_pred             cCCcEEEecCC--CCCcCChhh--ccCCCEEECCCC-ccccCChhhh--ccccEEECcCC-ccCcCChhHh--CCCCEEE
Confidence            57999999433  455777654  368999999999 6889997654  58999999986 5789998875  5899999


Q ss_pred             ecCCC
Q 048347          322 SWWPR  326 (351)
Q Consensus       322 l~~~~  326 (351)
                      +++..
T Consensus       269 Ls~N~  273 (754)
T PRK15370        269 LFHNK  273 (754)
T ss_pred             CcCCc
Confidence            98754

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.01  E-value=0.0047  Score=54.96  Aligned_cols=32  Identities=9%  Similarity=0.222  Sum_probs=25.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD   72 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~   72 (351)
                      ++...|.++||+|.||||+.++++.+  ....+.
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~h--l~~~~~   48 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSH--LHAKKT   48 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHH--HhhccC
Confidence            45567778899999999999999988  444443

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=96.01  E-value=0.013  Score=59.35  Aligned_cols=75  Identities=7%  Similarity=-0.074  Sum_probs=54.6

Q ss_pred             CCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEEEe-CCHHHHHHHHHHH
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVYYQ-LSLDMMLDAIMKS   93 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~~-~~~~~~~~~i~~~   93 (351)
                      --++++|.++-.+.+...+....    -+.++|+.|+||||+|+.+.+.  +... |...+++..+ .+..++++.++.+
T Consensus        16 ~~~~viG~~~a~~~l~~a~~~~~----~~ll~G~pG~GKT~la~~la~~--l~~~~~~~~~~~~n~~~~~~~~~~~v~~~   89 (608)
T TIGR00764        16 LIDQVIGQEEAVEIIKKAAKQKR----NVLLIGEPGVGKSMLAKAMAEL--LPDEELEDILVYPNPEDPNMPRIVEVPAG   89 (608)
T ss_pred             hHhhccCHHHHHHHHHHHHHcCC----CEEEECCCCCCHHHHHHHHHHH--cCchhheeEEEEeCCCCCchHHHHHHHHh
Confidence            34668899988888887776542    3448999999999999999987  5443 3444444444 6777888888887


Q ss_pred             hCC
Q 048347           94 LMP   96 (351)
Q Consensus        94 ~~~   96 (351)
                      ++.
T Consensus        90 ~g~   92 (608)
T TIGR00764        90 EGR   92 (608)
T ss_pred             hch
Confidence            765

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

>PRK04296 thymidine kinase; Provisional

Probab=96.00  E-value=0.01  Score=50.97  Aligned_cols=110  Identities=10%  Similarity=-0.074  Sum_probs=60.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      .++.|.|..|.||||+|.....+  ...+-..++.+ -+ ++.......++.+++.+...  .......++.+.+.+ ..
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~--~~~~g~~v~i~-k~~~d~~~~~~~i~~~lg~~~~~--~~~~~~~~~~~~~~~-~~   76 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYN--YEERGMKVLVF-KPAIDDRYGEGKVVSRIGLSREA--IPVSSDTDIFELIEE-EG   76 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHH--HHHcCCeEEEE-eccccccccCCcEecCCCCcccc--eEeCChHHHHHHHHh-hC
Confidence            46778999999999999888877  33333333333 22 34333344556666532221  112344555555555 33


Q ss_pred             CceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347          121 NKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus       121 ~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ++.-+||+|.+.-.  ++...+...+  ...|..|++ .++.
T Consensus        77 ~~~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~  116 (190)
T PRK04296         77 EKIDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDT  116 (190)
T ss_pred             CCCCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCc
Confidence            34458999999432  2223333332  234667777 6654

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.99  E-value=0.025  Score=51.09  Aligned_cols=40  Identities=10%  Similarity=0.125  Sum_probs=29.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      ++-+++.|.|.+|+|||+||.++.... .+ .=+.+++++..
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~-a~-~Ge~vlyis~E   73 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQ-AS-RGNPVLFVTVE   73 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHH-Hh-CCCcEEEEEec
Confidence            456888999999999999999875542 12 23456777765

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK08149 ATP synthase SpaL; Validated

Probab=95.98  E-value=0.026  Score=54.34  Aligned_cols=87  Identities=11%  Similarity=0.087  Sum_probs=51.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC--ccC-CCC--------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL--SEI-LDN--------  106 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~--~~~-~~~--------  106 (351)
                      -..++|+|..|+|||||++.++.....    +.++...+.   -++.++..+...........  ... +..        
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~~----dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~  226 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSEA----DVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAA  226 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCCC----CeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHH
Confidence            357899999999999999999886322    233333333   66777777776643322110  000 111        


Q ss_pred             -CHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          107 -DFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       107 -~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                       ..-.+.+.+++  ++|+.|+++||+-.
T Consensus       227 ~~a~tiAE~fr~--~G~~Vll~~DslTr  252 (428)
T PRK08149        227 LVATTVAEYFRD--QGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHH--cCCCEEEEccchHH
Confidence             11122333443  48999999999943

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=95.95  E-value=0.024  Score=54.62  Aligned_cols=94  Identities=6%  Similarity=0.079  Sum_probs=53.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCH------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDF------  108 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~------  108 (351)
                      -..++|+|..|+|||||++.+...  ...  +.++.+-+.   -.+.++..+++..-..+...   ...+....      
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~--~~~--dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRG--TTA--DVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGC  237 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccC--CCC--CEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHH
Confidence            357899999999999999999876  222  455555444   55566666654432111100   00011111      


Q ss_pred             ---HHHHHHHHHhcCCceEEEEEeCCCCh-hhHHHH
Q 048347          109 ---EMKKNTLHNYLKNKRYLIVIQDVWRG-DIWDFL  140 (351)
Q Consensus       109 ---~~~~~~l~~~L~~k~~LlVLDdv~~~-~~~~~l  140 (351)
                         -.+.+.+++  ++++.|+++||+-.. .++..+
T Consensus       238 ~~A~tiAEyfrd--~G~~VLl~~DslTR~A~A~REI  271 (444)
T PRK08972        238 ETATTIAEYFRD--QGLNVLLLMDSLTRYAQAQREI  271 (444)
T ss_pred             HHHHHHHHHHHH--cCCCEEEEEcChHHHHHHHHHH
Confidence               112334443  589999999999433 333433

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.95  E-value=0.0055  Score=51.85  Aligned_cols=23  Identities=13%  Similarity=0.287  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++.|.|+.|+||||+|+.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            37889999999999999998776

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.

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=95.95  E-value=0.00097  Score=64.84  Aligned_cols=65  Identities=18%  Similarity=0.228  Sum_probs=33.6

Q ss_pred             eeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          259 LVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       259 lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      +|..++.+.+|+.|.+..| .+..+|.+.+.| .|..||++ |+++-.+|-.+.+|+.|++|-|.+-|
T Consensus       181 lpsql~~l~slr~l~vrRn-~l~~lp~El~~L-pLi~lDfS-cNkis~iPv~fr~m~~Lq~l~LenNP  245 (722)
T KOG0532|consen  181 LPSQLGYLTSLRDLNVRRN-HLEDLPEELCSL-PLIRLDFS-CNKISYLPVDFRKMRHLQVLQLENNP  245 (722)
T ss_pred             chHHhhhHHHHHHHHHhhh-hhhhCCHHHhCC-ceeeeecc-cCceeecchhhhhhhhheeeeeccCC
Confidence            3444444444444444444 344444444422 25555665 45666666666666666666665543

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.95  E-value=0.03  Score=52.09  Aligned_cols=25  Identities=16%  Similarity=0.325  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+++++|+.|+||||++..+...
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~  137 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHK  137 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4689999999999999999998876

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

Probab=95.95  E-value=0.021  Score=54.44  Aligned_cols=75  Identities=15%  Similarity=0.155  Sum_probs=50.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      .-..+-|||..|.|||-|++++.+.  ...+......+++  +.+.+..++...+..+             -.+.+++..
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~--~~~~~~~a~v~y~--~se~f~~~~v~a~~~~-------------~~~~Fk~~y  174 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNE--ALANGPNARVVYL--TSEDFTNDFVKALRDN-------------EMEKFKEKY  174 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHH--HHhhCCCceEEec--cHHHHHHHHHHHHHhh-------------hHHHHHHhh
Confidence            3568889999999999999999999  6666664333343  3445555555444432             144555555


Q ss_pred             CCceEEEEEeCCCC
Q 048347          120 KNKRYLIVIQDVWR  133 (351)
Q Consensus       120 ~~k~~LlVLDdv~~  133 (351)
                        .-=++++||++-
T Consensus       175 --~~dlllIDDiq~  186 (408)
T COG0593         175 --SLDLLLIDDIQF  186 (408)
T ss_pred             --ccCeeeechHhH
Confidence              333788899964

>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=95.93  E-value=0.068  Score=44.68  Aligned_cols=112  Identities=10%  Similarity=0.082  Sum_probs=57.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccc-C--CCe---eEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKN-Y--FDC---CAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKK  112 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~-~--F~~---~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~  112 (351)
                      -.+++|+|..|.|||||++.+........ .  ++.   +.++.-.  +....+...+...   ...    .....+...
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~---~~~----~LS~G~~~r   99 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYP---WDD----VLSGGEQQR   99 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEECCCCccccccHHHHhhcc---CCC----CCCHHHHHH
Confidence            45899999999999999999987732111 0  111   1111111  1111233333211   111    222334444


Q ss_pred             HHHHHhcCCceEEEEEeCCCCh---hhHHHHHhhcCCCCCCcEEEE-Eeeccc
Q 048347          113 NTLHNYLKNKRYLIVIQDVWRG---DIWDFLKEALPDHQNGSRILT-ALIHIV  161 (351)
Q Consensus       113 ~~l~~~L~~k~~LlVLDdv~~~---~~~~~l~~~l~~~~~gs~Iiv-TR~~~v  161 (351)
                      -.+.+.+..+.-++++|+--..   .....+...+...  +..+|+ |++...
T Consensus       100 v~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~  150 (166)
T cd03223         100 LAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSL  150 (166)
T ss_pred             HHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhH
Confidence            5556666677778889877533   2233333333222  355666 876543

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

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.90  E-value=0.029  Score=54.91  Aligned_cols=56  Identities=13%  Similarity=0.028  Sum_probs=34.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~   96 (351)
                      -.|++++|+.|+||||++.+++.....+..-..+..+...   ....+-++..++..+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGV  314 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGV  314 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCC
Confidence            4799999999999999999998763222222234455444   2333444444554443

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.89  E-value=0.008  Score=50.59  Aligned_cols=25  Identities=20%  Similarity=0.294  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+++|+|..|+|||||++.+...
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~   29 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPA   29 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHH
Confidence            5679999999999999999999877

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=95.89  E-value=0.035  Score=46.94  Aligned_cols=24  Identities=8%  Similarity=0.152  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|.|..|+|||||++.+.--
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            358999999999999999999877

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.89  E-value=0.0062  Score=51.86  Aligned_cols=36  Identities=6%  Similarity=0.084  Sum_probs=28.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY   78 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~   78 (351)
                      .+++.|+|+.|+|||||++++...  ....|...+..+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~--~~~~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQE--FPDKFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHH--STTTEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh--cccccccceeec
Confidence            468889999999999999999988  666775444443

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 ....

>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=95.88  E-value=0.091  Score=42.82  Aligned_cols=24  Identities=4%  Similarity=0.124  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|.|..|.|||||++.+..-
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~   49 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGE   49 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            368999999999999999999887

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.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.88  E-value=0.011  Score=58.76  Aligned_cols=34  Identities=24%  Similarity=0.370  Sum_probs=27.3

Q ss_pred             HHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           31 LDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        31 ~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.+.....++.+|+|.|..|+||||||+.+...
T Consensus        55 ~qlL~~~~~~riIIGIaGpSGSGKTTLAk~Lagl   88 (656)
T PLN02318         55 CQLLAQKNDGIILVGVAGPSGAGKTVFTEKVLNF   88 (656)
T ss_pred             HHHHHhcCCCeEEEEEECCCCCcHHHHHHHHHhh
Confidence            3344434456899999999999999999999876

>PRK04040 adenylate kinase; Provisional

Probab=95.88  E-value=0.0063  Score=52.14  Aligned_cols=46  Identities=15%  Similarity=0.231  Sum_probs=31.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMP   96 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~   96 (351)
                      .+|+|+|+.|+||||+++.+...  ....+.   +++    ..++...++...+.
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~--l~~~~~---~~~----~g~~~~~~a~~~g~   48 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEK--LKEDYK---IVN----FGDVMLEVAKEEGL   48 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH--hccCCe---EEe----cchHHHHHHHHcCC
Confidence            58999999999999999999887  421222   222    24566666655554

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.88  E-value=0.0068  Score=51.30  Aligned_cols=23  Identities=13%  Similarity=0.315  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+|+.|+||||||+.+...
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            47899999999999999999886

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.

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=95.87  E-value=0.018  Score=57.84  Aligned_cols=26  Identities=12%  Similarity=0.241  Sum_probs=23.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-++.-+.|++|+||||||..++.+
T Consensus       324 P~kKilLL~GppGlGKTTLAHViAkq  349 (877)
T KOG1969|consen  324 PPKKILLLCGPPGLGKTTLAHVIAKQ  349 (877)
T ss_pred             CccceEEeecCCCCChhHHHHHHHHh
Confidence            34578889999999999999999888

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.87  E-value=0.024  Score=54.76  Aligned_cols=87  Identities=9%  Similarity=0.065  Sum_probs=50.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHH-----
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFE-----  109 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~-----  109 (351)
                      -..++|.|..|+|||||++.+....+  .  +.++++-+.   -.+.++..+.+.+-..+...   ..-+.....     
T Consensus       158 Gqri~I~G~sG~GKTtLL~~I~~~~~--~--d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~  233 (442)
T PRK08927        158 GQRMGIFAGSGVGKSVLLSMLARNAD--A--DVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAA  233 (442)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccC--C--CEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHH
Confidence            46789999999999999999998732  2  344444454   55556665554432211100   000111111     


Q ss_pred             ----HHHHHHHHhcCCceEEEEEeCCCC
Q 048347          110 ----MKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       110 ----~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                          .+.+.+++  ++++.|+++||+-.
T Consensus       234 ~~a~tiAEyfrd--~G~~Vll~~DslTr  259 (442)
T PRK08927        234 YLTLAIAEYFRD--QGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHHHHHHHHHH--CCCcEEEEEeCcHH
Confidence                12344443  48999999999943

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.87  E-value=0.048  Score=47.68  Aligned_cols=22  Identities=5%  Similarity=-0.022  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~   23 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEK   23 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4778999999999999999776

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.83  E-value=0.054  Score=50.85  Aligned_cols=67  Identities=10%  Similarity=-0.009  Sum_probs=43.0

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC----CCeeEEEEEe--CCHHHHHHHHHHHhCC
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY----FDCCAWVYYQ--LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~~--~~~~~~~~~i~~~~~~   96 (351)
                      .|-.+|..+=+.-.++-|.|..|+|||+||..++-.......    -..++||+..  |.++.+ .+|++.+..
T Consensus       111 ~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~  183 (342)
T PLN03186        111 ELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGL  183 (342)
T ss_pred             HHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCC
Confidence            344444333355688889999999999999887744222111    1257888877  677665 455666543

>PRK06217 hypothetical protein; Validated

Probab=95.83  E-value=0.0063  Score=51.84  Aligned_cols=24  Identities=13%  Similarity=0.022  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ..|.|.|++|+||||+|+++....
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            358899999999999999999873

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=95.82  E-value=0.0008  Score=60.59  Aligned_cols=86  Identities=16%  Similarity=0.150  Sum_probs=64.4

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccC--hhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFP--EELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP--~~i~~  313 (351)
                      ..+..+++|..|+||+|..  ..+.-.-..+-+.+.|.|++| .++.+. .+++|.+|.+||+++ ++++.+-  .+||+
T Consensus       323 ~nLa~L~~L~~LDLS~N~L--s~~~Gwh~KLGNIKtL~La~N-~iE~LS-GL~KLYSLvnLDl~~-N~Ie~ldeV~~IG~  397 (490)
T KOG1259|consen  323 QNLAELPQLQLLDLSGNLL--AECVGWHLKLGNIKTLKLAQN-KIETLS-GLRKLYSLVNLDLSS-NQIEELDEVNHIGN  397 (490)
T ss_pred             hhhhhcccceEeecccchh--HhhhhhHhhhcCEeeeehhhh-hHhhhh-hhHhhhhheeccccc-cchhhHHHhccccc
Confidence            3456678999999954422  122222345667889999998 577776 688999999999998 4677665  37899


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      |+-|+++.+.+.|
T Consensus       398 LPCLE~l~L~~NP  410 (490)
T KOG1259|consen  398 LPCLETLRLTGNP  410 (490)
T ss_pred             ccHHHHHhhcCCC
Confidence            9999999999877

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=95.82  E-value=0.014  Score=58.50  Aligned_cols=56  Identities=14%  Similarity=0.242  Sum_probs=45.5

Q ss_pred             CCCCCccccchhhHHHHHHHHHc----cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIE----RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      -+-+++-.|+++-++++.+.+.-    +..+-++++.+|+.|+|||.+|+.++.-  ....|
T Consensus       407 ~iLdeDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~A--LnRkF  466 (906)
T KOG2004|consen  407 EILDEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARA--LNRKF  466 (906)
T ss_pred             HhhcccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHH--hCCce
Confidence            34467789999999999998853    3456789999999999999999999887  55554

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.82  E-value=0.0054  Score=52.45  Aligned_cols=22  Identities=14%  Similarity=0.075  Sum_probs=20.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|.+|+||||+|+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999887

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>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=95.82  E-value=0.034  Score=46.82  Aligned_cols=116  Identities=13%  Similarity=0.016  Sum_probs=57.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHhCCCCCCc--cC-C--CCCHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSALS--EI-L--DNDFEMK  111 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~~~--~~-~--~~~~~~~  111 (351)
                      -.+++|+|..|.|||||.+.+..-  ... ....+++.-.    .......+.+.. +.......  .. +  ....+..
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~--~~~-~~G~i~~~g~~~~~~~~~~~~~~i~~-~~q~~~~~~~tv~~~lLS~G~~q  103 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGL--LRP-TSGRVRLDGADISQWDPNELGDHVGY-LPQDDELFSGSIAENILSGGQRQ  103 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc--cCC-CCCeEEECCEEcccCCHHHHHhheEE-ECCCCccccCcHHHHCcCHHHHH
Confidence            458999999999999999999876  222 2222332211    122222111110 00000000  00 0  1122333


Q ss_pred             HHHHHHhcCCceEEEEEeCCCCh---hhHHHHHhhcCC-CCCCcEEEE-Eeecc
Q 048347          112 KNTLHNYLKNKRYLIVIQDVWRG---DIWDFLKEALPD-HQNGSRILT-ALIHI  160 (351)
Q Consensus       112 ~~~l~~~L~~k~~LlVLDdv~~~---~~~~~l~~~l~~-~~~gs~Iiv-TR~~~  160 (351)
                      .-.+...+..+.-++++|+--..   .....+...+.. ...|..||+ |.+.+
T Consensus       104 rv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  157 (173)
T cd03246         104 RLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPE  157 (173)
T ss_pred             HHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            44456666677778899988544   223333333321 223666777 87664

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

>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=95.82  E-value=0.0073  Score=51.32  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=20.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|..|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999887

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=95.81  E-value=0.016  Score=51.63  Aligned_cols=39  Identities=18%  Similarity=0.285  Sum_probs=30.0

Q ss_pred             hHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           26 KMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        26 ~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...++++.+.....+..+|||.|++|+||+||..++...
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~   52 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRE   52 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHH
Confidence            455677777666567899999999999999999887665

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>PRK00625 shikimate kinase; Provisional

Probab=95.81  E-value=0.0057  Score=51.66  Aligned_cols=22  Identities=9%  Similarity=-0.017  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.++||.|+||||+|+.+.+.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3778999999999999999877

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.81  E-value=0.062  Score=52.49  Aligned_cols=100  Identities=17%  Similarity=0.067  Sum_probs=56.3

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCcc-CCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSE-ILD  105 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~-~~~  105 (351)
                      .+++-..|-.+=..-.++.|.|.+|+|||||+.++...  ....-..++|++..-+..++... ++.++.....-. ...
T Consensus        66 i~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~--~a~~g~~vlYvs~Ees~~qi~~r-a~rlg~~~~~l~~~~e  142 (446)
T PRK11823         66 IGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAAR--LAAAGGKVLYVSGEESASQIKLR-AERLGLPSDNLYLLAE  142 (446)
T ss_pred             cHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEccccHHHHHHH-HHHcCCChhcEEEeCC
Confidence            34455555443344578899999999999999999876  33222345666644333333222 444443211000 122


Q ss_pred             CCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347          106 NDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus       106 ~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      .+.+++.+.+.+   .+.-++|+|.+.
T Consensus       143 ~~l~~i~~~i~~---~~~~lVVIDSIq  166 (446)
T PRK11823        143 TNLEAILATIEE---EKPDLVVIDSIQ  166 (446)
T ss_pred             CCHHHHHHHHHh---hCCCEEEEechh
Confidence            345555555533   355689999984

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

Probab=95.80  E-value=0.029  Score=49.82  Aligned_cols=50  Identities=12%  Similarity=0.054  Sum_probs=36.7

Q ss_pred             CCccccchhhHHH---HHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCCcc
Q 048347           17 NKVDLDLEDKMEE---LLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNSSY   66 (351)
Q Consensus        17 ~~~~vGr~~~~~~---l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~~~   66 (351)
                      -+++||.++.+.+   |++.|...    +.-.+-|-.+|+.|.|||.+|+++.+..+
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~k  176 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAK  176 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccC
Confidence            3568898777665   44555432    23356677899999999999999999943

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.79  E-value=0.0063  Score=50.97  Aligned_cols=24  Identities=13%  Similarity=0.062  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|.+.|++|+||||+|+.+...
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            357889999999999999999988

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=95.79  E-value=0.017  Score=56.06  Aligned_cols=90  Identities=10%  Similarity=0.110  Sum_probs=54.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCH-----HH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDF-----EM  110 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~-----~~  110 (351)
                      ..++|.|.+|+|||||+.++...... .+-+.++++-+.   -.+.++..++...-......   ...+....     ..
T Consensus       144 QR~gIfa~~G~GKt~Ll~~~~~~~~~-~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~  222 (461)
T PRK12597        144 GKTGLFGGAGVGKTVLMMELIFNISK-QHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVL  222 (461)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHh-hCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHH
Confidence            56899999999999999988877322 244666666555   66667777766432211110   00011111     11


Q ss_pred             HHHHHHHhc---CCceEEEEEeCCC
Q 048347          111 KKNTLHNYL---KNKRYLIVIQDVW  132 (351)
Q Consensus       111 ~~~~l~~~L---~~k~~LlVLDdv~  132 (351)
                      ..-.+.+++   .+++.|+++|++-
T Consensus       223 ~a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        223 TGLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHhcCCceEEEeccch
Confidence            123344555   3799999999994

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=95.79  E-value=0.014  Score=59.18  Aligned_cols=74  Identities=8%  Similarity=-0.030  Sum_probs=57.5

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccc-cCCCeeEEEEEe-CCHHHHHHHHHHHh
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVK-NYFDCCAWVYYQ-LSLDMMLDAIMKSL   94 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~~-~~~~~~~~~i~~~~   94 (351)
                      -++++|.++-++.|...+...    +-+.++|..|+||||+|+.+...  +. .+|+..+|...+ .+...+++.++.+.
T Consensus        30 ~~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~--l~~~~~~~~~~~~np~~~~~~~~~~v~~~~  103 (637)
T PRK13765         30 IDQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAEL--LPKEELQDILVYPNPEDPNNPKIRTVPAGK  103 (637)
T ss_pred             HHHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHH--cChHhHHHheEeeCCCcchHHHHHHHHHhc
Confidence            356889888888888777654    35778999999999999999877  33 235777887777 88888888888766


Q ss_pred             CC
Q 048347           95 MP   96 (351)
Q Consensus        95 ~~   96 (351)
                      +.
T Consensus       104 G~  105 (637)
T PRK13765        104 GK  105 (637)
T ss_pred             CH
Confidence            65

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=95.78  E-value=0.0044  Score=59.38  Aligned_cols=79  Identities=22%  Similarity=0.188  Sum_probs=45.3

Q ss_pred             CceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEe
Q 048347          243 HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLES  322 (351)
Q Consensus       243 ~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l  322 (351)
                      +|+.|++  .......+|..++.++.|+.|++++| .+.++|...+.+.+|+.|++++ ..+..+|..++.+.+|++|.+
T Consensus       141 nL~~L~l--~~N~i~~l~~~~~~l~~L~~L~l~~N-~l~~l~~~~~~~~~L~~L~ls~-N~i~~l~~~~~~~~~L~~l~~  216 (394)
T COG4886         141 NLKELDL--SDNKIESLPSPLRNLPNLKNLDLSFN-DLSDLPKLLSNLSNLNNLDLSG-NKISDLPPEIELLSALEELDL  216 (394)
T ss_pred             hcccccc--cccchhhhhhhhhccccccccccCCc-hhhhhhhhhhhhhhhhheeccC-CccccCchhhhhhhhhhhhhh
Confidence            5666666  22233344444556666666666666 4666665555666666666665 356666665555555666666


Q ss_pred             cCC
Q 048347          323 WWP  325 (351)
Q Consensus       323 ~~~  325 (351)
                      ++-
T Consensus       217 ~~N  219 (394)
T COG4886         217 SNN  219 (394)
T ss_pred             cCC
Confidence            554

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=95.78  E-value=0.052  Score=50.57  Aligned_cols=56  Identities=7%  Similarity=0.064  Sum_probs=38.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC----CeeEEEEEe--CCHHHHHHHHHHHhC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF----DCCAWVYYQ--LSLDMMLDAIMKSLM   95 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~~~--~~~~~~~~~i~~~~~   95 (351)
                      +.-.++-|+|.+|+|||+||.+++-.......+    ..++||+..  |.+..+.+ +++.++
T Consensus       100 ~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g  161 (317)
T PRK04301        100 ETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALG  161 (317)
T ss_pred             cCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcC
Confidence            556889999999999999999987652222111    357888876  67666554 444443

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=95.77  E-value=0.074  Score=49.35  Aligned_cols=67  Identities=10%  Similarity=0.065  Sum_probs=42.8

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc----CCCeeEEEEEe--CCHHHHHHHHHHHhCC
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN----YFDCCAWVYYQ--LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~~--~~~~~~~~~i~~~~~~   96 (351)
                      .|-.+|-.+=+.-+++-|+|..|+|||+||.+++-..+...    .=..++||+..  |..+.+.+ +++.++.
T Consensus        84 ~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~  156 (313)
T TIGR02238        84 ALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGV  156 (313)
T ss_pred             HHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            34444433335568899999999999999988764322221    11356788776  67776654 5666544

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.76  E-value=0.066  Score=50.24  Aligned_cols=57  Identities=7%  Similarity=0.034  Sum_probs=39.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccc---C-CCeeEEEEEe--CCHHHHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN---Y-FDCCAWVYYQ--LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~---~-F~~~~wv~~~--~~~~~~~~~i~~~~~~   96 (351)
                      +.-++.-|.|..|+|||+|+.+++-..+...   . -..++||+..  |.++.+.+ +++.++.
T Consensus       124 ~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~  186 (344)
T PLN03187        124 ETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGM  186 (344)
T ss_pred             CCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            5568888999999999999988864422221   1 2356788876  77777655 5666554

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.76  E-value=0.0095  Score=50.26  Aligned_cols=25  Identities=12%  Similarity=-0.005  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|.|.|+.|+||||+|+++...
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999887

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=95.75  E-value=0.011  Score=61.28  Aligned_cols=55  Identities=20%  Similarity=0.121  Sum_probs=41.7

Q ss_pred             CcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          267 PRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       267 ~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      .+|+.|++++| .+..+|..   ..+|+.|++++ ..+..+|.+++++++|+.|++++.+
T Consensus       402 s~L~~LdLS~N-~LssIP~l---~~~L~~L~Ls~-NqLt~LP~sl~~L~~L~~LdLs~N~  456 (788)
T PRK15387        402 SELKELMVSGN-RLTSLPML---PSGLLSLSVYR-NQLTRLPESLIHLSSETTVNLEGNP  456 (788)
T ss_pred             cCCCEEEccCC-cCCCCCcc---hhhhhhhhhcc-CcccccChHHhhccCCCeEECCCCC
Confidence            45667777776 46666643   24577788887 4688899999999999999998865

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

Probab=95.73  E-value=0.0099  Score=51.47  Aligned_cols=54  Identities=17%  Similarity=0.071  Sum_probs=36.9

Q ss_pred             ccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE
Q 048347           21 LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY   78 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~   78 (351)
                      ..+..+....++.|..    ..++.+.|++|.|||.||-+..-+.-..+.|+..+++.
T Consensus         3 ~p~~~~Q~~~~~al~~----~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~R   56 (205)
T PF02562_consen    3 KPKNEEQKFALDALLN----NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITR   56 (205)
T ss_dssp             ---SHHHHHHHHHHHH-----SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE
T ss_pred             cCCCHHHHHHHHHHHh----CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            4566777888888873    45888999999999999988877654557787776654

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

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.73  E-value=0.008  Score=48.69  Aligned_cols=22  Identities=9%  Similarity=0.344  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++|+|+.|+|||||++.+...
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhc
Confidence            3689999999999999999887

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.

>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=95.73  E-value=0.0099  Score=54.05  Aligned_cols=35  Identities=29%  Similarity=0.403  Sum_probs=26.0

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+++.+....   +-+-++|+.|+|||++++.....
T Consensus        22 ~~~ll~~l~~~~---~pvLl~G~~GtGKT~li~~~l~~   56 (272)
T PF12775_consen   22 YSYLLDLLLSNG---RPVLLVGPSGTGKTSLIQNFLSS   56 (272)
T ss_dssp             HHHHHHHHHHCT---EEEEEESSTTSSHHHHHHHHHHC
T ss_pred             HHHHHHHHHHcC---CcEEEECCCCCchhHHHHhhhcc
Confidence            345666666543   34468999999999999998765

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.71  E-value=0.057  Score=55.78  Aligned_cols=49  Identities=16%  Similarity=0.043  Sum_probs=38.6

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      -..++|.....+.+.+.+..-...-.-|-|.|..|+|||++|+.+++..
T Consensus       375 ~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s  423 (686)
T PRK15429        375 FGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS  423 (686)
T ss_pred             ccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            3469999998888887776433334466789999999999999999873

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.69  E-value=0.017  Score=52.84  Aligned_cols=79  Identities=6%  Similarity=-0.021  Sum_probs=44.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC--CeeEEEEEe-CC-HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF--DCCAWVYYQ-LS-LDMMLDAIMKSLMPLSALSEILDNDFEMKKNT  114 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~~~-~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  114 (351)
                      +...+|||.|..|+||||+|+.+..-  .....  ..+..++.. |. ..+....    .+......-++..+.+.+.+.
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~l--l~~~~~~g~V~vi~~D~f~~~~~~l~~----~g~~~~~g~P~s~D~~~l~~~  133 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQAL--LSRWPEHRKVELITTDGFLHPNQVLKE----RNLMKKKGFPESYDMHRLVKF  133 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HhhcCCCCceEEEecccccccHHHHHH----cCCccccCCChhccHHHHHHH
Confidence            45689999999999999999877544  22111  123344444 22 2222222    221111011356677777777


Q ss_pred             HHHhcCCce
Q 048347          115 LHNYLKNKR  123 (351)
Q Consensus       115 l~~~L~~k~  123 (351)
                      +...-.++.
T Consensus       134 L~~Lk~g~~  142 (290)
T TIGR00554       134 LSDLKSGKP  142 (290)
T ss_pred             HHHHHCCCC
Confidence            777666553

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.68  E-value=0.075  Score=50.63  Aligned_cols=71  Identities=15%  Similarity=0.074  Sum_probs=48.9

Q ss_pred             HHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCC
Q 048347           27 MEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        27 ~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~   96 (351)
                      .++|.++|-.+       .+...||-.+|.-|.||||.|..+.+.  .+.+=..+.-|...   +...+-++.++.|+..
T Consensus        79 ~eELv~llG~~~~~~~l~~~~P~vImmvGLQGsGKTTt~~KLA~~--lkk~~~kvllVaaD~~RpAA~eQL~~La~q~~v  156 (451)
T COG0541          79 YEELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKY--LKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGV  156 (451)
T ss_pred             HHHHHHHhCCCCcccccCCCCCeEEEEEeccCCChHhHHHHHHHH--HHHcCCceEEEecccCChHHHHHHHHHHHHcCC
Confidence            35566666432       134688999999999999999998887  55522223344444   7777788899999887


Q ss_pred             CCC
Q 048347           97 LSA   99 (351)
Q Consensus        97 ~~~   99 (351)
                      +.-
T Consensus       157 ~~f  159 (451)
T COG0541         157 PFF  159 (451)
T ss_pred             cee
Confidence            644

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

Probab=95.66  E-value=0.0087  Score=48.67  Aligned_cols=35  Identities=14%  Similarity=0.223  Sum_probs=25.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccc-cCCCeeEEEE
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVK-NYFDCCAWVY   78 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~   78 (351)
                      ++|.|+|..|+|||||++.+.+.  .. ..+...+..+
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~--l~~~g~~v~~ik~   36 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINE--LKRRGYRVAVIKH   36 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HhHcCCceEEEEE
Confidence            48999999999999999999998  44 3344443443

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=95.66  E-value=0.017  Score=53.79  Aligned_cols=48  Identities=8%  Similarity=0.219  Sum_probs=41.9

Q ss_pred             CCccccchhhHHHHHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++++|.++.++++++.+...    +.+-+|+-++|+-|.||||||+.+.+-
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~  111 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRG  111 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHH
Confidence            457999999999999988754    356789999999999999999998776

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PTZ00035 Rad51 protein; Provisional

Probab=95.64  E-value=0.11  Score=48.70  Aligned_cols=68  Identities=9%  Similarity=-0.000  Sum_probs=41.8

Q ss_pred             HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccc---c-CCCeeEEEEEe--CCHHHHHHHHHHHhCC
Q 048347           28 EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVK---N-YFDCCAWVYYQ--LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        28 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~---~-~F~~~~wv~~~--~~~~~~~~~i~~~~~~   96 (351)
                      ..|-.+|..+=+.-.++.|+|..|+|||||+..++-..+..   . .=..++|++..  |..+. +.++++.+..
T Consensus       105 ~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g~  178 (337)
T PTZ00035        105 TQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFGL  178 (337)
T ss_pred             HHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhCC
Confidence            33444443333567899999999999999999886542221   1 11245677766  66666 3444555443

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

Probab=95.63  E-value=0.072  Score=50.50  Aligned_cols=59  Identities=8%  Similarity=0.022  Sum_probs=34.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSA   99 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~   99 (351)
                      -++|.++|+.|+||||-..+++.+......=..+..|+..   -...+-++.-++-+..+..
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~  264 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLE  264 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceE
Confidence            6899999999999998555544442212222345677766   2333344444444444444

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.63  E-value=0.068  Score=49.73  Aligned_cols=67  Identities=15%  Similarity=0.014  Sum_probs=41.8

Q ss_pred             HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc----CCCeeEEEEEe--CCHHHHHHHHHHHhC
Q 048347           28 EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN----YFDCCAWVYYQ--LSLDMMLDAIMKSLM   95 (351)
Q Consensus        28 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~~--~~~~~~~~~i~~~~~   95 (351)
                      +.+-.+|..+=+.-.++.|.|..|+||||||..++.......    .-..++|++..  +.... +.++++.+.
T Consensus        83 ~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~  155 (316)
T TIGR02239        83 KELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYG  155 (316)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcC
Confidence            344444444335678999999999999999998875322211    11246788766  66665 344555443

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>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=95.62  E-value=0.013  Score=48.42  Aligned_cols=35  Identities=6%  Similarity=-0.141  Sum_probs=27.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY   78 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~   78 (351)
                      .||-+.|..|+||||||+++...  ....-..+..+.
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~--L~~~g~~~~~LD   37 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERR--LFARGIKVYLLD   37 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHH--HHHTTS-EEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEec
Confidence            57778899999999999999988  655555555554

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 ....

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=95.62  E-value=0.027  Score=50.76  Aligned_cols=102  Identities=20%  Similarity=0.127  Sum_probs=55.9

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC----CCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC--
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY----FDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL--  100 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~--  100 (351)
                      .|-++|..+=..-.+.-|+|.+|+|||+||-+++-..++...    =..++|++-.  |..+.+. +|+++...+...  
T Consensus        26 ~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l  104 (256)
T PF08423_consen   26 SLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEIL  104 (256)
T ss_dssp             HHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHH
T ss_pred             HHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhh
Confidence            344444332234578999999999999999887655333322    1247788766  7776665 566654332110  


Q ss_pred             c---cCCCCCHHHHHHHHH---Hhc-CCceEEEEEeCC
Q 048347          101 S---EILDNDFEMKKNTLH---NYL-KNKRYLIVIQDV  131 (351)
Q Consensus       101 ~---~~~~~~~~~~~~~l~---~~L-~~k~~LlVLDdv  131 (351)
                      .   -....+.+++.+.+.   ..+ .++--|||+|.+
T Consensus       105 ~~I~v~~~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSI  142 (256)
T PF08423_consen  105 DNIFVIRVFDLEELLELLEQLPKLLSESKIKLIVIDSI  142 (256)
T ss_dssp             HTEEEEE-SSHHHHHHHHHHHHHHHHHSCEEEEEEETS
T ss_pred             hceeeeecCCHHHHHHHHHHHHhhccccceEEEEecch
Confidence            0   012233444443332   223 234558888887

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK13947 shikimate kinase; Provisional

Probab=95.61  E-value=0.0074  Score=50.60  Aligned_cols=22  Identities=18%  Similarity=0.218  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+||.|+||||+|+.+.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~   24 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATT   24 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            4788999999999999999887

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=95.60  E-value=0.0035  Score=60.10  Aligned_cols=81  Identities=20%  Similarity=0.139  Sum_probs=46.4

Q ss_pred             CCCceEEEEecccccCceeeeCCCCCC-cccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHGGFP-RQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~~l~-~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      ++.+..|.+  ..-....+|.....+. +|+.|+++++ .+..+|..++.++.|+.|++++| .+..+|...+.+++|+.
T Consensus       115 ~~~l~~L~l--~~n~i~~i~~~~~~~~~nL~~L~l~~N-~i~~l~~~~~~l~~L~~L~l~~N-~l~~l~~~~~~~~~L~~  190 (394)
T COG4886         115 LTNLTSLDL--DNNNITDIPPLIGLLKSNLKELDLSDN-KIESLPSPLRNLPNLKNLDLSFN-DLSDLPKLLSNLSNLNN  190 (394)
T ss_pred             ccceeEEec--CCcccccCccccccchhhccccccccc-chhhhhhhhhccccccccccCCc-hhhhhhhhhhhhhhhhh
Confidence            355666666  3333345555555553 6666666666 46666555666666666666663 46666665556666666


Q ss_pred             EEecCC
Q 048347          320 LESWWP  325 (351)
Q Consensus       320 L~l~~~  325 (351)
                      |++++.
T Consensus       191 L~ls~N  196 (394)
T COG4886         191 LDLSGN  196 (394)
T ss_pred             eeccCC
Confidence            666553

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.60  E-value=0.042  Score=45.79  Aligned_cols=109  Identities=9%  Similarity=-0.048  Sum_probs=58.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      -.+++|.|..|.|||||.+.++..  .. .....+++.-.    .+..+..+   +.+.-   .+  +....+...-.+.
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~--~~-~~~G~v~~~g~~~~~~~~~~~~~---~~i~~---~~--qLS~G~~qrl~la   94 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGL--YK-PDSGEILVDGKEVSFASPRDARR---AGIAM---VY--QLSVGERQMVEIA   94 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--CC-CCCeEEEECCEECCcCCHHHHHh---cCeEE---EE--ecCHHHHHHHHHH
Confidence            358999999999999999999877  32 23344443322    11111110   00100   00  1223334455566


Q ss_pred             HhcCCceEEEEEeCCCCh---hhHHHHHhhcCC-CCCCcEEEE-Eeecc
Q 048347          117 NYLKNKRYLIVIQDVWRG---DIWDFLKEALPD-HQNGSRILT-ALIHI  160 (351)
Q Consensus       117 ~~L~~k~~LlVLDdv~~~---~~~~~l~~~l~~-~~~gs~Iiv-TR~~~  160 (351)
                      +.+..+.-++++|+--..   .....+...+.. ...|..||+ |++..
T Consensus        95 ral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  143 (163)
T cd03216          95 RALARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLD  143 (163)
T ss_pred             HHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            677777788889987543   223333333321 123556666 77654

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.

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

Probab=95.59  E-value=0.0046  Score=47.76  Aligned_cols=21  Identities=14%  Similarity=0.235  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |-|+|.+|+|||++|+.+..+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999998877

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

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.59  E-value=0.055  Score=45.46  Aligned_cols=24  Identities=17%  Similarity=0.169  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|.|..|.|||||.+.++.-
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC
Confidence            468999999999999999999887

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.

>COG3903 Predicted ATPase [General function prediction only]

Probab=95.59  E-value=0.006  Score=57.41  Aligned_cols=110  Identities=18%  Similarity=0.141  Sum_probs=70.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe-eEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC-CAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      ..+.+.++|.|||||||++-.+..   +...|.. ++++...  .+...+.-.....+.-...       +.+.....+.
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~-------~g~~~~~~~~   82 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQ-------PGDSAVDTLV   82 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhcccccc-------cchHHHHHHH
Confidence            367899999999999999998877   4556654 5555555  5555555555555655443       3334556677


Q ss_pred             HhcCCceEEEEEeCCCCh-hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347          117 NYLKNKRYLIVIQDVWRG-DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus       117 ~~L~~k~~LlVLDdv~~~-~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ....+++.++|+||..+. +.--.+...+..+...-.|+. +|+.
T Consensus        83 ~~~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~  127 (414)
T COG3903          83 RRIGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREA  127 (414)
T ss_pred             HHHhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhh
Confidence            777899999999999655 223333344443333444554 4443

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=95.55  E-value=0.046  Score=49.43  Aligned_cols=99  Identities=13%  Similarity=0.103  Sum_probs=57.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccc--ccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHH----
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYV--KNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFE----  109 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~----  109 (351)
                      ..++|.|-.|+|||+|+..+.++.++  +.+-+.++++-+.   -++.++..++...=..+...   .+.+.....    
T Consensus        70 QR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a  149 (276)
T cd01135          70 QKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIIT  149 (276)
T ss_pred             CEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHH
Confidence            56889999999999999998877331  1234566777666   77777777776542211110   000111111    


Q ss_pred             -HHHHHHHHhc---CCceEEEEEeCCCCh-hhHHHH
Q 048347          110 -MKKNTLHNYL---KNKRYLIVIQDVWRG-DIWDFL  140 (351)
Q Consensus       110 -~~~~~l~~~L---~~k~~LlVLDdv~~~-~~~~~l  140 (351)
                       ...-.+.+++   ++++.|+++||+-.. +++.++
T Consensus       150 ~~~a~aiAEyfrd~~g~~VLl~~D~ltr~A~A~rEi  185 (276)
T cd01135         150 PRMALTTAEYLAYEKGKHVLVILTDMTNYAEALREI  185 (276)
T ss_pred             HHHHHHHHHHHHhccCCeEEEEEcChhHHHHHHHHH
Confidence             1122334444   378999999999543 344444

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>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=95.55  E-value=0.0074  Score=50.89  Aligned_cols=38  Identities=8%  Similarity=-0.081  Sum_probs=28.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccc-cCCCeeEEEEEe
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVK-NYFDCCAWVYYQ   80 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~~   80 (351)
                      ..++-+.|+.|+|||.||+.+..-  +. ......+-+..+
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~--l~~~~~~~~~~~d~s   41 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAEL--LFVGSERPLIRIDMS   41 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHH--HT-SSCCEEEEEEGG
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHH--hccCCccchHHHhhh
Confidence            467788999999999999999887  54 455555555555

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 ....

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=95.55  E-value=0.0084  Score=49.12  Aligned_cols=22  Identities=5%  Similarity=0.166  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+.|+.|+||||+|+.+...
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            3678899999999999999887

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.54  E-value=0.011  Score=50.49  Aligned_cols=23  Identities=9%  Similarity=0.265  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++.|+|+.|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            37889999999999999999777

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.54  E-value=0.018  Score=48.56  Aligned_cols=25  Identities=8%  Similarity=0.226  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      -.++.|.|++|+||+||+++++++.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3678899999999999999999993

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=95.54  E-value=0.0072  Score=51.30  Aligned_cols=22  Identities=9%  Similarity=0.144  Sum_probs=20.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ||.|.|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999887

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.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.54  E-value=0.008  Score=50.99  Aligned_cols=97  Identities=11%  Similarity=0.013  Sum_probs=48.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      .|.|.|.+|+||||+|+.+.+...+ .|.+.-.|.... ....++-..+...+....-      -+.+-....+.+.+..
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i-~hlstgd~~r~~~~~~t~lg~~~k~~i~~g~l------v~d~i~~~~v~~rl~~   74 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGL-PHLDTGDILRAAIAERTELGEEIKKYIDKGEL------VPDEIVNGLVKERLDE   74 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC-cEEcHhHHhHhhhccCChHHHHHHHHHHcCCc------cchHHHHHHHHHHHHh
Confidence            4678999999999999999888332 122211111111 1223333333333333221      1222223334444422


Q ss_pred             --ceEEEEEeCCCCh-hhHHHHHhhcCC
Q 048347          122 --KRYLIVIQDVWRG-DIWDFLKEALPD  146 (351)
Q Consensus       122 --k~~LlVLDdv~~~-~~~~~l~~~l~~  146 (351)
                        .+.-+|+|+.=.. .++..+...+..
T Consensus        75 ~d~~~~~I~dg~PR~~~qa~~l~r~l~~  102 (178)
T COG0563          75 ADCKAGFILDGFPRTLCQARALKRLLKE  102 (178)
T ss_pred             hcccCeEEEeCCCCcHHHHHHHHHHHHH
Confidence              2227888888544 455556555544

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.54  E-value=0.042  Score=45.13  Aligned_cols=22  Identities=5%  Similarity=0.092  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|.|.|..|+||||+|+.+...
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            4778999999999999998877

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.54  E-value=0.011  Score=51.29  Aligned_cols=24  Identities=8%  Similarity=0.185  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+|+|+|+.|+||||||+.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999887

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=95.52  E-value=0.033  Score=48.70  Aligned_cols=86  Identities=13%  Similarity=0.190  Sum_probs=49.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCC--CccCCCCC---------
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSA--LSEILDND---------  107 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~--~~~~~~~~---------  107 (351)
                      ..++|.|..|+|||+|+..+.+.  ..  -+..+++-+.   -.+.++.+++...-..+..  .......+         
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~--~~--~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~   91 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANN--QD--ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPY   91 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH--CT--TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhc--cc--ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhc
Confidence            46788999999999999999887  32  2233454444   5556666666433111100  00001111         


Q ss_pred             -HHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          108 -FEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       108 -~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                       .-...+.+++  .+|+.|+++||+-.
T Consensus        92 ~a~t~AEyfrd--~G~dVlli~Dsltr  116 (215)
T PF00006_consen   92 TALTIAEYFRD--QGKDVLLIIDSLTR  116 (215)
T ss_dssp             HHHHHHHHHHH--TTSEEEEEEETHHH
T ss_pred             cchhhhHHHhh--cCCceeehhhhhHH
Confidence             1122344444  69999999999943

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PRK13949 shikimate kinase; Provisional

Probab=95.49  E-value=0.0096  Score=50.08  Aligned_cols=22  Identities=14%  Similarity=0.164  Sum_probs=20.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|+|+.|+||||+|+.+...
T Consensus         3 ~I~liG~~GsGKstl~~~La~~   24 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARE   24 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999888

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

Probab=95.49  E-value=0.017  Score=55.97  Aligned_cols=52  Identities=15%  Similarity=0.083  Sum_probs=38.9

Q ss_pred             CccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           18 KVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      .++.|.++.++++.+.+...           -...+-+.++|+.|.|||++|+.+++.  ....|
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~e--l~~~f  245 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE--TSATF  245 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHh--hCCCE
Confidence            45678999999998877421           022345678999999999999999998  54444

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.49  E-value=0.01  Score=50.08  Aligned_cols=23  Identities=0%  Similarity=0.034  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.+.|++|+||||+|+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            57889999999999999999877

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.48  E-value=0.12  Score=52.80  Aligned_cols=50  Identities=16%  Similarity=0.171  Sum_probs=35.4

Q ss_pred             CccccchhhHHHHHHHH---HccC-------CCeEEEEEEcCCCChHHHHHHHHhCCccc
Q 048347           18 KVDLDLEDKMEELLDLL---IERQ-------PQLSLVAIIDTMGFDRTAFIGEAYNSSYV   67 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L---~~~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~   67 (351)
                      .++.|.|+-+++|.+.+   ....       .-.+=+-++|+.|.|||.||++++-...|
T Consensus       311 kDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgV  370 (774)
T KOG0731|consen  311 KDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGV  370 (774)
T ss_pred             ccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCC
Confidence            45778887777766655   3221       12233668899999999999999999443

>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=95.48  E-value=0.023  Score=47.14  Aligned_cols=37  Identities=19%  Similarity=0.363  Sum_probs=30.7

Q ss_pred             hhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           24 EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        24 ~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      .+.+++|.+.+..     +++.++|..|+|||||.+.+....
T Consensus        23 ~~g~~~l~~~l~~-----k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   23 GEGIEELKELLKG-----KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTTHHHHHHHHTT-----SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CcCHHHHHHHhcC-----CEEEEECCCCCCHHHHHHHHHhhc
Confidence            4567888888843     588889999999999999999883

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.47  E-value=0.014  Score=50.44  Aligned_cols=26  Identities=8%  Similarity=0.073  Sum_probs=23.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++..+|+|.|+.|+||||||+.+...
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~   47 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEA   47 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45689999999999999999999886

>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=95.47  E-value=0.0097  Score=48.28  Aligned_cols=22  Identities=14%  Similarity=0.148  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|.|.|..|+||||+|+.+...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~   22 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKK   22 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999876

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.47  E-value=0.0078  Score=32.13  Aligned_cols=19  Identities=21%  Similarity=0.057  Sum_probs=9.4

Q ss_pred             ccEEEEecCCcccccccccc
Q 048347          269 QEILHLKSMLWLEEWKMETG  288 (351)
Q Consensus       269 L~~L~L~~~~~l~~lp~~i~  288 (351)
                      |++|++++| .++.+|.+++
T Consensus         2 L~~Ldls~n-~l~~ip~~~~   20 (22)
T PF00560_consen    2 LEYLDLSGN-NLTSIPSSFS   20 (22)
T ss_dssp             ESEEEETSS-EESEEGTTTT
T ss_pred             ccEEECCCC-cCEeCChhhc
Confidence            455555555 4445554443

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>PRK13975 thymidylate kinase; Provisional

Probab=95.47  E-value=0.01  Score=50.99  Aligned_cols=23  Identities=9%  Similarity=0.004  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999988

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.47  E-value=0.031  Score=53.83  Aligned_cols=91  Identities=11%  Similarity=0.114  Sum_probs=49.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCC---ccCCCCCHHH-----H
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSAL---SEILDNDFEM-----K  111 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~~-----~  111 (351)
                      -..++|.|..|+|||||++.+...  .+...-.++++-.. -.+.++..+.+..-..+...   ...+......     .
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~--~~~~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~~  217 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARN--TDADVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAYT  217 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCC--CCCCEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHHH
Confidence            357899999999999999999887  33221112222222 55556665544332211110   0001111111     1


Q ss_pred             HHHHHHhc--CCceEEEEEeCCCC
Q 048347          112 KNTLHNYL--KNKRYLIVIQDVWR  133 (351)
Q Consensus       112 ~~~l~~~L--~~k~~LlVLDdv~~  133 (351)
                      .-.+.+++  ++++.|+++||+-.
T Consensus       218 a~~iAEyfrd~G~~Vll~~DslTr  241 (418)
T TIGR03498       218 ATAIAEYFRDQGKDVLLLMDSVTR  241 (418)
T ss_pred             HHHHHHHHHHcCCCEEEeccchhH
Confidence            12233444  57999999999943

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=95.46  E-value=0.11  Score=47.07  Aligned_cols=121  Identities=12%  Similarity=0.012  Sum_probs=78.2

Q ss_pred             CCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEE-EEe--CCHHHHHHHH
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWV-YYQ--LSLDMMLDAI   90 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv-~~~--~~~~~~~~~i   90 (351)
                      ......++|.... .++..++......-+.+.|+|+.|+|||+-++.+++.  .     ..+|+ ..+  ++...+...+
T Consensus        68 ~~~~~~~l~tkt~-r~~~~~~~~A~k~g~l~~vyg~~g~gKt~a~~~y~~s--~-----p~~~l~~~~p~~~a~~~i~~i  139 (297)
T COG2842          68 EKLAPDFLETKTV-RRIFFRTRPASKTGSLVVVYGYAGLGKTQAAKNYAPS--N-----PNALLIEADPSYTALVLILII  139 (297)
T ss_pred             ccccccccccchh-HhHhhhhhhhhhcCceEEEeccccchhHHHHHhhccc--C-----ccceeecCChhhHHHHHHHHH
Confidence            3345556664332 2233444333333348889999999999999999988  2     23443 333  6666666666


Q ss_pred             HHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCC
Q 048347           91 MKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQ  148 (351)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~  148 (351)
                      ...+.....      ....+....+...+++..-+++.|+....  +.++.++.-....+
T Consensus       140 ~~~~~~~~~------~~~~d~~~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~d~~G  193 (297)
T COG2842         140 CAAAFGATD------GTINDLTERLMIRLRDTVRLIIVDEADRLPYRALEELRRIHDKTG  193 (297)
T ss_pred             HHHHhcccc------hhHHHHHHHHHHHHccCcceeeeehhhccChHHHHHHHHHHHhhC
Confidence            655555433      46667788888888899999999988765  56777766554443

>TIGR00416 sms DNA repair protein RadA

Probab=95.46  E-value=0.087  Score=51.53  Aligned_cols=100  Identities=14%  Similarity=0.028  Sum_probs=55.0

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCcc-CCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSE-ILD  105 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~-~~~  105 (351)
                      ..++-.+|..+=..-.++.|.|..|+|||||+.++...  ....-..++|++..-...++.. -+..++....... ...
T Consensus        80 i~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~--~a~~g~kvlYvs~EEs~~qi~~-ra~rlg~~~~~l~~~~e  156 (454)
T TIGR00416        80 FGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQ--LAKNQMKVLYVSGEESLQQIKM-RAIRLGLPEPNLYVLSE  156 (454)
T ss_pred             cHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHH--HHhcCCcEEEEECcCCHHHHHH-HHHHcCCChHHeEEcCC
Confidence            44555555444355678899999999999999998766  3332234567654433333222 1223332211000 223


Q ss_pred             CCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347          106 NDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus       106 ~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      .+.+++.+.+.+   .+.-++|+|.+-
T Consensus       157 ~~~~~I~~~i~~---~~~~~vVIDSIq  180 (454)
T TIGR00416       157 TNWEQICANIEE---ENPQACVIDSIQ  180 (454)
T ss_pred             CCHHHHHHHHHh---cCCcEEEEecch
Confidence            445555555433   245579999884

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

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.45  E-value=0.0082  Score=32.04  Aligned_cols=22  Identities=18%  Similarity=0.258  Sum_probs=17.2

Q ss_pred             CccEEeecCCccccccChhhhcC
Q 048347          292 KLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       292 ~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      +|++|++++| .+..+|.++++|
T Consensus         1 ~L~~Ldls~n-~l~~ip~~~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGN-NLTSIPSSFSNL   22 (22)
T ss_dssp             TESEEEETSS-EESEEGTTTTT-
T ss_pred             CccEEECCCC-cCEeCChhhcCC
Confidence            5889999997 677899887654

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.45  E-value=0.073  Score=52.69  Aligned_cols=122  Identities=12%  Similarity=0.095  Sum_probs=69.0

Q ss_pred             cchhhHHHHHHHHHccC-----------CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHH
Q 048347           22 DLEDKMEELLDLLIERQ-----------PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAI   90 (351)
Q Consensus        22 Gr~~~~~~l~~~L~~~~-----------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i   90 (351)
                      |.++-+.++...+...-           .-..=|-.||+.|.|||.||++|+|.  ..-+|     +++-  -.+++.. 
T Consensus       515 aL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANE--ag~NF-----isVK--GPELlNk-  584 (802)
T KOG0733|consen  515 ALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANE--AGANF-----ISVK--GPELLNK-  584 (802)
T ss_pred             cHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhh--ccCce-----Eeec--CHHHHHH-
Confidence            35566666665554321           11233568999999999999999999  54554     3332  0111111 


Q ss_pred             HHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh-------------hhHHHHHhhcCCC--CCCcEEEE
Q 048347           91 MKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG-------------DIWDFLKEALPDH--QNGSRILT  155 (351)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~-------------~~~~~l~~~l~~~--~~gs~Iiv  155 (351)
                         -.         ..++....+.+.+.=.+-.|.|.+|.++..             ....++.+.+...  -.|--||-
T Consensus       585 ---YV---------GESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~via  652 (802)
T KOG0733|consen  585 ---YV---------GESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIA  652 (802)
T ss_pred             ---Hh---------hhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEe
Confidence               00         112334444445555678899999999532             2345555555542  23444555


Q ss_pred             -Eeeccc---hhhc
Q 048347          156 -ALIHIV---GLSS  165 (351)
Q Consensus       156 -TR~~~v---~lL~  165 (351)
                       |...++   ++|+
T Consensus       653 ATNRPDiIDpAiLR  666 (802)
T KOG0733|consen  653 ATNRPDIIDPAILR  666 (802)
T ss_pred             ecCCCcccchhhcC
Confidence             777776   5554

>PLN02348 phosphoribulokinase

Probab=95.43  E-value=0.062  Score=50.99  Aligned_cols=27  Identities=7%  Similarity=0.236  Sum_probs=24.4

Q ss_pred             CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           38 QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        38 ~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++..+|||.|.+|+||||+|+.+.+.
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L~~~   72 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRLTSV   72 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            356789999999999999999999887

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=95.39  E-value=0.035  Score=49.07  Aligned_cols=57  Identities=12%  Similarity=-0.011  Sum_probs=40.6

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      |.+.-.++=|.|-.++++.+.+.-.           -+..+=|-.+|+.|.|||.||++|.++  .+..|
T Consensus       150 pdvsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~--t~a~f  217 (408)
T KOG0727|consen  150 PDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH--TTAAF  217 (408)
T ss_pred             CCccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhc--cchhe
Confidence            5454556667888888887776321           022344568999999999999999999  55554

>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=95.39  E-value=0.011  Score=47.71  Aligned_cols=21  Identities=19%  Similarity=0.227  Sum_probs=19.1

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |-++|..|+|||+||+.++..
T Consensus         2 vlL~G~~G~GKt~l~~~la~~   22 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAAL   22 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999887

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.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.37  E-value=0.047  Score=52.70  Aligned_cols=90  Identities=13%  Similarity=0.189  Sum_probs=48.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHHHH--
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFEMK--  111 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~~~--  111 (351)
                      +-..++|.|..|+|||||++.+.+.  ..  .+...+.-+.   ..+.+++.+....=..+...   ..-+.......  
T Consensus       154 ~GqrigI~G~sG~GKSTLL~~I~~~--~~--~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a  229 (433)
T PRK07594        154 EGQRVGIFSAPGVGKSTLLAMLCNA--PD--ADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRA  229 (433)
T ss_pred             CCCEEEEECCCCCCccHHHHHhcCC--CC--CCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHH
Confidence            3457899999999999999999887  22  3334444444   55555555543211000000   00011111111  


Q ss_pred             ---HHHHHHhc--CCceEEEEEeCCCC
Q 048347          112 ---KNTLHNYL--KNKRYLIVIQDVWR  133 (351)
Q Consensus       112 ---~~~l~~~L--~~k~~LlVLDdv~~  133 (351)
                         .-.+.+++  ++++.|+++||+-.
T Consensus       230 ~~~a~tiAEyfrd~G~~VLl~~Dsltr  256 (433)
T PRK07594        230 LFVATTIAEFFRDNGKRVVLLADSLTR  256 (433)
T ss_pred             HHHHHHHHHHHHHCCCcEEEEEeCHHH
Confidence               12233333  48899999999953

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=95.34  E-value=0.0039  Score=61.01  Aligned_cols=82  Identities=18%  Similarity=0.243  Sum_probs=38.2

Q ss_pred             CCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhh-cCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELW-RIK  315 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~-~L~  315 (351)
                      .-++.|++|+||+|..  ..+|.. +..-.++++|+|++| .++.+-.. +..|.+|-+|.|+. ..+..+|.-+. +|+
T Consensus       146 ~~l~alrslDLSrN~i--s~i~~~sfp~~~ni~~L~La~N-~It~l~~~~F~~lnsL~tlkLsr-NrittLp~r~Fk~L~  221 (873)
T KOG4194|consen  146 SALPALRSLDLSRNLI--SEIPKPSFPAKVNIKKLNLASN-RITTLETGHFDSLNSLLTLKLSR-NRITTLPQRSFKRLP  221 (873)
T ss_pred             HhHhhhhhhhhhhchh--hcccCCCCCCCCCceEEeeccc-cccccccccccccchheeeeccc-CcccccCHHHhhhcc
Confidence            3445555555533321  122221 222234555555555 34444332 44555555555555 34555554332 355


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      .|+.|++..
T Consensus       222 ~L~~LdLnr  230 (873)
T KOG4194|consen  222 KLESLDLNR  230 (873)
T ss_pred             hhhhhhccc
Confidence            555555543

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.33  E-value=0.044  Score=53.00  Aligned_cols=88  Identities=7%  Similarity=0.122  Sum_probs=48.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEE-e-CCHHHHHHHHHHHhCCCCC--CccCCCCC---------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYY-Q-LSLDMMLDAIMKSLMPLSA--LSEILDND---------  107 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~-~-~~~~~~~~~i~~~~~~~~~--~~~~~~~~---------  107 (351)
                      -.+++|+|..|+|||||++.+....+   ....+++..- . -++.++....+.......-  ..+.+...         
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~---pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~  241 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADA---FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLT  241 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC---CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHH
Confidence            35789999999999999998876622   1223333321 1 4555555444444322110  01101111         


Q ss_pred             HHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          108 FEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       108 ~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                      .-.+.+.+++  ++++.|+++||+-.
T Consensus       242 a~~iAEyfrd--~G~~Vll~~DslTr  265 (450)
T PRK06002        242 ATAIAEYFRD--RGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHH--cCCCEEEeccchHH
Confidence            1122344443  48999999999943

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.32  E-value=0.21  Score=46.68  Aligned_cols=40  Identities=13%  Similarity=0.106  Sum_probs=28.4

Q ss_pred             CceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347          121 NKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus       121 ~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      +++-.+|+|+++..  .+.+.+...+.....++.+|+ |.+.+
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~  147 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPS  147 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChh
Confidence            44445678999865  678888888877666777777 76554

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.31  E-value=0.022  Score=52.64  Aligned_cols=38  Identities=18%  Similarity=0.218  Sum_probs=29.2

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+.+.+.....+..+|+|.|.+|+|||||+..+...
T Consensus        20 ~~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~   57 (300)
T TIGR00750        20 AKQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGME   57 (300)
T ss_pred             HHHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            34455555444456899999999999999999998775

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.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.31  E-value=0.057  Score=50.25  Aligned_cols=87  Identities=8%  Similarity=0.102  Sum_probs=48.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCC-------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDND-------  107 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~-------  107 (351)
                      -..++|+|..|+|||||++.+...  ...  +.....-+.   -++.++.......-......   .+.+...       
T Consensus        69 Gqri~I~G~sG~GKTtLl~~Ia~~--~~~--~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~  144 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGMIARG--TTA--DVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAA  144 (326)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCC--CCC--CEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHH
Confidence            357899999999999999999887  322  233333333   55555555554432211000   0001111       


Q ss_pred             --HHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          108 --FEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       108 --~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                        .-.+.+.+++  ++|..|+++||+-.
T Consensus       145 ~~a~~~AEyfr~--~g~~Vll~~Dsltr  170 (326)
T cd01136         145 YTATAIAEYFRD--QGKDVLLLMDSLTR  170 (326)
T ss_pred             HHHHHHHHHHHH--cCCCeEEEeccchH
Confidence              1122344443  58999999999843

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.31  E-value=0.087  Score=52.07  Aligned_cols=102  Identities=12%  Similarity=0.013  Sum_probs=60.1

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCC------
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSAL------  100 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~------  100 (351)
                      ..++-++|-.+=.+-+++-|.|.+|+||||||.++...  ...+-+.+++++..=+..++.... +.++-+...      
T Consensus       249 i~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~--~~~~ge~~~y~s~eEs~~~i~~~~-~~lg~~~~~~~~~g~  325 (484)
T TIGR02655       249 VVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLEN--ACANKERAILFAYEESRAQLLRNA-YSWGIDFEEMEQQGL  325 (484)
T ss_pred             hHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEeeCCHHHHHHHH-HHcCCChHHHhhCCc
Confidence            45566666554456788899999999999999998776  333344566666544455555553 344322110      


Q ss_pred             -----ccCCCCCHHHHHHHHHHhcCC-ceEEEEEeCC
Q 048347          101 -----SEILDNDFEMKKNTLHNYLKN-KRYLIVIQDV  131 (351)
Q Consensus       101 -----~~~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv  131 (351)
                           ..+.....++..+.+.+.++. +.-.+|+|.+
T Consensus       326 l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi  362 (484)
T TIGR02655       326 LKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSL  362 (484)
T ss_pred             EEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCH
Confidence                 001223345566666666643 3346777776

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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.30  E-value=0.029  Score=52.35  Aligned_cols=38  Identities=24%  Similarity=0.313  Sum_probs=29.1

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++.+.+.....+..+|+|.|..|+|||||+..+...
T Consensus        42 ~~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~   79 (332)
T PRK09435         42 AQELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMH   79 (332)
T ss_pred             HHHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            34555555443456789999999999999999987666

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.29  E-value=0.067  Score=51.67  Aligned_cols=87  Identities=13%  Similarity=0.134  Sum_probs=50.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC--ccCCCCCH-------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL--SEILDNDF-------  108 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~--~~~~~~~~-------  108 (351)
                      -..++|.|..|+|||||.+.+++.  ...  +.++.+-+.   -.+.++....+..-..+...  -...+.+.       
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~--~~~--dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRS--AEV--DVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAG  237 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcC--CCC--CEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHH
Confidence            457899999999999999999998  322  455555555   55555554433321111000  00011111       


Q ss_pred             ---HHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          109 ---EMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       109 ---~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                         -.+.+.+++  .+|+.|+++|++-.
T Consensus       238 ~~a~tiAEyfrd--~G~~Vll~~DslTR  263 (439)
T PRK06936        238 FVATSIAEYFRD--QGKRVLLLMDSVTR  263 (439)
T ss_pred             HHHHHHHHHHHH--cCCCEEEeccchhH
Confidence               123444444  48999999999943

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=95.28  E-value=0.014  Score=50.97  Aligned_cols=24  Identities=8%  Similarity=0.249  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      .-|+|+|++|+|||||+.++..+.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCc
Confidence            467799999999999999998873

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.27  E-value=0.013  Score=49.50  Aligned_cols=23  Identities=9%  Similarity=0.174  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|.|+|+.|+||||+|+.+...
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHH
Confidence            46889999999999999999877

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=95.27  E-value=0.057  Score=49.75  Aligned_cols=116  Identities=16%  Similarity=0.144  Sum_probs=66.6

Q ss_pred             CCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHH
Q 048347           16 DNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAI   90 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i   90 (351)
                      +...++|...+..++-.++...  .....-+.|+|+.|.|||+|...+..+  .+..=+...-|...   ..-+-.++.|
T Consensus        22 ~~~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~--~q~~~E~~l~v~Lng~~~~dk~al~~I   99 (408)
T KOG2228|consen   22 PHINLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSD--IQENGENFLLVRLNGELQTDKIALKGI   99 (408)
T ss_pred             CCcceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhh--HHhcCCeEEEEEECccchhhHHHHHHH
Confidence            5667899999999999988643  011234557899999999999888777  33332333344444   2223355666


Q ss_pred             HHHhCCCCCCccCCCCCHHHHHHHHHHhcC------CceEEEEEeCCCC
Q 048347           91 MKSLMPLSALSEILDNDFEMKKNTLHNYLK------NKRYLIVIQDVWR  133 (351)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~------~k~~LlVLDdv~~  133 (351)
                      .+|+..+....-....+..+-..++-..|+      +-+.++|+|..+-
T Consensus       100 ~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDl  148 (408)
T KOG2228|consen  100 TRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDL  148 (408)
T ss_pred             HHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhc
Confidence            666544221100122333333444444443      2357778877753

>PRK13948 shikimate kinase; Provisional

Probab=95.24  E-value=0.013  Score=49.88  Aligned_cols=25  Identities=20%  Similarity=0.200  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+.|.++||.|+||||+++.+...
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~   33 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRA   33 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4567889999999999999999887

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.24  E-value=0.07  Score=51.96  Aligned_cols=99  Identities=10%  Similarity=0.125  Sum_probs=55.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCC--eeEEEEEe---CCHHHHHHHHHHHhCCCCCC--ccCCCC-C-----H
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD--CCAWVYYQ---LSLDMMLDAIMKSLMPLSAL--SEILDN-D-----F  108 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~~---~~~~~~~~~i~~~~~~~~~~--~~~~~~-~-----~  108 (351)
                      ..++|.|-.|+|||||+..+.+..+..+.+.  .++++-+.   -.+.+++.++...=..+...  -...+. .     .
T Consensus       142 QR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a  221 (458)
T TIGR01041       142 QKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVT  221 (458)
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHH
Confidence            4688999999999999999988744332222  33344444   66667777766432211100  000111 1     1


Q ss_pred             HHHHHHHHHhcC---CceEEEEEeCCCCh-hhHHHH
Q 048347          109 EMKKNTLHNYLK---NKRYLIVIQDVWRG-DIWDFL  140 (351)
Q Consensus       109 ~~~~~~l~~~L~---~k~~LlVLDdv~~~-~~~~~l  140 (351)
                      ....-.+.++++   +++.|+++||+-.. .++..+
T Consensus       222 ~~~a~tiAEyfr~d~G~~VLli~DslTR~A~A~REI  257 (458)
T TIGR01041       222 PRMALTAAEYLAFEKDMHVLVILTDMTNYCEALREI  257 (458)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcChhHHHHHHHHH
Confidence            111233455554   68899999999433 333443

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.21  E-value=0.035  Score=54.99  Aligned_cols=90  Identities=10%  Similarity=0.067  Sum_probs=47.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccc-CCCeeEEEEEe----CCHHHHHHHHHHHhCCCCCCcc-CCCCCHHHHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKN-YFDCCAWVYYQ----LSLDMMLDAIMKSLMPLSALSE-ILDNDFEMKKNTL  115 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv~~~----~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~l  115 (351)
                      ....|+|..|+|||||++.+.+.  +.. +=++.++|-+.    -.+.++.+.+-.++........ ........+.-.+
T Consensus       417 QR~LIvgpp~aGKTtLL~~IAn~--i~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~  494 (672)
T PRK12678        417 QRGLIVSPPKAGKTTILQNIANA--ITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIER  494 (672)
T ss_pred             CEeEEeCCCCCCHHHHHHHHHHH--HhhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHH
Confidence            46789999999999999999987  433 23444443333    3333443333111111111000 0001111122223


Q ss_pred             HHhc--CCceEEEEEeCCCC
Q 048347          116 HNYL--KNKRYLIVIQDVWR  133 (351)
Q Consensus       116 ~~~L--~~k~~LlVLDdv~~  133 (351)
                      .+++  .++.+||++|++-.
T Consensus       495 Ae~fre~G~dVlillDSlTR  514 (672)
T PRK12678        495 AKRLVELGKDVVVLLDSITR  514 (672)
T ss_pred             HHHHHHcCCCEEEEEeCchH
Confidence            3444  68999999999943

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.21  E-value=0.018  Score=49.21  Aligned_cols=24  Identities=17%  Similarity=0.187  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|+|++|+|||||++++...
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            578899999999999999999887

>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=95.20  E-value=0.021  Score=51.76  Aligned_cols=23  Identities=13%  Similarity=0.003  Sum_probs=18.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|.|.|.+|+||||+|+++...
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH
Confidence            46889999999999999999887

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.20  E-value=0.027  Score=49.56  Aligned_cols=24  Identities=8%  Similarity=0.101  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      +-.++||+|.+|.||||||+.+.-
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhc
Confidence            346899999999999999999854

>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=95.20  E-value=0.015  Score=47.60  Aligned_cols=21  Identities=19%  Similarity=0.229  Sum_probs=19.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|+.|+||||+|+.+...
T Consensus         2 i~l~G~~GsGKstla~~la~~   22 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKA   22 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            678999999999999999877

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.

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=95.19  E-value=0.019  Score=44.24  Aligned_cols=22  Identities=23%  Similarity=0.126  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHh
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      -..++|.|+.|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4678999999999999999986

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.19  E-value=0.035  Score=53.77  Aligned_cols=91  Identities=9%  Similarity=0.152  Sum_probs=54.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC--ccCCCC-CHH-----H
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL--SEILDN-DFE-----M  110 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~--~~~~~~-~~~-----~  110 (351)
                      ..++|.|.+|+|||+|+.++....+ +.+-+.++++-+.   -.+.++..++...=..+...  ...... ...     .
T Consensus       139 Qr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~  217 (449)
T TIGR03305       139 GKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGH  217 (449)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHH
Confidence            5689999999999999999877722 2233567777666   56666777765432111100  000111 111     1


Q ss_pred             HHHHHHHhcC---CceEEEEEeCCCC
Q 048347          111 KKNTLHNYLK---NKRYLIVIQDVWR  133 (351)
Q Consensus       111 ~~~~l~~~L~---~k~~LlVLDdv~~  133 (351)
                      ..-.+.++++   +++.|+++||+-.
T Consensus       218 ~a~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       218 TALTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHHHhcCCceEEEecChHH
Confidence            2334455554   5899999999943

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=95.19  E-value=0.071  Score=51.80  Aligned_cols=89  Identities=11%  Similarity=0.191  Sum_probs=52.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCC-CeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHH-----
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYF-DCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFE-----  109 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~-----  109 (351)
                      ..++|.|..|+|||||+..+...  ..... +.++++-+.   -.+.++..++...-..+...   ...+.....     
T Consensus       145 QR~gIfa~~GvGKt~Ll~~i~~~--~~~~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~  222 (463)
T PRK09280        145 GKIGLFGGAGVGKTVLIQELINN--IAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVA  222 (463)
T ss_pred             CEEEeecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            56899999999999999988666  22221 345555554   66667777776542211100   000111111     


Q ss_pred             HHHHHHHHhc---CCceEEEEEeCCC
Q 048347          110 MKKNTLHNYL---KNKRYLIVIQDVW  132 (351)
Q Consensus       110 ~~~~~l~~~L---~~k~~LlVLDdv~  132 (351)
                      ...-.+.+++   ++++.|+++|++-
T Consensus       223 ~~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        223 LTGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHHhcCCceEEEecchH
Confidence            1123345555   5799999999994

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.19  E-value=0.19  Score=44.96  Aligned_cols=45  Identities=13%  Similarity=0.072  Sum_probs=32.8

Q ss_pred             cccchhhHHHHHHHHHcc----C-------CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           20 DLDLEDKMEELLDLLIER----Q-------PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~----~-------~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +=|-.+.++++.+.+...    +       +..+=|-.+|+.|.|||.+|++|.|+
T Consensus       179 vggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanr  234 (435)
T KOG0729|consen  179 VGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANR  234 (435)
T ss_pred             ccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcc
Confidence            445677777777765322    0       22345668999999999999999999

>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=95.17  E-value=0.016  Score=45.21  Aligned_cols=23  Identities=13%  Similarity=0.446  Sum_probs=19.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCCcc
Q 048347           44 VAIIDTMGFDRTAFIGEAYNSSY   66 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~~~   66 (351)
                      |.|+|..|+|||||.+.+.....
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            67899999999999999987743

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.

>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=95.15  E-value=0.031  Score=47.38  Aligned_cols=44  Identities=11%  Similarity=0.036  Sum_probs=30.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHH
Q 048347           44 VAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDA   89 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~   89 (351)
                      +.|.|.+|+|||+||.++...  .-..=..++|++...+..++.+.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~--~~~~g~~v~~~s~e~~~~~~~~~   45 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYA--GLARGEPGLYVTLEESPEELIEN   45 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH--HHHCCCcEEEEECCCCHHHHHHH
Confidence            568899999999999987665  22222456777665555555544

A related protein is found in archaea.

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=95.14  E-value=0.046  Score=52.61  Aligned_cols=25  Identities=16%  Similarity=0.274  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-..++|+|..|+|||||++.+...
T Consensus       136 ~Gqri~I~G~sG~GKTtLl~~i~~~  160 (413)
T TIGR03497       136 KGQRVGIFAGSGVGKSTLLGMIARN  160 (413)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999998886

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=95.12  E-value=0.043  Score=50.87  Aligned_cols=99  Identities=15%  Similarity=0.045  Sum_probs=57.5

Q ss_pred             HHHHHHHccC-CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCc-cCCCC
Q 048347           29 ELLDLLIERQ-PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALS-EILDN  106 (351)
Q Consensus        29 ~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~-~~~~~  106 (351)
                      .|-..|-.++ ++-+++-|+|..|+||||||-++...  ....-..++||...   ..+-...+..++.+...- -....
T Consensus        40 ~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e---~~ld~~~a~~lGvdl~rllv~~P~  114 (322)
T PF00154_consen   40 ALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAE---HALDPEYAESLGVDLDRLLVVQPD  114 (322)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESS---S---HHHHHHTT--GGGEEEEE-S
T ss_pred             ccchhhccCccccCceEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCc---ccchhhHHHhcCccccceEEecCC
Confidence            3444443232 56689999999999999999998877  54455568898865   123334455555433210 01234


Q ss_pred             CHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          107 DFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       107 ~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                      ..++....+...++. .--++|+|-|-
T Consensus       115 ~~E~al~~~e~lirsg~~~lVVvDSv~  141 (322)
T PF00154_consen  115 TGEQALWIAEQLIRSGAVDLVVVDSVA  141 (322)
T ss_dssp             SHHHHHHHHHHHHHTTSESEEEEE-CT
T ss_pred             cHHHHHHHHHHHhhcccccEEEEecCc
Confidence            456666666666654 34588999984

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.10  E-value=0.013  Score=48.77  Aligned_cols=21  Identities=5%  Similarity=0.189  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|+.|+||||+|+.+...
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            468899999999999999887

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.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.10  E-value=0.018  Score=50.06  Aligned_cols=26  Identities=15%  Similarity=0.317  Sum_probs=23.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++++|+++|..|+|||||.+++...
T Consensus        20 ~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        20 HGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             cCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            46999999999999999999998876

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.10  E-value=0.046  Score=49.82  Aligned_cols=31  Identities=13%  Similarity=0.284  Sum_probs=26.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      .+..++.|.|..|+|||||++++.+.  .+...
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~--l~~~~  132 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMR--LKDSV  132 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--hccCC
Confidence            46899999999999999999999888  54443

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

Probab=95.06  E-value=0.016  Score=55.73  Aligned_cols=48  Identities=15%  Similarity=0.086  Sum_probs=35.2

Q ss_pred             CCccccchhhHHHHHHHHHcc------------C--CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER------------Q--PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~------------~--~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..++|.|+-++.+...+...            +  ..-.-+.++|+.|+|||++|+.+...
T Consensus        70 ~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~  131 (412)
T PRK05342         70 DQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARI  131 (412)
T ss_pred             hhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            356899999888886555211            0  01245778999999999999999876

>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=95.05  E-value=0.016  Score=51.62  Aligned_cols=32  Identities=16%  Similarity=0.071  Sum_probs=20.9

Q ss_pred             EEcCCCChHHHHHHHHhCCcccccCCCeeEEEEE
Q 048347           46 IIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYY   79 (351)
Q Consensus        46 I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~   79 (351)
                      |+||+|+||||+++.+.+.  ....-..++-|+.
T Consensus         1 ViGpaGSGKTT~~~~~~~~--~~~~~~~~~~vNL   32 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEW--LESNGRDVYIVNL   32 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHH--HTTT-S-EEEEE-
T ss_pred             CCCCCCCCHHHHHHHHHHH--HHhccCCceEEEc
Confidence            6899999999999999887  3333333344443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.05  E-value=0.048  Score=50.57  Aligned_cols=94  Identities=12%  Similarity=0.144  Sum_probs=51.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHh
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNY  118 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~  118 (351)
                      -..+.|.|..|+|||||++.+...  +..... .+.+.-.  .....  .....-......    .....-...+.++..
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~--~~~~~~-iv~ied~~El~~~~--~~~~~l~~~~~~----~~~~~~~~~~~l~~~  214 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDE--IPKDER-IITIEDTREIFLPH--PNYVHLFYSKGG----QGLAKVTPKDLLQSC  214 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcc--CCcccc-EEEEcCccccCCCC--CCEEEEEecCCC----CCcCccCHHHHHHHH
Confidence            468889999999999999999877  333222 2222111  11110  000000000000    111122345666777


Q ss_pred             cCCceEEEEEeCCCChhhHHHHHhh
Q 048347          119 LKNKRYLIVIQDVWRGDIWDFLKEA  143 (351)
Q Consensus       119 L~~k~~LlVLDdv~~~~~~~~l~~~  143 (351)
                      |+...=.+++|.+...+.++.+...
T Consensus       215 Lr~~pd~ii~gE~r~~e~~~~l~a~  239 (308)
T TIGR02788       215 LRMRPDRIILGELRGDEAFDFIRAV  239 (308)
T ss_pred             hcCCCCeEEEeccCCHHHHHHHHHH
Confidence            8888888999999987777644333

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.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.04  E-value=0.02  Score=49.43  Aligned_cols=24  Identities=17%  Similarity=0.110  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|.|++|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999988

>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=95.03  E-value=0.016  Score=49.57  Aligned_cols=22  Identities=14%  Similarity=0.152  Sum_probs=20.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|+.|+||||+++.+.+.
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~   23 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAER   23 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999999888

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

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.03  E-value=0.049  Score=52.40  Aligned_cols=24  Identities=13%  Similarity=0.202  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|.|..|+|||||++.+...
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~  160 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARY  160 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            357899999999999999999877

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon

Probab=95.02  E-value=0.018  Score=51.08  Aligned_cols=23  Identities=17%  Similarity=0.307  Sum_probs=20.6

Q ss_pred             EEEEEEcC-CCChHHHHHHHHhCC
Q 048347           42 SLVAIIDT-MGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~-gGiGKTtLa~~v~~~   64 (351)
                      ++|+|+|+ ||+||||++..+..-
T Consensus         2 ~~iai~s~kGGvG~TTltAnLA~a   25 (243)
T PF06564_consen    2 KVIAIVSPKGGVGKTTLTANLAWA   25 (243)
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHH
Confidence            68999999 999999999988765

It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.02  E-value=0.12  Score=51.69  Aligned_cols=57  Identities=16%  Similarity=-0.021  Sum_probs=41.3

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      +.+.-+++=|.|+-+.+|.+.+...           -+..+=|-.+|++|.|||++|+++.+.  ..-.|
T Consensus       429 p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne--~~~nF  496 (693)
T KOG0730|consen  429 PNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANE--AGMNF  496 (693)
T ss_pred             CCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhh--hcCCe
Confidence            4454455566888888887766532           134566778999999999999999999  44444

>TIGR00991 3a0901s02IAP34 GTP-binding protein (Chloroplast Envelope Protein Translocase)

Probab=95.02  E-value=0.045  Score=50.37  Aligned_cols=40  Identities=15%  Similarity=0.262  Sum_probs=29.9

Q ss_pred             hHHHHHHHH---HccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           26 KMEELLDLL---IERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        26 ~~~~l~~~L---~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ...+|.++|   .+.+.....|.|+|.+|+|||+++..+....
T Consensus        20 tq~~l~~~l~~l~~~~~~~~rIllvGktGVGKSSliNsIlG~~   62 (313)
T TIGR00991        20 TQTKLLELLGKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGER   62 (313)
T ss_pred             HHHHHHHHHHhcccccccceEEEEECCCCCCHHHHHHHHhCCC
Confidence            344555555   4445556678899999999999999998763

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.02  E-value=0.017  Score=47.87  Aligned_cols=22  Identities=14%  Similarity=0.274  Sum_probs=20.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |++|+|+.|+|||||+.++...
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~   22 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKA   22 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999987

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

>PRK14530 adenylate kinase; Provisional

Probab=95.01  E-value=0.018  Score=50.34  Aligned_cols=23  Identities=4%  Similarity=0.078  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|+|+.|+||||+|+.+...
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            36889999999999999999876

>PRK13946 shikimate kinase; Provisional

Probab=95.00  E-value=0.016  Score=49.45  Aligned_cols=23  Identities=13%  Similarity=0.160  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.+.|+.|+||||+|+.+.+.
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~~   33 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLATM   33 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999988

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=94.99  E-value=0.14  Score=49.68  Aligned_cols=88  Identities=11%  Similarity=0.101  Sum_probs=48.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHH-----
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFE-----  109 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~-----  109 (351)
                      -..++|+|..|+|||||++.+...  ..  .+.++...+.   .++.++...+...-......   ..-+.....     
T Consensus       168 GqrigI~G~sG~GKSTLl~~I~g~--~~--~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~  243 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRF--TE--ADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAA  243 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC--CC--CCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHH
Confidence            357899999999999999999876  21  2233333333   44555555554332211100   000111111     


Q ss_pred             ----HHHHHHHHhcCCceEEEEEeCCCCh
Q 048347          110 ----MKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus       110 ----~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                          .+.+.+++  ++++.|+++||+-..
T Consensus       244 ~~a~aiAEyfrd--~G~~VLl~~DslTR~  270 (451)
T PRK05688        244 MYCTRIAEYFRD--KGKNVLLLMDSLTRF  270 (451)
T ss_pred             HHHHHHHHHHHH--CCCCEEEEecchhHH
Confidence                12344443  589999999999543

>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=94.99  E-value=0.022  Score=45.72  Aligned_cols=23  Identities=17%  Similarity=0.309  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||.+.++..
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEEccCCCccccceeeeccc
Confidence            58899999999999999999776

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 ....

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=94.98  E-value=0.018  Score=47.93  Aligned_cols=20  Identities=30%  Similarity=0.298  Sum_probs=18.7

Q ss_pred             EEEEEcCCCChHHHHHHHHh
Q 048347           43 LVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~   62 (351)
                      .|+|.|.+|+||||+|+.+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58899999999999999987

>TIGR01351 adk adenylate kinases

Probab=94.97  E-value=0.11  Score=45.17  Aligned_cols=21  Identities=5%  Similarity=0.086  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKsT~a~~La~~   22 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEK   22 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668999999999999999876

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.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=94.97  E-value=0.26  Score=49.06  Aligned_cols=119  Identities=14%  Similarity=0.092  Sum_probs=61.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcc-cccCCCeeEEEEEe--------CC----H------------HHHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSY-VKNYFDCCAWVYYQ--------LS----L------------DMMLDAIMKSLM   95 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~~~--------~~----~------------~~~~~~i~~~~~   95 (351)
                      -..|+|+|+.|+|||||.+.+..... .......-.-+.++        ..    +            +.-.+..+.++.
T Consensus       348 g~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~  427 (530)
T COG0488         348 GDRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFG  427 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcC
Confidence            35789999999999999999965511 11111000001122        01    0            122222222222


Q ss_pred             CCCCC--ccCC-CCCHHHHHHHHHHhcCCceEEEEEeCCCCh---hhHHHHHhhcCCCCCCcEEEEEeecc
Q 048347           96 PLSAL--SEIL-DNDFEMKKNTLHNYLKNKRYLIVIQDVWRG---DIWDFLKEALPDHQNGSRILTALIHI  160 (351)
Q Consensus        96 ~~~~~--~~~~-~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~---~~~~~l~~~l~~~~~gs~IivTR~~~  160 (351)
                      -....  ..+. ....+...-.+...+-.+.-++|||.=-+.   +..+.+..++.... |+.|+||.++.
T Consensus       428 F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f~-Gtvl~VSHDr~  497 (530)
T COG0488         428 FTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDFE-GTVLLVSHDRY  497 (530)
T ss_pred             CChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhCC-CeEEEEeCCHH
Confidence            21110  0012 223333445556667788899999965444   34455555555443 77777688775

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.96  E-value=0.07  Score=51.96  Aligned_cols=101  Identities=18%  Similarity=0.103  Sum_probs=58.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      +..-+-+.|++|+|||+||..+...    ..|+.+--++    ++++.       +-.      +..-...+.+...+..
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKiiS----pe~mi-------G~s------EsaKc~~i~k~F~DAY  595 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKIIS----PEDMI-------GLS------ESAKCAHIKKIFEDAY  595 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEeC----hHHcc-------Ccc------HHHHHHHHHHHHHHhh
Confidence            4455667899999999999999987    4555422221    11110       000      1122233455556666


Q ss_pred             CCceEEEEEeCCCChhhHH------------HHHhhcC-CCCCCcEEEE-Eeeccc
Q 048347          120 KNKRYLIVIQDVWRGDIWD------------FLKEALP-DHQNGSRILT-ALIHIV  161 (351)
Q Consensus       120 ~~k~~LlVLDdv~~~~~~~------------~l~~~l~-~~~~gs~Iiv-TR~~~v  161 (351)
                      ++.--.+|+||+...-+|-            .+...+. ...+|-|.+| +-...+
T Consensus       596 kS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~  651 (744)
T KOG0741|consen  596 KSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRR  651 (744)
T ss_pred             cCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHH
Confidence            7788899999997664443            3333343 2455777777 444444

>PRK13768 GTPase; Provisional

Probab=94.94  E-value=0.024  Score=50.98  Aligned_cols=23  Identities=17%  Similarity=0.197  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++.|+|+||+||||++..+...
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~~   25 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSDW   25 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHHH
Confidence            57889999999999999887665

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=94.94  E-value=0.018  Score=48.24  Aligned_cols=22  Identities=14%  Similarity=0.190  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++||.|+||||+.+++...
T Consensus         4 ~IvLiG~mGaGKSTIGr~LAk~   25 (172)
T COG0703           4 NIVLIGFMGAGKSTIGRALAKA   25 (172)
T ss_pred             cEEEEcCCCCCHhHHHHHHHHH
Confidence            4678999999999999999876

>PRK04182 cytidylate kinase; Provisional

Probab=94.94  E-value=0.018  Score=48.52  Aligned_cols=22  Identities=14%  Similarity=0.143  Sum_probs=20.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|.|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~   23 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999887

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=94.94  E-value=0.044  Score=52.92  Aligned_cols=24  Identities=13%  Similarity=0.255  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -..++|.|..|+|||||++.+...
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~  180 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKG  180 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhc
Confidence            458899999999999999999876

>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=94.93  E-value=0.0097  Score=47.25  Aligned_cols=27  Identities=19%  Similarity=0.188  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCCcccccCCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNSSYVKNYFD   72 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~~~~~~~F~   72 (351)
                      |-++|..|+||||+|+.+...  +...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~~--~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS--LGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH--TT--EE
T ss_pred             EeeECCCccHHHHHHHHHHHH--cCCcee
Confidence            458999999999999999988  555553

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=94.92  E-value=0.062  Score=50.65  Aligned_cols=93  Identities=11%  Similarity=0.124  Sum_probs=54.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      -..+.|.|+.|+||||+++.+...  +..+...+++.--. .++-..... ..+..+..   . ..+.....+.++..|+
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~--i~~~~~~~i~tiEd-p~E~~~~~~-~~~i~q~e---v-g~~~~~~~~~l~~~lr  193 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDY--INKNAAGHIITIED-PIEYVHRNK-RSLINQRE---V-GLDTLSFANALRAALR  193 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh--hCcCCCCEEEEEcC-ChhhhccCc-cceEEccc---c-CCCCcCHHHHHHHhhc
Confidence            368889999999999999998876  55444444443211 111110000 00000000   1 1122345667788888


Q ss_pred             CceEEEEEeCCCChhhHHHHH
Q 048347          121 NKRYLIVIQDVWRGDIWDFLK  141 (351)
Q Consensus       121 ~k~~LlVLDdv~~~~~~~~l~  141 (351)
                      ...=.+++|.+.+.+.+....
T Consensus       194 ~~pd~i~vgEird~~~~~~~l  214 (343)
T TIGR01420       194 EDPDVILIGEMRDLETVELAL  214 (343)
T ss_pred             cCCCEEEEeCCCCHHHHHHHH
Confidence            888899999998877665433

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.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=94.92  E-value=0.097  Score=50.59  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|.|..|+|||||++.+...
T Consensus       154 ~GQ~igI~G~sGaGKSTLl~~I~g~  178 (434)
T PRK07196        154 KGQRVGLMAGSGVGKSVLLGMITRY  178 (434)
T ss_pred             cceEEEEECCCCCCccHHHHHHhcc
Confidence            3467999999999999999998876

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=94.90  E-value=0.0031  Score=50.59  Aligned_cols=83  Identities=23%  Similarity=0.136  Sum_probs=66.9

Q ss_pred             CCCCCCceEEEEecccccCceeeeCC-CCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGH-GGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~-~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      +.....|...+|+.|.  .+.+|..+ ..|+..+.|++++| .+.++|.++..++.|+.|++++ +.+...|+-|..|.+
T Consensus        49 l~~~~el~~i~ls~N~--fk~fp~kft~kf~t~t~lNl~~n-eisdvPeE~Aam~aLr~lNl~~-N~l~~~p~vi~~L~~  124 (177)
T KOG4579|consen   49 LSKGYELTKISLSDNG--FKKFPKKFTIKFPTATTLNLANN-EISDVPEELAAMPALRSLNLRF-NPLNAEPRVIAPLIK  124 (177)
T ss_pred             HhCCceEEEEecccch--hhhCCHHHhhccchhhhhhcchh-hhhhchHHHhhhHHhhhccccc-CccccchHHHHHHHh
Confidence            3456778888995443  33566553 45678999999999 7999999999999999999998 568889999999999


Q ss_pred             CCEEEecC
Q 048347          317 LRKLESWW  324 (351)
Q Consensus       317 L~~L~l~~  324 (351)
                      |-.|+.-+
T Consensus       125 l~~Lds~~  132 (177)
T KOG4579|consen  125 LDMLDSPE  132 (177)
T ss_pred             HHHhcCCC
Confidence            98888765

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=94.90  E-value=0.098  Score=54.08  Aligned_cols=99  Identities=14%  Similarity=0.005  Sum_probs=62.3

Q ss_pred             HHHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCc-c
Q 048347           27 MEELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALS-E  102 (351)
Q Consensus        27 ~~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~-~  102 (351)
                      ...|-.+|- .+=++-+++-|.|..|+||||||.+++..  ....-..++|++..  ++     ...+++++.+...- -
T Consensus        45 i~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~--a~~~G~~v~yId~E~t~~-----~~~A~~lGvDl~~llv  117 (790)
T PRK09519         45 SIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFIDAEHALD-----PDYAKKLGVDTDSLLV  117 (790)
T ss_pred             cHHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchh-----HHHHHHcCCChhHeEE
Confidence            344555554 23356788889999999999999887665  22333557888765  33     24667776543210 0


Q ss_pred             CCCCCHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          103 ILDNDFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                      ....+.+++...+...++. +--++|+|.+-
T Consensus       118 ~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        118 SQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             ecCCCHHHHHHHHHHHhhcCCCeEEEEcchh
Confidence            2334455666666666644 55689999984

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

Probab=94.89  E-value=0.089  Score=43.65  Aligned_cols=117  Identities=6%  Similarity=-0.126  Sum_probs=59.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCC-----CCccCCCCCH-------
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLS-----ALSEILDNDF-------  108 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~-----~~~~~~~~~~-------  108 (351)
                      ..|-|++-.|.||||+|-...-+  .-.+=..+.++.+- -....--..+++.+..-.     ........+.       
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~r--a~~~g~~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a   80 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALR--ALGHGYRVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAA   80 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHH
Confidence            46778888899999999887666  33333344555544 111111222333332100     0000000111       


Q ss_pred             HHHHHHHHHhcCCc-eEEEEEeCCCCh-----hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347          109 EMKKNTLHNYLKNK-RYLIVIQDVWRG-----DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus       109 ~~~~~~l~~~L~~k-~~LlVLDdv~~~-----~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      ....+..++.++.. -=|+|||++-..     -..+.+...+.....+.-+|+ .|+..
T Consensus        81 ~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          81 AEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            11233344555443 449999999544     234555555555555666777 77654

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.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=94.89  E-value=0.022  Score=46.87  Aligned_cols=22  Identities=14%  Similarity=0.193  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+++|.+|+|||||++.+...
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~   23 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYD   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4778999999999999999866

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

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

Probab=94.88  E-value=0.086  Score=47.72  Aligned_cols=107  Identities=12%  Similarity=0.129  Sum_probs=58.0

Q ss_pred             ccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCC
Q 048347           21 LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLS   98 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~   98 (351)
                      .|..++..+....+....  ..+|.|.|..|.||||+++.+.+.  +...-..++-+.-.  +....+     .|+..  
T Consensus        62 lg~~~~~~~~l~~~~~~~--~GlilisG~tGSGKTT~l~all~~--i~~~~~~iitiEdp~E~~~~~~-----~q~~v--  130 (264)
T cd01129          62 LGLKPENLEIFRKLLEKP--HGIILVTGPTGSGKTTTLYSALSE--LNTPEKNIITVEDPVEYQIPGI-----NQVQV--  130 (264)
T ss_pred             cCCCHHHHHHHHHHHhcC--CCEEEEECCCCCcHHHHHHHHHhh--hCCCCCeEEEECCCceecCCCc-----eEEEe--
Confidence            454444444333333322  357889999999999999988766  43221122222211  111100     01111  


Q ss_pred             CCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCChhhHHHHHhh
Q 048347           99 ALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEA  143 (351)
Q Consensus        99 ~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~~~~l~~~  143 (351)
                           .........+.++..|+...=.++++++.+.+....+...
T Consensus       131 -----~~~~~~~~~~~l~~~lR~~PD~i~vgEiR~~e~a~~~~~a  170 (264)
T cd01129         131 -----NEKAGLTFARGLRAILRQDPDIIMVGEIRDAETAEIAVQA  170 (264)
T ss_pred             -----CCcCCcCHHHHHHHHhccCCCEEEeccCCCHHHHHHHHHH
Confidence                 1111123566777778877888999999887655444333

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.87  E-value=0.046  Score=48.43  Aligned_cols=50  Identities=16%  Similarity=0.148  Sum_probs=33.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAI   90 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i   90 (351)
                      ++-.++.|.|..|+||||||.++.... .+.. ..+++++..-+..++.+.+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~-~~~g-~~~~yi~~e~~~~~~~~~~   71 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGF-LQNG-YSVSYVSTQLTTTEFIKQM   71 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH-HhCC-CcEEEEeCCCCHHHHHHHH
Confidence            445699999999999999987665542 2232 3445665335556666665

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=94.86  E-value=0.015  Score=56.28  Aligned_cols=82  Identities=18%  Similarity=0.177  Sum_probs=34.0

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      ++.+.+|..|++  ..-.++.+...+..+++|++|++++| .++.+. .+..+..|+.|++.+| .+..++ ++..+.+|
T Consensus        91 l~~~~~l~~l~l--~~n~i~~i~~~l~~~~~L~~L~ls~N-~I~~i~-~l~~l~~L~~L~l~~N-~i~~~~-~~~~l~~L  164 (414)
T KOG0531|consen   91 LSKLKSLEALDL--YDNKIEKIENLLSSLVNLQVLDLSFN-KITKLE-GLSTLTLLKELNLSGN-LISDIS-GLESLKSL  164 (414)
T ss_pred             cccccceeeeec--cccchhhcccchhhhhcchheecccc-cccccc-chhhccchhhheeccC-cchhcc-CCccchhh
Confidence            344444555555  22222222222344455555555554 344444 2444444555555442 233222 23334444


Q ss_pred             CEEEecCC
Q 048347          318 RKLESWWP  325 (351)
Q Consensus       318 ~~L~l~~~  325 (351)
                      +.+++++.
T Consensus       165 ~~l~l~~n  172 (414)
T KOG0531|consen  165 KLLDLSYN  172 (414)
T ss_pred             hcccCCcc
Confidence            44444443

>smart00072 GuKc Guanylate kinase homologues

Probab=94.86  E-value=0.027  Score=47.94  Aligned_cols=24  Identities=8%  Similarity=0.213  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.|.|+|+.|+||+|+++.+...
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~   25 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQE   25 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhc
Confidence            367889999999999999999888

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.

>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=94.83  E-value=0.026  Score=43.90  Aligned_cols=21  Identities=24%  Similarity=0.327  Sum_probs=19.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+|+|+.|+|||||.+.+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999974

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 ....

>PRK09099 type III secretion system ATPase; Provisional

Probab=94.81  E-value=0.07  Score=51.70  Aligned_cols=91  Identities=11%  Similarity=0.163  Sum_probs=49.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHH----
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFE----  109 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~----  109 (351)
                      +-.+++|.|..|+|||||++.+....+  .  +....+-+.   -.+.++...+...-......   ..-+.....    
T Consensus       162 ~Gq~~~I~G~sG~GKTtLl~~ia~~~~--~--d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a  237 (441)
T PRK09099        162 EGQRMGIFAPAGVGKSTLMGMFARGTQ--C--DVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKA  237 (441)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC--C--CeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHH
Confidence            346789999999999999999987732  2  222222223   55555555554332111000   000111111    


Q ss_pred             -HHHHHHHHhc--CCceEEEEEeCCCCh
Q 048347          110 -MKKNTLHNYL--KNKRYLIVIQDVWRG  134 (351)
Q Consensus       110 -~~~~~l~~~L--~~k~~LlVLDdv~~~  134 (351)
                       ...-.+.+++  ++++.|+++|++-..
T Consensus       238 ~~~a~tiAEyfrd~G~~VLl~~DslTr~  265 (441)
T PRK09099        238 AYVATAIAEYFRDRGLRVLLMMDSLTRF  265 (441)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchhHH
Confidence             1122233333  489999999999443

>PRK14527 adenylate kinase; Provisional

Probab=94.81  E-value=0.021  Score=48.91  Aligned_cols=26  Identities=8%  Similarity=0.038  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      +..+|.|.|++|+||||+|+.+.+..
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998763

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=94.80  E-value=0.024  Score=48.03  Aligned_cols=23  Identities=4%  Similarity=-0.000  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+||||+++.+...
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~   26 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAAL   26 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999999987

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=94.77  E-value=0.03  Score=46.39  Aligned_cols=50  Identities=14%  Similarity=0.085  Sum_probs=33.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSAL  100 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~  100 (351)
                      .+++.|+|.+|+||||+.+.+-..  .  -+...      .+.-++.-+++..-+.....
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~--l--~~~~i------vNyG~~Mle~A~k~glve~r   53 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKE--L--VKHKI------VNYGDLMLEIAKKKGLVEHR   53 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHH--H--hhcee------eeHhHHHHHHHHHhCCcccH
Confidence            579999999999999998887666  2  11111      24456666777766665443

>cd04163 Era Era subfamily

Probab=94.77  E-value=0.032  Score=45.65  Aligned_cols=24  Identities=13%  Similarity=0.274  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+++|..|+|||||++++...
T Consensus         3 ~~~i~~~G~~g~GKttl~~~l~~~   26 (168)
T cd04163           3 SGFVAIVGRPNVGKSTLLNALVGQ   26 (168)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999999998765

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.

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

Probab=94.76  E-value=0.071  Score=52.85  Aligned_cols=97  Identities=12%  Similarity=0.030  Sum_probs=59.3

Q ss_pred             CCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCH
Q 048347           15 WDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSL   83 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~   83 (351)
                      +.-.++.|.++..+.+.+.+...           -...+.+-++|+.|.|||+||+++.+.  ...+|-.+..    +  
T Consensus       239 v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~--~~~~fi~v~~----~--  310 (494)
T COG0464         239 VTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE--SRSRFISVKG----S--  310 (494)
T ss_pred             cceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhh--CCCeEEEeeC----H--
Confidence            33344566677766666655321           123557889999999999999999996  4444422211    0  


Q ss_pred             HHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           84 DMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        84 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                           ++...-         -...+..+.+.+....+...+.+.+|+++.
T Consensus       311 -----~l~sk~---------vGesek~ir~~F~~A~~~~p~iiFiDEiDs  346 (494)
T COG0464         311 -----ELLSKW---------VGESEKNIRELFEKARKLAPSIIFIDEIDS  346 (494)
T ss_pred             -----HHhccc---------cchHHHHHHHHHHHHHcCCCcEEEEEchhh
Confidence                 111111         122344555666666678899999999963

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=94.73  E-value=0.074  Score=54.50  Aligned_cols=47  Identities=11%  Similarity=0.030  Sum_probs=36.4

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|.+....++.+.+..-...-.-|-|+|..|+||+++|+.+++.
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHh
Confidence            45889888888877777543323334669999999999999999987

>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=94.73  E-value=0.065  Score=50.74  Aligned_cols=74  Identities=14%  Similarity=0.165  Sum_probs=45.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccc----ccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYV----KNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~----~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      .+=+-|||.-|.|||.|+-..|+...+    +-||+.            +..++-+.+..-..    ....    ...+.
T Consensus        62 ~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~------------Fm~~vh~~l~~~~~----~~~~----l~~va  121 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHE------------FMLDVHSRLHQLRG----QDDP----LPQVA  121 (362)
T ss_pred             CceEEEECCCCCchhHHHHHHHHhCCccccccccccH------------HHHHHHHHHHHHhC----CCcc----HHHHH
Confidence            445778999999999999999998443    223433            33333333322111    1112    44455


Q ss_pred             HhcCCceEEEEEeCCCCh
Q 048347          117 NYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus       117 ~~L~~k~~LlVLDdv~~~  134 (351)
                      +.+.++..+|++|.+.=.
T Consensus       122 ~~l~~~~~lLcfDEF~V~  139 (362)
T PF03969_consen  122 DELAKESRLLCFDEFQVT  139 (362)
T ss_pred             HHHHhcCCEEEEeeeecc
Confidence            666677779999988533

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

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

Probab=94.73  E-value=0.047  Score=46.61  Aligned_cols=110  Identities=12%  Similarity=0.073  Sum_probs=57.3

Q ss_pred             hhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCC
Q 048347           25 DKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEIL  104 (351)
Q Consensus        25 ~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~  104 (351)
                      ++..++.......   -..+.|.|..|+||||+++.+..-  +..... .+-+  . +..++...-...+..........
T Consensus        12 ~~~~~~l~~~v~~---g~~i~I~G~tGSGKTTll~aL~~~--i~~~~~-~i~i--e-d~~E~~~~~~~~~~~~~~~~~~~   82 (186)
T cd01130          12 PLQAAYLWLAVEA---RKNILISGGTGSGKTTLLNALLAF--IPPDER-IITI--E-DTAELQLPHPNWVRLVTRPGNVE   82 (186)
T ss_pred             HHHHHHHHHHHhC---CCEEEEECCCCCCHHHHHHHHHhh--cCCCCC-EEEE--C-CccccCCCCCCEEEEEEecCCCC
Confidence            3444444444433   358899999999999999998876  332221 1111  1 11110000000000000000001


Q ss_pred             CCCHHHHHHHHHHhcCCceEEEEEeCCCChhhHHHHHhh
Q 048347          105 DNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEA  143 (351)
Q Consensus       105 ~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~~~~l~~~  143 (351)
                      ........+.++..++..+=.++++.+.+.+.+..+...
T Consensus        83 ~~~~~~~~~~l~~~lR~~pd~i~igEir~~ea~~~~~a~  121 (186)
T cd01130          83 GSGEVTMADLLRSALRMRPDRIIVGEVRGGEALDLLQAM  121 (186)
T ss_pred             CCCccCHHHHHHHHhccCCCEEEEEccCcHHHHHHHHHH
Confidence            112234556667777777778899999988877755543

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.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=94.71  E-value=0.026  Score=45.83  Aligned_cols=24  Identities=13%  Similarity=0.196  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      +.|-++|..|+|||||++.+-...
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            467789999999999999997763

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

>cd01862 Rab7 Rab7 subfamily

Probab=94.71  E-value=0.027  Score=46.82  Aligned_cols=22  Identities=23%  Similarity=0.400  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|+|.+|+|||||++++.+.
T Consensus         2 ki~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           2 KVIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3678999999999999998776

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>TIGR01287 nifH nitrogenase iron protein

Probab=94.71  E-value=0.022  Score=51.82  Aligned_cols=23  Identities=13%  Similarity=0.163  Sum_probs=19.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|+|.|-||+||||+|..+...
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~   23 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAA   23 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHH
Confidence            46889999999999988777655

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=94.70  E-value=0.018  Score=56.58  Aligned_cols=97  Identities=20%  Similarity=0.180  Sum_probs=58.1

Q ss_pred             CCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccCh-hhhcCCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPE-ELWRIKALR  318 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~L~  318 (351)
                      ..+|..|+| .++.-..--..++..++.||+|||+.| .+.++|.. +..=.++++|+|++ ..+..+-. .+..|.+|-
T Consensus       124 sghl~~L~L-~~N~I~sv~se~L~~l~alrslDLSrN-~is~i~~~sfp~~~ni~~L~La~-N~It~l~~~~F~~lnsL~  200 (873)
T KOG4194|consen  124 SGHLEKLDL-RHNLISSVTSEELSALPALRSLDLSRN-LISEIPKPSFPAKVNIKKLNLAS-NRITTLETGHFDSLNSLL  200 (873)
T ss_pred             ccceeEEee-eccccccccHHHHHhHhhhhhhhhhhc-hhhcccCCCCCCCCCceEEeecc-ccccccccccccccchhe
Confidence            345777777 333222112234667777888888887 67777764 55556788888887 45655543 245677888


Q ss_pred             EEEecCCC-----hhHHhhccccccCc
Q 048347          319 KLESWWPR-----PELRQSLHKFEEID  340 (351)
Q Consensus       319 ~L~l~~~~-----~~~~~~l~~~~~~~  340 (351)
                      +|.++.-.     .-...++.+++.++
T Consensus       201 tlkLsrNrittLp~r~Fk~L~~L~~Ld  227 (873)
T KOG4194|consen  201 TLKLSRNRITTLPQRSFKRLPKLESLD  227 (873)
T ss_pred             eeecccCcccccCHHHhhhcchhhhhh
Confidence            88887633     22233455555443

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.70  E-value=0.18  Score=51.32  Aligned_cols=99  Identities=11%  Similarity=0.048  Sum_probs=62.0

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc---------C-CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-C
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER---------Q-PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-L   81 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~---------~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~   81 (351)
                      |.+.=+++=|.|+-+.+|.+-+.-.         + .+.+=|-.+|+.|.|||.+||+|+..  .+     ..|++|- +
T Consensus       667 PnV~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATE--cs-----L~FlSVKGP  739 (953)
T KOG0736|consen  667 PNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATE--CS-----LNFLSVKGP  739 (953)
T ss_pred             CccchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhh--ce-----eeEEeecCH
Confidence            3333345567888888888777431         1 22344668999999999999999887  22     2345543 2


Q ss_pred             CHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh
Q 048347           82 SLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus        82 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                      .   ++.-   .+          ..+++...+...+.=..+.|.|.+|.+++.
T Consensus       740 E---LLNM---YV----------GqSE~NVR~VFerAR~A~PCVIFFDELDSl  776 (953)
T KOG0736|consen  740 E---LLNM---YV----------GQSEENVREVFERARSAAPCVIFFDELDSL  776 (953)
T ss_pred             H---HHHH---Hh----------cchHHHHHHHHHHhhccCCeEEEecccccc
Confidence            1   1111   11          123445555555555678999999999644

>PRK00698 tmk thymidylate kinase; Validated

Probab=94.69  E-value=0.025  Score=48.76  Aligned_cols=23  Identities=13%  Similarity=0.069  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|+|.|+.|+||||+++.+.+.
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~   26 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKEL   26 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999876

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=94.69  E-value=0.024  Score=47.26  Aligned_cols=22  Identities=14%  Similarity=0.143  Sum_probs=20.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|+.|+||||+|+.+.+.
T Consensus         2 iI~i~G~~GSGKstia~~la~~   23 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEK   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            7899999999999999999876

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.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=94.67  E-value=0.04  Score=49.93  Aligned_cols=38  Identities=21%  Similarity=0.275  Sum_probs=30.6

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++..+.....+..||||.|.+|+||+||...+-..
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~   74 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRE   74 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHH
Confidence            34566666666667889999999999999999887666

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=94.67  E-value=0.028  Score=51.07  Aligned_cols=28  Identities=7%  Similarity=0.152  Sum_probs=24.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      ++|+|+|.+|+|||||+.++...  .+...
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~--L~~~G   29 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDR--LSGRG   29 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--HHhCC
Confidence            58999999999999999999888  55554

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=94.67  E-value=0.32  Score=43.19  Aligned_cols=97  Identities=19%  Similarity=0.231  Sum_probs=58.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~  116 (351)
                      +-.++.|.|.-|+|||.+++.....  ..+.  .++=|.+.   .....+...|+.++..+...  .-.....++...+.
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s--~~~d--~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~--~~~~~~e~~~~~L~  123 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLAS--LNED--QVAVVVIDKPTLSDATLLEAIVADLESQPKV--NVNAVLEQIDRELA  123 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHh--cCCC--ceEEEEecCcchhHHHHHHHHHHHhccCccc--hhHHHHHHHHHHHH
Confidence            4568889999999999999955433  1111  12224444   77788999999999884320  01112222333333


Q ss_pred             Hhc-CCce-EEEEEeCCCCh--hhHHHHHh
Q 048347          117 NYL-KNKR-YLIVIQDVWRG--DIWDFLKE  142 (351)
Q Consensus       117 ~~L-~~k~-~LlVLDdv~~~--~~~~~l~~  142 (351)
                      ... ++++ ..+++|+....  +..+.++-
T Consensus       124 al~~~g~r~v~l~vdEah~L~~~~le~Lrl  153 (269)
T COG3267         124 ALVKKGKRPVVLMVDEAHDLNDSALEALRL  153 (269)
T ss_pred             HHHHhCCCCeEEeehhHhhhChhHHHHHHH
Confidence            333 5677 88888988644  44554443

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=94.66  E-value=0.075  Score=51.42  Aligned_cols=24  Identities=8%  Similarity=0.178  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -..++|.|..|+|||||++.+...
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~  198 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARY  198 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCC
Confidence            467899999999999999999877

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=94.64  E-value=0.028  Score=48.93  Aligned_cols=24  Identities=13%  Similarity=0.148  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.++.-
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G~   50 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNGL   50 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999765

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=94.63  E-value=0.12  Score=51.58  Aligned_cols=52  Identities=15%  Similarity=0.096  Sum_probs=37.5

Q ss_pred             CCCccccchhhHHHHHHHHH---ccC-------CCeEEEEEEcCCCChHHHHHHHHhCCccc
Q 048347           16 DNKVDLDLEDKMEELLDLLI---ERQ-------PQLSLVAIIDTMGFDRTAFIGEAYNSSYV   67 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~---~~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~   67 (351)
                      .-.++-|.|+.++++.+.+.   +..       .=.+=|..+|+.|.|||.||+++.....+
T Consensus       148 ~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~V  209 (596)
T COG0465         148 TFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGV  209 (596)
T ss_pred             ChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCC
Confidence            33567799888888766663   221       11344778899999999999999999544

>PLN02796 D-glycerate 3-kinase

Probab=94.63  E-value=0.071  Score=49.79  Aligned_cols=25  Identities=12%  Similarity=0.103  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-+|+|.|..|+||||||+.+...
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~l  123 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYL  123 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            5678999999999999999999887

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

Probab=94.62  E-value=0.031  Score=53.73  Aligned_cols=48  Identities=13%  Similarity=0.070  Sum_probs=35.7

Q ss_pred             CCccccchhhHHHHHHHHH-------c---cC--C----CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLI-------E---RQ--P----QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~-------~---~~--~----~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..++|.++-++.+...+.       .   ..  +    .-..+.++|+.|+|||++|+.+...
T Consensus        76 ~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~  139 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARI  139 (413)
T ss_pred             cceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHh
Confidence            4568999999988866552       1   11  1    1246889999999999999999876

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=94.62  E-value=0.16  Score=50.65  Aligned_cols=102  Identities=11%  Similarity=0.072  Sum_probs=58.9

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCC-------
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSA-------   99 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~-------   99 (351)
                      ...|-++|..+=++-.++.|.|..|+|||+||.++...  ....-+.++|++..-+..++.+.+ ..++-+..       
T Consensus       259 i~~lD~~l~GG~~~g~~~li~G~~G~GKT~l~~~~~~~--~~~~g~~~~yis~e~~~~~i~~~~-~~~g~~~~~~~~~g~  335 (509)
T PRK09302        259 VPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEA--ACRRGERCLLFAFEESRAQLIRNA-RSWGIDLEKMEEKGL  335 (509)
T ss_pred             cHHHHHhhcCCCCCCcEEEEEcCCCCCHHHHHHHHHHH--HHhCCCcEEEEEecCCHHHHHHHH-HHcCCChHHHhhcCC
Confidence            34455555334355678889999999999999998766  333446678887664455555443 34432110       


Q ss_pred             --C--ccCCCCCHHHHHHHHHHhcCC-ceEEEEEeCC
Q 048347          100 --L--SEILDNDFEMKKNTLHNYLKN-KRYLIVIQDV  131 (351)
Q Consensus       100 --~--~~~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv  131 (351)
                        .  ........+.....+.+.++. +.-++|+|.+
T Consensus       336 l~i~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDsl  372 (509)
T PRK09302        336 LKIICARPESYGLEDHLIIIKREIEEFKPSRVAIDPL  372 (509)
T ss_pred             ceeecCCcccCCHHHHHHHHHHHHHHcCCCEEEEcCH
Confidence              0  001222344555555555533 3346778877

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=94.62  E-value=0.032  Score=46.40  Aligned_cols=23  Identities=9%  Similarity=0.286  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+|..|+|||||++++...
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~   24 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPA   24 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999877

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=94.61  E-value=0.0037  Score=62.67  Aligned_cols=80  Identities=20%  Similarity=0.225  Sum_probs=45.9

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      .-++.|+.|+|++|.+..  .. .+..+++|+.|||++| .+..+|.--..=.+|+.|.+++ +.++.| .+|.+|++|+
T Consensus       184 qll~ale~LnLshNk~~~--v~-~Lr~l~~LkhLDlsyN-~L~~vp~l~~~gc~L~~L~lrn-N~l~tL-~gie~LksL~  257 (1096)
T KOG1859|consen  184 QLLPALESLNLSHNKFTK--VD-NLRRLPKLKHLDLSYN-CLRHVPQLSMVGCKLQLLNLRN-NALTTL-RGIENLKSLY  257 (1096)
T ss_pred             HHHHHhhhhccchhhhhh--hH-HHHhcccccccccccc-hhccccccchhhhhheeeeecc-cHHHhh-hhHHhhhhhh
Confidence            345677777775443322  11 3556666777777776 5666664211123477777776 345544 3667777777


Q ss_pred             EEEecC
Q 048347          319 KLESWW  324 (351)
Q Consensus       319 ~L~l~~  324 (351)
                      .||++.
T Consensus       258 ~LDlsy  263 (1096)
T KOG1859|consen  258 GLDLSY  263 (1096)
T ss_pred             ccchhH
Confidence            777654

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

Probab=94.60  E-value=0.05  Score=47.54  Aligned_cols=22  Identities=14%  Similarity=0.176  Sum_probs=16.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..|+|++|.||||++..+...
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~   40 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQ   40 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHHH
Confidence            7888999999999877666555

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

Probab=94.59  E-value=0.027  Score=41.70  Aligned_cols=22  Identities=9%  Similarity=0.256  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+.|.+|+||||++..+...
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~   22 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAA   22 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4678899999999999998877

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

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

Probab=94.59  E-value=0.019  Score=46.47  Aligned_cols=45  Identities=18%  Similarity=0.067  Sum_probs=32.1

Q ss_pred             ccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           21 LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ||.....+++.+.+..-.....-|-|.|..|+||+++|+.++...
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~   45 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYS   45 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhc
Confidence            566677777777775432334556789999999999999998873

>CHL00195 ycf46 Ycf46; Provisional

Probab=94.58  E-value=0.1  Score=51.40  Aligned_cols=47  Identities=11%  Similarity=-0.009  Sum_probs=31.6

Q ss_pred             CccccchhhHHHHHHHHHc--------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIE--------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~--------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++-|.+.-++.+.+....        +-+..+-|-++|+.|.|||.+|+.+.+.
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e  282 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAND  282 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            4466766655555442211        1123345778999999999999999887

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=94.58  E-value=0.14  Score=47.62  Aligned_cols=57  Identities=12%  Similarity=0.037  Sum_probs=42.5

Q ss_pred             CCccccchhhHHH---HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe
Q 048347           17 NKVDLDLEDKMEE---LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC   73 (351)
Q Consensus        17 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~   73 (351)
                      .+.+||-.+.++.   +++++.++--.-+-|-++|+.|.|||+||-.+....--.-.|-.
T Consensus        38 ~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~   97 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVA   97 (450)
T ss_pred             CCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCcee
Confidence            4568998777776   57777666444578889999999999999999888444445533

>PRK05922 type III secretion system ATPase; Validated

Probab=94.56  E-value=0.13  Score=49.65  Aligned_cols=96  Identities=9%  Similarity=0.133  Sum_probs=51.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCCHHH----
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDNDFEM----  110 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~~~~----  110 (351)
                      -..++|.|..|+|||||.+.+...  ...  +....+-++   ..+.+++.+.......+...   ..-+......    
T Consensus       157 GqrigI~G~nG~GKSTLL~~Ia~~--~~~--d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~  232 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKG--SKS--TINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAG  232 (434)
T ss_pred             CcEEEEECCCCCChHHHHHHHhcc--CCC--CceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHH
Confidence            356899999999999999999877  222  233333333   44455555554333221110   0001111111    


Q ss_pred             -HHHHHHHhc--CCceEEEEEeCCCCh-hhHHHH
Q 048347          111 -KKNTLHNYL--KNKRYLIVIQDVWRG-DIWDFL  140 (351)
Q Consensus       111 -~~~~l~~~L--~~k~~LlVLDdv~~~-~~~~~l  140 (351)
                       ..-.+.+++  ++++.|+++||+-.. .+...+
T Consensus       233 ~~a~tiAEyfrd~G~~VLl~~DslTR~A~A~REi  266 (434)
T PRK05922        233 RAAMTIAEYFRDQGHRVLFIMDSLSRWIAALQEV  266 (434)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchhHHHHHHHHH
Confidence             112233333  489999999999433 333444

>cd00879 Sar1 Sar1 subfamily

Probab=94.56  E-value=0.056  Score=45.92  Aligned_cols=25  Identities=4%  Similarity=0.056  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|+|+|.+|+|||||++.+...
T Consensus        18 ~~~ki~ilG~~~~GKStLi~~l~~~   42 (190)
T cd00879          18 KEAKILFLGLDNAGKTTLLHMLKDD   42 (190)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3455689999999999999999875

Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=94.55  E-value=0.03  Score=46.16  Aligned_cols=22  Identities=14%  Similarity=0.255  Sum_probs=19.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCCc
Q 048347           44 VAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      |.++|.+|+|||||+.++.+..
T Consensus         3 i~~vG~~~vGKTsli~~l~~~~   24 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEGR   24 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999998763

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.55  E-value=0.13  Score=43.28  Aligned_cols=82  Identities=9%  Similarity=-0.059  Sum_probs=44.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                      ++.|.|..|+||||+|..+...  ...   ...++.-. ....+..+.|..+.......-. ......++.+.+.....+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~--~~~---~~~~iat~~~~~~e~~~ri~~h~~~R~~~w~-t~E~~~~l~~~i~~~~~~   76 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQ--SGL---QVLYIATAQPFDDEMAARIAHHRQRRPAHWQ-TVEEPLDLAELLRADAAP   76 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHH--cCC---CcEeCcCCCCChHHHHHHHHHHHhcCCCCCe-EecccccHHHHHHhhcCC
Confidence            5789999999999999998766  211   12222222 4455666666655443211100 111122344445443433


Q ss_pred             ceEEEEEeCC
Q 048347          122 KRYLIVIQDV  131 (351)
Q Consensus       122 k~~LlVLDdv  131 (351)
                       .-++++|.+
T Consensus        77 -~~~VlID~L   85 (170)
T PRK05800         77 -GRCVLVDCL   85 (170)
T ss_pred             -CCEEEehhH
Confidence             336888887

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=94.55  E-value=0.026  Score=47.36  Aligned_cols=23  Identities=9%  Similarity=0.067  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|+|+.|+||||+|+.+...
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~   25 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQA   25 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            35778999999999999999887

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=94.55  E-value=0.03  Score=48.99  Aligned_cols=24  Identities=17%  Similarity=0.194  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+..-
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            468999999999999999999765

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>PRK08356 hypothetical protein; Provisional

Probab=94.54  E-value=0.037  Score=47.64  Aligned_cols=22  Identities=9%  Similarity=0.086  Sum_probs=19.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHh
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      ..+|+|.|+.|+||||+|+.+-
T Consensus         5 ~~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          5 KMIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             cEEEEEECCCCCCHHHHHHHHH
Confidence            3678999999999999999993

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=94.53  E-value=0.083  Score=46.19  Aligned_cols=23  Identities=9%  Similarity=0.164  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+++.|.|+-|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            47888999999999999999874

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

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=94.53  E-value=0.031  Score=47.27  Aligned_cols=24  Identities=13%  Similarity=0.191  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGL   49 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999866

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. 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.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=94.53  E-value=0.092  Score=50.91  Aligned_cols=90  Identities=12%  Similarity=0.163  Sum_probs=52.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC--ccCCCCC-HHH----
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL--SEILDND-FEM----  110 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~--~~~~~~~-~~~----  110 (351)
                      ..++|.|..|+|||||+..+...  .... =..++++-+.   -.+.+++.++...=..+...  -.....+ ...    
T Consensus       144 Qr~~If~~~G~GKt~L~~~~~~~--~~~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~  221 (461)
T TIGR01039       144 GKIGLFGGAGVGKTVLIQELINN--IAKEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVA  221 (461)
T ss_pred             CEEEeecCCCCChHHHHHHHHHH--HHhcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            56889999999999999998766  3222 1345555554   66677777775432111100  0001111 111    


Q ss_pred             -HHHHHHHhc---CCceEEEEEeCCCC
Q 048347          111 -KKNTLHNYL---KNKRYLIVIQDVWR  133 (351)
Q Consensus       111 -~~~~l~~~L---~~k~~LlVLDdv~~  133 (351)
                       ..-.+.+++   ++++.|+++|++-.
T Consensus       222 ~~a~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       222 LTGLTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEecchhH
Confidence             123445555   46899999999943

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=94.52  E-value=0.023  Score=54.51  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++.|+|+|..|+||||||+++...
T Consensus       218 ~~~~IvI~G~~gsGKTTL~~~La~~  242 (399)
T PRK08099        218 FVRTVAILGGESSGKSTLVNKLANI  242 (399)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4688999999999999999999876

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=94.52  E-value=0.029  Score=51.20  Aligned_cols=23  Identities=4%  Similarity=0.081  Sum_probs=19.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|+|+|-||+||||+|..+..-
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~   24 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAA   24 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            57889999999999988776555

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=94.52  E-value=0.08  Score=51.42  Aligned_cols=24  Identities=13%  Similarity=0.260  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -..++|.|..|+|||||++.+...
T Consensus       163 Gq~~~I~G~sG~GKStLl~~I~~~  186 (440)
T TIGR01026       163 GQRIGIFAGSGVGKSTLLGMIARN  186 (440)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999999887

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>PRK04328 hypothetical protein; Provisional

Probab=94.51  E-value=0.1  Score=46.74  Aligned_cols=58  Identities=10%  Similarity=0.080  Sum_probs=37.8

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHH
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLD   88 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~   88 (351)
                      .|-++|..+=++-+++-|.|.+|+|||+||.++.... . ..-+.++|++..-+..++.+
T Consensus        11 ~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~-~-~~ge~~lyis~ee~~~~i~~   68 (249)
T PRK04328         11 GMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNG-L-QMGEPGVYVALEEHPVQVRR   68 (249)
T ss_pred             hHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHH-H-hcCCcEEEEEeeCCHHHHHH
Confidence            3444444443556788899999999999998865551 2 23456778876644444433

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=94.51  E-value=0.028  Score=49.00  Aligned_cols=23  Identities=13%  Similarity=0.144  Sum_probs=19.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|+|.|-||+||||++..+..-
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~   23 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAA   23 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHH
Confidence            46889999999999988776555

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PTZ00185 ATPase alpha subunit; Provisional

Probab=94.50  E-value=0.12  Score=50.61  Aligned_cols=90  Identities=10%  Similarity=0.026  Sum_probs=49.5

Q ss_pred             EEEEEEcCCCChHHHHH-HHHhCCcccc-----cCCCeeEEEEEe---CCHHHHHHHHHHHhC-CCCCC----cc-----
Q 048347           42 SLVAIIDTMGFDRTAFI-GEAYNSSYVK-----NYFDCCAWVYYQ---LSLDMMLDAIMKSLM-PLSAL----SE-----  102 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa-~~v~~~~~~~-----~~F~~~~wv~~~---~~~~~~~~~i~~~~~-~~~~~----~~-----  102 (351)
                      ..++|.|-.|+|||+|| ..+.+...+.     ++-..++++-++   -++.++.+.+- +-+ .+...    ..     
T Consensus       190 QR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~-e~GaL~~TvVV~AtAdep~~  268 (574)
T PTZ00185        190 QRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLR-SYGALRYTTVMAATAAEPAG  268 (574)
T ss_pred             CEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHH-hcCCccceEEEEECCCCCHH
Confidence            56889999999999997 6677764221     233455666666   44444333332 222 11000    00     


Q ss_pred             ---CCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh
Q 048347          103 ---ILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus       103 ---~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                         ......-.+.+.+++  +++..|+|+||+-..
T Consensus       269 ~r~~Apy~a~tiAEYFrd--~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        269 LQYLAPYSGVTMGEYFMN--RGRHCLCVYDDLSKQ  301 (574)
T ss_pred             HHHHHHHHHHHHHHHHHH--cCCCEEEEEcCchHH
Confidence               011122233444443  489999999999543

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=94.50  E-value=0.034  Score=48.52  Aligned_cols=25  Identities=8%  Similarity=0.174  Sum_probs=22.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+ .+++|+|..|+|||||++.+..-
T Consensus        22 ~~-e~~~i~G~nGsGKSTLl~~l~G~   46 (214)
T cd03297          22 NE-EVTGIFGASGAGKSTLLRCIAGL   46 (214)
T ss_pred             cc-eeEEEECCCCCCHHHHHHHHhCC
Confidence            45 89999999999999999999765

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. 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.

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=94.50  E-value=0.028  Score=50.79  Aligned_cols=23  Identities=13%  Similarity=0.161  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|+|.|-||+||||+|..+..-
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~   24 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAA   24 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHH
Confidence            57888899999999998887666

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=94.50  E-value=0.028  Score=51.05  Aligned_cols=23  Identities=13%  Similarity=0.161  Sum_probs=19.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|+|.|-||+||||+|..+..-
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~~   24 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTAA   24 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH
Confidence            57888899999999988777554

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=94.49  E-value=0.041  Score=54.55  Aligned_cols=56  Identities=16%  Similarity=0.222  Sum_probs=42.6

Q ss_pred             CccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEE
Q 048347           18 KVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWV   77 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv   77 (351)
                      ++++--...++++..||...   ....+++.+.|++|+||||.++.+++.  .  .|+.+-|.
T Consensus        19 ~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~e--l--g~~v~Ew~   77 (519)
T PF03215_consen   19 DELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKE--L--GFEVQEWI   77 (519)
T ss_pred             HHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHH--h--CCeeEEec
Confidence            44555667889999999753   334678999999999999999999887  2  35555564

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=94.47  E-value=0.031  Score=48.78  Aligned_cols=24  Identities=13%  Similarity=0.236  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+..-
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl   52 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGI   52 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            368999999999999999999765

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=94.47  E-value=0.031  Score=46.09  Aligned_cols=22  Identities=9%  Similarity=0.206  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|+|.+|+|||||++++.+.
T Consensus         2 ki~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3678999999999999999765

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK13236 nitrogenase reductase; Reviewed

Probab=94.46  E-value=0.036  Score=51.09  Aligned_cols=26  Identities=8%  Similarity=0.175  Sum_probs=21.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+++++.|-||+||||+|..+..-
T Consensus         4 ~~~~~~~~~GKGGVGKTt~a~NLA~~   29 (296)
T PRK13236          4 ENIRQIAFYGKGGIGKSTTSQNTLAA   29 (296)
T ss_pred             cCceEEEEECCCcCCHHHHHHHHHHH
Confidence            35799999999999999977666544

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=94.46  E-value=0.12  Score=40.61  Aligned_cols=52  Identities=6%  Similarity=-0.195  Sum_probs=31.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHh
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSL   94 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~   94 (351)
                      .+.|.|..|.|||+.+...............++++.-. .-..+....+....
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~   54 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELF   54 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHh
Confidence            35688999999999988876663332334455666544 33334444444444

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

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

Probab=94.45  E-value=0.035  Score=46.11  Aligned_cols=24  Identities=13%  Similarity=0.278  Sum_probs=22.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|++|+|+.|+|||||..++...
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~   25 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRK   25 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHH
Confidence            479999999999999999999877

>PLN02200 adenylate kinase family protein

Probab=94.45  E-value=0.034  Score=49.41  Aligned_cols=25  Identities=4%  Similarity=0.018  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+|.|.|+.|+||||+|+.+...
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~   66 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVET   66 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3568899999999999999999776

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=94.44  E-value=0.14  Score=46.25  Aligned_cols=52  Identities=15%  Similarity=0.096  Sum_probs=38.2

Q ss_pred             CccccchhhHHHHHHHHHcc--------C---CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           18 KVDLDLEDKMEELLDLLIER--------Q---PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~--------~---~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      .++=|.|..+++|.+.+.-.        +   ...+=|.++|..|.|||.||++|+|.  ....|
T Consensus       185 ~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANq--TSATF  247 (440)
T KOG0726|consen  185 ADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQ--TSATF  247 (440)
T ss_pred             cccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcc--cchhh
Confidence            34557899999998877422        0   22344668999999999999999999  54444

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=94.44  E-value=0.052  Score=50.42  Aligned_cols=47  Identities=15%  Similarity=0.067  Sum_probs=30.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDA   89 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~   89 (351)
                      .+++.+.|.||+||||+|.+..-.  .........=|+..  .+..+++..
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~--lA~~g~kvLlvStDPAhsL~d~f~~   50 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVK--LAESGKKVLLVSTDPAHSLGDVFDL   50 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHH--HHHcCCcEEEEEeCCCCchHhhhcc
Confidence            478889999999999999885544  33333334445444  555554443

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=94.44  E-value=0.034  Score=44.78  Aligned_cols=23  Identities=4%  Similarity=0.249  Sum_probs=20.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCc
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      .|+++|..|+|||||+.++....
T Consensus         3 ki~~~G~~~~GKstl~~~l~~~~   25 (161)
T TIGR00231         3 KIVIVGDPNVGKSTLLNRLLGNK   25 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47799999999999999998874

This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=94.43  E-value=0.031  Score=48.89  Aligned_cols=22  Identities=18%  Similarity=0.205  Sum_probs=19.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|.|-||+||||+|..+...
T Consensus         2 kIaI~GKGG~GKTtiaalll~~   23 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKR   23 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHH
Confidence            6899999999999999885555

>cd03114 ArgK-like The function of this protein family is unkown

Probab=94.43  E-value=0.039  Score=45.32  Aligned_cols=22  Identities=14%  Similarity=0.327  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++.|.+|+||||++..+...
T Consensus         1 ~i~~~G~~GsGKTt~~~~l~~~   22 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITA   22 (148)
T ss_pred             CEEEECCCCCcHHHHHHHHHHH
Confidence            4788999999999999998766

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=94.43  E-value=0.11  Score=51.96  Aligned_cols=51  Identities=12%  Similarity=-0.029  Sum_probs=41.0

Q ss_pred             CCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....+.++|.....+++.+.+..-...-.-|-|+|..|+|||++|+.+++.
T Consensus       192 ~~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       192 SGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             cCccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHh
Confidence            345678999999999998888654333445669999999999999999987

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.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=94.43  E-value=0.034  Score=48.08  Aligned_cols=24  Identities=4%  Similarity=0.147  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|||.|+.|+||||.|+.+-+-
T Consensus         2 ~~iIglTG~igsGKStva~~~~~~   25 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAEL   25 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHHc
Confidence            468999999999999999988663

>PRK05973 replicative DNA helicase; Provisional

Probab=94.42  E-value=0.12  Score=45.96  Aligned_cols=51  Identities=12%  Similarity=-0.042  Sum_probs=34.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      ++-.++.|.|.+|+|||+||.++...  .-.+-+.+++++...+..++...+.
T Consensus        62 ~~Gsl~LIaG~PG~GKT~lalqfa~~--~a~~Ge~vlyfSlEes~~~i~~R~~  112 (237)
T PRK05973         62 KPGDLVLLGARPGHGKTLLGLELAVE--AMKSGRTGVFFTLEYTEQDVRDRLR  112 (237)
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEEEeCCHHHHHHHHH
Confidence            34567888999999999999988665  2223345666666555666666653

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=94.42  E-value=0.26  Score=44.64  Aligned_cols=97  Identities=12%  Similarity=0.051  Sum_probs=54.1

Q ss_pred             EEEEEEcCCCChHHHHH-HHHhCCcccccCCCee-EEEEEe---CCHHHHHHHHHHHhCCCCCC---ccCCCCC------
Q 048347           42 SLVAIIDTMGFDRTAFI-GEAYNSSYVKNYFDCC-AWVYYQ---LSLDMMLDAIMKSLMPLSAL---SEILDND------  107 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~~-~wv~~~---~~~~~~~~~i~~~~~~~~~~---~~~~~~~------  107 (351)
                      ..++|.|..|+|||+|| ..+.+.  ..  -+.+ +++-+.   -.+.++..++...-..+...   ...+...      
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~--~~--~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a  145 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQ--KG--KKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLA  145 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHh--cC--CCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHH
Confidence            46889999999999996 666655  22  2333 344334   55556666665432111000   0001111      


Q ss_pred             ---HHHHHHHHHHhcCCceEEEEEeCCCCh-hhHHHHHhhc
Q 048347          108 ---FEMKKNTLHNYLKNKRYLIVIQDVWRG-DIWDFLKEAL  144 (351)
Q Consensus       108 ---~~~~~~~l~~~L~~k~~LlVLDdv~~~-~~~~~l~~~l  144 (351)
                         .-.+.+.+++  +++..|+++||+-.. +++..+...+
T Consensus       146 ~~~a~aiAE~fr~--~G~~Vlvl~DslTr~A~A~rEisl~~  184 (274)
T cd01132         146 PYTGCAMGEYFMD--NGKHALIIYDDLSKQAVAYRQMSLLL  184 (274)
T ss_pred             HHHHHHHHHHHHH--CCCCEEEEEcChHHHHHHHHHHHHhc
Confidence               1223444444  489999999999544 5566665444

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>cd04155 Arl3 Arl3 subfamily

Probab=94.41  E-value=0.039  Score=46.00  Aligned_cols=25  Identities=8%  Similarity=0.105  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|+|+|..|+|||||.+.+...
T Consensus        13 ~~~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          13 EEPRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             CccEEEEEccCCCCHHHHHHHHhcC
Confidence            3456889999999999999999876

Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=94.40  E-value=0.032  Score=46.37  Aligned_cols=21  Identities=14%  Similarity=0.139  Sum_probs=17.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+|.|..|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999866

>PRK06761 hypothetical protein; Provisional

Probab=94.39  E-value=0.049  Score=49.59  Aligned_cols=24  Identities=17%  Similarity=0.171  Sum_probs=22.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ++|.|.|+.|+||||+|+.+++..
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L   27 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDIL   27 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            578899999999999999999883

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=94.39  E-value=0.035  Score=47.49  Aligned_cols=24  Identities=8%  Similarity=0.163  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|.|..|+|||||++.+..-
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G~   41 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNGL   41 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998765

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>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=94.38  E-value=0.036  Score=46.95  Aligned_cols=100  Identities=7%  Similarity=-0.110  Sum_probs=54.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEE---EeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVY---YQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHN  117 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~  117 (351)
                      -.+++|+|..|+|||||++.+..-  .+. ....+++.   +++..             +..    .....+...-.+..
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl--~~p-~~G~i~~~g~~i~~~~-------------q~~----~LSgGq~qrv~lar   84 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQ--LIP-NGDNDEWDGITPVYKP-------------QYI----DLSGGELQRVAIAA   84 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC--CCC-CCcEEEECCEEEEEEc-------------ccC----CCCHHHHHHHHHHH
Confidence            458999999999999999999876  222 22222221   11000             000    01223334455566


Q ss_pred             hcCCceEEEEEeCCCCh---hhHHHHHhhcCC-CCC-CcEEEE-Eeecc
Q 048347          118 YLKNKRYLIVIQDVWRG---DIWDFLKEALPD-HQN-GSRILT-ALIHI  160 (351)
Q Consensus       118 ~L~~k~~LlVLDdv~~~---~~~~~l~~~l~~-~~~-gs~Iiv-TR~~~  160 (351)
                      .+..+.-++++|+--..   .....+...+.. ... +..||+ |.+..
T Consensus        85 al~~~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~  133 (177)
T cd03222          85 ALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLA  133 (177)
T ss_pred             HHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHH
Confidence            67677788889987533   223333333321 112 245666 77654

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.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=94.38  E-value=0.033  Score=47.71  Aligned_cols=23  Identities=13%  Similarity=0.023  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|+|.|..|+||||+|+.+.+.
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~   26 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKL   26 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999887

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.

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=94.38  E-value=0.12  Score=49.96  Aligned_cols=101  Identities=12%  Similarity=0.144  Sum_probs=54.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCC--CccCCCCCH--H----HH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSA--LSEILDNDF--E----MK  111 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~--~~~~~~~~~--~----~~  111 (351)
                      -..++|.|..|+|||||++.++...  +.....++.+--. ..+.+++...+..-+....  .......+.  .    ..
T Consensus       156 Gqri~I~G~sG~GKTtLl~~Ia~~~--~~~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~~~  233 (432)
T PRK06793        156 GQKIGIFAGSGVGKSTLLGMIAKNA--KADINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAAKL  233 (432)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccC--CCCeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHHHH
Confidence            4578999999999999999998873  2221111111111 6777777766555322110  000011111  1    11


Q ss_pred             HHHHHHhc--CCceEEEEEeCCCCh-hhHHHHHhh
Q 048347          112 KNTLHNYL--KNKRYLIVIQDVWRG-DIWDFLKEA  143 (351)
Q Consensus       112 ~~~l~~~L--~~k~~LlVLDdv~~~-~~~~~l~~~  143 (351)
                      ...+.+++  ++++.|+++|++-.. +....+...
T Consensus       234 a~~iAEyfr~~G~~VLlilDslTr~a~A~reisl~  268 (432)
T PRK06793        234 ATSIAEYFRDQGNNVLLMMDSVTRFADARRSVDIA  268 (432)
T ss_pred             HHHHHHHHHHcCCcEEEEecchHHHHHHHHHHHHH
Confidence            22233333  479999999999544 344444433

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=94.37  E-value=0.068  Score=53.75  Aligned_cols=48  Identities=13%  Similarity=0.003  Sum_probs=35.6

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....+-|.+-.+.|.+......++-.+|.+.|+.|+||||+|+.++..
T Consensus       368 pP~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~  415 (568)
T PRK05537        368 IPEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVK  415 (568)
T ss_pred             CChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHH
Confidence            344566666666666655444455668889999999999999999987

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.37  E-value=0.047  Score=50.36  Aligned_cols=90  Identities=14%  Similarity=0.147  Sum_probs=51.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCC-eeEEEEEeCCHHHHHHHHHHHhCCCCCC-ccCCCCCHHHHHHHHHHhc
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD-CCAWVYYQLSLDMMLDAIMKSLMPLSAL-SEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~l~~~L  119 (351)
                      +-+.|.|..|+||||+++.+...  +....+ .++ +++. +..++.      +..+... .+... ......+.++..|
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~--i~~~~~~~ri-~tiE-d~~El~------~~~~~~v~~~~~~-~~~~~~~~l~~aL  201 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAE--IAKNDPTDRV-VIIE-DTRELQ------CAAPNVVQLRTSD-DAISMTRLLKATL  201 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--hhccCCCceE-EEEC-Cchhhc------CCCCCEEEEEecC-CCCCHHHHHHHHh
Confidence            35669999999999999999877  433221 122 2222 111111      0011000 00000 1115667778888


Q ss_pred             CCceEEEEEeCCCChhhHHHHHh
Q 048347          120 KNKRYLIVIQDVWRGDIWDFLKE  142 (351)
Q Consensus       120 ~~k~~LlVLDdv~~~~~~~~l~~  142 (351)
                      +...=-+|+..+.+.+.+..+..
T Consensus       202 R~~pD~iivGEiR~~ea~~~l~a  224 (299)
T TIGR02782       202 RLRPDRIIVGEVRGGEALDLLKA  224 (299)
T ss_pred             cCCCCEEEEeccCCHHHHHHHHH
Confidence            88888889999998887765433

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.

>PRK13695 putative NTPase; Provisional

Probab=94.37  E-value=0.035  Score=46.74  Aligned_cols=22  Identities=14%  Similarity=0.199  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|..|+|||||++.+++.
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998877

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=94.35  E-value=0.057  Score=43.86  Aligned_cols=23  Identities=9%  Similarity=0.143  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .=|-|.|.+|+||||||.++...
T Consensus         8 PNILvtGTPG~GKstl~~~lae~   30 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEK   30 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHH
Confidence            34668899999999999999865

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=94.35  E-value=0.066  Score=42.38  Aligned_cols=47  Identities=4%  Similarity=-0.047  Sum_probs=33.9

Q ss_pred             CccccchhhHHHHHHHHHc----c-CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIE----R-QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~----~-~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|-.--.+.+.+.+..    . +++.-|++.+|..|+|||.+|+.+++.
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            4567766555666555532    2 467889999999999999977776555

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

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=94.34  E-value=0.031  Score=51.71  Aligned_cols=23  Identities=9%  Similarity=0.037  Sum_probs=19.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++-+.|-||+||||+|....-.
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~   24 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALA   24 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHH
Confidence            57888999999999999776554

...

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	351
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-12
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	8e-07

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 71.0 bits (173), Expect = 2e-13
 Identities = 60/356 (16%), Positives = 115/356 (32%), Gaps = 86/356 (24%)

Query: 24  EDKMEELLDLLIERQPQLSLVAIIDTM-GFDRTAFIGEAYNSSYVKNYFDC-CAWVYY-- 79
                +L   L+E +P  +++  ID + G  +T    +   S  V+   D    W+    
Sbjct: 134 LQPYLKLRQALLELRPAKNVL--IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN 191

Query: 80  ----QLSLDMMLDAIMKSLMPLSALSEILDN---DFEMKKNTLHNYLKNKRY---LIVIQ 129
               +  L+M+   + +     ++ S+   N        +  L   LK+K Y   L+V+ 
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251

Query: 130 DVWRGDIWD-FLKEALPDHQNGSRIL--TALIHIVGLSSCRLENDEKIRLDLVPPKGKL- 185
           +V     W+ F      +     +IL  T    +       L       + L      L 
Sbjct: 252 NVQNAKAWNAF------NL--SCKILLTTRFKQVTD----FLSAATTTHISLDHHSMTLT 299

Query: 186 --RARQLYQLWI----------AEAFIPDNCESTAEEYLKELIDR--GFIQVNKKDLE-- 229
               + L   ++               P      AE  +++ +     +  VN   L   
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES-IRDGLATWDNWKHVNCDKLTTI 358

Query: 230 LEDDPMPAPEKLPHLKVLK--LKRSSYSGRKLVCGHGGFPR-----QEILHLKSMLWLEE 282
           +E            L VL+    R  +   +L      FP        +L   S++W + 
Sbjct: 359 IESS----------LNVLEPAEYRKMF--DRLSV----FPPSAHIPTILL---SLIWFDV 399

Query: 283 WKMETGA-MQKL--KSLIVNPCAYLRKFPEELWRIKALRKLESWWPRPELRQSLHK 335
            K +    + KL   SL+       ++  E    I ++        + E   +LH+
Sbjct: 400 IKSDVMVVVNKLHKYSLV------EKQPKESTISIPSIYLELK--VKLENEYALHR 447

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.8 bits (123), Expect = 2e-07
 Identities = 60/390 (15%), Positives = 108/390 (27%), Gaps = 106/390 (27%)

Query: 21  LDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD--C----- 73
           L +     EL  LL  +  +  L+ ++               N+      F+  C     
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLL-VLL-----------NVQNAKAWN-AFNLSCKILLT 271

Query: 74  ----------CAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDF-----EMKK-NTLHN 117
                      A     +SLD     +    +  S L + LD        E+   N    
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEV-KSLLLKYLDCRPQDLPREVLTTNPRR- 329

Query: 118 YLKNKRYLIVIQDVWRGDI--WDFLKEALPDHQNGSRILTALIHIVGLSSCRLENDEKIR 175
                  L +I +  R  +  WD  K     H N  +    L  I+  S   LE  E  +
Sbjct: 330 -------LSIIAESIRDGLATWDNWK-----HVNCDK----LTTIIESSLNVLEPAEYRK 373

Query: 176 L--DLV--PPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVNKK----- 226
           +   L   PP   +    L  +W       D  +S     + +L     ++   K     
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIW------FDVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427

Query: 227 --DLELEDDPMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQE---IL-----HLKS 276
              + LE       E   H  ++      Y+  K        P             HLK+
Sbjct: 428 IPSIYLELKVKLENEYALHRSIV----DHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483

Query: 277 MLWLEEWKM----------------ETGAMQKLKSLIVNPCAYLRKF-----PEELWRIK 315
           +   E   +                           I+N    L+ +       +    +
Sbjct: 484 IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYER 543

Query: 316 ALRKLESWWPRPELRQSLHKFEEIDRLDMQ 345
            +  +  + P+ E      K+ ++ R+ + 
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIALM 573

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.5 bits (117), Expect = 1e-06
 Identities = 52/407 (12%), Positives = 115/407 (28%), Gaps = 100/407 (24%)

Query: 18  KVDLDLED---------KMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVK 68
             + D +D           EE+  +++ +      + +  T+   +   + +        
Sbjct: 30  VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI 89

Query: 69  NYFDCCAWVYYQLSLD-----MMLDAIMKSLMPLSALSEILDNDF---EMKKNTLHNYLK 120
           NY     ++   +  +     MM    ++    L   +++              L   L 
Sbjct: 90  NY----KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145

Query: 121 NKR---YLIV--------------------IQDVWRGDI-W-DFLKEALPDHQNGSRILT 155
             R    +++                    +Q      I W +      P+      +L 
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV--LEMLQ 203

Query: 156 ALIHIVGLSSC-RLENDEKIRLDLVPPKGKLR---ARQLYQ-----------LWIAEAFI 200
            L++ +  +   R ++   I+L +   + +LR     + Y+                AF 
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF- 262

Query: 201 PD-NCE---STAEEYLKELIDR-GFIQVNKKDLELEDDPMPAPEKLP------HLKVLKL 249
            + +C+   +T     K++ D           L+     +   E           +   L
Sbjct: 263 -NLSCKILLTTRF---KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318

Query: 250 KRSSYSGRKLVCGH-GGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRK-- 306
            R   +             R  +    +   +   K+ T     L  L   P A  RK  
Sbjct: 319 PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL--EP-AEYRKMF 375

Query: 307 -----FPEELWRI--KALRKLESWWPRPE-----LRQSLHKFEEIDR 341
                FP     I    L  +  W+   +     +   LHK+  +++
Sbjct: 376 DRLSVFPPSAH-IPTILLSLI--WFDVIKSDVMVVVNKLHKYSLVEK 419

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.1 bits (98), Expect = 2e-04
 Identities = 35/227 (15%), Positives = 69/227 (30%), Gaps = 88/227 (38%)

Query: 15  WDNKVDLDLEDKMEELLD-LLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC 73
           W + +  D+   + +L    L+E+QP+ S ++I                           
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI--------------------------- 428

Query: 74  CAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR 133
                  + L+               L   L+N++ + ++ + +Y   K +         
Sbjct: 429 -----PSIYLE---------------LKVKLENEYALHRSIVDHYNIPKTF--------- 459

Query: 134 GDIWDFLKEALPDHQNGSRILTALIHIVG--LSSCRLEND----EKIRLDLVPPKGKLRA 187
            D  D +   L  +       +   HI G  L +            + LD    + K+R 
Sbjct: 460 -DSDDLIPPYLDQY-----FYS---HI-GHHLKNIEHPERMTLFRMVFLDFRFLEQKIRH 509

Query: 188 RQ------------LYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQ 222
                         L QL   + +I DN     E  +  ++D  F+ 
Sbjct: 510 DSTAWNASGSILNTLQQLKFYKPYICDNDP-KYERLVNAILD--FLP 553

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 67.2 bits (164), Expect = 2e-12
 Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 15/140 (10%)

Query: 24  EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSY-VKNYFDCC-AWVY--- 78
           +  +  +   L + + +   V I    G  ++    EA      ++  F     WV    
Sbjct: 130 KKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGK 189

Query: 79  -YQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL--KNKRYLIVIQDVWRGD 135
             +  L M L  +   L    + S+ L  + E  K+ L   +  K+ R L+++ DVW   
Sbjct: 190 QDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSW 249

Query: 136 IWDFLKEALPDHQNGSRILT 155
           +            +  +IL 
Sbjct: 250 VLKAFD-------SQCQILL 262

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 49.6 bits (118), Expect = 8e-07
 Identities = 21/150 (14%), Positives = 42/150 (28%), Gaps = 31/150 (20%)

Query: 24  EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIG--------EAYNSS--YVKNYFDC 73
           E  ++ ++  L E     S    +           G        +A + S   +   +D 
Sbjct: 134 EYHVDRVIKKLDEMCDLDSFFLFLHGRA-------GSGKSVIASQALSKSDQLIGINYDS 186

Query: 74  CAWVY----YQLSLDMMLDAIMKSLMPLSALSEILDNDFEM----KKNTLHNYLKNKRYL 125
             W+        S   +   I+  L     L      +       K+   +  +     L
Sbjct: 187 IVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTL 246

Query: 126 IVIQDVWRGDIWDFLKEALPDHQNGSRILT 155
            V  DV +    + ++ A    +   R L 
Sbjct: 247 FVFDDVVQ---EETIRWAQ---ELRLRCLV 270

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	351
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.96
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.89
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.88
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.83
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.19
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.98
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.98
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.96
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.93
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.91
2fna_A	357	Conserved hypothetical protein; structural genomic	98.82
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	98.77
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	98.73
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	98.71
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.69
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.67
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	98.61
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	98.59
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	98.55
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.54
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	98.54
3e6j_A	229	Variable lymphocyte receptor diversity region; var	98.53
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	98.53
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	98.52
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.5
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	98.49
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	98.48
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	98.48
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.47
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	98.47
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	98.46
3e6j_A	229	Variable lymphocyte receptor diversity region; var	98.45
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	98.44
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	98.43
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	98.43
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.42
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	98.4
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	98.39
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.37
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	98.37
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	98.36
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	98.35
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	98.33
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	98.33
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	98.33
3m19_A	251	Variable lymphocyte receptor A diversity region; a	98.32
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	98.31
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	98.3
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.28
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	98.27
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	98.27
3m19_A	251	Variable lymphocyte receptor A diversity region; a	98.27
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.26
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	98.26
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	98.26
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	98.26
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	98.25
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	98.25
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	98.24
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	98.24
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	98.23
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.23
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	98.21
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	98.21
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	98.21
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	98.21
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	98.2
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	98.2
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	98.19
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	98.19
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	98.19
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	98.19
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	98.19
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	98.19
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	98.18
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	98.18
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	98.17
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	98.17
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	98.17
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	98.16
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	98.16
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	98.15
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	98.15
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	98.15
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.14
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	98.14
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.14
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	98.13
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	98.13
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	98.13
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	98.12
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	98.11
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	98.11
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	98.1
1o6v_A	466	Internalin A; bacterial infection, extracellular r	98.1
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	98.1
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	98.09
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	98.08
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	98.08
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	98.08
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	98.08
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	98.08
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	98.08
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	98.07
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	98.07
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	98.06
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	98.06
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	98.05
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	98.05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	98.05
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.04
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	98.04
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	98.03
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	98.03
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	98.02
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	98.01
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	97.98
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.98
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.98
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	97.97
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	97.96
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	97.96
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	97.95
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	97.94
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	97.93
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	97.92
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	97.92
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	97.91
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	97.88
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	97.88
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	97.87
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	97.86
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	97.85
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	97.84
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	97.83
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	97.83
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.82
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	97.82
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.82
1o6v_A	466	Internalin A; bacterial infection, extracellular r	97.81
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	97.8
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.78
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.77
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.72
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.71
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	97.68
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	97.68
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	97.68
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.68
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.64
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.64
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	97.63
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.63
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.63
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.59
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.58
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	97.58
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	97.57
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.56
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.54
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	97.53
3pvs_A	447	Replication-associated recombination protein A; ma	97.51
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	97.49
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	97.48
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.46
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	97.46
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.46
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.44
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.43
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	97.42
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.39
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	97.35
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.32
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.31
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.3
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.29
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.26
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.25
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.25
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.21
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	97.16
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.14
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.11
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.09
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.05
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.02
3co5_A	143	Putative two-component system transcriptional RES	97.01
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.0
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.0
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.91
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.9
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.88
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.86
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.83
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.82
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.82
3bos_A	242	Putative DNA replication factor; P-loop containing	96.82
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.77
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.77
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.76
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.73
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	96.68
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.67
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.64
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	96.6
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.58
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.57
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.56
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.56
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.54
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.52
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.52
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.52
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	96.49
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.48
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	96.48
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.47
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.44
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.42
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	96.41
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	96.41
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	96.41
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.37
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.3
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.29
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.29
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.28
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	96.26
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.22
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.22
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.21
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	96.19
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.18
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.17
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.16
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.13
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.1
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.09
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.08
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.08
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.05
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.03
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.02
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.01
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.01
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	95.99
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	95.99
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	95.97
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.97
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.96
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.95
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	95.95
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.94
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.94
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.92
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.92
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.92
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.92
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.91
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	95.89
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.89
2xxa_A	433	Signal recognition particle protein; protein trans	95.89
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.87
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.86
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	95.85
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.83
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.82
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.82
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.81
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.8
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.8
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.78
3ice_A	422	Transcription termination factor RHO; transcriptio	95.78
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.77
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.76
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.76
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.74
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.74
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.72
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.7
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.69
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.68
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.68
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.68
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.68
3io5_A	333	Recombination and repair protein; storage dimer, i	95.67
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.67
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.66
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.66
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.65
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.65
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.65
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.65
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.64
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.62
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.62
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.62
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.61
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.6
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.6
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.6
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.6
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.59
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.57
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.56
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.56
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.56
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.55
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.54
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.54
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.52
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.5
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.5
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.49
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.47
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.46
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.46
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.45
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.44
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.42
1via_A	175	Shikimate kinase; structural genomics, transferase	95.4
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.38
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.35
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.34
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.33
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.33
2qgz_A	308	Helicase loader, putative primosome component; str	95.32
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.31
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.3
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.29
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.28
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.26
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.26
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.24
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.24
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.23
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.21
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.19
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.19
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.18
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.18
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.16
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.16
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.15
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.15
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.13
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.13
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	95.12
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.11
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	95.1
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.09
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.09
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.07
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.07
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	95.06
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.03
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.02
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.96
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	94.96
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.95
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.94
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.93
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	94.9
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.88
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	94.88
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.85
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.83
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.81
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	94.81
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.77
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.77
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.74
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	94.73
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.71
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	94.71
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.71
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.69
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.68
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.67
1g6h_A	257	High-affinity branched-chain amino acid transport	94.66
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.65
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.64
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	94.63
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.61
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.6
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.6
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.59
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.58
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.57
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.57
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	94.55
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.55
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.55
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.54
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.53
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.53
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	94.52
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.52
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.51
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	94.5
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	94.48
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.48
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.48
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	94.47
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.46
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.45
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.43
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.4
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.39
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.38
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	94.38
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.38
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.33
2og2_A	359	Putative signal recognition particle receptor; nuc	94.33
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.33
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	94.32
3end_A	307	Light-independent protochlorophyllide reductase ir	94.32
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.31
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.3
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.28
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.28
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	94.27
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.25
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.24
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.23
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.23
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.21
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.2
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.19
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.14
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	94.13
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.1
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	94.06
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.04
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.04
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	94.03
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	94.03
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.02
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.02
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.0
3l0o_A	427	Transcription termination factor RHO; helicase, RH	93.98
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	93.97
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.96
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.95
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.92
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	93.9
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	93.89
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.88
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.88
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.88
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	93.87
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	93.86
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.81
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.79
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.78
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	93.76
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.75
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.74
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.68
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.67
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	93.67
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.63
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.63
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.62
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.56
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.5
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.48
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	93.45
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.43
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.43
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.43
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.38
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.38
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.37
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.37
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.32
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	93.31
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	93.29
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.29
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.28
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.27
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.26
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.22
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	93.19
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.19
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.18
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.17
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.15
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.15
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.09
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.07
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	93.05
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.05
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.05
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	93.04
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.03
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	92.96
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.94
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	92.94
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	92.94

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=99.96  E-value=5.7e-28  Score=239.63  Aligned_cols=195  Identities=16%  Similarity=0.141  Sum_probs=153.2

Q ss_pred             ccchhhHHHHHHHHHcc-CCCeEEEEEEcCCCChHHHHHHHHhC--CcccccCCCeeEEEEEe--C--CHHHHHHHHHHH
Q 048347           21 LDLEDKMEELLDLLIER-QPQLSLVAIIDTMGFDRTAFIGEAYN--SSYVKNYFDCCAWVYYQ--L--SLDMMLDAIMKS   93 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~-~~~~~vv~I~G~gGiGKTtLa~~v~~--~~~~~~~F~~~~wv~~~--~--~~~~~~~~i~~~   93 (351)
                      |||++++++|.++|..+ ++..++|+|+||||+||||||+++|+  +.+++.+|+.++||+++  +  ++.++++.|+.+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            69999999999999765 44689999999999999999999998  56799999999999999  3  689999999999


Q ss_pred             hCCCCC---CccCCCCCHHHHHHHHHHhcCCc-eEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccchh-----
Q 048347           94 LMPLSA---LSEILDNDFEMKKNTLHNYLKNK-RYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIVGL-----  163 (351)
Q Consensus        94 ~~~~~~---~~~~~~~~~~~~~~~l~~~L~~k-~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v~l-----  163 (351)
                      ++....   ....+..+.+.+...+++.|+++ |+||||||||+.+++ .+..     .+||+||| ||++.|+.     
T Consensus       211 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~~~~  284 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVEISNAASQT  284 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGGGGGGCCSC
T ss_pred             HhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHHHHHHcCCC
Confidence            987532   12234456778899999999996 999999999998765 2221     16999999 99977711     


Q ss_pred             -------------------------------------------------------hc---cc-----------cCCCC--
Q 048347          164 -------------------------------------------------------SS---CR-----------LENDE--  172 (351)
Q Consensus       164 -------------------------------------------------------L~---w~-----------l~~~~--  172 (351)
                                                                             ++   |+           ...+.  
T Consensus       285 ~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~w~~~~~l~~~l~~~~~~~i~  364 (549)
T 2a5y_B          285 CEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVE  364 (549)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHHHCSSTTC
T ss_pred             CeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccchHHHHHHhHHHhhcccHHHHH
Confidence                                                                   00   11           00000  


Q ss_pred             c-----------------e-----------EEccCCCCeEEeccchHHHHHHc--CCCC-----CCHHHHHHHHHHHHHH
Q 048347          173 K-----------------I-----------RLDLVPPKGKLRARQLYQLWIAE--AFIP-----DNCESTAEEYLKELID  217 (351)
Q Consensus       173 ~-----------------i-----------y~~~fp~~~~~~~~~l~~~w~~e--g~i~-----~~~~~~~~~~~~~L~~  217 (351)
                      .                 .           |||+||+++.++    +.+|+++  ||+.     .+.++.++ ||++|++
T Consensus       365 ~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~~~~~~~-~l~~L~~  439 (549)
T 2a5y_B          365 CITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQLDDEVAD-RLKRLSK  439 (549)
T ss_dssp             CCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCCTHHHHH-HHHHTTT
T ss_pred             HHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCCHHHHHH-HHHHHHH
Confidence            0                 1           999999999998    8999999  9996     34677777 9999999


Q ss_pred             CCCceeecc
Q 048347          218 RGFIQVNKK  226 (351)
Q Consensus       218 ~~~l~~~~~  226 (351)
                      +|++++...
T Consensus       440 rsLl~~~~~  448 (549)
T 2a5y_B          440 RGALLSGKR  448 (549)
T ss_dssp             BSSCSEEEC
T ss_pred             cCCeeEecC
Confidence            999998753

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=99.89  E-value=8.9e-23  Score=219.55  Aligned_cols=201  Identities=19%  Similarity=0.280  Sum_probs=155.9

Q ss_pred             ccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccc-ccCC-CeeEEEEEe-C---CHHH
Q 048347           12 GLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYV-KNYF-DCCAWVYYQ-L---SLDM   85 (351)
Q Consensus        12 ~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~-~~~F-~~~~wv~~~-~---~~~~   85 (351)
                      +++.....+|||++++++|.++|...+...++|+|+||||+||||||+++|++.+. ..+| +.++||+++ .   ....
T Consensus       118 ~~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~  197 (1249)
T 3sfz_A          118 GVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLM  197 (1249)
T ss_dssp             TCCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHH
T ss_pred             CCCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHH
Confidence            35566778999999999999999876667899999999999999999999999544 4556 457799998 2   3345


Q ss_pred             HHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCc--eEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccch
Q 048347           86 MLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNK--RYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIVG  162 (351)
Q Consensus        86 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k--~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v~  162 (351)
                      .+..++..+............+.+.+.+.++..+.++  |+||||||||+.++|..+       .+|++||+ ||++.++
T Consensus       198 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~  270 (1249)
T 3sfz_A          198 KLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVT  270 (1249)
T ss_dssp             HHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTT
T ss_pred             HHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHH
Confidence            5677888887654433334567888999999999887  999999999998765543       56899999 9999762


Q ss_pred             h-----------------------------------------------------------hc-----c------------
Q 048347          163 L-----------------------------------------------------------SS-----C------------  166 (351)
Q Consensus       163 l-----------------------------------------------------------L~-----w------------  166 (351)
                      .                                                           ++     |            
T Consensus       271 ~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~~~~~~~l~~l~~~~~  350 (1249)
T 3sfz_A          271 DSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQF  350 (1249)
T ss_dssp             TTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSSSCHHHHHHHHHSCCC
T ss_pred             HhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcChhHHHHHHHHHhhhhh
Confidence            0                                                           00     1            


Q ss_pred             ccCCCC------c--------------------eEEccCCCCeEEeccchHHHHHHcCCCCCCHHHHHHHHHHHHHHCCC
Q 048347          167 RLENDE------K--------------------IRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGF  220 (351)
Q Consensus       167 ~l~~~~------~--------------------iy~~~fp~~~~~~~~~l~~~w~~eg~i~~~~~~~~~~~~~~L~~~~~  220 (351)
                      ......      .                    .||++||+++.+++..++.+|.++       ++.+++++++|+++++
T Consensus       351 ~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~-------~~~~~~~l~~L~~~sl  423 (1249)
T 3sfz_A          351 KRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEFVNKSL  423 (1249)
T ss_dssp             CCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCC-------HHHHHHHHHHHHHTTS
T ss_pred             hhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCC-------HHHHHHHHHHHHhccc
Confidence            000000      0                    199999999999999999999554       4678999999999999


Q ss_pred             ceeecc
Q 048347          221 IQVNKK  226 (351)
Q Consensus       221 l~~~~~  226 (351)
                      ++....
T Consensus       424 ~~~~~~  429 (1249)
T 3sfz_A          424 LFCNRN  429 (1249)
T ss_dssp             CEEEES
T ss_pred             eEEecC
Confidence            987654

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.88  E-value=1.8e-23  Score=214.06  Aligned_cols=192  Identities=18%  Similarity=0.233  Sum_probs=147.9

Q ss_pred             ccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCe-eEEEEEe--CCHHHHHHHHHHHhC
Q 048347           19 VDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC-CAWVYYQ--LSLDMMLDAIMKSLM   95 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~~--~~~~~~~~~i~~~~~   95 (351)
                      ..|||++++++|.++|...+ ..++|+|+||||+||||||+++|++.+++.+|+. ++|++++  ++...++..|+..+.
T Consensus       129 ~~VGRe~eLeeL~elL~~~d-~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~  207 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLELR-PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY  207 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHCC-SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhccC-CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHh
Confidence            34999999999999998643 4789999999999999999999988778999997 8999999  888888888877543


Q ss_pred             CCC---CCcc----CCCCCHHHHHHHHHHhc---CCceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccch--
Q 048347           96 PLS---ALSE----ILDNDFEMKKNTLHNYL---KNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIVG--  162 (351)
Q Consensus        96 ~~~---~~~~----~~~~~~~~~~~~l~~~L---~~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v~--  162 (351)
                      ...   ....    ....+.+.+.+.+++.|   .+||+||||||||+.+.|+.+.       .||+||| ||++.++  
T Consensus       208 ~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va~~  280 (1221)
T 1vt4_I          208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDF  280 (1221)
T ss_dssp             HHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHHHH
T ss_pred             hcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHHHh
Confidence            211   1000    00123455667777766   7899999999999988887652       6999999 9998762  


Q ss_pred             ----------------hhc-----------------------------------------------cccCCCCc------
Q 048347          163 ----------------LSS-----------------------------------------------CRLENDEK------  173 (351)
Q Consensus       163 ----------------lL~-----------------------------------------------w~l~~~~~------  173 (351)
                                      .|.                                               |.......      
T Consensus       281 l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~eeL~~eICgGLPLALkLaGs~Lr~k~~s~eeW~~~~~~~I~aaLe  360 (1221)
T 1vt4_I          281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE  360 (1221)
T ss_dssp             HHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTTHHHHHCCCCHHHHHHHHHHHHHSCSSHHHHHHCSCHHHHHHHH
T ss_pred             cCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHHHHHHHhCCCHHHHHHHHHHHhCCCCCHHHHhcCChhHHHHHHH
Confidence                            111                                               21111100      


Q ss_pred             ---------------eEEccCCCCeEEeccchHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCceee
Q 048347          174 ---------------IRLDLVPPKGKLRARQLYQLWIAEAFIPDNCESTAEEYLKELIDRGFIQVN  224 (351)
Q Consensus       174 ---------------iy~~~fp~~~~~~~~~l~~~w~~eg~i~~~~~~~~~~~~~~L~~~~~l~~~  224 (351)
                                     .|||+||+++.+++..++.+|.++|      ++.+..++++|+++||++..
T Consensus       361 lSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeG------eedAe~~L~eLvdRSLLq~d  420 (1221)
T 1vt4_I          361 SSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI------KSDVMVVVNKLHKYSLVEKQ  420 (1221)
T ss_dssp             HHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC------SHHHHHHHHHHHTSSSSSBC
T ss_pred             HHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC------HHHHHHHHHHHHhhCCEEEe
Confidence                           1899999999999999999998886      24588999999999999875

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.83  E-value=3.8e-20  Score=184.98  Aligned_cols=142  Identities=18%  Similarity=0.218  Sum_probs=109.0

Q ss_pred             cCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccc-ccCCC-eeEEEEEe-CCHHHHHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYV-KNYFD-CCAWVYYQ-LSLDMMLDA   89 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~-~~~F~-~~~wv~~~-~~~~~~~~~   89 (351)
                      ++.....+|||++++++|.++|.....+.++|+|+||||+||||||+++|++..+ +.+|. .++|++++ .+...++..
T Consensus       119 ~P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~~~~~~~~~  198 (591)
T 1z6t_A          119 VPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMK  198 (591)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESCCHHHHHHH
T ss_pred             CCCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCCchHHHHHH
Confidence            4556778999999999999999865556899999999999999999999999655 78895 79999999 655555554


Q ss_pred             H---HHHhCCCCCCccCCCCCHHHHHHHHHHhcCC--ceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccc
Q 048347           90 I---MKSLMPLSALSEILDNDFEMKKNTLHNYLKN--KRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIV  161 (351)
Q Consensus        90 i---~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~--k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v  161 (351)
                      +   +..+............+.+.+...++..+.+  +++||||||+|+...+..    +   ..|++||+ ||++.+
T Consensus       199 l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~----l---~~~~~ilvTsR~~~~  269 (591)
T 1z6t_A          199 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKA----F---DSQCQILLTTRDKSV  269 (591)
T ss_dssp             HHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHT----T---CSSCEEEEEESCGGG
T ss_pred             HHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHH----h---cCCCeEEEECCCcHH
Confidence            4   3455432211112455677888888888876  789999999998655432    2   46899999 999875

>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=99.19  E-value=5.9e-11  Score=112.65  Aligned_cols=117  Identities=13%  Similarity=0.017  Sum_probs=83.2

Q ss_pred             cCCCCCccccchhhHHHHHHHH-Hcc--C--CCeEEEEE--EcCCCChHHHHHHHHhCCccccc-----CCCe-eEEEEE
Q 048347           13 LSWDNKVDLDLEDKMEELLDLL-IER--Q--PQLSLVAI--IDTMGFDRTAFIGEAYNSSYVKN-----YFDC-CAWVYY   79 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L-~~~--~--~~~~vv~I--~G~gGiGKTtLa~~v~~~~~~~~-----~F~~-~~wv~~   79 (351)
                      +......++||+++++++.+++ ..-  +  .....+.|  +|++|+||||||+++++.  ...     .|.. .+|++.
T Consensus        17 ~~~~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~--~~~~~~~~~~~~~~~~~~~   94 (412)
T 1w5s_A           17 ENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVNA   94 (412)
T ss_dssp             TTCCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEEG
T ss_pred             CccCCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHH--HHHHHhccCCceeEEEEEC
Confidence            3344578999999999999988 421  1  12344555  999999999999999987  433     2232 456654


Q ss_pred             e--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh
Q 048347           80 Q--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG  134 (351)
Q Consensus        80 ~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~  134 (351)
                      .  .+..+++..++.+++....   ....+...+...+.+.+.  +++++|||||++..
T Consensus        95 ~~~~~~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l  150 (412)
T 1w5s_A           95 FNAPNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQSM  150 (412)
T ss_dssp             GGCCSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHH
T ss_pred             CCCCCHHHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHH
Confidence            3  7788999999999866432   122345666777777775  67999999999764

>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=98.98  E-value=1.4e-09  Score=101.80  Aligned_cols=143  Identities=12%  Similarity=0.073  Sum_probs=93.6

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC---eeEEEEEe--CCHHH
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD---CCAWVYYQ--LSLDM   85 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~---~~~wv~~~--~~~~~   85 (351)
                      +....+.++||+++++.+.+++...  ......+.|+|++|+||||||+.+++.  ....+.   ..+|++..  .+...
T Consensus        15 ~~~~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~~~   92 (386)
T 2qby_A           15 PDYIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTPYR   92 (386)
T ss_dssp             SSCCCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSHHH
T ss_pred             CccCCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCHHH
Confidence            4445578999999999999988752  334568889999999999999999987  444432   24455544  67778


Q ss_pred             HHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh------hhHHHHHhhcCC-CCCCcEEEE-
Q 048347           86 MLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG------DIWDFLKEALPD-HQNGSRILT-  155 (351)
Q Consensus        86 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~------~~~~~l~~~l~~-~~~gs~Iiv-  155 (351)
                      ++..++.+++....   ....+..+..+.+.+.+.  +++.++|||+++..      +.+..+...+.. ...+..+|+ 
T Consensus        93 ~~~~i~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~  169 (386)
T 2qby_A           93 VLADLLESLDVKVP---FTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGI  169 (386)
T ss_dssp             HHHHHTTTTSCCCC---SSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEE
T ss_pred             HHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEE
Confidence            88888877754322   122345566666666664  45899999999653      233344333322 223445566 


Q ss_pred             Eeecc
Q 048347          156 ALIHI  160 (351)
Q Consensus       156 TR~~~  160 (351)
                      |+...
T Consensus       170 ~~~~~  174 (386)
T 2qby_A          170 TNDVK  174 (386)
T ss_dssp             ESCGG
T ss_pred             ECCCC
Confidence            76554

>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=98.98  E-value=2.3e-09  Score=100.71  Aligned_cols=140  Identities=14%  Similarity=0.004  Sum_probs=93.1

Q ss_pred             CCccccchhhHHHHHHHHHc--cCCCeEEEEEEcCCCChHHHHHHHHhCCcccc----cCC--CeeEEEEEe--C-CHHH
Q 048347           17 NKVDLDLEDKMEELLDLLIE--RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVK----NYF--DCCAWVYYQ--L-SLDM   85 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~----~~F--~~~~wv~~~--~-~~~~   85 (351)
                      .+.++||+++++++.+++..  .....+.+.|+|++|+|||+||+.+++...-.    ..+  ...+|++..  . +...
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   98 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQA   98 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHH
Confidence            47899999999999988865  23345688899999999999999999872111    112  234455544  5 8889


Q ss_pred             HHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCChhh---HHH-HHhhcCCCCCCcEEEE-Eeec
Q 048347           86 MLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDI---WDF-LKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        86 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~---~~~-l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ++..++.++......  ....+...+.+.+.+.++.++.++||||++....   .+. +...+... .+.++|. |+..
T Consensus        99 ~~~~l~~~l~~~~~~--~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~~  174 (384)
T 2qby_B           99 VLSSLAGKLTGFSVP--KHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISNDI  174 (384)
T ss_dssp             HHHHHHHHHHCSCCC--SSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSST
T ss_pred             HHHHHHHHhcCCCCC--CCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECCC
Confidence            999999888432110  1233446677788888877777999999976432   222 22222222 5667777 7655

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.96  E-value=2.6e-09  Score=100.21  Aligned_cols=117  Identities=14%  Similarity=0.029  Sum_probs=84.4

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC-----C-eeEEEEEe--CC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF-----D-CCAWVYYQ--LS   82 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F-----~-~~~wv~~~--~~   82 (351)
                      +....+.++||+++++++.+++..-  ......+.|+|++|+||||+|+.+++.  ....+     . ..+|++..  .+
T Consensus        14 ~~~~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~   91 (387)
T 2v1u_A           14 PDYVPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARHRET   91 (387)
T ss_dssp             TTCCCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTTSCS
T ss_pred             CccCCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCcCCC
Confidence            3444578999999999999988542  334567889999999999999999987  32211     1 23444443  67


Q ss_pred             HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc--CCceEEEEEeCCCCh
Q 048347           83 LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL--KNKRYLIVIQDVWRG  134 (351)
Q Consensus        83 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L--~~k~~LlVLDdv~~~  134 (351)
                      ...++..++.++.....   ....+..++.+.+.+.+  .+++.+++||+++..
T Consensus        92 ~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l  142 (387)
T 2v1u_A           92 PYRVASAIAEAVGVRVP---FTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFL  142 (387)
T ss_dssp             HHHHHHHHHHHHSCCCC---SSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHH
T ss_pred             HHHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhh
Confidence            78899999999966433   12344666677777776  356899999999765

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.93  E-value=2.1e-09  Score=99.37  Aligned_cols=136  Identities=9%  Similarity=0.088  Sum_probs=89.3

Q ss_pred             ccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-C-------CH
Q 048347           12 GLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-L-------SL   83 (351)
Q Consensus        12 ~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~-------~~   83 (351)
                      .+......++||++++++|.+++..+    +++.|+|++|+|||||++++++.  .    . .+|++.. .       +.
T Consensus         6 ~~~~~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~--~----~-~~~~~~~~~~~~~~~~~~   74 (350)
T 2qen_A            6 RPKTRREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNE--R----P-GILIDCRELYAERGHITR   74 (350)
T ss_dssp             SCCCSGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHH--S----S-EEEEEHHHHHHTTTCBCH
T ss_pred             CCCCChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHH--c----C-cEEEEeecccccccCCCH
Confidence            45556778999999999999998653    58889999999999999999877  3    1 4555544 2       56


Q ss_pred             HHHHHHHHHHhCCC--------------CCCccCCCCCHHHHHHHHHHhcCC-ceEEEEEeCCCChhh---------HHH
Q 048347           84 DMMLDAIMKSLMPL--------------SALSEILDNDFEMKKNTLHNYLKN-KRYLIVIQDVWRGDI---------WDF  139 (351)
Q Consensus        84 ~~~~~~i~~~~~~~--------------~~~~~~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~~~~~---------~~~  139 (351)
                      ..+.+.+.+.+...              .........+..++.+.+.+..+. ++.++||||++..+.         +..
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~  154 (350)
T 2qen_A           75 EELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLAL  154 (350)
T ss_dssp             HHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHH
Confidence            67777777665430              000001124556666777666643 389999999976432         333


Q ss_pred             HHhhcCCCCCCcEEEE-Eeec
Q 048347          140 LKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus       140 l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      +....... .+.++|+ ++..
T Consensus       155 L~~~~~~~-~~~~~il~g~~~  174 (350)
T 2qen_A          155 FAYAYDSL-PNLKIILTGSEV  174 (350)
T ss_dssp             HHHHHHHC-TTEEEEEEESSH
T ss_pred             HHHHHHhc-CCeEEEEECCcH
Confidence            33322222 3667777 6554

>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=98.91  E-value=1.3e-08  Score=95.55  Aligned_cols=142  Identities=13%  Similarity=0.063  Sum_probs=96.5

Q ss_pred             CCCCCccccchhhHHHHHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC-CeeEEEEEe--CCHHHH
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF-DCCAWVYYQ--LSLDMM   86 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~~~--~~~~~~   86 (351)
                      ....+.++||+++++++..++...    ....+.+.|+|+.|+||||||+.+++.  ..... ...++++..  .+...+
T Consensus        13 ~~~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~i~~~~~~~~~~~   90 (389)
T 1fnn_A           13 SYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAI   90 (389)
T ss_dssp             TCCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHH
T ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHH--HhhhcCeeEEEEeCccCCCHHHH
Confidence            334478999999999999998752    222347889999999999999999987  43332 233455544  667889


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh--hhHHHHHhhcCCCC----CCcEEEE-Ee
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG--DIWDFLKEALPDHQ----NGSRILT-AL  157 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~--~~~~~l~~~l~~~~----~gs~Iiv-TR  157 (351)
                      ...++.+++....   ....+...+.+.+.+.+.  +++.+++||+++..  +....+...+....    .+..+|+ |+
T Consensus        91 ~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~  167 (389)
T 1fnn_A           91 IGEIARSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGH  167 (389)
T ss_dssp             HHHHHHHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEES
T ss_pred             HHHHHHHhCccCC---CCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEEC
Confidence            9999988865432   123355666666666664  56889999999764  44555555554321    3566666 77


Q ss_pred             ecc
Q 048347          158 IHI  160 (351)
Q Consensus       158 ~~~  160 (351)
                      +..
T Consensus       168 ~~~  170 (389)
T 1fnn_A          168 NDA  170 (389)
T ss_dssp             STH
T ss_pred             Cch
Confidence            653

>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=98.82  E-value=5.9e-09  Score=96.53  Aligned_cols=136  Identities=13%  Similarity=0.063  Sum_probs=83.4

Q ss_pred             ccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-C------CHH
Q 048347           12 GLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-L------SLD   84 (351)
Q Consensus        12 ~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~------~~~   84 (351)
                      .+......++||+++++.|.+ +..     +++.|+|++|+|||+|++++++.  ...   ..+|++.. .      +..
T Consensus         7 ~~~~~~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~--~~~---~~~~~~~~~~~~~~~~~~~   75 (357)
T 2fna_A            7 SPKDNRKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINE--LNL---PYIYLDLRKFEERNYISYK   75 (357)
T ss_dssp             SCCCSGGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHH--HTC---CEEEEEGGGGTTCSCCCHH
T ss_pred             CCCCCHHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHh--cCC---CEEEEEchhhccccCCCHH
Confidence            344566789999999999999 643     58999999999999999999987  332   24666654 3      345


Q ss_pred             HHHHHHHHHhCC-------------CC---CCcc----C-----CCCCHHHHHHHHHHhcCCceEEEEEeCCCChh----
Q 048347           85 MMLDAIMKSLMP-------------LS---ALSE----I-----LDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGD----  135 (351)
Q Consensus        85 ~~~~~i~~~~~~-------------~~---~~~~----~-----~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~----  135 (351)
                      .+...+.+.+..             ..   ..+.    .     .......+.+.+.+.-+ ++.+|||||++..+    
T Consensus        76 ~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~  154 (357)
T 2fna_A           76 DFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRG  154 (357)
T ss_dssp             HHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTT
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCc
Confidence            555555544311             00   0000    0     12345556666655433 48999999997632    


Q ss_pred             -h-HHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347          136 -I-WDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus       136 -~-~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                       + +..+....... .+.++|+ +|...
T Consensus       155 ~~~~~~l~~~~~~~-~~~~~i~~g~~~~  181 (357)
T 2fna_A          155 VNLLPALAYAYDNL-KRIKFIMSGSEMG  181 (357)
T ss_dssp             CCCHHHHHHHHHHC-TTEEEEEEESSHH
T ss_pred             hhHHHHHHHHHHcC-CCeEEEEEcCchH
Confidence             2 23333222222 3667777 77543

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=98.77  E-value=8.8e-09  Score=95.00  Aligned_cols=88  Identities=27%  Similarity=0.335  Sum_probs=56.0

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .++.+++|++|+++.+.  +..+|..++.+++|++|++++|...+.+|..++.+++|++|++++|...+.+|.+++++++
T Consensus       201 ~l~~l~~L~~L~L~~N~--l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~~  278 (328)
T 4fcg_A          201 SIANLQNLKSLKIRNSP--LSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQ  278 (328)
T ss_dssp             GGGGCTTCCEEEEESSC--CCCCCGGGGGCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGGGCTT
T ss_pred             hhcCCCCCCEEEccCCC--CCcCchhhccCCCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchhhhcCCC
Confidence            34556666666663322  2245555666666777777766555666666666777777777766666667766777777


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |++|++++++
T Consensus       279 L~~L~L~~n~  288 (328)
T 4fcg_A          279 LEKLDLRGCV  288 (328)
T ss_dssp             CCEEECTTCT
T ss_pred             CCEEeCCCCC
Confidence            7777776643

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=98.73  E-value=1.9e-08  Score=85.51  Aligned_cols=89  Identities=11%  Similarity=0.134  Sum_probs=54.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +.+..+++|++|+++.+. .....|..++.+++|++|++++|......|..++.+++|++|++++|..+..+| .+.+++
T Consensus        82 ~~l~~l~~L~~L~l~~n~-l~~~~~~~l~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~  159 (197)
T 4ezg_A           82 NPISGLSNLERLRIMGKD-VTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLP  159 (197)
T ss_dssp             GGGTTCTTCCEEEEECTT-CBGGGSCCCTTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCS
T ss_pred             hhhhcCCCCCEEEeECCc-cCcccChhhcCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCC
Confidence            345566677777773322 222244556667777777777763223455566777777777777755466666 567777


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|+++++.
T Consensus       160 ~L~~L~l~~n~  170 (197)
T 4ezg_A          160 ELKSLNIQFDG  170 (197)
T ss_dssp             SCCEEECTTBC
T ss_pred             CCCEEECCCCC
Confidence            77777776654

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=98.71  E-value=2e-08  Score=92.61  Aligned_cols=88  Identities=24%  Similarity=0.235  Sum_probs=79.9

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +.+..+++|++|++ .++.....+|..++.+++|++|++++|...+.+|..++.+++|++|+|++|..++.+|+++++|+
T Consensus       223 ~~l~~l~~L~~L~L-s~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~iP~~l~~L~  301 (328)
T 4fcg_A          223 PAIHHLPKLEELDL-RGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLP  301 (328)
T ss_dssp             GGGGGCTTCCEEEC-TTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEECTTCTTCCCCCGGGGGSC
T ss_pred             hhhccCCCCCEEEC-cCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeCCCCCchhhccHHHhhcc
Confidence            45678999999999 55556668898899999999999999988899999999999999999999999999999999999


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|+.+++..
T Consensus       302 ~L~~l~l~~  310 (328)
T 4fcg_A          302 ANCIILVPP  310 (328)
T ss_dssp             TTCEEECCG
T ss_pred             CceEEeCCH
Confidence            999998874

>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=98.69  E-value=7.9e-08  Score=82.43  Aligned_cols=120  Identities=8%  Similarity=0.007  Sum_probs=73.0

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHH
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMK   92 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~   92 (351)
                      -.+++|+++.++.+.+++....  ...+.|+|++|+|||++|+.+++.  .........++.+.    .....+...+. 
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   90 (226)
T 2chg_A           16 LDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARD--LFGENWRDNFIEMNASDERGIDVVRHKIK-   90 (226)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSTTSSHHHHHHHHHHH--HHGGGGGGGEEEEETTCTTCHHHHHHHHH-
T ss_pred             HHHHcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHH--HhccccccceEEeccccccChHHHHHHHH-
Confidence            3568999999999999997653  223789999999999999999876  32222222334443    12211111111 


Q ss_pred             HhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           93 SLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      .+.....                  .-.+++.++|+||++..  +..+.+...+.....+.++|+ |+..
T Consensus        91 ~~~~~~~------------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~  142 (226)
T 2chg_A           91 EFARTAP------------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYV  142 (226)
T ss_dssp             HHHTSCC------------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             HHhcccC------------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCCh
Confidence            1111000                  01257889999999765  445566655554455667777 6544

>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=98.67  E-value=9.3e-08  Score=83.00  Aligned_cols=136  Identities=13%  Similarity=0.030  Sum_probs=74.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      .+++|+++.++.+..++..+. ....+.|+|++|+||||||+.+++.  ....+....+-+  ..... ...+.......
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~   96 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKG--LNCETGITATPC--GVCDN-CREIEQGRFVD   96 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHH--HHCTTCSCSSCC--SCSHH-HHHHHTTCCSS
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHH--hcCCCCCCCCCC--cccHH-HHHHhccCCcc
Confidence            469999999999999997653 2347889999999999999999876  322221100000  00000 01111000000


Q ss_pred             CC-CccCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCC--hhhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           98 SA-LSEILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWR--GDIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        98 ~~-~~~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~--~~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      .. .........+.+.+.+...    ..+++.++|+||++.  .+.++.+...+.....+.++|+ |+..
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~  166 (250)
T 1njg_A           97 LIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDP  166 (250)
T ss_dssp             EEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCG
T ss_pred             eEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCCh
Confidence            00 0000011112222222221    135678999999965  3567777776655555677777 7654

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=98.61  E-value=3.5e-08  Score=101.29  Aligned_cols=91  Identities=15%  Similarity=0.128  Sum_probs=79.4

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhc
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ..+.++.+++|++|+++.+... ..+|..++.+++|++|+|++|...+.+|..++.|++|++|+|++|...+.+|..+++
T Consensus       624 ~~~~~~~l~~L~~LdLs~N~l~-g~ip~~l~~l~~L~~L~Ls~N~l~g~ip~~l~~L~~L~~LdLs~N~l~g~ip~~l~~  702 (768)
T 3rgz_A          624 TSPTFDNNGSMMFLDMSYNMLS-GYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSA  702 (768)
T ss_dssp             CCCSCSSSBCCCEEECCSSCCB-SCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEECCCGGGGG
T ss_pred             CchhhhccccccEEECcCCccc-ccCCHHHhccccCCEEeCcCCccCCCCChHHhCCCCCCEEECCCCcccCcCChHHhC
Confidence            3456778899999999655444 478999999999999999999656699999999999999999998877899999999


Q ss_pred             CCCCCEEEecCC
Q 048347          314 IKALRKLESWWP  325 (351)
Q Consensus       314 L~~L~~L~l~~~  325 (351)
                      |++|++|++++.
T Consensus       703 l~~L~~L~ls~N  714 (768)
T 3rgz_A          703 LTMLTEIDLSNN  714 (768)
T ss_dssp             CCCCSEEECCSS
T ss_pred             CCCCCEEECcCC
Confidence            999999999875

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=98.59  E-value=1e-07  Score=80.92  Aligned_cols=89  Identities=10%  Similarity=0.066  Sum_probs=72.8

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ++.+..+++|++|+++ ++ .+..++ .+..+++|++|++++|......|..++.+++|++|++++|......|..++++
T Consensus        59 l~~l~~l~~L~~L~l~-~n-~~~~~~-~l~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~Ls~n~i~~~~~~~l~~l  135 (197)
T 4ezg_A           59 LTGIEYAHNIKDLTIN-NI-HATNYN-PISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTL  135 (197)
T ss_dssp             CTTGGGCTTCSEEEEE-SC-CCSCCG-GGTTCTTCCEEEEECTTCBGGGSCCCTTCTTCCEEECCSSBCBGGGHHHHTTC
T ss_pred             hHHHhcCCCCCEEEcc-CC-CCCcch-hhhcCCCCCEEEeECCccCcccChhhcCCCCCCEEEecCCccCcHhHHHHhhC
Confidence            3467889999999995 44 444444 68889999999999994333578889999999999999976555678899999


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|+++++.
T Consensus       136 ~~L~~L~L~~n~  147 (197)
T 4ezg_A          136 PKVNSIDLSYNG  147 (197)
T ss_dssp             SSCCEEECCSCT
T ss_pred             CCCCEEEccCCC
Confidence            999999999986

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=98.55  E-value=4.2e-08  Score=98.60  Aligned_cols=67  Identities=12%  Similarity=0.131  Sum_probs=44.8

Q ss_pred             eeeCCCCCCcccEEEEecCCcccc------------------cccccc--ccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          259 LVCGHGGFPRQEILHLKSMLWLEE------------------WKMETG--AMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       259 lp~~~~~l~~L~~L~L~~~~~l~~------------------lp~~i~--~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      +|..++.+++|++|+|++|. +..                  +|..++  ++++|++|++++|...+.+|..++++++|+
T Consensus       198 ip~~l~~l~~L~~L~Ls~n~-l~~~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~  276 (636)
T 4eco_A          198 VSKAVMRLTKLRQFYMGNSP-FVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQ  276 (636)
T ss_dssp             ECGGGGGCTTCCEEEEESCC-CCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEECCTTCSSCCTTTTTCSSCC
T ss_pred             CCHHHhcccCCCEEECcCCc-cccccccccccccccchhcccCchhhhhcccCCCCEEEecCCcCCccChHHHhcCCCCC
Confidence            55566666777777777763 444                  676666  677777777776666666777777777777


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|+++++.
T Consensus       277 ~L~Ls~n~  284 (636)
T 4eco_A          277 LINVACNR  284 (636)
T ss_dssp             EEECTTCT
T ss_pred             EEECcCCC
Confidence            77776654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.54  E-value=3.5e-07  Score=83.57  Aligned_cols=113  Identities=12%  Similarity=0.100  Sum_probs=75.9

Q ss_pred             cccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCCccccc---CCCeeEEEEEe----CCHHHHHHHH
Q 048347           20 DLDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN---YFDCCAWVYYQ----LSLDMMLDAI   90 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~---~F~~~~wv~~~----~~~~~~~~~i   90 (351)
                      +.|||++.+++...|...  +.+..-+-|+|+.|+|||++|+.|++..+-..   ......++++.    .+...++..|
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I  101 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKI  101 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHH
Confidence            789999999999888652  33556778999999999999999998832111   11134556666    6778899999


Q ss_pred             HHHhCCCCCCccCCCCCHHHHHHHHHHh--cCCceEEEEEeCCCChh
Q 048347           91 MKSLMPLSALSEILDNDFEMKKNTLHNY--LKNKRYLIVIQDVWRGD  135 (351)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~--L~~k~~LlVLDdv~~~~  135 (351)
                      ++++......   .......+.+.+...  -.+++++++||+++...
T Consensus       102 ~~~L~g~~~~---~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~  145 (318)
T 3te6_A          102 WFAISKENLC---GDISLEALNFYITNVPKAKKRKTLILIQNPENLL  145 (318)
T ss_dssp             HHHHSCCC-----CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC
T ss_pred             HHHhcCCCCC---chHHHHHHHHHHHHhhhccCCceEEEEecHHHhh
Confidence            9999764321   122333344433332  24678999999998653

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=98.54  E-value=6e-08  Score=88.71  Aligned_cols=89  Identities=11%  Similarity=-0.019  Sum_probs=43.6

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .+..+++|++|+++.++.....+|..++.+++|++|++++|...+.+|..++.+++|++|++++|.....+|..++++++
T Consensus        71 ~l~~l~~L~~L~L~~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~~  150 (313)
T 1ogq_A           71 SLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPN  150 (313)
T ss_dssp             GGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTT
T ss_pred             hHhCCCCCCeeeCCCCCcccccCChhHhcCCCCCEEECcCCeeCCcCCHHHhCCCCCCEEeCCCCccCCcCChHHhcCCC
Confidence            34455555555553111122234544555555555555555222245555555555555555554332345555555555


Q ss_pred             CCEEEecCC
Q 048347          317 LRKLESWWP  325 (351)
Q Consensus       317 L~~L~l~~~  325 (351)
                      |++|++++.
T Consensus       151 L~~L~L~~N  159 (313)
T 1ogq_A          151 LVGITFDGN  159 (313)
T ss_dssp             CCEEECCSS
T ss_pred             CCeEECcCC
Confidence            555555543

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=98.53  E-value=2.7e-07  Score=80.45  Aligned_cols=83  Identities=18%  Similarity=0.176  Sum_probs=44.1

Q ss_pred             CCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccCh-hhhcCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPE-ELWRIK  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~  315 (351)
                      +..+++|++|+|+.+  .+..+|.. +..+++|++|++++| .+..+|..++.+++|++|+|++| .+..+|. .+.+++
T Consensus        84 ~~~l~~L~~L~Ls~N--~l~~l~~~~~~~l~~L~~L~Ls~N-~l~~lp~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~  159 (229)
T 3e6j_A           84 FDSLTQLTVLDLGTN--QLTVLPSAVFDRLVHLKELFMCCN-KLTELPRGIERLTHLTHLALDQN-QLKSIPHGAFDRLS  159 (229)
T ss_dssp             TTTCTTCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCSCCTTGGGCTTCSEEECCSS-CCCCCCTTTTTTCT
T ss_pred             cccCCCcCEEECCCC--cCCccChhHhCcchhhCeEeccCC-cccccCcccccCCCCCEEECCCC-cCCccCHHHHhCCC
Confidence            345555666666322  22233332 355566666666665 45566655666666666666653 4555553 245566


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|+.|++++
T Consensus       160 ~L~~L~l~~  168 (229)
T 3e6j_A          160 SLTHAYLFG  168 (229)
T ss_dssp             TCCEEECTT
T ss_pred             CCCEEEeeC
Confidence            666666654

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=98.53  E-value=2e-07  Score=76.85  Aligned_cols=85  Identities=16%  Similarity=0.201  Sum_probs=69.0

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccc-ccccccccCCccEEeecCCccccccC--hhhhc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEE-WKMETGAMQKLKSLIVNPCAYLRKFP--EELWR  313 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~-lp~~i~~L~~L~~L~l~~c~~l~~lP--~~i~~  313 (351)
                      .+..+++|++|+++.+.  +..+ ..+..+++|++|++++| .+.. +|..++.+++|++|++++| .+..+|  ..+.+
T Consensus        44 ~~~~l~~L~~L~l~~n~--l~~~-~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~l~~  118 (168)
T 2ell_A           44 LTAEFVNLEFLSLINVG--LISV-SNLPKLPKLKKLELSEN-RIFGGLDMLAEKLPNLTHLNLSGN-KLKDISTLEPLKK  118 (168)
T ss_dssp             CCGGGGGCCEEEEESSC--CCCC-SSCCCCSSCCEEEEESC-CCCSCCCHHHHHCTTCCEEECBSS-SCCSSGGGGGGSS
T ss_pred             HHHhCCCCCEEeCcCCC--CCCh-hhhccCCCCCEEECcCC-cCchHHHHHHhhCCCCCEEeccCC-ccCcchhHHHHhc
Confidence            34788999999995443  3344 56888999999999999 5665 7777778999999999986 678877  78899


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|++++++
T Consensus       119 l~~L~~L~l~~N~  131 (168)
T 2ell_A          119 LECLKSLDLFNCE  131 (168)
T ss_dssp             CSCCCEEECCSSG
T ss_pred             CCCCCEEEeeCCc
Confidence            9999999999875

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=98.52  E-value=1.5e-07  Score=76.09  Aligned_cols=86  Identities=12%  Similarity=0.153  Sum_probs=69.9

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccc-ccccccccCCccEEeecCCccccccC--hhhh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEE-WKMETGAMQKLKSLIVNPCAYLRKFP--EELW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~-lp~~i~~L~~L~~L~l~~c~~l~~lP--~~i~  312 (351)
                      +.+..+++|++|+++.+  .+..+ ..++.+++|++|++++| .+.. +|..++.+++|++|++++| .+..+|  ..++
T Consensus        36 ~~~~~l~~L~~L~l~~n--~l~~~-~~~~~l~~L~~L~Ls~n-~i~~~~~~~~~~l~~L~~L~ls~N-~i~~~~~~~~~~  110 (149)
T 2je0_A           36 GLTDEFEELEFLSTINV--GLTSI-ANLPKLNKLKKLELSDN-RVSGGLEVLAEKCPNLTHLNLSGN-KIKDLSTIEPLK  110 (149)
T ss_dssp             SCCTTCTTCCEEECTTS--CCCCC-TTCCCCTTCCEEECCSS-CCCSCTHHHHHHCTTCCEEECTTS-CCCSHHHHGGGG
T ss_pred             HHHhhcCCCcEEECcCC--CCCCc-hhhhcCCCCCEEECCCC-cccchHHHHhhhCCCCCEEECCCC-cCCChHHHHHHh
Confidence            45578999999999433  33344 56888999999999999 5665 8877888999999999986 577765  7899


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++++
T Consensus       111 ~l~~L~~L~l~~N~  124 (149)
T 2je0_A          111 KLENLKSLDLFNCE  124 (149)
T ss_dssp             GCTTCCEEECTTCG
T ss_pred             hCCCCCEEeCcCCc
Confidence            99999999999875

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.50  E-value=1.2e-07  Score=93.85  Aligned_cols=87  Identities=18%  Similarity=0.111  Sum_probs=75.0

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccccc--Chhhh
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKF--PEELW  312 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~l--P~~i~  312 (351)
                      ++.++.+++|+.|+|+.+  .+..+|..++.+++|++|+|++| .+..+| .++.|++|++|+|++| .+..+  |..++
T Consensus       456 lp~~~~l~~L~~L~Ls~N--~l~~lp~~~~~l~~L~~L~Ls~N-~l~~lp-~l~~l~~L~~L~Ls~N-~l~~~~~p~~l~  530 (567)
T 1dce_A          456 LCHLEQLLLVTHLDLSHN--RLRALPPALAALRCLEVLQASDN-ALENVD-GVANLPRLQELLLCNN-RLQQSAAIQPLV  530 (567)
T ss_dssp             CCCGGGGTTCCEEECCSS--CCCCCCGGGGGCTTCCEEECCSS-CCCCCG-GGTTCSSCCEEECCSS-CCCSSSTTGGGG
T ss_pred             CcCccccccCcEeecCcc--cccccchhhhcCCCCCEEECCCC-CCCCCc-ccCCCCCCcEEECCCC-CCCCCCCcHHHh
Confidence            455788899999999544  33478989999999999999999 688899 8999999999999985 57777  89999


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      +|++|+.|++++.+
T Consensus       531 ~l~~L~~L~L~~N~  544 (567)
T 1dce_A          531 SCPRLVLLNLQGNS  544 (567)
T ss_dssp             GCTTCCEEECTTSG
T ss_pred             cCCCCCEEEecCCc
Confidence            99999999999865

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=98.49  E-value=4.5e-08  Score=99.87  Aligned_cols=86  Identities=20%  Similarity=0.100  Sum_probs=73.2

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .+..+++|++|+|+.+  .+..+|..++.+++|++|+|++| .+..+|..++.|.+|++|+|++| .+..+|.++++|++
T Consensus       242 ~~~~l~~L~~L~Ls~N--~l~~lp~~~~~l~~L~~L~Ls~N-~l~~lp~~~~~l~~L~~L~L~~N-~l~~lp~~~~~l~~  317 (727)
T 4b8c_D          242 NIFKYDFLTRLYLNGN--SLTELPAEIKNLSNLRVLDLSHN-RLTSLPAELGSCFQLKYFYFFDN-MVTTLPWEFGNLCN  317 (727)
T ss_dssp             GGGGCCSCSCCBCTTS--CCSCCCGGGGGGTTCCEEECTTS-CCSSCCSSGGGGTTCSEEECCSS-CCCCCCSSTTSCTT
T ss_pred             hhcCCCCCCEEEeeCC--cCcccChhhhCCCCCCEEeCcCC-cCCccChhhcCCCCCCEEECCCC-CCCccChhhhcCCC
Confidence            4457899999999433  33378888899999999999999 68899999999999999999985 68899999999999


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |++|++++.+
T Consensus       318 L~~L~L~~N~  327 (727)
T 4b8c_D          318 LQFLGVEGNP  327 (727)
T ss_dssp             CCCEECTTSC
T ss_pred             ccEEeCCCCc
Confidence            9999998865

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=98.48  E-value=6.8e-08  Score=98.54  Aligned_cols=87  Identities=16%  Similarity=0.037  Sum_probs=73.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      ..+..+++|+.|+|+ ++ .+..+|..+..+++|++|+|++| .+..+|..++.|++|++|+|++| .+..+|.++++|+
T Consensus       218 ~~~~~l~~L~~L~Ls-~n-~l~~l~~~~~~l~~L~~L~Ls~N-~l~~lp~~~~~l~~L~~L~Ls~N-~l~~lp~~~~~l~  293 (727)
T 4b8c_D          218 DSKYDDQLWHALDLS-NL-QIFNISANIFKYDFLTRLYLNGN-SLTELPAEIKNLSNLRVLDLSHN-RLTSLPAELGSCF  293 (727)
T ss_dssp             ----CCCCCCEEECT-TS-CCSCCCGGGGGCCSCSCCBCTTS-CCSCCCGGGGGGTTCCEEECTTS-CCSSCCSSGGGGT
T ss_pred             hhhccCCCCcEEECC-CC-CCCCCChhhcCCCCCCEEEeeCC-cCcccChhhhCCCCCCEEeCcCC-cCCccChhhcCCC
Confidence            456788999999994 33 34478888889999999999999 68899999999999999999996 5779999999999


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|+++++.
T Consensus       294 ~L~~L~L~~N~  304 (727)
T 4b8c_D          294 QLKYFYFFDNM  304 (727)
T ss_dssp             TCSEEECCSSC
T ss_pred             CCCEEECCCCC
Confidence            99999999864

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=98.48  E-value=2.6e-07  Score=76.96  Aligned_cols=84  Identities=18%  Similarity=0.128  Sum_probs=58.4

Q ss_pred             CCCCC-CceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccc-cccCCccEEeecCCccccccCh--hhhc
Q 048347          238 PEKLP-HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMET-GAMQKLKSLIVNPCAYLRKFPE--ELWR  313 (351)
Q Consensus       238 l~~l~-~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i-~~L~~L~~L~l~~c~~l~~lP~--~i~~  313 (351)
                      +..+. +|++|+++.+  .+..+ ..+..+++|++|++++| .+..+|..+ +.+++|++|++++| .+..+|.  .+++
T Consensus        37 ~~~~~~~L~~L~Ls~N--~l~~~-~~l~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N-~i~~~~~~~~l~~  111 (176)
T 1a9n_A           37 LGATLDQFDAIDFSDN--EIRKL-DGFPLLRRLKTLLVNNN-RICRIGEGLDQALPDLTELILTNN-SLVELGDLDPLAS  111 (176)
T ss_dssp             GGGGTTCCSEEECCSS--CCCEE-CCCCCCSSCCEEECCSS-CCCEECSCHHHHCTTCCEEECCSC-CCCCGGGGGGGGG
T ss_pred             hhhcCCCCCEEECCCC--CCCcc-cccccCCCCCEEECCCC-cccccCcchhhcCCCCCEEECCCC-cCCcchhhHhhhc
Confidence            33443 7888888433  23344 45677788888888887 577777654 77888888888874 5677776  6777


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|++++.+
T Consensus       112 l~~L~~L~l~~N~  124 (176)
T 1a9n_A          112 LKSLTYLCILRNP  124 (176)
T ss_dssp             CTTCCEEECCSSG
T ss_pred             CCCCCEEEecCCC
Confidence            8888888887765

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.47  E-value=2.7e-07  Score=76.99  Aligned_cols=82  Identities=17%  Similarity=0.105  Sum_probs=68.6

Q ss_pred             CCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIKAL  317 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L  317 (351)
                      .++|++|+++.+.  +..+ |..+..+++|++|+|++| .+..+|.. ++.+++|++|+|++ ..+..+|.+ ++++++|
T Consensus        32 ~~~L~~L~Ls~N~--l~~~~~~~~~~l~~L~~L~Ls~N-~l~~i~~~~~~~l~~L~~L~L~~-N~l~~l~~~~~~~l~~L  107 (174)
T 2r9u_A           32 PTDKQRLWLNNNQ--ITKLEPGVFDHLVNLQQLYFNSN-KLTAIPTGVFDKLTQLTQLDLND-NHLKSIPRGAFDNLKSL  107 (174)
T ss_dssp             CTTCSEEECCSSC--CCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCS-SCCCCCCTTTTTTCTTC
T ss_pred             CCCCcEEEeCCCC--ccccCHHHhcCCcCCCEEECCCC-CCCccChhHhCCcchhhEEECCC-CccceeCHHHhccccCC
Confidence            3789999994333  3344 566889999999999999 79999987 58999999999998 468889986 8899999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++.+
T Consensus       108 ~~L~L~~N~  116 (174)
T 2r9u_A          108 THIYLYNNP  116 (174)
T ss_dssp             SEEECCSSC
T ss_pred             CEEEeCCCC
Confidence            999998854

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=98.47  E-value=1.1e-07  Score=78.37  Aligned_cols=88  Identities=23%  Similarity=0.238  Sum_probs=73.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccc--ccccccCCccEEeecCCccccccCh----
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWK--METGAMQKLKSLIVNPCAYLRKFPE----  309 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp--~~i~~L~~L~~L~l~~c~~l~~lP~----  309 (351)
                      +.+..+++|++|+++.+.... .+|..+..+++|++|++++| .+..+|  ..++.+++|++|++++| .+..+|.    
T Consensus        65 ~~~~~l~~L~~L~Ls~N~l~~-~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~l~~l~~L~~L~l~~N-~l~~~~~~~~~  141 (168)
T 2ell_A           65 SNLPKLPKLKKLELSENRIFG-GLDMLAEKLPNLTHLNLSGN-KLKDISTLEPLKKLECLKSLDLFNC-EVTNLNDYRES  141 (168)
T ss_dssp             SSCCCCSSCCEEEEESCCCCS-CCCHHHHHCTTCCEEECBSS-SCCSSGGGGGGSSCSCCCEEECCSS-GGGTSTTHHHH
T ss_pred             hhhccCCCCCEEECcCCcCch-HHHHHHhhCCCCCEEeccCC-ccCcchhHHHHhcCCCCCEEEeeCC-cCcchHHHHHH
Confidence            677889999999995444332 36766667999999999999 688877  67899999999999996 5777886    


Q ss_pred             hhhcCCCCCEEEecCCC
Q 048347          310 ELWRIKALRKLESWWPR  326 (351)
Q Consensus       310 ~i~~L~~L~~L~l~~~~  326 (351)
                      .+.++++|++|+++++.
T Consensus       142 ~~~~l~~L~~L~l~~n~  158 (168)
T 2ell_A          142 VFKLLPQLTYLDGYDRE  158 (168)
T ss_dssp             HHTTCSSCCEETTEETT
T ss_pred             HHHhCccCcEecCCCCC
Confidence            78899999999999876

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=98.46  E-value=2.2e-07  Score=78.68  Aligned_cols=87  Identities=21%  Similarity=0.153  Sum_probs=69.0

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhcCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      +..+++|++|+++.+ ......|..+..+++|++|+|++| .+..+|.. ++.+++|++|+|++|......|..++.+++
T Consensus        50 ~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~  127 (192)
T 1w8a_A           50 FGRLPHLVKLELKRN-QLTGIEPNAFEGASHIQELQLGEN-KIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNS  127 (192)
T ss_dssp             GGGCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSC-CCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTT
T ss_pred             cccCCCCCEEECCCC-CCCCcCHhHcCCcccCCEEECCCC-cCCccCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCC
Confidence            678899999999443 333234667889999999999999 67777665 889999999999996544455778899999


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |++|++++.+
T Consensus       128 L~~L~L~~N~  137 (192)
T 1w8a_A          128 LTSLNLASNP  137 (192)
T ss_dssp             CCEEECTTCC
T ss_pred             CCEEEeCCCC
Confidence            9999998754

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=98.45  E-value=5.4e-07  Score=78.46  Aligned_cols=88  Identities=20%  Similarity=0.166  Sum_probs=73.8

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhh
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELW  312 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~  312 (351)
                      ...+..+++|++|+|+.+.  +..+|.. +..+++|++|+|++| .+..+|.. ++.+++|++|+|++| .+..+|.++.
T Consensus        57 ~~~~~~l~~L~~L~L~~N~--l~~i~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~~~~l~~L~~L~Ls~N-~l~~lp~~~~  132 (229)
T 3e6j_A           57 PGVFDSLINLKELYLGSNQ--LGALPVGVFDSLTQLTVLDLGTN-QLTVLPSAVFDRLVHLKELFMCCN-KLTELPRGIE  132 (229)
T ss_dssp             TTTTTTCTTCCEEECCSSC--CCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCSCCTTGG
T ss_pred             HHHhhCccCCcEEECCCCC--CCCcChhhcccCCCcCEEECCCC-cCCccChhHhCcchhhCeEeccCC-cccccCcccc
Confidence            3456789999999994443  3466654 688999999999999 68888876 689999999999984 6889999999


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++..
T Consensus       133 ~l~~L~~L~L~~N~  146 (229)
T 3e6j_A          133 RLTHLTHLALDQNQ  146 (229)
T ss_dssp             GCTTCSEEECCSSC
T ss_pred             cCCCCCEEECCCCc
Confidence            99999999998754

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=98.44  E-value=4.3e-07  Score=78.63  Aligned_cols=84  Identities=13%  Similarity=0.097  Sum_probs=38.6

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCcccccc-ChhhhcCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKF-PEELWRIK  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~  315 (351)
                      +..+++|++|+|+ ++......|..+..+++|++|+|++| .+..+|.. ++.+++|++|+|++| .+..+ |..+.+++
T Consensus        52 ~~~l~~L~~L~Ls-~N~i~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~f~~l~~L~~L~L~~N-~l~~~~~~~~~~l~  128 (220)
T 2v9t_B           52 FSPYKKLRRIDLS-NNQISELAPDAFQGLRSLNSLVLYGN-KITELPKSLFEGLFSLQLLLLNAN-KINCLRVDAFQDLH  128 (220)
T ss_dssp             STTCTTCCEEECC-SSCCCEECTTTTTTCSSCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCT
T ss_pred             hhCCCCCCEEECC-CCcCCCcCHHHhhCCcCCCEEECCCC-cCCccCHhHccCCCCCCEEECCCC-CCCEeCHHHcCCCC
Confidence            3445555555552 22111112334555555555555555 34555544 344555555555553 23333 33344555


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|++|++++
T Consensus       129 ~L~~L~L~~  137 (220)
T 2v9t_B          129 NLNLLSLYD  137 (220)
T ss_dssp             TCCEEECCS
T ss_pred             CCCEEECCC
Confidence            555555544

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=98.43  E-value=2.1e-07  Score=77.58  Aligned_cols=90  Identities=16%  Similarity=0.094  Sum_probs=75.4

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCC-CCCCcccEEEEecCCccccccc--cccccCCccEEeecCCccccccChh--
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGH-GGFPRQEILHLKSMLWLEEWKM--ETGAMQKLKSLIVNPCAYLRKFPEE--  310 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~-~~l~~L~~L~L~~~~~l~~lp~--~i~~L~~L~~L~l~~c~~l~~lP~~--  310 (351)
                      +.+..+++|++|+++.+  .+..+|... ..+++|++|++++| .++.+|.  .++.+++|++|++++| .+..+|..  
T Consensus        58 ~~l~~l~~L~~L~Ls~N--~l~~~~~~~~~~l~~L~~L~L~~N-~i~~~~~~~~l~~l~~L~~L~l~~N-~i~~~~~~~~  133 (176)
T 1a9n_A           58 DGFPLLRRLKTLLVNNN--RICRIGEGLDQALPDLTELILTNN-SLVELGDLDPLASLKSLTYLCILRN-PVTNKKHYRL  133 (176)
T ss_dssp             CCCCCCSSCCEEECCSS--CCCEECSCHHHHCTTCCEEECCSC-CCCCGGGGGGGGGCTTCCEEECCSS-GGGGSTTHHH
T ss_pred             cccccCCCCCEEECCCC--cccccCcchhhcCCCCCEEECCCC-cCCcchhhHhhhcCCCCCEEEecCC-CCCCcHhHHH
Confidence            56788999999999433  344677554 78999999999999 6899997  7899999999999995 57788986  


Q ss_pred             --hhcCCCCCEEEecCCChhH
Q 048347          311 --LWRIKALRKLESWWPRPEL  329 (351)
Q Consensus       311 --i~~L~~L~~L~l~~~~~~~  329 (351)
                        ++.+++|+.|++++...+-
T Consensus       134 ~~~~~l~~L~~Ld~~~n~~~~  154 (176)
T 1a9n_A          134 YVIYKVPQVRVLDFQKVKLKE  154 (176)
T ss_dssp             HHHHHCTTCSEETTEECCHHH
T ss_pred             HHHHHCCccceeCCCcCCHHH
Confidence              8999999999999887443

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=98.43  E-value=4.1e-07  Score=73.39  Aligned_cols=84  Identities=19%  Similarity=0.093  Sum_probs=69.5

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccc-cChhhhcCCCCC
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRK-FPEELWRIKALR  318 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~-lP~~i~~L~~L~  318 (351)
                      ..++|+.|+++.+......+|..+..+++|++|++++| .+..+ ..++.+++|++|++++|. +.. +|..++++++|+
T Consensus        15 ~~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n-~l~~~-~~~~~l~~L~~L~Ls~n~-i~~~~~~~~~~l~~L~   91 (149)
T 2je0_A           15 TPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINV-GLTSI-ANLPKLNKLKKLELSDNR-VSGGLEVLAEKCPNLT   91 (149)
T ss_dssp             CGGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTS-CCCCC-TTCCCCTTCCEEECCSSC-CCSCTHHHHHHCTTCC
T ss_pred             CCccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCC-CCCCc-hhhhcCCCCCEEECCCCc-ccchHHHHhhhCCCCC
Confidence            34789999994443332478888899999999999999 68877 679999999999999965 555 888888899999


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|+++++.
T Consensus        92 ~L~ls~N~   99 (149)
T 2je0_A           92 HLNLSGNK   99 (149)
T ss_dssp             EEECTTSC
T ss_pred             EEECCCCc
Confidence            99999876

>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=98.42  E-value=2.2e-07  Score=84.79  Aligned_cols=116  Identities=9%  Similarity=0.107  Sum_probs=71.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~   96 (351)
                      .+++|+++.++.+.+++..+..  ..+.++|++|+|||++|+.+++.  +........++.+. .+              
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~--------------   82 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDGNM--PHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASD--------------   82 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCCC--CCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTS--------------
T ss_pred             HHHHCCHHHHHHHHHHHHcCCC--CeEEEECcCCCCHHHHHHHHHHH--hcCCcccCCEEEecCcc--------------
Confidence            5689999999999999976542  22789999999999999999887  32211111223332 11              


Q ss_pred             CCCCccCCCCCHHHHHHHHHHh------c-CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           97 LSALSEILDNDFEMKKNTLHNY------L-KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~l~~~------L-~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                              ....+.+.+.+...      + .+++.++|+||++..  +.++.+...+.....+.++|+ |+..
T Consensus        83 --------~~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~  147 (323)
T 1sxj_B           83 --------DRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  147 (323)
T ss_dssp             --------CCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             --------ccChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCCh
Confidence                    01122222222221      1 356889999999764  455555555554445677777 7543

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=98.40  E-value=9.6e-07  Score=73.44  Aligned_cols=87  Identities=22%  Similarity=0.251  Sum_probs=69.0

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhh-h
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEEL-W  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i-~  312 (351)
                      ..+..+++|++|+++.+  .+..+|.. +..+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|..+ .
T Consensus        46 ~~~~~l~~L~~L~l~~n--~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~  121 (177)
T 2o6r_A           46 GVFDKLTQLTKLSLSQN--QIQSLPDGVFDKLTKLTILYLHEN-KLQSLPNGVFDKLTQLKELALDTN-QLKSVPDGIFD  121 (177)
T ss_dssp             TTTTTCTTCSEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTT
T ss_pred             HHhcCcccccEEECCCC--cceEeChhHccCCCccCEEECCCC-CccccCHHHhhCCcccCEEECcCC-cceEeCHHHhc
Confidence            34578899999999433  33455544 578999999999998 68888776 688999999999985 678888875 7


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++.+
T Consensus       122 ~l~~L~~L~l~~N~  135 (177)
T 2o6r_A          122 RLTSLQKIWLHTNP  135 (177)
T ss_dssp             TCTTCCEEECCSSC
T ss_pred             CCcccCEEEecCCC
Confidence            79999999998765

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=98.39  E-value=1.8e-07  Score=85.56  Aligned_cols=92  Identities=11%  Similarity=0.048  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhc
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ....+..+++|++|+++.+. ....+|..+..+++|++|++++|...+.+|..++.+++|++|++++|.....+|..+++
T Consensus        93 ~p~~l~~l~~L~~L~Ls~n~-l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~  171 (313)
T 1ogq_A           93 IPPAIAKLTQLHYLYITHTN-VSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGS  171 (313)
T ss_dssp             CCGGGGGCTTCSEEEEEEEC-CEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGC
T ss_pred             CChhHhcCCCCCEEECcCCe-eCCcCCHHHhCCCCCCEEeCCCCccCCcCChHHhcCCCCCeEECcCCcccCcCCHHHhh
Confidence            33456777888888884333 22356767777888888888887433367777888888888888876544477877777


Q ss_pred             CC-CCCEEEecCCC
Q 048347          314 IK-ALRKLESWWPR  326 (351)
Q Consensus       314 L~-~L~~L~l~~~~  326 (351)
                      ++ +|++|++++..
T Consensus       172 l~~~L~~L~L~~N~  185 (313)
T 1ogq_A          172 FSKLFTSMTISRNR  185 (313)
T ss_dssp             CCTTCCEEECCSSE
T ss_pred             hhhcCcEEECcCCe
Confidence            77 77888777643

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.37  E-value=6.7e-07  Score=74.16  Aligned_cols=82  Identities=18%  Similarity=0.113  Sum_probs=67.8

Q ss_pred             CCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIKAL  317 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L  317 (351)
                      .++|++|+++.+  .+..+ |..+..+++|++|+|++| .+..+|.. ++.+++|++|+|++| .+..+|.+ +.++++|
T Consensus        29 ~~~l~~L~L~~N--~i~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~f~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L  104 (170)
T 3g39_A           29 PTTTQVLYLYDN--QITKLEPGVFDRLTQLTRLDLDNN-QLTVLPAGVFDKLTQLTQLSLNDN-QLKSIPRGAFDNLKSL  104 (170)
T ss_dssp             CTTCSEEECCSS--CCCCCCTTTTTTCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTC
T ss_pred             CCCCcEEEcCCC--cCCccChhhhcCcccCCEEECCCC-CcCccChhhccCCCCCCEEECCCC-ccCEeCHHHhcCCCCC
Confidence            478999999433  33344 556889999999999999 68888887 589999999999984 68888875 7899999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++.+
T Consensus       105 ~~L~L~~N~  113 (170)
T 3g39_A          105 THIWLLNNP  113 (170)
T ss_dssp             CEEECCSSC
T ss_pred             CEEEeCCCC
Confidence            999998853

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=98.37  E-value=1.6e-07  Score=97.25  Aligned_cols=67  Identities=13%  Similarity=0.243  Sum_probs=52.6

Q ss_pred             eeeCCCCCCcccEEEEecCCcccc------------------cccccc--ccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          259 LVCGHGGFPRQEILHLKSMLWLEE------------------WKMETG--AMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       259 lp~~~~~l~~L~~L~L~~~~~l~~------------------lp~~i~--~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      +|..++.+++|++|+|++|. +..                  +|..++  ++++|++|+|++|.....+|..+++|++|+
T Consensus       440 IP~~l~~L~~L~~L~Ls~N~-Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~N~l~~~iP~~l~~L~~L~  518 (876)
T 4ecn_A          440 ISKAIQRLTKLQIIYFANSP-FTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQ  518 (876)
T ss_dssp             ECGGGGGCTTCCEEEEESCC-CCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEESCTTCCSCCGGGGGCSSCC
T ss_pred             hhHHHhcCCCCCEEECcCCc-CCCCcccccccccccccccccCChhhhhccCCCCCEEECcCCCCCccChHHHhCCCCCC
Confidence            66677788888888888884 554                  787777  888888888888777778888888888888


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      .|+++++.
T Consensus       519 ~L~Ls~N~  526 (876)
T 4ecn_A          519 SLNIACNR  526 (876)
T ss_dssp             EEECTTCT
T ss_pred             EEECcCCC
Confidence            88887764

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=98.36  E-value=6.8e-07  Score=80.78  Aligned_cols=82  Identities=21%  Similarity=0.206  Sum_probs=38.5

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhh-hcCCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEEL-WRIKA  316 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i-~~L~~  316 (351)
                      ..+++|++|+++.+  .+..+|..+..+++|++|++++| .+..+|. .++.+++|++|++++| .+..+|.++ .++++
T Consensus        74 ~~l~~L~~L~Ls~N--~l~~l~~~~~~l~~L~~L~l~~N-~l~~l~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~  149 (290)
T 1p9a_G           74 GTLPVLGTLDLSHN--QLQSLPLLGQTLPALTVLDVSFN-RLTSLPLGALRGLGELQELYLKGN-ELKTLPPGLLTPTPK  149 (290)
T ss_dssp             SCCTTCCEEECCSS--CCSSCCCCTTTCTTCCEEECCSS-CCCCCCSSTTTTCTTCCEEECTTS-CCCCCCTTTTTTCTT
T ss_pred             CCCCcCCEEECCCC--cCCcCchhhccCCCCCEEECCCC-cCcccCHHHHcCCCCCCEEECCCC-CCCccChhhcccccC
Confidence            34455555555222  22244444455555555555555 3444442 2455555555555543 344444432 34555


Q ss_pred             CCEEEecC
Q 048347          317 LRKLESWW  324 (351)
Q Consensus       317 L~~L~l~~  324 (351)
                      |+.|++++
T Consensus       150 L~~L~L~~  157 (290)
T 1p9a_G          150 LEKLSLAN  157 (290)
T ss_dssp             CCEEECTT
T ss_pred             CCEEECCC
Confidence            55555544

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=98.35  E-value=2e-07  Score=93.59  Aligned_cols=90  Identities=8%  Similarity=0.055  Sum_probs=59.2

Q ss_pred             CCCCCCCCceEEEEecccccCce-----------------eeeCCC--CCCcccEEEEecCCccccccccccccCCccEE
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRK-----------------LVCGHG--GFPRQEILHLKSMLWLEEWKMETGAMQKLKSL  296 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~-----------------lp~~~~--~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L  296 (351)
                      +.++++++|++|+|+.+...+ .                 +|..++  .+++|++|++++|...+.+|..++++++|++|
T Consensus       200 ~~l~~l~~L~~L~Ls~n~l~~-~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L  278 (636)
T 4eco_A          200 KAVMRLTKLRQFYMGNSPFVA-ENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLI  278 (636)
T ss_dssp             GGGGGCTTCCEEEEESCCCCG-GGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEECCTTCSSCCTTTTTCSSCCEE
T ss_pred             HHHhcccCCCEEECcCCcccc-ccccccccccccchhcccCchhhhhcccCCCCEEEecCCcCCccChHHHhcCCCCCEE
Confidence            346677777777774443222 1                 676666  77777777777775566777777777777777


Q ss_pred             eecCCcccc--ccChhhhcC------CCCCEEEecCCC
Q 048347          297 IVNPCAYLR--KFPEELWRI------KALRKLESWWPR  326 (351)
Q Consensus       297 ~l~~c~~l~--~lP~~i~~L------~~L~~L~l~~~~  326 (351)
                      ++++|..+.  .+|.++++|      ++|++|+++++.
T Consensus       279 ~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~  316 (636)
T 4eco_A          279 NVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNN  316 (636)
T ss_dssp             ECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSC
T ss_pred             ECcCCCCCccccchHHHHhhhccccCCCCCEEECCCCc
Confidence            777765233  477777665      677777776643

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=98.33  E-value=9.1e-07  Score=76.55  Aligned_cols=86  Identities=13%  Similarity=0.063  Sum_probs=52.2

Q ss_pred             CCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCcccccc-Chhhhc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKF-PEELWR  313 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~l-P~~i~~  313 (351)
                      .+..+++|++|+++.+. . ..++ ..+..+++|++|+|++| .+..+ |..++.+++|++|+|++| .+..+ |..+..
T Consensus        76 ~~~~l~~L~~L~Ls~N~-l-~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~  151 (220)
T 2v70_A           76 AFEGASGVNEILLTSNR-L-ENVQHKMFKGLESLKTLMLRSN-RITCVGNDSFIGLSSVRLLSLYDN-QITTVAPGAFDT  151 (220)
T ss_dssp             TTTTCTTCCEEECCSSC-C-CCCCGGGGTTCSSCCEEECTTS-CCCCBCTTSSTTCTTCSEEECTTS-CCCCBCTTTTTT
T ss_pred             HhCCCCCCCEEECCCCc-c-CccCHhHhcCCcCCCEEECCCC-cCCeECHhHcCCCccCCEEECCCC-cCCEECHHHhcC
Confidence            45566677777773222 2 2333 33666777777777777 45544 445667777777777764 34444 566677


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|+.|++++.+
T Consensus       152 l~~L~~L~L~~N~  164 (220)
T 2v70_A          152 LHSLSTLNLLANP  164 (220)
T ss_dssp             CTTCCEEECCSCC
T ss_pred             CCCCCEEEecCcC
Confidence            7777777776643

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=98.33  E-value=8.4e-07  Score=75.18  Aligned_cols=87  Identities=16%  Similarity=0.110  Sum_probs=65.8

Q ss_pred             CCCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChh-hh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEE-LW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~-i~  312 (351)
                      ..+..+++|++|+++.+.  +..++ ..+..+++|++|+|++| .+..+|. .++.+++|++|+|++| .+..+|.+ +.
T Consensus        48 ~~~~~l~~L~~L~Ls~N~--i~~i~~~~f~~l~~L~~L~Ls~N-~l~~i~~~~f~~l~~L~~L~L~~N-~l~~~~~~~~~  123 (193)
T 2wfh_A           48 KELSNYKHLTLIDLSNNR--ISTLSNQSFSNMTQLLTLILSYN-RLRCIPPRTFDGLKSLRLLSLHGN-DISVVPEGAFN  123 (193)
T ss_dssp             GGGGGCTTCCEEECCSSC--CCCCCTTTTTTCTTCCEEECCSS-CCCBCCTTTTTTCTTCCEEECCSS-CCCBCCTTTTT
T ss_pred             HHhhcccCCCEEECCCCc--CCEeCHhHccCCCCCCEEECCCC-ccCEeCHHHhCCCCCCCEEECCCC-CCCeeChhhhh
Confidence            345678889999994332  33444 45788899999999998 5777765 4888999999999984 67788875 67


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|+.|++++.+
T Consensus       124 ~l~~L~~L~L~~N~  137 (193)
T 2wfh_A          124 DLSALSHLAIGANP  137 (193)
T ss_dssp             TCTTCCEEECCSSC
T ss_pred             cCccccEEEeCCCC
Confidence            88999999998743

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=98.33  E-value=1.1e-06  Score=76.00  Aligned_cols=85  Identities=16%  Similarity=0.225  Sum_probs=69.6

Q ss_pred             CCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCcccccc-ChhhhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKF-PEELWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~l-P~~i~~L  314 (351)
                      +..+++|++|+++.+  .+..++. .+..+++|++|+|++| .+..+|.. ++.+++|++|+|++| .+..+ |..+.++
T Consensus        53 ~~~l~~L~~L~L~~N--~i~~i~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l  128 (220)
T 2v70_A           53 FKKLPQLRKINFSNN--KITDIEEGAFEGASGVNEILLTSN-RLENVQHKMFKGLESLKTLMLRSN-RITCVGNDSFIGL  128 (220)
T ss_dssp             GGGCTTCCEEECCSS--CCCEECTTTTTTCTTCCEEECCSS-CCCCCCGGGGTTCSSCCEEECTTS-CCCCBCTTSSTTC
T ss_pred             hccCCCCCEEECCCC--cCCEECHHHhCCCCCCCEEECCCC-ccCccCHhHhcCCcCCCEEECCCC-cCCeECHhHcCCC
Confidence            578999999999433  3445554 6889999999999999 67777665 889999999999996 45555 6788999


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++..
T Consensus       129 ~~L~~L~L~~N~  140 (220)
T 2v70_A          129 SSVRLLSLYDNQ  140 (220)
T ss_dssp             TTCSEEECTTSC
T ss_pred             ccCCEEECCCCc
Confidence            999999998864

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=98.32  E-value=1.6e-06  Score=76.38  Aligned_cols=84  Identities=18%  Similarity=0.241  Sum_probs=47.1

Q ss_pred             CCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccCh-hhhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPE-ELWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L  314 (351)
                      +..+++|++|+++.+  .+..+|.. +..+++|++|++++| .+..+|. .++.+++|++|+|++| .+..+|. .+.++
T Consensus       103 ~~~l~~L~~L~L~~N--~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l  178 (251)
T 3m19_A          103 FDHLTQLDKLYLGGN--QLKSLPSGVFDRLTKLKELRLNTN-QLQSIPAGAFDKLTNLQTLSLSTN-QLQSVPHGAFDRL  178 (251)
T ss_dssp             TTTCTTCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTC
T ss_pred             hcccCCCCEEEcCCC--cCCCcChhHhccCCcccEEECcCC-cCCccCHHHcCcCcCCCEEECCCC-cCCccCHHHHhCC
Confidence            345566666666322  22234433 355666666666666 4555555 3566666666666664 3444544 45566


Q ss_pred             CCCCEEEecCC
Q 048347          315 KALRKLESWWP  325 (351)
Q Consensus       315 ~~L~~L~l~~~  325 (351)
                      ++|++|++++.
T Consensus       179 ~~L~~L~l~~N  189 (251)
T 3m19_A          179 GKLQTITLFGN  189 (251)
T ss_dssp             TTCCEEECCSC
T ss_pred             CCCCEEEeeCC
Confidence            66666666653

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=98.31  E-value=1.9e-06  Score=73.50  Aligned_cols=82  Identities=21%  Similarity=0.219  Sum_probs=39.4

Q ss_pred             CCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIK  315 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~  315 (351)
                      ..+++|++|+++.+  .+..+|.. +..+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.. +.+++
T Consensus        73 ~~l~~L~~L~Ls~n--~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~l~  148 (208)
T 2o6s_A           73 NKLTSLTYLNLSTN--QLQSLPNGVFDKLTQLKELALNTN-QLQSLPDGVFDKLTQLKDLRLYQN-QLKSVPDGVFDRLT  148 (208)
T ss_dssp             TTCTTCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCT
T ss_pred             CCCCCcCEEECCCC--cCCccCHhHhcCccCCCEEEcCCC-cCcccCHhHhccCCcCCEEECCCC-ccceeCHHHhccCC
Confidence            44555555555222  12223322 345555555555555 34444443 455555555555553 34444443 34555


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|+.|++++
T Consensus       149 ~L~~L~l~~  157 (208)
T 2o6s_A          149 SLQYIWLHD  157 (208)
T ss_dssp             TCCEEECCS
T ss_pred             CccEEEecC
Confidence            555555554

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=98.30  E-value=2.2e-06  Score=73.15  Aligned_cols=87  Identities=20%  Similarity=0.253  Sum_probs=70.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~  312 (351)
                      ..+..+++|++|+++.+  .+..+|.. +..+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.. +.
T Consensus        46 ~~~~~l~~L~~L~l~~n--~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~  121 (208)
T 2o6s_A           46 GVFDELTSLTQLYLGGN--KLQSLPNGVFNKLTSLTYLNLSTN-QLQSLPNGVFDKLTQLKELALNTN-QLQSLPDGVFD  121 (208)
T ss_dssp             TTTTTCTTCSEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTT
T ss_pred             hhhcccccCcEEECCCC--ccCccChhhcCCCCCcCEEECCCC-cCCccCHhHhcCccCCCEEEcCCC-cCcccCHhHhc
Confidence            34678999999999433  33456554 578999999999999 68888876 689999999999985 67788876 68


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++..
T Consensus       122 ~l~~L~~L~l~~N~  135 (208)
T 2o6s_A          122 KLTQLKDLRLYQNQ  135 (208)
T ss_dssp             TCTTCCEEECCSSC
T ss_pred             cCCcCCEEECCCCc
Confidence            99999999998754

>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=98.28  E-value=6.7e-07  Score=81.69  Aligned_cols=118  Identities=8%  Similarity=-0.013  Sum_probs=71.9

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHH--HHHHHHHHh
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDM--MLDAIMKSL   94 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~--~~~~i~~~~   94 (351)
                      .+++|+++.++.+.+++..+.  ..-+.++|+.|+||||+|+.+++.  +........++.+. .+...  ..+...   
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~---   97 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERGINVIREKV---   97 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHHHHTTHHHH---
T ss_pred             HHhhCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCceEEeeccccCchHHHHHHH---
Confidence            459999999999999987653  333789999999999999999887  32221112233333 22111  011111   


Q ss_pred             CCCCCCccCCCCCHHHHHHHHHH-hc-CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           95 MPLSALSEILDNDFEMKKNTLHN-YL-KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~l~~-~L-~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                                       .+.... .+ .+++.++|+|+++..  +.++.+...+.....+.++|+ |...
T Consensus        98 -----------------~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~  150 (327)
T 1iqp_A           98 -----------------KEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYS  150 (327)
T ss_dssp             -----------------HHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             -----------------HHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCc
Confidence                             111100 01 256789999999754  456667666655455677777 6543

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=98.27  E-value=1.7e-06  Score=86.04  Aligned_cols=89  Identities=20%  Similarity=0.128  Sum_probs=63.3

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCcccc-ccChhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLR-KFPEELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~-~lP~~i~~  313 (351)
                      ..+..+++|++|+++ ++......|..++.+++|++|++++| .+..+| ..++++.+|++|++++|.... .+|..+++
T Consensus        74 ~~~~~l~~L~~L~Ls-~n~l~~~~p~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~  151 (606)
T 3vq2_A           74 KAWHGLHHLSNLILT-GNPIQSFSPGSFSGLTSLENLVAVET-KLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSN  151 (606)
T ss_dssp             TTTTTCTTCCEEECT-TCCCCCCCTTSSTTCTTCCEEECTTS-CCCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGT
T ss_pred             HHhhchhhcCEeECC-CCcccccChhhcCCcccCCEEEccCC-ccccccccccCCCCCCCEEeCCCCcccceechHhHhh
Confidence            345677888888883 33322233666788888888888888 566665 558888888888888854322 57888888


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|+++++.
T Consensus       152 l~~L~~L~Ls~n~  164 (606)
T 3vq2_A          152 LTNLVHVDLSYNY  164 (606)
T ss_dssp             CTTCCEEECCSSC
T ss_pred             cCCCCEEEccCCc
Confidence            8888888888754

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=98.27  E-value=1.1e-06  Score=87.31  Aligned_cols=87  Identities=14%  Similarity=0.100  Sum_probs=70.4

Q ss_pred             CCCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccC-hhhh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFP-EELW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP-~~i~  312 (351)
                      ..+..+++|++|+++ ++ .+..+ |..++.+++|++|++++| .+..+ |..++.+++|++|++++| .+..+| ..++
T Consensus        50 ~~~~~l~~L~~L~Ls-~n-~l~~i~~~~~~~l~~L~~L~Ls~n-~l~~~~p~~~~~l~~L~~L~L~~n-~l~~~~~~~~~  125 (606)
T 3vq2_A           50 YSFSNFSELQWLDLS-RC-EIETIEDKAWHGLHHLSNLILTGN-PIQSFSPGSFSGLTSLENLVAVET-KLASLESFPIG  125 (606)
T ss_dssp             TTTTTCTTCCEEECT-TC-CCCEECTTTTTTCTTCCEEECTTC-CCCCCCTTSSTTCTTCCEEECTTS-CCCCSSSSCCT
T ss_pred             hhccCCccCcEEeCC-CC-cccccCHHHhhchhhcCEeECCCC-cccccChhhcCCcccCCEEEccCC-ccccccccccC
Confidence            457789999999994 33 33455 556889999999999999 56666 777999999999999996 465666 6789


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|+++++.
T Consensus       126 ~l~~L~~L~L~~n~  139 (606)
T 3vq2_A          126 QLITLKKLNVAHNF  139 (606)
T ss_dssp             TCTTCCEEECCSSC
T ss_pred             CCCCCCEEeCCCCc
Confidence            99999999998864

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=98.27  E-value=2.7e-06  Score=74.94  Aligned_cols=88  Identities=19%  Similarity=0.149  Sum_probs=71.7

Q ss_pred             CCCCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccCh-hh
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPE-EL  311 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~-~i  311 (351)
                      ...+..+++|++|+++ ++. +..+| ..+..+++|++|++++| .+..+|.. ++.+++|++|+|++| .+..+|. .+
T Consensus        76 ~~~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~  151 (251)
T 3m19_A           76 AGVFDDLTELGTLGLA-NNQ-LASLPLGVFDHLTQLDKLYLGGN-QLKSLPSGVFDRLTKLKELRLNTN-QLQSIPAGAF  151 (251)
T ss_dssp             TTTTTTCTTCCEEECT-TSC-CCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTT
T ss_pred             HhHhccCCcCCEEECC-CCc-ccccChhHhcccCCCCEEEcCCC-cCCCcChhHhccCCcccEEECcCC-cCCccCHHHc
Confidence            3446789999999994 333 33455 44689999999999999 68888876 689999999999995 6888887 58


Q ss_pred             hcCCCCCEEEecCCC
Q 048347          312 WRIKALRKLESWWPR  326 (351)
Q Consensus       312 ~~L~~L~~L~l~~~~  326 (351)
                      +++++|++|++++..
T Consensus       152 ~~l~~L~~L~L~~N~  166 (251)
T 3m19_A          152 DKLTNLQTLSLSTNQ  166 (251)
T ss_dssp             TTCTTCCEEECCSSC
T ss_pred             CcCcCCCEEECCCCc
Confidence            899999999998864

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.26  E-value=1.1e-06  Score=87.10  Aligned_cols=78  Identities=18%  Similarity=0.104  Sum_probs=67.9

Q ss_pred             CceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEe
Q 048347          243 HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLES  322 (351)
Q Consensus       243 ~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l  322 (351)
                      .|++|+++.+  .+..+|. ++.+++|++|+|++| .+..+|..++.|++|++|+|++| .+..+| ++++|++|+.|++
T Consensus       442 ~L~~L~Ls~n--~l~~lp~-~~~l~~L~~L~Ls~N-~l~~lp~~~~~l~~L~~L~Ls~N-~l~~lp-~l~~l~~L~~L~L  515 (567)
T 1dce_A          442 DVRVLHLAHK--DLTVLCH-LEQLLLVTHLDLSHN-RLRALPPALAALRCLEVLQASDN-ALENVD-GVANLPRLQELLL  515 (567)
T ss_dssp             TCSEEECTTS--CCSSCCC-GGGGTTCCEEECCSS-CCCCCCGGGGGCTTCCEEECCSS-CCCCCG-GGTTCSSCCEEEC
T ss_pred             CceEEEecCC--CCCCCcC-ccccccCcEeecCcc-cccccchhhhcCCCCCEEECCCC-CCCCCc-ccCCCCCCcEEEC
Confidence            5889999433  4445786 899999999999999 68899999999999999999985 677899 8999999999999


Q ss_pred             cCCC
Q 048347          323 WWPR  326 (351)
Q Consensus       323 ~~~~  326 (351)
                      ++..
T Consensus       516 s~N~  519 (567)
T 1dce_A          516 CNNR  519 (567)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8754

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=98.26  E-value=8.3e-07  Score=91.09  Aligned_cols=86  Identities=16%  Similarity=0.110  Sum_probs=48.6

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      ..+++|++|+++ ++.....+|..+..+++|++|++++|...+.+|..++.+++|++|++++|...+.+|..++++++|+
T Consensus       463 ~~l~~L~~L~L~-~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~  541 (768)
T 3rgz_A          463 MYVKTLETLILD-FNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLI  541 (768)
T ss_dssp             GGCTTCCEEECC-SSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCC
T ss_pred             cCCCCceEEEec-CCcccCcCCHHHhcCCCCCEEEccCCccCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCC
Confidence            344555555552 2222224455555666666666666643335666666666666666666555456666666666666


Q ss_pred             EEEecCC
Q 048347          319 KLESWWP  325 (351)
Q Consensus       319 ~L~l~~~  325 (351)
                      .|+++++
T Consensus       542 ~L~Ls~N  548 (768)
T 3rgz_A          542 WLDLNTN  548 (768)
T ss_dssp             EEECCSS
T ss_pred             EEECCCC
Confidence            6666543

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=98.26  E-value=1.5e-06  Score=79.08  Aligned_cols=81  Identities=19%  Similarity=0.126  Sum_probs=37.0

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .+..+++|++|+++.+  .+..++. +..+++|++|++++| .+..+| .++.+++|++|++++| .+..+|. +.++++
T Consensus        58 ~~~~l~~L~~L~L~~n--~i~~~~~-~~~l~~L~~L~L~~n-~l~~~~-~~~~l~~L~~L~l~~n-~l~~~~~-l~~l~~  130 (308)
T 1h6u_A           58 GVQYLNNLIGLELKDN--QITDLAP-LKNLTKITELELSGN-PLKNVS-AIAGLQSIKTLDLTST-QITDVTP-LAGLSN  130 (308)
T ss_dssp             TGGGCTTCCEEECCSS--CCCCCGG-GTTCCSCCEEECCSC-CCSCCG-GGTTCTTCCEEECTTS-CCCCCGG-GTTCTT
T ss_pred             hhhccCCCCEEEccCC--cCCCChh-HccCCCCCEEEccCC-cCCCch-hhcCCCCCCEEECCCC-CCCCchh-hcCCCC
Confidence            3444555555555222  2223333 445555555555555 344444 3444555555555543 2333432 444444


Q ss_pred             CCEEEecC
Q 048347          317 LRKLESWW  324 (351)
Q Consensus       317 L~~L~l~~  324 (351)
                      |++|++++
T Consensus       131 L~~L~l~~  138 (308)
T 1h6u_A          131 LQVLYLDL  138 (308)
T ss_dssp             CCEEECCS
T ss_pred             CCEEECCC
Confidence            44444444

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=98.26  E-value=2.4e-06  Score=77.82  Aligned_cols=85  Identities=15%  Similarity=0.189  Sum_probs=53.5

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCC-----CcccEEEEecCCcccccc-ccccccCCccEEeecCCccccc--cChh
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGF-----PRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRK--FPEE  310 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l-----~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~--lP~~  310 (351)
                      ..+++|++|+++.+....  +|..++.+     ++|++|++++| .+..+| ..++.+++|++|++++|...+.  +|..
T Consensus       118 ~~l~~L~~L~Ls~N~l~~--~~~~~~~l~~~~~~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~  194 (312)
T 1wwl_A          118 ATGPDLNILNLRNVSWAT--RDAWLAELQQWLKPGLKVLSIAQA-HSLNFSCEQVRVFPALSTLDLSDNPELGERGLISA  194 (312)
T ss_dssp             CCSCCCSEEEEESCBCSS--SSSHHHHHHTTCCTTCCEEEEESC-SCCCCCTTTCCCCSSCCEEECCSCTTCHHHHHHHH
T ss_pred             hcCCCccEEEccCCCCcc--hhHHHHHHHHhhcCCCcEEEeeCC-CCccchHHHhccCCCCCEEECCCCCcCcchHHHHH
Confidence            667777777774433222  24434444     67777777777 455555 4577777777777777543333  4555


Q ss_pred             h--hcCCCCCEEEecCCC
Q 048347          311 L--WRIKALRKLESWWPR  326 (351)
Q Consensus       311 i--~~L~~L~~L~l~~~~  326 (351)
                      +  +++++|++|+++++.
T Consensus       195 ~~~~~l~~L~~L~L~~N~  212 (312)
T 1wwl_A          195 LCPLKFPTLQVLALRNAG  212 (312)
T ss_dssp             SCTTSCTTCCEEECTTSC
T ss_pred             HHhccCCCCCEEECCCCc
Confidence            5  677777777777754

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=98.25  E-value=4.3e-07  Score=94.13  Aligned_cols=91  Identities=10%  Similarity=0.050  Sum_probs=64.3

Q ss_pred             CCCCCCCCceEEEEecccccCc----------------eeeeCCC--CCCcccEEEEecCCccccccccccccCCccEEe
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGR----------------KLVCGHG--GFPRQEILHLKSMLWLEEWKMETGAMQKLKSLI  297 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~----------------~lp~~~~--~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~  297 (351)
                      +.++++++|++|+|+.+...+.                .+|..++  .+++|++|+|++|...+.+|..+++|++|++|+
T Consensus       442 ~~l~~L~~L~~L~Ls~N~Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~N~l~~~iP~~l~~L~~L~~L~  521 (876)
T 4ecn_A          442 KAIQRLTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQSLN  521 (876)
T ss_dssp             GGGGGCTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEESCTTCCSCCGGGGGCSSCCEEE
T ss_pred             HHHhcCCCCCEEECcCCcCCCCcccccccccccccccccCChhhhhccCCCCCEEECcCCCCCccChHHHhCCCCCCEEE
Confidence            3567788888888854443331                2677777  888888888888866677887788888888888


Q ss_pred             ecCCcccc--ccChhhhcCC-------CCCEEEecCCC
Q 048347          298 VNPCAYLR--KFPEELWRIK-------ALRKLESWWPR  326 (351)
Q Consensus       298 l~~c~~l~--~lP~~i~~L~-------~L~~L~l~~~~  326 (351)
                      |++|..+.  .+|.++++++       +|++|+++++.
T Consensus       522 Ls~N~~lsg~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~  559 (876)
T 4ecn_A          522 IACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNN  559 (876)
T ss_dssp             CTTCTTSCHHHHHHHHHHHHHCTTTTTTCCEEECCSSC
T ss_pred             CcCCCCcccccchHHHHhhhhcccccCCccEEEeeCCc
Confidence            88765243  4777776665       77777777654

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=98.25  E-value=1.8e-06  Score=89.42  Aligned_cols=88  Identities=20%  Similarity=0.190  Sum_probs=46.2

Q ss_pred             CCCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChh--h
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEE--L  311 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~--i  311 (351)
                      ..+..+++|++|+++ ++.....+ |..++++++|++|+|++| .+..+ |..++.+++|++|+|++|.....+|.+  +
T Consensus        42 ~~~~~l~~L~~LdLs-~n~~~~~i~~~~f~~L~~L~~L~Ls~N-~l~~~~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~  119 (844)
T 3j0a_A           42 SSFPFLEQLQLLELG-SQYTPLTIDKEAFRNLPNLRILDLGSS-KIYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYF  119 (844)
T ss_dssp             SSCSSCCSCSEEEEC-TTCCCCEECTTTTSSCTTCCEEECTTC-CCCEECTTSSCSCSSCCCEECTTCCCSSCCSTTCCC
T ss_pred             hHCcccccCeEEeCC-CCCCccccCHHHhcCCCCCCEEECCCC-cCcccCHhHccCCcccCEeeCcCCCCCcccccCccc
Confidence            344556666666663 33223344 344556666666666665 34333 445566666666666654333334443  5


Q ss_pred             hcCCCCCEEEecCC
Q 048347          312 WRIKALRKLESWWP  325 (351)
Q Consensus       312 ~~L~~L~~L~l~~~  325 (351)
                      ++|++|++|+++++
T Consensus       120 ~~L~~L~~L~Ls~N  133 (844)
T 3j0a_A          120 RNLKALTRLDLSKN  133 (844)
T ss_dssp             SSCSSCCEEEEESC
T ss_pred             cccCCCCEEECCCC
Confidence            55566666665553

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=98.24  E-value=1.7e-06  Score=85.91  Aligned_cols=84  Identities=15%  Similarity=0.179  Sum_probs=44.3

Q ss_pred             CCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWR  313 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~  313 (351)
                      .+..+++|++|+|+ ++ .+..+|. .+.++++|++|+|++| .+..+|.. ++.|.+|++|++++| .+..+|.. +++
T Consensus        71 ~f~~l~~L~~L~Ls-~N-~i~~i~~~~f~~L~~L~~L~Ls~N-~l~~l~~~~f~~L~~L~~L~Ls~N-~l~~l~~~~~~~  146 (635)
T 4g8a_A           71 SFFSFPELQVLDLS-RC-EIQTIEDGAYQSLSHLSTLILTGN-PIQSLALGAFSGLSSLQKLVAVET-NLASLENFPIGH  146 (635)
T ss_dssp             TTTTCTTCCEEECT-TC-CCCEECTTTTTTCTTCCEEECTTC-CCCEECGGGGTTCTTCCEEECTTS-CCCCSTTCCCTT
T ss_pred             HHhCCCCCCEEECC-CC-cCCCcChhHhcCCCCCCEEEccCC-cCCCCCHHHhcCCCCCCEEECCCC-cCCCCChhhhhc
Confidence            34555666666662 22 2334433 3455566666666665 45555543 455666666666653 34445442 455


Q ss_pred             CCCCCEEEecC
Q 048347          314 IKALRKLESWW  324 (351)
Q Consensus       314 L~~L~~L~l~~  324 (351)
                      |++|++|++++
T Consensus       147 L~~L~~L~Ls~  157 (635)
T 4g8a_A          147 LKTLKELNVAH  157 (635)
T ss_dssp             CTTCCEEECCS
T ss_pred             CcccCeecccc
Confidence            55566665554

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=98.24  E-value=2.2e-06  Score=76.79  Aligned_cols=86  Identities=22%  Similarity=0.208  Sum_probs=51.3

Q ss_pred             CCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChh-hhc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEE-LWR  313 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~  313 (351)
                      .+..+++|++|+++ ++.....+ |..+..+++|++|++++| .+..+ |..++.+++|++|++++| .+..+|.. +++
T Consensus        75 ~~~~l~~L~~L~l~-~n~~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~  151 (285)
T 1ozn_A           75 AFTGLALLEQLDLS-DNAQLRSVDPATFHGLGRLHTLHLDRC-GLQELGPGLFRGLAALQYLYLQDN-ALQALPDDTFRD  151 (285)
T ss_dssp             TTTTCTTCCEEECC-SCTTCCCCCTTTTTTCTTCCEEECTTS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTT
T ss_pred             hcCCccCCCEEeCC-CCCCccccCHHHhcCCcCCCEEECCCC-cCCEECHhHhhCCcCCCEEECCCC-cccccCHhHhcc
Confidence            45566667777763 33223333 445666677777777776 35444 344666777777777764 45555543 566


Q ss_pred             CCCCCEEEecCC
Q 048347          314 IKALRKLESWWP  325 (351)
Q Consensus       314 L~~L~~L~l~~~  325 (351)
                      +++|++|++++.
T Consensus       152 l~~L~~L~l~~n  163 (285)
T 1ozn_A          152 LGNLTHLFLHGN  163 (285)
T ss_dssp             CTTCCEEECCSS
T ss_pred             CCCccEEECCCC
Confidence            777777777664

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=98.23  E-value=2.2e-06  Score=83.49  Aligned_cols=86  Identities=16%  Similarity=0.023  Sum_probs=67.0

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccc-ccChhhhcCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLR-KFPEELWRIK  315 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~-~lP~~i~~L~  315 (351)
                      .+..+++|++|+++ ++......|..++.+++|++|++++| .+..+|..  .+++|++|++++|.... .+|..+++++
T Consensus        40 ~~~~l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~lp~~--~l~~L~~L~L~~N~l~~~~~p~~~~~l~  115 (520)
T 2z7x_B           40 DILSLSKLRILIIS-HNRIQYLDISVFKFNQELEYLDLSHN-KLVKISCH--PTVNLKHLDLSFNAFDALPICKEFGNMS  115 (520)
T ss_dssp             HHTTCTTCCEEECC-SSCCCEEEGGGGTTCTTCCEEECCSS-CCCEEECC--CCCCCSEEECCSSCCSSCCCCGGGGGCT
T ss_pred             hccccccccEEecC-CCccCCcChHHhhcccCCCEEecCCC-ceeecCcc--ccCCccEEeccCCccccccchhhhccCC
Confidence            35678899999994 33333233667889999999999998 68888876  88999999999865333 4678999999


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|++++..
T Consensus       116 ~L~~L~L~~n~  126 (520)
T 2z7x_B          116 QLKFLGLSTTH  126 (520)
T ss_dssp             TCCEEEEEESS
T ss_pred             cceEEEecCcc
Confidence            99999998865

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.23  E-value=1.4e-06  Score=72.59  Aligned_cols=47  Identities=13%  Similarity=0.199  Sum_probs=39.4

Q ss_pred             CCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-+.++||++.++++.+.+....  .+.+.|+|+.|+|||++|+.+++.
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           20 KLDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccccccchHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHH
Confidence            34669999999999999987643  345678999999999999999877

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=98.21  E-value=1.3e-06  Score=82.06  Aligned_cols=87  Identities=15%  Similarity=0.019  Sum_probs=54.5

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .+..+++|+.|+++ ++......|..+..+++|++|++++| .+..+|..++.+++|++|++++| .+..+|..++++++
T Consensus       243 ~l~~l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~l~~  319 (390)
T 3o6n_A          243 WLLNYPGLVEVDLS-YNELEKIMYHPFVKMQRLERLYISNN-RLVALNLYGQPIPTLKVLDLSHN-HLLHVERNQPQFDR  319 (390)
T ss_dssp             GGGGCTTCSEEECC-SSCCCEEESGGGTTCSSCCEEECCSS-CCCEEECSSSCCTTCCEEECCSS-CCCCCGGGHHHHTT
T ss_pred             HHcCCCCccEEECC-CCcCCCcChhHccccccCCEEECCCC-cCcccCcccCCCCCCCEEECCCC-cceecCccccccCc
Confidence            34556677777773 33222233555666777777777776 56666666666777777777764 46666766666666


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |++|++++.+
T Consensus       320 L~~L~L~~N~  329 (390)
T 3o6n_A          320 LENLYLDHNS  329 (390)
T ss_dssp             CSEEECCSSC
T ss_pred             CCEEECCCCc
Confidence            7776666654

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=98.21  E-value=3.3e-06  Score=75.65  Aligned_cols=84  Identities=18%  Similarity=0.114  Sum_probs=45.9

Q ss_pred             CCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccCh-hhhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPE-ELWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L  314 (351)
                      +..+++|++|+++ ++ .+..+|. .+..+++|++|++++| .+..+ |..++.+++|+.|++++| .+..+|. .+.++
T Consensus       149 ~~~l~~L~~L~l~-~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l  224 (285)
T 1ozn_A          149 FRDLGNLTHLFLH-GN-RISSVPERAFRGLHSLDRLLLHQN-RVAHVHPHAFRDLGRLMTLYLFAN-NLSALPTEALAPL  224 (285)
T ss_dssp             TTTCTTCCEEECC-SS-CCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSS-CCSCCCHHHHTTC
T ss_pred             hccCCCccEEECC-CC-cccccCHHHhcCccccCEEECCCC-cccccCHhHccCcccccEeeCCCC-cCCcCCHHHcccC
Confidence            4455666666662 22 2234443 2555666666666666 34433 545666666666666664 3444553 35666


Q ss_pred             CCCCEEEecCC
Q 048347          315 KALRKLESWWP  325 (351)
Q Consensus       315 ~~L~~L~l~~~  325 (351)
                      ++|+.|++++.
T Consensus       225 ~~L~~L~l~~N  235 (285)
T 1ozn_A          225 RALQYLRLNDN  235 (285)
T ss_dssp             TTCCEEECCSS
T ss_pred             cccCEEeccCC
Confidence            66666666654

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=98.21  E-value=2.1e-06  Score=85.42  Aligned_cols=88  Identities=17%  Similarity=0.021  Sum_probs=66.3

Q ss_pred             CCCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ..++.+++|++|+|+ ++. +..+| ..++.+++|++|+|++| .+..+|.. ++.+++|++|+|++|......|..+++
T Consensus        93 ~~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~  169 (597)
T 3oja_B           93 YAFAYAHTIQKLYMG-FNA-IRYLPPHVFQNVPLLTVLVLERN-DLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQA  169 (597)
T ss_dssp             TTTTTCTTCCEEECC-SSC-CCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTT
T ss_pred             HHhcCCCCCCEEECC-CCc-CCCCCHHHHcCCCCCCEEEeeCC-CCCCCCHHHhccCCCCCEEEeeCCcCCCCChhhhhc
Confidence            467788999999994 333 33344 44688899999999998 68888877 488999999999986543444456888


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|+++++.
T Consensus       170 l~~L~~L~L~~N~  182 (597)
T 3oja_B          170 TTSLQNLQLSSNR  182 (597)
T ss_dssp             CTTCCEEECTTSC
T ss_pred             CCcCcEEECcCCC
Confidence            9999999988764

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=98.21  E-value=4.1e-06  Score=74.73  Aligned_cols=83  Identities=20%  Similarity=0.193  Sum_probs=39.7

Q ss_pred             CCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L  314 (351)
                      +..+++|++|+++.+  .+..+|.. ++.+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.. ++++
T Consensus       129 ~~~l~~L~~L~L~~n--~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l  204 (272)
T 3rfs_A          129 FDKLTNLTYLNLAHN--QLQSLPKGVFDKLTNLTELDLSYN-QLQSLPEGVFDKLTQLKDLRLYQN-QLKSVPDGVFDRL  204 (272)
T ss_dssp             TTTCTTCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTC
T ss_pred             hccCCCCCEEECCCC--ccCccCHHHhccCccCCEEECCCC-CcCccCHHHhcCCccCCEEECCCC-cCCccCHHHHhCC
Confidence            344555555555222  12233322 345555555555555 34444433 355555555555553 23334332 3555


Q ss_pred             CCCCEEEecC
Q 048347          315 KALRKLESWW  324 (351)
Q Consensus       315 ~~L~~L~l~~  324 (351)
                      ++|+.|++++
T Consensus       205 ~~L~~L~l~~  214 (272)
T 3rfs_A          205 TSLQYIWLHD  214 (272)
T ss_dssp             TTCCEEECCS
T ss_pred             cCCCEEEccC
Confidence            5555555554

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=98.20  E-value=4.3e-06  Score=74.55  Aligned_cols=87  Identities=20%  Similarity=0.180  Sum_probs=69.8

Q ss_pred             CCCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~  312 (351)
                      ..+..+++|++|+++ ++. +..+|. .++.+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.. ++
T Consensus       103 ~~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~  178 (272)
T 3rfs_A          103 GVFDKLTNLKELVLV-ENQ-LQSLPDGVFDKLTNLTYLNLAHN-QLQSLPKGVFDKLTNLTELDLSYN-QLQSLPEGVFD  178 (272)
T ss_dssp             TTTTTCTTCCEEECT-TSC-CCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTT
T ss_pred             hHhcCCcCCCEEECC-CCc-CCccCHHHhccCCCCCEEECCCC-ccCccCHHHhccCccCCEEECCCC-CcCccCHHHhc
Confidence            346789999999994 333 334554 3788999999999999 68888766 689999999999996 56677765 58


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|+++++.
T Consensus       179 ~l~~L~~L~L~~N~  192 (272)
T 3rfs_A          179 KLTQLKDLRLYQNQ  192 (272)
T ss_dssp             TCTTCCEEECCSSC
T ss_pred             CCccCCEEECCCCc
Confidence            99999999998764

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=98.20  E-value=3.1e-06  Score=75.52  Aligned_cols=86  Identities=22%  Similarity=0.247  Sum_probs=62.2

Q ss_pred             CCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccc--cChhhh
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRK--FPEELW  312 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~--lP~~i~  312 (351)
                      .+..+++|++|+++ ++. +..++ ..+..+++|++|++++| .+..++. .++.+++|++|++++| .+..  +|..++
T Consensus        71 ~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~l~~~~~  146 (276)
T 2z62_A           71 AYQSLSHLSTLILT-GNP-IQSLALGAFSGLSSLQKLVAVET-NLASLENFPIGHLKTLKELNVAHN-LIQSFKLPEYFS  146 (276)
T ss_dssp             TTTTCTTCCEEECT-TCC-CCEECTTTTTTCTTCCEEECTTS-CCCCSTTCCCTTCTTCCEEECCSS-CCCCCCCCGGGG
T ss_pred             HccCCcCCCEEECC-CCc-cCccChhhhcCCccccEEECCCC-CccccCchhcccCCCCCEEECcCC-ccceecCchhhc
Confidence            45677888888883 332 33343 45777888888888888 5666655 5788888888888885 4544  688888


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++..
T Consensus       147 ~l~~L~~L~Ls~N~  160 (276)
T 2z62_A          147 NLTNLEHLDLSSNK  160 (276)
T ss_dssp             GCTTCCEEECCSSC
T ss_pred             cCCCCCEEECCCCC
Confidence            88899999888754

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=98.19  E-value=3.4e-06  Score=76.17  Aligned_cols=80  Identities=18%  Similarity=0.116  Sum_probs=35.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+++|++|+++.+  .+..++. +..+++|++|++++| .+..+|. ++.+++|++|++++| .+..+| .+.++++|
T Consensus        64 ~~~l~~L~~L~L~~n--~l~~~~~-l~~l~~L~~L~l~~n-~l~~~~~-l~~l~~L~~L~L~~n-~i~~~~-~l~~l~~L  136 (291)
T 1h6t_A           64 IQYLPNVTKLFLNGN--KLTDIKP-LANLKNLGWLFLDEN-KVKDLSS-LKDLKKLKSLSLEHN-GISDIN-GLVHLPQL  136 (291)
T ss_dssp             GGGCTTCCEEECCSS--CCCCCGG-GTTCTTCCEEECCSS-CCCCGGG-GTTCTTCCEEECTTS-CCCCCG-GGGGCTTC
T ss_pred             HhcCCCCCEEEccCC--ccCCCcc-cccCCCCCEEECCCC-cCCCChh-hccCCCCCEEECCCC-cCCCCh-hhcCCCCC
Confidence            444555555555222  1222332 445555555555554 3444442 444455555555543 233332 34444444


Q ss_pred             CEEEecC
Q 048347          318 RKLESWW  324 (351)
Q Consensus       318 ~~L~l~~  324 (351)
                      +.|++++
T Consensus       137 ~~L~l~~  143 (291)
T 1h6t_A          137 ESLYLGN  143 (291)
T ss_dssp             CEEECCS
T ss_pred             CEEEccC
Confidence            4444444

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=98.19  E-value=4.4e-06  Score=74.39  Aligned_cols=82  Identities=21%  Similarity=0.219  Sum_probs=38.0

Q ss_pred             CCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIK  315 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~  315 (351)
                      ..+++|++|+++.+  .+..+|.. +..+++|++|++++| .+..+|.. +..+++|++|++++| .+..+|.+ +.+++
T Consensus       130 ~~l~~L~~L~Ls~n--~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~  205 (270)
T 2o6q_A          130 DSLTKLTYLSLGYN--ELQSLPKGVFDKLTSLKELRLYNN-QLKRVPEGAFDKLTELKTLKLDNN-QLKRVPEGAFDSLE  205 (270)
T ss_dssp             TTCTTCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCT
T ss_pred             CcCcCCCEEECCCC--cCCccCHhHccCCcccceeEecCC-cCcEeChhHhccCCCcCEEECCCC-cCCcCCHHHhcccc
Confidence            34455555555221  12223322 344555555555555 34444433 445555555555553 34444443 34455


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|+.|++++
T Consensus       206 ~L~~L~l~~  214 (270)
T 2o6q_A          206 KLKMLQLQE  214 (270)
T ss_dssp             TCCEEECCS
T ss_pred             CCCEEEecC
Confidence            555555544

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=98.19  E-value=1.9e-06  Score=82.45  Aligned_cols=85  Identities=18%  Similarity=0.232  Sum_probs=44.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccc-ccccc--ccccCCccEEeecCCcccccc-Chh-hh
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLE-EWKME--TGAMQKLKSLIVNPCAYLRKF-PEE-LW  312 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~-~lp~~--i~~L~~L~~L~l~~c~~l~~l-P~~-i~  312 (351)
                      +..+++|++|+++ ++......|..++.+++|++|++++|. +. ..|..  ++.+++|++|++++|. +..+ |.. ++
T Consensus        75 ~~~l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~  151 (455)
T 3v47_A           75 FRGLSSLIILKLD-YNQFLQLETGAFNGLANLEVLTLTQCN-LDGAVLSGNFFKPLTSLEMLVLRDNN-IKKIQPASFFL  151 (455)
T ss_dssp             TTTCTTCCEEECT-TCTTCEECTTTTTTCTTCCEEECTTSC-CBTHHHHSSTTTTCTTCCEEECCSSB-CCSCCCCGGGG
T ss_pred             ccccccCCEEeCC-CCccCccChhhccCcccCCEEeCCCCC-CCccccCcccccCcccCCEEECCCCc-cCccCcccccC
Confidence            4555666666662 222222234455566666666666663 33 23433  5566666666666643 3333 443 55


Q ss_pred             cCCCCCEEEecCC
Q 048347          313 RIKALRKLESWWP  325 (351)
Q Consensus       313 ~L~~L~~L~l~~~  325 (351)
                      ++++|++|++++.
T Consensus       152 ~l~~L~~L~L~~n  164 (455)
T 3v47_A          152 NMRRFHVLDLTFN  164 (455)
T ss_dssp             GCTTCCEEECTTC
T ss_pred             CCCcccEEeCCCC
Confidence            6666666666654

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=98.19  E-value=2.2e-06  Score=72.60  Aligned_cols=82  Identities=17%  Similarity=0.136  Sum_probs=68.0

Q ss_pred             CCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccCh-hhhcCCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPE-ELWRIKALR  318 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~L~  318 (351)
                      .++|+.|+++.+  .+..+|..+..+++|++|+|++| .+..+|. .++.+++|++|+|++| .+..+|. .+.++++|+
T Consensus        30 ~~~l~~L~L~~n--~i~~ip~~~~~l~~L~~L~Ls~N-~i~~i~~~~f~~l~~L~~L~Ls~N-~l~~i~~~~f~~l~~L~  105 (193)
T 2wfh_A           30 PRDVTELYLDGN--QFTLVPKELSNYKHLTLIDLSNN-RISTLSNQSFSNMTQLLTLILSYN-RLRCIPPRTFDGLKSLR  105 (193)
T ss_dssp             CTTCCEEECCSS--CCCSCCGGGGGCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCBCCTTTTTTCTTCC
T ss_pred             CCCCCEEECCCC--cCchhHHHhhcccCCCEEECCCC-cCCEeCHhHccCCCCCCEEECCCC-ccCEeCHHHhCCCCCCC
Confidence            368999999433  34478888899999999999999 6887775 4899999999999995 5777765 688999999


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|++++..
T Consensus       106 ~L~L~~N~  113 (193)
T 2wfh_A          106 LLSLHGND  113 (193)
T ss_dssp             EEECCSSC
T ss_pred             EEECCCCC
Confidence            99998754

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=98.19  E-value=3.2e-06  Score=83.10  Aligned_cols=87  Identities=23%  Similarity=0.246  Sum_probs=64.7

Q ss_pred             CCCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCcccc--ccChhh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLR--KFPEEL  311 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~--~lP~~i  311 (351)
                      ..+..+++|++|+++ ++. +..+| ..++.+++|++|++++| .+..+|. .++.+++|++|++++|. +.  .+|..+
T Consensus        70 ~~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~l~~L~~L~L~~n~-l~~~~lp~~~  145 (570)
T 2z63_A           70 GAYQSLSHLSTLILT-GNP-IQSLALGAFSGLSSLQKLVAVET-NLASLENFPIGHLKTLKELNVAHNL-IQSFKLPEYF  145 (570)
T ss_dssp             TTTTTCTTCCEEECT-TCC-CCEECTTTTTTCTTCCEEECTTS-CCCCSTTCSCTTCTTCCEEECCSSC-CCCCCCCGGG
T ss_pred             ccccCchhCCEEeCc-CCc-CCccCHhhhcCcccccccccccc-ccccCCCccccccccccEEecCCCc-cceecChhhh
Confidence            346678888888883 332 33444 45778888888888888 5777765 58888899999998854 44  478888


Q ss_pred             hcCCCCCEEEecCCC
Q 048347          312 WRIKALRKLESWWPR  326 (351)
Q Consensus       312 ~~L~~L~~L~l~~~~  326 (351)
                      +++++|++|+++++.
T Consensus       146 ~~l~~L~~L~l~~n~  160 (570)
T 2z63_A          146 SNLTNLEHLDLSSNK  160 (570)
T ss_dssp             GGCTTCCEEECTTSC
T ss_pred             cccCCCCEEeCcCCc
Confidence            999999999988764

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=98.19  E-value=4.8e-06  Score=71.95  Aligned_cols=88  Identities=15%  Similarity=0.078  Sum_probs=71.0

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChh-h
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEE-L  311 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~-i  311 (351)
                      ...+..+++|++|+|+.+  .+..+|.. +..+++|++|+|++| .+..+ |..++.+++|++|+|++| .+..+|.+ +
T Consensus        73 ~~~~~~l~~L~~L~Ls~N--~l~~l~~~~f~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~  148 (220)
T 2v9t_B           73 PDAFQGLRSLNSLVLYGN--KITELPKSLFEGLFSLQLLLLNAN-KINCLRVDAFQDLHNLNLLSLYDN-KLQTIAKGTF  148 (220)
T ss_dssp             TTTTTTCSSCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTT
T ss_pred             HHHhhCCcCCCEEECCCC--cCCccCHhHccCCCCCCEEECCCC-CCCEeCHHHcCCCCCCCEEECCCC-cCCEECHHHH
Confidence            356788999999999443  34466665 578999999999999 57766 456899999999999995 57777764 7


Q ss_pred             hcCCCCCEEEecCCC
Q 048347          312 WRIKALRKLESWWPR  326 (351)
Q Consensus       312 ~~L~~L~~L~l~~~~  326 (351)
                      ..+++|++|++++.+
T Consensus       149 ~~l~~L~~L~L~~N~  163 (220)
T 2v9t_B          149 SPLRAIQTMHLAQNP  163 (220)
T ss_dssp             TTCTTCCEEECCSSC
T ss_pred             hCCCCCCEEEeCCCC
Confidence            889999999998754

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=98.18  E-value=2.9e-06  Score=79.59  Aligned_cols=87  Identities=17%  Similarity=0.068  Sum_probs=63.4

Q ss_pred             CCCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCcccccc-Chhhh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKF-PEELW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~l-P~~i~  312 (351)
                      ..+..+++|++|+++ ++. +..+ |..++.+++|++|++++| .+..+|.. ++.+++|++|++++|. +..+ |..++
T Consensus        87 ~~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~  162 (390)
T 3o6n_A           87 YAFAYAHTIQKLYMG-FNA-IRYLPPHVFQNVPLLTVLVLERN-DLSSLPRGIFHNTPKLTTLSMSNNN-LERIEDDTFQ  162 (390)
T ss_dssp             TTTTTCTTCCEEECC-SSC-CCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTS
T ss_pred             hhccCCCCcCEEECC-CCC-CCcCCHHHhcCCCCCCEEECCCC-ccCcCCHHHhcCCCCCcEEECCCCc-cCccChhhcc
Confidence            456778888888883 332 3334 444778888888888888 67888877 4788888888888854 4455 44578


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++..
T Consensus       163 ~l~~L~~L~l~~n~  176 (390)
T 3o6n_A          163 ATTSLQNLQLSSNR  176 (390)
T ss_dssp             SCTTCCEEECCSSC
T ss_pred             CCCCCCEEECCCCc
Confidence            88888888888754

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=98.18  E-value=1.9e-06  Score=79.77  Aligned_cols=85  Identities=15%  Similarity=0.078  Sum_probs=45.9

Q ss_pred             CCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccCh--hhh
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPE--ELW  312 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~--~i~  312 (351)
                      .+..+++|++|+++ ++ .+..+ |..+..+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.  .++
T Consensus        71 ~~~~l~~L~~L~L~-~n-~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~  146 (353)
T 2z80_A           71 DLQRCVNLQALVLT-SN-GINTIEEDSFSSLGSLEHLDLSYN-YLSNLSSSWFKPLSSLTFLNLLGN-PYKTLGETSLFS  146 (353)
T ss_dssp             TTTTCTTCCEEECT-TS-CCCEECTTTTTTCTTCCEEECCSS-CCSSCCHHHHTTCTTCSEEECTTC-CCSSSCSSCSCT
T ss_pred             HhccCCCCCEEECC-CC-ccCccCHhhcCCCCCCCEEECCCC-cCCcCCHhHhCCCccCCEEECCCC-CCcccCchhhhc
Confidence            34556666666662 22 22233 233555666666666665 45555554 555666666666653 4555554  455


Q ss_pred             cCCCCCEEEecCC
Q 048347          313 RIKALRKLESWWP  325 (351)
Q Consensus       313 ~L~~L~~L~l~~~  325 (351)
                      ++++|++|+++++
T Consensus       147 ~l~~L~~L~l~~n  159 (353)
T 2z80_A          147 HLTKLQILRVGNM  159 (353)
T ss_dssp             TCTTCCEEEEEES
T ss_pred             cCCCCcEEECCCC
Confidence            5666666666554

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=98.17  E-value=4.9e-07  Score=82.96  Aligned_cols=90  Identities=13%  Similarity=0.068  Sum_probs=52.4

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccc--ccChhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLR--KFPEELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~--~lP~~i~~  313 (351)
                      +.+..+++|++|+++.+......+|..+..+++|++|++++|......|..++.+++|++|++++|..+.  .+|..+.+
T Consensus        87 ~~~~~~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~L~~~~~l~~~~l~~~~~~  166 (336)
T 2ast_B           87 AEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSS  166 (336)
T ss_dssp             CSCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHH
T ss_pred             hhhccCCCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcCcccCHHHHHHHhcCCCCCEEECCCCCCCCHHHHHHHHhc
Confidence            3345667777777733222212255556666677777777663222455556666677777776664444  35555666


Q ss_pred             CCCCCEEEecCC
Q 048347          314 IKALRKLESWWP  325 (351)
Q Consensus       314 L~~L~~L~l~~~  325 (351)
                      +++|++|+++++
T Consensus       167 ~~~L~~L~l~~~  178 (336)
T 2ast_B          167 CSRLDELNLSWC  178 (336)
T ss_dssp             CTTCCEEECCCC
T ss_pred             CCCCCEEcCCCC
Confidence            666666666665

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=98.17  E-value=5.6e-06  Score=73.68  Aligned_cols=85  Identities=16%  Similarity=0.166  Sum_probs=57.5

Q ss_pred             CCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L  314 (351)
                      +..+++|++|+++.+  .+..+|. .+..+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.+ ++++
T Consensus        81 ~~~l~~L~~L~l~~n--~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l  156 (270)
T 2o6q_A           81 FKELKNLETLWVTDN--KLQALPIGVFDQLVNLAELRLDRN-QLKSLPPRVFDSLTKLTYLSLGYN-ELQSLPKGVFDKL  156 (270)
T ss_dssp             TSSCTTCCEEECCSS--CCCCCCTTTTTTCSSCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTC
T ss_pred             hcCCCCCCEEECCCC--cCCcCCHhHcccccCCCEEECCCC-ccCeeCHHHhCcCcCCCEEECCCC-cCCccCHhHccCC
Confidence            355677777777322  2334443 3567778888888877 56666554 677888888888874 56677765 5778


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++..
T Consensus       157 ~~L~~L~L~~n~  168 (270)
T 2o6q_A          157 TSLKELRLYNNQ  168 (270)
T ss_dssp             TTCCEEECCSSC
T ss_pred             cccceeEecCCc
Confidence            888888887653

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=98.17  E-value=2.6e-06  Score=81.78  Aligned_cols=61  Identities=23%  Similarity=0.230  Sum_probs=27.6

Q ss_pred             CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhcCCCCCEEEecCC
Q 048347          263 HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWP  325 (351)
Q Consensus       263 ~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  325 (351)
                      +..+++|++|++++|..++.+|.. ++.+++|++|++++| .+..+| .+..+++|+.|++++.
T Consensus       167 ~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n-~l~~~~-~~~~l~~L~~L~Ls~N  228 (452)
T 3zyi_A          167 FNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMC-NIKDMP-NLTPLVGLEELEMSGN  228 (452)
T ss_dssp             TTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTS-CCSSCC-CCTTCTTCCEEECTTS
T ss_pred             HhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCC-cccccc-cccccccccEEECcCC
Confidence            334444444444443334444432 444445555555442 344444 2445555555555543

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=98.16  E-value=5.1e-06  Score=74.98  Aligned_cols=86  Identities=22%  Similarity=0.174  Sum_probs=63.6

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      ..+..+++|++|+++.+  .+..+|.. +..+++|++|++++| .+..+|.. +..+++|++|+|++| .+..+|.++..
T Consensus       118 ~~~~~l~~L~~L~L~~N--~l~~~~~~~~~~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~L~L~~N-~l~~ip~~~~~  193 (290)
T 1p9a_G          118 GALRGLGELQELYLKGN--ELKTLPPGLLTPTPKLEKLSLANN-NLTELPAGLLNGLENLDTLLLQEN-SLYTIPKGFFG  193 (290)
T ss_dssp             STTTTCTTCCEEECTTS--CCCCCCTTTTTTCTTCCEEECTTS-CCSCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTT
T ss_pred             HHHcCCCCCCEEECCCC--CCCccChhhcccccCCCEEECCCC-cCCccCHHHhcCcCCCCEEECCCC-cCCccChhhcc
Confidence            34567788888888333  23345443 567788888888888 67788876 467888888888874 67788888888


Q ss_pred             CCCCCEEEecCC
Q 048347          314 IKALRKLESWWP  325 (351)
Q Consensus       314 L~~L~~L~l~~~  325 (351)
                      +.+|+.|++++.
T Consensus       194 ~~~L~~l~L~~N  205 (290)
T 1p9a_G          194 SHLLPFAFLHGN  205 (290)
T ss_dssp             TCCCSEEECCSC
T ss_pred             cccCCeEEeCCC
Confidence            888888888763

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=98.16  E-value=1.7e-06  Score=86.22  Aligned_cols=88  Identities=15%  Similarity=0.020  Sum_probs=55.8

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +.+..+++|+.|+++ ++......|..++.+++|++|+|++| .+..+|..++.+++|++|+|++| .+..+|..++.++
T Consensus       248 ~~l~~l~~L~~L~Ls-~N~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~~L~~L~Ls~N-~l~~i~~~~~~l~  324 (597)
T 3oja_B          248 AWLLNYPGLVEVDLS-YNELEKIMYHPFVKMQRLERLYISNN-RLVALNLYGQPIPTLKVLDLSHN-HLLHVERNQPQFD  324 (597)
T ss_dssp             GGGGGCTTCSEEECC-SSCCCEEESGGGTTCSSCCEEECTTS-CCCEEECSSSCCTTCCEEECCSS-CCCCCGGGHHHHT
T ss_pred             hhhccCCCCCEEECC-CCccCCCCHHHhcCccCCCEEECCCC-CCCCCCcccccCCCCcEEECCCC-CCCccCcccccCC
Confidence            334566777777773 33333334555667777777777776 56666666666777777777764 4556776666666


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|+.|+++++.
T Consensus       325 ~L~~L~L~~N~  335 (597)
T 3oja_B          325 RLENLYLDHNS  335 (597)
T ss_dssp             TCSEEECCSSC
T ss_pred             CCCEEECCCCC
Confidence            67766666644

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=98.15  E-value=2.8e-06  Score=74.08  Aligned_cols=84  Identities=15%  Similarity=0.122  Sum_probs=39.3

Q ss_pred             CCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEec-CCccccccc-cccccCCccEEeecCCccccccChhhhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKS-MLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~-~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      +..+++|++|+++ ++..+..++. .+..+++|++|++++ | .+..+|. .++.+++|++|++++| .+..+|. ++++
T Consensus        51 ~~~l~~L~~L~l~-~n~~l~~i~~~~f~~l~~L~~L~l~~~n-~l~~i~~~~f~~l~~L~~L~l~~n-~l~~lp~-~~~l  126 (239)
T 2xwt_C           51 FSNLPNISRIYVS-IDVTLQQLESHSFYNLSKVTHIEIRNTR-NLTYIDPDALKELPLLKFLGIFNT-GLKMFPD-LTKV  126 (239)
T ss_dssp             TTTCTTCCEEEEE-CCSSCCEECTTTEESCTTCCEEEEEEET-TCCEECTTSEECCTTCCEEEEEEE-CCCSCCC-CTTC
T ss_pred             ccCCCCCcEEeCC-CCCCcceeCHhHcCCCcCCcEEECCCCC-CeeEcCHHHhCCCCCCCEEeCCCC-CCccccc-cccc
Confidence            4445555555552 2222333433 244555555555555 3 4555443 2445555555555553 3444443 4444


Q ss_pred             CCCC---EEEecCC
Q 048347          315 KALR---KLESWWP  325 (351)
Q Consensus       315 ~~L~---~L~l~~~  325 (351)
                      ++|+   .|++++.
T Consensus       127 ~~L~~L~~L~l~~N  140 (239)
T 2xwt_C          127 YSTDIFFILEITDN  140 (239)
T ss_dssp             CBCCSEEEEEEESC
T ss_pred             cccccccEEECCCC
Confidence            4444   5544443

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=98.15  E-value=3.4e-06  Score=83.24  Aligned_cols=85  Identities=20%  Similarity=0.106  Sum_probs=65.5

Q ss_pred             CCCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccccc--Chhhh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKF--PEELW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~l--P~~i~  312 (351)
                      ..+..+++|++|+++ ++ .+..+ |..+..+++|++|++++| .+..+|..  .+++|++|++++| .+..+  |..++
T Consensus        70 ~~~~~l~~L~~L~Ls-~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~lp~~--~l~~L~~L~Ls~N-~l~~l~~p~~~~  143 (562)
T 3a79_B           70 PDISFLSELRVLRLS-HN-RIRSLDFHVFLFNQDLEYLDVSHN-RLQNISCC--PMASLRHLDLSFN-DFDVLPVCKEFG  143 (562)
T ss_dssp             GGTTTCTTCCEEECC-SC-CCCEECTTTTTTCTTCCEEECTTS-CCCEECSC--CCTTCSEEECCSS-CCSBCCCCGGGG
T ss_pred             hhhccCCCccEEECC-CC-CCCcCCHHHhCCCCCCCEEECCCC-cCCccCcc--ccccCCEEECCCC-CccccCchHhhc
Confidence            356788899999994 33 33344 556888899999999998 58888876  7899999999985 45554  47888


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++..
T Consensus       144 ~l~~L~~L~L~~n~  157 (562)
T 3a79_B          144 NLTKLTFLGLSAAK  157 (562)
T ss_dssp             GCTTCCEEEEECSB
T ss_pred             ccCcccEEecCCCc
Confidence            99999999998754

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=98.15  E-value=4.1e-06  Score=75.80  Aligned_cols=85  Identities=13%  Similarity=0.064  Sum_probs=39.8

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhhhcC-C
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWRI-K  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L-~  315 (351)
                      +..+++|++|+++ ++......|..+..+++|++|++++| .+..+|. .++.+++|++|++++|......|..+.++ +
T Consensus       171 ~~~l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~  248 (306)
T 2z66_A          171 FTELRNLTFLDLS-QCQLEQLSPTAFNSLSSLQVLNMSHN-NFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPS  248 (306)
T ss_dssp             CTTCTTCCEEECT-TSCCCEECTTTTTTCTTCCEEECTTS-CCSBCCSGGGTTCTTCCEEECTTSCCCBCSSSSCCCCCT
T ss_pred             HhhCcCCCEEECC-CCCcCCcCHHHhcCCCCCCEEECCCC-ccCccChhhccCcccCCEeECCCCCCcccCHHHHHhhhc
Confidence            3445555555552 22111112334445555555555555 3444433 34555555555555543333344445555 3


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|++|++++
T Consensus       249 ~L~~L~L~~  257 (306)
T 2z66_A          249 SLAFLNLTQ  257 (306)
T ss_dssp             TCCEEECTT
T ss_pred             cCCEEEccC
Confidence            555555555

>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=98.14  E-value=5.9e-06  Score=76.89  Aligned_cols=54  Identities=13%  Similarity=0.065  Sum_probs=41.7

Q ss_pred             ccccccCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347            8 DNFRGLSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus         8 ~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++...+  .+++|+++.++.+...+..+. ....+.|+|+.|+||||+|+.+.+.
T Consensus         8 ~k~rp~~~--~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~~   61 (373)
T 1jr3_A            8 RKWRPQTF--ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKG   61 (373)
T ss_dssp             HHTCCCST--TTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HhhCCCch--hhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34444433  459999999999999997653 2346779999999999999999775

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=98.14  E-value=4.3e-06  Score=76.97  Aligned_cols=83  Identities=13%  Similarity=0.118  Sum_probs=47.1

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +.+..+++|++|+++ ++ ....++. +..+++|++|++++| .+..+| .++.+++|++|++++| .+..+|. +.+++
T Consensus        60 ~~~~~~~~L~~L~l~-~n-~i~~~~~-~~~l~~L~~L~L~~n-~i~~~~-~~~~l~~L~~L~l~~n-~i~~~~~-~~~l~  132 (347)
T 4fmz_A           60 QGIEYLTNLEYLNLN-GN-QITDISP-LSNLVKLTNLYIGTN-KITDIS-ALQNLTNLRELYLNED-NISDISP-LANLT  132 (347)
T ss_dssp             TTGGGCTTCCEEECC-SS-CCCCCGG-GTTCTTCCEEECCSS-CCCCCG-GGTTCTTCSEEECTTS-CCCCCGG-GTTCT
T ss_pred             hhhhhcCCccEEEcc-CC-ccccchh-hhcCCcCCEEEccCC-cccCch-HHcCCCcCCEEECcCC-cccCchh-hccCC
Confidence            345556667777773 22 2333443 566666666666666 455555 4666666666666653 3555554 55566


Q ss_pred             CCCEEEecCC
Q 048347          316 ALRKLESWWP  325 (351)
Q Consensus       316 ~L~~L~l~~~  325 (351)
                      +|++|+++++
T Consensus       133 ~L~~L~l~~n  142 (347)
T 4fmz_A          133 KMYSLNLGAN  142 (347)
T ss_dssp             TCCEEECTTC
T ss_pred             ceeEEECCCC
Confidence            6666666554

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.14  E-value=5.1e-06  Score=76.61  Aligned_cols=88  Identities=13%  Similarity=-0.055  Sum_probs=70.5

Q ss_pred             CCCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      |.++.+++|+.|+|+ +.-.+..+| ..+..+++|++|+|++| .+..+|. .++.|++|++|+|++ ..+..+|.++..
T Consensus        25 p~l~~~~~L~~L~l~-~~n~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~l~~-N~l~~~~~~~~~  101 (347)
T 2ifg_A           25 HHLPGAENLTELYIE-NQQHLQHLELRDLRGLGELRNLTIVKS-GLRFVAPDAFHFTPRLSRLNLSF-NALESLSWKTVQ  101 (347)
T ss_dssp             TTSCSCSCCSEEECC-SCSSCCEECGGGSCSCCCCSEEECCSS-CCCEECTTGGGSCSCCCEEECCS-SCCSCCCSTTTC
T ss_pred             CCCCCCCCeeEEEcc-CCCCCCCcChhHhccccCCCEEECCCC-ccceeCHHHhcCCcCCCEEeCCC-CccceeCHHHcc
Confidence            337888999999993 323444666 56899999999999999 6877766 479999999999998 578899988766


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      ..+|+.|++.+.+
T Consensus       102 ~~~L~~l~l~~N~  114 (347)
T 2ifg_A          102 GLSLQELVLSGNP  114 (347)
T ss_dssp             SCCCCEEECCSSC
T ss_pred             cCCceEEEeeCCC
Confidence            5559999998743

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=98.13  E-value=3.7e-06  Score=80.36  Aligned_cols=85  Identities=14%  Similarity=0.028  Sum_probs=39.8

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      ++.+++|++|+++ ++......|..+..+++|++|++++| .+..+ |..++.+++|++|++++|......|..++++++
T Consensus       295 ~~~l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~  372 (455)
T 3v47_A          295 FSHFTDLEQLTLA-QNEINKIDDNAFWGLTHLLKLNLSQN-FLGSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPN  372 (455)
T ss_dssp             TTTCTTCCEEECT-TSCCCEECTTTTTTCTTCCEEECCSS-CCCEECGGGGTTCTTCCEEECCSSCCCEECTTTTTTCTT
T ss_pred             cccCCCCCEEECC-CCcccccChhHhcCcccCCEEECCCC-ccCCcChhHhcCcccCCEEECCCCcccccChhhcccccc
Confidence            4455555555552 22222122334455555555555555 33433 333455555555555554322222444555555


Q ss_pred             CCEEEecC
Q 048347          317 LRKLESWW  324 (351)
Q Consensus       317 L~~L~l~~  324 (351)
                      |++|++++
T Consensus       373 L~~L~L~~  380 (455)
T 3v47_A          373 LKELALDT  380 (455)
T ss_dssp             CCEEECCS
T ss_pred             ccEEECCC
Confidence            55555554

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=98.13  E-value=3.9e-06  Score=80.89  Aligned_cols=85  Identities=16%  Similarity=0.102  Sum_probs=38.2

Q ss_pred             CCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChhhhcCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +..+++|++|+|+.+  .+..+|.. +..+++|++|++++|. +..+ |..++.+++|++|++++|......|..+.+++
T Consensus        76 ~~~l~~L~~L~L~~n--~l~~~~~~~~~~l~~L~~L~Ls~n~-i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~  152 (477)
T 2id5_A           76 FNNLFNLRTLGLRSN--RLKLIPLGVFTGLSNLTKLDISENK-IVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLN  152 (477)
T ss_dssp             TTTCTTCCEEECCSS--CCCSCCTTSSTTCTTCCEEECTTSC-CCEECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCT
T ss_pred             hhCCccCCEEECCCC--cCCccCcccccCCCCCCEEECCCCc-cccCChhHccccccCCEEECCCCccceeChhhccCCC
Confidence            344455555555211  12233322 3445555555555552 3322 33345555555555555322222233455566


Q ss_pred             CCCEEEecCC
Q 048347          316 ALRKLESWWP  325 (351)
Q Consensus       316 ~L~~L~l~~~  325 (351)
                      +|++|+++++
T Consensus       153 ~L~~L~l~~n  162 (477)
T 2id5_A          153 SLEQLTLEKC  162 (477)
T ss_dssp             TCCEEEEESC
T ss_pred             CCCEEECCCC
Confidence            6666666554

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=98.13  E-value=2.5e-06  Score=83.57  Aligned_cols=85  Identities=20%  Similarity=0.098  Sum_probs=46.4

Q ss_pred             CCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCcccc--ccChhhh
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLR--KFPEELW  312 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~--~lP~~i~  312 (351)
                      .+..+++|++|+++ ++. +..++ ..++.+++|++|++++| .+..+|.. ++.+++|++|++++|. +.  ..|..++
T Consensus        45 ~~~~l~~L~~L~Ls-~n~-i~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~  120 (549)
T 2z81_A           45 DLRACANLQVLILK-SSR-INTIEGDAFYSLGSLEHLDLSDN-HLSSLSSSWFGPLSSLKYLNLMGNP-YQTLGVTSLFP  120 (549)
T ss_dssp             TTSSCTTCCEEECT-TSC-CCEECTTTTTTCTTCCEEECTTS-CCCSCCHHHHTTCTTCCEEECTTCC-CSSSCSSCSCT
T ss_pred             hhhcCCcccEEECC-CCC-cCccChhhccccccCCEEECCCC-ccCccCHHHhccCCCCcEEECCCCc-ccccchhhhhh
Confidence            44566666666662 222 22332 34566666666666666 35544443 6666666666666542 33  2345556


Q ss_pred             cCCCCCEEEecCC
Q 048347          313 RIKALRKLESWWP  325 (351)
Q Consensus       313 ~L~~L~~L~l~~~  325 (351)
                      ++++|++|+++++
T Consensus       121 ~l~~L~~L~L~~n  133 (549)
T 2z81_A          121 NLTNLQTLRIGNV  133 (549)
T ss_dssp             TCTTCCEEEEEES
T ss_pred             ccCCccEEECCCC
Confidence            6666666666554

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=98.12  E-value=3.3e-06  Score=76.48  Aligned_cols=89  Identities=17%  Similarity=0.131  Sum_probs=59.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccCh-hhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPE-ELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~  313 (351)
                      ..+..+++|++|+++.+......+|..+..+++|++|++++| .+..+ |..++.+++|++|++++| .+..+|. .+.+
T Consensus       144 ~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~  221 (306)
T 2z66_A          144 GIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC-QLEQLSPTAFNSLSSLQVLNMSHN-NFFSLDTFPYKC  221 (306)
T ss_dssp             TTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECTTS-CCSBCCSGGGTT
T ss_pred             hhcccCcCCCEEECCCCccccccchhHHhhCcCCCEEECCCC-CcCCcCHHHhcCCCCCCEEECCCC-ccCccChhhccC
Confidence            345667777777774333322246666777788888888887 45555 555777888888888875 3555544 5677


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|+.|++++..
T Consensus       222 l~~L~~L~L~~N~  234 (306)
T 2z66_A          222 LNSLQVLDYSLNH  234 (306)
T ss_dssp             CTTCCEEECTTSC
T ss_pred             cccCCEeECCCCC
Confidence            7888888887654

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=98.11  E-value=5.3e-06  Score=75.48  Aligned_cols=82  Identities=15%  Similarity=0.147  Sum_probs=45.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+++|++|+++.+  .+..++. +..+++|++|++++| .+..+|. ++.+++|+.|++++| .+..+|. +.++++|
T Consensus       125 l~~l~~L~~L~l~~n--~l~~~~~-l~~l~~L~~L~l~~n-~l~~~~~-l~~l~~L~~L~l~~n-~l~~~~~-l~~l~~L  197 (308)
T 1h6u_A          125 LAGLSNLQVLYLDLN--QITNISP-LAGLTNLQYLSIGNA-QVSDLTP-LANLSKLTTLKADDN-KISDISP-LASLPNL  197 (308)
T ss_dssp             GTTCTTCCEEECCSS--CCCCCGG-GGGCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSS-CCCCCGG-GGGCTTC
T ss_pred             hcCCCCCCEEECCCC--ccCcCcc-ccCCCCccEEEccCC-cCCCChh-hcCCCCCCEEECCCC-ccCcChh-hcCCCCC
Confidence            455666666666322  2222332 455566666666666 4555554 566666666666653 3555553 5566666


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|+++++.
T Consensus       198 ~~L~L~~N~  206 (308)
T 1h6u_A          198 IEVHLKNNQ  206 (308)
T ss_dssp             CEEECTTSC
T ss_pred             CEEEccCCc
Confidence            666666544

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=98.11  E-value=5e-06  Score=73.89  Aligned_cols=56  Identities=16%  Similarity=0.058  Sum_probs=35.1

Q ss_pred             CcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          267 PRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       267 ~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      ++|++|++++| .+..+| .++.+++|+.|++++| .+..+| .++++++|++|+++++.
T Consensus       106 ~~L~~L~L~~N-~l~~~~-~l~~l~~L~~L~Ls~N-~i~~~~-~l~~l~~L~~L~L~~N~  161 (263)
T 1xeu_A          106 ACLSRLFLDNN-ELRDTD-SLIHLKNLEILSIRNN-KLKSIV-MLGFLSKLEVLDLHGNE  161 (263)
T ss_dssp             SSCCEEECCSS-CCSBSG-GGTTCTTCCEEECTTS-CCCBCG-GGGGCTTCCEEECTTSC
T ss_pred             CcccEEEccCC-ccCCCh-hhcCcccccEEECCCC-cCCCCh-HHccCCCCCEEECCCCc
Confidence            45555555555 455554 4666777777777764 466665 56777777777777654

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=98.10  E-value=5.5e-06  Score=74.78  Aligned_cols=82  Identities=20%  Similarity=0.179  Sum_probs=42.9

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+++|++|+++.+  .+..++ .+..+++|++|++++| .+..++ .++.+++|+.|++++| .+..+|. +.++++|
T Consensus       108 l~~l~~L~~L~L~~n--~i~~~~-~l~~l~~L~~L~l~~n-~l~~~~-~l~~l~~L~~L~L~~N-~l~~~~~-l~~l~~L  180 (291)
T 1h6t_A          108 LKDLKKLKSLSLEHN--GISDIN-GLVHLPQLESLYLGNN-KITDIT-VLSRLTKLDTLSLEDN-QISDIVP-LAGLTKL  180 (291)
T ss_dssp             GTTCTTCCEEECTTS--CCCCCG-GGGGCTTCCEEECCSS-CCCCCG-GGGGCTTCSEEECCSS-CCCCCGG-GTTCTTC
T ss_pred             hccCCCCCEEECCCC--cCCCCh-hhcCCCCCCEEEccCC-cCCcch-hhccCCCCCEEEccCC-ccccchh-hcCCCcc
Confidence            455566666666222  122232 3445556666666665 455542 4555666666666653 3444544 5566666


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|+++++.
T Consensus       181 ~~L~L~~N~  189 (291)
T 1h6t_A          181 QNLYLSKNH  189 (291)
T ss_dssp             CEEECCSSC
T ss_pred             CEEECCCCc
Confidence            666665543

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=98.10  E-value=5.2e-06  Score=79.91  Aligned_cols=85  Identities=11%  Similarity=0.097  Sum_probs=59.4

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ++.+..+++|++|+++.+  ....+|. +..+++|++|++++| .+..+|. ++++++|++|++++| .+..+|. +.++
T Consensus        61 l~~~~~l~~L~~L~Ls~n--~l~~~~~-~~~l~~L~~L~l~~n-~l~~~~~-~~~l~~L~~L~L~~n-~l~~~~~-~~~l  133 (466)
T 1o6v_A           61 IDGVEYLNNLTQINFSNN--QLTDITP-LKNLTKLVDILMNNN-QIADITP-LANLTNLTGLTLFNN-QITDIDP-LKNL  133 (466)
T ss_dssp             CTTGGGCTTCCEEECCSS--CCCCCGG-GTTCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSS-CCCCCGG-GTTC
T ss_pred             CcchhhhcCCCEEECCCC--ccCCchh-hhccccCCEEECCCC-ccccChh-hcCCCCCCEEECCCC-CCCCChH-HcCC
Confidence            445667788888888332  3334554 777888888888887 5666665 778888888888875 5666665 7777


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|+++++.
T Consensus       134 ~~L~~L~l~~n~  145 (466)
T 1o6v_A          134 TNLNRLELSSNT  145 (466)
T ss_dssp             TTCSEEEEEEEE
T ss_pred             CCCCEEECCCCc
Confidence            888888777654

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=98.10  E-value=4e-06  Score=83.58  Aligned_cols=60  Identities=15%  Similarity=0.109  Sum_probs=31.1

Q ss_pred             CCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          263 HGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       263 ~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      +..+++|++|+|++| .+..+| .++.|++|+.|+|++| .+..+ ..+++|++|+.|+++++.
T Consensus       105 l~~l~~L~~L~Ls~N-~l~~l~-~l~~l~~L~~L~Ls~N-~l~~l-~~l~~l~~L~~L~Ls~N~  164 (605)
T 1m9s_A          105 LKDLKKLKSLSLEHN-GISDIN-GLVHLPQLESLYLGNN-KITDI-TVLSRLTKLDTLSLEDNQ  164 (605)
T ss_dssp             STTCTTCCEEECTTS-CCCCCG-GGGGCTTCSEEECCSS-CCCCC-GGGGSCTTCSEEECCSSC
T ss_pred             hccCCCCCEEEecCC-CCCCCc-cccCCCccCEEECCCC-ccCCc-hhhcccCCCCEEECcCCc
Confidence            445555555555555 344443 3555555555555553 34444 345555666666665543

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=98.09  E-value=8e-06  Score=72.58  Aligned_cols=58  Identities=19%  Similarity=0.115  Sum_probs=29.2

Q ss_pred             CCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecC
Q 048347          263 HGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWW  324 (351)
Q Consensus       263 ~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  324 (351)
                      +..+++|++|++++| .+..+| .++.+++|++|++++| .+..+ ..+.++++|+.|++++
T Consensus       124 l~~l~~L~~L~Ls~N-~i~~~~-~l~~l~~L~~L~L~~N-~i~~~-~~l~~l~~L~~L~l~~  181 (263)
T 1xeu_A          124 LIHLKNLEILSIRNN-KLKSIV-MLGFLSKLEVLDLHGN-EITNT-GGLTRLKKVNWIDLTG  181 (263)
T ss_dssp             GTTCTTCCEEECTTS-CCCBCG-GGGGCTTCCEEECTTS-CCCBC-TTSTTCCCCCEEEEEE
T ss_pred             hcCcccccEEECCCC-cCCCCh-HHccCCCCCEEECCCC-cCcch-HHhccCCCCCEEeCCC
Confidence            445555555555555 344444 3555555555555553 33333 3445555555555544

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=98.08  E-value=5.5e-06  Score=75.58  Aligned_cols=82  Identities=15%  Similarity=0.002  Sum_probs=66.5

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+++|++|+++ ++ .+..++. ...+++|++|++++| .+..+|..++.+++|++|++++| .+..+|..+..+++|+.
T Consensus       167 ~l~~L~~L~L~-~N-~l~~~~~-~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~~L~~L~L~~N-~l~~l~~~~~~l~~L~~  241 (317)
T 3o53_A          167 SSDTLEHLNLQ-YN-FIYDVKG-QVVFAKLKTLDLSSN-KLAFMGPEFQSAAGVTWISLRNN-KLVLIEKALRFSQNLEH  241 (317)
T ss_dssp             GTTTCCEEECT-TS-CCCEEEC-CCCCTTCCEEECCSS-CCCEECGGGGGGTTCSEEECTTS-CCCEECTTCCCCTTCCE
T ss_pred             ccCcCCEEECC-CC-cCccccc-ccccccCCEEECCCC-cCCcchhhhcccCcccEEECcCC-cccchhhHhhcCCCCCE
Confidence            57888888883 32 3445554 345889999999998 68888888999999999999985 67889999999999999


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |++++.+
T Consensus       242 L~l~~N~  248 (317)
T 3o53_A          242 FDLRGNG  248 (317)
T ss_dssp             EECTTCC
T ss_pred             EEccCCC
Confidence            9998865

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=98.08  E-value=4.6e-06  Score=79.69  Aligned_cols=86  Identities=22%  Similarity=0.224  Sum_probs=55.7

Q ss_pred             CCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      .+..+++|++|+++ ++ .+..+|. .+..+++|++|++++|..+..+|.. ++.+++|++|++++| .+..+| .+.++
T Consensus       131 ~~~~l~~L~~L~L~-~N-~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n-~l~~~~-~~~~l  206 (440)
T 3zyj_A          131 AFVYLSKLKELWLR-NN-PIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMC-NLREIP-NLTPL  206 (440)
T ss_dssp             TSCSCSSCCEEECC-SC-CCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEECTTS-CCSSCC-CCTTC
T ss_pred             HhhccccCceeeCC-CC-cccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecCCCC-cCcccc-ccCCC
Confidence            35566777777773 22 2334443 4666777777777776566666653 667777777777774 566676 46777


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|+.|++++..
T Consensus       207 ~~L~~L~Ls~N~  218 (440)
T 3zyj_A          207 IKLDELDLSGNH  218 (440)
T ss_dssp             SSCCEEECTTSC
T ss_pred             cccCEEECCCCc
Confidence            777788777654

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=98.08  E-value=5.6e-06  Score=73.78  Aligned_cols=86  Identities=15%  Similarity=0.155  Sum_probs=67.7

Q ss_pred             CCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccccCh-hhhc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRKFPE-ELWR  313 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~  313 (351)
                      .+..+++|++|+++ ++ .+..++. .+..+++|++|++++| .+..+| ..++.+++|++|++++| .+..+|. .+++
T Consensus        47 ~~~~l~~L~~L~l~-~n-~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~  122 (276)
T 2z62_A           47 SFFSFPELQVLDLS-RC-EIQTIEDGAYQSLSHLSTLILTGN-PIQSLALGAFSGLSSLQKLVAVET-NLASLENFPIGH  122 (276)
T ss_dssp             TTTTCTTCSEEECT-TC-CCCEECTTTTTTCTTCCEEECTTC-CCCEECTTTTTTCTTCCEEECTTS-CCCCSTTCCCTT
T ss_pred             HhccccCCcEEECC-CC-cCCccCHHHccCCcCCCEEECCCC-ccCccChhhhcCCccccEEECCCC-CccccCchhccc
Confidence            56788999999993 33 3445554 5788999999999999 577666 45889999999999985 4666665 6889


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|++++..
T Consensus       123 l~~L~~L~l~~n~  135 (276)
T 2z62_A          123 LKTLKELNVAHNL  135 (276)
T ss_dssp             CTTCCEEECCSSC
T ss_pred             CCCCCEEECcCCc
Confidence            9999999998754

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=98.08  E-value=1.2e-06  Score=80.42  Aligned_cols=107  Identities=15%  Similarity=0.104  Sum_probs=69.7

Q ss_pred             CCCCCCCceEEEEecccccCc--eeeeCCCCCCcccEEEEecCCcccc--ccccccccC-CccEEeecCCc-cc--cccC
Q 048347          237 APEKLPHLKVLKLKRSSYSGR--KLVCGHGGFPRQEILHLKSMLWLEE--WKMETGAMQ-KLKSLIVNPCA-YL--RKFP  308 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~--~lp~~~~~l~~L~~L~L~~~~~l~~--lp~~i~~L~-~L~~L~l~~c~-~l--~~lP  308 (351)
                      .+..+++|++|++ .++....  .++..+..+++|++|++++|..+..  +|..++.++ +|++|++++|. .+  ..+|
T Consensus       137 ~l~~~~~L~~L~L-~~~~~l~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~  215 (336)
T 2ast_B          137 TLAKNSNLVRLNL-SGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLS  215 (336)
T ss_dssp             HHTTCTTCSEEEC-TTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHH
T ss_pred             HHhcCCCCCEEEC-CCCCCCCHHHHHHHHhcCCCCCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHH
Confidence            3456788888888 3442222  3555566778888888888844553  666677888 88888888864 23  5667


Q ss_pred             hhhhcCCCCCEEEecCCC---hhHHhhccccccCceeeE
Q 048347          309 EELWRIKALRKLESWWPR---PELRQSLHKFEEIDRLDM  344 (351)
Q Consensus       309 ~~i~~L~~L~~L~l~~~~---~~~~~~l~~~~~~~~~~~  344 (351)
                      ..+.++++|++|+++++.   .+....+..+...+...+
T Consensus       216 ~~~~~~~~L~~L~l~~~~~l~~~~~~~l~~l~~L~~L~l  254 (336)
T 2ast_B          216 TLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSL  254 (336)
T ss_dssp             HHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEEC
T ss_pred             HHHhhCCCCCEEeCCCCCcCCHHHHHHHhCCCCCCEeeC
Confidence            777788888888888876   233444444444433333

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=98.08  E-value=6.7e-06  Score=71.66  Aligned_cols=83  Identities=14%  Similarity=0.156  Sum_probs=68.5

Q ss_pred             CCceEEEEecccccCceeee-CCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccCh-hhhcCCCCC
Q 048347          242 PHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPE-ELWRIKALR  318 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~L~  318 (351)
                      ++|++|+++.+  .+..+|. .+..+++|++|++++|..++.+|. .++.+++|++|++++|..+..+|. .+.++++|+
T Consensus        31 ~~l~~L~l~~n--~l~~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L~  108 (239)
T 2xwt_C           31 PSTQTLKLIET--HLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLK  108 (239)
T ss_dssp             TTCCEEEEESC--CCSEECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTTCC
T ss_pred             CcccEEEEeCC--cceEECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCCC
Confidence            48999999433  3556665 588999999999999944888887 588999999999998667888885 568999999


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|+++++.
T Consensus       109 ~L~l~~n~  116 (239)
T 2xwt_C          109 FLGIFNTG  116 (239)
T ss_dssp             EEEEEEEC
T ss_pred             EEeCCCCC
Confidence            99998764

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=98.08  E-value=5.7e-06  Score=76.98  Aligned_cols=85  Identities=21%  Similarity=0.201  Sum_probs=50.4

Q ss_pred             CCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChhh---
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEEL---  311 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~i---  311 (351)
                      .+..+++|++|+|+.+  .+..++. .+..+++|++|+|++| .+..+ |..++.+++|+.|+|++| .+..+|..+   
T Consensus        83 ~~~~l~~L~~L~Ls~N--~l~~~~~~~~~~l~~L~~L~L~~N-~i~~~~~~~~~~l~~L~~L~L~~N-~l~~l~~~~~~~  158 (361)
T 2xot_A           83 AFVPVPNLRYLDLSSN--HLHTLDEFLFSDLQALEVLLLYNN-HIVVVDRNAFEDMAQLQKLYLSQN-QISRFPVELIKD  158 (361)
T ss_dssp             TTTTCTTCCEEECCSS--CCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSS-CCCSCCGGGTC-
T ss_pred             hccCCCCCCEEECCCC--cCCcCCHHHhCCCcCCCEEECCCC-cccEECHHHhCCcccCCEEECCCC-cCCeeCHHHhcC
Confidence            3556666777777322  2334443 3566677777777776 45554 344666777777777763 566666655   


Q ss_pred             -hcCCCCCEEEecCC
Q 048347          312 -WRIKALRKLESWWP  325 (351)
Q Consensus       312 -~~L~~L~~L~l~~~  325 (351)
                       .++++|+.|++++.
T Consensus       159 ~~~l~~L~~L~L~~N  173 (361)
T 2xot_A          159 GNKLPKLMLLDLSSN  173 (361)
T ss_dssp             ---CTTCCEEECCSS
T ss_pred             cccCCcCCEEECCCC
Confidence             45677777777654

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=98.07  E-value=5.4e-06  Score=81.48  Aligned_cols=85  Identities=21%  Similarity=0.217  Sum_probs=42.8

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccCh-hhhcCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPE-ELWRIK  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~  315 (351)
                      +..+++|++|+++.+......+|..+..+++|++|++++| .+..+ |..++.+++|++|++++| .+..+|. .+.+++
T Consensus       441 ~~~l~~L~~L~l~~n~l~~~~~p~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~  518 (570)
T 2z63_A          441 FNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC-QLEQLSPTAFNSLSSLQVLNMASN-QLKSVPDGIFDRLT  518 (570)
T ss_dssp             TTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCT
T ss_pred             hhcCCcCcEEECcCCcCccccchhhhhcccCCCEEECCCC-ccccCChhhhhcccCCCEEeCCCC-cCCCCCHHHhhccc
Confidence            3445555555552222221245555555566666666655 33333 445555666666666654 3333433 345566


Q ss_pred             CCCEEEecC
Q 048347          316 ALRKLESWW  324 (351)
Q Consensus       316 ~L~~L~l~~  324 (351)
                      +|+.|++++
T Consensus       519 ~L~~L~l~~  527 (570)
T 2z63_A          519 SLQKIWLHT  527 (570)
T ss_dssp             TCCEEECCS
T ss_pred             CCcEEEecC
Confidence            666666655

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=98.07  E-value=7.2e-06  Score=76.29  Aligned_cols=82  Identities=18%  Similarity=0.117  Sum_probs=50.2

Q ss_pred             CCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCcccccc-ChhhhcCCC
Q 048347          240 KLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKF-PEELWRIKA  316 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~l-P~~i~~L~~  316 (351)
                      .+++|++|+|+.+  .+..++ ..+..+++|++|+|++| .+..+|.. +..+++|++|+|++|. +..+ |..+.++++
T Consensus        62 ~l~~L~~L~L~~N--~i~~i~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N~-i~~~~~~~~~~l~~  137 (361)
T 2xot_A           62 RLTNLHSLLLSHN--HLNFISSEAFVPVPNLRYLDLSSN-HLHTLDEFLFSDLQALEVLLLYNNH-IVVVDRNAFEDMAQ  137 (361)
T ss_dssp             CCTTCCEEECCSS--CCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTT
T ss_pred             cccccCEEECCCC--cCCccChhhccCCCCCCEEECCCC-cCCcCCHHHhCCCcCCCEEECCCCc-ccEECHHHhCCccc
Confidence            5667777777322  233444 34666777777777776 46666553 5667777777777643 4444 455667777


Q ss_pred             CCEEEecCC
Q 048347          317 LRKLESWWP  325 (351)
Q Consensus       317 L~~L~l~~~  325 (351)
                      |++|++++.
T Consensus       138 L~~L~L~~N  146 (361)
T 2xot_A          138 LQKLYLSQN  146 (361)
T ss_dssp             CCEEECCSS
T ss_pred             CCEEECCCC
Confidence            777777654

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=98.06  E-value=9e-06  Score=74.53  Aligned_cols=85  Identities=18%  Similarity=0.125  Sum_probs=63.4

Q ss_pred             CCCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChh-hhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEE-LWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~  313 (351)
                      ..+..+++|++|+++ ++. +..+ |..++.+++|++|++++| .+..+|..+.  ++|++|++++| .+..+|.. +.+
T Consensus        72 ~~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~--~~L~~L~l~~n-~i~~~~~~~~~~  145 (332)
T 2ft3_A           72 DDFKGLQHLYALVLV-NNK-ISKIHEKAFSPLRKLQKLYISKN-HLVEIPPNLP--SSLVELRIHDN-RIRKVPKGVFSG  145 (332)
T ss_dssp             TTTTTCTTCCEEECC-SSC-CCEECGGGSTTCTTCCEEECCSS-CCCSCCSSCC--TTCCEEECCSS-CCCCCCSGGGSS
T ss_pred             hHhhCCCCCcEEECC-CCc-cCccCHhHhhCcCCCCEEECCCC-cCCccCcccc--ccCCEEECCCC-ccCccCHhHhCC
Confidence            356778888888883 333 3344 666888888888888888 6778887665  78888888874 56667754 678


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|++++..
T Consensus       146 l~~L~~L~l~~n~  158 (332)
T 2ft3_A          146 LRNMNCIEMGGNP  158 (332)
T ss_dssp             CSSCCEEECCSCC
T ss_pred             CccCCEEECCCCc
Confidence            8889999888765

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=98.06  E-value=9.4e-06  Score=74.30  Aligned_cols=85  Identities=16%  Similarity=0.071  Sum_probs=49.1

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccCh-hhhcCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPE-ELWRIK  315 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~  315 (351)
                      .+..+++|++|+++ ++......|..+..+++|++|++++| .+..+|..+.  ++|++|++++| .+..+|. .+++++
T Consensus        71 ~~~~l~~L~~L~L~-~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~l~~~~~--~~L~~L~l~~n-~l~~~~~~~~~~l~  145 (330)
T 1xku_A           71 DFKNLKNLHTLILI-NNKISKISPGAFAPLVKLERLYLSKN-QLKELPEKMP--KTLQELRVHEN-EITKVRKSVFNGLN  145 (330)
T ss_dssp             TTTTCTTCCEEECC-SSCCCCBCTTTTTTCTTCCEEECCSS-CCSBCCSSCC--TTCCEEECCSS-CCCBBCHHHHTTCT
T ss_pred             hhccCCCCCEEECC-CCcCCeeCHHHhcCCCCCCEEECCCC-cCCccChhhc--ccccEEECCCC-cccccCHhHhcCCc
Confidence            45667777777773 32222223555667777777777776 4666665543  56666666654 3444443 345666


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|++++..
T Consensus       146 ~L~~L~l~~n~  156 (330)
T 1xku_A          146 QMIVVELGTNP  156 (330)
T ss_dssp             TCCEEECCSSC
T ss_pred             cccEEECCCCc
Confidence            66666666543

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=98.05  E-value=8e-06  Score=78.31  Aligned_cols=87  Identities=17%  Similarity=0.064  Sum_probs=50.6

Q ss_pred             CCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChh-hhc
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEE-LWR  313 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~-i~~  313 (351)
                      .+..+++|++|+|+.+  .+..+|.. +..+++|++|+|++| .+..+|. .++.+++|++|++++|..+..+|.. +.+
T Consensus       118 ~~~~l~~L~~L~L~~n--~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~  194 (452)
T 3zyi_A          118 AFNGLASLNTLELFDN--WLTVIPSGAFEYLSKLRELWLRNN-PIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEG  194 (452)
T ss_dssp             TTTTCTTCCEEECCSS--CCSBCCTTTSSSCTTCCEEECCSC-CCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTT
T ss_pred             hccCcccCCEEECCCC--cCCccChhhhcccCCCCEEECCCC-CcceeCHhHHhcCCcccEEeCCCCCCccccChhhccC
Confidence            3455666666666322  22234332 555666666666666 4555554 3566666666666666666666653 566


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|+++++.
T Consensus       195 l~~L~~L~L~~n~  207 (452)
T 3zyi_A          195 LFNLKYLNLGMCN  207 (452)
T ss_dssp             CTTCCEEECTTSC
T ss_pred             CCCCCEEECCCCc
Confidence            7777777776654

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=98.05  E-value=8.2e-06  Score=84.56  Aligned_cols=86  Identities=15%  Similarity=0.079  Sum_probs=70.1

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChhhhcCCCCC
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALR  318 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~  318 (351)
                      ..++|++|+|+.+ ......|..+..+++|++|+|++|.....+ |..++++++|++|+|++|......|..++++++|+
T Consensus        22 lp~~l~~LdLs~N-~i~~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L~  100 (844)
T 3j0a_A           22 VLNTTERLLLSFN-YIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLF  100 (844)
T ss_dssp             SCTTCCEEEEESC-CCCEECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSCC
T ss_pred             CCCCcCEEECCCC-cCCccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCcccC
Confidence            4579999999543 333334667999999999999999667788 66699999999999999654444588999999999


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|+++++.
T Consensus       101 ~L~Ls~n~  108 (844)
T 3j0a_A          101 ELRLYFCG  108 (844)
T ss_dssp             CEECTTCC
T ss_pred             EeeCcCCC
Confidence            99999875

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=98.05  E-value=7.2e-06  Score=75.46  Aligned_cols=82  Identities=15%  Similarity=0.080  Sum_probs=39.7

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+++|++|+++.+  ....+| .+..+++|++|++++| .+..+|. ++.+++|++|++++|..+..+| .+.++++|
T Consensus        84 ~~~l~~L~~L~L~~n--~i~~~~-~~~~l~~L~~L~l~~n-~i~~~~~-~~~l~~L~~L~l~~n~~~~~~~-~~~~l~~L  157 (347)
T 4fmz_A           84 LSNLVKLTNLYIGTN--KITDIS-ALQNLTNLRELYLNED-NISDISP-LANLTKMYSLNLGANHNLSDLS-PLSNMTGL  157 (347)
T ss_dssp             GTTCTTCCEEECCSS--CCCCCG-GGTTCTTCSEEECTTS-CCCCCGG-GTTCTTCCEEECTTCTTCCCCG-GGTTCTTC
T ss_pred             hhcCCcCCEEEccCC--cccCch-HHcCCCcCCEEECcCC-cccCchh-hccCCceeEEECCCCCCccccc-chhhCCCC
Confidence            445555666666222  222333 2455555555555555 3445543 5555555555555544333333 24444455


Q ss_pred             CEEEecCC
Q 048347          318 RKLESWWP  325 (351)
Q Consensus       318 ~~L~l~~~  325 (351)
                      ++|+++++
T Consensus       158 ~~L~l~~~  165 (347)
T 4fmz_A          158 NYLTVTES  165 (347)
T ss_dssp             CEEECCSS
T ss_pred             cEEEecCC
Confidence            55554443

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.04  E-value=2.2e-07  Score=78.97  Aligned_cols=85  Identities=15%  Similarity=0.108  Sum_probs=42.5

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccCh--hhhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPE--ELWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~--~i~~L  314 (351)
                      .+..+++|++|+++.+.  +..+|..+..+++|++|++++| .+..+| .++.+++|++|++++| .+..+|.  .+.++
T Consensus        65 ~~~~l~~L~~L~l~~n~--l~~l~~~~~~~~~L~~L~L~~N-~l~~l~-~~~~l~~L~~L~l~~N-~i~~~~~~~~l~~l  139 (198)
T 1ds9_A           65 SLSGMENLRILSLGRNL--IKKIENLDAVADTLEELWISYN-QIASLS-GIEKLVNLRVLYMSNN-KITNWGEIDKLAAL  139 (198)
T ss_dssp             CHHHHTTCCEEEEEEEE--ECSCSSHHHHHHHCSEEEEEEE-ECCCHH-HHHHHHHSSEEEESEE-ECCCHHHHHHHTTT
T ss_pred             ccccCCCCCEEECCCCC--cccccchhhcCCcCCEEECcCC-cCCcCC-ccccCCCCCEEECCCC-cCCchhHHHHHhcC
Confidence            33444555555552221  1134433334455555555555 444554 4555555666666553 3444443  45566


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++.+
T Consensus       140 ~~L~~L~l~~N~  151 (198)
T 1ds9_A          140 DKLEDLLLAGNP  151 (198)
T ss_dssp             TTCSEEEECSCH
T ss_pred             CCCCEEEecCCc
Confidence            666666666554

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=98.04  E-value=8.5e-06  Score=80.85  Aligned_cols=85  Identities=14%  Similarity=0.096  Sum_probs=50.1

Q ss_pred             CCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhhhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      .+..+++|++|+|+ ++ .+..+ |..+.++++|++|+|++| .+..+|. .++.+++|++|+|++|......|..+.++
T Consensus       489 ~~~~l~~L~~L~Ls-~N-~L~~l~~~~f~~l~~L~~L~Ls~N-~l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~l~~l  565 (635)
T 4g8a_A          489 IFTELRNLTFLDLS-QC-QLEQLSPTAFNSLSSLQVLNMSHN-NFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHF  565 (635)
T ss_dssp             CCTTCTTCCEEECT-TS-CCCEECTTTTTTCTTCCEEECTTS-CCCBCCCGGGTTCTTCCEEECTTSCCCBCCSSCTTCC
T ss_pred             hhhhccccCEEECC-CC-ccCCcChHHHcCCCCCCEEECCCC-cCCCCChhHHhCCCCCCEEECCCCcCCCCCHHHHHhh
Confidence            34556667777773 32 23333 444666777777777776 4665544 36667777777777654333334455665


Q ss_pred             -CCCCEEEecC
Q 048347          315 -KALRKLESWW  324 (351)
Q Consensus       315 -~~L~~L~l~~  324 (351)
                       ++|+.|++++
T Consensus       566 ~~~L~~L~L~~  576 (635)
T 4g8a_A          566 PSSLAFLNLTQ  576 (635)
T ss_dssp             CTTCCEEECTT
T ss_pred             hCcCCEEEeeC
Confidence             5677777765

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=98.03  E-value=6.8e-06  Score=81.93  Aligned_cols=85  Identities=19%  Similarity=0.187  Sum_probs=52.1

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ++.+..+++|+.|+|+.+.  +..++ .+..+++|+.|+|++| .+..+ ..++.+++|+.|+|++| .+..+|. +.++
T Consensus       102 l~~l~~l~~L~~L~Ls~N~--l~~l~-~l~~l~~L~~L~Ls~N-~l~~l-~~l~~l~~L~~L~Ls~N-~l~~~~~-l~~l  174 (605)
T 1m9s_A          102 LSSLKDLKKLKSLSLEHNG--ISDIN-GLVHLPQLESLYLGNN-KITDI-TVLSRLTKLDTLSLEDN-QISDIVP-LAGL  174 (605)
T ss_dssp             CTTSTTCTTCCEEECTTSC--CCCCG-GGGGCTTCSEEECCSS-CCCCC-GGGGSCTTCSEEECCSS-CCCCCGG-GTTC
T ss_pred             ChhhccCCCCCEEEecCCC--CCCCc-cccCCCccCEEECCCC-ccCCc-hhhcccCCCCEEECcCC-cCCCchh-hccC
Confidence            3456667777777773222  22333 3566677777777776 46655 35667777777777764 3555544 6667


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|+.|+++++.
T Consensus       175 ~~L~~L~Ls~N~  186 (605)
T 1m9s_A          175 TKLQNLYLSKNH  186 (605)
T ss_dssp             TTCCEEECCSSC
T ss_pred             CCCCEEECcCCC
Confidence            777777776654

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=98.03  E-value=4.5e-06  Score=75.97  Aligned_cols=83  Identities=18%  Similarity=0.130  Sum_probs=39.9

Q ss_pred             CCCceEEEEecccccCceeeeCC--CCCCcccEEEEecCCcccccccccccc-----CCccEEeecCCccccccC-hhhh
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGH--GGFPRQEILHLKSMLWLEEWKMETGAM-----QKLKSLIVNPCAYLRKFP-EELW  312 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~--~~l~~L~~L~L~~~~~l~~lp~~i~~L-----~~L~~L~l~~c~~l~~lP-~~i~  312 (351)
                      +++|++|+++.+... ..+|..+  ..+++|++|++++| .+..+|..++.+     ++|++|++++|. +..+| ..++
T Consensus        94 l~~L~~L~L~~n~l~-~~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~l~~~~~~~L~~L~L~~N~-l~~~~~~~~~  170 (312)
T 1wwl_A           94 ISGLQELTLENLEVT-GTAPPPLLEATGPDLNILNLRNV-SWATRDAWLAELQQWLKPGLKVLSIAQAH-SLNFSCEQVR  170 (312)
T ss_dssp             TSCCCEEEEEEEBCB-SCCCCCSSSCCSCCCSEEEEESC-BCSSSSSHHHHHHTTCCTTCCEEEEESCS-CCCCCTTTCC
T ss_pred             cCCccEEEccCCccc-chhHHHHHHhcCCCccEEEccCC-CCcchhHHHHHHHHhhcCCCcEEEeeCCC-CccchHHHhc
Confidence            455555555322221 2344433  45555555555555 344445444444     555555555532 33333 4455


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|++++..
T Consensus       171 ~l~~L~~L~Ls~N~  184 (312)
T 1wwl_A          171 VFPALSTLDLSDNP  184 (312)
T ss_dssp             CCSSCCEEECCSCT
T ss_pred             cCCCCCEEECCCCC
Confidence            55555555555543

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=98.02  E-value=7.8e-06  Score=68.96  Aligned_cols=81  Identities=15%  Similarity=0.197  Sum_probs=64.9

Q ss_pred             CCceEEEEecccccCceeeeC--CCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChh-hhcCCCC
Q 048347          242 PHLKVLKLKRSSYSGRKLVCG--HGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEE-LWRIKAL  317 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~--~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L  317 (351)
                      ++|++|+++.+  .+..++..  ++.+++|++|+|++| .+..+ |..++.+++|++|+|++| .+..+|.. +.++++|
T Consensus        29 ~~l~~L~l~~n--~i~~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L  104 (192)
T 1w8a_A           29 LHTTELLLNDN--ELGRISSDGLFGRLPHLVKLELKRN-QLTGIEPNAFEGASHIQELQLGEN-KIKEISNKMFLGLHQL  104 (192)
T ss_dssp             TTCSEEECCSC--CCCSBCCSCSGGGCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSC-CCCEECSSSSTTCTTC
T ss_pred             CCCCEEECCCC--cCCccCCccccccCCCCCEEECCCC-CCCCcCHhHcCCcccCCEEECCCC-cCCccCHHHhcCCCCC
Confidence            48999999433  34455543  789999999999999 57666 667999999999999995 56666654 7899999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++..
T Consensus       105 ~~L~L~~N~  113 (192)
T 1w8a_A          105 KTLNLYDNQ  113 (192)
T ss_dssp             CEEECCSSC
T ss_pred             CEEECCCCc
Confidence            999999864

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=98.01  E-value=8.5e-06  Score=80.86  Aligned_cols=84  Identities=13%  Similarity=0.054  Sum_probs=41.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCcccccc--ChhhhcC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKF--PEELWRI  314 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~l--P~~i~~L  314 (351)
                      +..+++|++|+++ ++......|..++.+++|++|++++| .+..+ |..++.+++|++|++++|. +..+  |.. ..+
T Consensus        77 ~~~l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~L~~n-~i~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~-~~l  152 (606)
T 3t6q_A           77 FQSQHRLDTLVLT-ANPLIFMAETALSGPKALKHLFFIQT-GISSIDFIPLHNQKTLESLYLGSNH-ISSIKLPKG-FPT  152 (606)
T ss_dssp             TTTCTTCCEEECT-TCCCSEECTTTTSSCTTCCEEECTTS-CCSCGGGSCCTTCTTCCEEECCSSC-CCCCCCCTT-CCC
T ss_pred             ccCccccCeeeCC-CCcccccChhhhcccccccEeecccc-CcccCCcchhccCCcccEEECCCCc-ccccCcccc-cCC
Confidence            4455555555552 22222222444555555555555555 34444 3445556666666666532 3333  322 236


Q ss_pred             CCCCEEEecCC
Q 048347          315 KALRKLESWWP  325 (351)
Q Consensus       315 ~~L~~L~l~~~  325 (351)
                      ++|++|++++.
T Consensus       153 ~~L~~L~L~~n  163 (606)
T 3t6q_A          153 EKLKVLDFQNN  163 (606)
T ss_dssp             TTCCEEECCSS
T ss_pred             cccCEEEcccC
Confidence            66666666554

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=97.98  E-value=1.5e-05  Score=66.06  Aligned_cols=82  Identities=16%  Similarity=0.161  Sum_probs=66.5

Q ss_pred             CCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIKAL  317 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L  317 (351)
                      .++|+.|+++.+.  +..+|.. +..+++|++|++++| .+..+|.. ++.+++|++|++++| .+..+|.. ++++++|
T Consensus        27 ~~~l~~L~l~~n~--l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~l~~L  102 (177)
T 2o6r_A           27 PSSATRLELESNK--LQSLPHGVFDKLTQLTKLSLSQN-QIQSLPDGVFDKLTKLTILYLHEN-KLQSLPNGVFDKLTQL  102 (177)
T ss_dssp             CTTCSEEECCSSC--CCCCCTTTTTTCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTC
T ss_pred             CCCCcEEEeCCCc--ccEeCHHHhcCcccccEEECCCC-cceEeChhHccCCCccCEEECCCC-CccccCHHHhhCCccc
Confidence            4789999994333  3355543 688999999999999 68888876 689999999999985 67788876 5899999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++..
T Consensus       103 ~~L~l~~N~  111 (177)
T 2o6r_A          103 KELALDTNQ  111 (177)
T ss_dssp             CEEECCSSC
T ss_pred             CEEECcCCc
Confidence            999998754

>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=97.98  E-value=7.5e-06  Score=74.35  Aligned_cols=119  Identities=8%  Similarity=-0.028  Sum_probs=69.5

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~   96 (351)
                      .+++|+++..+.+.+++..+.  ...+.++|+.|+|||++|+.+++.  +........++.+. .+.             
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~-------------   79 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARD--LFGENWRDNFIEMNASDE-------------   79 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTC--CCCEEEESSSSSSHHHHHHHHHHH--HHTTCHHHHCEEEETTST-------------
T ss_pred             HHHhCCHHHHHHHHHHHhCCC--CCeEEEECcCCcCHHHHHHHHHHH--hcCCcccCCeEEEeCccc-------------
Confidence            458999999999999886643  223789999999999999999876  31111011122222 110             


Q ss_pred             CCCCccCCCCCHHHHHHHHHHh--c-CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           97 LSALSEILDNDFEMKKNTLHNY--L-KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~l~~~--L-~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                        .    ...............  + .+++.++|+|+++..  +..+.+...+.....+.++|+ |...
T Consensus        80 --~----~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~  142 (319)
T 2chq_A           80 --R----GIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYV  142 (319)
T ss_dssp             --T----CTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCG
T ss_pred             --c----ChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCh
Confidence              0    001111112222111  2 256789999999754  445666666665555666666 6543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.98  E-value=1.3e-05  Score=64.40  Aligned_cols=46  Identities=9%  Similarity=-0.120  Sum_probs=35.5

Q ss_pred             ccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++|+++..+++.+.+..-...-.-|-|+|..|+|||++|+.+++.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHh
Confidence            5789999999999888543222234569999999999999999987

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=97.97  E-value=1.6e-05  Score=73.51  Aligned_cols=82  Identities=15%  Similarity=0.076  Sum_probs=68.0

Q ss_pred             CCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccccChh-hhcCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRKFPEE-LWRIKAL  317 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L  317 (351)
                      .++|++|+++ ++ .+..+|. .+..+++|++|++++| .+..++ ..++.+++|++|++++| .+..+|.. ++++++|
T Consensus        51 ~~~L~~L~l~-~n-~i~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L  126 (353)
T 2z80_A           51 TEAVKSLDLS-NN-RITYISNSDLQRCVNLQALVLTSN-GINTIEEDSFSSLGSLEHLDLSYN-YLSNLSSSWFKPLSSL  126 (353)
T ss_dssp             CTTCCEEECT-TS-CCCEECTTTTTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECCSS-CCSSCCHHHHTTCTTC
T ss_pred             cccCcEEECC-CC-cCcccCHHHhccCCCCCEEECCCC-ccCccCHhhcCCCCCCCEEECCCC-cCCcCCHhHhCCCccC
Confidence            3689999993 33 3456665 6889999999999999 677765 45999999999999985 68888887 7899999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++..
T Consensus       127 ~~L~L~~n~  135 (353)
T 2z80_A          127 TFLNLLGNP  135 (353)
T ss_dssp             SEEECTTCC
T ss_pred             CEEECCCCC
Confidence            999999865

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=97.96  E-value=1.8e-05  Score=78.43  Aligned_cols=86  Identities=17%  Similarity=0.177  Sum_probs=53.9

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChh-hhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEE-LWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L  314 (351)
                      .+..+++|++|+++ ++ .+..+|..+..+++|++|++++| .+..+ |..++.+++|++|++++|.....+|.+ ++++
T Consensus       273 ~~~~l~~L~~L~l~-~n-~l~~lp~~l~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l  349 (606)
T 3t6q_A          273 TFHCFSGLQELDLT-AT-HLSELPSGLVGLSTLKKLVLSAN-KFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENL  349 (606)
T ss_dssp             TTTTCTTCSEEECT-TS-CCSCCCSSCCSCTTCCEEECTTC-CCSBGGGGCGGGCTTCSEEECCSCSSCCBCCSSTTTTC
T ss_pred             HhccccCCCEEecc-CC-ccCCCChhhcccccCCEEECccC-CcCcCchhhhhccCcCCEEECCCCCcccccchhhhhcc
Confidence            35667778888873 22 34467777777777777777777 35444 445666777777777765444455543 5566


Q ss_pred             CCCCEEEecCC
Q 048347          315 KALRKLESWWP  325 (351)
Q Consensus       315 ~~L~~L~l~~~  325 (351)
                      ++|++|+++++
T Consensus       350 ~~L~~L~l~~n  360 (606)
T 3t6q_A          350 ENLRELDLSHD  360 (606)
T ss_dssp             TTCCEEECCSS
T ss_pred             CcCCEEECCCC
Confidence            66666666554

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=97.96  E-value=1.1e-05  Score=73.86  Aligned_cols=82  Identities=18%  Similarity=0.102  Sum_probs=58.5

Q ss_pred             CCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhhhcCCCCCEE
Q 048347          242 PHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKL  320 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  320 (351)
                      ++|++|+++ ++......|..+..+++|++|++++| .+..+|. .++.+++|++|++++| .+..+|.++.++++|++|
T Consensus       192 ~~L~~L~l~-~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~lp~~l~~l~~L~~L  268 (330)
T 1xku_A          192 PSLTELHLD-GNKITKVDAASLKGLNNLAKLGLSFN-SISAVDNGSLANTPHLRELHLNNN-KLVKVPGGLADHKYIQVV  268 (330)
T ss_dssp             TTCSEEECT-TSCCCEECTGGGTTCTTCCEEECCSS-CCCEECTTTGGGSTTCCEEECCSS-CCSSCCTTTTTCSSCCEE
T ss_pred             ccCCEEECC-CCcCCccCHHHhcCCCCCCEEECCCC-cCceeChhhccCCCCCCEEECCCC-cCccCChhhccCCCcCEE
Confidence            567777773 33222222456778888888888888 5666554 5778888888888885 577888888888888888


Q ss_pred             EecCCC
Q 048347          321 ESWWPR  326 (351)
Q Consensus       321 ~l~~~~  326 (351)
                      ++++.+
T Consensus       269 ~l~~N~  274 (330)
T 1xku_A          269 YLHNNN  274 (330)
T ss_dssp             ECCSSC
T ss_pred             ECCCCc
Confidence            887754

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=97.95  E-value=3e-07  Score=78.09  Aligned_cols=84  Identities=17%  Similarity=0.151  Sum_probs=70.4

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .+..+++|++|+++.+.  +..+| .+..+++|++|++++| .+..+|..++.+++|++|++++| .+..+| .++++++
T Consensus        43 ~~~~l~~L~~L~ls~n~--l~~l~-~~~~l~~L~~L~l~~n-~l~~l~~~~~~~~~L~~L~L~~N-~l~~l~-~~~~l~~  116 (198)
T 1ds9_A           43 TLSTLKACKHLALSTNN--IEKIS-SLSGMENLRILSLGRN-LIKKIENLDAVADTLEELWISYN-QIASLS-GIEKLVN  116 (198)
T ss_dssp             HHHHTTTCSEEECSEEE--ESCCC-CHHHHTTCCEEEEEEE-EECSCSSHHHHHHHCSEEEEEEE-ECCCHH-HHHHHHH
T ss_pred             HHhcCCCCCEEECCCCC--Ccccc-ccccCCCCCEEECCCC-CcccccchhhcCCcCCEEECcCC-cCCcCC-ccccCCC
Confidence            45678999999994433  33477 7788899999999999 68899988888999999999985 677888 7899999


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |++|++++..
T Consensus       117 L~~L~l~~N~  126 (198)
T 1ds9_A          117 LRVLYMSNNK  126 (198)
T ss_dssp             SSEEEESEEE
T ss_pred             CCEEECCCCc
Confidence            9999998864

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=97.94  E-value=1.4e-05  Score=66.30  Aligned_cols=77  Identities=13%  Similarity=0.113  Sum_probs=61.8

Q ss_pred             ceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChhh-hcCCCCCEEE
Q 048347          244 LKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEEL-WRIKALRKLE  321 (351)
Q Consensus       244 L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~i-~~L~~L~~L~  321 (351)
                      -+.++++  ...+..+|..+.  ++|++|+|++| .+..+ |..++.+++|++|+|++| .+..+|.++ .++++|++|+
T Consensus        14 ~~~l~~~--~n~l~~iP~~~~--~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~i~~~~~~~l~~L~~L~   87 (174)
T 2r9u_A           14 QTLVNCQ--NIRLASVPAGIP--TDKQRLWLNNN-QITKLEPGVFDHLVNLQQLYFNSN-KLTAIPTGVFDKLTQLTQLD   87 (174)
T ss_dssp             SSEEECC--SSCCSSCCSCCC--TTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEE
T ss_pred             CcEEEeC--CCCCCccCCCcC--CCCcEEEeCCC-CccccCHHHhcCCcCCCEEECCCC-CCCccChhHhCCcchhhEEE
Confidence            3677883  334457787553  89999999999 67777 556899999999999995 788999875 7999999999


Q ss_pred             ecCCC
Q 048347          322 SWWPR  326 (351)
Q Consensus       322 l~~~~  326 (351)
                      +++..
T Consensus        88 L~~N~   92 (174)
T 2r9u_A           88 LNDNH   92 (174)
T ss_dssp             CCSSC
T ss_pred             CCCCc
Confidence            98754

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=97.93  E-value=1.5e-05  Score=78.05  Aligned_cols=82  Identities=15%  Similarity=0.072  Sum_probs=67.0

Q ss_pred             CCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccccChh-hhcCCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRKFPEE-LWRIKAL  317 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L  317 (351)
                      .++|++|+++ ++. +..+ |..+..+++|++|++++| .+..+| ..++.+++|++|++++| .+..+|.. ++++++|
T Consensus        25 ~~~L~~L~Ls-~n~-l~~~~~~~~~~l~~L~~L~Ls~n-~i~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L  100 (549)
T 2z81_A           25 TAAMKSLDLS-FNK-ITYIGHGDLRACANLQVLILKSS-RINTIEGDAFYSLGSLEHLDLSDN-HLSSLSSSWFGPLSSL  100 (549)
T ss_dssp             CTTCCEEECC-SSC-CCEECSSTTSSCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECTTS-CCCSCCHHHHTTCTTC
T ss_pred             CCCccEEECc-CCc-cCccChhhhhcCCcccEEECCCC-CcCccChhhccccccCCEEECCCC-ccCccCHHHhccCCCC
Confidence            3789999994 333 3344 567899999999999999 577665 56999999999999996 56667765 9999999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|+++++.
T Consensus       101 ~~L~Ls~n~  109 (549)
T 2z81_A          101 KYLNLMGNP  109 (549)
T ss_dssp             CEEECTTCC
T ss_pred             cEEECCCCc
Confidence            999999875

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=97.92  E-value=5.9e-06  Score=75.37  Aligned_cols=86  Identities=15%  Similarity=0.039  Sum_probs=66.3

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCC-CCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGH-GGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~-~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      .+..+++|++|+++ ++......+..+ ..+++|++|++++| .+..+|. ...+++|++|++++| .+..+|.++.+++
T Consensus       139 ~~~~l~~L~~L~Ls-~N~l~~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~-~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~  214 (317)
T 3o53_A          139 DEGCRSRVQYLDLK-LNEIDTVNFAELAASSDTLEHLNLQYN-FIYDVKG-QVVFAKLKTLDLSSN-KLAFMGPEFQSAA  214 (317)
T ss_dssp             CTGGGSSEEEEECT-TSCCCEEEGGGGGGGTTTCCEEECTTS-CCCEEEC-CCCCTTCCEEECCSS-CCCEECGGGGGGT
T ss_pred             hhhccCCCCEEECC-CCCCCcccHHHHhhccCcCCEEECCCC-cCccccc-ccccccCCEEECCCC-cCCcchhhhcccC
Confidence            45668899999994 333222223333 46889999999999 6888874 446899999999985 6888999999999


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|+.|++++..
T Consensus       215 ~L~~L~L~~N~  225 (317)
T 3o53_A          215 GVTWISLRNNK  225 (317)
T ss_dssp             TCSEEECTTSC
T ss_pred             cccEEECcCCc
Confidence            99999999875

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=97.92  E-value=1.5e-05  Score=77.35  Aligned_cols=82  Identities=15%  Similarity=0.003  Sum_probs=64.7

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+++|++|+|+.+.  +..+|. ...+++|++|+|++| .+..+|..++.+++|+.|+|++| .+..+|..++.+++|+.
T Consensus       167 ~l~~L~~L~Ls~N~--l~~~~~-~~~l~~L~~L~Ls~N-~l~~~~~~~~~l~~L~~L~Ls~N-~l~~lp~~l~~l~~L~~  241 (487)
T 3oja_A          167 SSDTLEHLNLQYNF--IYDVKG-QVVFAKLKTLDLSSN-KLAFMGPEFQSAAGVTWISLRNN-KLVLIEKALRFSQNLEH  241 (487)
T ss_dssp             GTTTCCEEECTTSC--CCEEEC-CCCCTTCCEEECCSS-CCCEECGGGGGGTTCSEEECTTS-CCCEECTTCCCCTTCCE
T ss_pred             hCCcccEEecCCCc--cccccc-cccCCCCCEEECCCC-CCCCCCHhHcCCCCccEEEecCC-cCcccchhhccCCCCCE
Confidence            57888888884332  334443 446888999999998 68888888889999999999985 57789988889999999


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |++++.+
T Consensus       242 L~l~~N~  248 (487)
T 3oja_A          242 FDLRGNG  248 (487)
T ss_dssp             EECTTCC
T ss_pred             EEcCCCC
Confidence            9998865

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=97.91  E-value=5.3e-06  Score=83.56  Aligned_cols=86  Identities=21%  Similarity=0.106  Sum_probs=64.5

Q ss_pred             CCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccccChhhhcCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      +..+++|++|+++.+  .+..+|. .++.+++|++|++++| .+..+| ..++.+++|++|++++|......|..+++++
T Consensus        69 ~~~l~~L~~L~L~~n--~l~~l~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~  145 (680)
T 1ziw_A           69 CQKLPMLKVLNLQHN--ELSQLSDKTFAFCTNLTELHLMSN-SIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLE  145 (680)
T ss_dssp             HHHCTTCCEEECCSS--CCCCCCTTTTTTCTTCSEEECCSS-CCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCT
T ss_pred             HhcccCcCEEECCCC--ccCccChhhhccCCCCCEEECCCC-ccCccChhHccccCCCCEEECCCCcccccCchhhcccc
Confidence            456788888888433  3445665 4788889999999988 567776 4588899999999998755455566778899


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|++++..
T Consensus       146 ~L~~L~L~~n~  156 (680)
T 1ziw_A          146 NLQELLLSNNK  156 (680)
T ss_dssp             TCCEEECCSSC
T ss_pred             cCCEEEccCCc
Confidence            99999988753

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=97.88  E-value=1.1e-05  Score=81.20  Aligned_cols=87  Identities=17%  Similarity=0.028  Sum_probs=63.6

Q ss_pred             CCCCCCCceEEEEecccccCceee-eCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChh-hh--
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLV-CGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEE-LW--  312 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp-~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~-i~--  312 (351)
                      .+..+++|++|+++ ++. ...+| ..++.+++|++|++++|......|..++.+++|++|++++| .+..+|.. ++  
T Consensus        92 ~~~~l~~L~~L~L~-~n~-l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~~  168 (680)
T 1ziw_A           92 TFAFCTNLTELHLM-SNS-IQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNN-KIQALKSEELDIF  168 (680)
T ss_dssp             TTTTCTTCSEEECC-SSC-CCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSS-CCCCBCHHHHGGG
T ss_pred             hhccCCCCCEEECC-CCc-cCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEEccCC-cccccCHHHhhcc
Confidence            47788999999994 333 33454 56888999999999998433344556889999999999985 45666543 33  


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|+++++.
T Consensus       169 ~~~~L~~L~L~~n~  182 (680)
T 1ziw_A          169 ANSSLKKLELSSNQ  182 (680)
T ss_dssp             TTCEESEEECTTCC
T ss_pred             ccccccEEECCCCc
Confidence            56889999998763

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=97.88  E-value=1.1e-05  Score=78.22  Aligned_cols=86  Identities=15%  Similarity=0.039  Sum_probs=66.4

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCC-CCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHG-GFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~-~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      .++.+++|++|+++ ++......|..+. .+++|++|+|++| .+..+|. ...+++|++|+|++| .+..+|.++++++
T Consensus       139 ~~~~l~~L~~L~Ls-~N~l~~~~~~~l~~~l~~L~~L~Ls~N-~l~~~~~-~~~l~~L~~L~Ls~N-~l~~~~~~~~~l~  214 (487)
T 3oja_A          139 DEGCRSRVQYLDLK-LNEIDTVNFAELAASSDTLEHLNLQYN-FIYDVKG-QVVFAKLKTLDLSSN-KLAFMGPEFQSAA  214 (487)
T ss_dssp             CGGGGSSEEEEECT-TSCCCEEEGGGGGGGTTTCCEEECTTS-CCCEEEC-CCCCTTCCEEECCSS-CCCEECGGGGGGT
T ss_pred             hhcCCCCCCEEECC-CCCCCCcChHHHhhhCCcccEEecCCC-ccccccc-cccCCCCCEEECCCC-CCCCCCHhHcCCC
Confidence            45678899999994 3333333455554 6889999999998 5777764 446899999999985 6888988899999


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|+.|++++..
T Consensus       215 ~L~~L~Ls~N~  225 (487)
T 3oja_A          215 GVTWISLRNNK  225 (487)
T ss_dssp             TCSEEECTTSC
T ss_pred             CccEEEecCCc
Confidence            99999998865

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=97.87  E-value=2.5e-05  Score=76.06  Aligned_cols=84  Identities=19%  Similarity=0.180  Sum_probs=61.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChh-hhcCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEE-LWRIKA  316 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~  316 (351)
                      +..+++|+.|+++ ++......|..+.  ++|++|++++| .+..+|..+..+++|++|++++| .+..+|.. +.++++
T Consensus       395 ~~~l~~L~~L~Ls-~N~l~~~~~~~l~--~~L~~L~Ls~N-~l~~ip~~~~~l~~L~~L~L~~N-~l~~l~~~~~~~l~~  469 (520)
T 2z7x_B          395 CSWTKSLLSLNMS-SNILTDTIFRCLP--PRIKVLDLHSN-KIKSIPKQVVKLEALQELNVASN-QLKSVPDGIFDRLTS  469 (520)
T ss_dssp             CCCCTTCCEEECC-SSCCCGGGGGSCC--TTCCEEECCSS-CCCCCCGGGGGCTTCCEEECCSS-CCCCCCTTTTTTCTT
T ss_pred             hccCccCCEEECc-CCCCCcchhhhhc--ccCCEEECCCC-cccccchhhhcCCCCCEEECCCC-cCCccCHHHhccCCc
Confidence            4566778888884 3332233443322  67888888888 67788888888889999999885 57788887 788888


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |++|++++.+
T Consensus       470 L~~L~l~~N~  479 (520)
T 2z7x_B          470 LQKIWLHTNP  479 (520)
T ss_dssp             CCEEECCSSC
T ss_pred             ccEEECcCCC
Confidence            9999988754

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=97.86  E-value=2.2e-05  Score=75.53  Aligned_cols=79  Identities=20%  Similarity=0.067  Sum_probs=41.3

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKA  316 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~  316 (351)
                      .++.+++|++|+++.+.  +..+|  ++.+++|++|++++| .+..+|  ++.+++|++|++++| .+..+|  ++++++
T Consensus        59 ~l~~l~~L~~L~Ls~n~--l~~~~--~~~l~~L~~L~Ls~N-~l~~~~--~~~l~~L~~L~L~~N-~l~~l~--~~~l~~  128 (457)
T 3bz5_A           59 GIEKLTGLTKLICTSNN--ITTLD--LSQNTNLTYLACDSN-KLTNLD--VTPLTKLTYLNCDTN-KLTKLD--VSQNPL  128 (457)
T ss_dssp             TGGGCTTCSEEECCSSC--CSCCC--CTTCTTCSEEECCSS-CCSCCC--CTTCTTCCEEECCSS-CCSCCC--CTTCTT
T ss_pred             hhcccCCCCEEEccCCc--CCeEc--cccCCCCCEEECcCC-CCceee--cCCCCcCCEEECCCC-cCCeec--CCCCCc
Confidence            45556666666663222  22233  455566666666665 355443  555556666666553 344444  455555


Q ss_pred             CCEEEecCC
Q 048347          317 LRKLESWWP  325 (351)
Q Consensus       317 L~~L~l~~~  325 (351)
                      |++|+++++
T Consensus       129 L~~L~l~~N  137 (457)
T 3bz5_A          129 LTYLNCARN  137 (457)
T ss_dssp             CCEEECTTS
T ss_pred             CCEEECCCC
Confidence            555555543

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=97.85  E-value=2.8e-05  Score=74.84  Aligned_cols=87  Identities=16%  Similarity=0.103  Sum_probs=58.8

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccCh-hhhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPE-ELWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L  314 (351)
                      .+..+++|++|+++ ++......|..+..+++|++|++++| .+..+ |..++.+++|+.|++++| .+..+|. .+.++
T Consensus        99 ~~~~l~~L~~L~Ls-~n~i~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~l~~l  175 (477)
T 2id5_A           99 VFTGLSNLTKLDIS-ENKIVILLDYMFQDLYNLKSLEVGDN-DLVYISHRAFSGLNSLEQLTLEKC-NLTSIPTEALSHL  175 (477)
T ss_dssp             SSTTCTTCCEEECT-TSCCCEECTTTTTTCTTCCEEEECCT-TCCEECTTSSTTCTTCCEEEEESC-CCSSCCHHHHTTC
T ss_pred             cccCCCCCCEEECC-CCccccCChhHccccccCCEEECCCC-ccceeChhhccCCCCCCEEECCCC-cCcccChhHhccc
Confidence            35677888888883 33333233555777788888888887 45544 445777888888888875 4666664 46778


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|+.|++++..
T Consensus       176 ~~L~~L~l~~n~  187 (477)
T 2id5_A          176 HGLIVLRLRHLN  187 (477)
T ss_dssp             TTCCEEEEESCC
T ss_pred             CCCcEEeCCCCc
Confidence            888888887654

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=97.84  E-value=3.6e-05  Score=73.46  Aligned_cols=89  Identities=13%  Similarity=0.133  Sum_probs=61.8

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccccChh-hh
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRKFPEE-LW  312 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~lP~~-i~  312 (351)
                      ++.+..+++|+.|+++ ++......|..+..+++|++|++++| .+..++ ..++.+++|+.|+|++| .+..+|.. +.
T Consensus       200 ~~~~~~l~~L~~L~Ls-~N~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~  276 (440)
T 3zyj_A          200 IPNLTPLIKLDELDLS-GNHLSAIRPGSFQGLMHLQKLWMIQS-QIQVIERNAFDNLQSLVEINLAHN-NLTLLPHDLFT  276 (440)
T ss_dssp             CCCCTTCSSCCEEECT-TSCCCEECTTTTTTCTTCCEEECTTC-CCCEECTTSSTTCTTCCEEECTTS-CCCCCCTTTTS
T ss_pred             ccccCCCcccCEEECC-CCccCccChhhhccCccCCEEECCCC-ceeEEChhhhcCCCCCCEEECCCC-CCCccChhHhc
Confidence            3456677788888883 33222223556778888888888888 466554 34778888888888885 56677765 46


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|+.|++++.+
T Consensus       277 ~l~~L~~L~L~~Np  290 (440)
T 3zyj_A          277 PLHHLERIHLHHNP  290 (440)
T ss_dssp             SCTTCCEEECCSSC
T ss_pred             cccCCCEEEcCCCC
Confidence            78888888887744

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=97.83  E-value=2.9e-05  Score=64.13  Aligned_cols=78  Identities=13%  Similarity=0.048  Sum_probs=62.4

Q ss_pred             CceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccChhh-hcCCCCCEE
Q 048347          243 HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFPEEL-WRIKALRKL  320 (351)
Q Consensus       243 ~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP~~i-~~L~~L~~L  320 (351)
                      ..+.++++  ...+..+|..+  .++|++|+|++| .+..+ |..++.+++|++|+|++| .+..+|.++ .++++|++|
T Consensus        10 ~~~~l~~s--~n~l~~ip~~~--~~~l~~L~L~~N-~i~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~f~~l~~L~~L   83 (170)
T 3g39_A           10 SGTTVDCS--GKSLASVPTGI--PTTTQVLYLYDN-QITKLEPGVFDRLTQLTRLDLDNN-QLTVLPAGVFDKLTQLTQL   83 (170)
T ss_dssp             ETTEEECT--TSCCSSCCSCC--CTTCSEEECCSS-CCCCCCTTTTTTCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEE
T ss_pred             CCCEEEeC--CCCcCccCccC--CCCCcEEEcCCC-cCCccChhhhcCcccCCEEECCCC-CcCccChhhccCCCCCCEE
Confidence            35678883  33455677654  488999999999 68777 556899999999999985 688898875 799999999


Q ss_pred             EecCCC
Q 048347          321 ESWWPR  326 (351)
Q Consensus       321 ~l~~~~  326 (351)
                      ++++..
T Consensus        84 ~L~~N~   89 (170)
T 3g39_A           84 SLNDNQ   89 (170)
T ss_dssp             ECCSSC
T ss_pred             ECCCCc
Confidence            998754

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=97.83  E-value=3.1e-05  Score=76.31  Aligned_cols=84  Identities=17%  Similarity=0.157  Sum_probs=59.7

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChh-hhcCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEE-LWRIKA  316 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~  316 (351)
                      +..+++|++|+++.+.. ....|..+.  ++|++|++++| .+..+|..++.+++|++|++++| .+..+|.+ +.++++
T Consensus       424 ~~~l~~L~~L~l~~n~l-~~~~~~~l~--~~L~~L~L~~N-~l~~ip~~~~~l~~L~~L~L~~N-~l~~l~~~~~~~l~~  498 (562)
T 3a79_B          424 CAWAESILVLNLSSNML-TGSVFRCLP--PKVKVLDLHNN-RIMSIPKDVTHLQALQELNVASN-QLKSVPDGVFDRLTS  498 (562)
T ss_dssp             CCCCTTCCEEECCSSCC-CGGGGSSCC--TTCSEEECCSS-CCCCCCTTTTSSCCCSEEECCSS-CCCCCCTTSTTTCTT
T ss_pred             hcCcccCCEEECCCCCC-Ccchhhhhc--CcCCEEECCCC-cCcccChhhcCCCCCCEEECCCC-CCCCCCHHHHhcCCC
Confidence            45566677777733322 223333222  57888888888 68888888888888999999885 57788887 788888


Q ss_pred             CCEEEecCCC
Q 048347          317 LRKLESWWPR  326 (351)
Q Consensus       317 L~~L~l~~~~  326 (351)
                      |+.|++++.+
T Consensus       499 L~~L~l~~N~  508 (562)
T 3a79_B          499 LQYIWLHDNP  508 (562)
T ss_dssp             CCCEECCSCC
T ss_pred             CCEEEecCCC
Confidence            9999888754

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.82  E-value=2.5e-05  Score=69.93  Aligned_cols=51  Identities=12%  Similarity=0.044  Sum_probs=40.1

Q ss_pred             CCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.-++++|.++.++++.+.+...           -...+-+.|+|+.|+|||+||+.+++.
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            344567999999999998887431           123345779999999999999999887

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=97.82  E-value=1.2e-05  Score=73.73  Aligned_cols=60  Identities=15%  Similarity=0.080  Sum_probs=26.9

Q ss_pred             CCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhhhcCCCCCEEEecC
Q 048347          263 HGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWW  324 (351)
Q Consensus       263 ~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  324 (351)
                      +..+++|++|++++| .+..+|. .++.+++|+.|++++| .+..+|.+++++++|++|++++
T Consensus       213 l~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~lp~~l~~l~~L~~L~l~~  273 (332)
T 2ft3_A          213 LLRYSKLYRLGLGHN-QIRMIENGSLSFLPTLRELHLDNN-KLSRVPAGLPDLKLLQVVYLHT  273 (332)
T ss_dssp             STTCTTCSCCBCCSS-CCCCCCTTGGGGCTTCCEEECCSS-CCCBCCTTGGGCTTCCEEECCS
T ss_pred             hcCCCCCCEEECCCC-cCCcCChhHhhCCCCCCEEECCCC-cCeecChhhhcCccCCEEECCC
Confidence            444444444444444 2333332 3444444444444442 3444444444444444444443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.82  E-value=4e-05  Score=69.38  Aligned_cols=46  Identities=7%  Similarity=-0.027  Sum_probs=36.2

Q ss_pred             ccccchhhHHHHHHHHHcc-------------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIER-------------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~-------------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++|.++.++.+.+++..-             .....-+.|+|+.|+|||++|+.+++.
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~   90 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGL   90 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999988776421             233446779999999999999988776

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=97.81  E-value=2.1e-05  Score=75.60  Aligned_cols=80  Identities=11%  Similarity=0.119  Sum_probs=66.9

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+++++.|.++  ......+|. +..+++|++|++++| .+..+|. ++.+++|++|++++| .+..+|. ++++++|++
T Consensus        44 ~l~~l~~L~l~--~~~i~~l~~-~~~l~~L~~L~Ls~n-~l~~~~~-~~~l~~L~~L~l~~n-~l~~~~~-~~~l~~L~~  116 (466)
T 1o6v_A           44 DLDQVTTLQAD--RLGIKSIDG-VEYLNNLTQINFSNN-QLTDITP-LKNLTKLVDILMNNN-QIADITP-LANLTNLTG  116 (466)
T ss_dssp             HHHTCCEEECC--SSCCCCCTT-GGGCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSS-CCCCCGG-GTTCTTCCE
T ss_pred             HhccccEEecC--CCCCccCcc-hhhhcCCCEEECCCC-ccCCchh-hhccccCCEEECCCC-ccccChh-hcCCCCCCE
Confidence            46789999993  334445663 778999999999999 6888886 999999999999986 5777776 999999999


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |+++++.
T Consensus       117 L~L~~n~  123 (466)
T 1o6v_A          117 LTLFNNQ  123 (466)
T ss_dssp             EECCSSC
T ss_pred             EECCCCC
Confidence            9999875

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=97.80  E-value=8e-06  Score=74.21  Aligned_cols=89  Identities=24%  Similarity=0.189  Sum_probs=51.4

Q ss_pred             CCCCCCCCceEEEEecccccC-ceeee--CCCCCCcccEEEEecCCcccccccc----ccccCCccEEeecCCcccccc-
Q 048347          236 PAPEKLPHLKVLKLKRSSYSG-RKLVC--GHGGFPRQEILHLKSMLWLEEWKME----TGAMQKLKSLIVNPCAYLRKF-  307 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~-~~lp~--~~~~l~~L~~L~L~~~~~l~~lp~~----i~~L~~L~~L~l~~c~~l~~l-  307 (351)
                      ..+..+++|++|+++.+.... ..++.  ....+++|++|++++| .+..+|..    ++.+++|++|+|++|. +..+ 
T Consensus       163 ~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~~~l~~L~~L~Ls~N~-l~~~~  240 (310)
T 4glp_A          163 EQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNT-GMETPTGVCAALAAAGVQPHSLDLSHNS-LRATV  240 (310)
T ss_dssp             TSCCCCTTCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSS-CCCCHHHHHHHHHHHTCCCSSEECTTSC-CCCCC
T ss_pred             HHhccCCCCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCC-CCCchHHHHHHHHhcCCCCCEEECCCCC-CCccc
Confidence            455677788888884433221 01222  2356677777777777 45555442    3566777777777654 3333 


Q ss_pred             ChhhhcC---CCCCEEEecCCC
Q 048347          308 PEELWRI---KALRKLESWWPR  326 (351)
Q Consensus       308 P~~i~~L---~~L~~L~l~~~~  326 (351)
                      |..++.+   ++|++|++++..
T Consensus       241 p~~~~~~~~~~~L~~L~Ls~N~  262 (310)
T 4glp_A          241 NPSAPRCMWSSALNSLNLSFAG  262 (310)
T ss_dssp             CSCCSSCCCCTTCCCEECCSSC
T ss_pred             hhhHHhccCcCcCCEEECCCCC
Confidence            6666655   477777776543

>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=97.78  E-value=3.3e-05  Score=64.23  Aligned_cols=91  Identities=8%  Similarity=0.045  Sum_probs=49.9

Q ss_pred             hhhHHHHHHHHHccC-CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCcc
Q 048347           24 EDKMEELLDLLIERQ-PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSE  102 (351)
Q Consensus        24 ~~~~~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~  102 (351)
                      .+..+.+.+++..-. ++-..+.|+|+.|+||||||+.+++.......+. +.++    +..++...+.........   
T Consensus        20 ~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~-~~~~----~~~~~~~~~~~~~~~~~~---   91 (180)
T 3ec2_A           20 NRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR-GYFF----DTKDLIFRLKHLMDEGKD---   91 (180)
T ss_dssp             HHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC-CCEE----EHHHHHHHHHHHHHHTCC---
T ss_pred             HHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe-EEEE----EHHHHHHHHHHHhcCchH---
Confidence            334444444443321 2346889999999999999999988732122222 2333    344555555443322211   


Q ss_pred             CCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          103 ILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                          .  ...+.+.     +.-++||||+..
T Consensus        92 ----~--~~~~~~~-----~~~llilDE~~~  111 (180)
T 3ec2_A           92 ----T--KFLKTVL-----NSPVLVLDDLGS  111 (180)
T ss_dssp             ----S--HHHHHHH-----TCSEEEEETCSS
T ss_pred             ----H--HHHHHhc-----CCCEEEEeCCCC
Confidence                1  2222222     445889999973

>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=97.77  E-value=5.5e-05  Score=69.06  Aligned_cols=116  Identities=11%  Similarity=0.086  Sum_probs=68.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLM   95 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~   95 (351)
                      -++++|.++.++.+.+++..+. ...++-+.|+.|+|||++|+.+.+.  ...   ..+.++.+ .... ..+.++..+.
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~--l~~---~~~~i~~~~~~~~-~i~~~~~~~~   97 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHD--VNA---DMMFVNGSDCKID-FVRGPLTNFA   97 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHH--TTE---EEEEEETTTCCHH-HHHTHHHHHH
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHH--hCC---CEEEEcccccCHH-HHHHHHHHHH
Confidence            3679999999999999998653 2356667788999999999999877  321   12222222 2221 1121111111


Q ss_pred             CCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCChh---hHHHHHhhcCCCCCCcEEEE-Eee
Q 048347           96 PLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGD---IWDFLKEALPDHQNGSRILT-ALI  158 (351)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~---~~~~l~~~l~~~~~gs~Iiv-TR~  158 (351)
                      ...                   ...+++.++++|++....   ..+.+...+.....+.++|. |..
T Consensus        98 ~~~-------------------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~  145 (324)
T 3u61_B           98 SAA-------------------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANN  145 (324)
T ss_dssp             HBC-------------------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESS
T ss_pred             hhc-------------------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            100                   012477899999998653   45555555443333456666 543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.72  E-value=7.2e-05  Score=63.33  Aligned_cols=96  Identities=13%  Similarity=0.141  Sum_probs=53.9

Q ss_pred             Cccccchh----hHHHHHHHHHccCCC--eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           18 KVDLDLED----KMEELLDLLIERQPQ--LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        18 ~~~vGr~~----~~~~l~~~L~~~~~~--~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      +++++.+.    ..+.+.+++......  ...+.|+|++|+|||+||+.+++.  .......+++++.    .++...+.
T Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~--~~~~~~~~~~~~~----~~~~~~~~   98 (202)
T 2w58_A           25 SDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANE--LAKRNVSSLIVYV----PELFRELK   98 (202)
T ss_dssp             TSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEEEH----HHHHHHHH
T ss_pred             hhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEh----HHHHHHHH
Confidence            44665443    344455555543221  157789999999999999999987  4444444555543    34444444


Q ss_pred             HHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           92 KSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                      .....         .......+.+.    +. -+|||||++.
T Consensus        99 ~~~~~---------~~~~~~~~~~~----~~-~~lilDei~~  126 (202)
T 2w58_A           99 HSLQD---------QTMNEKLDYIK----KV-PVLMLDDLGA  126 (202)
T ss_dssp             HC------------CCCHHHHHHHH----HS-SEEEEEEECC
T ss_pred             HHhcc---------chHHHHHHHhc----CC-CEEEEcCCCC
Confidence            32211         11223333333    22 3899999954

>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=97.71  E-value=9e-05  Score=65.24  Aligned_cols=49  Identities=8%  Similarity=0.011  Sum_probs=37.0

Q ss_pred             CCCccccchhhHHHHHHHHHc---cC-------CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIE---RQ-------PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~---~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .=++++|.++.++.+.+++..   ..       ...+-+.++|+.|+|||++|+.+++.
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~   62 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE   62 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            346789999988888776532   11       22345679999999999999999886

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=97.68  E-value=3.7e-05  Score=73.92  Aligned_cols=82  Identities=17%  Similarity=0.097  Sum_probs=68.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCC
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIK  315 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~  315 (351)
                      ..++.+++|++|+++.+  .+..+| .++.+++|++|++++| .+..+|  ++.+++|++|++++| .+..+|  +++++
T Consensus        36 ~~~~~l~~L~~L~Ls~n--~l~~~~-~l~~l~~L~~L~Ls~n-~l~~~~--~~~l~~L~~L~Ls~N-~l~~~~--~~~l~  106 (457)
T 3bz5_A           36 ISEEQLATLTSLDCHNS--SITDMT-GIEKLTGLTKLICTSN-NITTLD--LSQNTNLTYLACDSN-KLTNLD--VTPLT  106 (457)
T ss_dssp             EEHHHHTTCCEEECCSS--CCCCCT-TGGGCTTCSEEECCSS-CCSCCC--CTTCTTCSEEECCSS-CCSCCC--CTTCT
T ss_pred             cChhHcCCCCEEEccCC--CcccCh-hhcccCCCCEEEccCC-cCCeEc--cccCCCCCEEECcCC-CCceee--cCCCC
Confidence            34567899999999443  333456 6889999999999999 688887  899999999999996 577776  88999


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|+++++.
T Consensus       107 ~L~~L~L~~N~  117 (457)
T 3bz5_A          107 KLTYLNCDTNK  117 (457)
T ss_dssp             TCCEEECCSSC
T ss_pred             cCCEEECCCCc
Confidence            99999999875

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=97.68  E-value=0.0001  Score=73.60  Aligned_cols=76  Identities=20%  Similarity=0.052  Sum_probs=63.1

Q ss_pred             CCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEE
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKL  320 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  320 (351)
                      +++|+.|+++.+  .+..+|   ..+++|++|++++| .+..+|.   .+++|++|+|++| .+..+|.+++++++|+.|
T Consensus       220 ~~~L~~L~Ls~N--~L~~lp---~~l~~L~~L~Ls~N-~L~~lp~---~~~~L~~L~Ls~N-~L~~lp~~l~~l~~L~~L  289 (622)
T 3g06_A          220 PSGLKELIVSGN--RLTSLP---VLPSELKELMVSGN-RLTSLPM---LPSGLLSLSVYRN-QLTRLPESLIHLSSETTV  289 (622)
T ss_dssp             CTTCCEEECCSS--CCSCCC---CCCTTCCEEECCSS-CCSCCCC---CCTTCCEEECCSS-CCCSCCGGGGGSCTTCEE
T ss_pred             CCCCCEEEccCC--ccCcCC---CCCCcCcEEECCCC-CCCcCCc---ccccCcEEeCCCC-CCCcCCHHHhhccccCEE
Confidence            478888998433  333466   56788999999999 6888987   6789999999996 678999999999999999


Q ss_pred             EecCCC
Q 048347          321 ESWWPR  326 (351)
Q Consensus       321 ~l~~~~  326 (351)
                      ++++.+
T Consensus       290 ~L~~N~  295 (622)
T 3g06_A          290 NLEGNP  295 (622)
T ss_dssp             ECCSCC
T ss_pred             EecCCC
Confidence            999876

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=97.68  E-value=6.4e-05  Score=68.16  Aligned_cols=86  Identities=15%  Similarity=0.099  Sum_probs=64.1

Q ss_pred             CCCCCceEEEEecccccCceee----eCCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccc--cChh-
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLV----CGHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRK--FPEE-  310 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp----~~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~--lP~~-  310 (351)
                      ..+++|++|+++.+.... ..+    ..+..+++|++|++++| .+..+| ..++.+++|++|+|++|.....  +|.. 
T Consensus       114 ~~~~~L~~L~Ls~n~i~~-~~~~~~~~~~~~~~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~  191 (310)
T 4glp_A          114 ATGLALSSLRLRNVSWAT-GRSWLAELQQWLKPGLKVLSIAQA-HSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAAL  191 (310)
T ss_dssp             CCCBCCSSCEEESCCCSS-TTSSHHHHHTTBCSCCCEEEEECC-SSCCCCTTSCCCCTTCCEEECCSCTTCHHHHHHTTS
T ss_pred             ccCCCCCEEEeecccccc-hhhhhHHHHhhhccCCCEEEeeCC-CcchhhHHHhccCCCCCEEECCCCCCccchhhhHHH
Confidence            789999999996554332 222    23457899999999999 566655 5689999999999999753321  4333 


Q ss_pred             -hhcCCCCCEEEecCCC
Q 048347          311 -LWRIKALRKLESWWPR  326 (351)
Q Consensus       311 -i~~L~~L~~L~l~~~~  326 (351)
                       ++++++|++|+++++.
T Consensus       192 ~~~~l~~L~~L~Ls~N~  208 (310)
T 4glp_A          192 CPHKFPAIQNLALRNTG  208 (310)
T ss_dssp             CTTSSCCCCSCBCCSSC
T ss_pred             hhhcCCCCCEEECCCCC
Confidence             3789999999999875

>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=97.68  E-value=3.7e-05  Score=70.87  Aligned_cols=46  Identities=11%  Similarity=-0.031  Sum_probs=38.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+++.++.+..++..+...  -+.++|+.|+||||+|+.+.+.
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~~~--~~ll~G~~G~GKT~la~~la~~   81 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSANLP--HMLFYGPPGTGKTSTILALTKE   81 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTTCC--CEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHhcCCCC--EEEEECCCCCCHHHHHHHHHHH
Confidence            356899999999999998765322  2789999999999999999887

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.64  E-value=0.00034  Score=64.82  Aligned_cols=48  Identities=15%  Similarity=0.043  Sum_probs=36.1

Q ss_pred             CCccccchhhHHHH---HHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEEL---LDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l---~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|++..++.+   ...+..+....+.+-|+|+.|+|||++|+.+.+.
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            34689999887774   4444443322357779999999999999999987

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.64  E-value=3e-05  Score=64.16  Aligned_cols=46  Identities=11%  Similarity=0.151  Sum_probs=38.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|+++.++.+.+.+....  ..-+.|+|+.|+|||++|+.+++.
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~--~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRT--KNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             cchhhcchHHHHHHHHHHhCCC--CCceEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999987643  345679999999999999999876

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=97.63  E-value=6.6e-05  Score=69.09  Aligned_cols=77  Identities=14%  Similarity=0.119  Sum_probs=61.5

Q ss_pred             EEEEecccccCceeeeCCCCCCcccEEEEec-CCccccccc-cccccCCccEEeecCCccccccCh-hhhcCCCCCEEEe
Q 048347          246 VLKLKRSSYSGRKLVCGHGGFPRQEILHLKS-MLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPE-ELWRIKALRKLES  322 (351)
Q Consensus       246 ~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~-~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l  322 (351)
                      .++++ +...+..+|. +..+.+|++|+|++ | .+..+|. .++.|.+|+.|+|++| .+..+|. .+++|++|+.|+|
T Consensus        12 ~v~~~-~~n~l~~ip~-l~~~~~L~~L~l~~~n-~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~l   87 (347)
T 2ifg_A           12 GLRCT-RDGALDSLHH-LPGAENLTELYIENQQ-HLQHLELRDLRGLGELRNLTIVKS-GLRFVAPDAFHFTPRLSRLNL   87 (347)
T ss_dssp             CEECC-SSCCCTTTTT-SCSCSCCSEEECCSCS-SCCEECGGGSCSCCCCSEEECCSS-CCCEECTTGGGSCSCCCEEEC
T ss_pred             EEEcC-CCCCCCccCC-CCCCCCeeEEEccCCC-CCCCcChhHhccccCCCEEECCCC-ccceeCHHHhcCCcCCCEEeC
Confidence            34662 2214567888 99999999999997 7 7888885 5999999999999996 5776765 5699999999999


Q ss_pred             cCCC
Q 048347          323 WWPR  326 (351)
Q Consensus       323 ~~~~  326 (351)
                      ++..
T Consensus        88 ~~N~   91 (347)
T 2ifg_A           88 SFNA   91 (347)
T ss_dssp             CSSC
T ss_pred             CCCc
Confidence            8754

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.63  E-value=4.7e-05  Score=63.21  Aligned_cols=83  Identities=11%  Similarity=0.084  Sum_probs=59.3

Q ss_pred             CCceEEEEecccccCc-eeeeCCCCCCcccEEEEecCCccccccc-ccccc----CCccEEeecCCcccccc-ChhhhcC
Q 048347          242 PHLKVLKLKRSSYSGR-KLVCGHGGFPRQEILHLKSMLWLEEWKM-ETGAM----QKLKSLIVNPCAYLRKF-PEELWRI  314 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~-~lp~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L----~~L~~L~l~~c~~l~~l-P~~i~~L  314 (351)
                      .+|+.|+++ ++.-.. .+ ..+.++++|+.|+|++|..+++--. .++.+    ++|++|+|++|+.+..- -..+.++
T Consensus        61 ~~L~~LDLs-~~~Itd~GL-~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~  138 (176)
T 3e4g_A           61 YKIQAIDAT-DSCIMSIGF-DHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHF  138 (176)
T ss_dssp             CCEEEEEEE-SCCCCGGGG-GGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGC
T ss_pred             ceEeEEeCc-CCCccHHHH-HHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcC
Confidence            369999995 443221 22 2367899999999999977764322 24444    47999999999877531 1245688


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++|+
T Consensus       139 ~~L~~L~L~~c~  150 (176)
T 3e4g_A          139 RNLKYLFLSDLP  150 (176)
T ss_dssp             TTCCEEEEESCT
T ss_pred             CCCCEEECCCCC
Confidence            999999999997

>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=97.63  E-value=0.00015  Score=66.91  Aligned_cols=45  Identities=13%  Similarity=-0.006  Sum_probs=35.8

Q ss_pred             CccccchhhHHHHHHHH-HccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLL-IERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L-~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.++..+.+.+++ ..+. ... +.|+|+.|+||||+|+.+...
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~-~~~-~ll~Gp~G~GKTtl~~~la~~   59 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRD-LPH-LLLYGPNGTGKKTRCMALLES   59 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTC-CCC-EEEECSTTSSHHHHHHTHHHH
T ss_pred             HHhcCCHHHHHHHHHHHhhCCC-CCe-EEEECCCCCCHHHHHHHHHHH
Confidence            45899999999998888 4432 223 889999999999999988663

>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=97.59  E-value=7.9e-05  Score=71.27  Aligned_cols=101  Identities=17%  Similarity=0.178  Sum_probs=57.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK  120 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~  120 (351)
                      ..-+.|+|+.|+||||||+.+++.  ....+...-+++++  ..++..++...+...         .    ...+.+.+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~--l~~~~~~~~v~~v~--~~~~~~~~~~~~~~~---------~----~~~~~~~~~  192 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYIT--SEKFLNDLVDSMKEG---------K----LNEFREKYR  192 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHH--HHHHCCSSCEEEEE--HHHHHHHHHHHHHTT---------C----HHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEee--HHHHHHHHHHHHHcc---------c----HHHHHHHhc
Confidence            556889999999999999999987  54444332233333  223344444333221         1    122334444


Q ss_pred             CceEEEEEeCCCChh----hHHHHHhhcCC-CCCCcEEEE-Eee
Q 048347          121 NKRYLIVIQDVWRGD----IWDFLKEALPD-HQNGSRILT-ALI  158 (351)
Q Consensus       121 ~k~~LlVLDdv~~~~----~~~~l~~~l~~-~~~gs~Iiv-TR~  158 (351)
                      .+.-+++|||+....    ..+.+...+.. ...|..||+ |.+
T Consensus       193 ~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          193 KKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             TTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            356789999996442    23344443321 234667777 664

>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=97.58  E-value=0.0002  Score=65.42  Aligned_cols=52  Identities=13%  Similarity=0.051  Sum_probs=39.7

Q ss_pred             cCCCCCccccchhhHHHHHHHHHc----------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIE----------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+.=++++|.++.++.+.+.+..          .....+-+-++|+.|+|||+||+.+++.
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHH
T ss_pred             CCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            334446789999999999988831          1122345779999999999999999887

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=97.58  E-value=9.6e-05  Score=73.00  Aligned_cols=77  Identities=13%  Similarity=0.034  Sum_probs=60.2

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCc-------cEEeecCCccccccChhhh
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKL-------KSLIVNPCAYLRKFPEELW  312 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L-------~~L~l~~c~~l~~lP~~i~  312 (351)
                      .+++|++|+++.|.  +..+|. +.  ++|++|+|++| .+..+|. ++.  +|       +.|+|++| .+..+|.++.
T Consensus       158 ~l~~L~~L~Ls~N~--L~~lp~-l~--~~L~~L~Ls~N-~L~~lp~-~~~--~L~~~~~~L~~L~Ls~N-~l~~lp~~l~  227 (571)
T 3cvr_A          158 LPTSLEVLSVRNNQ--LTFLPE-LP--ESLEALDVSTN-LLESLPA-VPV--RNHHSEETEIFFRCREN-RITHIPENIL  227 (571)
T ss_dssp             CCTTCCEEECCSSC--CSCCCC-CC--TTCCEEECCSS-CCSSCCC-CC----------CCEEEECCSS-CCCCCCGGGG
T ss_pred             cCCCcCEEECCCCC--CCCcch-hh--CCCCEEECcCC-CCCchhh-HHH--hhhcccccceEEecCCC-cceecCHHHh
Confidence            46788888884332  334666 44  88999999999 6889997 655  77       99999985 6889999999


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|+.|++++.+
T Consensus       228 ~l~~L~~L~L~~N~  241 (571)
T 3cvr_A          228 SLDPTCTIILEDNP  241 (571)
T ss_dssp             GSCTTEEEECCSSS
T ss_pred             cCCCCCEEEeeCCc
Confidence            99999999999876

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=97.57  E-value=0.00017  Score=69.22  Aligned_cols=56  Identities=14%  Similarity=0.076  Sum_probs=24.0

Q ss_pred             CCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecC
Q 048347          263 HGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWW  324 (351)
Q Consensus       263 ~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  324 (351)
                      ++.+++|++|++++| .+..+|..+   .+|++|++++| .+..+| +++++++|++|++++
T Consensus       149 ~~~l~~L~~L~l~~N-~l~~lp~~~---~~L~~L~L~~n-~l~~l~-~~~~l~~L~~L~l~~  204 (454)
T 1jl5_A          149 LQNSSFLKIIDVDNN-SLKKLPDLP---PSLEFIAAGNN-QLEELP-ELQNLPFLTAIYADN  204 (454)
T ss_dssp             CTTCTTCCEEECCSS-CCSCCCCCC---TTCCEEECCSS-CCSSCC-CCTTCTTCCEEECCS
T ss_pred             cCCCCCCCEEECCCC-cCcccCCCc---ccccEEECcCC-cCCcCc-cccCCCCCCEEECCC
Confidence            444444555554444 343444322   24444444442 233344 344444444444443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.56  E-value=0.00082  Score=61.38  Aligned_cols=99  Identities=14%  Similarity=0.093  Sum_probs=60.1

Q ss_pred             CCCCCccccchhhHHHHHHHHHcc----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIER----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LS   82 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~   82 (351)
                      .+.=++++|.++.++.|.+.+...          ....+-+-++|+.|+|||+||+.+++.  ..    ..-++.++ .+
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~--~~----~~~~~~i~~~~   81 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE--AN----NSTFFSISSSD   81 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH--TT----SCEEEEEECCS
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH--cC----CCcEEEEEhHH
Confidence            344467899999999998877421          112356779999999999999999987  31    12344444 11


Q ss_pred             HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh
Q 048347           83 LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus        83 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                      .           ....     .......+...+...-..+..+|+||+++..
T Consensus        82 l-----------~~~~-----~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l  117 (322)
T 1xwi_A           82 L-----------VSKW-----LGESEKLVKNLFQLARENKPSIIFIDEIDSL  117 (322)
T ss_dssp             S-----------CCSS-----CCSCHHHHHHHHHHHHHTSSEEEEEETTTGG
T ss_pred             H-----------Hhhh-----hhHHHHHHHHHHHHHHhcCCcEEEeecHHHh
Confidence            1           0110     1112333333333333467889999999754

>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=97.54  E-value=3.2e-05  Score=70.53  Aligned_cols=48  Identities=13%  Similarity=0.089  Sum_probs=38.4

Q ss_pred             CCccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|+++..+.+..++..-   ......+.|+|+.|+|||++|+.+++.
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~   61 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHE   61 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHH
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            467999999999988887531   122356778999999999999999886

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=97.53  E-value=1.8e-05  Score=74.08  Aligned_cols=88  Identities=19%  Similarity=0.147  Sum_probs=64.0

Q ss_pred             CCCCCCCceEEEEeccccc---CceeeeCCCCCCcccEEEEecCCcccc-----ccccc--cccCCccEEeecCCccccc
Q 048347          237 APEKLPHLKVLKLKRSSYS---GRKLVCGHGGFPRQEILHLKSMLWLEE-----WKMET--GAMQKLKSLIVNPCAYLRK  306 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~---~~~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i--~~L~~L~~L~l~~c~~l~~  306 (351)
                      .+..+++|++|+|+.+...   ...+|..+..+++|++|+|++|. +..     +|..+  +.+++|++|+|++|. +..
T Consensus       211 ~l~~~~~L~~L~Ls~n~l~~~g~~~l~~~l~~~~~L~~L~L~~n~-i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~-i~~  288 (386)
T 2ca6_A          211 GLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNE-IEL  288 (386)
T ss_dssp             TGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBH
T ss_pred             HhhcCCCccEEECcCCCCCcHHHHHHHHHHccCCCcCEEECCCCC-CchhhHHHHHHHHhhccCCCeEEEECcCCc-CCH
Confidence            5667888999999433321   14567677788889999999884 543     45555  458889999998864 554


Q ss_pred             -----cChhh-hcCCCCCEEEecCCC
Q 048347          307 -----FPEEL-WRIKALRKLESWWPR  326 (351)
Q Consensus       307 -----lP~~i-~~L~~L~~L~l~~~~  326 (351)
                           +|..+ .++++|++|++++++
T Consensus       289 ~g~~~l~~~l~~~l~~L~~L~l~~N~  314 (386)
T 2ca6_A          289 DAVRTLKTVIDEKMPDLLFLELNGNR  314 (386)
T ss_dssp             HHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             HHHHHHHHHHHhcCCCceEEEccCCc
Confidence                 88888 678999999988754

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.51  E-value=0.00013  Score=69.96  Aligned_cols=47  Identities=9%  Similarity=0.040  Sum_probs=38.4

Q ss_pred             CCCccccchhhH---HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKM---EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~---~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|.+..+   ..+...+..+.  ...+.++|+.|+||||+|+.+++.
T Consensus        24 ~l~~ivGq~~~~~~~~~L~~~i~~~~--~~~vLL~GppGtGKTtlAr~ia~~   73 (447)
T 3pvs_A           24 NLAQYIGQQHLLAAGKPLPRAIEAGH--LHSMILWGPPGTGKTTLAEVIARY   73 (447)
T ss_dssp             STTTCCSCHHHHSTTSHHHHHHHHTC--CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CHHHhCCcHHHHhchHHHHHHHHcCC--CcEEEEECCCCCcHHHHHHHHHHH
Confidence            346689998888   67777776653  467789999999999999999987

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=97.49  E-value=9.2e-05  Score=71.09  Aligned_cols=88  Identities=23%  Similarity=0.188  Sum_probs=44.0

Q ss_pred             CCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccc--ccChhhhcC-----
Q 048347          242 PHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLR--KFPEELWRI-----  314 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~--~lP~~i~~L-----  314 (351)
                      ++|++|+++.+.  ...+|.   .+++|++|++++| .+..+|.   .+++|++|++++|....  .+|.++++|     
T Consensus       317 ~~L~~L~Ls~N~--l~~lp~---~~~~L~~L~L~~N-~l~~lp~---~l~~L~~L~L~~N~l~~l~~ip~~l~~L~~n~~  387 (454)
T 1jl5_A          317 PSLEELNVSNNK--LIELPA---LPPRLERLIASFN-HLAEVPE---LPQNLKQLHVEYNPLREFPDIPESVEDLRMNSH  387 (454)
T ss_dssp             TTCCEEECCSSC--CSCCCC---CCTTCCEEECCSS-CCSCCCC---CCTTCCEEECCSSCCSSCCCCCTTCCEEECCC-
T ss_pred             CcCCEEECCCCc--cccccc---cCCcCCEEECCCC-ccccccc---hhhhccEEECCCCCCCcCCCChHHHHhhhhccc
Confidence            367777773322  223443   3577888888888 5777886   47888899998865444  677888887     


Q ss_pred             --------CCCCEEEecCCCh----hHHhhcccccc
Q 048347          315 --------KALRKLESWWPRP----ELRQSLHKFEE  338 (351)
Q Consensus       315 --------~~L~~L~l~~~~~----~~~~~l~~~~~  338 (351)
                              ++|+.|++++.+-    .+...+..+..
T Consensus       388 ~~~i~~~~~~L~~L~ls~N~l~~~~~iP~sl~~L~~  423 (454)
T 1jl5_A          388 LAEVPELPQNLKQLHVETNPLREFPDIPESVEDLRM  423 (454)
T ss_dssp             ------------------------------------
T ss_pred             ccccccccCcCCEEECCCCcCCccccchhhHhheeC
Confidence                    7888888887542    34444444443

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=97.48  E-value=0.00014  Score=67.18  Aligned_cols=55  Identities=16%  Similarity=0.116  Sum_probs=25.1

Q ss_pred             ccEEEEecCCccccccccccccCCccEEeecCCccccccChhh-hcCCCCCEEEecC
Q 048347          269 QEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEEL-WRIKALRKLESWW  324 (351)
Q Consensus       269 L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i-~~L~~L~~L~l~~  324 (351)
                      +++|++++| .++.+|.......+|+.|++.++..+..+|.++ .++++|+.|++++
T Consensus       156 l~~L~L~~N-~i~~i~~~~f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~  211 (350)
T 4ay9_X          156 SVILWLNKN-GIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISR  211 (350)
T ss_dssp             CEEEECCSS-CCCEECTTSSTTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTT
T ss_pred             hhhhccccc-cccCCChhhccccchhHHhhccCCcccCCCHHHhccCcccchhhcCC
Confidence            444444444 344444444444444444444444444444432 4444444444444

>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=97.46  E-value=0.00037  Score=63.06  Aligned_cols=98  Identities=11%  Similarity=0.019  Sum_probs=60.9

Q ss_pred             CCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLS   82 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~   82 (351)
                      .+.-++++|.++.++++.+++...           -...+.+.++|+.|+|||+||+.+++.  ...     -++.+.  
T Consensus        11 ~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~--~~~-----~~i~v~--   81 (301)
T 3cf0_A           11 QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQA-----NFISIK--   81 (301)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH--TTC-----EEEEEC--
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH--hCC-----CEEEEE--
Confidence            334456999999999988877531           123456789999999999999999987  322     233333  


Q ss_pred             HHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           83 LDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        83 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                      ..++.....   +..          ...+...+.........++++|++..
T Consensus        82 ~~~l~~~~~---g~~----------~~~~~~~f~~a~~~~p~il~iDEid~  119 (301)
T 3cf0_A           82 GPELLTMWF---GES----------EANVREIFDKARQAAPCVLFFDELDS  119 (301)
T ss_dssp             HHHHHHHHH---TTC----------TTHHHHHHHHHHHTCSEEEEECSTTH
T ss_pred             hHHHHhhhc---Cch----------HHHHHHHHHHHHhcCCeEEEEEChHH
Confidence            333332221   111          11233334444445678999999964

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=97.46  E-value=5.4e-05  Score=70.80  Aligned_cols=87  Identities=15%  Similarity=0.109  Sum_probs=46.3

Q ss_pred             CCCCCceEEEEecccccCc---eeeeCCCCCCcccEEEEecCCcccc-----cccccccc---------CCccEEeecCC
Q 048347          239 EKLPHLKVLKLKRSSYSGR---KLVCGHGGFPRQEILHLKSMLWLEE-----WKMETGAM---------QKLKSLIVNPC  301 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~---~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~~L---------~~L~~L~l~~c  301 (351)
                      ..+++|++|+|+.+.....   .+|..+..+++|++|+|++|. ++.     ++..+..+         ++|++|++++|
T Consensus        91 ~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~-l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~~n  169 (386)
T 2ca6_A           91 LKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNG-LGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRN  169 (386)
T ss_dssp             TTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSC-CHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSS
T ss_pred             hhCCcccEEECCCCcCCHHHHHHHHHHHHhCCCCCEEECcCCC-CCHHHHHHHHHHHHHHhhhhhcccCCCCcEEECCCC
Confidence            4556666666633322211   244455566667777776663 332     22223333         66777777665


Q ss_pred             ccc-cccC---hhhhcCCCCCEEEecCCC
Q 048347          302 AYL-RKFP---EELWRIKALRKLESWWPR  326 (351)
Q Consensus       302 ~~l-~~lP---~~i~~L~~L~~L~l~~~~  326 (351)
                      ..- ..+|   ..+.++++|++|+++++.
T Consensus       170 ~l~~~~~~~l~~~l~~~~~L~~L~L~~n~  198 (386)
T 2ca6_A          170 RLENGSMKEWAKTFQSHRLLHTVKMVQNG  198 (386)
T ss_dssp             CCTGGGHHHHHHHHHHCTTCCEEECCSSC
T ss_pred             CCCcHHHHHHHHHHHhCCCcCEEECcCCC
Confidence            321 2344   455666777777777665

>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=97.46  E-value=0.00013  Score=71.15  Aligned_cols=48  Identities=8%  Similarity=0.012  Sum_probs=39.9

Q ss_pred             CCccccchhhHHHHHHHHHccC---------------CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQ---------------PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~---------------~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|+++.++++.+++....               ...+.+.|+|+.|+||||+|+.+++.
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~  100 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE  100 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3569999999999999997510               12467889999999999999999987

>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=97.44  E-value=0.00066  Score=60.22  Aligned_cols=47  Identities=15%  Similarity=0.088  Sum_probs=35.6

Q ss_pred             CccccchhhHHHHHHH-------HHc-cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDL-------LIE-RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~-------L~~-~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.++..+++...       +.. ......-+-|+|+.|+|||++|+.+++.
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4678888877776662       321 1345677889999999999999999887

>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=97.43  E-value=0.00025  Score=65.86  Aligned_cols=49  Identities=6%  Similarity=-0.057  Sum_probs=38.9

Q ss_pred             CCCccccchhhHHHHHHHHHc----------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIE----------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|.++.++.+.+.+..          .....+-+.|+|+.|+|||+||+.+++.
T Consensus        82 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~  140 (357)
T 3d8b_A           82 NWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ  140 (357)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            345689999999999988753          1123456779999999999999999877

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=97.42  E-value=0.00021  Score=65.93  Aligned_cols=82  Identities=16%  Similarity=0.122  Sum_probs=50.9

Q ss_pred             CCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccCh-hhhcCCCCC
Q 048347          242 PHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPE-ELWRIKALR  318 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~-~i~~L~~L~  318 (351)
                      ++++.|+|+.+  .+..+|.. +.++++|++|+|++|...+.+|.. +.++++|..+...++..+..+|. .+.++++|+
T Consensus        30 ~~l~~L~Ls~N--~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~~L~  107 (350)
T 4ay9_X           30 RNAIELRFVLT--KLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQ  107 (350)
T ss_dssp             TTCSEEEEESC--CCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCTTCC
T ss_pred             CCCCEEEccCC--cCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCCcccccCchhhhhccccc
Confidence            46777777332  34566653 577777777777777444556653 56676666554444456666644 346677777


Q ss_pred             EEEecCC
Q 048347          319 KLESWWP  325 (351)
Q Consensus       319 ~L~l~~~  325 (351)
                      +|++++.
T Consensus       108 ~L~l~~n  114 (350)
T 4ay9_X          108 YLLISNT  114 (350)
T ss_dssp             EEEEEEE
T ss_pred             ccccccc
Confidence            7777654

>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=97.39  E-value=0.00039  Score=63.93  Aligned_cols=45  Identities=11%  Similarity=0.078  Sum_probs=36.5

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|.++-++.+...+..+.  ..-+.++|+.|+||||+|+.+...
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~--~~~~ll~Gp~G~GKTtla~~la~~   69 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALARE   69 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHH
Confidence            447898888888888887653  222789999999999999998876

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=97.35  E-value=0.00038  Score=69.52  Aligned_cols=58  Identities=17%  Similarity=0.154  Sum_probs=30.8

Q ss_pred             CCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccCh
Q 048347          242 PHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPE  309 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~  309 (351)
                      ++|++|+++.+  .+..+|.   .+++|++|+|++| .+..+|.   .+++|++|++++| .+..+|.
T Consensus        61 ~~L~~L~L~~N--~l~~lp~---~l~~L~~L~Ls~N-~l~~lp~---~l~~L~~L~Ls~N-~l~~l~~  118 (622)
T 3g06_A           61 AHITTLVIPDN--NLTSLPA---LPPELRTLEVSGN-QLTSLPV---LPPGLLELSIFSN-PLTHLPA  118 (622)
T ss_dssp             TTCSEEEECSC--CCSCCCC---CCTTCCEEEECSC-CCSCCCC---CCTTCCEEEECSC-CCCCCCC
T ss_pred             CCCcEEEecCC--CCCCCCC---cCCCCCEEEcCCC-cCCcCCC---CCCCCCEEECcCC-cCCCCCC
Confidence            56666666322  2334444   4556666666666 4555654   4455555555553 3444443

>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=97.32  E-value=0.00032  Score=64.03  Aligned_cols=38  Identities=18%  Similarity=0.190  Sum_probs=27.8

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+..++.........+.|+|+.|+||||||+.+++.
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~   60 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE   60 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            34455555443323456779999999999999999987

>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=97.31  E-value=0.0014  Score=62.65  Aligned_cols=50  Identities=12%  Similarity=0.050  Sum_probs=38.6

Q ss_pred             CCCCccccchhhHHHHHHHHHc---------c-CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIE---------R-QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~---------~-~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.=++++|.++.++.|.+.+..         + ....+-+.++|+.|+|||+||+.+++.
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3345689999999999887731         0 122356779999999999999999987

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.30  E-value=0.00033  Score=63.31  Aligned_cols=47  Identities=9%  Similarity=0.175  Sum_probs=38.1

Q ss_pred             CccccchhhHHHHHHHHHccC-------CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQ-------PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.+..++.+...+....       .....+.++|+.|+|||++|+.++..
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~   70 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT   70 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHH
Confidence            457899999999888886531       12357889999999999999999887

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.29  E-value=0.00028  Score=63.42  Aligned_cols=50  Identities=8%  Similarity=0.013  Sum_probs=39.2

Q ss_pred             CCCCccccchhhHHHHHHHHHcc----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIER----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..-++++|.++.++.+.+.+...          ....+-+.|+|+.|+||||+|+.+++.
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~   77 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE   77 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            34467999999999998887431          112456779999999999999999887

>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=97.26  E-value=0.00097  Score=61.78  Aligned_cols=50  Identities=14%  Similarity=0.054  Sum_probs=38.1

Q ss_pred             CCCCccccchhhHHHHHHHHHcc----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIER----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.=++++|.++.++.|.+.+...          ....+-|.++|+.|+|||+||+.+++.
T Consensus        48 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~  107 (355)
T 2qp9_X           48 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE  107 (355)
T ss_dssp             CCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            33456899999999998887321          112234678999999999999999987

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.25  E-value=0.00077  Score=63.23  Aligned_cols=48  Identities=8%  Similarity=0.007  Sum_probs=37.8

Q ss_pred             CCccccchhhHHHHHHHHHcc----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|.+..++.+...+...          ....+-+-|+|..|+|||+||+.+++.
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~  171 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE  171 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            356899999999999888321          112356779999999999999999876

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.25  E-value=0.00092  Score=60.56  Aligned_cols=47  Identities=15%  Similarity=0.098  Sum_probs=37.1

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|.+....++.+.+..-.....-|-|+|..|+|||++|+.+++.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHh
Confidence            56899999999998888653222334568999999999999999885

>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=97.21  E-value=0.00043  Score=71.77  Aligned_cols=46  Identities=13%  Similarity=0.274  Sum_probs=38.2

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+.++||+++++.+.+.+.....  .-+.++|..|+|||++|+.++..
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~~--~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRTK--NNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSC--CCCEEEECTTSCHHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCCC--CceEEEcCCCCCHHHHHHHHHHH
Confidence            35689999999999999876532  23568999999999999999876

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=97.16  E-value=0.00058  Score=67.42  Aligned_cols=74  Identities=15%  Similarity=0.009  Sum_probs=45.2

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC--
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL--  317 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L--  317 (351)
                      .+++|+.|+++.+.  +..+|.   .+++|++|++++| .+..+|. ++  ++|++|+|++| .+..+|. +..  +|  
T Consensus       138 ~l~~L~~L~Ls~N~--l~~lp~---~l~~L~~L~Ls~N-~L~~lp~-l~--~~L~~L~Ls~N-~L~~lp~-~~~--~L~~  204 (571)
T 3cvr_A          138 LPALLEYINADNNQ--LTMLPE---LPTSLEVLSVRNN-QLTFLPE-LP--ESLEALDVSTN-LLESLPA-VPV--RNHH  204 (571)
T ss_dssp             CCTTCCEEECCSSC--CSCCCC---CCTTCCEEECCSS-CCSCCCC-CC--TTCCEEECCSS-CCSSCCC-CC-------
T ss_pred             cCccccEEeCCCCc--cCcCCC---cCCCcCEEECCCC-CCCCcch-hh--CCCCEEECcCC-CCCchhh-HHH--hhhc
Confidence            45677777773332  223554   4567777777777 5666776 55  77777777774 5667776 543  55  


Q ss_pred             -----CEEEecCCC
Q 048347          318 -----RKLESWWPR  326 (351)
Q Consensus       318 -----~~L~l~~~~  326 (351)
                           +.|++++..
T Consensus       205 ~~~~L~~L~Ls~N~  218 (571)
T 3cvr_A          205 SEETEIFFRCRENR  218 (571)
T ss_dssp             ---CCEEEECCSSC
T ss_pred             ccccceEEecCCCc
Confidence                 777777643

>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=97.14  E-value=0.0011  Score=67.67  Aligned_cols=45  Identities=16%  Similarity=0.183  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++||+++++.+.+.|....  ..-+.++|..|+|||++|+.++..
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~--~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhccC--CCCeEEEcCCCCCHHHHHHHHHHH
Confidence            568999999999999887653  233568999999999999999876

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.11  E-value=0.00087  Score=58.87  Aligned_cols=49  Identities=12%  Similarity=0.026  Sum_probs=35.6

Q ss_pred             CCCccccchhhHHHHHHHHHc---c-------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIE---R-------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~---~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|.++.++++.+.+..   .       ....+-+.|+|+.|+||||||+.+++.
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            335689999888887765432   1       011233779999999999999999887

>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=97.09  E-value=0.0025  Score=57.68  Aligned_cols=115  Identities=11%  Similarity=-0.040  Sum_probs=65.3

Q ss_pred             cchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC-cccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCC
Q 048347           22 DLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS-SYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        22 Gr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~-~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~   97 (351)
                      |-++-.+.+.+.+..+.  ....-++|+.|+||||+|+.+.+. ......+.....+..+   ..+ +-.+++...+...
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~i-d~ir~li~~~~~~   77 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGI-DDIRTIKDFLNYS   77 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCH-HHHHHHHHHHTSC
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCH-HHHHHHHHHHhhc
Confidence            34555667777776553  678889999999999999998763 1111112222333211   111 1112222222211


Q ss_pred             CCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           98 SALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        98 ~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      .                    ..+++-++|+|+++..  ++.+.+...+......+++|+ |.+.
T Consensus        78 p--------------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~  122 (305)
T 2gno_A           78 P--------------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  122 (305)
T ss_dssp             C--------------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             c--------------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence            0                    1245678899999754  567778877776666777777 6543

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.05  E-value=0.00027  Score=62.75  Aligned_cols=85  Identities=20%  Similarity=0.212  Sum_probs=47.8

Q ss_pred             CCCCceEEEEecccccC-ceeeeCCCCCCcccEEEEecCCccccccccccccC--CccEEeecCCccccccCh-------
Q 048347          240 KLPHLKVLKLKRSSYSG-RKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQ--KLKSLIVNPCAYLRKFPE-------  309 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~-~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~--~L~~L~l~~c~~l~~lP~-------  309 (351)
                      ++++|+.|+|+.|.... ..+|..+..+++|++|+|++| .+..+. .++.+.  +|+.|+|.+|.....+|.       
T Consensus       168 ~l~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N-~i~~~~-~l~~l~~l~L~~L~L~~Npl~~~~~~~~~y~~~  245 (267)
T 3rw6_A          168 NIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGN-ELKSER-ELDKIKGLKLEELWLDGNSLCDTFRDQSTYISA  245 (267)
T ss_dssp             HCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTS-CCCSGG-GGGGGTTSCCSEEECTTSTTGGGCSSHHHHHHH
T ss_pred             hCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCC-ccCCch-hhhhcccCCcceEEccCCcCccccCcchhHHHH
Confidence            35677777774333221 123333446777777777777 465552 344444  777777777554444542       


Q ss_pred             hhhcCCCCCEEEecCCC
Q 048347          310 ELWRIKALRKLESWWPR  326 (351)
Q Consensus       310 ~i~~L~~L~~L~l~~~~  326 (351)
                      -+..+++|+.||-...+
T Consensus       246 il~~~P~L~~LDg~~v~  262 (267)
T 3rw6_A          246 IRERFPKLLRLDGHELP  262 (267)
T ss_dssp             HHHHCTTCCEESSCBCC
T ss_pred             HHHHCcccCeECCcCCC
Confidence            24566777777655443

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.02  E-value=0.0017  Score=53.77  Aligned_cols=89  Identities=16%  Similarity=0.154  Sum_probs=58.3

Q ss_pred             eeeCCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccC-hhhhcC----CCCCEEEecCCC---hhH
Q 048347          259 LVCGHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFP-EELWRI----KALRKLESWWPR---PEL  329 (351)
Q Consensus       259 lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP-~~i~~L----~~L~~L~l~~~~---~~~  329 (351)
                      +|.....-.+|+.|++++|. ++.. -..+..+++|+.|+|++|..+..-- ..+..+    ++|++|++++|+   ..-
T Consensus        53 LP~~~~~~~~L~~LDLs~~~-Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~G  131 (176)
T 3e4g_A           53 LPTGPLDKYKIQAIDATDSC-IMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKG  131 (176)
T ss_dssp             SCCCSTTCCCEEEEEEESCC-CCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHH
T ss_pred             CCcccCCCceEeEEeCcCCC-ccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHH
Confidence            45433233579999999995 5432 2246789999999999998765321 123333    369999999986   333


Q ss_pred             HhhccccccCceeeEEecC
Q 048347          330 RQSLHKFEEIDRLDMQIYP  348 (351)
Q Consensus       330 ~~~l~~~~~~~~~~~~~~P  348 (351)
                      ...+.+...+....+...|
T Consensus       132 l~~L~~~~~L~~L~L~~c~  150 (176)
T 3e4g_A          132 IIALHHFRNLKYLFLSDLP  150 (176)
T ss_dssp             HHHGGGCTTCCEEEEESCT
T ss_pred             HHHHhcCCCCCEEECCCCC
Confidence            4455666666666666655

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.01  E-value=0.00019  Score=57.42  Aligned_cols=47  Identities=11%  Similarity=-0.047  Sum_probs=34.0

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+++|.++..+++.+.+..-.....-|-|+|..|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            46889999999988887542111233668999999999999999988

>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=97.00  E-value=0.0026  Score=54.09  Aligned_cols=87  Identities=10%  Similarity=-0.004  Sum_probs=49.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCC-------CCcc-CCCCCHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLS-------ALSE-ILDNDFE  109 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~-------~~~~-~~~~~~~  109 (351)
                      .-.++.|.|.+|+||||||..+.. .    .-..++|++..  ++...+.. +...+....       .... .......
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-~----~~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-L----SGKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQR   92 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-H----HCSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-H----cCCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHH
Confidence            446899999999999999999987 1    12346666654  45544443 333322210       0000 0111123


Q ss_pred             HHHHHHHHhcCCceEEEEEeCCC
Q 048347          110 MKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus       110 ~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      +....++..++.+.-++|+|..-
T Consensus        93 ~~~~~~~~l~~~~~~lliiD~~~  115 (220)
T 2cvh_A           93 RVIGSLKKTVDSNFALVVVDSIT  115 (220)
T ss_dssp             HHHHHHHHHCCTTEEEEEEECCC
T ss_pred             HHHHHHHHHhhcCCCEEEEcCcH
Confidence            34445555554456788899874

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.00  E-value=0.00031  Score=64.38  Aligned_cols=48  Identities=10%  Similarity=0.053  Sum_probs=39.2

Q ss_pred             CCccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|+++.++++..++...   ......+.|+|+.|+|||++|+.+++.
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~   78 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYE   78 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            356899999999999988652   233455789999999999999999776

>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=96.91  E-value=0.0053  Score=56.21  Aligned_cols=128  Identities=9%  Similarity=-0.012  Sum_probs=64.5

Q ss_pred             hhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCccccc--CCCeeEEEEEeCCHHHHHHHHHHHhCCCC---
Q 048347           24 EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN--YFDCCAWVYYQLSLDMMLDAIMKSLMPLS---   98 (351)
Q Consensus        24 ~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~--~F~~~~wv~~~~~~~~~~~~i~~~~~~~~---   98 (351)
                      ++..+.+.+.+..+. -...+-++|+.|+|||++|+.+........  .+..+-       .-..-+.+...-..+.   
T Consensus         8 ~~~~~~l~~~i~~~~-~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~-------~c~~c~~~~~~~~~d~~~~   79 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG-------HCRGCQLMQAGTHPDYYTL   79 (334)
T ss_dssp             HHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCS-------CSHHHHHHHHTCCTTEEEE
T ss_pred             HHHHHHHHHHHHcCC-cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCC-------CCHHHHHHhcCCCCCEEEE
Confidence            455666677665442 345677899999999999998865411110  000000       0000111110000000   


Q ss_pred             CCc-cCCCCCHHHHHHHHHHh----cCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           99 ALS-EILDNDFEMKKNTLHNY----LKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        99 ~~~-~~~~~~~~~~~~~l~~~----L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ... .......+++.+.+...    ..+++-++|+|+++..  +..+.+...+.....+..+|+ |.+.
T Consensus        80 ~~~~~~~~~~i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~  148 (334)
T 1a5t_A           80 APEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREP  148 (334)
T ss_dssp             CCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             eccccCCCCCHHHHHHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence            000 00112333333322221    1356778999999754  566777777776665677776 7654

>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=96.90  E-value=0.00051  Score=62.39  Aligned_cols=71  Identities=13%  Similarity=0.117  Sum_probs=46.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      -+++.|+|++|+|||+||.++...     .-..+.|++.. ...          +  ..     -..+.+...+.+.+.+
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs~~~eE~----------v--~~-----~~~~le~~l~~i~~~l  180 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-----LGGKDKYATVRFGEP----------L--SG-----YNTDFNVFVDDIARAM  180 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-----HHTTSCCEEEEBSCS----------S--TT-----CBCCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-----CCCCEEEEEecchhh----------h--hh-----hhcCHHHHHHHHHHHH
Confidence            456789999999999999999765     11134566662 000          0  00     0134566666677777


Q ss_pred             CCceEEEEEeCCCCh
Q 048347          120 KNKRYLIVIQDVWRG  134 (351)
Q Consensus       120 ~~k~~LlVLDdv~~~  134 (351)
                      +..+ ++|+|++...
T Consensus       181 ~~~~-LLVIDsI~aL  194 (331)
T 2vhj_A          181 LQHR-VIVIDSLKNV  194 (331)
T ss_dssp             HHCS-EEEEECCTTT
T ss_pred             hhCC-EEEEeccccc
Confidence            6666 9999999643

>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=96.88  E-value=0.0016  Score=57.49  Aligned_cols=47  Identities=17%  Similarity=0.098  Sum_probs=34.1

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|.+....++.+.+..-...-.-|-|+|..|+|||++|+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            35789999999888777542222245668999999999999999987

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.86  E-value=0.002  Score=61.22  Aligned_cols=52  Identities=12%  Similarity=-0.011  Sum_probs=39.5

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.+.=+++.|.++.+++|.+.+...           -...+=|-++|++|.|||+||+++++.
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            4444466789999999988877431           122355668999999999999999998

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.83  E-value=0.0015  Score=61.17  Aligned_cols=48  Identities=13%  Similarity=0.092  Sum_probs=37.0

Q ss_pred             CCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      =+++.|.++.+++|.+.+.-.           -+..+=|-++|++|.|||.||+++++.
T Consensus       147 ~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          147 YDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHh
Confidence            355789999999988777431           122344668999999999999999988

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.82  E-value=0.00091  Score=56.89  Aligned_cols=39  Identities=23%  Similarity=0.268  Sum_probs=29.4

Q ss_pred             hHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           26 KMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        26 ~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.++|.+.+....++-.+|+|+|..|+|||||++.+...
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~   45 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAA   45 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            344555555433345689999999999999999998776

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.82  E-value=0.00088  Score=64.49  Aligned_cols=45  Identities=13%  Similarity=0.194  Sum_probs=37.5

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+||++++++.+...+..... . -+.++|..|+|||++|+.++..
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~~-~-~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRTK-N-NPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSS-C-EEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccCC-C-CeEEECCCCCCHHHHHHHHHHH
Confidence            4699999999999999876432 2 3458999999999999999877

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.82  E-value=0.0019  Score=55.58  Aligned_cols=60  Identities=8%  Similarity=0.012  Sum_probs=38.9

Q ss_pred             CCccccc---hhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           17 NKVDLDL---EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        17 ~~~~vGr---~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      -++++|.   ++.++.+..++...  ....+.|+|+.|+||||||+.+++.  .......+.+++..
T Consensus        27 ~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~   89 (242)
T 3bos_A           27 FTSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLG   89 (242)
T ss_dssp             TTTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGG
T ss_pred             hhhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHH
Confidence            3567763   34455566655443  3467789999999999999999887  43333344555543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.77  E-value=0.0022  Score=60.96  Aligned_cols=50  Identities=12%  Similarity=0.007  Sum_probs=38.0

Q ss_pred             CCCCccccchhhHHHHHHHHHc-----------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIE-----------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.=+++.|.++.+++|.+.+..           +-...+=|-++|+.|.|||+||+++++.
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e  266 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANR  266 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHH
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhc
Confidence            3335688999999999887632           1123445668999999999999999988

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.77  E-value=0.0024  Score=60.51  Aligned_cols=52  Identities=13%  Similarity=-0.000  Sum_probs=39.2

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.+.-+++.|.++.+++|.+.+...           -+..+=|-++|++|.|||+||+++++.
T Consensus       167 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~  229 (428)
T 4b4t_K          167 PDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS  229 (428)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3344466889999999998877421           122344678999999999999999988

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.76  E-value=0.0016  Score=55.00  Aligned_cols=42  Identities=12%  Similarity=0.154  Sum_probs=33.6

Q ss_pred             chhhHHHHHHHHHcc-CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           23 LEDKMEELLDLLIER-QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        23 r~~~~~~l~~~L~~~-~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |++..+++.+.+... ..+..+|+|.|..|+||||+++.+...
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~   45 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQT   45 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            456677787777653 245689999999999999999998765

>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=96.73  E-value=0.0013  Score=63.66  Aligned_cols=93  Identities=9%  Similarity=0.042  Sum_probs=57.7

Q ss_pred             CccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      ++++|.++.++++.+++...           ....+-|-|+|..|+|||++|+.+++.  ...     -++.+.  ..++
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~--~~~-----~fv~vn--~~~l  274 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE--TGA-----FFFLIN--GPEI  274 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHH--CSS-----EEEEEE--HHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHH--hCC-----CEEEEE--chHh
Confidence            45899999999998887532           123345779999999999999999877  322     233333  1111


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      .    ..+.         ..........+.....++..+|+||+++
T Consensus       275 ~----~~~~---------g~~~~~~~~~f~~A~~~~p~iLfLDEId  307 (489)
T 3hu3_A          275 M----SKLA---------GESESNLRKAFEEAEKNAPAIIFIDELD  307 (489)
T ss_dssp             H----TSCT---------THHHHHHHHHHHHHHHTCSEEEEEESHH
T ss_pred             h----hhhc---------chhHHHHHHHHHHHHhcCCcEEEecchh
Confidence            1    0000         1112233444444555677899999993

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=96.68  E-value=0.00064  Score=66.92  Aligned_cols=84  Identities=18%  Similarity=0.104  Sum_probs=51.9

Q ss_pred             CCCCceEEEEecccccCce--eeeCCCCCCcccEEEEecCCcccc-----ccccccccCCccEEeecCCc-cc--cccCh
Q 048347          240 KLPHLKVLKLKRSSYSGRK--LVCGHGGFPRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIVNPCA-YL--RKFPE  309 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~--lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l~~c~-~l--~~lP~  309 (351)
                      .+++|++|+++ ++.....  ++.....+++|++|++++|. +..     ++.-...+++|+.|++++|. .+  ..++.
T Consensus       128 ~~~~L~~L~L~-~~~~~~~~~l~~~~~~~~~L~~L~L~~~~-i~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~l~~  205 (594)
T 2p1m_B          128 SFKNFKVLVLS-SCEGFSTDGLAAIAATCRNLKELDLRESD-VDDVSGHWLSHFPDTYTSLVSLNISCLASEVSFSALER  205 (594)
T ss_dssp             HCTTCCEEEEE-SCEEEEHHHHHHHHHHCTTCCEEECTTCE-EECCCGGGGGGSCTTCCCCCEEECTTCCSCCCHHHHHH
T ss_pred             hCCCCcEEeCC-CcCCCCHHHHHHHHHhCCCCCEEeCcCCc-cCCcchHHHHHHhhcCCcCcEEEecccCCcCCHHHHHH
Confidence            46788888883 4322222  44444467888888888874 332     33333466788888888764 11  12222


Q ss_pred             hhhcCCCCCEEEecCC
Q 048347          310 ELWRIKALRKLESWWP  325 (351)
Q Consensus       310 ~i~~L~~L~~L~l~~~  325 (351)
                      -+.++++|++|+++++
T Consensus       206 l~~~~~~L~~L~L~~~  221 (594)
T 2p1m_B          206 LVTRCPNLKSLKLNRA  221 (594)
T ss_dssp             HHHHCTTCCEEECCTT
T ss_pred             HHHhCCCCcEEecCCC
Confidence            3355788888888887

>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=96.67  E-value=0.003  Score=64.49  Aligned_cols=94  Identities=10%  Similarity=0.062  Sum_probs=58.8

Q ss_pred             CccccchhhHHHHHHHHHc---cC--------CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIE---RQ--------PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~---~~--------~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      +++.|.++.+++|.+.+.-   ..        ...+=|-++|+.|.|||+||+++++.  ...+|     +.++  ..++
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~e--lg~~~-----~~v~--~~~l  274 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE--TGAFF-----FLIN--GPEI  274 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTT--TTCEE-----EEEE--HHHH
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH--hCCeE-----EEEE--hHHh
Confidence            4578899999998887632   11        22345778999999999999999998  43332     2332  1111


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                          .    ...     .......+.+.+....+...++|+||+++.
T Consensus       275 ----~----sk~-----~gese~~lr~lF~~A~~~~PsIIfIDEiDa  308 (806)
T 3cf2_A          275 ----M----SKL-----AGESESNLRKAFEEAEKNAPAIIFIDELDA  308 (806)
T ss_dssp             ----H----SSC-----TTHHHHHHHHHHHHHTTSCSEEEEEESGGG
T ss_pred             ----h----ccc-----chHHHHHHHHHHHHHHHcCCeEEEEehhcc
Confidence                1    111     112233444455555567889999999963

>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=96.64  E-value=0.0011  Score=60.80  Aligned_cols=47  Identities=15%  Similarity=0.068  Sum_probs=36.7

Q ss_pred             CccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.+..++.+...+...   +.....+.++|+.|+||||||+.++..
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~   74 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASE   74 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            45789888778777666542   233457889999999999999999887

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=96.60  E-value=0.00044  Score=65.88  Aligned_cols=86  Identities=19%  Similarity=0.210  Sum_probs=62.7

Q ss_pred             CCCCCceEEEEecccccC---ceeeeCCCCCCcccEEEEecCCcccc-ccccc-cccC----CccEEeecCCcccc----
Q 048347          239 EKLPHLKVLKLKRSSYSG---RKLVCGHGGFPRQEILHLKSMLWLEE-WKMET-GAMQ----KLKSLIVNPCAYLR----  305 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~---~~lp~~~~~l~~L~~L~L~~~~~l~~-lp~~i-~~L~----~L~~L~l~~c~~l~----  305 (351)
                      ..+++|++|+++.+....   ..++..+..+++|++|++++| .+.. -+..+ ..+.    +|++|++++|. +.    
T Consensus        25 ~~~~~L~~L~L~~~~l~~~~~~~l~~~l~~~~~L~~L~Ls~n-~l~~~~~~~l~~~l~~~~~~L~~L~L~~n~-i~~~~~  102 (461)
T 1z7x_W           25 PLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSN-ELGDVGVHCVLQGLQTPSCKIQKLSLQNCC-LTGAGC  102 (461)
T ss_dssp             HHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTC-CCHHHHHHHHHHTTCSTTCCCCEEECTTSC-CBGGGH
T ss_pred             hhcCCccEEEccCCCCCHHHHHHHHHHHHhCCCcCEEeCCCC-cCChHHHHHHHHHHhhCCCceeEEEccCCC-CCHHHH
Confidence            467899999995443221   145666777899999999998 4554 23333 3355    69999999975 44    


Q ss_pred             -ccChhhhcCCCCCEEEecCCC
Q 048347          306 -KFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       306 -~lP~~i~~L~~L~~L~l~~~~  326 (351)
                       .+|..+.++++|++|+++++.
T Consensus       103 ~~l~~~l~~~~~L~~L~Ls~n~  124 (461)
T 1z7x_W          103 GVLSSTLRTLPTLQELHLSDNL  124 (461)
T ss_dssp             HHHHHHTTSCTTCCEEECCSSB
T ss_pred             HHHHHHHccCCceeEEECCCCc
Confidence             678889999999999999876

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.58  E-value=0.0034  Score=53.71  Aligned_cols=89  Identities=16%  Similarity=0.030  Sum_probs=49.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCc---------c---------
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALS---------E---------  102 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~---------~---------  102 (351)
                      -.+++|.|..|+|||||++.+...  ....-..+.|+.......++...+. ++.......         .         
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~--~~~~~~~v~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAK--GLRDGDPCIYVTTEESRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEKEDQW   99 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHH--HHHHTCCEEEEESSSCHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC----CTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH--HHHCCCeEEEEEcccCHHHHHHHHH-HhcchHHHHhhCCEEEEeccccccCcee
Confidence            368999999999999999999865  2222123455543344444444332 333211000         0         


Q ss_pred             -CCCCCHHHHHHHHHHhcCC-c--eEEEEEeCCC
Q 048347          103 -ILDNDFEMKKNTLHNYLKN-K--RYLIVIQDVW  132 (351)
Q Consensus       103 -~~~~~~~~~~~~l~~~L~~-k--~~LlVLDdv~  132 (351)
                       ....+..++...+...+.. +  ..++|+|..-
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~  133 (235)
T 2w0m_A          100 SLVNLTPEELVNKVIEAKQKLGYGKARLVIDSVS  133 (235)
T ss_dssp             BCSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGG
T ss_pred             eecCCCHHHHHHHHHHHHHhhCCCceEEEEECch
Confidence             0112555665555555432 2  3489999986

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.57  E-value=0.0023  Score=60.65  Aligned_cols=51  Identities=12%  Similarity=0.066  Sum_probs=38.4

Q ss_pred             CCCCCccccchhhHHHHHHHHHc----c-------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIE----R-------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.=+++.|.++.+++|.+.+..    .       -+..+=|-++|++|.|||+||+++++.
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e  238 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQ  238 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHH
Confidence            33345688999999998877532    1       123455668999999999999999988

>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=96.56  E-value=0.0012  Score=59.31  Aligned_cols=47  Identities=13%  Similarity=0.092  Sum_probs=37.2

Q ss_pred             CccccchhhHHHHHHHHHcc------------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIER------------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.++.++.+...+...            .....-+-++|..|+|||++|+.+.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   73 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            56899999999998887541            112345668999999999999999887

>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=96.56  E-value=0.002  Score=61.94  Aligned_cols=47  Identities=15%  Similarity=0.094  Sum_probs=35.2

Q ss_pred             CccccchhhHHHHHHHHHc--c--------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIE--R--------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~--~--------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.++.++++.+.+..  .        ..-.+-|.++|+.|+|||+||+.+++.
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~   72 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGE   72 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4689999988888776532  1        011123679999999999999999987

>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=96.52  E-value=0.0047  Score=57.07  Aligned_cols=99  Identities=14%  Similarity=-0.004  Sum_probs=59.6

Q ss_pred             HHHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCc-c
Q 048347           27 MEELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALS-E  102 (351)
Q Consensus        27 ~~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~-~  102 (351)
                      ...|-..|- .+=++-.++.|.|..|+||||||.++...  ....-..++|++..  ++..     .+++++...... -
T Consensus        46 ~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~--~~~~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i  118 (356)
T 3hr8_A           46 SLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAE--AQKMGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLI  118 (356)
T ss_dssp             CHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEE
T ss_pred             CHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEecccccchH-----HHHHcCCchhhhhh
Confidence            344555453 22244579999999999999999999876  33322345677655  4432     455555432110 0


Q ss_pred             CCCCCHHHHHHHHHHhcC-CceEEEEEeCCC
Q 048347          103 ILDNDFEMKKNTLHNYLK-NKRYLIVIQDVW  132 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~-~k~~LlVLDdv~  132 (351)
                      ....+.+++...+...++ .+.-++|+|.+-
T Consensus       119 ~~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~  149 (356)
T 3hr8_A          119 SQPDHGEQALEIVDELVRSGVVDLIVVDSVA  149 (356)
T ss_dssp             ECCSSHHHHHHHHHHHHHTSCCSEEEEECTT
T ss_pred             hhccCHHHHHHHHHHHhhhcCCCeEEehHhh
Confidence            134456666666666554 445588899874

>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=96.52  E-value=0.0057  Score=58.01  Aligned_cols=25  Identities=12%  Similarity=0.141  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|.++|.+|+||||++..+...
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~  120 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYF  120 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999988765

>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=96.52  E-value=0.0028  Score=56.93  Aligned_cols=93  Identities=11%  Similarity=0.011  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHc----cCCCeEEEEEEcCCCChHHHHHHHHhCCccccc-CCCeeEEEEEe--CCHHHHHHHHHHHhC---
Q 048347           26 KMEELLDLLIE----RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN-YFDCCAWVYYQ--LSLDMMLDAIMKSLM---   95 (351)
Q Consensus        26 ~~~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv~~~--~~~~~~~~~i~~~~~---   95 (351)
                      -.+.|.+.+..    ...+..+|+|.|..|+||||||+.+........ .......|+..  +-..+....+.....   
T Consensus        12 ~~~~l~~~i~~~~~~~~~~~~ii~I~G~sGsGKSTla~~L~~~l~~~g~~~~~~~iv~~D~f~~~~~~~~~l~~~~~~~~   91 (290)
T 1odf_A           12 TIEFLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNK   91 (290)
T ss_dssp             HHHHHHHHHHHHHTTTCCSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCG
T ss_pred             HHHHHHHHHHHhhhccCCCCeEEEEECCCCCCHHHHHHHHHHHhhhcCCCCceEEEeccccccCChHHHHHHhccccccc
Confidence            34444444433    345678999999999999999999877622211 12233333444  222344444443311   


Q ss_pred             ---CCCCCccCCCCCHHHHHHHHHHhcCC
Q 048347           96 ---PLSALSEILDNDFEMKKNTLHNYLKN  121 (351)
Q Consensus        96 ---~~~~~~~~~~~~~~~~~~~l~~~L~~  121 (351)
                         ....   ++..+...+.+.+...-.+
T Consensus        92 l~~~~g~---p~a~d~~~l~~~l~~l~~g  117 (290)
T 1odf_A           92 LLQGRGL---PGTHDMKLLQEVLNTIFNN  117 (290)
T ss_dssp             GGSSSCS---TTSBCHHHHHHHHHHHTC-
T ss_pred             hhhhccC---cchhHHHHHHHHHHHhhcc
Confidence               1111   2445566666666655444

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=96.49  E-value=0.0032  Score=55.81  Aligned_cols=60  Identities=23%  Similarity=0.089  Sum_probs=48.4

Q ss_pred             CCCCcccEEEEecCCccccc---cccccccCCccEEeecCCccccccChhhhcCC--CCCEEEecCCC
Q 048347          264 GGFPRQEILHLKSMLWLEEW---KMETGAMQKLKSLIVNPCAYLRKFPEELWRIK--ALRKLESWWPR  326 (351)
Q Consensus       264 ~~l~~L~~L~L~~~~~l~~l---p~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~--~L~~L~l~~~~  326 (351)
                      ..+++|++|+|++| .+..+   |..++.+++|+.|+|++| .+..+ .++..++  +|++|++++.+
T Consensus       167 ~~l~~L~~L~Ls~N-~l~~l~~l~~~~~~l~~L~~L~Ls~N-~i~~~-~~l~~l~~l~L~~L~L~~Np  231 (267)
T 3rw6_A          167 ENIPELLSLNLSNN-RLYRLDDMSSIVQKAPNLKILNLSGN-ELKSE-RELDKIKGLKLEELWLDGNS  231 (267)
T ss_dssp             HHCTTCCEEECTTS-CCCCCGGGTTHHHHSTTCCEEECTTS-CCCSG-GGGGGGTTSCCSEEECTTST
T ss_pred             hhCCCCCEEECCCC-CCCCCccchhHHhhCCCCCEEECCCC-ccCCc-hhhhhcccCCcceEEccCCc
Confidence            46889999999999 56654   456779999999999984 57666 4566666  99999999866

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.48  E-value=0.0021  Score=65.62  Aligned_cols=46  Identities=13%  Similarity=0.197  Sum_probs=38.1

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+.+||+++.++.+...+..... .. +.++|..|+|||++|+.+...
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~~-~~-vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRTK-NN-PVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSS-CE-EEEESCTTTTTHHHHHHHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCCC-CC-eEEECCCCCCHHHHHHHHHHH
Confidence            35699999999999999976432 23 568999999999999999876

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=96.48  E-value=0.00097  Score=61.68  Aligned_cols=85  Identities=14%  Similarity=-0.009  Sum_probs=47.7

Q ss_pred             CCCC-CceEEEEecccccCceeeeCCCC-----CCcccEEEEecCCccccc-cccccc----c-CCccEEeecCCccccc
Q 048347          239 EKLP-HLKVLKLKRSSYSGRKLVCGHGG-----FPRQEILHLKSMLWLEEW-KMETGA----M-QKLKSLIVNPCAYLRK  306 (351)
Q Consensus       239 ~~l~-~L~~L~l~~~~~~~~~lp~~~~~-----l~~L~~L~L~~~~~l~~l-p~~i~~----L-~~L~~L~l~~c~~l~~  306 (351)
                      ..++ +|++|+++.+.... ..+..+..     +++|++|++++| .++.. +..++.    + ++|++|++++|. +..
T Consensus        47 ~~~~~~L~~L~Ls~N~l~~-~~~~~l~~~l~~~~~~L~~L~Ls~n-~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~  123 (362)
T 3goz_A           47 ANTPASVTSLNLSGNSLGF-KNSDELVQILAAIPANVTSLNLSGN-FLSYKSSDELVKTLAAIPFTITVLDLGWND-FSS  123 (362)
T ss_dssp             HTCCTTCCEEECCSSCGGG-SCHHHHHHHHHTSCTTCCEEECCSS-CGGGSCHHHHHHHHHTSCTTCCEEECCSSC-GGG
T ss_pred             HhCCCceeEEECcCCCCCH-HHHHHHHHHHhccCCCccEEECcCC-cCChHHHHHHHHHHHhCCCCccEEECcCCc-CCc
Confidence            3566 78888884332221 22222222     267888888887 35543 333333    3 678888888754 444


Q ss_pred             cCh-hh----hc-CCCCCEEEecCCC
Q 048347          307 FPE-EL----WR-IKALRKLESWWPR  326 (351)
Q Consensus       307 lP~-~i----~~-L~~L~~L~l~~~~  326 (351)
                      .+. .+    .. .++|++|+++++.
T Consensus       124 ~~~~~l~~~l~~~~~~L~~L~Ls~N~  149 (362)
T 3goz_A          124 KSSSEFKQAFSNLPASITSLNLRGND  149 (362)
T ss_dssp             SCHHHHHHHHTTSCTTCCEEECTTSC
T ss_pred             HHHHHHHHHHHhCCCceeEEEccCCc
Confidence            443 22    23 2578888888765

>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=96.47  E-value=0.0074  Score=55.14  Aligned_cols=25  Identities=16%  Similarity=0.157  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|+.|+||||+++.+...
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~  152 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANW  152 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999998766

>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=96.44  E-value=0.0047  Score=55.90  Aligned_cols=89  Identities=9%  Similarity=0.043  Sum_probs=47.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHH--HHHHHHHHhCCCCCCccCCCCCHHH-HHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDM--MLDAIMKSLMPLSALSEILDNDFEM-KKNTL  115 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~--~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~l  115 (351)
                      ...+++|+|.+|+||||++..+...  .+..-..+..+... +....  -+...++......- .+....+... ..+.+
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~--l~~~g~kV~lv~~D~~r~~a~eqL~~~~~~~gl~~~-~~~s~~~~~~v~~~al  179 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKM--FVDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVI-SHSEGADPAAVAFDAV  179 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH--HHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCEEE-CCSTTCCHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHH--HHhcCCEEEEEccccccHHHHHHHHHHHHHcCCcEE-ecCCccCHHHHHHHHH
Confidence            4579999999999999999999876  33332234455544 33321  22334444432211 0111112222 23345


Q ss_pred             HHhcCCceEEEEEeCC
Q 048347          116 HNYLKNKRYLIVIQDV  131 (351)
Q Consensus       116 ~~~L~~k~~LlVLDdv  131 (351)
                      ...+..+.-++++|-.
T Consensus       180 ~~a~~~~~dvvIiDtp  195 (306)
T 1vma_A          180 AHALARNKDVVIIDTA  195 (306)
T ss_dssp             HHHHHTTCSEEEEEEC
T ss_pred             HHHHhcCCCEEEEECC
Confidence            5545444457777865

>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=96.42  E-value=0.0015  Score=53.26  Aligned_cols=92  Identities=10%  Similarity=-0.038  Sum_probs=47.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCC-cc-----CCCCCHHHHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSAL-SE-----ILDNDFEMKKNTL  115 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~-~~-----~~~~~~~~~~~~l  115 (351)
                      .+|+|.|+.|+||||+|+.+ ..  .  .|.   +++    ..++++.....-...... ..     ..........+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~--~--g~~---~i~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KE--R--GAK---VIV----MSDVVRKRYSIEAKPGERLMDFAKRLREIYGDGVVARLC   69 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HH--T--TCE---EEE----HHHHHHHHHHHHC---CCHHHHHHHHHHHHCTTHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH-HH--C--CCc---EEE----HhHHHHHHHHhcCCChhHHHHHHHHHHhhCCHHHHHHHH
Confidence            47899999999999999999 33  1  121   222    234444443332210000 00     0000111223344


Q ss_pred             HHhc-CCceEEEEEeCCCChhhHHHHHhhcC
Q 048347          116 HNYL-KNKRYLIVIQDVWRGDIWDFLKEALP  145 (351)
Q Consensus       116 ~~~L-~~k~~LlVLDdv~~~~~~~~l~~~l~  145 (351)
                      .+.+ ......+|+|++....+...+.....
T Consensus        70 ~~~l~~~~~~~vi~dg~~~~~~~~~l~~~~~  100 (179)
T 3lw7_A           70 VEELGTSNHDLVVFDGVRSLAEVEEFKRLLG  100 (179)
T ss_dssp             HHHHCSCCCSCEEEECCCCHHHHHHHHHHHC
T ss_pred             HHHHHhcCCCeEEEeCCCCHHHHHHHHHHhC
Confidence            4455 23344578899966666666666553

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=96.41  E-value=0.00096  Score=65.64  Aligned_cols=61  Identities=16%  Similarity=0.105  Sum_probs=40.6

Q ss_pred             CCCcccEEEEecCCccc--cccccccccCCccEEeecCCccc-cccChhhhcCCCCCEEEecCCC
Q 048347          265 GFPRQEILHLKSMLWLE--EWKMETGAMQKLKSLIVNPCAYL-RKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       265 ~l~~L~~L~L~~~~~l~--~lp~~i~~L~~L~~L~l~~c~~l-~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      .+++|++|++++|. +.  .+|..+..+++|++|++++|..- ..+|..+.++++|+.|++++++
T Consensus       461 ~~~~L~~L~L~~n~-l~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~ls~n~  524 (592)
T 3ogk_B          461 YSPNVRWMLLGYVG-ESDEGLMEFSRGCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYR  524 (592)
T ss_dssp             SCTTCCEEEECSCC-SSHHHHHHHHTCCTTCCEEEEESCCCBHHHHHHHHHHCSSCCEEEEESCB
T ss_pred             hCccceEeeccCCC-CCHHHHHHHHhcCcccCeeeccCCCCcHHHHHHHHHhcCccCeeECcCCc
Confidence            36677777777773 43  24544567788888888887621 2245555678888888888776

>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=96.41  E-value=0.0013  Score=58.11  Aligned_cols=49  Identities=14%  Similarity=0.053  Sum_probs=36.5

Q ss_pred             CCCccccchhhHHHHHHHHHc----------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIE----------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|.++.++.+.+.+..          +....+-+.++|+.|+|||+||+.+++.
T Consensus         9 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A            9 RFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             CSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHH
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            346799999998888877641          0011223668999999999999999987

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=96.41  E-value=0.00063  Score=64.77  Aligned_cols=83  Identities=18%  Similarity=0.129  Sum_probs=54.9

Q ss_pred             CCceEEEEecccccCc---eeeeCCCCCCcccEEEEecCCccccc-cccccc-----cCCccEEeecCCcccc-----cc
Q 048347          242 PHLKVLKLKRSSYSGR---KLVCGHGGFPRQEILHLKSMLWLEEW-KMETGA-----MQKLKSLIVNPCAYLR-----KF  307 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~---~lp~~~~~l~~L~~L~L~~~~~l~~l-p~~i~~-----L~~L~~L~l~~c~~l~-----~l  307 (351)
                      ++|++|+++.+.....   .++..+..+++|++|++++| .+... +..+..     .++|++|++++|. +.     .+
T Consensus       313 ~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n-~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~-i~~~~~~~l  390 (461)
T 1z7x_W          313 CQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNN-RLEDAGVRELCQGLGQPGSVLRVLWLADCD-VSDSSCSSL  390 (461)
T ss_dssp             CCCCEEECTTSCCBGGGHHHHHHHHHHCSSCCEEECCSS-BCHHHHHHHHHHHHTSTTCCCCEEECTTSC-CCHHHHHHH
T ss_pred             ccceeeEcCCCCCchHHHHHHHHHHhhCCCccEEEccCC-ccccccHHHHHHHHcCCCCceEEEECCCCC-CChhhHHHH
Confidence            4677777732222111   13444556678888888888 45543 333332     5688999998864 54     78


Q ss_pred             ChhhhcCCCCCEEEecCCC
Q 048347          308 PEELWRIKALRKLESWWPR  326 (351)
Q Consensus       308 P~~i~~L~~L~~L~l~~~~  326 (351)
                      |..+.++++|++|++++++
T Consensus       391 ~~~l~~~~~L~~L~l~~N~  409 (461)
T 1z7x_W          391 AATLLANHSLRELDLSNNC  409 (461)
T ss_dssp             HHHHHHCCCCCEEECCSSS
T ss_pred             HHHHHhCCCccEEECCCCC
Confidence            8888888999999998875

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.37  E-value=0.0051  Score=57.95  Aligned_cols=52  Identities=13%  Similarity=0.012  Sum_probs=38.6

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+.=+++.|.|+.+++|.+.+...           -+..+=|-++|+.|.|||.||+++++.
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHH
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHH
Confidence            3333355788999999988876421           122345668999999999999999988

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.30  E-value=0.012  Score=56.90  Aligned_cols=51  Identities=16%  Similarity=0.070  Sum_probs=36.9

Q ss_pred             CCCCCccccchhhHHHHHHHHHc--cC--------CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIE--RQ--------PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~--~~--------~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.-++++|.++.++++.+.+..  ..        .-.+=+.|+|+.|+||||||+.++..
T Consensus        27 ~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~   87 (499)
T 2dhr_A           27 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   87 (499)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            34446789999888887776532  10        00112789999999999999999987

>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=96.29  E-value=0.0087  Score=51.55  Aligned_cols=93  Identities=4%  Similarity=-0.027  Sum_probs=50.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccc----CCCeeEEEEEe--CCHHHHHHHHHHHhCCCC-----CCccCCCCCH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKN----YFDCCAWVYYQ--LSLDMMLDAIMKSLMPLS-----ALSEILDNDF  108 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~-----~~~~~~~~~~  108 (351)
                      .-.++.|+|..|+||||||..+........    .-..++|++..  +....+ ..+++.+....     ...-....+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL-LAVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH-HHHHHHcCCCHHHHhhCeEEEecCCH
Confidence            346899999999999999999876411211    12356676655  344443 34445554321     0000012223


Q ss_pred             HHH---HHHHHHhcC-CceEEEEEeCCCC
Q 048347          109 EMK---KNTLHNYLK-NKRYLIVIQDVWR  133 (351)
Q Consensus       109 ~~~---~~~l~~~L~-~k~~LlVLDdv~~  133 (351)
                      .+.   .+.+.+.+. .+.-++|+|.+..
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEeCchH
Confidence            332   233444443 4667888998853

>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=96.29  E-value=0.0025  Score=53.04  Aligned_cols=24  Identities=8%  Similarity=0.068  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999876

>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=96.28  E-value=0.0091  Score=56.66  Aligned_cols=25  Identities=8%  Similarity=0.208  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|.++|.+|+||||++..+...
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~  123 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARY  123 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHH
Confidence            4689999999999999999888765

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=96.26  E-value=0.0023  Score=59.38  Aligned_cols=95  Identities=18%  Similarity=0.209  Sum_probs=61.3

Q ss_pred             CCCCceEEEEecc--cccCc----eeee--CCCCCCcccEEEEecCCccccccccc---cccCCccEEeecCCccccc--
Q 048347          240 KLPHLKVLKLKRS--SYSGR----KLVC--GHGGFPRQEILHLKSMLWLEEWKMET---GAMQKLKSLIVNPCAYLRK--  306 (351)
Q Consensus       240 ~l~~L~~L~l~~~--~~~~~----~lp~--~~~~l~~L~~L~L~~~~~l~~lp~~i---~~L~~L~~L~l~~c~~l~~--  306 (351)
                      .+|+|+.|+|+.+  .+.+.    .+..  ....+++|++|+|++|......+..+   +.+++|++|+|+.| .+..  
T Consensus       217 ~lp~L~~L~L~~~~~~~~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n-~L~d~G  295 (362)
T 2ra8_A          217 DLPNLEKLVLYVGVEDYGFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAG-VLTDEG  295 (362)
T ss_dssp             BCTTCCEEEEECBCGGGTCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSS-CCBHHH
T ss_pred             cCCCCcEEEEeccccccccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCC-CCChHH
Confidence            5788888888421  11111    1111  12468999999999884322233222   46889999999875 4543  


Q ss_pred             ---cChhhhcCCCCCEEEecCCC--hhHHhhccc
Q 048347          307 ---FPEELWRIKALRKLESWWPR--PELRQSLHK  335 (351)
Q Consensus       307 ---lP~~i~~L~~L~~L~l~~~~--~~~~~~l~~  335 (351)
                         ++.++.++++|+.|+++++.  .+....+.+
T Consensus       296 ~~~L~~~L~~l~~L~~L~L~~n~i~d~~~~~l~~  329 (362)
T 2ra8_A          296 ARLLLDHVDKIKHLKFINMKYNYLSDEMKKELQK  329 (362)
T ss_dssp             HHHHHTTHHHHTTCSEEECCSBBCCHHHHHHHHH
T ss_pred             HHHHHhhcccCCcceEEECCCCcCCHHHHHHHHH
Confidence               67777889999999998764  455555554

>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=96.22  E-value=0.0022  Score=52.17  Aligned_cols=23  Identities=4%  Similarity=0.024  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999876

>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=96.22  E-value=0.011  Score=53.18  Aligned_cols=25  Identities=8%  Similarity=0.191  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++++|.+|+||||++..+...
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~  128 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAI  128 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4569999999999999999998766

>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=96.21  E-value=0.002  Score=52.92  Aligned_cols=23  Identities=0%  Similarity=0.039  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~   26 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999999887

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=96.19  E-value=0.0015  Score=64.29  Aligned_cols=86  Identities=15%  Similarity=0.029  Sum_probs=58.7

Q ss_pred             CCCCceEEEEecccccCceeeeCCC-CCCcccEEEEecCCcccc--ccccccccCCccEEeecCCcccc----ccChhhh
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHG-GFPRQEILHLKSMLWLEE--WKMETGAMQKLKSLIVNPCAYLR----KFPEELW  312 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~-~l~~L~~L~L~~~~~l~~--lp~~i~~L~~L~~L~l~~c~~l~----~lP~~i~  312 (351)
                      .+++|++|+++.+. .....+..+. .+++|++|++++|..++.  ++.-..++++|++|++++|..-.    .++.-..
T Consensus       103 ~~~~L~~L~L~~~~-~~~~~~~~l~~~~~~L~~L~L~~~~~~~~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~  181 (594)
T 2p1m_B          103 SYTWLEEIRLKRMV-VTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPD  181 (594)
T ss_dssp             HCTTCCEEEEESCB-CCHHHHHHHHHHCTTCCEEEEESCEEEEHHHHHHHHHHCTTCCEEECTTCEEECCCGGGGGGSCT
T ss_pred             hCCCCCeEEeeCcE-EcHHHHHHHHHhCCCCcEEeCCCcCCCCHHHHHHHHHhCCCCCEEeCcCCccCCcchHHHHHHhh
Confidence            57889999995433 2222222232 578999999999865654  56556689999999999875211    2333334


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ++++|++|+++++.
T Consensus       182 ~~~~L~~L~l~~~~  195 (594)
T 2p1m_B          182 TYTSLVSLNISCLA  195 (594)
T ss_dssp             TCCCCCEEECTTCC
T ss_pred             cCCcCcEEEecccC
Confidence            67799999999886

>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=96.18  E-value=0.0025  Score=55.86  Aligned_cols=26  Identities=4%  Similarity=0.038  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|+.|+||||+|+.+...
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~   45 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQL   45 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999999775

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.17  E-value=0.0025  Score=52.82  Aligned_cols=24  Identities=8%  Similarity=0.167  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|+|+.|+|||||++.+...
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999999764

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.16  E-value=0.0026  Score=53.55  Aligned_cols=25  Identities=12%  Similarity=0.101  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|.|+|+.|+||||+|+.+...
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~   48 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARK   48 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            3468999999999999999999876

>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=96.13  E-value=0.015  Score=53.01  Aligned_cols=92  Identities=11%  Similarity=0.079  Sum_probs=52.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccC----CCeeEEEEEe--CCHHHHHHHHHHHhCCCCC-----CccCCCCCH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY----FDCCAWVYYQ--LSLDMMLDAIMKSLMPLSA-----LSEILDNDF  108 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~-----~~~~~~~~~  108 (351)
                      .-.++.|.|..|+||||||.++.........    -..++|++..  ++.+.+. .++..++....     ..-....+.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCH
Confidence            3468899999999999999998765221111    2356777766  5566554 34555543211     000012233


Q ss_pred             H---HHHHHHHHhcC--CceEEEEEeCCC
Q 048347          109 E---MKKNTLHNYLK--NKRYLIVIQDVW  132 (351)
Q Consensus       109 ~---~~~~~l~~~L~--~k~~LlVLDdv~  132 (351)
                      +   ++.+.+...++  .+--++|+|.+-
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  213 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVT  213 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTT
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcH
Confidence            3   23445555553  456788888884

>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=96.10  E-value=0.011  Score=54.76  Aligned_cols=99  Identities=12%  Similarity=0.013  Sum_probs=58.2

Q ss_pred             HHHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-cc
Q 048347           27 MEELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SE  102 (351)
Q Consensus        27 ~~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~  102 (351)
                      ...|-.+|. .+=++-.++.|.|.+|+||||||.++...  ....-..++|++..  ++..     .++.++..... .-
T Consensus        59 ~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~--~~~~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i  131 (366)
T 1xp8_A           59 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQ--AQKAGGTCAFIDAEHALDPV-----YARALGVNTDELLV  131 (366)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEE
T ss_pred             CHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHH--HHHCCCeEEEEECCCChhHH-----HHHHcCCCHHHcee
Confidence            334444443 12133467888999999999999988776  32222357788776  3332     24444432110 00


Q ss_pred             CCCCCHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          103 ILDNDFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                      .+..+.+++.+.+....+. +--+||+|.+-
T Consensus       132 ~~~~~~e~~l~~l~~l~~~~~~~lVVIDsl~  162 (366)
T 1xp8_A          132 SQPDNGEQALEIMELLVRSGAIDVVVVDSVA  162 (366)
T ss_dssp             ECCSSHHHHHHHHHHHHTTTCCSEEEEECTT
T ss_pred             ecCCcHHHHHHHHHHHHhcCCCCEEEEeChH
Confidence            1234566777777666653 34588999884

>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=96.09  E-value=0.026  Score=51.76  Aligned_cols=57  Identities=5%  Similarity=0.018  Sum_probs=37.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccc----CCCeeEEEEEe--CCHHHHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN----YFDCCAWVYYQ--LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~~--~~~~~~~~~i~~~~~~   96 (351)
                      +.-.++.|.|..|+||||||.+++.......    .-..++|++..  ++...+. .++..++.
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~  182 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNV  182 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            4567899999999999999999876522211    12356777766  5665554 34455443

>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=96.08  E-value=0.0047  Score=53.96  Aligned_cols=48  Identities=17%  Similarity=0.120  Sum_probs=34.7

Q ss_pred             CCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|.++..+++.++...-           ..... +.|+|+.|+||||||+.++..
T Consensus        14 ~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g-~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           14 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCCCCHHHHHHHHHHH
Confidence            3356889887777776654321           01123 889999999999999999987

>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=96.08  E-value=0.0032  Score=58.33  Aligned_cols=46  Identities=13%  Similarity=0.037  Sum_probs=36.1

Q ss_pred             ccccchhhHHHHHHHHHc-------------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIE-------------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~-------------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.++.++.+...+..             ......-+.++|+.|+|||++|+.+++.
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~   74 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARL   74 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            479999999998888731             1112345778999999999999999987

>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=96.05  E-value=0.0038  Score=52.52  Aligned_cols=25  Identities=4%  Similarity=0.042  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|+|+|+.|+||||+|+.+...
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999999887

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.03  E-value=0.0037  Score=51.22  Aligned_cols=22  Identities=14%  Similarity=0.247  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+|.|.|+.|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5788999999999999999987

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.02  E-value=0.0023  Score=51.49  Aligned_cols=24  Identities=4%  Similarity=0.069  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -..++|+|..|+|||||++.++..
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~   59 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQ   59 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            458889999999999999999887

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.01  E-value=0.0053  Score=54.62  Aligned_cols=49  Identities=20%  Similarity=0.087  Sum_probs=33.8

Q ss_pred             CCCCccccchhhHHHHHHHHHcc------------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           15 WDNKVDLDLEDKMEELLDLLIER------------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~------------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.=+++.|.++-+++|.+.+...            ..... +.++|+.|+||||||+.++..
T Consensus         7 ~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G-vlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A            7 VTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG-VLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             -----CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE-EEEESSTTSCHHHHHHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe-EEEECCCCCcHHHHHHHHHHH
Confidence            33456888888888887765211            11223 889999999999999999886

>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=96.01  E-value=0.0047  Score=50.57  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.+++|.|+.|+||||+|+.+...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            3578999999999999999998765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=95.99  E-value=0.0055  Score=54.44  Aligned_cols=50  Identities=16%  Similarity=0.098  Sum_probs=36.2

Q ss_pred             CCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           14 SWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        14 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.-++++|.++.++++.++...-           ..... +.|+|+.|+||||||+.++..
T Consensus        36 ~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~~   96 (278)
T 1iy2_A           36 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   96 (278)
T ss_dssp             CCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHHH
Confidence            344456899988877776655321           01123 789999999999999999987

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=95.99  E-value=0.0018  Score=59.81  Aligned_cols=82  Identities=15%  Similarity=0.011  Sum_probs=56.3

Q ss_pred             CCceEEEEecccccCceeee----CCCCC-CcccEEEEecCCcccccccc-cc----cc-CCccEEeecCCcccc-----
Q 048347          242 PHLKVLKLKRSSYSGRKLVC----GHGGF-PRQEILHLKSMLWLEEWKME-TG----AM-QKLKSLIVNPCAYLR-----  305 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~----~~~~l-~~L~~L~L~~~~~l~~lp~~-i~----~L-~~L~~L~l~~c~~l~-----  305 (351)
                      ++|++|+++.+.... ..+.    .+..+ ++|++|++++| .++..+.. ++    .+ .+|++|+|++|. +.     
T Consensus        80 ~~L~~L~Ls~n~l~~-~~~~~l~~~l~~~~~~L~~L~Ls~N-~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~~~~~  156 (362)
T 3goz_A           80 ANVTSLNLSGNFLSY-KSSDELVKTLAAIPFTITVLDLGWN-DFSSKSSSEFKQAFSNLPASITSLNLRGND-LGIKSSD  156 (362)
T ss_dssp             TTCCEEECCSSCGGG-SCHHHHHHHHHTSCTTCCEEECCSS-CGGGSCHHHHHHHHTTSCTTCCEEECTTSC-GGGSCHH
T ss_pred             CCccEEECcCCcCCh-HHHHHHHHHHHhCCCCccEEECcCC-cCCcHHHHHHHHHHHhCCCceeEEEccCCc-CCHHHHH
Confidence            899999995443222 2222    13344 78999999999 56665542 33    32 589999999864 44     


Q ss_pred             ccChhhhcCC-CCCEEEecCCC
Q 048347          306 KFPEELWRIK-ALRKLESWWPR  326 (351)
Q Consensus       306 ~lP~~i~~L~-~L~~L~l~~~~  326 (351)
                      .++..+..+. +|++|+++++.
T Consensus       157 ~l~~~l~~~~~~L~~L~Ls~n~  178 (362)
T 3goz_A          157 ELIQILAAIPANVNSLNLRGNN  178 (362)
T ss_dssp             HHHHHHHTSCTTCCEEECTTSC
T ss_pred             HHHHHHhcCCccccEeeecCCC
Confidence            5666677776 99999999876

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=95.97  E-value=0.0028  Score=51.78  Aligned_cols=23  Identities=9%  Similarity=0.174  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|+|.|+.|+||||+++.+...
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999876

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.97  E-value=0.0039  Score=51.17  Aligned_cols=23  Identities=30%  Similarity=0.592  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      -.+++|+|+.|+|||||++.++.
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHcc
Confidence            46899999999999999997553

>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=95.96  E-value=0.012  Score=54.20  Aligned_cols=99  Identities=15%  Similarity=0.004  Sum_probs=57.5

Q ss_pred             HHHHHHHHH-ccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCcc-
Q 048347           27 MEELLDLLI-ERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALSE-  102 (351)
Q Consensus        27 ~~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~-  102 (351)
                      ...|-.+|. .+=++-.++.|.|..|+||||||.++...  ....=..++|++..  ++..     .++.++....... 
T Consensus        46 ~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~--~~~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i  118 (349)
T 2zr9_A           46 SISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLV  118 (349)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEE
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEE
Confidence            334444443 22234568999999999999999998866  33232356787766  4332     2445543211000 


Q ss_pred             CCCCCHHHHHHHHHHhcCC-ceEEEEEeCCC
Q 048347          103 ILDNDFEMKKNTLHNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       103 ~~~~~~~~~~~~l~~~L~~-k~~LlVLDdv~  132 (351)
                      ....+.++..+.++...+. +.-++|+|.+-
T Consensus       119 ~~~~~~e~~l~~~~~l~~~~~~~lIVIDsl~  149 (349)
T 2zr9_A          119 SQPDTGEQALEIADMLVRSGALDIIVIDSVA  149 (349)
T ss_dssp             ECCSSHHHHHHHHHHHHTTTCCSEEEEECGG
T ss_pred             ecCCCHHHHHHHHHHHHhcCCCCEEEEcChH
Confidence            1233556666655555543 45688999884

>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=95.95  E-value=0.0042  Score=51.62  Aligned_cols=22  Identities=14%  Similarity=0.138  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+++|.|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999975

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=95.95  E-value=0.011  Score=58.13  Aligned_cols=84  Identities=12%  Similarity=-0.096  Sum_probs=52.8

Q ss_pred             CCCCCceEEEEeccccc--CceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCcccc--ccChhhhcC
Q 048347          239 EKLPHLKVLKLKRSSYS--GRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLR--KFPEELWRI  314 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~--~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~--~lP~~i~~L  314 (351)
                      ..+++|+.|.++.....  ....+..+..+++|+.|+++++ ....+|..+..+++|++|++++|. +.  .++..+.++
T Consensus       240 ~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~-~~~~l~~~~~~~~~L~~L~Ls~~~-l~~~~~~~~~~~~  317 (592)
T 3ogk_B          240 KAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYM-GPNEMPILFPFAAQIRKLDLLYAL-LETEDHCTLIQKC  317 (592)
T ss_dssp             HHCTTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTC-CTTTGGGGGGGGGGCCEEEETTCC-CCHHHHHHHHTTC
T ss_pred             hhhhHHHhhcccccccccchHHHHHHhhccccccccCcccc-chhHHHHHHhhcCCCcEEecCCCc-CCHHHHHHHHHhC
Confidence            34566666666211111  0123344566677778877775 466777777788888888888876 32  223345778


Q ss_pred             CCCCEEEecC
Q 048347          315 KALRKLESWW  324 (351)
Q Consensus       315 ~~L~~L~l~~  324 (351)
                      ++|++|++++
T Consensus       318 ~~L~~L~L~~  327 (592)
T 3ogk_B          318 PNLEVLETRN  327 (592)
T ss_dssp             TTCCEEEEEG
T ss_pred             cCCCEEeccC
Confidence            8888888874

>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=95.94  E-value=0.0048  Score=52.09  Aligned_cols=26  Identities=8%  Similarity=0.106  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...+|+|.|+.|+||||+|+.+...
T Consensus        19 ~~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           19 SKTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34679999999999999999999876

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.94  E-value=0.0048  Score=56.18  Aligned_cols=43  Identities=14%  Similarity=0.109  Sum_probs=36.4

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|+++.++.+...+..+.    -+-++|..|+|||+||+.+.+.
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~----~vll~G~pGtGKT~la~~la~~   69 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG----HILLEGVPGLAKTLSVNTLAKT   69 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC----CEEEESCCCHHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHcCC----eEEEECCCCCcHHHHHHHHHHH
Confidence            578999999999888887642    4668999999999999999876

>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=95.92  E-value=0.0066  Score=58.13  Aligned_cols=47  Identities=13%  Similarity=-0.005  Sum_probs=35.4

Q ss_pred             CccccchhhHHHHHHHH---HccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLL---IERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L---~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.++.++.+..++   ..+....+-+-++|+.|+|||++|+.+.+.
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            67899999888665544   333222244668999999999999999988

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.92  E-value=0.0039  Score=52.36  Aligned_cols=23  Identities=17%  Similarity=0.280  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||++.+...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHhh
Confidence            58999999999999999998764

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.92  E-value=0.0038  Score=51.74  Aligned_cols=23  Identities=4%  Similarity=0.172  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|.|+.|+||||+|+.+...
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~   24 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57889999999999999999887

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.92  E-value=0.0039  Score=52.50  Aligned_cols=25  Identities=12%  Similarity=0.165  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.+++|.|+.|+||||+|+.+...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~   52 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADE   52 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999999876

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.91  E-value=0.0046  Score=52.30  Aligned_cols=25  Identities=8%  Similarity=0.077  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|+|.|..|+|||||++.+...
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999999998775

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=95.89  E-value=0.0025  Score=59.43  Aligned_cols=84  Identities=15%  Similarity=0.048  Sum_probs=52.2

Q ss_pred             CCCceEEEEecccccCc---eeeeCC-CCCCcccEEEEecCCcccc-----ccccccccCCccEEeecCCcccc-----c
Q 048347          241 LPHLKVLKLKRSSYSGR---KLVCGH-GGFPRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIVNPCAYLR-----K  306 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~---~lp~~~-~~l~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l~~c~~l~-----~  306 (351)
                      +++|+.|+|+.+.....   .+...+ ...++|++|+|++| .++.     ++..+...++|++|+|++|. +.     .
T Consensus       125 L~~L~~L~Ls~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls~n-~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~-l~~~g~~~  202 (372)
T 3un9_A          125 FLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNN-PLTAAGVAVLMEGLAGNTSVTHLSLLHTG-LGDEGLEL  202 (372)
T ss_dssp             HHTEEEEECCSSCCCHHHHHHHHHHHHSTTCCCCEEECCSS-CCHHHHHHHHHHHHHTCSSCCEEECTTSS-CHHHHHHH
T ss_pred             HHhccHhhcCCCCCCHHHHHHHHHHHHhcCCccceeeCCCC-CCChHHHHHHHHHHhcCCCcCEEeCCCCC-CCcHHHHH
Confidence            45677888843322110   111111 24567888888888 4543     44445677888888888864 43     3


Q ss_pred             cChhhhcCCCCCEEEecCCC
Q 048347          307 FPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       307 lP~~i~~L~~L~~L~l~~~~  326 (351)
                      ++..+.+.++|++|+++++.
T Consensus       203 L~~~L~~~~~L~~L~Ls~N~  222 (372)
T 3un9_A          203 LAAQLDRNRQLQELNVAYNG  222 (372)
T ss_dssp             HHHHGGGCSCCCEEECCSSC
T ss_pred             HHHHHhcCCCcCeEECCCCC
Confidence            45667777888888888875

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.89  E-value=0.028  Score=53.35  Aligned_cols=38  Identities=18%  Similarity=0.197  Sum_probs=28.3

Q ss_pred             HHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++.+++...       ..+.++|.++|.+|+||||+|..+...
T Consensus        79 ~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~~  123 (433)
T 2xxa_A           79 RNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKF  123 (433)
T ss_dssp             HHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45566666432       134689999999999999999888765

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.87  E-value=0.0041  Score=51.41  Aligned_cols=24  Identities=21%  Similarity=0.238  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.|.++|+.|+||||+|+.+...
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~   28 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKL   28 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            357889999999999999999876

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.86  E-value=0.022  Score=51.27  Aligned_cols=38  Identities=13%  Similarity=-0.009  Sum_probs=27.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      ..+++++|.+|+||||++..+...  ....-..+.++...
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~--~~~~g~~v~l~~~D  135 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF--YKKKGFKVGLVGAD  135 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEecC
Confidence            579999999999999999998766  32222234455444

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=95.85  E-value=0.0021  Score=59.86  Aligned_cols=85  Identities=15%  Similarity=0.153  Sum_probs=62.1

Q ss_pred             CCCCceEEEEecccccC---ceeeeCCCCCCcccEEEEecCCcccc-----ccccccccCCccEEeecCCcccc-----c
Q 048347          240 KLPHLKVLKLKRSSYSG---RKLVCGHGGFPRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIVNPCAYLR-----K  306 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~---~~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l~~c~~l~-----~  306 (351)
                      ..++|+.|+|+.+....   ..++..+...++|++|+|++| .++.     ++..+...++|+.|+|++|. +.     .
T Consensus       153 ~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N-~l~~~g~~~L~~~L~~~~~L~~L~Ls~N~-i~~~g~~~  230 (372)
T 3un9_A          153 DQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHT-GLGDEGLELLAAQLDRNRQLQELNVAYNG-AGDTAALA  230 (372)
T ss_dssp             TTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTS-SCHHHHHHHHHHHGGGCSCCCEEECCSSC-CCHHHHHH
T ss_pred             cCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCC-CCCcHHHHHHHHHHhcCCCcCeEECCCCC-CCHHHHHH
Confidence            46789999995443211   224444567888999999999 4653     35556778899999999974 43     4


Q ss_pred             cChhhhcCCCCCEEEecCCC
Q 048347          307 FPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       307 lP~~i~~L~~L~~L~l~~~~  326 (351)
                      ++..+...++|++|++++++
T Consensus       231 l~~~L~~~~~L~~L~Ls~N~  250 (372)
T 3un9_A          231 LARAAREHPSLELLHLYFNE  250 (372)
T ss_dssp             HHHHHHHCSSCCEEECTTSS
T ss_pred             HHHHHHhCCCCCEEeccCCC
Confidence            55667788999999999876

>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=95.83  E-value=0.0055  Score=50.84  Aligned_cols=24  Identities=8%  Similarity=0.084  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999999999876

>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=95.82  E-value=0.0051  Score=51.50  Aligned_cols=26  Identities=8%  Similarity=0.126  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++..+|+|.|+.|+||||+|+.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            35689999999999999999999875

>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=95.82  E-value=0.0048  Score=52.37  Aligned_cols=24  Identities=8%  Similarity=0.181  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+...
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhh
Confidence            468999999999999999999876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.81  E-value=0.0097  Score=54.13  Aligned_cols=26  Identities=4%  Similarity=-0.005  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|..|+||||||+.+..-
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~l  115 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKAL  115 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999998655

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.80  E-value=0.0039  Score=52.24  Aligned_cols=22  Identities=23%  Similarity=0.354  Sum_probs=20.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|+.|+||||+|+.+...
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~   23 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKK   23 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHh
Confidence            6889999999999999999876

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.80  E-value=0.0034  Score=52.82  Aligned_cols=24  Identities=4%  Similarity=0.093  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~   41 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEA   41 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999776

>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=95.78  E-value=0.025  Score=51.28  Aligned_cols=93  Identities=8%  Similarity=0.075  Sum_probs=53.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccc---------CC-----CeeEEEEEe--CCHHHHHHHHHHHhCCCCC---
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKN---------YF-----DCCAWVYYQ--LSLDMMLDAIMKSLMPLSA---   99 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~---------~F-----~~~~wv~~~--~~~~~~~~~i~~~~~~~~~---   99 (351)
                      +.-.++.|.|..|+||||||.+++.......         ..     ..++|++..  ++.+++.+ ++..++....   
T Consensus        96 ~~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~  174 (322)
T 2i1q_A           96 ESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVL  174 (322)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHh
Confidence            3457899999999999999998875422211         11     356677666  55666553 4555543211   


Q ss_pred             --CccCCCCCHH---HHHHHHHHhcC--CceEEEEEeCCC
Q 048347          100 --LSEILDNDFE---MKKNTLHNYLK--NKRYLIVIQDVW  132 (351)
Q Consensus       100 --~~~~~~~~~~---~~~~~l~~~L~--~k~~LlVLDdv~  132 (351)
                        ..-....+.+   ++.+.+.+.++  .+--++|+|.+-
T Consensus       175 ~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          175 DNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             HTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             cCEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence              0001122333   23444555554  345688889884

>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=95.78  E-value=0.011  Score=54.97  Aligned_cols=24  Identities=13%  Similarity=-0.006  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -..++|+|..|+|||||++.+.+.
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~  197 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQS  197 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHH
Confidence            358889999999999999998775

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.77  E-value=0.0052  Score=51.65  Aligned_cols=24  Identities=8%  Similarity=0.171  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+||||+++.+...
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999999776

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.76  E-value=0.0055  Score=55.68  Aligned_cols=26  Identities=8%  Similarity=0.116  Sum_probs=21.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+||+|.|-|||||||.|..+.--
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~a   71 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAA   71 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHH
Confidence            35899999999999999987766544

>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=95.76  E-value=0.0042  Score=51.46  Aligned_cols=23  Identities=17%  Similarity=0.179  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~   26 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDN   26 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999876

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.74  E-value=0.016  Score=52.73  Aligned_cols=39  Identities=10%  Similarity=0.050  Sum_probs=27.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      +..+++|+|.+|+||||++..+...  ....-..+.++...
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~--l~~~g~kVllid~D  142 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANY--YAELGYKVLIAAAD  142 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEeCC
Confidence            4679999999999999999998776  33332234454444

>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=95.74  E-value=0.0059  Score=51.46  Aligned_cols=22  Identities=14%  Similarity=0.214  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+|+|.|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>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=95.72  E-value=0.016  Score=55.28  Aligned_cols=48  Identities=8%  Similarity=0.137  Sum_probs=32.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCC-CeeEEEEEe---CCHHHHHHHHHH
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYF-DCCAWVYYQ---LSLDMMLDAIMK   92 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~~~---~~~~~~~~~i~~   92 (351)
                      .++|+|..|+||||||+.+...  ....+ +.++++-+.   ....+++.++..
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~--~~~~~~~i~V~~~iGerttev~el~~~l~~  204 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHN--IAQEHGGISVFAGVGERTREGNDLYHEMKD  204 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHH--HHHHTCCCEEEEEESSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhh--hhhccCcEEEEeeeccCchHHHHHHHHhhh
Confidence            5889999999999999999887  33333 334454444   445566665543

>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=95.70  E-value=0.0053  Score=50.88  Aligned_cols=22  Identities=14%  Similarity=0.271  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|+|..|+|||||++.+...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999998765

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.69  E-value=0.012  Score=54.14  Aligned_cols=44  Identities=18%  Similarity=0.270  Sum_probs=31.8

Q ss_pred             ccchhhHHHHHHHHHcc--CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           21 LDLEDKMEELLDLLIER--QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        21 vGr~~~~~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+.++-.+++.+.+...  ......|.|+|+.|+||||+|+.++..
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~   47 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQI   47 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHH
Confidence            44555666666666432  234567889999999999999988776

>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=95.68  E-value=0.0095  Score=51.87  Aligned_cols=40  Identities=13%  Similarity=-0.039  Sum_probs=28.3

Q ss_pred             hhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           25 DKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        25 ~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....++.........+..+|+|.|+.|+||||+|+.+.+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           13 DLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             HHHHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3344444443333335678999999999999999999765

>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=95.68  E-value=0.012  Score=54.31  Aligned_cols=38  Identities=18%  Similarity=0.143  Sum_probs=28.5

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++.+.+.....+..+|+|+|.+|+|||||+..+...
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~  102 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMH  102 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            33445555444456789999999999999999998654

>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=95.68  E-value=0.016  Score=53.53  Aligned_cols=86  Identities=13%  Similarity=0.011  Sum_probs=50.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-ccCCCCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SEILDNDFEMKKNTLH  116 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~l~  116 (351)
                      +-+++.|.|.+|+||||||.++...  ....-..++|++..  ++..     .+..++..... .-.+..+.+++.+.++
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~--~~~~g~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~  134 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  134 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHH
Confidence            4468889999999999999998776  33232356787766  4432     24444432110 0012234555555555


Q ss_pred             HhcC-CceEEEEEeCCC
Q 048347          117 NYLK-NKRYLIVIQDVW  132 (351)
Q Consensus       117 ~~L~-~k~~LlVLDdv~  132 (351)
                      ...+ .+--++|+|.+-
T Consensus       135 ~l~~~~~~~lVVIDsl~  151 (356)
T 1u94_A          135 ALARSGAVDVIVVDSVA  151 (356)
T ss_dssp             HHHHHTCCSEEEEECGG
T ss_pred             HHHhccCCCEEEEcCHH
Confidence            4432 344588889873

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.68  E-value=0.007  Score=50.83  Aligned_cols=26  Identities=12%  Similarity=0.174  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|+.|+||||+|+.+...
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35678999999999999999999865

>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=95.67  E-value=0.053  Score=49.03  Aligned_cols=83  Identities=8%  Similarity=0.080  Sum_probs=50.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccC--CCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCc-cCCCCCHHHH-HHHHH
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNY--FDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALS-EILDNDFEMK-KNTLH  116 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~-~~~l~  116 (351)
                      ++-|.|..|+||||||-++...  ....  =..++||+..  ++..     -+++++.+...- -....+.+++ .+.+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~--~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~  102 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSS--YMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVN  102 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH--HHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHH
Confidence            7899999999999999888776  3332  2356787755  4442     366676543210 0123455555 33332


Q ss_pred             Hh--c-CCceEEEEEeCCC
Q 048347          117 NY--L-KNKRYLIVIQDVW  132 (351)
Q Consensus       117 ~~--L-~~k~~LlVLDdv~  132 (351)
                      ..  + +++.-++|+|-+-
T Consensus       103 ~l~~i~~~~~~lvVIDSI~  121 (333)
T 3io5_A          103 QLDAIERGEKVVVFIDSLG  121 (333)
T ss_dssp             HHHTCCTTCCEEEEEECST
T ss_pred             HHHHhhccCceEEEEeccc
Confidence            22  3 4567899999884

>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=95.67  E-value=0.0058  Score=51.40  Aligned_cols=22  Identities=5%  Similarity=0.163  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+|+|.|+.|+||||+|+.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            4799999999999999999976

>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=95.66  E-value=0.0054  Score=50.88  Aligned_cols=25  Identities=16%  Similarity=0.049  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|+|.|+.|+||||+|+.+...
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            4568999999999999999999775

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.66  E-value=0.0097  Score=57.56  Aligned_cols=43  Identities=9%  Similarity=0.030  Sum_probs=36.7

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.++.++.+...+..+.    -|-++|+.|+|||+||+.+.+.
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~----~VLL~GpPGtGKT~LAraLa~~   64 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFA   64 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC----EEEEECCSSSSHHHHHHHGGGG
T ss_pred             hhhHHHHHHHHHHHHHHhcCC----eeEeecCchHHHHHHHHHHHHH
Confidence            568999999988888777653    4668999999999999999987

>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=95.65  E-value=0.0059  Score=50.16  Aligned_cols=25  Identities=4%  Similarity=0.111  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++++|.|..|+|||||+.++...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            4679999999999999999999876

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.65  E-value=0.0045  Score=52.14  Aligned_cols=23  Identities=9%  Similarity=0.287  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+|+.|+|||||++.+...
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~   27 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQE   27 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            57899999999999999998653

>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=95.65  E-value=0.0052  Score=50.62  Aligned_cols=24  Identities=21%  Similarity=0.223  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|.|+.|+||||+|+.+...
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH
Confidence            457889999999999999999866

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.65  E-value=0.0063  Score=53.42  Aligned_cols=23  Identities=13%  Similarity=-0.031  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|.|+.|+||||||+.+...
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhc
Confidence            57899999999999999999876

>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=95.64  E-value=0.008  Score=62.20  Aligned_cols=46  Identities=7%  Similarity=0.150  Sum_probs=36.4

Q ss_pred             ccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.++.++.+...+...       ......+.|+|+.|+|||++|+.+++.
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~  611 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT  611 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            4789999888888877532       112357889999999999999999876

>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=95.62  E-value=0.0042  Score=53.52  Aligned_cols=110  Identities=12%  Similarity=-0.062  Sum_probs=60.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL  119 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L  119 (351)
                      +-.++.|.|..|+||||++..+..+  ...+-..++.+....+.. ....|+++++....  ........++.+.+.+.+
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r--~~~~g~kVli~~~~~d~r-~~~~i~srlG~~~~--~~~~~~~~~i~~~i~~~~   85 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHR--LEYADVKYLVFKPKIDTR-SIRNIQSRTGTSLP--SVEVESAPEILNYIMSNS   85 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHH--HHHTTCCEEEEEECCCGG-GCSSCCCCCCCSSC--CEEESSTHHHHHHHHSTT
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHH--HHhcCCEEEEEEeccCch-HHHHHHHhcCCCcc--ccccCCHHHHHHHHHHHh
Confidence            3578888999999999999888877  333322333333333322 22334444432211  112234456677777666


Q ss_pred             CCceE-EEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Ee
Q 048347          120 KNKRY-LIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-AL  157 (351)
Q Consensus       120 ~~k~~-LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR  157 (351)
                      .+.++ +|++|.+-..  +..+.+.... +.  |..||+ -+
T Consensus        86 ~~~~~dvViIDEaQ~l~~~~ve~l~~L~-~~--gi~Vil~Gl  124 (223)
T 2b8t_A           86 FNDETKVIGIDEVQFFDDRICEVANILA-EN--GFVVIISGL  124 (223)
T ss_dssp             SCTTCCEEEECSGGGSCTHHHHHHHHHH-HT--TCEEEEECC
T ss_pred             hCCCCCEEEEecCccCcHHHHHHHHHHH-hC--CCeEEEEec
Confidence            55544 8999998532  3333333222 21  556665 54

>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=95.62  E-value=0.0033  Score=52.58  Aligned_cols=23  Identities=9%  Similarity=0.287  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|+|++|+|||||++++..+
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            45779999999999999999765

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.62  E-value=0.0076  Score=49.92  Aligned_cols=25  Identities=12%  Similarity=0.021  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|.|.|+.|+||||+|+.+...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999887

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.61  E-value=0.013  Score=49.85  Aligned_cols=39  Identities=13%  Similarity=0.200  Sum_probs=28.7

Q ss_pred             hhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           24 EDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        24 ~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++..+.+...+..  .+..+|.|+|.+|+|||||+.++...
T Consensus        23 ~~~a~~~r~~~~~--~~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           23 KRLADKNRKLLNK--HGVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             HHHHHHHHHHHHH--TTCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3344455555433  35788999999999999999998766

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.60  E-value=0.04  Score=49.91  Aligned_cols=53  Identities=11%  Similarity=0.122  Sum_probs=38.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHh
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSL   94 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~   94 (351)
                      .-.++.|.|.+|+||||||.++..+...++  ..++|++.-.+..++...+....
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE~s~~~l~~R~~~~~  119 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEMGKKENIKRLIVTA  119 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESSSCHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECCCCHHHHHHHHHHHH
Confidence            346888899999999999999876622222  45667665577777777776654

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.60  E-value=0.012  Score=50.04  Aligned_cols=43  Identities=19%  Similarity=0.166  Sum_probs=32.6

Q ss_pred             cccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           20 DLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-+.++..+.+.+.+...  +..+|+|+|.+|+|||||+.++...
T Consensus        11 l~~~~~~~~~~~~~~~~~--~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           11 LAENKRLAEKNREALRES--GTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             CHHHHHHHHHHHHHHHHH--TCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HhhcHHHHHHHHHhhccc--CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            344555666666665433  5789999999999999999998766

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.60  E-value=0.005  Score=51.98  Aligned_cols=24  Identities=8%  Similarity=0.278  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|+|+.|+||||+++.+...
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            467889999999999999999776

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.60  E-value=0.0057  Score=50.90  Aligned_cols=24  Identities=4%  Similarity=0.109  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~   32 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQK   32 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999875

>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=95.59  E-value=0.0095  Score=55.35  Aligned_cols=47  Identities=11%  Similarity=0.043  Sum_probs=36.0

Q ss_pred             CccccchhhHHHHHHHHHc----------------------------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIE----------------------------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~----------------------------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.++-++.+...+..                            ......-+.++|+.|+|||++|+.+++.
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999988877721                            0112345779999999999999999887

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=95.57  E-value=0.016  Score=52.12  Aligned_cols=25  Identities=12%  Similarity=0.036  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+++|+|.+|+||||++..++..
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~  121 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALY  121 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999998876

>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=95.56  E-value=0.0066  Score=51.89  Aligned_cols=23  Identities=9%  Similarity=0.153  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|+|+|+.|+||||+|+.+...
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~   28 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEA   28 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999765

>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=95.56  E-value=0.0075  Score=54.72  Aligned_cols=26  Identities=4%  Similarity=0.095  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|..|+|||||++.+..-
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gl  113 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQAL  113 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhh
Confidence            45689999999999999999998775

>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=95.56  E-value=0.0068  Score=51.30  Aligned_cols=24  Identities=4%  Similarity=0.043  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl   43 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRER   43 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999998654

>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=95.55  E-value=0.0064  Score=52.91  Aligned_cols=24  Identities=13%  Similarity=0.108  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|+|+.|+|||||++.+...
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~   50 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQN   50 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999844

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.54  E-value=0.0066  Score=50.32  Aligned_cols=24  Identities=8%  Similarity=0.057  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999998765

>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=95.54  E-value=0.0062  Score=55.70  Aligned_cols=47  Identities=13%  Similarity=0.058  Sum_probs=33.4

Q ss_pred             CCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .=++++|.+..++.+...+....  ..-+-++|..|+|||++|+.+++.
T Consensus        22 ~f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           22 PFSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             CchhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHHh
Confidence            33568999886665544443322  123778999999999999999876

>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=95.52  E-value=0.0077  Score=53.00  Aligned_cols=24  Identities=13%  Similarity=0.259  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~   27 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKI   27 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            568999999999999999999875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.50  E-value=0.0061  Score=49.57  Aligned_cols=25  Identities=16%  Similarity=0.256  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+|+|.|+.|+||||+|+.+...
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~   30 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLA   30 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999876

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.50  E-value=0.0084  Score=52.19  Aligned_cols=25  Identities=4%  Similarity=0.049  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|+|.|..|+|||||++.+...
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~   48 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMEL   48 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999998764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.49  E-value=0.043  Score=53.01  Aligned_cols=25  Identities=8%  Similarity=0.111  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|.|+|.+|+||||++.++...
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~  124 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYY  124 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999998854

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.47  E-value=0.015  Score=52.12  Aligned_cols=26  Identities=8%  Similarity=0.107  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....+|.|.|+.|+||||+|+.+...
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~~   56 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFEE   56 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34578889999999999999999765

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.46  E-value=0.0084  Score=49.49  Aligned_cols=24  Identities=8%  Similarity=0.007  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+|++.|+.|+||||+|+.+...
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~   27 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQE   27 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999999865

>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=95.46  E-value=0.0089  Score=48.49  Aligned_cols=25  Identities=12%  Similarity=0.210  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.+++++|..|+|||||++.+..-
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g~   56 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            4579999999999999999998765

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=95.45  E-value=0.019  Score=54.92  Aligned_cols=50  Identities=12%  Similarity=0.080  Sum_probs=37.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccc-cCCCeeEEEEEe---CCHHHHHHHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVK-NYFDCCAWVYYQ---LSLDMMLDAIMKS   93 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~~---~~~~~~~~~i~~~   93 (351)
                      ..++|.|..|+|||+|+..+.+.  +. .+-+.++++-+.   -.+.++..++...
T Consensus       166 qr~gIfgg~GvGKT~L~~~l~~~--~a~~~~~v~V~~~iGER~rEv~e~~~~~~~~  219 (498)
T 1fx0_B          166 GKIGLFGGAGVGKTVLIMELINN--IAKAHGGVSVFGGVGERTREGNDLYMEMKES  219 (498)
T ss_dssp             CCEEEEECSSSSHHHHHHHHHHH--TTTTCSSCEEEEEESCCSHHHHHHHHHHHHT
T ss_pred             CeEEeecCCCCCchHHHHHHHHH--HHhhCCCEEEEEEcccCcHHHHHHHHhhhcc
Confidence            46888999999999999988776  32 334667777666   5667777777654

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.44  E-value=0.0079  Score=50.64  Aligned_cols=24  Identities=13%  Similarity=-0.047  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            368899999999999999999886

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.42  E-value=0.0061  Score=52.19  Aligned_cols=24  Identities=17%  Similarity=0.281  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+...
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            358999999999999999998764

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.40  E-value=0.0063  Score=49.89  Aligned_cols=23  Identities=13%  Similarity=0.209  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|.|+.|+||||+|+.+...
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            36889999999999999999876

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.38  E-value=0.0069  Score=50.51  Aligned_cols=23  Identities=13%  Similarity=0.144  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|+|.|+.|+||||+|+.+...
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999876

>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=95.35  E-value=0.0083  Score=50.56  Aligned_cols=25  Identities=12%  Similarity=0.202  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-++++|+|+.|+|||||++.+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhh
Confidence            4578999999999999999998765

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.34  E-value=0.0086  Score=52.46  Aligned_cols=24  Identities=8%  Similarity=0.126  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+|+|.|+.|+||||+++.+...
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~   50 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAES   50 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999865

>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=95.33  E-value=0.011  Score=49.68  Aligned_cols=26  Identities=8%  Similarity=0.166  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....+|+|.|+.|+||||+|+.+...
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHHh
Confidence            35789999999999999999999775

>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=95.33  E-value=0.0099  Score=49.14  Aligned_cols=24  Identities=8%  Similarity=0.095  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~   29 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999875

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.32  E-value=0.016  Score=52.33  Aligned_cols=39  Identities=10%  Similarity=0.254  Sum_probs=28.1

Q ss_pred             hHHHHHHHHHccCC-CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           26 KMEELLDLLIERQP-QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        26 ~~~~l~~~L~~~~~-~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+.+.+++....+ ...-+.++|..|+|||+||..+++.
T Consensus       136 ~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          136 AFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             HHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHH
Confidence            34455566654221 2356779999999999999999987

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.31  E-value=0.0076  Score=49.97  Aligned_cols=22  Identities=23%  Similarity=0.249  Sum_probs=20.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~   23 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEY   23 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999999886

>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=95.30  E-value=0.02  Score=51.68  Aligned_cols=26  Identities=4%  Similarity=0.011  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|..|+|||||++.+...
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~  103 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQAL  103 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999999998775

>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=95.29  E-value=0.0063  Score=49.53  Aligned_cols=23  Identities=13%  Similarity=0.101  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|.|+.|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~   25 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARA   25 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.28  E-value=0.0085  Score=48.54  Aligned_cols=22  Identities=14%  Similarity=0.009  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRS   23 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999876

>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=95.26  E-value=0.0068  Score=50.02  Aligned_cols=22  Identities=5%  Similarity=0.055  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|.|.|+.|+||||+|+.+...
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~   25 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKA   25 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999876

>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=95.26  E-value=0.011  Score=52.69  Aligned_cols=23  Identities=9%  Similarity=0.148  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHh
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      +..+|+|.|+.|+||||+|+.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            46799999999999999999998

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.24  E-value=0.0068  Score=49.84  Aligned_cols=24  Identities=13%  Similarity=0.108  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~   28 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHER   28 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHh
Confidence            458899999999999999999765

>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=95.24  E-value=0.009  Score=50.46  Aligned_cols=24  Identities=4%  Similarity=-0.022  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~   32 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEA   32 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999877

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.23  E-value=0.015  Score=55.41  Aligned_cols=50  Identities=16%  Similarity=0.173  Sum_probs=36.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccc-ccCCCeeEEEEEe---CCHHHHHHHHHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYV-KNYFDCCAWVYYQ---LSLDMMLDAIMKS   93 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~-~~~F~~~~wv~~~---~~~~~~~~~i~~~   93 (351)
                      ..++|.|..|+|||+|+..+.+.  + +.+-+.++++-+.   -.+.++.+++...
T Consensus       154 Qr~~Ifgg~G~GKT~L~~~i~~~--~~~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          154 GKIGLFGGAGVGKTVLIMELINN--VAKAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH--TTTTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             CeeeeecCCCCChHHHHHHHHHh--hHhhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            57889999999999999998776  3 2233556665555   6667777777654

>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=95.21  E-value=0.012  Score=48.32  Aligned_cols=25  Identities=12%  Similarity=-0.059  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|+|.|+.|+||||+++.+...
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~   28 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEY   28 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3468899999999999999999875

>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=95.19  E-value=0.01  Score=49.75  Aligned_cols=24  Identities=13%  Similarity=-0.056  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHT
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH
Confidence            357899999999999999999887

>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=95.19  E-value=0.01  Score=50.92  Aligned_cols=25  Identities=16%  Similarity=0.234  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|+.|+|||||++.+...
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc
Confidence            3468999999999999999998765

>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=95.18  E-value=0.011  Score=50.34  Aligned_cols=24  Identities=8%  Similarity=0.155  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .-.+++|+|..|+|||||++.+..
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g   47 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAV   47 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999975

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.16  E-value=0.054  Score=49.54  Aligned_cols=65  Identities=17%  Similarity=0.050  Sum_probs=41.6

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHh
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSL   94 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~   94 (351)
                      ...|-.++ .+=..-.++.|.|.+|+||||||..++.+  ....=..++|++.-.+..++...++...
T Consensus        33 ~~~LD~~~-gGl~~G~LiiIaG~pG~GKTt~al~ia~~--~a~~g~~Vl~fSlEms~~ql~~Rlls~~   97 (338)
T 4a1f_A           33 FVQLDNYT-SGFNKGSLVIIGARPSMGKTSLMMNMVLS--ALNDDRGVAVFSLEMSAEQLALRALSDL   97 (338)
T ss_dssp             CHHHHHHH-CSBCTTCEEEEEECTTSCHHHHHHHHHHH--HHHTTCEEEEEESSSCHHHHHHHHHHHH
T ss_pred             ChHHHHHh-cCCCCCcEEEEEeCCCCCHHHHHHHHHHH--HHHcCCeEEEEeCCCCHHHHHHHHHHHh
Confidence            44444444 23233468888999999999999998877  3222234566554466777777765543

>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=95.16  E-value=0.012  Score=49.35  Aligned_cols=25  Identities=8%  Similarity=-0.011  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+|.|.|+.|+||||+|+.+...
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~   43 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEK   43 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3458899999999999999999876

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.15  E-value=0.01  Score=50.95  Aligned_cols=24  Identities=13%  Similarity=0.106  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999999875

>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=95.15  E-value=0.0094  Score=50.82  Aligned_cols=24  Identities=8%  Similarity=0.009  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|.|.|+.|+||||+|+.+...
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~   27 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQER   27 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            457889999999999999999876

>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=95.13  E-value=0.0052  Score=51.95  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|+.|+||||+|+.+...
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~   23 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGA   23 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            6899999999999999999766

>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=95.13  E-value=0.013  Score=49.83  Aligned_cols=23  Identities=13%  Similarity=0.209  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999965

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=95.12  E-value=0.019  Score=48.80  Aligned_cols=23  Identities=13%  Similarity=0.049  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||++.+..-
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998653

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.11  E-value=0.0084  Score=53.81  Aligned_cols=25  Identities=8%  Similarity=0.046  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+.+.++|+.|+|||+||+.+++.
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~   59 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRK   59 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3457778999999999999999988

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=95.10  E-value=0.015  Score=48.31  Aligned_cols=58  Identities=14%  Similarity=0.108  Sum_probs=27.0

Q ss_pred             CcccEEEEecCCcccc-----ccccccccCCccEEee--cCCccccc-----cChhhhcCCCCCEEEecCCC
Q 048347          267 PRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIV--NPCAYLRK-----FPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       267 ~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l--~~c~~l~~-----lP~~i~~L~~L~~L~l~~~~  326 (351)
                      ++|++|+|++| .++.     +...+...++|++|+|  ++| .+..     +.+.+...++|++|+++++.
T Consensus        93 ~~L~~L~L~~N-~i~~~g~~~l~~~L~~n~~L~~L~L~~~~N-~i~~~g~~~l~~~L~~n~~L~~L~L~~n~  162 (185)
T 1io0_A           93 NTLKSLNVESN-FISGSGILALVEALQSNTSLIELRIDNQSQ-PLGNNVEMEIANMLEKNTTLLKFGYHFTQ  162 (185)
T ss_dssp             SSCCEEECCSS-CCCHHHHHHHHHGGGGCSSCCEEECCCCSS-CCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             CCcCEEECcCC-cCCHHHHHHHHHHHHhCCCceEEEecCCCC-CCCHHHHHHHHHHHHhCCCcCEEeccCCC
Confidence            44555555555 3332     2333444455555555  432 2221     33334444555555555554

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.09  E-value=0.0072  Score=49.74  Aligned_cols=23  Identities=17%  Similarity=0.245  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+|..|+|||||++.+..-
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~   25 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPI   25 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998766

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.09  E-value=0.0096  Score=50.21  Aligned_cols=24  Identities=0%  Similarity=-0.212  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~   33 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEY   33 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999999876

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.07  E-value=0.019  Score=50.14  Aligned_cols=26  Identities=12%  Similarity=0.001  Sum_probs=22.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...+|.+.|+.|+||||+|+.+...
T Consensus        30 ~~~~~i~l~G~~GsGKSTla~~L~~~   55 (253)
T 2p5t_B           30 KQPIAILLGGQSGAGKTTIHRIKQKE   55 (253)
T ss_dssp             SSCEEEEEESCGGGTTHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34578999999999999999999776

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=95.06  E-value=0.012  Score=51.33  Aligned_cols=25  Identities=8%  Similarity=0.218  Sum_probs=21.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +. .+++|+|+.|+|||||.+.+.--
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl   47 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCC
Confidence            45 79999999999999999998654

>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=95.03  E-value=0.015  Score=49.26  Aligned_cols=25  Identities=4%  Similarity=-0.072  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.+|.|.|+.|+||||+|+.+...
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999876

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.02  E-value=0.0077  Score=51.83  Aligned_cols=24  Identities=8%  Similarity=0.167  Sum_probs=16.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHh-CC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAY-NS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~-~~   64 (351)
                      -.+++|+|+.|+|||||++.+. ..
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC--
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcC
Confidence            3689999999999999999998 54

>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=94.96  E-value=0.013  Score=50.79  Aligned_cols=24  Identities=13%  Similarity=0.137  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999999654

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=94.96  E-value=0.0097  Score=50.83  Aligned_cols=24  Identities=8%  Similarity=-0.176  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|.|.|+.|+||||+|+.+...
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            457889999999999999999876

>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=94.95  E-value=0.013  Score=52.99  Aligned_cols=25  Identities=16%  Similarity=0.193  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|++|+||||+++.+..-
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagl  125 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRY  125 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            3569999999999999999998754

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.94  E-value=0.013  Score=50.38  Aligned_cols=23  Identities=17%  Similarity=0.154  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999654

>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=94.93  E-value=0.016  Score=50.58  Aligned_cols=26  Identities=23%  Similarity=0.253  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..++.+.|.||+||||++..+...
T Consensus        12 ~~~~i~~~~GkgGvGKTTl~~~La~~   37 (262)
T 1yrb_A           12 MASMIVVFVGTAGSGKTTLTGEFGRY   37 (262)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            46788899999999999999999754

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=94.90  E-value=0.015  Score=49.80  Aligned_cols=26  Identities=4%  Similarity=0.093  Sum_probs=23.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.++|.|.|++|+||+|.|+.+..+
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            56789999999999999999999877

>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=94.88  E-value=0.012  Score=55.79  Aligned_cols=48  Identities=13%  Similarity=0.106  Sum_probs=36.5

Q ss_pred             CCccccchhhHHHHHHHHHcc------------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER------------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~------------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+++|.++-++.+...+...            ....+-+.++|+.|+||||+|+.+...
T Consensus        14 d~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~   73 (444)
T 1g41_A           14 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (444)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            356899999888887776321            112344778999999999999999877

>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=94.88  E-value=0.1  Score=50.40  Aligned_cols=54  Identities=6%  Similarity=0.001  Sum_probs=37.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      .-.++.|.|.+|+||||||.++..+  .... =..++|++...+..++...++....
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~--~a~~~g~~vl~~s~E~s~~~l~~r~~~~~~  295 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQ--WGTAMGKKVGLAMLEESVEETAEDLIGLHN  295 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHH--HTTTSCCCEEEEESSSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHH--HHHhcCCcEEEEeccCCHHHHHHHHHHHHc
Confidence            3467888999999999999998776  3322 2345666555667777777665543

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.85  E-value=0.012  Score=49.22  Aligned_cols=22  Identities=23%  Similarity=0.274  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++|+|..|+|||||++.+...
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhh
Confidence            6889999999999999998765

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.83  E-value=0.017  Score=52.11  Aligned_cols=25  Identities=16%  Similarity=0.298  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|..|+||||+++.+...
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~  123 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHR  123 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            3579999999999999999998765

>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=94.81  E-value=0.016  Score=47.86  Aligned_cols=24  Identities=17%  Similarity=0.278  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+++|.|..|+|||||++.+...
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHh
Confidence            578999999999999999999876

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=94.81  E-value=0.014  Score=49.53  Aligned_cols=22  Identities=5%  Similarity=0.086  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999766

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=94.77  E-value=0.046  Score=51.61  Aligned_cols=25  Identities=12%  Similarity=0.036  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+++|+|.+|+||||++..+...
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999998766

>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=94.77  E-value=0.015  Score=51.64  Aligned_cols=23  Identities=13%  Similarity=0.254  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||++.+.--
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            58999999999999999998653

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.74  E-value=0.016  Score=51.17  Aligned_cols=24  Identities=17%  Similarity=0.243  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999654

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=94.73  E-value=0.057  Score=48.84  Aligned_cols=77  Identities=12%  Similarity=0.046  Sum_probs=38.7

Q ss_pred             CCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCcc-EEeecCCccccccCh-hhhcCCC
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLK-SLIVNPCAYLRKFPE-ELWRIKA  316 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~-~L~l~~c~~l~~lP~-~i~~L~~  316 (351)
                      +++|+.++++  ...+..+|.. +.++.+|+.+++.++  +..++.. +..+.+|+ .+++.+  .+..+++ ...++++
T Consensus       225 ~~~L~~l~L~--~n~i~~I~~~aF~~~~~L~~l~l~~n--i~~I~~~aF~~~~~L~~~l~l~~--~l~~I~~~aF~~c~~  298 (329)
T 3sb4_A          225 MPNLVSLDIS--KTNATTIPDFTFAQKKYLLKIKLPHN--LKTIGQRVFSNCGRLAGTLELPA--SVTAIEFGAFMGCDN  298 (329)
T ss_dssp             CTTCCEEECT--TBCCCEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCEEEEECT--TCCEECTTTTTTCTT
T ss_pred             cCCCeEEECC--CCCcceecHhhhhCCCCCCEEECCcc--cceehHHHhhCChhccEEEEEcc--cceEEchhhhhCCcc
Confidence            4555555551  1123344442 445555666655553  5555543 45555565 555554  3444443 3345555


Q ss_pred             CCEEEec
Q 048347          317 LRKLESW  323 (351)
Q Consensus       317 L~~L~l~  323 (351)
                      |+.+++.
T Consensus       299 L~~l~l~  305 (329)
T 3sb4_A          299 LRYVLAT  305 (329)
T ss_dssp             EEEEEEC
T ss_pred             CCEEEeC
Confidence            6555553

>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=94.71  E-value=0.017  Score=50.20  Aligned_cols=24  Identities=17%  Similarity=0.411  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+..-
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999776

>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=94.71  E-value=0.071  Score=49.96  Aligned_cols=56  Identities=7%  Similarity=0.014  Sum_probs=34.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccc----CCCeeEEEEEe--CCHHHHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKN----YFDCCAWVYYQ--LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~~--~~~~~~~~~i~~~~~~   96 (351)
                      .-.++.|.|..|+|||||+..++-......    .-..++|++..  +.... ++.+++.++.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~r-l~~~a~~~gl  238 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVR-LVSIAQRFGL  238 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHH-HHHHHHHTTC
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHH-HHHHHHHcCC
Confidence            346899999999999999997652211111    22346777655  44443 3446666554

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.71  E-value=0.013  Score=51.44  Aligned_cols=23  Identities=17%  Similarity=0.117  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|+|+|+.|+||||+++.+...
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~   71 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARS   71 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999875

>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=94.69  E-value=0.017  Score=50.25  Aligned_cols=23  Identities=17%  Similarity=0.274  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||.+.++--
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999664

>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=94.68  E-value=0.016  Score=51.16  Aligned_cols=24  Identities=21%  Similarity=0.224  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999999764

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.67  E-value=0.013  Score=49.98  Aligned_cols=24  Identities=8%  Similarity=-0.045  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|.|.|+.|+||||+|+.+...
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~   28 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKE   28 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            357889999999999999999876

>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=94.66  E-value=0.017  Score=50.75  Aligned_cols=24  Identities=17%  Similarity=0.152  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999654

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.65  E-value=0.018  Score=52.61  Aligned_cols=23  Identities=17%  Similarity=0.179  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|+|.|+.|+||||||+.+...
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~   30 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKK   30 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHHH
Confidence            58999999999999999999876

>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=94.64  E-value=0.019  Score=49.99  Aligned_cols=24  Identities=13%  Similarity=0.086  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||.+.+..-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999998653

>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=94.63  E-value=0.018  Score=48.75  Aligned_cols=22  Identities=5%  Similarity=-0.016  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999765

>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=94.61  E-value=0.019  Score=48.15  Aligned_cols=22  Identities=9%  Similarity=0.098  Sum_probs=20.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +|+|.|+.|+||||+|+.+...
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~   25 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAA   25 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            8999999999999999999775

>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=94.60  E-value=0.036  Score=49.47  Aligned_cols=53  Identities=6%  Similarity=0.102  Sum_probs=34.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCC-eeEEEEEeCCHHHHHHHHHHHh
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD-CCAWVYYQLSLDMMLDAIMKSL   94 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~i~~~~   94 (351)
                      .-.+++|.|..|+|||||++.+...  ...... .++|++......++.+.+....
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~--~~~~~G~~v~~~~~e~~~~~~~~r~~~~~   87 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQ--WGTAMGKKVGLAMLEESVEETAEDLIGLH   87 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHH--HHHTSCCCEEEEESSSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHHHcCCeEEEEeCcCCHHHHHHHHHHHH
Confidence            3468999999999999999998877  332222 3455543344555555555544

>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=94.60  E-value=0.018  Score=50.83  Aligned_cols=24  Identities=17%  Similarity=0.194  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+.--
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcC
Confidence            368999999999999999998654

>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=94.59  E-value=0.018  Score=49.60  Aligned_cols=23  Identities=17%  Similarity=0.310  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999876

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.58  E-value=0.024  Score=51.79  Aligned_cols=24  Identities=8%  Similarity=0.158  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|+|+.|+||||||..+...
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999999987

>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=94.57  E-value=0.033  Score=53.52  Aligned_cols=25  Identities=16%  Similarity=0.284  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|..|+|||||++.+...
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgl  316 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQ  316 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHH
Confidence            4579999999999999999998765

>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=94.57  E-value=0.019  Score=50.26  Aligned_cols=23  Identities=9%  Similarity=0.091  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||++.+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999873

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=94.55  E-value=0.093  Score=47.42  Aligned_cols=81  Identities=10%  Similarity=0.022  Sum_probs=64.5

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeC-CCCCCccc-EEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-h
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQE-ILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-L  311 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~-~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i  311 (351)
                      ..+..+++|+.+.+. +.  +..++.. +.++.+|+ .+.+..  .+..++.. +..+.+|+.+++.+ ..+..++.. +
T Consensus       244 ~aF~~~~~L~~l~l~-~n--i~~I~~~aF~~~~~L~~~l~l~~--~l~~I~~~aF~~c~~L~~l~l~~-n~i~~I~~~aF  317 (329)
T 3sb4_A          244 FTFAQKKYLLKIKLP-HN--LKTIGQRVFSNCGRLAGTLELPA--SVTAIEFGAFMGCDNLRYVLATG-DKITTLGDELF  317 (329)
T ss_dssp             TTTTTCTTCCEEECC-TT--CCEECTTTTTTCTTCCEEEEECT--TCCEECTTTTTTCTTEEEEEECS-SCCCEECTTTT
T ss_pred             hhhhCCCCCCEEECC-cc--cceehHHHhhCChhccEEEEEcc--cceEEchhhhhCCccCCEEEeCC-CccCccchhhh
Confidence            346788999999994 32  6677654 77888999 999987  58888754 88999999999987 578888874 5


Q ss_pred             hcCCCCCEEEe
Q 048347          312 WRIKALRKLES  322 (351)
Q Consensus       312 ~~L~~L~~L~l  322 (351)
                      .++++|+.++.
T Consensus       318 ~~~~~L~~ly~  328 (329)
T 3sb4_A          318 GNGVPSKLIYK  328 (329)
T ss_dssp             CTTCCCCEEEC
T ss_pred             cCCcchhhhcc
Confidence            68899998864

>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=94.55  E-value=0.019  Score=50.16  Aligned_cols=23  Identities=9%  Similarity=0.182  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||++.+..-
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999665

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.55  E-value=0.027  Score=47.64  Aligned_cols=37  Identities=11%  Similarity=0.091  Sum_probs=26.6

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+..++..- ++..-+.|+|++|+||||+|..+++.
T Consensus        45 ~~~l~~~~~~i-Pkkn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           45 LGALKSFLKGT-PKKNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             HHHHHHHHHTC-TTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-CcccEEEEECCCCCCHHHHHHHHHHH
Confidence            45555555432 23345789999999999999888776

>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=94.54  E-value=0.016  Score=49.53  Aligned_cols=23  Identities=13%  Similarity=0.228  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            57899999999999999999765

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.53  E-value=0.043  Score=54.37  Aligned_cols=43  Identities=12%  Similarity=0.073  Sum_probs=35.8

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|.+.-++.+...+..+    ..+.|+|+.|+||||||+.+...
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~   83 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAEL   83 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHT
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhcc
Confidence            34789888888877777654    37889999999999999999887

>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=94.53  E-value=0.035  Score=51.64  Aligned_cols=26  Identities=8%  Similarity=0.093  Sum_probs=22.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-.+++|+|+.|+|||||++.+...
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~  192 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLEL  192 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            44579999999999999999999864

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=94.52  E-value=0.019  Score=52.19  Aligned_cols=25  Identities=12%  Similarity=0.332  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+++|.|+.|+|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            5789999999999999999999855

>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=94.52  E-value=0.019  Score=50.42  Aligned_cols=24  Identities=13%  Similarity=0.097  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.++--
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999764

>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=94.51  E-value=0.019  Score=50.73  Aligned_cols=24  Identities=13%  Similarity=0.122  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.++.-
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999874

>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=94.50  E-value=0.017  Score=49.71  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=22.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++-.+|+|.|+.|+||||+++.+...
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc
Confidence            34579999999999999999998765

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=94.48  E-value=0.016  Score=53.72  Aligned_cols=83  Identities=18%  Similarity=0.119  Sum_probs=53.6

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccc-ccccccc--ccCCccEEeecCCcc-------ccccC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLE-EWKMETG--AMQKLKSLIVNPCAY-------LRKFP  308 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~-~lp~~i~--~L~~L~~L~l~~c~~-------l~~lP  308 (351)
                      ..+|+|+.|.++ ++... .++. + .+++|+.|+|..|. +. +-...++  .+++|+.|+|..+..       +..+-
T Consensus       169 ~~~P~L~~L~L~-g~~~l-~l~~-~-~~~~L~~L~L~~~~-l~~~~l~~l~~~~lp~L~~L~L~~~~~~~~~~~~~~~l~  243 (362)
T 2ra8_A          169 DAMPLLNNLKIK-GTNNL-SIGK-K-PRPNLKSLEIISGG-LPDSVVEDILGSDLPNLEKLVLYVGVEDYGFDGDMNVFR  243 (362)
T ss_dssp             HTCTTCCEEEEE-CCBTC-BCCS-C-BCTTCSEEEEECSB-CCHHHHHHHHHSBCTTCCEEEEECBCGGGTCCSCGGGTG
T ss_pred             hcCCCCcEEEEe-CCCCc-eecc-c-cCCCCcEEEEecCC-CChHHHHHHHHccCCCCcEEEEeccccccccchhHHHHH
Confidence            567999999994 43222 3443 3 37899999999874 43 2222333  789999999863211       22222


Q ss_pred             hhh--hcCCCCCEEEecCCC
Q 048347          309 EEL--WRIKALRKLESWWPR  326 (351)
Q Consensus       309 ~~i--~~L~~L~~L~l~~~~  326 (351)
                      ..+  +.+++|++|+++++.
T Consensus       244 ~~l~~~~~p~Lr~L~L~~~~  263 (362)
T 2ra8_A          244 PLFSKDRFPNLKWLGIVDAE  263 (362)
T ss_dssp             GGSCTTTCTTCCEEEEESCT
T ss_pred             HHHhcCCCCCcCEEeCCCCC
Confidence            222  357899999998876

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.48  E-value=0.03  Score=57.08  Aligned_cols=47  Identities=6%  Similarity=0.119  Sum_probs=37.5

Q ss_pred             CccccchhhHHHHHHHHHccC-------CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQ-------PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~-------~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.++.++.+...+....       .....+-++|+.|+|||++|+.+++.
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~  544 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAES  544 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999988888886421       22346889999999999999999887

>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=94.48  E-value=0.029  Score=45.19  Aligned_cols=23  Identities=9%  Similarity=0.163  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|+|+|.+|+|||||.+.+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            56889999999999999999875

>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=94.47  E-value=0.043  Score=50.26  Aligned_cols=35  Identities=17%  Similarity=0.175  Sum_probs=26.1

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..-+.....+..+|+|+|.+|+|||||+..+...
T Consensus        45 ~~~~l~~~~~~~~~i~i~G~~g~GKSTl~~~l~~~   79 (341)
T 2p67_A           45 LLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGML   79 (341)
T ss_dssp             HHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HHHhCCcccCCCEEEEEEcCCCCCHHHHHHHHHHH
Confidence            33333333356789999999999999999998643

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.46  E-value=0.023  Score=45.15  Aligned_cols=23  Identities=9%  Similarity=0.222  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|.|+|.+|+|||||++++...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999766

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.45  E-value=0.021  Score=50.34  Aligned_cols=24  Identities=13%  Similarity=0.174  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+..-
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            358999999999999999999765

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.43  E-value=0.0099  Score=53.31  Aligned_cols=25  Identities=4%  Similarity=0.086  Sum_probs=19.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|+|.|..|+||||+|+.+...
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~   28 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQI   28 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999999775

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.40  E-value=0.021  Score=50.58  Aligned_cols=24  Identities=13%  Similarity=0.117  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.++.-
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999764

>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=94.39  E-value=0.022  Score=49.89  Aligned_cols=23  Identities=4%  Similarity=0.276  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl   49 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGM   49 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999999765

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.38  E-value=0.022  Score=50.38  Aligned_cols=24  Identities=4%  Similarity=0.047  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||.+.++--
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            358999999999999999998764

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=94.38  E-value=0.018  Score=54.62  Aligned_cols=88  Identities=7%  Similarity=0.105  Sum_probs=50.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCC----eeEEEEEe---CCHHHHHHHHHHHhCCCCC--CccCCCCCHH-HH-
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFD----CCAWVYYQ---LSLDMMLDAIMKSLMPLSA--LSEILDNDFE-MK-  111 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~----~~~wv~~~---~~~~~~~~~i~~~~~~~~~--~~~~~~~~~~-~~-  111 (351)
                      .++|.|..|+|||+|+.++.+..  ..+-+    .++++-+.   -.+.++..++...=..+..  .....+.+.. .. 
T Consensus       153 r~~Ifgg~G~GKt~L~~~Ia~~~--~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~  230 (465)
T 3vr4_D          153 KLPVFSGSGLPHKELAAQIARQA--TVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIA  230 (465)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHC--BCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHH
T ss_pred             EEEEeCCCCcChHHHHHHHHHHH--HhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHH
Confidence            46788999999999999998873  33222    34455555   6666777776543100000  0000111111 11 


Q ss_pred             ----HHHHHHhcC---CceEEEEEeCCC
Q 048347          112 ----KNTLHNYLK---NKRYLIVIQDVW  132 (351)
Q Consensus       112 ----~~~l~~~L~---~k~~LlVLDdv~  132 (351)
                          .-.+.++++   ++..|+++||+-
T Consensus       231 a~~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          231 TPRMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence                123344443   789999999994

>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=94.38  E-value=0.032  Score=45.69  Aligned_cols=26  Identities=8%  Similarity=0.084  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++...|+|+|.+|+|||||.+++...
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhcC
Confidence            34567889999999999999999876

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=94.33  E-value=0.036  Score=47.67  Aligned_cols=47  Identities=11%  Similarity=-0.035  Sum_probs=30.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHH
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDA   89 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~   89 (351)
                      -.++.|.|..|+||||||.++...  ....=..++|++......++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~--~~~~~~~v~~~~~e~~~~~~~~~   69 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWN--GLKMGEPGIYVALEEHPVQVRQN   69 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEESSSCHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEccCCHHHHHHH
Confidence            468899999999999999888655  22222345666544444444443

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.33  E-value=0.025  Score=52.23  Aligned_cols=25  Identities=16%  Similarity=0.298  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+++|+|..|+||||+++.++..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~  180 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHR  180 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhh
Confidence            3579999999999999999998765

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.33  E-value=0.022  Score=50.70  Aligned_cols=23  Identities=9%  Similarity=0.026  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||.+.+..-
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl   70 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAY   70 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999999764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=94.32  E-value=0.022  Score=49.92  Aligned_cols=23  Identities=9%  Similarity=0.313  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||.+.+..-
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999765

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.31  E-value=0.032  Score=45.72  Aligned_cols=25  Identities=8%  Similarity=0.142  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|+|+|..|+|||||.+.+...
T Consensus         6 ~~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            6 KSYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467889999999999999999875

>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=94.30  E-value=0.021  Score=48.40  Aligned_cols=22  Identities=0%  Similarity=-0.112  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEK   23 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999876

>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=94.28  E-value=0.026  Score=46.77  Aligned_cols=25  Identities=16%  Similarity=0.264  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..-.|+|+|..|+|||||.+.+...
T Consensus        28 ~~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           28 YLFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHhcC
Confidence            3567899999999999999999765

>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=94.28  E-value=0.022  Score=49.06  Aligned_cols=24  Identities=4%  Similarity=-0.038  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|.|.|+.|+||||+|+.+...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            457889999999999999999877

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=94.27  E-value=0.016  Score=48.12  Aligned_cols=86  Identities=14%  Similarity=0.053  Sum_probs=60.6

Q ss_pred             CCCCCCceEEEEeccc-ccC----ceeeeCCCCCCcccEEEEecCCcccc-----ccccccccCCccEEeecCCccccc-
Q 048347          238 PEKLPHLKVLKLKRSS-YSG----RKLVCGHGGFPRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIVNPCAYLRK-  306 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~-~~~----~~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l~~c~~l~~-  306 (351)
                      +...+.|+.|+|+ ++ ...    ..+...+...++|++|+|++| .++.     +...+...++|++|+|++| .+.. 
T Consensus        32 l~~~~~L~~L~L~-~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n-~i~~~g~~~l~~~L~~n~~L~~L~L~~N-~i~~~  108 (185)
T 1io0_A           32 QNNDPDLEEVNLN-NIMNIPVPTLKACAEALKTNTYVKKFSIVGT-RSNDPVAFALAEMLKVNNTLKSLNVESN-FISGS  108 (185)
T ss_dssp             HTTCTTCCEEECT-TCTTCCHHHHHHHHHHHTTCCSCCEEECTTS-CCCHHHHHHHHHHHHHCSSCCEEECCSS-CCCHH
T ss_pred             HhcCCCCCEEEec-CCCCCCHHHHHHHHHHHHhCCCcCEEECcCC-CCChHHHHHHHHHHHhCCCcCEEECcCC-cCCHH
Confidence            3467899999994 43 222    123444566788999999999 4543     3334555689999999986 3443 


Q ss_pred             ----cChhhhcCCCCCEEEe--cCCC
Q 048347          307 ----FPEELWRIKALRKLES--WWPR  326 (351)
Q Consensus       307 ----lP~~i~~L~~L~~L~l--~~~~  326 (351)
                          +...+.+.++|++|++  ++..
T Consensus       109 g~~~l~~~L~~n~~L~~L~L~~~~N~  134 (185)
T 1io0_A          109 GILALVEALQSNTSLIELRIDNQSQP  134 (185)
T ss_dssp             HHHHHHHGGGGCSSCCEEECCCCSSC
T ss_pred             HHHHHHHHHHhCCCceEEEecCCCCC
Confidence                5667788899999999  5544

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.25  E-value=0.022  Score=48.80  Aligned_cols=22  Identities=9%  Similarity=-0.015  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~   23 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDK   23 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999876

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.24  E-value=0.18  Score=47.79  Aligned_cols=55  Identities=15%  Similarity=-0.060  Sum_probs=38.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccC-CCeeEEEEEeCCHHHHHHHHHHHhC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-FDCCAWVYYQLSLDMMLDAIMKSLM   95 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~~~~~~~~~~~i~~~~~   95 (351)
                      ++-.++.|.|.+|+||||||..++..  +... =..++|++...+..++...++....
T Consensus       198 ~~G~l~ii~G~pg~GKT~lal~ia~~--~a~~~g~~vl~~slE~~~~~l~~R~~~~~~  253 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKTAFALTIAQN--AALKEGVGVGIYSLEMPAAQLTLRMMCSEA  253 (444)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHH--HHHTTCCCEEEEESSSCHHHHHHHHHHHHT
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHH--HHHhCCCeEEEEECCCCHHHHHHHHHHHHc
Confidence            34468889999999999999998877  3321 2245666554667777777665443

>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=94.23  E-value=0.024  Score=46.55  Aligned_cols=22  Identities=14%  Similarity=0.338  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|+|+|.+|+|||||.+.+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4679999999999999999875

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.23  E-value=0.026  Score=48.69  Aligned_cols=26  Identities=8%  Similarity=-0.050  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|.|+.|+||||+++.+...
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~~   39 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAKD   39 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            45678999999999999999999875

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.21  E-value=0.025  Score=48.92  Aligned_cols=24  Identities=8%  Similarity=0.189  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|.|.|+.|+||||+++.+...
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            367899999999999999999876

>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=94.20  E-value=0.026  Score=48.86  Aligned_cols=24  Identities=13%  Similarity=0.093  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~   32 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARA   32 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999876

>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=94.19  E-value=0.45  Score=40.66  Aligned_cols=91  Identities=12%  Similarity=0.096  Sum_probs=47.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC-cccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCCCC----------------c
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS-SYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLSAL----------------S  101 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~-~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~~~----------------~  101 (351)
                      +.+.|.|..|+||||+.....-+ ...........-+...   ....++.+.+...+......                .
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  156 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHA  156 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCSSS
T ss_pred             CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhccCCCCC
Confidence            57889999999999866554322 1111122222222222   23334445555444332110                0


Q ss_pred             cCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347          102 EILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus       102 ~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                      .+-..+.+.+...+...+.+-+ ++|+|+++.
T Consensus       157 ~Ivv~Tpg~l~~~l~~~l~~~~-~lVlDEah~  187 (235)
T 3llm_A          157 SIMFCTVGVLLRKLEAGIRGIS-HVIVDEIHE  187 (235)
T ss_dssp             EEEEEEHHHHHHHHHHCCTTCC-EEEECCTTS
T ss_pred             eEEEECHHHHHHHHHhhhcCCc-EEEEECCcc
Confidence            1222455666666766565544 678999976

>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=94.14  E-value=0.026  Score=50.99  Aligned_cols=24  Identities=21%  Similarity=0.102  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|.|+.|+||||||..++..
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~   26 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKR   26 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHh
Confidence            368899999999999999999876

>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=94.13  E-value=0.029  Score=52.77  Aligned_cols=24  Identities=21%  Similarity=0.314  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      ...+++|+|..|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            456999999999999999999987

>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=94.10  E-value=0.028  Score=50.20  Aligned_cols=23  Identities=13%  Similarity=0.238  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57889999999999999999873

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=94.06  E-value=0.053  Score=49.61  Aligned_cols=35  Identities=17%  Similarity=0.264  Sum_probs=26.7

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhC
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+.+.+...-.+..+++|+|..|+|||||.+.+..
T Consensus        43 ~~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           43 DLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHhCCcccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34444443334678999999999999999999874

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.04  E-value=0.12  Score=49.36  Aligned_cols=51  Identities=14%  Similarity=0.143  Sum_probs=35.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIM   91 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~   91 (351)
                      +-.++.|.|.+|+||||||..+....... .-..++|++...+..++...+.
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~-~g~~Vl~~s~E~s~~~l~~r~~  252 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATK-TNENVAIFSLEMSAQQLVMRML  252 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHH-SSCCEEEEESSSCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEEECCCCHHHHHHHHH
Confidence            34688899999999999999988773221 1224666665555566666654

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.04  E-value=0.045  Score=45.06  Aligned_cols=25  Identities=8%  Similarity=0.036  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|+|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4557889999999999999999876

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=94.03  E-value=0.028  Score=49.81  Aligned_cols=22  Identities=9%  Similarity=0.457  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|+|..|+|||||.+.++.-
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~   25 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKS   25 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5789999999999999998754

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=94.03  E-value=0.072  Score=46.67  Aligned_cols=37  Identities=11%  Similarity=0.214  Sum_probs=27.2

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ++.+.+.....+...|+|+|..|+|||||...+....
T Consensus        24 ~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           24 EFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3344444444456778899999999999999998763

>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=94.02  E-value=0.025  Score=53.36  Aligned_cols=26  Identities=27%  Similarity=0.402  Sum_probs=23.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....+|.|+|+.|+||||+|+.+..+
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            34678999999999999999999876

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.02  E-value=0.03  Score=50.84  Aligned_cols=23  Identities=4%  Similarity=0.085  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|+|+.|+||||||+.+...
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~   28 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADA   28 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            58899999999999999999876

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.00  E-value=0.035  Score=48.90  Aligned_cols=25  Identities=12%  Similarity=0.305  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.+++|+|+.|+|||||++.+..-
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~   48 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDY   48 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHh
Confidence            3479999999999999999998765

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=93.98  E-value=0.025  Score=52.52  Aligned_cols=35  Identities=20%  Similarity=0.181  Sum_probs=25.9

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++.+..=. +-..++|+|..|+|||+|+..+.+.
T Consensus       164 raID~l~Pig-rGQR~lIfg~~g~GKT~Ll~~Ia~~  198 (427)
T 3l0o_A          164 RLIDLFAPIG-KGQRGMIVAPPKAGKTTILKEIANG  198 (427)
T ss_dssp             HHHHHHSCCB-TTCEEEEEECTTCCHHHHHHHHHHH
T ss_pred             hhhhhccccc-CCceEEEecCCCCChhHHHHHHHHH
Confidence            4555554322 2347789999999999999998886

>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=93.97  E-value=0.033  Score=46.35  Aligned_cols=24  Identities=17%  Similarity=0.299  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...|+|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999999765

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.96  E-value=0.047  Score=44.11  Aligned_cols=25  Identities=16%  Similarity=0.333  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|+|+|..|+|||||..++...
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567889999999999999999765

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.95  E-value=0.032  Score=48.90  Aligned_cols=37  Identities=14%  Similarity=0.038  Sum_probs=25.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      ++|+|.|-||+||||+|..+...  ....=..++-|...
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~--la~~G~~VlliD~D   38 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSG--LHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEEEC
T ss_pred             cEEEEecCCCCcHHHHHHHHHHH--HHHCCCcEEEEcCC
Confidence            67888999999999999888766  33222234555554

>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=93.92  E-value=0.048  Score=55.61  Aligned_cols=99  Identities=10%  Similarity=0.032  Sum_probs=60.6

Q ss_pred             cCCCCCccccchhhHHHHHHHHHcc-----------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIER-----------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQL   81 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~   81 (351)
                      +.+.-.++.|.++.+++|.+.+...           -...+-+-++|+.|.|||.+|+++++.  ....     ++.++ 
T Consensus       472 p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e--~~~~-----f~~v~-  543 (806)
T 3cf2_A          472 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQAN-----FISIK-  543 (806)
T ss_dssp             CCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHT--TTCE-----EEECC-
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHH--hCCc-----eEEec-
Confidence            3444456778888888887776431           012234668999999999999999998  3222     23332 


Q ss_pred             CHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCC
Q 048347           82 SLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWR  133 (351)
Q Consensus        82 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~  133 (351)
                       ..++    +..-         -..++..+.+.+...-+...+.|++|+++.
T Consensus       544 -~~~l----~s~~---------vGese~~vr~lF~~Ar~~~P~IifiDEiDs  581 (806)
T 3cf2_A          544 -GPEL----LTMW---------FGESEANVREIFDKARQAAPCVLFFDELDS  581 (806)
T ss_dssp             -HHHH----HTTT---------CSSCHHHHHHHHHHHHTTCSEEEECSCGGG
T ss_pred             -cchh----hccc---------cchHHHHHHHHHHHHHHcCCceeechhhhH
Confidence             1121    1111         112344455555555566789999999963

>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=93.90  E-value=0.061  Score=54.74  Aligned_cols=47  Identities=9%  Similarity=0.123  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHHHcc-------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIER-------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.++.++.+...+...       ......+-++|+.|+|||++|+.+.+.
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~  511 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHH
Confidence            45889999888888777532       122346889999999999999999887

>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=93.89  E-value=0.028  Score=44.59  Aligned_cols=22  Identities=9%  Similarity=0.227  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.++|.+|+|||||++.+...
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            4779999999999999999765

>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=93.88  E-value=0.021  Score=50.11  Aligned_cols=26  Identities=8%  Similarity=0.222  Sum_probs=22.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+...|.|.|+.|+||||+|+.+.+.
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~~   47 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQL   47 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHh
Confidence            35688999999999999999998877

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.88  E-value=0.031  Score=49.27  Aligned_cols=23  Identities=17%  Similarity=0.213  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||.+.++.-
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999754

>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=93.88  E-value=0.026  Score=50.97  Aligned_cols=24  Identities=8%  Similarity=0.196  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+..-
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~gl  103 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFRF  103 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTTS
T ss_pred             CCEEEEECCCCchHHHHHHHHHcC
Confidence            368999999999999999998654

>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=93.87  E-value=0.045  Score=53.54  Aligned_cols=46  Identities=17%  Similarity=0.231  Sum_probs=34.4

Q ss_pred             ccccchhhHHHHHHHHHcc----CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIER----QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++|.++-.+.+.+.+.-.    .-+...+.++|+.|+||||||+.++..
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            4788877777775544321    123568899999999999999999887

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=93.86  E-value=0.081  Score=46.55  Aligned_cols=38  Identities=13%  Similarity=0.185  Sum_probs=27.3

Q ss_pred             HHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           28 EELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        28 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      .++.+.+...+.+...|.++|..|+|||||...++...
T Consensus        26 ~~~~~~~~~~~~~~~~I~vvG~~g~GKSSLin~l~~~~   63 (270)
T 1h65_A           26 LELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   63 (270)
T ss_dssp             HHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHhhcCCCCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            33444344444446678899999999999999998763

>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=93.81  E-value=0.04  Score=43.94  Aligned_cols=24  Identities=4%  Similarity=0.133  Sum_probs=20.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.|.|+|.+|+|||||.+.+...
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            456779999999999999998765

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=93.79  E-value=0.037  Score=49.22  Aligned_cols=24  Identities=13%  Similarity=0.162  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|+|.|-||+||||+|..+...
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~   25 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAA   25 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHH
Confidence            478888999999999999888766

>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=93.78  E-value=0.053  Score=48.83  Aligned_cols=26  Identities=12%  Similarity=0.171  Sum_probs=22.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-.+++|+|+.|+|||||++.+..-
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl  149 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHF  149 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhh
Confidence            34568999999999999999998654

>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=93.76  E-value=0.037  Score=47.69  Aligned_cols=25  Identities=20%  Similarity=0.360  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|.|.|+.|+||||+++.+...
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999887

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.75  E-value=0.044  Score=44.30  Aligned_cols=27  Identities=15%  Similarity=0.247  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      +..-.|+|+|..|+|||||...+....
T Consensus         7 ~~~~~i~v~G~~~~GKssl~~~l~~~~   33 (181)
T 3tw8_B            7 DHLFKLLIIGDSGVGKSSLLLRFADNT   33 (181)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHHCSCC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHhcCC
Confidence            345678899999999999999998763

>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=93.74  E-value=0.034  Score=49.24  Aligned_cols=24  Identities=8%  Similarity=0.056  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.++.|+|..|+||||||..+...
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~   53 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQ   53 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999998754

>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=93.68  E-value=0.032  Score=45.85  Aligned_cols=23  Identities=9%  Similarity=0.190  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.|.|+|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46779999999999999999765

>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=93.67  E-value=0.036  Score=52.54  Aligned_cols=24  Identities=8%  Similarity=0.152  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..+|.|+|.+|+||||+|..+...
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999988765

>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=93.67  E-value=0.043  Score=46.40  Aligned_cols=30  Identities=20%  Similarity=0.422  Sum_probs=24.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCe
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDC   73 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~   73 (351)
                      +.|+|-|+.|+||||+++.+.+.  ....++.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~--L~~~~~v   32 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHR--LVKDYDV   32 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH--HTTTSCE
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH--HHCCCCE
Confidence            57889999999999999999887  4444443

>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=93.63  E-value=0.042  Score=45.28  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|+|+|..|+|||||..++...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567889999999999999999876

>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=93.63  E-value=0.036  Score=49.59  Aligned_cols=24  Identities=17%  Similarity=0.236  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||.+.+..-
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            368999999999999999999776

>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=93.62  E-value=0.056  Score=43.45  Aligned_cols=24  Identities=17%  Similarity=0.205  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .--|+|+|..|+|||||.+++...
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            456789999999999999999776

>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=93.56  E-value=0.04  Score=43.98  Aligned_cols=22  Identities=14%  Similarity=0.123  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|+|+|.+|+|||||.+.+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            4678999999999999999765

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.50  E-value=0.043  Score=43.86  Aligned_cols=23  Identities=13%  Similarity=0.205  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      --|.|+|.+|+|||||.+++...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45779999999999999999875

>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=93.48  E-value=0.039  Score=50.97  Aligned_cols=24  Identities=13%  Similarity=0.130  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL   77 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLL   77 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcC
Confidence            368999999999999999998653

>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=93.45  E-value=0.044  Score=49.36  Aligned_cols=25  Identities=12%  Similarity=0.034  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|.|.|+.|+||||||..+...
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~   33 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKI   33 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHh
Confidence            3468899999999999999999866

>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=93.43  E-value=0.044  Score=44.91  Aligned_cols=21  Identities=14%  Similarity=0.169  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      +.+|+|..|+|||||+++++-
T Consensus        28 ~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            788999999999999999854

>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=93.43  E-value=0.044  Score=50.62  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...++|+|..|+|||||++.+..-
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999988654

>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=93.43  E-value=0.038  Score=43.94  Aligned_cols=24  Identities=17%  Similarity=0.234  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..-|+|+|..|+|||||.+.+...
T Consensus         4 ~~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            345789999999999999999765

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.38  E-value=0.046  Score=44.82  Aligned_cols=26  Identities=12%  Similarity=0.271  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ....|.|+|..|+|||||..++....
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHcCc
Confidence            34567899999999999999998763

>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=93.38  E-value=0.056  Score=43.64  Aligned_cols=26  Identities=12%  Similarity=0.181  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+...|+|+|..|+|||||.+++...
T Consensus         7 ~~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            7 SETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             SCEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhC
Confidence            34567889999999999999998766

>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=93.37  E-value=0.046  Score=44.43  Aligned_cols=23  Identities=9%  Similarity=0.092  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|+|+|..|+|||||.+.+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46789999999999999999875

>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=93.37  E-value=0.042  Score=50.68  Aligned_cols=24  Identities=17%  Similarity=0.170  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaGl   53 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAGF   53 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcC
Confidence            358999999999999999998653

>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=93.32  E-value=0.064  Score=42.85  Aligned_cols=23  Identities=13%  Similarity=0.199  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      --|+|+|..|+|||||...+...
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~~   25 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGGL   25 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhc
Confidence            45789999999999999998654

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=93.31  E-value=0.04  Score=52.48  Aligned_cols=90  Identities=12%  Similarity=0.109  Sum_probs=50.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCC--CeeEEEEEe---CCHHHHHHHHHHHhCCCCC--CccCCCCCHHH----
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYF--DCCAWVYYQ---LSLDMMLDAIMKSLMPLSA--LSEILDNDFEM----  110 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~~~---~~~~~~~~~i~~~~~~~~~--~~~~~~~~~~~----  110 (351)
                      ..++|.|..|+|||+|+.++.......+.-  +.++++-+.   -.+.++..++...=..+..  .....+.+...    
T Consensus       153 Qr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~r~~~  232 (469)
T 2c61_A          153 QKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVT  232 (469)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHHHHHH
Confidence            356778999999999999998874432211  245555555   6667777777643111100  00001111111    


Q ss_pred             --HHHHHHHhcC---CceEEEEEeCC
Q 048347          111 --KKNTLHNYLK---NKRYLIVIQDV  131 (351)
Q Consensus       111 --~~~~l~~~L~---~k~~LlVLDdv  131 (351)
                        ..-.+.++++   ++..|+++||+
T Consensus       233 ~~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          233 PRMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             HHHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeCH
Confidence              1223344443   69999999997

>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=93.29  E-value=0.042  Score=46.54  Aligned_cols=86  Identities=7%  Similarity=0.034  Sum_probs=47.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCC-----CccCCCCCHHHHHHHHHH
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSA-----LSEILDNDFEMKKNTLHN  117 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~-----~~~~~~~~~~~~~~~l~~  117 (351)
                      +|.|.|++|+||+|.|+.+..+..+       ..++    .-+++++-+..-+.-..     ..+-..-+.+-..+.+.+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g~-------~~is----tGdllR~~i~~~t~lg~~~~~~~~~G~lvpd~iv~~lv~~   70 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKGF-------VHIS----TGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEE   70 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCC-------EEEE----HHHHHHHHHHHTCHHHHHHHHHHHHTCCCCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC-------eEEc----HHHHHHHHHHhcChhhhhHHHHHhcCCcCCHHHHHHHHHH
Confidence            5778999999999999999877221       2222    23444332221100000     000122344556777788


Q ss_pred             hcCCceEEEEEeCCCCh-hhHHHH
Q 048347          118 YLKNKRYLIVIQDVWRG-DIWDFL  140 (351)
Q Consensus       118 ~L~~k~~LlVLDdv~~~-~~~~~l  140 (351)
                      .+..... +|||+.=.. .+.+.+
T Consensus        71 ~l~~~~~-~ilDGfPRt~~Qa~~l   93 (206)
T 3sr0_A           71 VFPKHGN-VIFDGFPRTVKQAEAL   93 (206)
T ss_dssp             HCCSSSC-EEEESCCCSHHHHHHH
T ss_pred             hhccCCc-eEecCCchhHHHHHHH
Confidence            8866554 678988433 343433

>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=93.29  E-value=0.073  Score=46.88  Aligned_cols=35  Identities=6%  Similarity=0.058  Sum_probs=25.5

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..|+....++..-+.++|++|.|||++|..+.+.
T Consensus        93 l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           93 FLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            44444443233445789999999999999999875

>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=93.28  E-value=0.042  Score=43.75  Aligned_cols=23  Identities=9%  Similarity=0.187  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      --|+|+|..|+|||||.+++.+.
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35779999999999999999765

>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=93.27  E-value=0.054  Score=45.54  Aligned_cols=23  Identities=17%  Similarity=0.049  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|.|..|+||||||.++..+
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            56789999999999999999877

>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=93.26  E-value=0.042  Score=43.98  Aligned_cols=24  Identities=8%  Similarity=0.048  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-.|.|+|..|+|||||.+++...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456789999999999999998765

>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=93.22  E-value=0.054  Score=44.29  Aligned_cols=25  Identities=8%  Similarity=0.092  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..-.|.|+|.+|+|||||++++...
T Consensus         6 ~~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            6 VKCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEEECCCCCCHHHHHHHHhcC
Confidence            3456779999999999999998765

>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=93.19  E-value=0.05  Score=44.48  Aligned_cols=22  Identities=5%  Similarity=0.077  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|+|.+|+|||||...+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4678999999999999999876

>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=93.19  E-value=0.044  Score=43.75  Aligned_cols=22  Identities=0%  Similarity=0.141  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|..|+|||||..++...
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            4778999999999999998765

>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=93.18  E-value=0.055  Score=45.05  Aligned_cols=34  Identities=9%  Similarity=0.099  Sum_probs=24.4

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+.+.-.. +...|+|+|.+|+|||||.+++...
T Consensus        15 ~l~~~~~~~-~~~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           15 VLQFLGLYK-KTGKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             HHHHHTCTT-CCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             HHHHhhccC-CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            444443322 2345789999999999999999765

>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=93.17  E-value=0.056  Score=43.68  Aligned_cols=25  Identities=20%  Similarity=0.335  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|.|+|..|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            4567889999999999999998765

>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=93.15  E-value=0.044  Score=43.79  Aligned_cols=24  Identities=8%  Similarity=0.169  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .--|.|+|..|+|||||.+.+...
T Consensus         6 ~~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            6 ELKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            345789999999999999998766

>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=93.15  E-value=0.048  Score=45.93  Aligned_cols=25  Identities=8%  Similarity=0.036  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|.|+|.+|+|||||+.++...
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4567889999999999999999876

>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=93.09  E-value=0.046  Score=43.41  Aligned_cols=23  Identities=13%  Similarity=0.208  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      --|+|+|..|+|||||..++...
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998755

>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=93.07  E-value=0.074  Score=47.80  Aligned_cols=22  Identities=5%  Similarity=0.214  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++++|+.|+|||||.+.+. .
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~-~  187 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT-G  187 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH-S
T ss_pred             cEEEEECCCCCCHHHHHHHHH-H
Confidence            588999999999999999998 6

>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=93.05  E-value=0.067  Score=49.17  Aligned_cols=26  Identities=8%  Similarity=0.119  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-.++.|+|..|+|||||+..++..
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~  154 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVM  154 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45589999999999999999998765

>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=93.05  E-value=0.058  Score=44.84  Aligned_cols=25  Identities=24%  Similarity=0.357  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....|+|+|..|+|||||...+...
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            4567889999999999999998765

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.05  E-value=0.051  Score=50.08  Aligned_cols=23  Identities=13%  Similarity=0.238  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||.+.+.--
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999998653

>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=93.04  E-value=0.037  Score=46.31  Aligned_cols=25  Identities=12%  Similarity=0.012  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-..|+|+|..|+|||||.+.+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3567999999999999999998765

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.03  E-value=0.061  Score=49.46  Aligned_cols=25  Identities=16%  Similarity=0.065  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+|+|+|..|+|||||.+.+...
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~   97 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKM   97 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            3789999999999999999998753

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=92.96  E-value=0.063  Score=46.16  Aligned_cols=25  Identities=4%  Similarity=0.001  Sum_probs=20.6

Q ss_pred             CeEEEEEEcC-CCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDT-MGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~-gGiGKTtLa~~v~~~   64 (351)
                      ..++|+|++. ||+||||+|..+...
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~~   28 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAFA   28 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHHH
Confidence            4678888855 999999999888665

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.94  E-value=0.098  Score=58.29  Aligned_cols=87  Identities=14%  Similarity=0.043  Sum_probs=53.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCCcc-CCCCCHHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSALSE-ILDNDFEMKKNTL  115 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~l  115 (351)
                      ++-+.+-|+|+.|+|||+||.++...  ...+=..++|+++.  ++...     ++.++.+...-. ....+.+++.+.+
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~e--a~~~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~ 1497 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEIC 1497 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHH--HHTTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHH
Confidence            34578889999999999999999776  33333345676655  33333     445543211000 1233445666666


Q ss_pred             HHhcC-CceEEEEEeCCC
Q 048347          116 HNYLK-NKRYLIVIQDVW  132 (351)
Q Consensus       116 ~~~L~-~k~~LlVLDdv~  132 (351)
                      +...+ .+..+||+|.+.
T Consensus      1498 ~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1498 DALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHHTCCSEEEESCGG
T ss_pred             HHHHhcCCCCEEEEcChh
Confidence            65543 456799999994

>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=92.94  E-value=0.076  Score=45.24  Aligned_cols=26  Identities=8%  Similarity=0.255  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+...|.|+|.+|+|||||...+...
T Consensus        27 ~~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           27 PHKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TTSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34567889999999999999999876

>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=92.94  E-value=0.048  Score=44.84  Aligned_cols=25  Identities=12%  Similarity=0.193  Sum_probs=20.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.--|.|+|.+|+|||||...+.+.
T Consensus        19 ~~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           19 PELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcC
Confidence            3456779999999999999887665

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	351
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-06

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

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]

 Score = 47.1 bits (111), Expect = 1e-06
 Identities = 19/142 (13%), Positives = 40/142 (28%), Gaps = 17/142 (11%)

Query: 24  EDKMEELLDLLIE-RQPQLSLVAIIDTMGFDRTAFIGEAYNSS--YVKNYFDCCAWVY-- 78
           E  ++ ++  L E        + +    G  ++    +A + S   +   +D   W+   
Sbjct: 26  EYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDS 85

Query: 79  YQLSLDMMLDAIMKSLMPLSAL------SEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW 132
                          LM  S        S        +K+   +  +     L V  DV 
Sbjct: 86  GTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV 145

Query: 133 RGDIWDFLKEALPDHQNGSRIL 154
           + +   +        +   R L
Sbjct: 146 QEETIRWA------QELRLRCL 161

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	351
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.9
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.67
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	98.65
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	98.44
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	98.4
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.38
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.36
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.31
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	98.28
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.28
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	98.24
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	98.2
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.16
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.13
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.09
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.09
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.07
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.06
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.03
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	98.03
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.03
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.0
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	97.97
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	97.97
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	97.93
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	97.93
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	97.91
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	97.89
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	97.87
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	97.86
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	97.81
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	97.77
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	97.72
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	97.72
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.71
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	97.71
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	97.68
d2ifga3	156	High affinity nerve growth factor receptor, N-term	97.67
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.66
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.63
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.63
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	97.54
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	97.5
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.41
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.41
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.41
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.37
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.33
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	97.27
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.26
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	97.25
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	97.22
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.21
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.12
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.0
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	96.99
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.99
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.98
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.97
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.95
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.91
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.9
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.86
d1okkd2	207	GTPase domain of the signal recognition particle r	96.85
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.79
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.78
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.78
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.71
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	96.7
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.69
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.66
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.66
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.65
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.64
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.64
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.63
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.62
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.61
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.59
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.58
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.54
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.54
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.5
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.4
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.36
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.3
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.3
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.29
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.27
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.27
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.2
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.1
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	96.06
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.04
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.02
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.01
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.0
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	95.99
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.92
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.9
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.9
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.89
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.85
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.84
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.82
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.7
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.69
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.66
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.62
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.61
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.61
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.59
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.59
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.57
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.53
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.5
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.48
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.48
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.47
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.44
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.35
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.33
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	95.32
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.28
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.25
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	95.23
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	95.22
d1g2912	240	Maltose transport protein MalK, N-terminal domain	95.13
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.07
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.04
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.03
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	95.02
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.01
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.99
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	94.93
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.92
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.9
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.9
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	94.9
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	94.87
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.87
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.87
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.84
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.82
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.81
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.72
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.66
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.66
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.6
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.59
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.57
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	94.56
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.55
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.52
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	94.51
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.44
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.44
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	94.4
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.35
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.29
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.18
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.18
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.05
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	94.02
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.02
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.99
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.98
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.97
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.96
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	93.89
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.81
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	93.79
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.75
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.74
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.74
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.72
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	93.7
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.66
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.65
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	93.64
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.63
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.62
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.58
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.58
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.57
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.49
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.48
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	93.39
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.33
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	93.3
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	93.24
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.23
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.23
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.21
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	93.21
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.13
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.09
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.09
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.06
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.05
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.03
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.03
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.02
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	93.02
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.99
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	92.95
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.91
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.9
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	92.88
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	92.88
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.87
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.8
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	92.76
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	92.74
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.73
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.69
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.56
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.55
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	92.55
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.5
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.49
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.44
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	92.32
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.24
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.23
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	92.2
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.17
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.14
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.11
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	92.11
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	92.1
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.1
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.1
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.96
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	91.94
d2fh5b1	207	Signal recognition particle receptor beta-subunit	91.93
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	91.88
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.84
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	91.83
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	91.77
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	91.66
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	91.65
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	91.59
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	91.39
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.32
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.32
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	91.23
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	91.15
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	90.78
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	90.67
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	90.45
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.23
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	90.22
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	90.19
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	90.07
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	89.83
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	89.5
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	89.31
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	89.27
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	89.16
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	88.86
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.48
d1tuea_	205	Replication protein E1 helicase domain {Human papi	88.1
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	87.88
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	87.88
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	87.27
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	87.03
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	86.95
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	86.77
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	86.23
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	86.2
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	85.84
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	85.13
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.09
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	84.88
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.69
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	83.68
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	83.62
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	83.28
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	81.15
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	80.8
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	80.14

>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=99.90  E-value=4.3e-24  Score=191.54  Aligned_cols=143  Identities=11%  Similarity=0.041  Sum_probs=109.8

Q ss_pred             CCCCccccchhhHHHHHHHHHc-cCCCeEEEEEEcCCCChHHHHHHHHhCCcc--cccCCCeeEEEEEe--CCHHHHHHH
Q 048347           15 WDNKVDLDLEDKMEELLDLLIE-RQPQLSLVAIIDTMGFDRTAFIGEAYNSSY--VKNYFDCCAWVYYQ--LSLDMMLDA   89 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~~~--~~~~~~~~~   89 (351)
                      ....+++||+.++++|+++|.. .++..++|+|+||||+||||||+++|++..  .+.+|++++||+++  ++...+...
T Consensus        17 p~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~   96 (277)
T d2a5yb3          17 PKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLF   96 (277)
T ss_dssp             BCCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHH
T ss_pred             CCCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHH
Confidence            3566788999999999999975 345689999999999999999999998743  67789999999999  776766666


Q ss_pred             HHHHh---CCCCC--Ccc-CCCCCHHHHHHHHHHhcCCceEEEEEeCCCChhhHHHHHhhcCCCCCCcEEEE-Eeeccch
Q 048347           90 IMKSL---MPLSA--LSE-ILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRGDIWDFLKEALPDHQNGSRILT-ALIHIVG  162 (351)
Q Consensus        90 i~~~~---~~~~~--~~~-~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Iiv-TR~~~v~  162 (351)
                      +...+   .....  .+. ............+.+.+.++|+|+||||||+.++|+.+.      ..|||||| ||++.|+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~------~~~srilvTTR~~~v~  170 (277)
T d2a5yb3          97 TDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQ------ELRLRCLVTTRDVEIS  170 (277)
T ss_dssp             HHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHH------HTTCEEEEEESBGGGG
T ss_pred             HHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhc------ccCceEEEEeehHHHH
Confidence            54443   22211  111 233344445567888999999999999999998887653      24899999 9999884


Q ss_pred             h
Q 048347          163 L  163 (351)
Q Consensus       163 l  163 (351)
                      .
T Consensus       171 ~  171 (277)
T d2a5yb3         171 N  171 (277)
T ss_dssp             G
T ss_pred             H
Confidence            4

>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=98.67  E-value=1.5e-07  Score=81.31  Aligned_cols=119  Identities=13%  Similarity=0.077  Sum_probs=83.2

Q ss_pred             cccCCCCCccccchhhHHHHHHHHHc----cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCee-EEEEEe--CCH
Q 048347           11 RGLSWDNKVDLDLEDKMEELLDLLIE----RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCC-AWVYYQ--LSL   83 (351)
Q Consensus        11 ~~~~~~~~~~vGr~~~~~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~-~wv~~~--~~~   83 (351)
                      .+|.+....++|||.+++++.++|..    .+.....+.|+|+.|+|||++|+.+++.  ....+... +++...  ...
T Consensus         9 l~~~y~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~~~   86 (276)
T d1fnna2           9 FSPSYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNF   86 (276)
T ss_dssp             GSTTCCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHH--HhcccCCcEEEecchhhhhh
Confidence            45666677899999999999998864    2334567889999999999999999988  55444432 333333  777


Q ss_pred             HHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcC--CceEEEEEeCCCCh
Q 048347           84 DMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLK--NKRYLIVIQDVWRG  134 (351)
Q Consensus        84 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~--~k~~LlVLDdv~~~  134 (351)
                      ......+..+......   ............+.+.+.  ......++|++++.
T Consensus        87 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~  136 (276)
T d1fnna2          87 TAIIGEIARSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL  136 (276)
T ss_dssp             HHHHHHHHHHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS
T ss_pred             hhhhhhhHHhhhhhhh---hhccchhHHHHHHHHHHhhcccccccchhHHHHh
Confidence            8888888888776544   134455666666655553  35667777777654

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.65  E-value=2.1e-08  Score=77.05  Aligned_cols=88  Identities=18%  Similarity=0.114  Sum_probs=73.5

Q ss_pred             CCCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccC--hhh
Q 048347          234 PMPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFP--EEL  311 (351)
Q Consensus       234 ~~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP--~~i  311 (351)
                      .++.++.+++|++|+++++  .+..+|..++.+++|++|++++| .+..+| .++.+++|+.|++++| .+..+|  ..+
T Consensus        12 ~l~~l~~l~~L~~L~ls~N--~l~~lp~~~~~l~~L~~L~l~~N-~i~~l~-~~~~l~~L~~L~l~~N-~i~~~~~~~~l   86 (124)
T d1dcea3          12 VLCHLEQLLLVTHLDLSHN--RLRALPPALAALRCLEVLQASDN-ALENVD-GVANLPRLQELLLCNN-RLQQSAAIQPL   86 (124)
T ss_dssp             SCCCGGGGTTCCEEECCSS--CCCCCCGGGGGCTTCCEEECCSS-CCCCCG-GGTTCSSCCEEECCSS-CCCSSSTTGGG
T ss_pred             CCcccccCCCCCEEECCCC--ccCcchhhhhhhhcccccccccc-cccccC-ccccccccCeEECCCC-ccCCCCCchhh
Confidence            3456778899999999443  45578888899999999999999 688998 5999999999999984 677777  367


Q ss_pred             hcCCCCCEEEecCCC
Q 048347          312 WRIKALRKLESWWPR  326 (351)
Q Consensus       312 ~~L~~L~~L~l~~~~  326 (351)
                      +++++|+.|++++-+
T Consensus        87 ~~~~~L~~L~l~~N~  101 (124)
T d1dcea3          87 VSCPRLVLLNLQGNS  101 (124)
T ss_dssp             GGCTTCCEEECTTSG
T ss_pred             cCCCCCCEEECCCCc
Confidence            899999999998854

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.44  E-value=1.3e-07  Score=72.44  Aligned_cols=76  Identities=18%  Similarity=0.104  Sum_probs=64.2

Q ss_pred             eEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecC
Q 048347          245 KVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWW  324 (351)
Q Consensus       245 ~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  324 (351)
                      |+|+++++  .+..++ .++.+++|++|++++| .+..+|..++.+++|++|++++ ..+..+| +++++++|++|++++
T Consensus         1 R~L~Ls~n--~l~~l~-~l~~l~~L~~L~ls~N-~l~~lp~~~~~l~~L~~L~l~~-N~i~~l~-~~~~l~~L~~L~l~~   74 (124)
T d1dcea3           1 RVLHLAHK--DLTVLC-HLEQLLLVTHLDLSHN-RLRALPPALAALRCLEVLQASD-NALENVD-GVANLPRLQELLLCN   74 (124)
T ss_dssp             SEEECTTS--CCSSCC-CGGGGTTCCEEECCSS-CCCCCCGGGGGCTTCCEEECCS-SCCCCCG-GGTTCSSCCEEECCS
T ss_pred             CEEEcCCC--CCCCCc-ccccCCCCCEEECCCC-ccCcchhhhhhhhccccccccc-ccccccC-ccccccccCeEECCC
Confidence            57888433  334565 4789999999999999 6999998899999999999999 4788887 599999999999988


Q ss_pred             CC
Q 048347          325 PR  326 (351)
Q Consensus       325 ~~  326 (351)
                      ..
T Consensus        75 N~   76 (124)
T d1dcea3          75 NR   76 (124)
T ss_dssp             SC
T ss_pred             Cc
Confidence            65

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=98.40  E-value=9.8e-08  Score=84.86  Aligned_cols=92  Identities=12%  Similarity=-0.008  Sum_probs=73.8

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      .+.++++++|++|+|+..+.....+|..++++++|++|+|++|...+..|..+..+.+|++++++.|.....+|.+++++
T Consensus        69 p~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~l~l~~N~~~~~~p~~l~~l  148 (313)
T d1ogqa_          69 PSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSL  148 (313)
T ss_dssp             CGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGC
T ss_pred             ChHHhcCccccccccccccccccccccccccccccchhhhccccccccccccccchhhhcccccccccccccCchhhccC
Confidence            45778999999999954233333689889999999999999994333445558889999999999888888899999999


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|+.+++++..
T Consensus       149 ~~L~~l~l~~n~  160 (313)
T d1ogqa_         149 PNLVGITFDGNR  160 (313)
T ss_dssp             TTCCEEECCSSC
T ss_pred             cccceeeccccc
Confidence            999999998754

>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=98.38  E-value=1.8e-07  Score=80.95  Aligned_cols=46  Identities=17%  Similarity=0.194  Sum_probs=38.4

Q ss_pred             cCCCCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |....+.+|||+++++++.+.      ..+.+.|+|++|+|||+|++++.++
T Consensus         7 p~~~~~~f~GR~~el~~l~~~------~~~~i~i~G~~G~GKTsLl~~~~~~   52 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEKLKGL------RAPITLVLGLRRTGKSSIIKIGINE   52 (283)
T ss_dssp             CCCSGGGSCCCHHHHHHHHHT------CSSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCChhhCCChHHHHHHHHhc------cCCEEEEEcCCCCcHHHHHHHHHHH
Confidence            445678899999999998763      2357889999999999999999876

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=6.3e-07  Score=71.41  Aligned_cols=89  Identities=12%  Similarity=-0.034  Sum_probs=73.8

Q ss_pred             CCCCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhh
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELW  312 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~  312 (351)
                      +..+..+++|+.|.+ .+...+..++. .+.++++|+.|++++| .+..+|.. +..+++|++|+|++ ..+..+|.++.
T Consensus        24 p~~l~~l~~l~~L~l-~~n~~l~~i~~~~f~~l~~L~~L~Ls~N-~l~~i~~~~f~~l~~L~~L~Ls~-N~l~~l~~~~~  100 (156)
T d2ifga3          24 LHHLPGAENLTELYI-ENQQHLQHLELRDLRGLGELRNLTIVKS-GLRFVAPDAFHFTPRLSRLNLSF-NALESLSWKTV  100 (156)
T ss_dssp             TTTSCSCSCCSEEEC-CSCSSCCEECGGGSCSCCCCSEEECCSS-CCCEECTTGGGSCSCCCEEECCS-SCCSCCCSTTT
T ss_pred             cccccCccccCeeec-CCCccccccCchhhccccccCcceeecc-ccCCcccccccccccccceeccC-CCCcccChhhh
Confidence            455677889999999 44445667765 4889999999999999 79998655 88999999999998 57999999887


Q ss_pred             cCCCCCEEEecCCC
Q 048347          313 RIKALRKLESWWPR  326 (351)
Q Consensus       313 ~L~~L~~L~l~~~~  326 (351)
                      ...+|+.|++++-+
T Consensus       101 ~~~~l~~L~L~~Np  114 (156)
T d2ifga3         101 QGLSLQELVLSGNP  114 (156)
T ss_dssp             CSCCCCEEECCSSC
T ss_pred             ccccccccccCCCc
Confidence            77789999998743

>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=98.31  E-value=9.3e-07  Score=76.62  Aligned_cols=116  Identities=13%  Similarity=0.061  Sum_probs=76.7

Q ss_pred             ccCCCCCccccchhhHHHHHHHHHc----c---CCCeEEEEEEcCCCChHHHHHHHHhCCcccccC-----C-CeeEEEE
Q 048347           12 GLSWDNKVDLDLEDKMEELLDLLIE----R---QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY-----F-DCCAWVY   78 (351)
Q Consensus        12 ~~~~~~~~~vGr~~~~~~l~~~L~~----~---~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~-----F-~~~~wv~   78 (351)
                      .+....+.++|||+++++|.+.+..    +   .+...++.++|+.|+|||++|+.+++.  +...     . ....++.
T Consensus        10 ~~~~~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~   87 (287)
T d1w5sa2          10 DENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVN   87 (287)
T ss_dssp             STTCCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEE
T ss_pred             CCccCCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHH--HHhhcccccCCceeeeec
Confidence            3555678899999999999887742    1   122334567899999999999999987  3221     1 1233444


Q ss_pred             Ee--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhc--CCceEEEEEeCCC
Q 048347           79 YQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYL--KNKRYLIVIQDVW  132 (351)
Q Consensus        79 ~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L--~~k~~LlVLDdv~  132 (351)
                      ..  .+.......+...+.....   ..........+.+.+..  .+...++++|.+.
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          88 AFNAPNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             GGGCCSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             cccccchhhHHHHHhhhcccccc---cccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence            33  6677777777777766443   13445556666666555  3466778888775

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.28  E-value=4.9e-07  Score=72.55  Aligned_cols=83  Identities=19%  Similarity=0.173  Sum_probs=67.4

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccc-cccCCccEEeecCCccccccCh--hhhcCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMET-GAMQKLKSLIVNPCAYLRKFPE--ELWRIK  315 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i-~~L~~L~~L~l~~c~~l~~lP~--~i~~L~  315 (351)
                      ..+++|++|+++++  .+..++ .+..+++|++|++++| .+..+|..+ ..+++|+.|++++| .+..+|+  .+.+++
T Consensus        38 ~~l~~L~~L~Ls~N--~i~~l~-~~~~l~~L~~L~ls~N-~i~~l~~~~~~~l~~L~~L~L~~N-~i~~~~~l~~l~~l~  112 (162)
T d1a9na_          38 ATLDQFDAIDFSDN--EIRKLD-GFPLLRRLKTLLVNNN-RICRIGEGLDQALPDLTELILTNN-SLVELGDLDPLASLK  112 (162)
T ss_dssp             GGTTCCSEEECCSS--CCCEEC-CCCCCSSCCEEECCSS-CCCEECSCHHHHCTTCCEEECCSC-CCCCGGGGGGGGGCT
T ss_pred             cccccCCEEECCCC--CCCccC-CcccCcchhhhhcccc-cccCCCccccccccccccceeccc-ccccccccccccccc
Confidence            45789999999543  455665 4788999999999999 688888764 57999999999985 5777764  678899


Q ss_pred             CCCEEEecCCC
Q 048347          316 ALRKLESWWPR  326 (351)
Q Consensus       316 ~L~~L~l~~~~  326 (351)
                      +|++|++++++
T Consensus       113 ~L~~L~l~~N~  123 (162)
T d1a9na_         113 SLTYLCILRNP  123 (162)
T ss_dssp             TCCEEECCSSG
T ss_pred             ccchhhcCCCc
Confidence            99999999976

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.28  E-value=6.1e-07  Score=73.88  Aligned_cols=87  Identities=18%  Similarity=0.108  Sum_probs=68.8

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L  314 (351)
                      .+..+++|+.|+++ ++......+..+..+++|++|+|++| .+..+|.. +.++++|++|+|++ ..+..+|++ +.++
T Consensus        49 ~f~~l~~L~~L~L~-~N~i~~~~~~~~~~~~~L~~L~Ls~N-~l~~l~~~~F~~l~~L~~L~L~~-N~l~~i~~~~f~~l  125 (192)
T d1w8aa_          49 LFGRLPHLVKLELK-RNQLTGIEPNAFEGASHIQELQLGEN-KIKEISNKMFLGLHQLKTLNLYD-NQISCVMPGSFEHL  125 (192)
T ss_dssp             SGGGCTTCCEEECC-SSCCCCBCTTTTTTCTTCCEEECCSC-CCCEECSSSSTTCTTCCEEECCS-SCCCEECTTSSTTC
T ss_pred             ccCCCceEeeeecc-ccccccccccccccccccceeeeccc-cccccCHHHHhCCCcccccccCC-ccccccCHHHhcCC
Confidence            34678999999994 43333334556788999999999999 68888775 78899999999998 468888776 5789


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++-+
T Consensus       126 ~~L~~l~L~~N~  137 (192)
T d1w8aa_         126 NSLTSLNLASNP  137 (192)
T ss_dssp             TTCCEEECTTCC
T ss_pred             cccccccccccc
Confidence            999999998743

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=1.3e-06  Score=69.96  Aligned_cols=83  Identities=14%  Similarity=0.120  Sum_probs=54.3

Q ss_pred             CCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhh-hcCCCC
Q 048347          239 EKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEEL-WRIKAL  317 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i-~~L~~L  317 (351)
                      .++..++.|+|+  +..+..++.....+++|++|+|++| .+.+++ .+..+++|++|++++| .+..+|.++ .++++|
T Consensus        15 ~n~~~lr~L~L~--~n~I~~i~~~~~~l~~L~~L~Ls~N-~i~~l~-~~~~l~~L~~L~ls~N-~i~~l~~~~~~~l~~L   89 (162)
T d1a9na_          15 TNAVRDRELDLR--GYKIPVIENLGATLDQFDAIDFSDN-EIRKLD-GFPLLRRLKTLLVNNN-RICRIGEGLDQALPDL   89 (162)
T ss_dssp             ECTTSCEEEECT--TSCCCSCCCGGGGTTCCSEEECCSS-CCCEEC-CCCCCSSCCEEECCSS-CCCEECSCHHHHCTTC
T ss_pred             cCcCcCcEEECC--CCCCCccCccccccccCCEEECCCC-CCCccC-CcccCcchhhhhcccc-cccCCCcccccccccc
Confidence            455567777772  2334455544456677777777777 577775 4677777777777774 466676654 457777


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++..
T Consensus        90 ~~L~L~~N~   98 (162)
T d1a9na_          90 TELILTNNS   98 (162)
T ss_dssp             CEEECCSCC
T ss_pred             ccceecccc
Confidence            777777754

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=98.20  E-value=9.9e-07  Score=78.11  Aligned_cols=85  Identities=15%  Similarity=0.151  Sum_probs=69.1

Q ss_pred             CCceEEEEecccccCc-eeeeCCCCCCcccEEEEecCCcc-ccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          242 PHLKVLKLKRSSYSGR-KLVCGHGGFPRQEILHLKSMLWL-EEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~-~lp~~~~~l~~L~~L~L~~~~~l-~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+++.|+|+.+...+. .+|..++.+++|++|+|+++..+ +.+|.++++|++|++|+|++|......|..+.++.+|+.
T Consensus        50 ~~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~  129 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVT  129 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCE
T ss_pred             EEEEEEECCCCCCCCCCCCChHHhcCccccccccccccccccccccccccccccchhhhccccccccccccccchhhhcc
Confidence            3689999965544443 58889999999999999974344 589999999999999999997655556677889999999


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      +++++..
T Consensus       130 l~l~~N~  136 (313)
T d1ogqa_         130 LDFSYNA  136 (313)
T ss_dssp             EECCSSE
T ss_pred             ccccccc
Confidence            9998743

>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=98.16  E-value=1.3e-06  Score=73.59  Aligned_cols=120  Identities=9%  Similarity=0.013  Sum_probs=69.3

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHh
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSL   94 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~   94 (351)
                      +++||.++.++.|.+|+..+.  ..-+-++|+.|+||||+|+.+++.  +.............   ..-.+.........
T Consensus        14 ~divg~~~~~~~L~~~i~~~~--~~~lLl~Gp~G~GKttl~~~la~~--l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~   89 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNASDDRGIDVVRNQIKDF   89 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTTSCCSHHHHHTHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChhHHHHHHHHH--hhcCCCcceeEEecccccCCeeeeecchhhc
Confidence            569999999999999997754  323558999999999999999876  32221111111111   11111111111111


Q ss_pred             CCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeec
Q 048347           95 MPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIH  159 (351)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~  159 (351)
                      ...                  .....+++..+|+|++...  .....+...+......+++++ |...
T Consensus        90 ~~~------------------~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~  139 (227)
T d1sxjc2          90 AST------------------RQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYA  139 (227)
T ss_dssp             HHB------------------CCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             ccc------------------ccccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcH
Confidence            000                  0011234557889999755  455666666665666777777 6543

>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=98.13  E-value=1.3e-06  Score=74.68  Aligned_cols=47  Identities=13%  Similarity=-0.007  Sum_probs=36.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|.++..+.|.+++.... ...-+.++|++|+||||+|+++++.
T Consensus        10 ~~diig~~~~~~~L~~~~~~~~-~~~~lll~Gp~G~GKTt~~~~la~~   56 (252)
T d1sxje2          10 LNALSHNEELTNFLKSLSDQPR-DLPHLLLYGPNGTGKKTRCMALLES   56 (252)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTT-CCCCEEEECSTTSSHHHHHHTHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCCeEEEECCCCCCHHHHHHHHHHh
Confidence            3569999998888888876543 2333559999999999999998765

>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=98.09  E-value=2.1e-06  Score=72.65  Aligned_cols=47  Identities=9%  Similarity=-0.004  Sum_probs=39.7

Q ss_pred             CCCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           16 DNKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        16 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .-++++|-++-++.+..++..+.  .+-+-++|+.|+||||+|+.+.+.
T Consensus        22 ~~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtla~~iak~   68 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALARE   68 (231)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCcHHHHHHHHHHH
Confidence            34679999999999999997763  444679999999999999999876

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.09  E-value=1.9e-06  Score=72.67  Aligned_cols=80  Identities=10%  Similarity=0.059  Sum_probs=51.4

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+++|+.|.++ ++ .....+ .++++++|+.|++++| .+..+|. ++.+++|++|++++| .+..+| .++++++|
T Consensus       147 ~~~~~~L~~L~l~-~n-~~~~~~-~l~~l~~L~~L~Ls~n-~l~~l~~-l~~l~~L~~L~Ls~N-~lt~i~-~l~~l~~L  219 (227)
T d1h6ua2         147 LAGLTNLQYLSIG-NA-QVSDLT-PLANLSKLTTLKADDN-KISDISP-LASLPNLIEVHLKNN-QISDVS-PLANTSNL  219 (227)
T ss_dssp             GGGCTTCCEEECC-SS-CCCCCG-GGTTCTTCCEEECCSS-CCCCCGG-GGGCTTCCEEECTTS-CCCBCG-GGTTCTTC
T ss_pred             hcccccccccccc-cc-ccccch-hhcccccceecccCCC-ccCCChh-hcCCCCCCEEECcCC-cCCCCc-ccccCCCC
Confidence            3456677777772 22 222222 2567777777777777 5666663 677777777777775 566666 36777777


Q ss_pred             CEEEecC
Q 048347          318 RKLESWW  324 (351)
Q Consensus       318 ~~L~l~~  324 (351)
                      +.|++++
T Consensus       220 ~~L~lsn  226 (227)
T d1h6ua2         220 FIVTLTN  226 (227)
T ss_dssp             CEEEEEE
T ss_pred             CEEEeeC
Confidence            7777753

>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=98.07  E-value=1.4e-05  Score=68.94  Aligned_cols=99  Identities=18%  Similarity=0.285  Sum_probs=59.4

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc---ccccCC-CeeEE-EEEeCCHHHHHHHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS---YVKNYF-DCCAW-VYYQLSLDMMLDAIMK   92 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~---~~~~~F-~~~~w-v~~~~~~~~~~~~i~~   92 (351)
                      +.++|||+++++++..|....++ .+ .++|.+|+|||+++..++.+.   ++.... ...+| ++.+            
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k~-n~-lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~------------   83 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRKN-NP-LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG------------   83 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSC-EE-EEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC------------
T ss_pred             CcccChHHHHHHHHHHHhcCccC-Cc-EEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeec------------
Confidence            46899999999999999765432 33 389999999999888877651   122222 23343 2221            


Q ss_pred             HhCCCCCCccCCCCCHHHHHHHHHHhc-CCceEEEEEeCCCCh
Q 048347           93 SLMPLSALSEILDNDFEMKKNTLHNYL-KNKRYLIVIQDVWRG  134 (351)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~l~~~L-~~k~~LlVLDdv~~~  134 (351)
                      .+.....    -....+...+.+.+.+ +.++.++++|++...
T Consensus        84 ~liag~~----~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l  122 (268)
T d1r6bx2          84 SLLAGTK----YRGDFEKRFKALLKQLEQDTNSILFIDEIHTI  122 (268)
T ss_dssp             ---CCCC----CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTT
T ss_pred             hHhccCc----cchhHHHHHHHHHHHhhccCCceEEecchHHH
Confidence            1111111    1234444444444444 456789999998644

>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=98.06  E-value=1.2e-06  Score=73.90  Aligned_cols=46  Identities=9%  Similarity=0.096  Sum_probs=38.2

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+++||-++-++.|.+++..+.  ..-+-++|+.|+||||+|+.+.+.
T Consensus        14 ~~d~ig~~~~~~~L~~~~~~~~--~~~~ll~Gp~G~GKTt~a~~la~~   59 (224)
T d1sxjb2          14 LSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAHE   59 (224)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHcCC--CCeEEEECCCCCCchhhHHHHHHH
Confidence            3568999999999999998764  233568999999999999988776

>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=98.03  E-value=9.9e-06  Score=68.85  Aligned_cols=136  Identities=11%  Similarity=0.007  Sum_probs=73.5

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMMLDAIMKSLMP   96 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~i~~~~~~   96 (351)
                      ++++|.++.++.+.+++..+. -...+-++|+.|+||||+|+.+.+.  +......    ... .......+.+...-..
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~--l~~~~~~----~~~~~~~~~~~~~i~~~~~~   84 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKG--LNCETGI----TATPCGVCDNCREIEQGRFV   84 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHHH--HHCTTCS----CSSCCSCSHHHHHHHHTCCT
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHH--hcCcccc----ccCccccchHHHHHHcCCCC
Confidence            578999999999999997653 2334568999999999999987654  2111100    000 0111111222211100


Q ss_pred             CCC-CccCCCCCHHHHHHHHHHhc----CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347           97 LSA-LSEILDNDFEMKKNTLHNYL----KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus        97 ~~~-~~~~~~~~~~~~~~~l~~~L----~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      ... ....+....+++.+.+...-    .++..++|||+++..  +....+...+......+++|. |.+.+
T Consensus        85 ~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~  156 (239)
T d1njfa_          85 DLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ  156 (239)
T ss_dssp             TEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGG
T ss_pred             eEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCcc
Confidence            000 00001122333332222211    245568899999865  455667777766666777777 76543

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.03  E-value=6.5e-06  Score=71.06  Aligned_cols=86  Identities=22%  Similarity=0.183  Sum_probs=67.7

Q ss_pred             CCCCCCCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ....+++++.|.++ ++ .+..+|.. ...+++|++|++++| .+..+|.. ++.+++|++|+|++| .+..+|+++..+
T Consensus       119 ~~~~l~~l~~L~l~-~n-~l~~l~~~~~~~l~~l~~l~l~~N-~l~~~~~~~~~~l~~L~~L~Ls~N-~L~~lp~~~~~~  194 (266)
T d1p9ag_         119 ALRGLGELQELYLK-GN-ELKTLPPGLLTPTPKLEKLSLANN-NLTELPAGLLNGLENLDTLLLQEN-SLYTIPKGFFGS  194 (266)
T ss_dssp             TTTTCTTCCEEECT-TS-CCCCCCTTTTTTCTTCCEEECTTS-CCSCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTT
T ss_pred             cccccccccccccc-cc-ccceeccccccccccchhcccccc-cccccCccccccccccceeecccC-CCcccChhHCCC
Confidence            34566777777773 22 33345443 567889999999999 68888765 788999999999995 688999999999


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|+.|++++-|
T Consensus       195 ~~L~~L~L~~Np  206 (266)
T d1p9ag_         195 HLLPFAFLHGNP  206 (266)
T ss_dssp             CCCSEEECCSCC
T ss_pred             CCCCEEEecCCC
Confidence            999999999743

>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=98.03  E-value=1.4e-06  Score=73.75  Aligned_cols=126  Identities=11%  Similarity=0.033  Sum_probs=69.7

Q ss_pred             CCccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccC---CCeeEEEEEe--CCHHHHHHHHH
Q 048347           17 NKVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNY---FDCCAWVYYQ--LSLDMMLDAIM   91 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~---F~~~~wv~~~--~~~~~~~~~i~   91 (351)
                      -++++|.++.++.+.+++....  ..-+-++|+.|+||||+|+.+++.  +...   ......+..+  .....+...+-
T Consensus        11 ~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtl~~~i~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTKE--LYGPDLMKSRILELNASDERGISIVREKVK   86 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHHH--HHHHHHHTTSEEEECSSSCCCHHHHTTHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChHHHHHHHHHH--HcCCcccccchhheeccccccchHHHHHHH
Confidence            3558999999999999997653  334678999999999999999876  3221   1112222223  22322222222


Q ss_pred             HHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE
Q 048347           92 KSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT  155 (351)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv  155 (351)
                      ........     ...    ...+......+.-.+|+|++...  ..+..+...+.......++++
T Consensus        87 ~~~~~~~~-----~~~----~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~  143 (237)
T d1sxjd2          87 NFARLTVS-----KPS----KHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCL  143 (237)
T ss_dssp             HHHHSCCC-----CCC----TTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEE
T ss_pred             HHhhhhhh-----hhh----HHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccc
Confidence            11111111     000    11222333445557899998755  455555554444444555655

>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=98.00  E-value=5.4e-06  Score=67.84  Aligned_cols=45  Identities=13%  Similarity=0.236  Sum_probs=36.6

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|||++++++...|....+.  =+.++|.+|+|||+++..++.+
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k~--n~lLvG~pGVGKTalv~~LA~r   66 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTKN--NPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSC--EEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhccCCC--CeEEEecCCcccHHHHHHHHHH
Confidence            56899999999999999865432  2457999999999998777664

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=97.97  E-value=4.7e-06  Score=68.36  Aligned_cols=82  Identities=15%  Similarity=0.147  Sum_probs=64.4

Q ss_pred             CCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCcccccc-ccccccCCccEEeecCCccccccChh-hhcCCCCC
Q 048347          242 PHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWK-METGAMQKLKSLIVNPCAYLRKFPEE-LWRIKALR  318 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L~  318 (351)
                      +++++|+|+.+.... .+ +..+..+++|+.|++++| .+..+| ..+..+++|++|+|+++ ++..+|.+ +.+|++|+
T Consensus        29 ~~l~~L~Ls~N~i~~-~~~~~~f~~l~~L~~L~L~~N-~i~~~~~~~~~~~~~L~~L~Ls~N-~l~~l~~~~F~~l~~L~  105 (192)
T d1w8aa_          29 LHTTELLLNDNELGR-ISSDGLFGRLPHLVKLELKRN-QLTGIEPNAFEGASHIQELQLGEN-KIKEISNKMFLGLHQLK  105 (192)
T ss_dssp             TTCSEEECCSCCCCS-BCCSCSGGGCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSC-CCCEECSSSSTTCTTCC
T ss_pred             CCCCEEEeCCCCCcc-cccccccCCCceEeeeecccc-ccccccccccccccccceeeeccc-cccccCHHHHhCCCccc
Confidence            689999995443322 33 344678999999999999 566554 45888999999999985 78888775 58899999


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|++++..
T Consensus       106 ~L~L~~N~  113 (192)
T d1w8aa_         106 TLNLYDNQ  113 (192)
T ss_dssp             EEECCSSC
T ss_pred             ccccCCcc
Confidence            99999865

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.97  E-value=7.7e-06  Score=67.39  Aligned_cols=85  Identities=11%  Similarity=0.126  Sum_probs=50.3

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ++.+..+++|++|+++ ++ .+..++. ++.+++|++|++++| ....+| .++.+++|+.|++++|. ...+ ..+.++
T Consensus        55 l~~l~~l~nL~~L~Ls-~N-~l~~~~~-l~~l~~L~~L~l~~n-~~~~~~-~l~~l~~L~~L~l~~~~-~~~~-~~~~~l  127 (199)
T d2omxa2          55 IDGVEYLNNLTQINFS-NN-QLTDITP-LKNLTKLVDILMNNN-QIADIT-PLANLTNLTGLTLFNNQ-ITDI-DPLKNL  127 (199)
T ss_dssp             CTTGGGCTTCCEEECC-SS-CCCCCGG-GTTCTTCCEEECCSS-CCCCCG-GGTTCTTCSEEECCSSC-CCCC-GGGTTC
T ss_pred             ccccccCCCcCcCccc-cc-cccCccc-ccCCccccccccccc-cccccc-ccccccccccccccccc-cccc-cccchh
Confidence            3445667788888883 33 2333443 667777777777777 455665 36666666666666543 2222 235566


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|+.|+++++.
T Consensus       128 ~~L~~L~l~~n~  139 (199)
T d2omxa2         128 TNLNRLELSSNT  139 (199)
T ss_dssp             TTCSEEECCSSC
T ss_pred             hhhHHhhhhhhh
Confidence            666666666543

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.93  E-value=4.3e-06  Score=75.47  Aligned_cols=82  Identities=13%  Similarity=0.116  Sum_probs=48.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..++.++.+.++.+  ....++ ....++++++|++++| .+..++ .+..+++|+.|++++| .+..+| +++++++|
T Consensus       281 ~~~~~~l~~l~~~~n--~l~~~~-~~~~~~~l~~L~ls~n-~l~~l~-~l~~l~~L~~L~L~~n-~l~~l~-~l~~l~~L  353 (384)
T d2omza2         281 LAGLTALTNLELNEN--QLEDIS-PISNLKNLTYLTLYFN-NISDIS-PVSSLTKLQRLFFANN-KVSDVS-SLANLTNI  353 (384)
T ss_dssp             GTTCTTCSEEECCSS--CCSCCG-GGGGCTTCSEEECCSS-CCSCCG-GGGGCTTCCEEECCSS-CCCCCG-GGGGCTTC
T ss_pred             ccccccccccccccc--cccccc-ccchhcccCeEECCCC-CCCCCc-ccccCCCCCEEECCCC-CCCCCh-hHcCCCCC
Confidence            445566666666222  222222 2456666777777766 466665 3666677777777765 455555 46667777


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      ++|++++++
T Consensus       354 ~~L~l~~N~  362 (384)
T d2omza2         354 NWLSAGHNQ  362 (384)
T ss_dssp             CEEECCSSC
T ss_pred             CEEECCCCc
Confidence            777776654

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.93  E-value=1.1e-05  Score=66.52  Aligned_cols=85  Identities=14%  Similarity=0.142  Sum_probs=62.6

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ++.+..+++|+.|.++ ++... .++ .+..+++|++|++++| .+..+| .+..+++|+.|++.+| .+..+| .++++
T Consensus        99 ~~~l~~l~~L~~L~l~-~~~~~-~~~-~~~~l~~L~~L~l~~n-~l~~~~-~l~~~~~L~~L~l~~n-~l~~l~-~l~~l  171 (199)
T d2omxa2          99 ITPLANLTNLTGLTLF-NNQIT-DID-PLKNLTNLNRLELSSN-TISDIS-ALSGLTSLQQLNFSSN-QVTDLK-PLANL  171 (199)
T ss_dssp             CGGGTTCTTCSEEECC-SSCCC-CCG-GGTTCTTCSEEECCSS-CCCCCG-GGTTCTTCSEEECCSS-CCCCCG-GGTTC
T ss_pred             cccccccccccccccc-ccccc-ccc-ccchhhhhHHhhhhhh-hhcccc-cccccccccccccccc-cccCCc-cccCC
Confidence            3446677888888883 33222 232 3677888999999888 577766 5788889999999875 567776 48889


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++++
T Consensus       172 ~~L~~L~ls~N~  183 (199)
T d2omxa2         172 TTLERLDISSNK  183 (199)
T ss_dssp             TTCCEEECCSSC
T ss_pred             CCCCEEECCCCC
Confidence            999999998875

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.91  E-value=7.7e-06  Score=71.80  Aligned_cols=83  Identities=18%  Similarity=0.089  Sum_probs=45.4

Q ss_pred             CCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccc-cccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKM-ETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      +++|+.|++ .++......+..+.+++.+++|++++| .+..+|. .+..+++|++|+|++| .+..+|.++.++++|++
T Consensus       170 ~~~L~~L~l-~~n~~~~~~~~~~~~~~~l~~L~~s~n-~l~~~~~~~~~~l~~L~~L~L~~N-~L~~lp~~l~~l~~L~~  246 (305)
T d1xkua_         170 PPSLTELHL-DGNKITKVDAASLKGLNNLAKLGLSFN-SISAVDNGSLANTPHLRELHLNNN-KLVKVPGGLADHKYIQV  246 (305)
T ss_dssp             CTTCSEEEC-TTSCCCEECTGGGTTCTTCCEEECCSS-CCCEECTTTGGGSTTCCEEECCSS-CCSSCCTTTTTCSSCCE
T ss_pred             CCccCEEEC-CCCcCCCCChhHhhccccccccccccc-cccccccccccccccceeeecccc-cccccccccccccCCCE
Confidence            455666666 233323233444555566666666665 4554433 3555666666666664 45566666666666666


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |++++..
T Consensus       247 L~Ls~N~  253 (305)
T d1xkua_         247 VYLHNNN  253 (305)
T ss_dssp             EECCSSC
T ss_pred             EECCCCc
Confidence            6666543

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.89  E-value=1.5e-05  Score=66.15  Aligned_cols=83  Identities=17%  Similarity=0.143  Sum_probs=53.5

Q ss_pred             CCCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcC
Q 048347          235 MPAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRI  314 (351)
Q Consensus       235 ~~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L  314 (351)
                      ++.+..+++|+.|+++.+  .+..++. ++.+++|++|++++| .+..+| .++.+++|+.|++.+|. +..+| .+.++
T Consensus        61 l~~l~~l~~L~~L~L~~n--~i~~l~~-~~~l~~L~~L~l~~n-~i~~l~-~l~~l~~L~~L~l~~~~-~~~~~-~l~~l  133 (210)
T d1h6ta2          61 VQGIQYLPNVTKLFLNGN--KLTDIKP-LANLKNLGWLFLDEN-KVKDLS-SLKDLKKLKSLSLEHNG-ISDIN-GLVHL  133 (210)
T ss_dssp             CTTGGGCTTCCEEECCSS--CCCCCGG-GTTCTTCCEEECCSS-CCCCGG-GGTTCTTCCEEECTTSC-CCCCG-GGGGC
T ss_pred             chhHhhCCCCCEEeCCCc--cccCccc-cccCccccccccccc-cccccc-ccccccccccccccccc-ccccc-ccccc
Confidence            345667888888888433  3334553 577888888888888 577777 57788888888888753 33333 34444


Q ss_pred             CCCCEEEecC
Q 048347          315 KALRKLESWW  324 (351)
Q Consensus       315 ~~L~~L~l~~  324 (351)
                      ++|+.+++++
T Consensus       134 ~~l~~l~~~~  143 (210)
T d1h6ta2         134 PQLESLYLGN  143 (210)
T ss_dssp             TTCCEEECCS
T ss_pred             cccccccccc
Confidence            4444444433

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.87  E-value=9.8e-06  Score=69.88  Aligned_cols=79  Identities=18%  Similarity=0.163  Sum_probs=53.4

Q ss_pred             CCceEEEEecccccCceeee-CCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEE
Q 048347          242 PHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKL  320 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  320 (351)
                      +++++|+|+.+  .+..+|. .+..+++|++|+|++| .++.+|. ++.+++|++|+|++| .+...|..+.++++|+.|
T Consensus        31 ~~l~~L~Ls~N--~i~~l~~~~f~~l~~L~~L~L~~N-~l~~l~~-~~~l~~L~~L~Ls~N-~l~~~~~~~~~l~~L~~L  105 (266)
T d1p9ag_          31 KDTTILHLSEN--LLYTFSLATLMPYTRLTQLNLDRA-ELTKLQV-DGTLPVLGTLDLSHN-QLQSLPLLGQTLPALTVL  105 (266)
T ss_dssp             TTCCEEECTTS--CCSEEEGGGGTTCTTCCEEECTTS-CCCEEEC-CSCCTTCCEEECCSS-CCSSCCCCTTTCTTCCEE
T ss_pred             cCCCEEECcCC--cCCCcCHHHhhccccccccccccc-ccccccc-ccccccccccccccc-cccccccccccccccccc
Confidence            46777777322  3445553 4677777777777777 5777763 567777777777774 566667777777777777


Q ss_pred             EecCC
Q 048347          321 ESWWP  325 (351)
Q Consensus       321 ~l~~~  325 (351)
                      ++++.
T Consensus       106 ~l~~~  110 (266)
T d1p9ag_         106 DVSFN  110 (266)
T ss_dssp             ECCSS
T ss_pred             ccccc
Confidence            77654

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.86  E-value=7.6e-06  Score=68.07  Aligned_cols=80  Identities=16%  Similarity=0.184  Sum_probs=65.8

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+..|+.|++ .+ ..+..++ .+..+++|++|++++| .+..+| .++.+++|++|++++| .+..+| .+.++++|+.
T Consensus        44 ~L~~L~~L~l-~~-~~i~~l~-~l~~l~~L~~L~L~~n-~i~~l~-~~~~l~~L~~L~l~~n-~i~~l~-~l~~l~~L~~  116 (210)
T d1h6ta2          44 ELNSIDQIIA-NN-SDIKSVQ-GIQYLPNVTKLFLNGN-KLTDIK-PLANLKNLGWLFLDEN-KVKDLS-SLKDLKKLKS  116 (210)
T ss_dssp             HHHTCCEEEC-TT-SCCCCCT-TGGGCTTCCEEECCSS-CCCCCG-GGTTCTTCCEEECCSS-CCCCGG-GGTTCTTCCE
T ss_pred             HhcCccEEEC-cC-CCCCCch-hHhhCCCCCEEeCCCc-cccCcc-ccccCccccccccccc-cccccc-cccccccccc
Confidence            4678899999 33 3444444 3678999999999999 688888 5789999999999985 688888 6899999999


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |++.++.
T Consensus       117 L~l~~~~  123 (210)
T d1h6ta2         117 LSLEHNG  123 (210)
T ss_dssp             EECTTSC
T ss_pred             ccccccc
Confidence            9999876

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.81  E-value=1.2e-05  Score=70.56  Aligned_cols=88  Identities=11%  Similarity=0.020  Sum_probs=70.8

Q ss_pred             CCCCCCCCceEEEEecccccCcee-eeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhh---
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKL-VCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEEL---  311 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~l-p~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i---  311 (351)
                      ..+..++.+++|+++ ++ .+..+ +..+.++++|++|+|++| .+..+|..++.+++|++|+|++| ++..+|...   
T Consensus       189 ~~~~~~~~l~~L~~s-~n-~l~~~~~~~~~~l~~L~~L~L~~N-~L~~lp~~l~~l~~L~~L~Ls~N-~i~~i~~~~f~~  264 (305)
T d1xkua_         189 ASLKGLNNLAKLGLS-FN-SISAVDNGSLANTPHLRELHLNNN-KLVKVPGGLADHKYIQVVYLHNN-NISAIGSNDFCP  264 (305)
T ss_dssp             GGGTTCTTCCEEECC-SS-CCCEECTTTGGGSTTCCEEECCSS-CCSSCCTTTTTCSSCCEEECCSS-CCCCCCTTSSSC
T ss_pred             hHhhccccccccccc-cc-cccccccccccccccceeeecccc-cccccccccccccCCCEEECCCC-ccCccChhhccC
Confidence            445778899999994 33 34455 445678899999999999 79999999999999999999995 688887532   


Q ss_pred             ----hcCCCCCEEEecCCCh
Q 048347          312 ----WRIKALRKLESWWPRP  327 (351)
Q Consensus       312 ----~~L~~L~~L~l~~~~~  327 (351)
                          ..+.+|+.|++++.+-
T Consensus       265 ~~~~~~~~~L~~L~L~~N~~  284 (305)
T d1xkua_         265 PGYNTKKASYSGVSLFSNPV  284 (305)
T ss_dssp             SSCCTTSCCCSEEECCSSSS
T ss_pred             cchhcccCCCCEEECCCCcC
Confidence                3578899999999873

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.77  E-value=1.3e-05  Score=72.15  Aligned_cols=80  Identities=13%  Similarity=0.155  Sum_probs=61.6

Q ss_pred             CCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCE
Q 048347          240 KLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRK  319 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  319 (351)
                      .+.+|+.|++  ....+..+. .++.+++|++|++++| .++.+|. +++|++|++|++++| .+..+| .++++++|+.
T Consensus        42 ~l~~l~~L~l--~~~~I~~l~-gl~~L~nL~~L~Ls~N-~l~~l~~-l~~L~~L~~L~L~~n-~i~~i~-~l~~l~~L~~  114 (384)
T d2omza2          42 DLDQVTTLQA--DRLGIKSID-GVEYLNNLTQINFSNN-QLTDITP-LKNLTKLVDILMNNN-QIADIT-PLANLTNLTG  114 (384)
T ss_dssp             HHTTCCEEEC--CSSCCCCCT-TGGGCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSS-CCCCCG-GGTTCTTCCE
T ss_pred             HhCCCCEEEC--CCCCCCCcc-ccccCCCCCEEeCcCC-cCCCCcc-ccCCccccccccccc-cccccc-cccccccccc
Confidence            4677889999  333444553 4678889999999998 6888884 888999999999985 466666 3788999999


Q ss_pred             EEecCCC
Q 048347          320 LESWWPR  326 (351)
Q Consensus       320 L~l~~~~  326 (351)
                      |++++..
T Consensus       115 L~~~~~~  121 (384)
T d2omza2         115 LTLFNNQ  121 (384)
T ss_dssp             EECCSSC
T ss_pred             ccccccc
Confidence            9987754

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=4.1e-05  Score=66.32  Aligned_cols=85  Identities=19%  Similarity=0.128  Sum_probs=64.6

Q ss_pred             CCCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCccccc-cccccccCCccEEeecCCccccccC-hhhh
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEW-KMETGAMQKLKSLIVNPCAYLRKFP-EELW  312 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~~c~~l~~lP-~~i~  312 (351)
                      ..+..+++|+.|+++ ++ .+..++. .+.++++|+++++++|. +..+ |..++.+++|++|++++| .+..+| ..++
T Consensus       147 ~~f~~~~~L~~L~l~-~N-~l~~l~~~~f~~l~~L~~l~l~~N~-l~~i~~~~f~~l~~L~~L~l~~N-~i~~~~~~~~~  222 (284)
T d1ozna_         147 DTFRDLGNLTHLFLH-GN-RISSVPERAFRGLHSLDRLLLHQNR-VAHVHPHAFRDLGRLMTLYLFAN-NLSALPTEALA  222 (284)
T ss_dssp             TTTTTCTTCCEEECC-SS-CCCEECTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSS-CCSCCCHHHHT
T ss_pred             hHhccccchhhcccc-cC-cccccchhhhccccccchhhhhhcc-ccccChhHhhhhhhccccccccc-ccccccccccc
Confidence            345678889999994 33 3445644 46788999999999984 5544 667899999999999985 456666 4668


Q ss_pred             cCCCCCEEEecC
Q 048347          313 RIKALRKLESWW  324 (351)
Q Consensus       313 ~L~~L~~L~l~~  324 (351)
                      ++++|++|++++
T Consensus       223 ~~~~L~~L~l~~  234 (284)
T d1ozna_         223 PLRALQYLRLND  234 (284)
T ss_dssp             TCTTCCEEECCS
T ss_pred             cccccCEEEecC
Confidence            899999999987

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=97.72  E-value=4.4e-05  Score=63.85  Aligned_cols=101  Identities=13%  Similarity=0.121  Sum_probs=69.3

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +...+.+..+.++ ++ ..... ..+..+++|++|++++| .+..++ .++.+++|+.|++++| .+..+|. ++++++|
T Consensus       125 ~~~~~~~~~l~~~-~~-~~~~~-~~~~~~~~L~~L~l~~n-~~~~~~-~l~~l~~L~~L~Ls~n-~l~~l~~-l~~l~~L  197 (227)
T d1h6ua2         125 LAGLSNLQVLYLD-LN-QITNI-SPLAGLTNLQYLSIGNA-QVSDLT-PLANLSKLTTLKADDN-KISDISP-LASLPNL  197 (227)
T ss_dssp             GTTCTTCCEEECC-SS-CCCCC-GGGGGCTTCCEEECCSS-CCCCCG-GGTTCTTCCEEECCSS-CCCCCGG-GGGCTTC
T ss_pred             hccccchhhhhch-hh-hhchh-hhhcccccccccccccc-ccccch-hhcccccceecccCCC-ccCCChh-hcCCCCC
Confidence            4455666677662 22 22222 23567788999999998 566665 4889999999999986 6888874 8999999


Q ss_pred             CEEEecCCChhHHhhccccccCceeeEE
Q 048347          318 RKLESWWPRPELRQSLHKFEEIDRLDMQ  345 (351)
Q Consensus       318 ~~L~l~~~~~~~~~~l~~~~~~~~~~~~  345 (351)
                      ++|++++++-.-...++.+......++.
T Consensus       198 ~~L~Ls~N~lt~i~~l~~l~~L~~L~ls  225 (227)
T d1h6ua2         198 IEVHLKNNQISDVSPLANTSNLFIVTLT  225 (227)
T ss_dssp             CEEECTTSCCCBCGGGTTCTTCCEEEEE
T ss_pred             CEEECcCCcCCCCcccccCCCCCEEEee
Confidence            9999999863322334445544445544

>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=97.71  E-value=6.2e-05  Score=68.30  Aligned_cols=44  Identities=14%  Similarity=0.326  Sum_probs=34.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhC
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      +.+||||++++++++.|....+...  .++|.+|+|||+++..++.
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k~n~--llvG~~GvGKtaiv~~la~   65 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTKNNP--VLIGEPGVGKTAIVEGLAQ   65 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSCCCC--EEEECTTSCHHHHHHHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhcCCCCCC--eEECCCCCCHHHHHHHHHH
Confidence            4589999999999999986643322  3579999999997765543

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=97.71  E-value=4.8e-07  Score=75.10  Aligned_cols=86  Identities=14%  Similarity=0.105  Sum_probs=52.7

Q ss_pred             CCCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccC--hhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFP--EELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP--~~i~~  313 (351)
                      +.+..+++|++|+++.+  .+..+|.....+++|++|++++| .+..++ .+..+++|++|++++| .+..+|  ..+.+
T Consensus        64 ~~l~~l~~L~~L~Ls~N--~i~~i~~~~~~~~~L~~L~l~~N-~i~~l~-~~~~l~~L~~L~L~~N-~i~~~~~~~~l~~  138 (198)
T d1m9la_          64 SSLSGMENLRILSLGRN--LIKKIENLDAVADTLEELWISYN-QIASLS-GIEKLVNLRVLYMSNN-KITNWGEIDKLAA  138 (198)
T ss_dssp             CCHHHHTTCCEEECCEE--EECSCSSHHHHHHHCCEEECSEE-ECCCHH-HHHHHHHSSEEEESEE-ECCCHHHHHHHTT
T ss_pred             ccccCCccccChhhccc--ccccccccccccccccccccccc-cccccc-cccccccccccccccc-hhccccccccccC
Confidence            34555666777777322  22234432333456777777776 566665 3667777788888763 566665  35677


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|++++.+
T Consensus       139 l~~L~~L~L~~N~  151 (198)
T d1m9la_         139 LDKLEDLLLAGNP  151 (198)
T ss_dssp             TTTCSEEEECSSH
T ss_pred             CCccceeecCCCc
Confidence            7888888887754

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.68  E-value=5.2e-06  Score=72.55  Aligned_cols=90  Identities=13%  Similarity=0.061  Sum_probs=56.7

Q ss_pred             CCCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccc--cChhhhcC
Q 048347          237 APEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRK--FPEELWRI  314 (351)
Q Consensus       237 ~l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~--lP~~i~~L  314 (351)
                      .......|++|+++.+......++..+..+++|++|++++|......+..++.+++|++|++++|+.+..  +..-..++
T Consensus        41 ~~~~~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c~~itd~~l~~l~~~~  120 (284)
T d2astb2          41 EHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSC  120 (284)
T ss_dssp             SCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHC
T ss_pred             hhccCCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCCCcHHHHHHhcCCCCcCccccccccccccccchhhHHH
Confidence            3345567888888322222233444466777888888888743335566677778888888888766642  22223567


Q ss_pred             CCCCEEEecCCC
Q 048347          315 KALRKLESWWPR  326 (351)
Q Consensus       315 ~~L~~L~l~~~~  326 (351)
                      ++|++|++++|.
T Consensus       121 ~~L~~L~ls~c~  132 (284)
T d2astb2         121 SRLDELNLSWCF  132 (284)
T ss_dssp             TTCCEEECCCCT
T ss_pred             Hhcccccccccc
Confidence            788888887764

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=4.3e-05  Score=60.32  Aligned_cols=81  Identities=12%  Similarity=0.093  Sum_probs=63.3

Q ss_pred             CceEEEEecccccCceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCCCCCEE
Q 048347          243 HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIKALRKL  320 (351)
Q Consensus       243 ~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L  320 (351)
                      ....++.+  .......|..+..+++|+.|+++++..++.+|.. +..|++|+.|++++| ++..+|.+ +.++++|++|
T Consensus         9 ~~~~l~c~--~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N-~l~~i~~~~f~~l~~L~~L   85 (156)
T d2ifga3           9 GSSGLRCT--RDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKS-GLRFVAPDAFHFTPRLSRL   85 (156)
T ss_dssp             SSSCEECC--SSCCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSS-CCCEECTTGGGSCSCCCEE
T ss_pred             CCCeEEec--CCCCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeecc-ccCCcccccccccccccce
Confidence            34456662  2233356777888899999999887669999865 889999999999984 68888654 7899999999


Q ss_pred             EecCCC
Q 048347          321 ESWWPR  326 (351)
Q Consensus       321 ~l~~~~  326 (351)
                      ++++..
T Consensus        86 ~Ls~N~   91 (156)
T d2ifga3          86 NLSFNA   91 (156)
T ss_dssp             ECCSSC
T ss_pred             eccCCC
Confidence            999865

>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=97.66  E-value=3.5e-05  Score=64.23  Aligned_cols=123  Identities=15%  Similarity=0.112  Sum_probs=69.2

Q ss_pred             CCccccchhh--HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHh
Q 048347           17 NKVDLDLEDK--MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSL   94 (351)
Q Consensus        17 ~~~~vGr~~~--~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~   94 (351)
                      ++.+||-..+  ...+.++....++....+-|||..|+|||.|++++++.  .......+++++    ..++...+...+
T Consensus        10 dnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~~----~~~~~~~~~~~~   83 (213)
T d1l8qa2          10 ENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSS----ADDFAQAMVEHL   83 (213)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEE----HHHHHHHHHHHH
T ss_pred             hhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHH--hccCccceEEec----hHHHHHHHHHHH
Confidence            3445664322  33345555443334444779999999999999999998  555555555554    345555554444


Q ss_pred             CCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh---hhHHH-HHhhcCC-CCCCcEEEE-Eeec
Q 048347           95 MPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG---DIWDF-LKEALPD-HQNGSRILT-ALIH  159 (351)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~---~~~~~-l~~~l~~-~~~gs~Iiv-TR~~  159 (351)
                      ...         ..    ..+.+.+++ --+++|||+...   ..|+. +...+.. ...|..||+ ++..
T Consensus        84 ~~~---------~~----~~~~~~~~~-~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~  140 (213)
T d1l8qa2          84 KKG---------TI----NEFRNMYKS-VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRH  140 (213)
T ss_dssp             HHT---------CH----HHHHHHHHT-CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             Hcc---------ch----hhHHHHHhh-ccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCc
Confidence            322         11    222233333 447899999744   45554 3333332 334667777 5543

>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=97.63  E-value=0.00016  Score=61.46  Aligned_cols=47  Identities=15%  Similarity=0.063  Sum_probs=35.3

Q ss_pred             CccccchhhHHHHHHHHH-------cc-CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLI-------ER-QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~-------~~-~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+||..++++.+++.+.       .. ....+-|-++|+.|+|||++|+++++.
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~   63 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE   63 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhc
Confidence            458898887777766553       11 123455779999999999999999987

>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=97.63  E-value=0.00018  Score=59.37  Aligned_cols=130  Identities=10%  Similarity=-0.024  Sum_probs=69.7

Q ss_pred             cchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcc--cccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCC
Q 048347           22 DLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSY--VKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSA   99 (351)
Q Consensus        22 Gr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~   99 (351)
                      +.++..+++.+.+..+. -..-+-++|+.|+||||+|+.+.+...  .......+       ....-.+.+.........
T Consensus         6 w~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~-------~~~~~~~~i~~~~~~~~~   77 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSC-------GHCRGCQLMQAGTHPDYY   77 (207)
T ss_dssp             GGHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCC-------SCSHHHHHHHHTCCTTEE
T ss_pred             ccHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccc-------cccchhhhhhhccccccc
Confidence            44566788888877653 234466899999999999997765310  00000000       000001111111111000


Q ss_pred             C----ccCCCCCHHHHHHHHHHhc-----CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347          100 L----SEILDNDFEMKKNTLHNYL-----KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus       100 ~----~~~~~~~~~~~~~~l~~~L-----~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      .    ........+++.+ +.+.+     .+++-++|+|+++..  ++...+...+.....+.++|. |++.+
T Consensus        78 ~~~~~~~~~~i~~~~ir~-l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~  149 (207)
T d1a5ta2          78 TLAPEKGKNTLGVDAVRE-VTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPE  149 (207)
T ss_dssp             EECCCTTCSSBCHHHHHH-HHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGG
T ss_pred             hhhhhhcccccccchhhH-HhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChh
Confidence            0    0001122333322 22322     356778999999865  578888888888777888887 77654

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.54  E-value=0.00011  Score=63.49  Aligned_cols=88  Identities=14%  Similarity=0.090  Sum_probs=66.3

Q ss_pred             CCCCCCCCceEEEEecccccCceeee-CCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChhhhc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSGRKLVC-GHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEELWR  313 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~~~lp~-~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~i~~  313 (351)
                      .....+++|+.++++.+  .+..+|. .+..+++|+.|++++| .+..+|.. +..+++|+++++.+|....-.|..+.+
T Consensus       123 ~~~~~~~~L~~l~l~~N--~l~~i~~~~f~~~~~L~~L~l~~N-~l~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~  199 (284)
T d1ozna_         123 GLFRGLAALQYLYLQDN--ALQALPDDTFRDLGNLTHLFLHGN-RISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRD  199 (284)
T ss_dssp             TTTTTCTTCCEEECCSS--CCCCCCTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTT
T ss_pred             cccchhcccchhhhccc--cccccChhHhccccchhhcccccC-cccccchhhhccccccchhhhhhccccccChhHhhh
Confidence            34556778888888333  3345543 4667888999999998 68877654 678999999999987655555788899


Q ss_pred             CCCCCEEEecCCC
Q 048347          314 IKALRKLESWWPR  326 (351)
Q Consensus       314 L~~L~~L~l~~~~  326 (351)
                      +++|++|++++..
T Consensus       200 l~~L~~L~l~~N~  212 (284)
T d1ozna_         200 LGRLMTLYLFANN  212 (284)
T ss_dssp             CTTCCEEECCSSC
T ss_pred             hhhcccccccccc
Confidence            9999999998743

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=97.50  E-value=2.4e-06  Score=70.71  Aligned_cols=83  Identities=17%  Similarity=0.151  Sum_probs=67.5

Q ss_pred             CCCCCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCC
Q 048347          238 PEKLPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKAL  317 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L  317 (351)
                      +..+++|++|+|+.+  .+..++ .+..+++|++|++++| .+..+|.....+++|+.|++++| .+..+| .+.++++|
T Consensus        44 l~~L~~L~~L~Ls~n--~I~~i~-~l~~l~~L~~L~Ls~N-~i~~i~~~~~~~~~L~~L~l~~N-~i~~l~-~~~~l~~L  117 (198)
T d1m9la_          44 LSTLKACKHLALSTN--NIEKIS-SLSGMENLRILSLGRN-LIKKIENLDAVADTLEELWISYN-QIASLS-GIEKLVNL  117 (198)
T ss_dssp             HHHTTTCCEEECSEE--EESCCC-CHHHHTTCCEEECCEE-EECSCSSHHHHHHHCCEEECSEE-ECCCHH-HHHHHHHS
T ss_pred             HhcccccceeECccc--CCCCcc-cccCCccccChhhccc-ccccccccccccccccccccccc-cccccc-cccccccc
Confidence            456899999999433  344565 4778899999999999 68899876667789999999985 677775 68899999


Q ss_pred             CEEEecCCC
Q 048347          318 RKLESWWPR  326 (351)
Q Consensus       318 ~~L~l~~~~  326 (351)
                      +.|++++..
T Consensus       118 ~~L~L~~N~  126 (198)
T d1m9la_         118 RVLYMSNNK  126 (198)
T ss_dssp             SEEEESEEE
T ss_pred             cccccccch
Confidence            999999854

>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=97.41  E-value=5.5e-05  Score=64.22  Aligned_cols=48  Identities=8%  Similarity=0.005  Sum_probs=39.7

Q ss_pred             CCccccchhhHHHHHHHHHc---------------cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIE---------------RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~---------------~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++++|.++.+++|.+++..               +....+.+.++|+.|+||||+|+.+++.
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~   75 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE   75 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            46799999999999999853               1123457889999999999999999987

>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=97.41  E-value=8.1e-05  Score=63.80  Aligned_cols=95  Identities=11%  Similarity=0.044  Sum_probs=57.3

Q ss_pred             CccccchhhHHHHHHHHHc-----------cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIE-----------RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      ++++|.|..+++|.+.+..           +-+..+-+-++|+.|+|||++|+++.+.  ...+|   .  .++  ..+ 
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~--~~~~~---~--~i~--~~~-   73 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE--TGAFF---F--LIN--GPE-   73 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHH--TTCEE---E--EEC--HHH-
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHH--hCCeE---E--EEE--chh-
Confidence            3588999999999887531           1122345678999999999999999887  32221   1  111  111 


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCCCh
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVWRG  134 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~~~  134 (351)
                             +.....     ......+.+.+...-..+++++++||++..
T Consensus        74 -------l~~~~~-----g~~~~~l~~~f~~A~~~~p~il~iDeid~l  109 (258)
T d1e32a2          74 -------IMSKLA-----GESESNLRKAFEEAEKNAPAIIFIDELDAI  109 (258)
T ss_dssp             -------HTTSCT-----THHHHHHHHHHHHHHHTCSEEEEESSGGGT
T ss_pred             -------hccccc-----ccHHHHHHHHHHHHHhcCCeEEEehhhhhh
Confidence                   111100     112333344444444678899999999753

>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=97.41  E-value=3e-05  Score=65.40  Aligned_cols=48  Identities=15%  Similarity=0.045  Sum_probs=38.0

Q ss_pred             CCccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      =+++||-++-+++|..++...   ++..+-+-++|+.|+||||+|+.+++.
T Consensus         8 ~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2           8 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhc
Confidence            366899999999999988532   222334568999999999999999887

>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=97.37  E-value=0.00013  Score=62.43  Aligned_cols=92  Identities=12%  Similarity=0.077  Sum_probs=56.9

Q ss_pred             CccccchhhHHHHHHHHH---cc-------CCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCHHHH
Q 048347           18 KVDLDLEDKMEELLDLLI---ER-------QPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSLDMM   86 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~---~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~~~~   86 (351)
                      ++++|.|+.+++|.+.+.   ..       ....+-+-++|+.|+|||++|+.+.+.  ...+     ++.++ .++.  
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~--~~~~-----~~~i~~~~l~--   82 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE--AKVP-----FFTISGSDFV--   82 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH--HTCC-----EEEECSCSST--
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHH--cCCC-----EEEEEhHHhh--
Confidence            578999999888876542   11       122345679999999999999999977  3222     22232 1110  


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                               .. .    -......+.+.+...-+..++++++||++
T Consensus        83 ---------~~-~----~g~~~~~l~~~f~~A~~~~P~il~iDeiD  114 (256)
T d1lv7a_          83 ---------EM-F----VGVGASRVRDMFEQAKKAAPCIIFIDEID  114 (256)
T ss_dssp             ---------TS-C----CCCCHHHHHHHHHHHHTTCSEEEEETTHH
T ss_pred             ---------hc-c----hhHHHHHHHHHHHHHHHcCCEEEEEEChh
Confidence                     00 0    11234445555555556788999999995

>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=97.33  E-value=6.6e-05  Score=63.31  Aligned_cols=47  Identities=13%  Similarity=0.112  Sum_probs=37.4

Q ss_pred             CccccchhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++||-++-++++..++...   ....+-+-++|+.|+||||+|+.+++.
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~   58 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHE   58 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            56899999999998888642   122344568999999999999999887

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.27  E-value=0.00038  Score=58.24  Aligned_cols=83  Identities=17%  Similarity=0.131  Sum_probs=61.6

Q ss_pred             CCceEEEEecccccCceeeeC-CCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccChh-hhcCCCCC
Q 048347          242 PHLKVLKLKRSSYSGRKLVCG-HGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPEE-LWRIKALR  318 (351)
Q Consensus       242 ~~L~~L~l~~~~~~~~~lp~~-~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L~  318 (351)
                      +++++|+++.+  .+..+|.. +.++++|++|++++|.....+|.. +..+++++.|.+..|..+..+|.. +.++++|+
T Consensus        29 ~~l~~L~Ls~n--~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~l~~L~  106 (242)
T d1xwdc1          29 RNAIELRFVLT--KLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQ  106 (242)
T ss_dssp             SCCSEEEEESC--CCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCCEECTTSEECCTTCC
T ss_pred             CCCCEEECcCC--cCCccChhHhhccchhhhhhhccccccceeecccccccccccccccccccccccccccccccccccc
Confidence            47899999433  35577764 678899999999998544555543 678889999988776667666654 57889999


Q ss_pred             EEEecCCC
Q 048347          319 KLESWWPR  326 (351)
Q Consensus       319 ~L~l~~~~  326 (351)
                      +|+++++.
T Consensus       107 ~l~l~~~~  114 (242)
T d1xwdc1         107 YLLISNTG  114 (242)
T ss_dssp             EEEEESCC
T ss_pred             ccccchhh
Confidence            99998764

>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=97.26  E-value=0.00016  Score=58.46  Aligned_cols=50  Identities=8%  Similarity=0.086  Sum_probs=34.0

Q ss_pred             hhHHHHHHHHHc-cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEE
Q 048347           25 DKMEELLDLLIE-RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAW   76 (351)
Q Consensus        25 ~~~~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~w   76 (351)
                      +.++.|.+.+.. +..+.-+|||.|..|+||||||+++...  .....-....
T Consensus         5 ~~~~~~~~~~~~~~~~~~~iIgI~G~~GSGKSTla~~L~~~--l~~~~~~~~~   55 (198)
T d1rz3a_           5 DRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQT--LREQGISVCV   55 (198)
T ss_dssp             HHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEE
T ss_pred             HHHHHHHHHHHhccCCCCEEEEEECCCCCCHHHHHHHHHHH--hcccccccee
Confidence            344555544433 2445678999999999999999999877  4444433333

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.25  E-value=6.7e-05  Score=65.16  Aligned_cols=85  Identities=19%  Similarity=0.118  Sum_probs=58.8

Q ss_pred             CCCceEEEEecccccC--ceeeeCCCCCCcccEEEEecCCccc-cccccccccCCccEEeecCCcccc-ccChhhhcCCC
Q 048347          241 LPHLKVLKLKRSSYSG--RKLVCGHGGFPRQEILHLKSMLWLE-EWKMETGAMQKLKSLIVNPCAYLR-KFPEELWRIKA  316 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~--~~lp~~~~~l~~L~~L~L~~~~~l~-~lp~~i~~L~~L~~L~l~~c~~l~-~lP~~i~~L~~  316 (351)
                      .++|+.|.++......  ..+..-...+++|++|++++|..++ ..+..++++++|++|++++|..+. .-+..++++++
T Consensus       147 ~~~L~~L~l~~~~~~i~~~~l~~l~~~~~~L~~L~L~~~~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~  226 (284)
T d2astb2         147 SETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPT  226 (284)
T ss_dssp             CTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTT
T ss_pred             ccccchhhhcccccccccccccccccccccccccccccccCCCchhhhhhcccCcCCEEECCCCCCCChHHHHHHhcCCC
Confidence            4678888883222222  1233333567889999999886665 455668888999999999987663 23345778889


Q ss_pred             CCEEEecCC
Q 048347          317 LRKLESWWP  325 (351)
Q Consensus       317 L~~L~l~~~  325 (351)
                      |+.|+++++
T Consensus       227 L~~L~l~~~  235 (284)
T d2astb2         227 LKTLQVFGI  235 (284)
T ss_dssp             CCEEECTTS
T ss_pred             CCEEeeeCC
Confidence            999999887

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=97.22  E-value=0.00025  Score=62.40  Aligned_cols=75  Identities=23%  Similarity=0.076  Sum_probs=57.5

Q ss_pred             CCCceEEEEecccccCceeeeCCCCCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEE
Q 048347          241 LPHLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKL  320 (351)
Q Consensus       241 l~~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  320 (351)
                      +++|++|+++  +..+..+|..   +.+|+.|++++| .+..++.-   .++|++|++++| .+..+|. .+++++|++|
T Consensus        57 ~~~L~~L~Ls--~N~l~~lp~~---~~~L~~L~l~~n-~l~~l~~l---p~~L~~L~L~~n-~l~~lp~-~~~l~~L~~L  125 (353)
T d1jl5a_          57 PPHLESLVAS--CNSLTELPEL---PQSLKSLLVDNN-NLKALSDL---PPLLEYLGVSNN-QLEKLPE-LQNSSFLKII  125 (353)
T ss_dssp             CTTCSEEECC--SSCCSSCCCC---CTTCCEEECCSS-CCSCCCSC---CTTCCEEECCSS-CCSSCCC-CTTCTTCCEE
T ss_pred             CCCCCEEECC--CCCCcccccc---hhhhhhhhhhhc-ccchhhhh---cccccccccccc-ccccccc-hhhhccceee
Confidence            4789999994  3355577754   457889999998 57776631   246999999985 6888985 6899999999


Q ss_pred             EecCCC
Q 048347          321 ESWWPR  326 (351)
Q Consensus       321 ~l~~~~  326 (351)
                      +++++.
T Consensus       126 ~l~~~~  131 (353)
T d1jl5a_         126 DVDNNS  131 (353)
T ss_dssp             ECCSSC
T ss_pred             cccccc
Confidence            998754

>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=97.21  E-value=7.5e-05  Score=59.68  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.|.|.|+.|+||||||+.+...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            688999999999999999999886

>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=97.12  E-value=0.00028  Score=59.88  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=36.9

Q ss_pred             cCCCCCccccchhhHHHHHHHHH---cc-------CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           13 LSWDNKVDLDLEDKMEELLDLLI---ER-------QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        13 ~~~~~~~~vGr~~~~~~l~~~L~---~~-------~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.+.=++++|.|+.++.|.+.+.   ..       ....+-+-++|+.|+|||++|+.+.+.
T Consensus         4 p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~   65 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   65 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHH
Confidence            33333578999988887765442   11       122345779999999999999999987

>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=97.00  E-value=0.00014  Score=57.23  Aligned_cols=24  Identities=17%  Similarity=0.278  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|++|+|..|+|||||++++...
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~   25 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPA   25 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999999876

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=96.99  E-value=0.00027  Score=62.07  Aligned_cols=54  Identities=24%  Similarity=0.178  Sum_probs=32.9

Q ss_pred             CCCcccEEEEecCCccccccccccccCCccEEeecCCccccccChhhhcCCCCCEEEecCCC
Q 048347          265 GFPRQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       265 ~l~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  326 (351)
                      .+++|++|++++| .+..+|..   +++|+.|++++| .+..+|+.   +++|++|++++++
T Consensus       282 ~~~~L~~L~Ls~N-~l~~lp~~---~~~L~~L~L~~N-~L~~l~~~---~~~L~~L~L~~N~  335 (353)
T d1jl5a_         282 LPPSLEELNVSNN-KLIELPAL---PPRLERLIASFN-HLAEVPEL---PQNLKQLHVEYNP  335 (353)
T ss_dssp             CCTTCCEEECCSS-CCSCCCCC---CTTCCEEECCSS-CCSCCCCC---CTTCCEEECCSSC
T ss_pred             cCCCCCEEECCCC-ccCccccc---cCCCCEEECCCC-cCCccccc---cCCCCEEECcCCc
Confidence            3556777777776 46666642   456666777664 46666643   3456667766654

>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=96.99  E-value=0.00019  Score=55.60  Aligned_cols=23  Identities=13%  Similarity=0.238  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|.|+.|+||||+|+++...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999998654

>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=96.98  E-value=0.0022  Score=52.23  Aligned_cols=107  Identities=11%  Similarity=0.021  Sum_probs=65.5

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC---eeEEEEEeCCHHHHHHHHHHHhCCCCCCccC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD---CCAWVYYQLSLDMMLDAIMKSLMPLSALSEI  103 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~---~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~  103 (351)
                      ++.+..++..+  ...-+-++|..|+|||++|..+.+.  +...+.   ...++.-.                  .    
T Consensus         3 ~~~l~~~i~~~--~~~~~l~~G~~g~gk~~~a~~l~~~--i~~~~~~h~D~~~i~~~------------------~----   56 (198)
T d2gnoa2           3 LETLKRIIEKS--EGISILINGEDLSYPREVSLELPEY--VEKFPPKASDVLEIDPE------------------G----   56 (198)
T ss_dssp             HHHHHHHHHTC--SSEEEEEECSSSSHHHHHHHHHHHH--HHTSCCCTTTEEEECCS------------------S----
T ss_pred             HHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHH--HhccccCCCCEEEEeCC------------------c----
Confidence            45566666544  3677789999999999999988765  322211   12332211                  0    


Q ss_pred             CCCCHHHHHHHHHHhc-----CCceEEEEEeCCCCh--hhHHHHHhhcCCCCCCcEEEE-Eeecc
Q 048347          104 LDNDFEMKKNTLHNYL-----KNKRYLIVIQDVWRG--DIWDFLKEALPDHQNGSRILT-ALIHI  160 (351)
Q Consensus       104 ~~~~~~~~~~~l~~~L-----~~k~~LlVLDdv~~~--~~~~~l~~~l~~~~~gs~Iiv-TR~~~  160 (351)
                      ..-..+++.+ +.+.+     .+++-++|+|+++..  ++++.+...+.....++.+|+ |.+.+
T Consensus        57 ~~I~Id~IR~-i~~~~~~~~~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~  120 (198)
T d2gnoa2          57 ENIGIDDIRT-IKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWH  120 (198)
T ss_dssp             SCBCHHHHHH-HHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGG
T ss_pred             CCCCHHHHHH-HHHHHhhCcccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChh
Confidence            0112233322 21222     245558899999855  688889888887777888877 76554

>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=96.97  E-value=7.8e-05  Score=58.23  Aligned_cols=23  Identities=9%  Similarity=0.174  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.+.|+.|+||||+|+.+...
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            35778899999999999999987

>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=96.95  E-value=0.00021  Score=56.28  Aligned_cols=23  Identities=13%  Similarity=0.135  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|.|+.|+||||+|+++...
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~   25 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999765

>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=96.91  E-value=0.00064  Score=56.11  Aligned_cols=57  Identities=7%  Similarity=-0.034  Sum_probs=40.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-C--CHHHHHHHHHHHhCCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-L--SLDMMLDAIMKSLMPL   97 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~--~~~~~~~~i~~~~~~~   97 (351)
                      .+..||.++|+.|+||||.+.+++..  ...+-..+..++.. |  ...+-++..++.+..+
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~--~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   68 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKM--FVDEGKSVVLAAADTFRAAAIEQLKIWGERVGAT   68 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHH--HHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCceEEEeecccccchhHHHHHHhhhcCcc
Confidence            45689999999999999988887766  33333457778777 3  3345666777777654

>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=96.90  E-value=0.00028  Score=60.57  Aligned_cols=93  Identities=12%  Similarity=0.064  Sum_probs=56.8

Q ss_pred             CccccchhhHHHHHHHHHc-----------cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           18 KVDLDLEDKMEELLDLLIE-----------RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      ++++|.++.+++|.+.+..           +-...+-|-++|+.|.|||+||++++..  ..-+     ++.++  ..++
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~--~~~~-----~~~~~--~~~l   77 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQAN-----FISIK--GPEL   77 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHH--TTCE-----EEEEC--HHHH
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHH--hCCc-----EEEEE--HHHh
Confidence            4578888888777776531           1123455779999999999999999888  3322     22222  1111


Q ss_pred             HHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCceEEEEEeCCC
Q 048347           87 LDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKRYLIVIQDVW  132 (351)
Q Consensus        87 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~~LlVLDdv~  132 (351)
                      ..       ..      .......+...+...-...+++++|||++
T Consensus        78 ~~-------~~------~~~~~~~l~~~f~~A~~~~p~il~ideid  110 (265)
T d1r7ra3          78 LT-------MW------FGESEANVREIFDKARQAAPCVLFFDELD  110 (265)
T ss_dssp             HT-------SC------TTTHHHHHHHHHHHHHHTCSEEEEESSGG
T ss_pred             hh-------cc------ccchHHHHHHHHHHHHhcCCcceeHHhhh
Confidence            11       10      11223334444444445678999999996

>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=96.86  E-value=0.00027  Score=55.95  Aligned_cols=25  Identities=12%  Similarity=-0.023  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.+|.+.|+.|+||||+|+++...
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~   29 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVT   29 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3468889999999999999999988

>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=96.85  E-value=0.00085  Score=55.09  Aligned_cols=56  Identities=14%  Similarity=0.017  Sum_probs=40.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~   97 (351)
                      +.+|+.++|+.|+||||.+.+++..  .+.+=..+..|+..   ....+-++..++.+..+
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~--~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRY--YQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEECCCCSSTTHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEEeccccccchhhHhhcccccCce
Confidence            4579999999999999988887766  33332356677766   56667777777777664

>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=96.79  E-value=0.00085  Score=55.12  Aligned_cols=56  Identities=11%  Similarity=-0.106  Sum_probs=38.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~   97 (351)
                      +.+|+.++|+.|+||||.+.++...  .+.+-..+..++..   ....+-++..++.+..+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~--~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALY--YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH--HHHTTCCEEEEECCSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEecccccchHHHHHHHHHHhcCCc
Confidence            4578999999999999988888766  33333345666665   33445666667666654

>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=96.78  E-value=0.001  Score=54.73  Aligned_cols=57  Identities=7%  Similarity=-0.116  Sum_probs=34.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCH--HHHHHHHHHHhCCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSL--DMMLDAIMKSLMPL   97 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~--~~~~~~i~~~~~~~   97 (351)
                      ++..||.++|+.|+||||.+.+++...+  ..=..+..|+.. +-.  .+-++..++.++.+
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~--~~g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYK--KKGFKVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHH--HTTCCEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH--HCCCceEEEEeeccccchhHHHHHhccccCcc
Confidence            4578999999999999998877776633  222346777776 333  34455566666554

>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=96.78  E-value=0.00022  Score=57.51  Aligned_cols=36  Identities=11%  Similarity=-0.117  Sum_probs=27.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEE
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWV   77 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv   77 (351)
                      +-.+|-+.|+.|+||||+|+.+...  ....+....++
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~--l~~~~~~~~~~   53 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEY--LVCHGIPCYTL   53 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHH--HHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHhcCCCccch
Confidence            3467889999999999999999887  54444444443

>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=96.71  E-value=0.00097  Score=54.83  Aligned_cols=58  Identities=9%  Similarity=-0.030  Sum_probs=39.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe-CCH--HHHHHHHHHHhCCCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ-LSL--DMMLDAIMKSLMPLS   98 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~-~~~--~~~~~~i~~~~~~~~   98 (351)
                      ++..||.++|+.|+||||.+.++...  .+..=..+..++.. |-.  .+-++..++.+..+.
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~--~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~   67 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQ--FEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPV   67 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHH--HHTTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEecccccccchhhhhhhhhhcCCcc
Confidence            45689999999999999988888766  33222334555555 444  456667777776653

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.70  E-value=0.0021  Score=53.45  Aligned_cols=80  Identities=16%  Similarity=0.147  Sum_probs=50.9

Q ss_pred             cccEEEEecCCccccccccccccCCccEEeecCCccccccChh-hhcCCCCCEEEecCCC-----hhHHhhccccccCce
Q 048347          268 RQEILHLKSMLWLEEWKMETGAMQKLKSLIVNPCAYLRKFPEE-LWRIKALRKLESWWPR-----PELRQSLHKFEEIDR  341 (351)
Q Consensus       268 ~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~-----~~~~~~l~~~~~~~~  341 (351)
                      .++.|+++++ .+..++....+..++..+....+..++++|.+ +.++++|+.|++++..     +....++.+++..+.
T Consensus       154 ~l~~L~l~~n-~l~~i~~~~~~~~~l~~~~~l~~n~l~~l~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~l~~  232 (242)
T d1xwdc1         154 ESVILWLNKN-GIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARST  232 (242)
T ss_dssp             SCEEEECCSS-CCCEECTTTTTTCCEEEEECTTCTTCCCCCTTTTTTSCCCSEEECTTSCCCCCCSSSCTTCCEEESSSE
T ss_pred             cceeeecccc-cccccccccccchhhhccccccccccccccHHHhcCCCCCCEEECCCCcCCccCHHHHcCCcccccCcC
Confidence            5677777776 57777776666666666655555677788765 4678888888887643     223345555555555


Q ss_pred             eeEEecC
Q 048347          342 LDMQIYP  348 (351)
Q Consensus       342 ~~~~~~P  348 (351)
                      ..+..+|
T Consensus       233 ~~l~~lp  239 (242)
T d1xwdc1         233 YNLKKLP  239 (242)
T ss_dssp             ESSSCSC
T ss_pred             CCCCcCC
Confidence            5555555

>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=96.69  E-value=0.00032  Score=55.18  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|.|.|++|+||||+|+.+..+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~   27 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASK   27 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            35678999999999999999876

>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=96.66  E-value=0.00031  Score=55.72  Aligned_cols=23  Identities=22%  Similarity=0.260  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|.|++|+|||||++++...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            46889999999999999999877

>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=96.66  E-value=0.00034  Score=55.70  Aligned_cols=23  Identities=17%  Similarity=0.179  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|+|.|+.|+||||+++.+...
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~   24 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDN   24 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999876

>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=96.65  E-value=0.00051  Score=54.18  Aligned_cols=24  Identities=8%  Similarity=0.068  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -++|.|.|+.|+||||+|+.+...
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999999877

>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=96.64  E-value=0.00081  Score=57.07  Aligned_cols=41  Identities=15%  Similarity=0.255  Sum_probs=28.9

Q ss_pred             hhhHHHHHHHHHcc---CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           24 EDKMEELLDLLIER---QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        24 ~~~~~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.+++.++.+..+   .+..+.|-++|+.|+||||||+.+++.
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~~   55 (273)
T d1gvnb_          12 ENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEE   55 (273)
T ss_dssp             HHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            33444444445333   234566889999999999999999987

>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=96.64  E-value=0.00057  Score=53.72  Aligned_cols=26  Identities=12%  Similarity=0.215  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+++.|.|+.|+||||+|+.+...
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~   29 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQ   29 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999999876

>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=96.63  E-value=0.00053  Score=55.60  Aligned_cols=27  Identities=11%  Similarity=0.165  Sum_probs=24.5

Q ss_pred             CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           38 QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        38 ~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++.+||.|.|++|+||||+|+.++.+
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            356899999999999999999999887

>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=96.62  E-value=0.00044  Score=54.55  Aligned_cols=23  Identities=4%  Similarity=0.083  Sum_probs=21.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++|+|..|+|||||+.++...
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~   24 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAA   24 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            68999999999999999999877

>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=96.61  E-value=0.00049  Score=54.23  Aligned_cols=26  Identities=19%  Similarity=0.144  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++...|.|.|+.|+||||+|+.+...
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            34566788999999999999999876

>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=96.59  E-value=0.00031  Score=55.49  Aligned_cols=21  Identities=5%  Similarity=0.091  Sum_probs=18.7

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++||.|+||||+|+.++..
T Consensus         4 IvliG~~G~GKSTig~~La~~   24 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKA   24 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            446699999999999999987

>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=96.58  E-value=0.00055  Score=55.39  Aligned_cols=26  Identities=8%  Similarity=0.112  Sum_probs=23.4

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++..+|.|+|++|+||||+|+.+++.
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999999876

>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=96.54  E-value=0.0005  Score=54.19  Aligned_cols=24  Identities=0%  Similarity=0.019  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|.|..|+||||+|+.+...
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~   26 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999887

>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=96.54  E-value=0.00053  Score=53.94  Aligned_cols=21  Identities=14%  Similarity=0.275  Sum_probs=19.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.+.||+|+||||+|+.++.+
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            567799999999999999888

>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=96.50  E-value=0.00081  Score=53.63  Aligned_cols=24  Identities=4%  Similarity=0.203  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.|.|+.|+||||+|+.+...
T Consensus         1 mkiivi~G~~GsGKTT~~~~La~~   24 (194)
T d1nksa_           1 MKIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            368889999999999999999877

>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=96.40  E-value=0.00081  Score=53.56  Aligned_cols=26  Identities=27%  Similarity=0.402  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++..+|.++|+.|+||||+|++++..
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            45679999999999999999998765

>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=96.36  E-value=0.0013  Score=57.72  Aligned_cols=47  Identities=9%  Similarity=0.172  Sum_probs=36.2

Q ss_pred             CccccchhhHHHHHHHHHc------c-CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           18 KVDLDLEDKMEELLDLLIE------R-QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~------~-~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++|-++-++.+...+..      + .....++..+|+.|+|||.+|+.+...
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~   76 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT   76 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHH
Confidence            4578999999988776642      1 223457889999999999999998776

>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=96.30  E-value=0.00064  Score=53.86  Aligned_cols=22  Identities=14%  Similarity=0.102  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.++|+.|+||||+|+.+++.
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            3557899999999999999887

>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=96.30  E-value=0.00062  Score=59.65  Aligned_cols=48  Identities=10%  Similarity=0.076  Sum_probs=36.1

Q ss_pred             CCccccchhhHHHHHHHHHc--------c----CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIE--------R----QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~--------~----~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..++|-++-++.+...+..        +    +...+-+.++|+.|+|||.||+++++.
T Consensus        13 ~~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          13 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhc
Confidence            34688999999888766621        0    112355668999999999999999886

>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=96.29  E-value=0.00091  Score=52.92  Aligned_cols=21  Identities=14%  Similarity=0.317  Sum_probs=19.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+|+|+.|+|||||++.+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhc
Confidence            789999999999999999876

>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=96.27  E-value=0.0018  Score=54.01  Aligned_cols=57  Identities=12%  Similarity=0.054  Sum_probs=40.2

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHH
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLD   88 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~   88 (351)
                      |-+.|..+=++-.++.|+|.+|+|||+||.++..+  ...+...++|++...+...+.+
T Consensus        15 LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~~~~~~~~   71 (242)
T d1tf7a2          15 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEESRAQLLR   71 (242)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSSCHHHHHH
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccCCHHHHHH
Confidence            33334333245678889999999999999999888  6677777888876544444433

>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=96.27  E-value=0.0011  Score=53.94  Aligned_cols=23  Identities=9%  Similarity=0.085  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.++|.+|+||||+|++++..
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~   25 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRY   25 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            57889999999999999999876

>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=96.20  E-value=0.001  Score=54.63  Aligned_cols=23  Identities=4%  Similarity=0.075  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -||||.|..|+||||+|+.+...
T Consensus         3 ~iIgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           3 FLIGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998776

>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=96.10  E-value=0.0029  Score=55.49  Aligned_cols=38  Identities=16%  Similarity=0.242  Sum_probs=29.4

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..++.+.+.....+..+|||.|++|+|||||..++...
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHH
Confidence            33445555555567899999999999999999888754

>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=96.06  E-value=0.0015  Score=55.55  Aligned_cols=24  Identities=17%  Similarity=0.205  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.|+|+|-||+||||+|-.+..-
T Consensus         1 mr~Iai~gKGGvGKTT~a~nLA~~   24 (269)
T d1cp2a_           1 MRQVAIYGKGGIGKSTTTQNLTSG   24 (269)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCcCCHHHHHHHHHHH
Confidence            378999999999999999887666

>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=96.04  E-value=0.0084  Score=50.95  Aligned_cols=87  Identities=15%  Similarity=0.065  Sum_probs=58.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-ccCCCCCHHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SEILDNDFEMKKNTL  115 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~l  115 (351)
                      +.-+++-|+|..|+||||||-+++..  ....-..++|+..-  ++.+.     +++++.+.+. --......++..+.+
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~--~q~~g~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~  130 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIA  130 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHH--HHHTTCEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHH--HhcCCCEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHH
Confidence            56688999999999999999888876  33333457888766  66543     4556554221 012345667777766


Q ss_pred             HHhcC-CceEEEEEeCCC
Q 048347          116 HNYLK-NKRYLIVIQDVW  132 (351)
Q Consensus       116 ~~~L~-~k~~LlVLDdv~  132 (351)
                      ....+ ++..|+|+|.+-
T Consensus       131 ~~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1         131 DMLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             HHHHHTTCEEEEEEECST
T ss_pred             HHHHhcCCCCEEEEeccc
Confidence            65554 457799999884

>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=96.02  E-value=0.0014  Score=52.94  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..+|+|-|..|+||||+|+.+...
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            45678999999999999999998766

>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=96.01  E-value=0.0011  Score=54.55  Aligned_cols=43  Identities=5%  Similarity=0.027  Sum_probs=31.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHh
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSL   94 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~   94 (351)
                      .+||+|-|++|+||||+|+.+.++..+       ..+    +.-+++++++...
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~gl-------~~i----StGdLlR~~a~~~   45 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQW-------HLL----DSGAIYRVLALAA   45 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHTC-------EEE----EHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCC-------cEE----CHHHHHHHHHHHH
Confidence            359999999999999999999988322       112    3446777766543

>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=96.00  E-value=0.0039  Score=54.74  Aligned_cols=36  Identities=17%  Similarity=0.186  Sum_probs=28.5

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+.+.....+..+|||.|.+|+|||||..++...
T Consensus        42 ~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          42 QLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             HHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            444445555567999999999999999999988755

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.99  E-value=0.0003  Score=55.53  Aligned_cols=61  Identities=18%  Similarity=-0.014  Sum_probs=44.3

Q ss_pred             CCCCcccEEEEecCCcccccc---ccccccCCccEEeecCCccccccChh-hhcCCCCCEEEecCCC
Q 048347          264 GGFPRQEILHLKSMLWLEEWK---METGAMQKLKSLIVNPCAYLRKFPEE-LWRIKALRKLESWWPR  326 (351)
Q Consensus       264 ~~l~~L~~L~L~~~~~l~~lp---~~i~~L~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~  326 (351)
                      ..+++|++|+|++| .++.++   ..+..+++|+.|+|++ ..+..+++- ..+..+|+.|++++.+
T Consensus        62 ~~~~~L~~L~Ls~N-~i~~l~~~~~~~~~l~~L~~L~Ls~-N~i~~l~~l~~l~~~~L~~L~L~~Np  126 (162)
T d1koha1          62 ENIPELLSLNLSNN-RLYRLDDMSSIVQKAPNLKILNLSG-NELKSERELDKIKGLKLEELWLDGNS  126 (162)
T ss_dssp             HHCTTCCCCCCCSS-CCCCCSGGGTHHHHSTTCCCCCCTT-SCCCCGGGHHHHTTCCCSSCCCTTST
T ss_pred             HhCCCCCEeeCCCc-cccCCchhHHHHhhCCccccccccc-CccccchhhhhhhccccceeecCCCC
Confidence            46788999999998 577654   3466789999999998 467777751 1233468888888754

>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=95.92  E-value=0.0049  Score=53.83  Aligned_cols=48  Identities=8%  Similarity=0.135  Sum_probs=38.4

Q ss_pred             CCccccchhhHHHHHHHHHc------c-CCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLIE------R-QPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~------~-~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..++|-++-++.+...+..      + +....++..+|+.|+|||.||+.+..-
T Consensus        21 ~~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~   75 (315)
T d1r6bx3          21 KMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA   75 (315)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhh
Confidence            46789999999998777741      1 233567889999999999999999876

>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=95.90  E-value=0.0076  Score=51.23  Aligned_cols=87  Identities=11%  Similarity=0.057  Sum_probs=58.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-ccCCCCCHHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SEILDNDFEMKKNTL  115 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~l  115 (351)
                      +.-+++-|+|..|+||||||-+++...+  ..=..++|++.-  ++.+     ++++++.+.+. .-....+.++..+.+
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~aq--k~g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~  127 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQAQ--KAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIM  127 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             cCceEEEEecCCccchHHHHHHHHHHHH--hCCCEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHH
Confidence            4557999999999999999988877733  322346788766  6663     66677664331 012345667777766


Q ss_pred             HHhcCC-ceEEEEEeCCC
Q 048347          116 HNYLKN-KRYLIVIQDVW  132 (351)
Q Consensus       116 ~~~L~~-k~~LlVLDdv~  132 (351)
                      ....+. +.-|+|+|-+-
T Consensus       128 ~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         128 ELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             HHHHTTTCCSEEEEECTT
T ss_pred             HHHHhcCCCcEEEEeccc
Confidence            666654 45688999883

>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=95.90  E-value=0.01  Score=51.37  Aligned_cols=79  Identities=8%  Similarity=0.046  Sum_probs=48.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCC--eeEEEEEe--CCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFD--CCAWVYYQ--LSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNT  114 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~~--~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  114 (351)
                      +..-+|||.|..|+||||+|+.+...  .+..+.  .+.-++..  +-..+.+..  +.+....  ..++..|.+.+.+.
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~l--L~~~~~~~~v~~Is~D~F~~~~~~l~~--~~~~~~~--g~Pes~D~~~L~~~  151 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQAL--LSRWPEHRRVELITTDGFLHPNQVLKE--RGLMKKK--GFPESYDMHRLVKF  151 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHH--HTTSTTCCCEEEEEGGGGBCCHHHHHH--HTCTTCT--TSGGGBCHHHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHH--HhhhcCCCceEEEeeeeeECCchHHHH--hcCCccC--CchHhhhHHHHHHH
Confidence            45689999999999999999999876  544332  23344444  222222221  1111111  11356788888888


Q ss_pred             HHHhcCCce
Q 048347          115 LHNYLKNKR  123 (351)
Q Consensus       115 l~~~L~~k~  123 (351)
                      +.....++.
T Consensus       152 L~~lk~g~~  160 (308)
T d1sq5a_         152 VSDLKSGVP  160 (308)
T ss_dssp             HHHHTTTCS
T ss_pred             HHHHHcCCC
Confidence            888776653

>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=95.89  E-value=0.002  Score=51.65  Aligned_cols=24  Identities=8%  Similarity=0.104  Sum_probs=20.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++| |.|++|+||||+|+.+...
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~   26 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKN   26 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHH
Confidence            45666 7899999999999999876

>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=95.85  E-value=0.0025  Score=51.20  Aligned_cols=23  Identities=9%  Similarity=0.186  Sum_probs=20.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHh
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      ..-+|||.|+.|+||||+|+.+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            35789999999999999999874

>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=95.84  E-value=0.002  Score=51.78  Aligned_cols=23  Identities=9%  Similarity=0.092  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+|.|.|++|+||||.|+.+++.
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999886

>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=95.82  E-value=0.0013  Score=52.99  Aligned_cols=22  Identities=9%  Similarity=0.303  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|+|+.|+|||||++++.++
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            4679999999999999999776

>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=95.70  E-value=0.0024  Score=51.40  Aligned_cols=25  Identities=16%  Similarity=0.157  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +...|.|.|+.|+||||+|+.+..+
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHH
Confidence            4556678899999999999999987

>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=95.69  E-value=0.0022  Score=51.14  Aligned_cols=23  Identities=4%  Similarity=0.108  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|+|+.|+|||||++.+..+
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            47889999999999999998765

>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=95.66  E-value=0.0014  Score=53.01  Aligned_cols=22  Identities=9%  Similarity=0.303  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|+|+.|+||||||+++...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHh
Confidence            3669999999999999998766

>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=95.62  E-value=0.0019  Score=51.60  Aligned_cols=23  Identities=9%  Similarity=0.206  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.|+|++|+|||||++++..+
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            57889999999999999998865

>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=95.61  E-value=0.0049  Score=52.50  Aligned_cols=102  Identities=15%  Similarity=0.159  Sum_probs=58.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCC--CCCCcc------CCCCCHHH
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMP--LSALSE------ILDNDFEM  110 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~--~~~~~~------~~~~~~~~  110 (351)
                      ..++|.|..|+|||+|+..+.++.+ +.+=+.++++-+.   ..+.++.+++.+.-..  .....+      ....+...
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~~-~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~  147 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNVA-KAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGA  147 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHT-TTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHH
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHHH-hhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCCHHH
Confidence            3588999999999999999876621 1222456666555   5566777777664211  100000      01112111


Q ss_pred             H------HHHHHHhcC---CceEEEEEeCCCCh-hhHHHHHhhc
Q 048347          111 K------KNTLHNYLK---NKRYLIVIQDVWRG-DIWDFLKEAL  144 (351)
Q Consensus       111 ~------~~~l~~~L~---~k~~LlVLDdv~~~-~~~~~l~~~l  144 (351)
                      .      .-.+.++++   +++.|+++||+-.. +++..+...+
T Consensus       148 r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~A~A~reis~~~  191 (276)
T d2jdid3         148 RARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALL  191 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHHHHHHHHHHHhc
Confidence            1      123445553   78999999999543 4555554433

>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=95.61  E-value=0.0028  Score=54.45  Aligned_cols=82  Identities=5%  Similarity=-0.021  Sum_probs=43.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe----CCHHHHHHHHHHHh---CCCCCCccCCCCCHHHHH
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ----LSLDMMLDAIMKSL---MPLSALSEILDNDFEMKK  112 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~----~~~~~~~~~i~~~~---~~~~~~~~~~~~~~~~~~  112 (351)
                      +..||||.|.+|+||||+|+.+.+.  .+..=-..+-++..    ++..+.-..+...-   ...-....++..+.+.+.
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i--~~~~~v~~~iI~~Dsfyr~~R~~~~~~~~~~~~~~~~~~~~~~P~A~d~dlL~   80 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQI--FRREGVKAVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELE   80 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHH--HHHHTCCEEEEEGGGGBSCCHHHHHHHHHHHHHHTCTTCSTTSGGGBCHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHH--HhhcCCCeEEEeCCCCCccchhhhhhhhhhhhhhhccCCCCCCcccccHHHHH
Confidence            5679999999999999999987665  32211112333333    34444333333221   111111123556777777


Q ss_pred             HHHHHhcCCce
Q 048347          113 NTLHNYLKNKR  123 (351)
Q Consensus       113 ~~l~~~L~~k~  123 (351)
                      +.++...+++.
T Consensus        81 ~~l~~L~~g~~   91 (288)
T d1a7ja_          81 RVFREYGETGQ   91 (288)
T ss_dssp             HHHHHHHHHSC
T ss_pred             HHHHHHHCCCc
Confidence            77777665544

>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=95.59  E-value=0.0019  Score=53.72  Aligned_cols=25  Identities=8%  Similarity=0.230  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+.|+|-|+.|+||||+|+.+...
T Consensus         1 ~~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           1 RIKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3589999999999999999998876

>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=95.59  E-value=0.0022  Score=52.72  Aligned_cols=45  Identities=9%  Similarity=-0.027  Sum_probs=32.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPL   97 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~   97 (351)
                      -+|+|-|++|+||||+|+.+..+..+       .++    +.-++++.++......
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~lg~-------~~i----stGdl~R~~a~~~~~~   48 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKDFGF-------TYL----DTGAMYRAATYMALKN   48 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCC-------EEE----EHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC-------cEE----CHHHHHHHHHHHHHHc
Confidence            46889999999999999999988322       122    3446777776555443

>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=95.57  E-value=0.0056  Score=52.03  Aligned_cols=36  Identities=14%  Similarity=0.262  Sum_probs=26.2

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+...+..  ++.+||.+.|-||+||||+|..+...
T Consensus         8 ~~~~~~~~~~--~~~~iii~sGKGGVGKTT~a~nLA~~   43 (279)
T d1ihua2           8 LSALVDDIAR--NEHGLIMLMGKGGVGKTTMAAAIAVR   43 (279)
T ss_dssp             HHHHHHHHHT--TSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhhc--CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4455555543  46889999999999999977666443

>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=95.53  E-value=0.0029  Score=50.06  Aligned_cols=21  Identities=5%  Similarity=0.099  Sum_probs=19.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|.|++|+||||+|+.+...
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668999999999999999876

>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=95.50  E-value=0.0029  Score=50.96  Aligned_cols=25  Identities=4%  Similarity=0.104  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++|.|.|++|+||||+|+.+.+.
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999999876

>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=95.48  E-value=0.011  Score=50.12  Aligned_cols=86  Identities=14%  Similarity=0.058  Sum_probs=54.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe--CCHHHHHHHHHHHhCCCCCC-ccCCCCCHHHHHHHH
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ--LSLDMMLDAIMKSLMPLSAL-SEILDNDFEMKKNTL  115 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~l  115 (351)
                      +.-+++-|+|..|+||||||-+++...  ...=..++|++..  ++..     .++.++.+.+. .-....+.++..+.+
T Consensus        52 ~~g~itei~G~~gsGKTtl~l~~~~~~--q~~g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i  124 (263)
T d1u94a1          52 PMGRIVEIYGPESSGKTTLTLQVIAAA--QREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEIC  124 (263)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHH--HcCCCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHH
Confidence            445788999999999999999988883  3343456777765  5543     35556554221 112344566666666


Q ss_pred             HHhcC-CceEEEEEeCC
Q 048347          116 HNYLK-NKRYLIVIQDV  131 (351)
Q Consensus       116 ~~~L~-~k~~LlVLDdv  131 (351)
                      ....+ ++.-|+|+|-+
T Consensus       125 ~~l~~~~~~~liViDSi  141 (263)
T d1u94a1         125 DALARSGAVDVIVVDSV  141 (263)
T ss_dssp             HHHHHHTCCSEEEEECG
T ss_pred             HHHHhcCCCCEEEEECc
Confidence            55554 34458888887

>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=95.48  E-value=0.0036  Score=53.79  Aligned_cols=24  Identities=13%  Similarity=0.162  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.|+|.|-||+||||+|..+...
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~   25 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAA   25 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHH
Confidence            467889999999999988877655

>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=95.47  E-value=0.0026  Score=51.00  Aligned_cols=22  Identities=9%  Similarity=-0.126  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||+|+.+.+.
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4668999999999999999877

>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=95.44  E-value=0.0045  Score=50.67  Aligned_cols=26  Identities=4%  Similarity=-0.072  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++-.+|-+.|++|+||||+|+++...
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~   47 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQ   47 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35678999999999999999999876

>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=95.35  E-value=0.0037  Score=49.68  Aligned_cols=22  Identities=5%  Similarity=0.074  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|++|+||||+|+.++.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3668999999999999999987

>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=95.33  E-value=0.0035  Score=49.80  Aligned_cols=22  Identities=9%  Similarity=0.034  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||+|+.+++.
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3668899999999999999877

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.0018  Score=58.59  Aligned_cols=85  Identities=18%  Similarity=0.154  Sum_probs=54.8

Q ss_pred             CCCCCceEEEEecccccC----ceeeeCCCCCCcccEEEEecCCcccc-----cccccc-ccCCccEEeecCCcccc---
Q 048347          239 EKLPHLKVLKLKRSSYSG----RKLVCGHGGFPRQEILHLKSMLWLEE-----WKMETG-AMQKLKSLIVNPCAYLR---  305 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~----~~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~-~L~~L~~L~l~~c~~l~---  305 (351)
                      +.++++++|+|+ ++.-.    +.+...+...++|++|+|++| .++.     +...+. .-.+|++|+|++|. +.   
T Consensus        24 ~~l~~l~~L~L~-~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N-~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~-it~~~  100 (460)
T d1z7xw1          24 PLLQQCQVVRLD-DCGLTEARCKDISSALRVNPALAELNLRSN-ELGDVGVHCVLQGLQTPSCKIQKLSLQNCC-LTGAG  100 (460)
T ss_dssp             HHHTTCSEEEEE-SSCCCHHHHHHHHHHHHTCTTCCEEECTTC-CCHHHHHHHHHHTTCSTTCCCCEEECTTSC-CBGGG
T ss_pred             HhCCCCCEEEeC-CCCCCHHHHHHHHHHHhcCCCCCEEECcCC-cCChHHHHHHHHHHhcCCCCCCEEECCCCC-ccccc
Confidence            456788888884 43211    133344567788999999888 4543     222222 22478999998874 43   


Q ss_pred             --ccChhhhcCCCCCEEEecCCC
Q 048347          306 --KFPEELWRIKALRKLESWWPR  326 (351)
Q Consensus       306 --~lP~~i~~L~~L~~L~l~~~~  326 (351)
                        .++..+..+++|++|++++..
T Consensus       101 ~~~l~~~l~~~~~L~~L~L~~N~  123 (460)
T d1z7xw1         101 CGVLSSTLRTLPTLQELHLSDNL  123 (460)
T ss_dssp             HHHHHHHTTSCTTCCEEECCSSB
T ss_pred             cccccchhhcccccccccccccc
Confidence              355667788899999998865

>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=95.28  E-value=0.0061  Score=49.83  Aligned_cols=28  Identities=4%  Similarity=-0.060  Sum_probs=23.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccccC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNSSYVKNY   70 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~   70 (351)
                      -..|+|-|+.|+||||+|+.+.+.  ...+
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~--L~~~   30 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEA--LCAA   30 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH--HHHT
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHH--HHHC
Confidence            357889999999999999999887  5444

>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=95.25  E-value=0.0044  Score=51.33  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ||+|.|+.|+|||||.+++...
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Confidence            7899999999999999998643

>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=95.23  E-value=0.013  Score=49.15  Aligned_cols=46  Identities=15%  Similarity=0.041  Sum_probs=35.5

Q ss_pred             ccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           19 VDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        19 ~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++||..+..+++.+.+..-...-.-|-|.|..|+|||++|+.++..
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            4788888888888887653322234568899999999999999865

>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=95.22  E-value=0.0038  Score=50.75  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.++.-
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcc
Confidence            358999999999999999999764

>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=95.13  E-value=0.0053  Score=51.30  Aligned_cols=23  Identities=9%  Similarity=0.176  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||++.++--
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl   52 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGL   52 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcC
Confidence            58999999999999999999654

>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=95.07  E-value=0.005  Score=48.85  Aligned_cols=23  Identities=13%  Similarity=0.200  Sum_probs=19.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +++| |.|+.|+||||+|+.+.+.
T Consensus         3 mrIv-l~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           3 IRMV-LIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             eEEE-EECCCCCCHHHHHHHHHHH
Confidence            3444 7799999999999999877

>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=95.04  E-value=0.0094  Score=52.99  Aligned_cols=45  Identities=7%  Similarity=0.104  Sum_probs=31.6

Q ss_pred             cccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           20 DLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|.++..-+....+..+.++-+.+.++|++|+|||++|+.+++.
T Consensus       133 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~~  177 (362)
T d1svma_         133 LPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLEL  177 (362)
T ss_dssp             STTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHHH
Confidence            344444444433434444456678889999999999999999988

>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=95.03  E-value=0.0057  Score=51.76  Aligned_cols=24  Identities=17%  Similarity=0.243  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+.--
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcC
Confidence            358999999999999999999654

>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=95.02  E-value=0.0059  Score=50.65  Aligned_cols=24  Identities=13%  Similarity=0.137  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~gl   54 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGCL   54 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCcchhhHhccCC
Confidence            358999999999999999988654

>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=95.01  E-value=0.0059  Score=50.99  Aligned_cols=24  Identities=13%  Similarity=0.130  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+.--
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~Gl   54 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNLL   54 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            368999999999999999999654

>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=94.99  E-value=0.01  Score=46.50  Aligned_cols=34  Identities=9%  Similarity=0.099  Sum_probs=24.7

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.+.+.... +...|.++|.+|+|||||..++...
T Consensus         3 ~~~~~~~~~-k~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_           3 VLQFLGLYK-KTGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             HHHHHTCTT-CCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             hHHhccccC-CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            344444443 3445669999999999999998665

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.93  E-value=0.0028  Score=49.68  Aligned_cols=86  Identities=19%  Similarity=0.114  Sum_probs=56.9

Q ss_pred             CCCCceEEEEeccccc-CceeeeCCCCCCcccEEEEecCCcccccccc-ccccCCccEEeecCCccccccCh-------h
Q 048347          240 KLPHLKVLKLKRSSYS-GRKLVCGHGGFPRQEILHLKSMLWLEEWKME-TGAMQKLKSLIVNPCAYLRKFPE-------E  310 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~-~~~lp~~~~~l~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l~~c~~l~~lP~-------~  310 (351)
                      .+++|++|+|+.+... ...++..+..+++|++|++++| .+.+++.- .....+|+.|++.++.-....+.       -
T Consensus        63 ~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N-~i~~l~~l~~l~~~~L~~L~L~~Npl~~~~~~~~~y~~~i  141 (162)
T d1koha1          63 NIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGN-ELKSERELDKIKGLKLEELWLDGNSLSDTFRDQSTYISAI  141 (162)
T ss_dssp             HCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTS-CCCCGGGHHHHTTCCCSSCCCTTSTTSSSSSSHHHHHHHH
T ss_pred             hCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccC-ccccchhhhhhhccccceeecCCCCcCcCcccchhHHHHH
Confidence            4789999999544321 1123333567899999999999 68888762 23445799999998643332222       2


Q ss_pred             hhcCCCCCEEEecCCC
Q 048347          311 LWRIKALRKLESWWPR  326 (351)
Q Consensus       311 i~~L~~L~~L~l~~~~  326 (351)
                      +..+++|+.||=...+
T Consensus       142 ~~~~P~L~~LDg~~v~  157 (162)
T d1koha1         142 RERFPKLLRLDGHELP  157 (162)
T ss_dssp             HTTSTTCCEETTEECC
T ss_pred             HHHCCCCCEECcCCCc
Confidence            4568899988754443

>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=94.92  E-value=0.0095  Score=46.67  Aligned_cols=28  Identities=7%  Similarity=0.069  Sum_probs=22.0

Q ss_pred             cCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           37 RQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        37 ~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++--.|.++|.+|+|||||..++...
T Consensus        12 ~~~~~~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          12 APDQEVRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             CCSSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHhcC
Confidence            3334445679999999999999999765

>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=94.90  E-value=0.0066  Score=50.39  Aligned_cols=23  Identities=9%  Similarity=0.206  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      -.+++|+|+.|+|||||.+.+.-
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999854

>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=94.90  E-value=0.006  Score=48.22  Aligned_cols=22  Identities=0%  Similarity=-0.112  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|.|+.|+||||.|+.++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3568899999999999999876

>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=94.90  E-value=0.0065  Score=50.41  Aligned_cols=24  Identities=8%  Similarity=0.189  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.|+|-|+-|+||||+++.+.+.
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH
Confidence            478999999999999999999765

>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=94.87  E-value=0.018  Score=49.01  Aligned_cols=99  Identities=12%  Similarity=0.070  Sum_probs=54.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEe---CCHHHHHHHHHHHhCCCC--------CCccCCCC----
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ---LSLDMMLDAIMKSLMPLS--------ALSEILDN----  106 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~---~~~~~~~~~i~~~~~~~~--------~~~~~~~~----  106 (351)
                      ..++|.|..|+|||+|+......  ...+-..++++-+.   ..+.++..++...=..+.        +.+.....    
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~  145 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPY  145 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHH
T ss_pred             ceEeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHH
Confidence            34778899999999999876554  33444566666666   444445544443211100        00000001    


Q ss_pred             CHHHHHHHHHHhcCCceEEEEEeCCCCh-hhHHHHHhhc
Q 048347          107 DFEMKKNTLHNYLKNKRYLIVIQDVWRG-DIWDFLKEAL  144 (351)
Q Consensus       107 ~~~~~~~~l~~~L~~k~~LlVLDdv~~~-~~~~~l~~~l  144 (351)
                      ..-.+.+.+++  .+++.|+++||+-.. +++..+...+
T Consensus       146 ~a~tiAEyfrd--~G~~Vlll~Dsltr~A~A~rEis~~~  182 (276)
T d1fx0a3         146 TGAALAEYFMY--RERHTLIIYDDLSKQAQAYRQMSLLL  182 (276)
T ss_dssp             HHHHHHHHHHH--TTCEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHH--cCCceeEEeeccHHHHHHHHHHHHHc
Confidence            11122344444  379999999999543 4555555443

>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=94.87  E-value=0.0068  Score=50.53  Aligned_cols=23  Identities=9%  Similarity=0.159  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      -.+++|+|+.|+|||||.+.+.-
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            35899999999999999999854

>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=94.87  E-value=0.0072  Score=49.68  Aligned_cols=38  Identities=8%  Similarity=0.011  Sum_probs=28.5

Q ss_pred             eEEEEEE-cCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           41 LSLVAII-DTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        41 ~~vv~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      ++||+|+ |-||+||||+|..+...  ....-..++.|...
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~~--la~~g~~VlliD~D   39 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGVA--LAQLGHDVTIVDAD   39 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             CEEEEEECCCCCChHHHHHHHHHHH--HHhCCCCEEEEeCC
Confidence            4789999 77999999999988776  44444456677654

>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=94.84  E-value=0.0068  Score=51.12  Aligned_cols=24  Identities=13%  Similarity=0.084  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl   64 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRF   64 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhcc
Confidence            358999999999999999999553

>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=94.82  E-value=0.0076  Score=50.43  Aligned_cols=24  Identities=13%  Similarity=0.122  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      +-.+++|+|+.|+|||||++.+..
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            347899999999999999999854

>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=94.81  E-value=0.0071  Score=50.57  Aligned_cols=24  Identities=8%  Similarity=0.113  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -..++|+|..|+|||||++.+..-
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            357999999999999999999664

>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=94.72  E-value=0.0079  Score=50.11  Aligned_cols=23  Identities=9%  Similarity=0.238  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||++.+..-
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl   47 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEEECCCCChHHHHHHHHHcC
Confidence            37889999999999999999654

>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=94.66  E-value=0.0081  Score=50.55  Aligned_cols=24  Identities=13%  Similarity=0.119  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|..|+|||||++.+..-
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcc
Confidence            468999999999999999998654

>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=94.66  E-value=0.0068  Score=49.41  Aligned_cols=23  Identities=13%  Similarity=0.278  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++|.|+|++|+|||||++.+..+
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            47889999999999999999765

>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=94.60  E-value=0.0075  Score=55.16  Aligned_cols=76  Identities=11%  Similarity=0.120  Sum_probs=48.7

Q ss_pred             CCccccchhhHHHHHHHHHc--------cCCC----eEEEEEEcCCCChHHHHHHHHhCCcccccCC---CeeEEEEEe-
Q 048347           17 NKVDLDLEDKMEELLDLLIE--------RQPQ----LSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF---DCCAWVYYQ-   80 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~~--------~~~~----~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~~~-   80 (351)
                      +.++||-|+-++.+--.+..        +..+    -+=|-++|+.|+|||.||+.++..  +.-.|   ++.-+..++ 
T Consensus        13 d~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~--l~VPFv~~daT~fTeaGY   90 (443)
T d1g41a_          13 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL--ANAPFIKVEATKFTEVGY   90 (443)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH--TTCCEEEEEGGGGC----
T ss_pred             cCcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHH--hCCCEEEeecceeeecce
Confidence            56789999988888766632        1100    112557899999999999999886  44444   222233333 


Q ss_pred             --CCHHHHHHHHHHHh
Q 048347           81 --LSLDMMLDAIMKSL   94 (351)
Q Consensus        81 --~~~~~~~~~i~~~~   94 (351)
                        -+++++.+.++...
T Consensus        91 vG~DVesii~~L~~~a  106 (443)
T d1g41a_          91 VGKEVDSIIRDLTDSA  106 (443)
T ss_dssp             CCCCTHHHHHHHHHHH
T ss_pred             eecchhHHHHHHHHHH
Confidence              77888888876544

>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=94.59  E-value=0.0074  Score=49.95  Aligned_cols=24  Identities=17%  Similarity=0.163  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+.--
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl   49 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGF   49 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999999553

>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=94.57  E-value=0.0086  Score=51.27  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||++.+.--
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            467999999999999999999765

>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=94.56  E-value=0.009  Score=49.92  Aligned_cols=23  Identities=17%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||.+.+.--
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999999664

>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=94.55  E-value=0.0082  Score=48.50  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=20.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|-|+.|+||||+++.+.+.
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~   23 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGA   23 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999876

>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=94.52  E-value=0.021  Score=46.80  Aligned_cols=42  Identities=5%  Similarity=0.078  Sum_probs=29.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccccCC----CeeEEEEEe
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF----DCCAWVYYQ   80 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~~~   80 (351)
                      ++-+++-|.|.+|+||||||-++.........+    ..++|++..
T Consensus        32 ~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          32 ETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             ESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            456788899999999999999987763332222    345666655

>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=94.51  E-value=0.0093  Score=49.74  Aligned_cols=24  Identities=13%  Similarity=0.097  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.+++|+|+.|+|||||.+.+..-
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~   51 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTL   51 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999999664

>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=94.44  E-value=0.011  Score=47.29  Aligned_cols=26  Identities=19%  Similarity=0.312  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++.|+|+|..|+|||||.+.+.+.
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            45678999999999999999999864

>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=94.44  E-value=0.0096  Score=50.81  Aligned_cols=24  Identities=8%  Similarity=0.008  Sum_probs=19.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|.+.|-||+||||+|..+...
T Consensus         8 p~~i~~sGKGGVGKTTvaa~lA~~   31 (296)
T d1ihua1           8 PPYLFFTGKGGVGKTSISCATAIR   31 (296)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCcChHHHHHHHHHHH
Confidence            567888999999999987776555

>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=94.40  E-value=0.01  Score=50.03  Aligned_cols=23  Identities=17%  Similarity=0.222  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|+.|+|||||++.+.--
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHCC
Confidence            58999999999999999999765

>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=94.35  E-value=0.02  Score=48.90  Aligned_cols=83  Identities=7%  Similarity=0.033  Sum_probs=48.7

Q ss_pred             cCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCC--C-eeEEEEEe--CCHHHHHHHHHHHhCCCCC---CccCCCCCH
Q 048347           37 RQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF--D-CCAWVYYQ--LSLDMMLDAIMKSLMPLSA---LSEILDNDF  108 (351)
Q Consensus        37 ~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F--~-~~~wv~~~--~~~~~~~~~i~~~~~~~~~---~~~~~~~~~  108 (351)
                      ..++.-+|||-|..|+||||||..+...  +...+  . .++-++..  +-..+=...+........-   ...+...|.
T Consensus        23 ~~~~P~iIGi~G~qGSGKSTl~~~l~~~--L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~  100 (286)
T d1odfa_          23 GNKCPLFIFFSGPQGSGKSFTSIQIYNH--LMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDM  100 (286)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHHH--HHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCH
T ss_pred             CCCCCEEEEeECCCCCCHHHHHHHHHHH--HHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhH
Confidence            3445679999999999999999988766  33322  2 23444544  2222223444444322100   011466788


Q ss_pred             HHHHHHHHHhcCC
Q 048347          109 EMKKNTLHNYLKN  121 (351)
Q Consensus       109 ~~~~~~l~~~L~~  121 (351)
                      +.+.+.+....++
T Consensus       101 ~ll~~~l~~l~~~  113 (286)
T d1odfa_         101 KLLQEVLNTIFNN  113 (286)
T ss_dssp             HHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHhh
Confidence            8788888777655

>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=94.29  E-value=0.011  Score=48.08  Aligned_cols=20  Identities=15%  Similarity=0.272  Sum_probs=18.3

Q ss_pred             EEEEEcCCCChHHHHHHHHh
Q 048347           43 LVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~   62 (351)
                      +|||.|+.|+||||.|+.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998763

>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=94.18  E-value=0.012  Score=44.90  Aligned_cols=21  Identities=5%  Similarity=0.042  Sum_probs=18.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|..|+|||||..++..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            558999999999999998654

>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=94.18  E-value=0.011  Score=45.52  Aligned_cols=21  Identities=14%  Similarity=0.164  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+|+|.+|+|||||.+++.++
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            669999999999999998766

>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=94.05  E-value=0.027  Score=48.05  Aligned_cols=35  Identities=17%  Similarity=0.087  Sum_probs=26.4

Q ss_pred             HHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           29 ELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        29 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++++.+..=. +-..++|.|..|+|||+|+..+.+.
T Consensus        32 r~ID~l~Pig-rGQr~~I~g~~g~GKT~l~~~i~~~   66 (289)
T d1xpua3          32 RVLDLASPIG-RGQRGLIVAPPKAGKTMLLQNIAQS   66 (289)
T ss_dssp             HHHHHHSCCB-TTCEEEEEECSSSSHHHHHHHHHHH
T ss_pred             eeeeeccccc-CCCeeeEeCCCCCCHHHHHHHHHHH
Confidence            4666665422 2357888999999999999999887

>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=94.02  E-value=0.018  Score=45.06  Aligned_cols=25  Identities=8%  Similarity=0.275  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+..|+|+|-.|+|||||.+++.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999999999865

>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=94.02  E-value=0.015  Score=45.05  Aligned_cols=21  Identities=5%  Similarity=0.105  Sum_probs=18.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|.+|+|||||.+++.+.
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            569999999999999998765

>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=93.99  E-value=0.017  Score=51.21  Aligned_cols=48  Identities=13%  Similarity=0.076  Sum_probs=34.5

Q ss_pred             CCccccchhhHHHHHHHHH----------------------------ccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           17 NKVDLDLEDKMEELLDLLI----------------------------ERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        17 ~~~~vGr~~~~~~l~~~L~----------------------------~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+||-|+-++.+...+-                            +.+...+-+-.+|+.|+|||-||+.+...
T Consensus        16 ~~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          16 DNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhh
Confidence            4678999998888765541                            01122344667899999999999998754

>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=93.98  E-value=0.0093  Score=49.76  Aligned_cols=23  Identities=17%  Similarity=0.193  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      -.+++|+|+.|+|||||++.+..
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            36899999999999999999855

>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=93.97  E-value=0.019  Score=45.03  Aligned_cols=25  Identities=12%  Similarity=0.255  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ....|+|+|..|+|||||.++++..
T Consensus         4 ~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           4 YSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999999865

>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=93.96  E-value=0.033  Score=43.40  Aligned_cols=25  Identities=4%  Similarity=0.081  Sum_probs=20.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.++ |.++|.+|+|||||..++.+.
T Consensus        11 k~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          11 KEMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CCEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             CeEE-EEEECCCCCCHHHHHHHHhcC
Confidence            3466 448899999999999999766

>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=93.89  E-value=0.01  Score=48.64  Aligned_cols=24  Identities=17%  Similarity=0.043  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -+.|+|-|+.|+||||+++.+.+.
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~   26 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKK   26 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHH
Confidence            367899999999999999999877

>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=93.81  E-value=0.018  Score=44.46  Aligned_cols=22  Identities=9%  Similarity=0.114  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|.+|+|||+|+.++.++
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999998765

>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=93.79  E-value=0.017  Score=44.73  Aligned_cols=21  Identities=5%  Similarity=0.232  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|..|+|||||+.++.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999988754

>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=93.75  E-value=0.018  Score=44.86  Aligned_cols=22  Identities=9%  Similarity=0.215  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|+|+|..|+|||||.+++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5889999999999999999764

>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=93.74  E-value=0.014  Score=45.60  Aligned_cols=21  Identities=14%  Similarity=0.276  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|..|+|||+|+.++.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            668999999999999997655

>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=93.74  E-value=0.017  Score=44.90  Aligned_cols=21  Identities=14%  Similarity=0.289  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|.+|+|||||..++..+
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568899999999999998765

>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=93.72  E-value=0.017  Score=45.46  Aligned_cols=28  Identities=14%  Similarity=0.203  Sum_probs=21.6

Q ss_pred             ccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           36 ERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        36 ~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...+..+++ ++|..|+|||||..++...
T Consensus        13 ~~~k~~KI~-lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          13 GSNKELRIL-ILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             TCSSCEEEE-EEEETTSSHHHHHHHTCCS
T ss_pred             CCCceEEEE-EECCCCCCHHHHHHHHhcC
Confidence            334445554 9999999999999998655

>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=93.70  E-value=0.012  Score=48.92  Aligned_cols=23  Identities=4%  Similarity=0.276  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|+|..|+|||||.+.+..-
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999998653

>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=93.66  E-value=0.019  Score=47.05  Aligned_cols=37  Identities=11%  Similarity=0.030  Sum_probs=26.3

Q ss_pred             EEEEEE-cCCCChHHHHHHHHhCCcccccCCCeeEEEEEe
Q 048347           42 SLVAII-DTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQ   80 (351)
Q Consensus        42 ~vv~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~   80 (351)
                      +||+|+ +-||+||||+|..+...  ....-..++-+...
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~--la~~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVA--LGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHH--HHhCCCCEEEEeCC
Confidence            689999 55999999999988766  33333345555543

>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=93.65  E-value=0.017  Score=46.68  Aligned_cols=21  Identities=14%  Similarity=0.189  Sum_probs=18.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHh
Q 048347           42 SLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      -+|||.|.-|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            489999999999999998774

>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=93.64  E-value=0.1  Score=42.73  Aligned_cols=50  Identities=6%  Similarity=-0.083  Sum_probs=32.7

Q ss_pred             HHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcc----cccCCCeeEEEEEe
Q 048347           31 LDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSY----VKNYFDCCAWVYYQ   80 (351)
Q Consensus        31 ~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~----~~~~F~~~~wv~~~   80 (351)
                      -.+|..+=+.-+++.|+|.+|+|||++|.++.....    ....+..+.|+...
T Consensus        27 D~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~   80 (258)
T d1v5wa_          27 DKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTE   80 (258)
T ss_dssp             HHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESS
T ss_pred             HHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechH
Confidence            343333335668999999999999999998864311    22234456666655

>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=93.63  E-value=0.016  Score=44.85  Aligned_cols=21  Identities=10%  Similarity=0.216  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|.+|+|||+|++++.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999998754

>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=93.62  E-value=0.017  Score=47.55  Aligned_cols=25  Identities=12%  Similarity=0.332  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.|..|.|.-|+|||||.+++...
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5789999999999999999998765

>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=93.58  E-value=0.016  Score=44.93  Aligned_cols=22  Identities=18%  Similarity=0.332  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|-+|+|||+|+.++.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999988654

>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=93.58  E-value=0.016  Score=47.00  Aligned_cols=23  Identities=13%  Similarity=0.101  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|+|-|+.|+||||+++.+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~   25 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVET   25 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            57889999999999999999876

>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=93.57  E-value=0.019  Score=45.42  Aligned_cols=22  Identities=14%  Similarity=0.259  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.|+|..|+|||||+.++.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3668999999999999998765

>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=93.49  E-value=0.02  Score=44.48  Aligned_cols=21  Identities=14%  Similarity=0.162  Sum_probs=18.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|..|+|||+|++++.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999998765

>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=93.48  E-value=0.017  Score=44.95  Aligned_cols=22  Identities=18%  Similarity=0.262  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|.+|+|||||..++..+
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3678999999999999988654

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.39  E-value=0.014  Score=52.34  Aligned_cols=82  Identities=12%  Similarity=0.009  Sum_probs=39.1

Q ss_pred             CceEEEEecccccCceeeeCCCCCCcccEEEEecCCccc-----cccccccccCCccEEeecCCcccc-----ccChhhh
Q 048347          243 HLKVLKLKRSSYSGRKLVCGHGGFPRQEILHLKSMLWLE-----EWKMETGAMQKLKSLIVNPCAYLR-----KFPEELW  312 (351)
Q Consensus       243 ~L~~L~l~~~~~~~~~lp~~~~~l~~L~~L~L~~~~~l~-----~lp~~i~~L~~L~~L~l~~c~~l~-----~lP~~i~  312 (351)
                      +|++|+++++......+..-+..++++++|+|++|. ++     .+...+..+++|+.|+|++| .+.     .+.+.+.
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~-i~~~~~~~l~~~L~~~~~L~~LdLs~N-~i~~~~~~~l~~~l~   80 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCG-LTEARCKDISSALRVNPALAELNLRSN-ELGDVGVHCVLQGLQ   80 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSC-CCHHHHHHHHHHHHTCTTCCEEECTTC-CCHHHHHHHHHHTTC
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCCC-CCHHHHHHHHHHHhcCCCCCEEECcCC-cCChHHHHHHHHHHh
Confidence            466666643333222222223345666666666662 33     22333455666666666654 232     1122221


Q ss_pred             c-CCCCCEEEecCCC
Q 048347          313 R-IKALRKLESWWPR  326 (351)
Q Consensus       313 ~-L~~L~~L~l~~~~  326 (351)
                      . ..+|++|+++++.
T Consensus        81 ~~~~~L~~L~L~~n~   95 (460)
T d1z7xw1          81 TPSCKIQKLSLQNCC   95 (460)
T ss_dssp             STTCCCCEEECTTSC
T ss_pred             cCCCCCCEEECCCCC
Confidence            1 2356666666654

>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=93.33  E-value=0.019  Score=44.81  Aligned_cols=22  Identities=14%  Similarity=0.330  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|.+|+|||+|.+++.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999998764

>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=93.30  E-value=0.055  Score=45.32  Aligned_cols=41  Identities=15%  Similarity=0.220  Sum_probs=30.0

Q ss_pred             hhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           25 DKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        25 ~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      ..+.++...+......--.|.++|..|+|||||...++.+.
T Consensus        16 ~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          16 TKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCCC
Confidence            34445555555554455567799999999999999998763

>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=93.24  E-value=0.03  Score=46.17  Aligned_cols=42  Identities=7%  Similarity=0.150  Sum_probs=28.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCcccc----cCCCeeEEEEEe
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNSSYVK----NYFDCCAWVYYQ   80 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~~~   80 (351)
                      +.-+++.|+|.+|+||||||.++..+....    .....++|+...
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~   79 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE   79 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESS
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEecc
Confidence            456899999999999999999886542211    122345666655

>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=93.23  E-value=0.016  Score=45.60  Aligned_cols=21  Identities=5%  Similarity=0.211  Sum_probs=19.2

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+|+|..|+|||||..++...
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999999754

>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=93.23  E-value=0.02  Score=44.31  Aligned_cols=22  Identities=9%  Similarity=0.255  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|..|+|||||..++.+.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3668999999999999998765

>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=93.21  E-value=0.013  Score=49.34  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      -..++|+|..|+|||||++.+..
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh
Confidence            36899999999999999998854

>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=93.21  E-value=0.02  Score=44.42  Aligned_cols=21  Identities=10%  Similarity=0.303  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|-+|+|||+|.+++.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999998765

>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=93.13  E-value=0.023  Score=46.94  Aligned_cols=24  Identities=4%  Similarity=0.016  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++|||.|..|+||||+|+.+.+.
T Consensus         1 M~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           1 MKLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHh
Confidence            368999999999999999998664

>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=93.09  E-value=0.026  Score=43.71  Aligned_cols=24  Identities=8%  Similarity=0.097  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..-|.|+|-.|+|||+|..++.++
T Consensus         4 ~~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           4 SRKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCcCHHHHHHHHHhC
Confidence            345778999999999999997654

>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=93.09  E-value=0.022  Score=44.37  Aligned_cols=21  Identities=0%  Similarity=0.177  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|..|+|||+|+.++.+.
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998754

>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=93.06  E-value=0.021  Score=45.73  Aligned_cols=23  Identities=9%  Similarity=0.086  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|.|+|.+|+|||||..++.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            36789999999999999999765

>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=93.05  E-value=0.022  Score=44.16  Aligned_cols=22  Identities=9%  Similarity=0.126  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|-+|+|||+|+.++.++
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999998654

>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=93.03  E-value=0.022  Score=44.44  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=19.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|.+|+|||||..++.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4679999999999999998654

>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=93.03  E-value=0.022  Score=44.47  Aligned_cols=22  Identities=9%  Similarity=0.246  Sum_probs=18.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|..|+|||+|+.++..+
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999987644

>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=93.02  E-value=0.026  Score=44.28  Aligned_cols=22  Identities=5%  Similarity=0.077  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|+|+|..|+|||||..++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999875

>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=93.02  E-value=0.041  Score=48.01  Aligned_cols=30  Identities=3%  Similarity=-0.051  Sum_probs=24.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccccCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYF   71 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F   71 (351)
                      ++..|.|-|+-|+||||+++.+.+.  .....
T Consensus         5 ~~~rI~iEG~iGsGKSTl~~~L~~~--l~~~~   34 (333)
T d1p6xa_           5 TIVRIYLDGVYGIGKSTTGRVMASA--ASGGS   34 (333)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHSG--GGCSS
T ss_pred             ceEEEEEECCccCCHHHHHHHHHHH--hccCC
Confidence            3567888899999999999999998  44443

>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=92.99  E-value=0.037  Score=42.92  Aligned_cols=23  Identities=13%  Similarity=0.049  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ..|.|+|.+|+|||||..++...
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            44668999999999999998765

>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=92.95  E-value=0.025  Score=45.15  Aligned_cols=26  Identities=8%  Similarity=0.020  Sum_probs=21.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-.++.|.|.+|+|||+||.++..+
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHH
Confidence            34568889999999999999888655

>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=92.91  E-value=0.024  Score=43.95  Aligned_cols=22  Identities=14%  Similarity=0.246  Sum_probs=19.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|-.|+|||+|..++.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3668999999999999998765

>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=92.90  E-value=0.024  Score=43.07  Aligned_cols=22  Identities=9%  Similarity=0.070  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .|.++|.+|+|||||..++.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4679999999999999998765

>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=92.88  E-value=0.041  Score=42.45  Aligned_cols=27  Identities=11%  Similarity=0.123  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcc
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNSSY   66 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~~~   66 (351)
                      .--+|.+.|-=|+||||+++.+.....
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg   58 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIG   58 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhcc
Confidence            456899999999999999999977643

>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=92.88  E-value=0.024  Score=43.84  Aligned_cols=21  Identities=10%  Similarity=0.271  Sum_probs=18.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|-.|+|||+|..++.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678899999999999998765

>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=92.87  E-value=0.024  Score=44.05  Aligned_cols=21  Identities=19%  Similarity=0.355  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|.+|+|||+|..++.++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            458899999999999998865

>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=92.80  E-value=0.033  Score=43.88  Aligned_cols=24  Identities=4%  Similarity=0.030  Sum_probs=19.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .--|.|+|.+|+|||+|.+++..+
T Consensus         5 ~iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           5 AIKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            334678999999999999988765

>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=92.76  E-value=0.025  Score=44.20  Aligned_cols=22  Identities=14%  Similarity=0.308  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|..|+|||||+.++.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4779999999999999988664

>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=92.74  E-value=0.024  Score=49.47  Aligned_cols=43  Identities=14%  Similarity=0.074  Sum_probs=30.2

Q ss_pred             CccccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHh
Q 048347           18 KVDLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        18 ~~~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      .+++|.+.-+..+.-.+.... ... |-+.|..|+||||||+.+.
T Consensus         7 ~~I~Gq~~~kral~laa~~~~-~h~-vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           7 SAIVGQEDMKLALLLTAVDPG-IGG-VLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGG-GCC-EEEECCGGGCTTHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHhccC-CCe-EEEECCCCccHHHHHHHHH
Confidence            578999877776554443211 112 4578999999999999885

>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=92.73  E-value=0.026  Score=45.06  Aligned_cols=22  Identities=9%  Similarity=0.234  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|.+|+|||||+.++...
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            4678999999999999998765

>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=92.69  E-value=0.026  Score=43.92  Aligned_cols=22  Identities=14%  Similarity=0.203  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|..|+|||+|..++.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3668999999999999987664

>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=92.56  E-value=0.033  Score=43.54  Aligned_cols=22  Identities=9%  Similarity=0.101  Sum_probs=18.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|..|+|||+|..++.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3568899999999999988765

>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=92.55  E-value=0.04  Score=42.89  Aligned_cols=23  Identities=13%  Similarity=0.193  Sum_probs=19.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      --|.|+|-+|+|||+|+.++.+.
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34669999999999999988754

>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=92.55  E-value=0.029  Score=43.43  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|-.|+|||+|..++...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568999999999999998655

>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=92.50  E-value=0.055  Score=44.31  Aligned_cols=34  Identities=15%  Similarity=0.301  Sum_probs=26.4

Q ss_pred             hHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           26 KMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        26 ~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+++|.++|..     +...++|..|+|||||..++..+
T Consensus        85 g~~~L~~~l~~-----kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          85 GIEELKEYLKG-----KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             THHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             hHhhHHHHhcC-----CeEEEECCCCCCHHHHHHhhcch
Confidence            36677776632     35667899999999999999876

>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=92.49  E-value=0.021  Score=45.05  Aligned_cols=22  Identities=5%  Similarity=0.156  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|+|+|.+++|||||..++...
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998653

>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=92.44  E-value=0.03  Score=43.46  Aligned_cols=21  Identities=0%  Similarity=0.181  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|..|+|||+|..++...
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            558899999999999987655

>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=92.32  E-value=0.03  Score=44.21  Aligned_cols=22  Identities=9%  Similarity=0.132  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|-+|+|||+|..++.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3778999999999999997765

>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=92.24  E-value=0.039  Score=42.17  Aligned_cols=21  Identities=10%  Similarity=0.156  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |+++|..|+|||||..++...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            569999999999999999754

>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=92.23  E-value=0.039  Score=42.96  Aligned_cols=22  Identities=14%  Similarity=0.191  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|.+|+|||+|++++...
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3668999999999999988654

>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=92.20  E-value=0.041  Score=46.85  Aligned_cols=99  Identities=11%  Similarity=0.067  Sum_probs=49.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccc-CC----C-eeEEEEEe---CCHHHHHHHHHHHhCCCCC--CccCCCCCH--
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKN-YF----D-CCAWVYYQ---LSLDMMLDAIMKSLMPLSA--LSEILDNDF--  108 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~-~F----~-~~~wv~~~---~~~~~~~~~i~~~~~~~~~--~~~~~~~~~--  108 (351)
                      ..++|.|..|+|||+|+..+....+..+ .-    . .++++-+.   -.+.++...+...-..+..  .......+.  
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~~~~~  148 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPL  148 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEEEEECCCCCHHH
Confidence            4567789999999999877654421111 11    1 23344343   4444555554433211100  000001111  


Q ss_pred             --------HHHHHHHHHhcCCceEEEEEeCCCCh-hhHHHHHh
Q 048347          109 --------EMKKNTLHNYLKNKRYLIVIQDVWRG-DIWDFLKE  142 (351)
Q Consensus       109 --------~~~~~~l~~~L~~k~~LlVLDdv~~~-~~~~~l~~  142 (351)
                              -.+.+.+++  ++|+.|+++||+-.. +++..+..
T Consensus       149 r~~~~~~a~tiAEyfrd--~G~~VLll~Dsltr~A~A~rEis~  189 (285)
T d2jdia3         149 QYLAPYSGCSMGEYFRD--NGKHALIIYDDLSKQAVAYRQMSL  189 (285)
T ss_dssp             HHHHHHHHHHHHHHHHH--TTCEEEEEEETHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH--cCCcEEEEEcChHHHHHHHHHHHH
Confidence                    123444443  589999999999433 44444443

>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=92.17  E-value=0.034  Score=42.87  Aligned_cols=21  Identities=10%  Similarity=0.194  Sum_probs=18.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|.+|+|||||..++...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            558899999999999988654

>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=92.14  E-value=0.036  Score=43.63  Aligned_cols=21  Identities=0%  Similarity=0.034  Sum_probs=17.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|-+|+|||+|.+++..+
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            458999999999999987544

>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=92.11  E-value=0.04  Score=43.24  Aligned_cols=23  Identities=17%  Similarity=0.268  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.|+|+|-.|+|||||..++.+.
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            34789999999999999999865

>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=92.11  E-value=0.024  Score=44.21  Aligned_cols=21  Identities=14%  Similarity=0.385  Sum_probs=17.2

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.|+|..|+|||+|..++.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668899999999999987665

>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=92.10  E-value=0.046  Score=44.67  Aligned_cols=26  Identities=12%  Similarity=0.207  Sum_probs=22.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-.++.|.|.+|+|||++|.++..+
T Consensus        32 ~~G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          32 ESQSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            34578899999999999999998654

>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=92.10  E-value=0.029  Score=43.79  Aligned_cols=26  Identities=12%  Similarity=0.003  Sum_probs=22.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++...|+|+|..++|||||.+++...
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34677899999999999999998664

>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=92.10  E-value=0.035  Score=43.09  Aligned_cols=22  Identities=14%  Similarity=0.271  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|-+|+|||+|++++.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4779999999999999987554

>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=91.96  E-value=0.048  Score=43.16  Aligned_cols=19  Identities=5%  Similarity=0.240  Sum_probs=16.9

Q ss_pred             EEEEEcCCCChHHHHHHHH
Q 048347           43 LVAIIDTMGFDRTAFIGEA   61 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v   61 (351)
                      -|.++|.+|+|||+|..++
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3568999999999999998

>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=91.94  E-value=0.036  Score=43.59  Aligned_cols=21  Identities=24%  Similarity=0.452  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|..|+|||||+.++.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668999999999999988764

>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=91.93  E-value=0.037  Score=44.44  Aligned_cols=22  Identities=9%  Similarity=0.066  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|.+|+|||||..++...
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999998764

>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=91.88  E-value=0.11  Score=45.12  Aligned_cols=98  Identities=11%  Similarity=0.150  Sum_probs=53.7

Q ss_pred             EEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCCCCCCccCCCCCHHHHHHHHHHhcCCce
Q 048347           44 VAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMPLSALSEILDNDFEMKKNTLHNYLKNKR  123 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~k~  123 (351)
                      |.|.|..|+||||+++++...  +...- .++-+.-....         ++.......+......-...+.++..|+...
T Consensus       169 ili~G~tgSGKTT~l~al~~~--i~~~~-rivtiEd~~El---------~l~~~~~~~~~~~~~~~~~~~ll~~~lR~~p  236 (323)
T d1g6oa_         169 VIVCGGTGSGKTTYIKSIMEF--IPKEE-RIISIEDTEEI---------VFKHHKNYTQLFFGGNITSADCLKSCLRMRP  236 (323)
T ss_dssp             EEEEESTTSSHHHHHHHHGGG--SCTTC-CEEEEESSCCC---------CCSSCSSEEEEECBTTBCHHHHHHHHTTSCC
T ss_pred             EEEEeeccccchHHHHHHhhh--ccccc-ceeeccchhhh---------hcccccccceeccccchhHHHHHHHHhccCC
Confidence            567899999999999999876  43322 12222111110         0000000001011111134556677787777


Q ss_pred             EEEEEeCCCChhhHHHHHhhcCCCCCCcEEE
Q 048347          124 YLIVIQDVWRGDIWDFLKEALPDHQNGSRIL  154 (351)
Q Consensus       124 ~LlVLDdv~~~~~~~~l~~~l~~~~~gs~Ii  154 (351)
                      =-+|+..+.+.+.|..+. +...+..|+--=
T Consensus       237 d~iivgEiR~~ea~~~l~-a~~tGh~g~~tT  266 (323)
T d1g6oa_         237 DRIILGELRSSEAYDFYN-VLCSGHKGTLTT  266 (323)
T ss_dssp             SEEEESCCCSTHHHHHHH-HHHTTCSCEEEE
T ss_pred             CcccCCccCchhHHHHHH-HHHhcCCcEEEE
Confidence            779999999888887554 444444455433

>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=91.84  E-value=0.038  Score=43.42  Aligned_cols=21  Identities=10%  Similarity=0.197  Sum_probs=18.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|..|+|||+|++++.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458999999999999988765

>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=91.83  E-value=0.039  Score=43.16  Aligned_cols=21  Identities=14%  Similarity=0.317  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|..|+|||+|.+++.+.
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            669999999999999987654

>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=91.77  E-value=0.097  Score=44.30  Aligned_cols=33  Identities=12%  Similarity=0.203  Sum_probs=27.3

Q ss_pred             HHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           32 DLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        32 ~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.|..-.+.+.||+|+|.-+.||+||+..++..
T Consensus        23 ~~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          23 KILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            344444557999999999999999999999876

>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=91.66  E-value=0.049  Score=47.21  Aligned_cols=23  Identities=9%  Similarity=0.128  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .++-++|++|+|||.||+.+...
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~  146 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEA  146 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHHH
Confidence            44556899999999999999987

>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=91.65  E-value=0.041  Score=42.68  Aligned_cols=21  Identities=10%  Similarity=0.324  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|-.|+|||+|..++.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            557899999999999998765

>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=91.59  E-value=0.042  Score=42.75  Aligned_cols=22  Identities=9%  Similarity=0.277  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|-+|+|||||+.++.++
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3779999999999999887654

>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=91.39  E-value=0.061  Score=41.62  Aligned_cols=24  Identities=17%  Similarity=0.234  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +.-|.|+|-+|+|||+|++++.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            345779999999999999997654

>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=91.32  E-value=0.046  Score=43.31  Aligned_cols=21  Identities=5%  Similarity=0.115  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|-.|+|||+|..++.+.
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            558899999999999887655

>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=91.32  E-value=0.048  Score=42.72  Aligned_cols=22  Identities=5%  Similarity=0.163  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.++|..|+|||+|..++.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4668999999999999988665

>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=91.23  E-value=0.049  Score=47.37  Aligned_cols=25  Identities=20%  Similarity=0.040  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           40 QLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        40 ~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+.+|.|-|.-|+||||+++.+.+.
T Consensus         3 ~~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           3 TLLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             CceEEEEECCcCCCHHHHHHHHHHH
Confidence            3567889999999999999999876

>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=91.15  E-value=0.062  Score=43.09  Aligned_cols=23  Identities=9%  Similarity=-0.058  Sum_probs=19.1

Q ss_pred             EEEEEEcCC-CChHHHHHHHHhCC
Q 048347           42 SLVAIIDTM-GFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~g-GiGKTtLa~~v~~~   64 (351)
                      +.+-|.|-| |+||||++..+..-
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~a   25 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQA   25 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHH
Confidence            567789998 99999988777665

>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=90.78  E-value=0.059  Score=42.45  Aligned_cols=21  Identities=14%  Similarity=0.178  Sum_probs=17.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 048347           44 VAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~~~   64 (351)
                      |.++|-+|+|||+|..++...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999988544

>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=90.67  E-value=0.063  Score=43.73  Aligned_cols=22  Identities=0%  Similarity=0.028  Sum_probs=18.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .-|.++|.+|+|||||.+++..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3467899999999999998753

>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=90.45  E-value=0.041  Score=44.63  Aligned_cols=56  Identities=13%  Similarity=0.056  Sum_probs=31.7

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHH
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMM   86 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~   86 (351)
                      |-+.|..+=+.-.++.|.|..|+|||+||.++........ -..++|++.......+
T Consensus        15 LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~-~~~~~~~s~e~~~~~~   70 (242)
T d1tf7a1          15 FDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF-DEPGVFVTFEETPQDI   70 (242)
T ss_dssp             HHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHH-CCCEEEEESSSCHHHH
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCcccccccCCHHHH
Confidence            3344433324457888899999999999987544311222 2234555443444443

>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=90.23  E-value=0.045  Score=42.57  Aligned_cols=22  Identities=14%  Similarity=0.181  Sum_probs=8.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|+|-.|+|||||..++..+
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999887654

>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=90.22  E-value=0.077  Score=46.16  Aligned_cols=24  Identities=13%  Similarity=0.138  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-.|.|-|.-|+||||+++.+.+.
T Consensus         5 ~lrI~IEG~iGsGKSTl~~~L~~~   28 (331)
T d1osna_           5 VLRIYLDGAYGIGKTTAAEEFLHH   28 (331)
T ss_dssp             EEEEEEEESSSSCTTHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            445788899999999999999887

>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=90.19  E-value=0.079  Score=44.83  Aligned_cols=25  Identities=12%  Similarity=0.118  Sum_probs=21.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 048347           39 PQLSLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        39 ~~~~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      +++|=|+|+|-+|.|||||+.++..
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHH
Confidence            3578899999999999999998853

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=90.07  E-value=0.042  Score=47.78  Aligned_cols=86  Identities=15%  Similarity=0.206  Sum_probs=57.5

Q ss_pred             CCCCCceEEEEecccccCc----eeeeCCCCCCcccEEEEecCCccc-----cccccccccCCccEEeecCCccccc---
Q 048347          239 EKLPHLKVLKLKRSSYSGR----KLVCGHGGFPRQEILHLKSMLWLE-----EWKMETGAMQKLKSLIVNPCAYLRK---  306 (351)
Q Consensus       239 ~~l~~L~~L~l~~~~~~~~----~lp~~~~~l~~L~~L~L~~~~~l~-----~lp~~i~~L~~L~~L~l~~c~~l~~---  306 (351)
                      ...+.|+.|+++.+....+    .+...+..+++|+.|++++|. ++     .+...+...++|++|+|++|. +..   
T Consensus       183 ~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~-i~~~g~~~L~~~l~~~~~L~~L~Ls~n~-i~~~g~  260 (344)
T d2ca6a1         183 QSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNT-FTHLGSSALAIALKSWPNLRELGLNDCL-LSARGA  260 (344)
T ss_dssp             HHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSC-CHHHHHHHHHHHGGGCTTCCEEECTTCC-CCHHHH
T ss_pred             hhhhhhcccccccccccccccccchhhhhcchhhhccccccccc-ccccccccccccccccccchhhhhhcCc-cCchhh
Confidence            3567899999944322211    133346678899999999984 43     245557788999999999974 332   


Q ss_pred             --cChhhhc--CCCCCEEEecCCC
Q 048347          307 --FPEELWR--IKALRKLESWWPR  326 (351)
Q Consensus       307 --lP~~i~~--L~~L~~L~l~~~~  326 (351)
                        +-+.+.+  -++|++|++++..
T Consensus       261 ~~l~~~l~~~~~~~L~~L~ls~N~  284 (344)
T d2ca6a1         261 AAVVDAFSKLENIGLQTLRLQYNE  284 (344)
T ss_dssp             HHHHHHHHTCSSCCCCEEECCSSC
T ss_pred             HHHHHHhhhccCCCCCEEECCCCc
Confidence              2223333  3579999999876

>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=89.83  E-value=0.085  Score=44.08  Aligned_cols=23  Identities=9%  Similarity=0.122  Sum_probs=18.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      .+..|+|.+|+||||||-+++-.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            46668999999999999877544

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=89.50  E-value=0.22  Score=41.46  Aligned_cols=54  Identities=6%  Similarity=0.051  Sum_probs=35.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccccCCCeeEEEEEeCCHHHHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNSSYVKNYFDCCAWVYYQLSLDMMLDAIMKSLMP   96 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~i~~~~~~   96 (351)
                      .++.|.|.+|+||||+|.++..+......+. +++++.-.+..++...++.....
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~-v~~~s~E~~~~~~~~r~~~~~~~   89 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGKK-VGLAMLEESVEETAEDLIGLHNR   89 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCCC-EEEEESSSCHHHHHHHHHHHHTT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhcccc-eeEeeeccchhhHHhHHHHHhhc
Confidence            5777889999999999988876522233333 34444336677777777665554

>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=89.31  E-value=0.11  Score=40.86  Aligned_cols=22  Identities=14%  Similarity=0.140  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|.|.+|+||||+|-.+..+
T Consensus        17 gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          17 GVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            3568899999999999998765

>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=89.27  E-value=0.035  Score=42.40  Aligned_cols=22  Identities=9%  Similarity=0.277  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|+++|..|+|||||.+++...
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

>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=89.16  E-value=0.093  Score=41.15  Aligned_cols=23  Identities=17%  Similarity=0.049  Sum_probs=19.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +-|.|.|.+|+||||+|..+..+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            34668899999999999987765

>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=88.86  E-value=0.12  Score=43.33  Aligned_cols=22  Identities=18%  Similarity=0.323  Sum_probs=19.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHh
Q 048347           41 LSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        41 ~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      +|-|+|+|-.|.|||||+.++.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            4679999999999999999873

>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=88.10  E-value=0.16  Score=40.63  Aligned_cols=37  Identities=11%  Similarity=0.091  Sum_probs=27.3

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ++.+..+|. +.++-.-+.++|+++.|||++|..+.+-
T Consensus        40 l~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~~   76 (205)
T d1tuea_          40 LGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIHF   76 (205)
T ss_dssp             HHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHHH
Confidence            455566664 3355677889999999999999887554

>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=87.88  E-value=0.22  Score=43.68  Aligned_cols=22  Identities=14%  Similarity=0.182  Sum_probs=18.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      ++..|.|.+|.||||++.++..
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~  185 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLA  185 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHHHH
Confidence            5788899999999998866543

>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=87.88  E-value=0.13  Score=40.02  Aligned_cols=22  Identities=18%  Similarity=0.104  Sum_probs=18.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|.|.|..|+||||+|-.+..+
T Consensus        17 gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          17 GVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4668999999999999887665

>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=87.27  E-value=0.25  Score=41.34  Aligned_cols=35  Identities=6%  Similarity=0.058  Sum_probs=25.9

Q ss_pred             HHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           30 LLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        30 l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      +..+|....++-..+.++|+|+.|||+++..+..-
T Consensus        93 l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~  127 (267)
T d1u0ja_          93 FLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHH
Confidence            33444444455677788999999999999888664

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=87.03  E-value=0.42  Score=36.62  Aligned_cols=83  Identities=11%  Similarity=0.036  Sum_probs=54.8

Q ss_pred             CCCCceEEEEecccccC-c----eeeeCCCCCCcccEEEEecCCcccc-----ccccccccCCccEEeecCCccccc---
Q 048347          240 KLPHLKVLKLKRSSYSG-R----KLVCGHGGFPRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIVNPCAYLRK---  306 (351)
Q Consensus       240 ~l~~L~~L~l~~~~~~~-~----~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l~~c~~l~~---  306 (351)
                      +.+.|+.|+|+ +...+ .    .+-..+...++|++|+|++| .++.     +-..+..-+.|+.|+|++|. +..   
T Consensus        13 n~~~L~~L~L~-~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n-~l~~~~~~~la~~L~~n~~L~~L~L~~n~-i~~~g~   89 (167)
T d1pgva_          13 DDTDLKEVNIN-NMKRVSKERIRSLIEAACNSKHIEKFSLANT-AISDSEARGLIELIETSPSLRVLNVESNF-LTPELL   89 (167)
T ss_dssp             TCSSCCEEECT-TCCSSCHHHHHHHHHHHTTCSCCCEEECTTS-CCBHHHHTTHHHHHHHCSSCCEEECCSSB-CCHHHH
T ss_pred             CCCCCcEEEeC-CCCCCCHHHHHHHHHHHhhCCccceeecccc-ccchhHHHHHhhhhhhcccccceeeehhh-cchHHH
Confidence            46889999994 32222 1    22234566788999999998 4542     22234456789999999973 432   


Q ss_pred             --cChhhhcCCCCCEEEecCC
Q 048347          307 --FPEELWRIKALRKLESWWP  325 (351)
Q Consensus       307 --lP~~i~~L~~L~~L~l~~~  325 (351)
                        +-..+.+-++|++|++++.
T Consensus        90 ~~l~~aL~~n~sL~~L~l~~n  110 (167)
T d1pgva_          90 ARLLRSTLVTQSIVEFKADNQ  110 (167)
T ss_dssp             HHHHHHTTTTCCCSEEECCCC
T ss_pred             HHHHHHHHhCCcCCEEECCCC
Confidence              2234556688999999864

>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=86.95  E-value=0.17  Score=41.19  Aligned_cols=22  Identities=9%  Similarity=0.365  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      .+|+|+|-.++|||||+.++..
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHh
Confidence            5799999999999999998854

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=86.77  E-value=0.17  Score=43.58  Aligned_cols=89  Identities=18%  Similarity=0.146  Sum_probs=60.2

Q ss_pred             CCCCCCCCceEEEEecccccC---ceeeeCCCCCCcccEEEEecCCccccc-----ccccc--ccCCccEEeecCCcccc
Q 048347          236 PAPEKLPHLKVLKLKRSSYSG---RKLVCGHGGFPRQEILHLKSMLWLEEW-----KMETG--AMQKLKSLIVNPCAYLR  305 (351)
Q Consensus       236 ~~l~~l~~L~~L~l~~~~~~~---~~lp~~~~~l~~L~~L~L~~~~~l~~l-----p~~i~--~L~~L~~L~l~~c~~l~  305 (351)
                      ..+..+++|+.|+++.+....   ..+...+..+++|++|++++| .++.-     =..+.  ....|+.|++++|. +.
T Consensus       209 ~~l~~~~~L~~L~Ls~N~i~~~g~~~L~~~l~~~~~L~~L~Ls~n-~i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~-i~  286 (344)
T d2ca6a1         209 EGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDC-LLSARGAAAVVDAFSKLENIGLQTLRLQYNE-IE  286 (344)
T ss_dssp             TTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTTC-CCCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CB
T ss_pred             hhhcchhhhcccccccccccccccccccccccccccchhhhhhcC-ccCchhhHHHHHHhhhccCCCCCEEECCCCc-CC
Confidence            345678999999995443221   234445677899999999999 45432     11222  23579999999864 43


Q ss_pred             -----ccChhhh-cCCCCCEEEecCCC
Q 048347          306 -----KFPEELW-RIKALRKLESWWPR  326 (351)
Q Consensus       306 -----~lP~~i~-~L~~L~~L~l~~~~  326 (351)
                           .+...+. ++++|++|++++..
T Consensus       287 ~~~~~~l~~~l~~~~~~L~~L~l~~N~  313 (344)
T d2ca6a1         287 LDAVRTLKTVIDEKMPDLLFLELNGNR  313 (344)
T ss_dssp             HHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             hHHHHHHHHHHHccCCCCCEEECCCCc
Confidence                 3555663 68899999998744

>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=86.23  E-value=0.2  Score=38.99  Aligned_cols=22  Identities=9%  Similarity=0.089  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|+|+|-.++|||||.+++...
T Consensus         7 nIaiiG~~naGKSTL~n~L~~~   28 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTEI   28 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTT
T ss_pred             EEEEEeCCCCcHHHHHHHHHHh
Confidence            5899999999999999998753

>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=86.20  E-value=0.26  Score=42.80  Aligned_cols=35  Identities=6%  Similarity=0.233  Sum_probs=27.6

Q ss_pred             HHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHh
Q 048347           27 MEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        27 ~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~   62 (351)
                      .+.+.+++.. .+++|=|+|+|-.|.|||||+.++.
T Consensus         4 ~~~~~~lm~~-~~~IRNI~iiGhvd~GKTTL~d~Ll   38 (341)
T d1n0ua2           4 VDQMRSLMDK-VTNVRNMSVIAHVDHGKSTLTDSLV   38 (341)
T ss_dssp             HHHHHHHHHC-GGGEEEEEEECCGGGTHHHHHHHHH
T ss_pred             HHHHHHHhcC-cccCcEEEEEeCCCCcHHHHHHHHH
Confidence            3556665544 4578889999999999999998885

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=85.84  E-value=0.097  Score=40.50  Aligned_cols=91  Identities=15%  Similarity=0.119  Sum_probs=58.0

Q ss_pred             CCCCCCceEEEEecccccC---ceeeeCCCCCCcccEEEEecCCcccc-----ccccccccCCccEEeecCCc--cc---
Q 048347          238 PEKLPHLKVLKLKRSSYSG---RKLVCGHGGFPRQEILHLKSMLWLEE-----WKMETGAMQKLKSLIVNPCA--YL---  304 (351)
Q Consensus       238 l~~l~~L~~L~l~~~~~~~---~~lp~~~~~l~~L~~L~L~~~~~l~~-----lp~~i~~L~~L~~L~l~~c~--~l---  304 (351)
                      +...++|+.|+++.+....   ..+-..+...+.|+.|++++| .++.     +-..+..-++|+.|++.++.  .+   
T Consensus        40 L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n-~i~~~g~~~l~~aL~~n~sL~~L~l~~n~~~~~g~~  118 (167)
T d1pgva_          40 ACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESN-FLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQ  118 (167)
T ss_dssp             HTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSS-BCCHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHH
T ss_pred             HhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehh-hcchHHHHHHHHHHHhCCcCCEEECCCCcCCCccHH
Confidence            4566889999994332211   122223345578999999999 4543     22234555789999998742  11   


Q ss_pred             --cccChhhhcCCCCCEEEecCCChhH
Q 048347          305 --RKFPEELWRIKALRKLESWWPRPEL  329 (351)
Q Consensus       305 --~~lP~~i~~L~~L~~L~l~~~~~~~  329 (351)
                        ..+...+..-++|+.|+++.+.++-
T Consensus       119 ~~~~l~~~L~~n~sL~~l~l~~~~~~~  145 (167)
T d1pgva_         119 VEMDMMMAIEENESLLRVGISFASMEA  145 (167)
T ss_dssp             HHHHHHHHHHHCSSCCEEECCCCCHHH
T ss_pred             HHHHHHHHHHhCCCccEeeCcCCCchH
Confidence              2244556667899999998877543

>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=85.13  E-value=0.11  Score=42.66  Aligned_cols=22  Identities=5%  Similarity=0.178  Sum_probs=18.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      ...++|..|+|||||.+++..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            4457899999999999999877

>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=84.88  E-value=0.82  Score=38.01  Aligned_cols=51  Identities=14%  Similarity=0.201  Sum_probs=33.8

Q ss_pred             CCCCccccchhhHHHHHHHHHcc---------CCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 048347           15 WDNKVDLDLEDKMEELLDLLIER---------QPQLSLVAIIDTMGFDRTAFIGEAYNSS   65 (351)
Q Consensus        15 ~~~~~~vGr~~~~~~l~~~L~~~---------~~~~~vv~I~G~gGiGKTtLa~~v~~~~   65 (351)
                      +...+..|..+..+.+.+.+...         ....-.|+|+|++.+||+||+..+....
T Consensus        77 isa~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~v~vvG~PNvGKSsliN~L~~~~  136 (273)
T d1puja_          77 INSVNGQGLNQIVPASKEILQEKFDRMRAKGVKPRAIRALIIGIPNVGKSTLINRLAKKN  136 (273)
T ss_dssp             CCTTTCTTGGGHHHHHHHHHHHHHHHHHHTTCCCCCEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             eecccCCCccccchhhhhhhhhhhhhhhhccCCCCceEEEEEecCccchhhhhhhhhccc
Confidence            33444455555555555544321         2345668999999999999999998864

>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=83.69  E-value=0.099  Score=40.90  Aligned_cols=21  Identities=5%  Similarity=0.118  Sum_probs=17.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      +..|+|+.|+||||+..+++-
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~   46 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVT   46 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            345679999999999998853

>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=83.68  E-value=0.53  Score=41.76  Aligned_cols=43  Identities=12%  Similarity=0.240  Sum_probs=29.7

Q ss_pred             cccchhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 048347           20 DLDLEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        20 ~vGr~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -.|..+..-+..+.+...  ...+|.|.|+.|.||||.+..+.+.
T Consensus       139 ~LG~~~~~~~~l~~l~~~--~~GliLvtGpTGSGKSTTl~~~l~~  181 (401)
T d1p9ra_         139 SLGMTAHNHDNFRRLIKR--PHGIILVTGPTGSGKSTTLYAGLQE  181 (401)
T ss_dssp             GSCCCHHHHHHHHHHHTS--SSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             hhcccHHHHHHHHHHHhh--hhceEEEEcCCCCCccHHHHHHhhh
Confidence            356555444444444433  3578889999999999999888765

>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=83.62  E-value=0.35  Score=42.96  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 048347           42 SLVAIIDTMGFDRTAFIGEAYN   63 (351)
Q Consensus        42 ~vv~I~G~gGiGKTtLa~~v~~   63 (351)
                      --|+|+|..|+|||||...+..
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4588999999999999999974

>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=83.28  E-value=0.29  Score=41.08  Aligned_cols=22  Identities=5%  Similarity=0.146  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 048347           43 LVAIIDTMGFDRTAFIGEAYNS   64 (351)
Q Consensus        43 vv~I~G~gGiGKTtLa~~v~~~   64 (351)
                      -|||+|++.+|||||-.++-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            5899999999999999988765

>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=81.15  E-value=0.41  Score=38.16  Aligned_cols=19  Identities=16%  Similarity=0.237  Sum_probs=17.4

Q ss_pred             EEEEcCCCChHHHHHHHHh
Q 048347           44 VAIIDTMGFDRTAFIGEAY   62 (351)
Q Consensus        44 v~I~G~gGiGKTtLa~~v~   62 (351)
                      |+|+|=.+.|||||+.++.
T Consensus         6 i~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHH
Confidence            7899999999999998874

>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=80.14  E-value=0.4  Score=40.62  Aligned_cols=65  Identities=11%  Similarity=0.070  Sum_probs=32.7

Q ss_pred             chhhHHHHHHHHHccCCCeEEEEEEcCCCChHHHHHHH-HhCCcccccCC--CeeEEEEEe-CCHHHHHHHHHHHh
Q 048347           23 LEDKMEELLDLLIERQPQLSLVAIIDTMGFDRTAFIGE-AYNSSYVKNYF--DCCAWVYYQ-LSLDMMLDAIMKSL   94 (351)
Q Consensus        23 r~~~~~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLa~~-v~~~~~~~~~F--~~~~wv~~~-~~~~~~~~~i~~~~   94 (351)
                      .+.+..++++.   .+ +  .+-|.|.+|.||||.+-+ +..-. .....  +.++.++.+ ....++...+....
T Consensus        12 L~~eQ~~~v~~---~~-g--~~lV~g~aGSGKTt~l~~ri~~ll-~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          12 LNKEQQEAVRT---TE-G--PLLIMAGAGSGKTRVLTHRIAYLM-AEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             SCHHHHHHHHC---CS-S--CEEEEECTTSCHHHHHHHHHHHHH-HTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC---CC-C--CEEEEecCCccHHHHHHHHHHHHH-HcCCCCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            44555566652   11 1  245779999999986533 21110 01112  234555555 44445555554443