Citrus Sinensis ID: 046115

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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-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-----
Protein Sequence
MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYDRACSL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHccHHHHHcccccEEEEEcccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHcccEEEEEEccccccccccHHHHHHHHcccccccEEEEEcccHHHHHHHccccEEEcccccHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccHHHHccccccccccHHHHHHHccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHccccccccccccccEEEEEEcHHHHHHHHHHHHccEEEEEccccccccccccccccEEEEEEEEccccccccccccccccccccccccccccccccccccHHHHHHccccccEEEcccccccccccccccccccccccccccEEEcccccccccccHHHcccccccEEEcccccccccccccccccccccEEEcccccccccccccccccccccccccEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHccHHHHHHccEEEEEEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccEEEEEEEccccccHHHHHHHHHHHHccccccEEEEEEccHHHHHHHccccccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccHHHHHHHHHcHHcccccccccccHHHHEcHccccHHHHHHHHEEEEccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHccccccccccEEEEHHHHHHHHHHHHccccEEEEEccccccccccccccccEEEEEEEEcccccccccccccHccccccccEcccccccccccccHHHHHHHccccEEEEccccccccccccHHHccccHcccHHHcEEEcccccccccccccccccHcHHEEEEcccHHHHHccHHHHccccccEEEEcccccHHccccccccHHHHccccEEEEEcccccEEcc
Coil and Loop (DISEMBL)
MGGIGKTTLAQFAYnngdvernfekrtwvcvsepfdEFRIARAIIEsltpgsakDLVEFQSLMQHIEECVAGKKFLLVLDDvwnedyykwepfYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAisgktigkreNLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLlsynelpskvkrcfsycavfpkdygirKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASrsffqdfnkyddgeiykckmHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLrrgasvpisiwgnvtglRGLRSLLVksdeyswssevlPQLFEKLTCLRALELQvreswprnnlikeIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYnlerlnvddcqnlrelprGIGKLRKLMYLhnedtgclrylpagiGELIRLRRVREFVvgggydracsl
Flexible Loop (DISEMBL)
mggigkttlaqfaynngdvernfeKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSlaisgktigkrenlEKIGREivkkckglplAAKTIASllrskntekEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTlrrgasvpisiwgnvtglRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELqvreswprnnlikEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLerlnvddcqnlrELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVvgggydracsl
Low Complexity Region (SEG)
MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYDRACSL
Disordered region (IsUnstruct)
******TTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYDR****
Disordered Region (DISOPRED)
MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTP**********SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAIS********NLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKG**EMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYD**CSL
Disordered Region (DISEMBL)
MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYDRACSL
Disordered Region (DISPRO)
**GIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYDR*C**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVGGGYDRACSL
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	505	2.2.26 [Sep-21-2011]
Q7XA40	992	Putative disease resistan	N/A	no	0.904	0.460	0.389	6e-84
Q7XA42	979	Putative disease resistan	N/A	no	0.885	0.456	0.376	9e-83
Q7XBQ9	970	Disease resistance protei	N/A	no	0.879	0.457	0.375	1e-81
Q7XA39	988	Putative disease resistan	N/A	no	0.885	0.452	0.382	9e-80
Q9LRR4	1054	Putative disease resistan	yes	no	0.938	0.449	0.339	2e-70
Q9LRR5	1424	Putative disease resistan	no	no	0.928	0.329	0.321	2e-67
Q38834	852	Disease resistance RPP13-	no	no	0.912	0.541	0.305	3e-57
Q39214	926	Disease resistance protei	no	no	0.873	0.476	0.304	9e-51
Q8W3K3	910	Putative disease resistan	no	no	0.883	0.490	0.295	4e-42
Q9M667	835	Disease resistance protei	no	no	0.586	0.354	0.335	2e-40

>sp|Q7XA40|RGA3_SOLBU Putative disease resistance protein RGA3 OS=Solanum bulbocastanum GN=RGA3 PE=2 SV=2

 Score =  311 bits (798), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 193/496 (38%), Positives = 283/496 (57%), Gaps = 39/496 (7%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGG+GKTTLAQ  +N+  +  +F  + WVCVS+ FDE R+ +AI+ES+   S  D+ +  
Sbjct: 183 MGGLGKTTLAQMVFNDQRITEHFNLKIWVCVSDDFDEKRLIKAIVESIEGKSLGDM-DLA 241

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
            L + ++E + GK++ LVLDDVWNED  KW+     LK     + ILITTR E +  IMG
Sbjct: 242 PLQKKLQELLNGKRYFLVLDDVWNEDQEKWDNLRAVLKIGASGASILITTRLEKIGSIMG 301

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           +  +  ++ LS+ +CW +F+  A   +T      L +IG+EIVKKC G+PLAAKT+  LL
Sbjct: 302 TLQLYQLSNLSQEDCWLLFKQRAFCHQT-ETSPKLMEIGKEIVKKCGGVPLAAKTLGGLL 360

Query: 181 RSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
           R K  E EW+++ ++EIW L   E  +L  L LSY+ LP  +++CF+YCAVFPKD  I K
Sbjct: 361 RFKREESEWEHVRDSEIWNLPQDENSVLPALRLSYHHLPLDLRQCFAYCAVFPKDTKIEK 420

Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHD 300
             LI LWMA  +L  KG  E+ED+G E +N L  RSFFQ+  +   G+ Y  KMHD++HD
Sbjct: 421 EYLIALWMAHSFLLSKGNMELEDVGNEVWNELYLRSFFQEI-EVKSGKTY-FKMHDLIHD 478

Query: 301 FAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRS 360
            A  + S    +  I       I+   ++ ++ +                 VT  + + S
Sbjct: 479 LATSMFSASASSRSIRQ-----INVKDDEDMMFI-----------------VTNYKDMMS 516

Query: 361 LLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL 420
           +       S+S    P LF++   LR L L        N+  +++P+++  L+HL+YL+L
Sbjct: 517 IGFSEVVSSYS----PSLFKRFVSLRVLNLS-------NSEFEQLPSSVGDLVHLRYLDL 565

Query: 421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG 480
            G  KI  LP+ LC+L NL+ L++ +CQ+L  LP+   KL  L  L   D   L  +P  
Sbjct: 566 SGN-KICSLPKRLCKLQNLQTLDLYNCQSLSCLPKQTSKLCSLRNL-VLDHCPLTSMPPR 623

Query: 481 IGELIRLRRVREFVVG 496
           IG L  L+ +  FVVG
Sbjct: 624 IGLLTCLKTLGYFVVG 639

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.
Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA42|RGA1_SOLBU Putative disease resistance protein RGA1 OS=Solanum bulbocastanum GN=RGA1 PE=2 SV=2

 Score =  308 bits (788), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 187/497 (37%), Positives = 265/497 (53%), Gaps = 50/497 (10%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGG+GKTTL+Q  +N+  V   F  + W+C+S+ F+E R+ +AI+ES+   S  D+ +  
Sbjct: 183 MGGLGKTTLSQMVFNDQRVTERFYPKIWICISDDFNEKRLIKAIVESIEGKSLSDM-DLA 241

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
            L + ++E + GK++ LVLDDVWNED +KW      LK     + +L TTR E V  IMG
Sbjct: 242 PLQKKLQELLNGKRYFLVLDDVWNEDQHKWANLRAVLKVGASGAFVLTTTRLEKVGSIMG 301

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           +     ++ LS  +CW +F   A  G       NL  IG+EIVKKC G+PLAAKT+  +L
Sbjct: 302 TLQPYELSNLSPEDCWFLFMQRAF-GHQEEINPNLMAIGKEIVKKCGGVPLAAKTLGGIL 360

Query: 181 RSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
           R K  E+EW+++ ++ IW L   E  +L  L LSY+ LP  +++CF YCAVFPKD  + K
Sbjct: 361 RFKREEREWEHVRDSPIWNLPQDESSILPALRLSYHHLPLDLRQCFVYCAVFPKDTKMAK 420

Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHD 300
             LI  WMA G+L  KG  E+ED+G E +N L  RSFFQ+  + + G+ Y  KMHD++HD
Sbjct: 421 ENLIAFWMAHGFLLSKGNLELEDVGNEVWNELYLRSFFQEI-EVESGKTY-FKMHDLIHD 478

Query: 301 FAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRS 360
            A  L S    +  I                                I  N  G      
Sbjct: 479 LATSLFSANTSSSNIR------------------------------EINANYDGYMMSIG 508

Query: 361 LLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL 420
                  YS      P L +K   LR L L       RN+ + ++P++I  L+HL+YL+L
Sbjct: 509 FAEVVSSYS------PSLLQKFVSLRVLNL-------RNSNLNQLPSSIGDLVHLRYLDL 555

Query: 421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGC-LRYLPA 479
            G  +I  LP+ LC+L NL+ L++  C +L  LP+   KL  L  L  +  GC L   P 
Sbjct: 556 SGNFRIRNLPKRLCKLQNLQTLDLHYCDSLSCLPKQTSKLGSLRNLLLD--GCSLTSTPP 613

Query: 480 GIGELIRLRRVREFVVG 496
            IG L  L+ +  FV+G
Sbjct: 614 RIGLLTCLKSLSCFVIG 630

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XBQ9|RGA2_SOLBU Disease resistance protein RGA2 OS=Solanum bulbocastanum GN=RGA2 PE=1 SV=1

 Score =  303 bits (777), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 188/501 (37%), Positives = 265/501 (52%), Gaps = 57/501 (11%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGG+GKTTLAQ  +N+  V  +F  + W+CVSE FDE R+ +AI+ES+        ++  
Sbjct: 183 MGGLGKTTLAQMVFNDQRVTEHFHSKIWICVSEDFDEKRLIKAIVESIEGRPLLGEMDLA 242

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
            L + ++E + GK++LLVLDDVWNED  KW      LK     + +L TTR E V  IMG
Sbjct: 243 PLQKKLQELLNGKRYLLVLDDVWNEDQQKWANLRAVLKVGASGASVLTTTRLEKVGSIMG 302

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           +     ++ LS+ +CW +F   A  G       NL  IG+EIVKK  G+PLAAKT+  +L
Sbjct: 303 TLQPYELSNLSQEDCWLLFMQRAF-GHQEEINPNLVAIGKEIVKKSGGVPLAAKTLGGIL 361

Query: 181 RSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
             K  E+ W+++ ++ IW L   E  +L  L LSY++LP  +K+CF+YCAVFPKD  + K
Sbjct: 362 CFKREERAWEHVRDSPIWNLPQDESSILPALRLSYHQLPLDLKQCFAYCAVFPKDAKMEK 421

Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHD 300
            KLI LWMA G+L  KG  E+ED+G+E +  L  RSFFQ+  +  DG+ Y  KMHD++HD
Sbjct: 422 EKLISLWMAHGFLLSKGNMELEDVGDEVWKELYLRSFFQEI-EVKDGKTY-FKMHDLIHD 479

Query: 301 FAQYLCSNECLAVEI-----HSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGL 355
            A  L S    +  I     HS   +    F E    +                      
Sbjct: 480 LATSLFSANTSSSNIREINKHSYTHMMSIGFAEVVFFY---------------------- 517

Query: 356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHL 415
                              LP L EK   LR L L        ++   ++P++I  L+HL
Sbjct: 518 ------------------TLPPL-EKFISLRVLNLG-------DSTFNKLPSSIGDLVHL 551

Query: 416 KYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLR 475
           +YLNL G   +  LP+ LC+L NL+ L++  C  L  LP+   KL  L  L  + +  L 
Sbjct: 552 RYLNLYGS-GMRSLPKQLCKLQNLQTLDLQYCTKLCCLPKETSKLGSLRNLLLDGSQSLT 610

Query: 476 YLPAGIGELIRLRRVREFVVG 496
            +P  IG L  L+ + +FVVG
Sbjct: 611 CMPPRIGSLTCLKTLGQFVVG 631

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth. Confers a broad resistance to all known races of P.infestans.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA39|RGA4_SOLBU Putative disease resistance protein RGA4 OS=Solanum bulbocastanum GN=RGA4 PE=2 SV=1

 Score =  298 bits (762), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 193/504 (38%), Positives = 268/504 (53%), Gaps = 57/504 (11%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS--AKDLVE 58
           MGG+GKTTLAQ  +N+  V ++F  + WVCVS+ FDE R+ + II ++   S   +DL  
Sbjct: 185 MGGLGKTTLAQMIFNDERVTKHFNPKIWVCVSDDFDEKRLIKTIIGNIERSSPHVEDLAS 244

Query: 59  FQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI 118
           FQ  +Q   E + GK++LLVLDDVWN+D  KW      L      + IL TTR E V  I
Sbjct: 245 FQKKLQ---ELLNGKRYLLVLDDVWNDDLEKWAKLRAVLTVGARGASILATTRLEKVGSI 301

Query: 119 MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS 178
           MG+     ++ LS  +   +F   A  G+      NL  IG+EIVKKC G+PLAAKT+  
Sbjct: 302 MGTLQPYHLSNLSPHDSLLLFMQRAF-GQQKEANPNLVAIGKEIVKKCGGVPLAAKTLGG 360

Query: 179 LLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGI 238
           LLR K  E EW+++ +NEIW L   E  +L  L LSY+ LP  +++CF+YCAVFPKD  +
Sbjct: 361 LLRFKREESEWEHVRDNEIWSLPQDESSILPALRLSYHHLPLDLRQCFAYCAVFPKDTKM 420

Query: 239 RKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIV 298
            K  LI LWMA G+L  KG  E+ED+G E +N L  RSFFQ+  +   G  Y  K+HD++
Sbjct: 421 IKENLITLWMAHGFLLSKGNLELEDVGNEVWNELYLRSFFQEI-EAKSGNTY-FKIHDLI 478

Query: 299 HDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGL 358
           HD A  L S       I    E+ +  +          T+  G +  +S +         
Sbjct: 479 HDLATSLFSASASCGNIR---EINVKDYKH--------TVSIGFAAVVSSYS-------- 519

Query: 359 RSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYL 418
                            P L +K   LR L L   +       ++++P++I  LLHL+YL
Sbjct: 520 -----------------PSLLKKFVSLRVLNLSYSK-------LEQLPSSIGDLLHLRYL 555

Query: 419 NLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGC-LRYL 477
           +L        LPE LC+L NL+ L+V +C +L  LP+   KL  L +L  +  GC L   
Sbjct: 556 DLSCN-NFRSLPERLCKLQNLQTLDVHNCYSLNCLPKQTSKLSSLRHLVVD--GCPLTST 612

Query: 478 PAGIGELIRLRRVREFVVGG--GY 499
           P  IG L  L+ +  F+VG   GY
Sbjct: 613 PPRIGLLTCLKTLGFFIVGSKKGY 636

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q9LRR4|R13L1_ARATH Putative disease resistance RPP13-like protein 1 OS=Arabidopsis thaliana GN=RPPL1 PE=3 SV=1

 Score =  266 bits (681), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 172/506 (33%), Positives = 267/506 (52%), Gaps = 32/506 (6%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           +GG+GKTTL+Q  YN+  V   F  + W  VSE FD F+I + + ES+T     +  +  
Sbjct: 204 IGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRPC-EFTDLD 262

Query: 61  SLMQHIEECVAGK--KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI 118
            L   ++E + G    FLLVLDD+WNE++  W+   +   ++   S+IL+TTR + VA I
Sbjct: 263 VLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPFIHAAQGSQILVTTRSQRVASI 322

Query: 119 MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS 178
           M + HV ++  LS+ +CWS+F       +       +  +   IV KC+GLPLA KT+  
Sbjct: 323 MCAVHVHNLQPLSDGDCWSLFMKTVFGNQEPCLNREIGDLAERIVHKCRGLPLAVKTLGG 382

Query: 179 LLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGI 238
           +LR +    EW+ +L + IW+L A +  LL  L +SY  LP+ +KRCF+YC++FPK +  
Sbjct: 383 VLRFEGKVIEWERVLSSRIWDLPADKSNLLPVLRVSYYYLPAHLKRCFAYCSIFPKGHAF 442

Query: 239 RKHKLIELWMAQGYLSE-KGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDI 297
            K K++ LWMA+G+L + + +K +E++G EYF+ L SRS  Q           +  MHD 
Sbjct: 443 EKDKVVLLWMAEGFLQQTRSSKNLEELGNEYFSELESRSLLQKTKT-------RYIMHDF 495

Query: 298 VHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRG 357
           +++ AQ+  S E  + +   G +L +S          L  LR   + P+     +  ++ 
Sbjct: 496 INELAQF-ASGE-FSSKFEDGCKLQVSERTR-----YLSYLRDNYAEPMEFEA-LREVKF 547

Query: 358 LRSLLVKSDEYSWSSEVLPQ-----LFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKL 412
           LR+ L  S   S  S  L Q     L   LT LR L L          + +  P   + +
Sbjct: 548 LRTFLPLSLTNSSRSCCLDQMVSEKLLPTLTRLRVLSLS------HYKIARLPPDFFKNI 601

Query: 413 LHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTG 472
            H ++L+L  + ++EKLP++LC +YNL+ L +  C +L+ELP  I  L  L YL    T 
Sbjct: 602 SHARFLDL-SRTELEKLPKSLCYMYNLQTLLLSYCSSLKELPTDISNLINLRYLDLIGTK 660

Query: 473 CLRYLPAGIGELIRLRRVREFVVGGG 498
            LR +P   G L  L+ +  F V   
Sbjct: 661 -LRQMPRRFGRLKSLQTLTTFFVSAS 685

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LRR5|DRL21_ARATH Putative disease resistance protein At3g14460 OS=Arabidopsis thaliana GN=At3g14460 PE=3 SV=1

 Score =  257 bits (656), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 162/504 (32%), Positives = 274/504 (54%), Gaps = 35/504 (6%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           M G+GKTTL +  +N+  V  +FE + W+     F+ F + +A+++ +T  SA +  +  
Sbjct: 201 MPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTVTKAVLQDIT-SSAVNTEDLP 259

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           SL   +++ ++GK+FLLVLDD W+E   +WE F     ++   SKI++TTR E V+ +  
Sbjct: 260 SLQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAFTDAEEGSKIVLTTRSEIVSTVAK 319

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGK-RENLEKIGREIVKKCKGLPLAAKTIASL 179
           +  +  + +++  ECW +    A    ++G   + LE IG+ I ++CKGLPLAA+ IAS 
Sbjct: 320 AEKIYQMKLMTNEECWELISRFAFGNISVGSINQELEGIGKRIAEQCKGLPLAARAIASH 379

Query: 180 LRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIR 239
           LRSK    +W  + +N      +    +L  L LSY+ LP ++KRCF+ C++FPK +   
Sbjct: 380 LRSKPNPDDWYAVSKN----FSSYTNSILPVLKLSYDSLPPQLKRCFALCSIFPKGHVFD 435

Query: 240 KHKLIELWMAQGYLSE-KGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIV 298
           + +L+ LWMA   L + + ++ +EDIG +Y   L ++SFFQ      D  +    MHD++
Sbjct: 436 REELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQSFFQRL----DITMTSFVMHDLM 491

Query: 299 HDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRR-GASVPISIWGNVTGLRG 357
           +D A+ +  + C  +E  +  E+  ++       H   +  +  ASV    + ++ G   
Sbjct: 492 NDLAKAVSGDFCFRLEDDNIPEIPSTT------RHFSFSRSQCDASV---AFRSICGAEF 542

Query: 358 LRSLLVKSDEYSWSS-----EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKL 412
           LR++L  +   S  S     +VL  L   L+ LR L L   +       I  +P +++ L
Sbjct: 543 LRTILPFNSPTSLESLQLTEKVLNPLLNALSGLRILSLSHYQ-------ITNLPKSLKGL 595

Query: 413 LHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTG 472
             L+YL+L    KI++LPE +C L NL+ L + +C++L  LP+ I +L  L  L    T 
Sbjct: 596 KLLRYLDL-SSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKSIAELINLRLLDLVGTP 654

Query: 473 CLRYLPAGIGELIRLRRVREFVVG 496
            L  +P GI +L  L+++  FV+G
Sbjct: 655 -LVEMPPGIKKLRSLQKLSNFVIG 677

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38834|R13L4_ARATH Disease resistance RPP13-like protein 4 OS=Arabidopsis thaliana GN=RPP13L4 PE=2 SV=2

 Score =  223 bits (568), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 152/497 (30%), Positives = 257/497 (51%), Gaps = 36/497 (7%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGG+GKTT+AQ  +N+ ++E  FE+R WV VS+ F E +I R+I+ +L   S  D  +  
Sbjct: 190 MGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRNLGDASVGD--DIG 247

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           +L++ I++ + GK++L+V+DDVW+++   W+  Y+ L        +++TTR E+VA+ + 
Sbjct: 248 TLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRG-QGGSVIVTTRSESVAKRVQ 306

Query: 121 S----THVISVNVLSEMECWSVFQSLAISGKT-IGKRENLEKIGREIVKKCKGLPLAAKT 175
           +    TH     +LS    W +F ++A +      +R  LE +G+EIV KCKGLPL  K 
Sbjct: 307 ARDDKTH--RPELLSPDNSWLLFCNVAFAANDGTCERPELEDVGKEIVTKCKGLPLTIKA 364

Query: 176 IASLLRSKN-TEKEWQNILENEIWELE---AIEKGLLAPLLLSYNELPSKVKRCFSYCAV 231
           +  LL  K+    EW+ I E+   EL    +    +++ L LSY+ELPS +K C    ++
Sbjct: 365 VGGLLLCKDHVYHEWRRIAEHFQDELRGNTSETDNVMSSLQLSYDELPSHLKSCILTLSL 424

Query: 232 FPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYK 291
           +P+D  I K +L+  W+ +G++  +  +   + GE+ F+ L +R   +  +K   G I  
Sbjct: 425 YPEDCVIPKQQLVHGWIGEGFVMWRNGRSATESGEDCFSGLTNRCLIEVVDKTYSGTIIT 484

Query: 292 CKMHDIVHDFAQYLCSNECLA-VEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWG 350
           CK+HD+V D    +   +  +  E  +   L IS   ++K + +   LR   S       
Sbjct: 485 CKIHDMVRDLVIDIAKKDSFSNPEGLNCRHLGISGNFDEKQIKVNHKLRGVVST------ 538

Query: 351 NVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIE 410
                        K+ E +  +  L + F     LR L++        +  + EI   I 
Sbjct: 539 ------------TKTGEVNKLNSDLAKKFTDCKYLRVLDISKS---IFDAPLSEILDEIA 583

Query: 411 KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNED 470
            L HL  L+L     + + P ++ +L+NL+ L+   CQNL++L   I   +KL+ L   +
Sbjct: 584 SLQHLACLSLSNTHPLIQFPRSMEDLHNLQILDASYCQNLKQLQPCIVLFKKLLVLDMTN 643

Query: 471 TGCLRYLPAGIGELIRL 487
            G L   P GIG L++L
Sbjct: 644 CGSLECFPKGIGSLVKL 660

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score =  201 bits (512), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 146/480 (30%), Positives = 246/480 (51%), Gaps = 39/480 (8%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDL---- 56
           MGG GKTTL+   + +  V R+FE   WV +S+ +    + R +I+     +   +    
Sbjct: 201 MGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADTQIPAEL 260

Query: 57  --VEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET 114
             + ++ L++ + E +  K++++VLDDVW      W      L + ++ S++++TTR   
Sbjct: 261 YSLGYRELVEKLVEYLQSKRYIVVLDDVWTTGL--WREISIALPDGIYGSRVMMTTRDMN 318

Query: 115 VARI---MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKR-ENLEKIGREIVKKCKGLP 170
           VA     +GST    + +L E E W +F + A        R +NLE I R++V++C+GLP
Sbjct: 319 VASFPYGIGSTKH-EIELLKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVERCQGLP 377

Query: 171 LAAKTIASLLRSKNTEKEWQNILENEIWELEAIE--KGLLAPLLLSYNELPSKVKRCFSY 228
           LA  ++ S++ +K  E EW+ +     WEL      K + + + LS+N+LP  +KRCF Y
Sbjct: 378 LAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLPYPLKRCFLY 437

Query: 229 CAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGE 288
           C++FP +Y +++ +LI +WMAQ ++      + E++ + Y N L  R+  Q       G 
Sbjct: 438 CSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKAEEVADSYLNELVYRNMLQVILWNPFGR 497

Query: 289 IYKCKMHDIVHDFAQYLCSNE--CLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPI 346
               KMHD++ + A  +   E  C      S  + A  +       HL +   +    P 
Sbjct: 498 PKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAETMENYGSRHLCI---QKEMTPD 554

Query: 347 SIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP 406
           SI         L SLLV S     S++   +L   L  LRAL+L+       ++ I ++P
Sbjct: 555 SIRAT-----NLHSLLVCS-----SAKHKMELLPSLNLLRALDLE-------DSSISKLP 597

Query: 407 TNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL 466
             +  + +LKYLNL  + ++++LP+   +L NLE LN    + + ELP G+ KL+KL YL
Sbjct: 598 DCLVTMFNLKYLNL-SKTQVKELPKNFHKLVNLETLNTKHSK-IEELPLGMWKLKKLRYL 655

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. 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. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W3K3|DRL8_ARATH Putative disease resistance protein At1g58400 OS=Arabidopsis thaliana GN=At1g58400 PE=3 SV=1

 Score =  172 bits (437), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 144/487 (29%), Positives = 238/487 (48%), Gaps = 41/487 (8%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLV--- 57
           MGG+GKTTLA+  +N+ DV+  F++  WVCVS+ F    + + I+++LT    KD +   
Sbjct: 192 MGGLGKTTLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSRETKDEILQM 251

Query: 58  EFQSLMQHIEECVAGKKFLLVLDDVWN-EDYYKWEPFYKCLKNSLHESKILITTRKETVA 116
           E   L   + + +   K L+V DD+W  ED+    P +   K      K+LIT+R ET+A
Sbjct: 252 EEAELHDELFQLLETSKSLIVFDDIWKEEDWGLINPIFPPKKG----WKVLITSRTETIA 307

Query: 117 RIMGSTHVISVN--VLSEMECWSVFQSLA---ISGKTIGKRENLEKIGREIVKKCKGLPL 171
            + G+   ++     L+ +E W +FQ +A   +        + +E +G++++K C GLPL
Sbjct: 308 -MHGNRRYVNFKPECLTILESWILFQRIAMPRVDESEFKVDKEMEMMGKQMIKYCGGLPL 366

Query: 172 AAKTIASLLRSKNTEKEWQNILENEIWEL-------EAIEKGLLAPLLLSYNELPSKVKR 224
           A K +  LL +K T  +W+ + EN    +       +     +   L LS+ ELPS +K 
Sbjct: 367 AVKVLGGLLAAKYTFHDWKRLSENIGCHIVGRTDFSDGNNSSVYHVLSLSFEELPSYLKH 426

Query: 225 CFSYCAVFPKDYGIRKHKLIELWMAQGYLSEK--GAKEMEDIGEEYFNILASRSFFQDFN 282
           CF Y A FP+D+ I+  KL   W A+G L  +    + + D+GE Y   L  R+      
Sbjct: 427 CFLYLAHFPEDHNIKVEKLSYCWAAEGILEPRHYHGQTIRDVGESYIEELVRRNMVIAER 486

Query: 283 KYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGA 342
                    C +HD++ +    L + E   V+I S      +S           T RR  
Sbjct: 487 DVTTLRFEACHLHDMMREVC-LLKAKEENFVQIASILPPTANSQYPG-------TSRRFV 538

Query: 343 S---VPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRN 399
           S     + +  ++   + L+SLL+  +    S ++L   F +L  LR L+L   +   RN
Sbjct: 539 SQNPTTLHVSRDINNPK-LQSLLIVWENRRKSWKLLGSSFIRLELLRVLDLYKAKFEGRN 597

Query: 400 NLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGK 459
                +P+ I KL+HL+YLNL    ++ +LP +L  L  L  L+++ C     +P  +  
Sbjct: 598 -----LPSGIGKLIHLRYLNLD-LARVSRLPSSLGNLRLLIYLDINVCTKSLFVPNCLMG 651

Query: 460 LRKLMYL 466
           + +L YL
Sbjct: 652 MHELRYL 658

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M667|RPP13_ARATH Disease resistance protein RPP13 OS=Arabidopsis thaliana GN=RPP13 PE=2 SV=2

 Score =  167 bits (423), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 104/310 (33%), Positives = 169/310 (54%), Gaps = 14/310 (4%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGG+GKT LA+  YN+ DV+  FE R W  VS+ +    I   II SL   S ++L + +
Sbjct: 193 MGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGEELEKIR 252

Query: 61  SLMQ-----HIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETV 115
              +     ++   + GKK+L+V+DD+W  +   W+   + L  +   S+++ITTR + V
Sbjct: 253 KFAEEELEVYLYGLLEGKKYLVVVDDIWERE--AWDSLKRALPCNHEGSRVIITTRIKAV 310

Query: 116 AR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAK 174
           A  + G  +   +  L+  E W +F+  A       K E+L K G+E+V+KC+GLPL   
Sbjct: 311 AEGVDGRFYAHKLRFLTFEESWELFEQRAFRNIQ-RKDEDLLKTGKEMVQKCRGLPLCIV 369

Query: 175 TIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLL--LSYNELPSKVKRCFSYCAVF 232
            +A LL S+ T  EW ++  N +W     +   +AP++  LS+ EL  + K CF Y ++F
Sbjct: 370 VLAGLL-SRKTPSEWNDVC-NSLWRRLKDDSIHVAPIVFDLSFKELRHESKLCFLYLSIF 427

Query: 233 PKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKC 292
           P+DY I   KLI L +A+G++       MED+   Y   L  RS  +   + + G++  C
Sbjct: 428 PEDYEIDLEKLIHLLVAEGFIQGDEEMMMEDVARYYIEELIDRSLLEAVRR-ERGKVMSC 486

Query: 293 KMHDIVHDFA 302
           ++HD++ D A
Sbjct: 487 RIHDLLRDVA 496

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 other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.

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	505
224114824	941	cc-nbs-lrr resistance protein [Populus t	0.962	0.516	0.466	1e-128
224115686	938	cc-nbs-lrr resistance protein [Populus t	0.950	0.511	0.495	1e-125
224114794	742	cc-nbs-lrr resistance protein [Populus t	0.920	0.626	0.473	1e-124
224122712	945	cc-nbs-lrr resistance protein [Populus t	0.954	0.510	0.465	1e-124
224115620	963	cc-nbs-lrr resistance protein [Populus t	0.958	0.502	0.491	1e-124
147825450	927	hypothetical protein VITISV_000086 [Viti	0.974	0.530	0.467	1e-123
224134406	987	cc-nbs-lrr resistance protein [Populus t	0.950	0.486	0.478	1e-123
359482769	904	PREDICTED: putative disease resistance p	0.964	0.538	0.461	1e-121
359482790	923	PREDICTED: putative disease resistance p	0.958	0.524	0.463	1e-121
359482784	919	PREDICTED: putative disease resistance p	0.964	0.529	0.464	1e-120

>gi|224114824|ref|XP_002332291.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222832453|gb|EEE70930.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  465 bits (1196), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 237/508 (46%), Positives = 341/508 (67%), Gaps = 22/508 (4%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGGIGKTTLAQ A+N+ +V  +FEK+ WVCVS+PFDE RI +AI+E L  G A DLVE Q
Sbjct: 201 MGGIGKTTLAQLAFNDDEVTAHFEKKIWVCVSDPFDEVRIGKAILEQLE-GRAPDLVELQ 259

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           SL+Q + E + G++FLLVLDDVW E++ +WE     L      S+IL+TTRK +VA +MG
Sbjct: 260 SLLQRVSESIKGERFLLVLDDVWTENHRQWEQLKPSLTGCARGSRILVTTRKHSVATMMG 319

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           + HVI++  LS+  C S+F  +A   ++  +RE L   G +I  KCKGLPLAAK +  L+
Sbjct: 320 TGHVINLEKLSDEVCRSIFNHVAFQQRSKDERERLTDTGDKIANKCKGLPLAAKVLGGLM 379

Query: 181 RSKNTEKEWQNILENEIWEL-----EAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKD 235
           +SK T +EW+ +  +E+W L     + +E+G+  PLLLSY +LPS V+RCF YCA+FPKD
Sbjct: 380 QSKRTREEWERVFCSELWGLDEVDRDQVERGIFLPLLLSYYDLPSMVRRCFLYCAMFPKD 439

Query: 236 YGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMH 295
           Y +RK++L+++W+AQGYL E    +ME +GE+YF +LA+RSFFQDF  YD  ++ + KMH
Sbjct: 440 YEMRKYELVKMWIAQGYLKETSGGDMEAVGEQYFQVLAARSFFQDFKTYDREDV-RFKMH 498

Query: 296 DIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGL 355
           DIVHDFAQY+  NECL V++++  E  + + +E ++ HL + L +    P+SI       
Sbjct: 499 DIVHDFAQYMTKNECLTVDVNNLREATVETSIE-RVRHLSMMLSKETYFPVSI----HKA 553

Query: 356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHL 415
           +GLRSL + + +  W    LP +F++LTC+R+L L +       +LIKEIP  + KL+HL
Sbjct: 554 KGLRSLFIDARD-PWLGAALPDVFKQLTCIRSLNLSM-------SLIKEIPNEVGKLIHL 605

Query: 416 KYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLR 475
           ++LNL    K+E LPE +C+L  L+ L+V  C++L ELP+ IGKL KL +L    +  + 
Sbjct: 606 RHLNLADCYKLESLPEIMCDLCKLQSLDVTTCRSLWELPKAIGKLIKLRHLRICGS-IVA 664

Query: 476 YLPAGIGELIRLRRVREFVV-GGGYDRA 502
           ++P GI  +  LR +  F V GGG D +
Sbjct: 665 FMPKGIERITCLRTLDWFAVCGGGEDES 692

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115686|ref|XP_002332117.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222874937|gb|EEF12068.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 250/505 (49%), Positives = 327/505 (64%), Gaps = 25/505 (4%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGGIGKTTLA+  YN+ DV  +F+KR WVCVS+PF+E  IA+AI+E LT GSA +L E Q
Sbjct: 203 MGGIGKTTLAKLVYNDHDVTTHFDKRIWVCVSDPFNEITIAKAILEDLT-GSAPNLNELQ 261

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           +L++H++E +  KKFLLVLDDVWNED  KWE     LK  L  S+I++TTRK  VA  MG
Sbjct: 262 TLVKHVQESIREKKFLLVLDDVWNEDSTKWEQLKDSLKCGLPGSRIMVTTRKTNVASSMG 321

Query: 121 S---THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIA 177
           S   T ++ + +LS  +CWS+F  LA   K   +R +LE IGR+I  KCKGLPLAAK++ 
Sbjct: 322 SSPSTDILELGLLSTDKCWSLFSQLAFFEKNSRERGDLEDIGRQIAAKCKGLPLAAKSLG 381

Query: 178 SLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYG 237
           SLLR K    EW+++L N +WE++  E  +LAPL LSYN+LPS ++RCFSYCAVFPKD+ 
Sbjct: 382 SLLRFKRIRAEWESVLNNHVWEIKEAESKILAPLWLSYNDLPSDMRRCFSYCAVFPKDFT 441

Query: 238 IRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFN-KYDDGEIYKCKMHD 296
             +  LI+LWMAQG+L E   KEME +G E F  LA+RSFFQDF    DDG IY CKMHD
Sbjct: 442 FERDTLIKLWMAQGFLRETQNKEMEVMGRECFEALAARSFFQDFEIDEDDGSIYACKMHD 501

Query: 297 IVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLR--RGASVPISIWGNVTG 354
           +VHDFAQ L  NEC +V+I    E  I SF  +   H ++  R  R  S P +I      
Sbjct: 502 MVHDFAQSLTKNECFSVDIDGVSESKIDSF-SRDTRHSMVVFRNYRTTSFPATI----HS 556

Query: 355 LRGLRSLLVKSDEYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLL 413
           L+ LRSL+V  D Y  S +  LP+L   L+CLR L L           I+E+P+NI KL+
Sbjct: 557 LKKLRSLIV--DGYPSSMNAALPKLIANLSCLRTLMLS-------ECGIEEVPSNIGKLI 607

Query: 414 HLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGC 473
           HL++++L    +I +LPE +CELYN+  L+V  C  L  LP  IGKL KL +L  ++   
Sbjct: 608 HLRHVDL-SWNEIRELPEEMCELYNMLTLDVSFCMKLERLPDNIGKLVKLRHLSVDNWQF 666

Query: 474 LRYLPAGIGELIRLRRVREFVVGGG 498
           ++    G+  L  LR + EF V G 
Sbjct: 667 VKM--RGVEGLSSLRELDEFHVSGS 689

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114794|ref|XP_002332284.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222832446|gb|EEE70923.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  453 bits (1165), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 230/486 (47%), Positives = 329/486 (67%), Gaps = 21/486 (4%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           +GGIGKTTLAQ AY + +V  +FEK+ WVCVSEPFDE RIA+AI+E L  GSA +L+E Q
Sbjct: 179 LGGIGKTTLAQLAYKDAEVTAHFEKKIWVCVSEPFDEVRIAKAILEQLE-GSAPNLIELQ 237

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           SL+Q + E + GK+ LLVLDDVW +++ +WE            S+IL+TTRK TVA IMG
Sbjct: 238 SLLQMVSESIKGKRLLLVLDDVWTDNHRQWEQLKPSFTGCARGSRILVTTRKGTVATIMG 297

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           + H I+V  LS+  C S+F  +A   ++  +RE L  IG +I  KCKGLPLAAK +  L+
Sbjct: 298 TDHQINVEKLSDEICRSIFNHVAFQERSKDERERLTDIGDKIANKCKGLPLAAKVLGGLM 357

Query: 181 RSKNTEKEWQNILENEIWEL-----EAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKD 235
           + K T +EW+ +L +E+W L     + +E+G+  PLLLSY +LPS V+RCF YCA+FPKD
Sbjct: 358 QFKRTREEWERVLSSELWGLDEVDRDQVERGIFLPLLLSYYDLPSVVRRCFLYCAMFPKD 417

Query: 236 YGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMH 295
           Y +RK++L+++W+AQGYL E    +ME +GEEYF +LA+R+FFQDF  Y   +I + KMH
Sbjct: 418 YEMRKYELVKMWIAQGYLKETSGGDMEAVGEEYFQVLAARAFFQDFKTYGREDI-RFKMH 476

Query: 296 DIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGL 355
           DIVHDFAQY+  NECL V++++     + + +E ++ HL + L    S P+SI       
Sbjct: 477 DIVHDFAQYMTKNECLTVDVNTLGGATVETSIE-RVRHLSIMLPNETSFPVSI----HKA 531

Query: 356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHL 415
           +GLRSLL+ + + +W    LP +F++L C+R+L L +       + IKEIP  + KL+HL
Sbjct: 532 KGLRSLLIDTRD-AWLGAALPDVFKQLRCIRSLNLSM-------SPIKEIPNEVGKLIHL 583

Query: 416 KYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLR 475
           ++LNL   +++E L ET+C+L NL+ L+V  C +L+ELP  IGKL KL +L    +G + 
Sbjct: 584 RHLNLVACRELESLSETMCDLCNLQSLDVAWCDSLKELPNAIGKLIKLRHLRISGSG-VA 642

Query: 476 YLPAGI 481
           ++P GI
Sbjct: 643 FIPKGI 648

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122712|ref|XP_002318907.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222859580|gb|EEE97127.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  451 bits (1161), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 234/503 (46%), Positives = 336/503 (66%), Gaps = 21/503 (4%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           +GGIGKTTLAQ A+N+ +V  +FEK+ WVCVSEPFDE RIA+AI+E L  G   +LVE Q
Sbjct: 205 LGGIGKTTLAQLAFNDSEVTAHFEKKIWVCVSEPFDEIRIAKAILEQLE-GRPTNLVELQ 263

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           SL+Q + E + GK+ LLVLDDVW E++ +WE     L      S+IL+TTRK+ VA +MG
Sbjct: 264 SLLQGVSESITGKRLLLVLDDVWTENHGQWEQLKPSLTGCARGSRILVTTRKDAVATMMG 323

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           + H I++  LS+  C S+F  +A   ++  +RE L  IG +I  KCKGLPLAAK +  L+
Sbjct: 324 TDHRINIEKLSDEICRSIFNHVAFQERSEDERERLTDIGDKIANKCKGLPLAAKVLGGLM 383

Query: 181 RSKNTEKEWQNILENEIWELEAIEKG-----LLAPLLLSYNELPSKVKRCFSYCAVFPKD 235
           +SK T +EW+ +L +E+W L+ +++      +  PLLLSY +LPS V+RCF YCA+FPKD
Sbjct: 384 QSKRTREEWERVLSSELWRLDEVDRDQVESRIFIPLLLSYYDLPSVVRRCFLYCAMFPKD 443

Query: 236 YGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMH 295
           Y + K++L+++WMAQGY+ E    +ME +GE YF++LA+RSFFQDF + D  E  K KMH
Sbjct: 444 YEMGKYELVKMWMAQGYIKETSGGDMELVGERYFHVLAARSFFQDF-ETDIFEGMKFKMH 502

Query: 296 DIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGL 355
           DIVHDFAQY+  NECL V++++     + + +E ++ HL + +    S P+SI       
Sbjct: 503 DIVHDFAQYMTKNECLTVDVNTLGGATVETSIE-RVRHLSMMVSEETSFPVSI----HKA 557

Query: 356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHL 415
           +GLRSLL+ + + S  +  LP LF++LTC+R+L L           IKEIP  + KL+HL
Sbjct: 558 KGLRSLLIDTRDPSLGA-ALPDLFKQLTCIRSLNLSASS-------IKEIPNEVGKLIHL 609

Query: 416 KYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLR 475
           +++NL    ++E LPET+C+L NL+ L+V  C++L+ELP  IGKL KL +L    +G + 
Sbjct: 610 RHVNLARCGELESLPETMCDLCNLQSLDVTWCRSLKELPNAIGKLIKLRHLRIYRSG-VD 668

Query: 476 YLPAGIGELIRLRRVREFVVGGG 498
           ++P GI  +  LR +  F V GG
Sbjct: 669 FIPKGIERITCLRTLDVFKVCGG 691

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115620|ref|XP_002332101.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222874921|gb|EEF12052.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  450 bits (1157), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 247/503 (49%), Positives = 325/503 (64%), Gaps = 19/503 (3%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGGIGKTTLAQ  YN+ +VE +F+KR WVCVS+PFDE +IA+AI+E+L  GSA DL+E Q
Sbjct: 204 MGGIGKTTLAQLVYNDHEVEIHFDKRIWVCVSDPFDETKIAKAILEALK-GSASDLIELQ 262

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
           +L+++I+  + GKKFLLVLDDVWNED  KWE     L   L  S IL+TTRK  VA  MG
Sbjct: 263 TLLENIQPLIRGKKFLLVLDDVWNEDSTKWEQLKYSLMCGLPGSSILVTTRKRNVASRMG 322

Query: 121 S--THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS 178
           S  T ++ + +LS  ECWS+F  LA   K   +R +LE IGR+I  KCKGLPLAAK++ S
Sbjct: 323 SSPTDILELGLLSTDECWSLFSRLAFFEKNSRERGDLEDIGRQIAAKCKGLPLAAKSLGS 382

Query: 179 LLRSKNTEKEWQNILENEIWE-LEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYG 237
           LLR K+  +EW+++L + +WE  E  E  +LAPL LSY +LPS ++RCFSYCAVFPKD+ 
Sbjct: 383 LLRFKSRIEEWESVLNSHVWESAEEAESKILAPLWLSYYDLPSDMRRCFSYCAVFPKDFT 442

Query: 238 IRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNK-YDDGEIYKCKMHD 296
             +  L++LWMAQG+L E   KEME IG + F  LA+RSFFQDF K   DG IY CKMHD
Sbjct: 443 FERDTLVKLWMAQGFLRETHNKEMEVIGRQCFEALAARSFFQDFQKETGDGSIYACKMHD 502

Query: 297 IVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLR 356
           +VHD AQ L  NEC +V+I    EL I SF      H ++  R   S P +I      L+
Sbjct: 503 MVHDLAQNLTKNECSSVDIDGPTELKIDSF-SINARHSMVVFRNYNSFPATI----HSLK 557

Query: 357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLK 416
            LRSL+V  D  S ++  LP L   L+CLR L+L           I+E+P+NI KL+HL+
Sbjct: 558 KLRSLIVDGDPSSMNA-ALPNLIANLSCLRTLKLS-------GCGIEEVPSNIGKLIHLR 609

Query: 417 YLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRY 476
           +++    + I++LPE + ELYN+  L+V  C  L  LP  IG+L KL +L   D   L +
Sbjct: 610 HVDFSWNENIKELPEEMFELYNMLTLDVSFCNKLERLPDNIGRLAKLRHLSIHDWRDLSF 669

Query: 477 LPA-GIGELIRLRRVREFVVGGG 498
           +   G+  L  LR + +F V G 
Sbjct: 670 VKMRGVKGLTSLRELDDFHVSGS 692

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147825450|emb|CAN71072.1| hypothetical protein VITISV_000086 [Vitis vinifera]

 Score =  449 bits (1154), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 236/505 (46%), Positives = 336/505 (66%), Gaps = 13/505 (2%)

Query: 2   GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQS 61
           GG+GKTTLAQ AY++ +VE +F++R WVCVS+PFD  R+ RAI+E+L   S  +L + ++
Sbjct: 205 GGMGKTTLAQLAYSHSEVEFHFDERIWVCVSDPFDPSRVCRAIVEALEKESC-NLHDLEA 263

Query: 62  LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGS 121
           L Q I+ C+ GKKFLLVLDDVW E++  WE     L      S+IL+TTR E V  +M +
Sbjct: 264 LQQKIQTCIGGKKFLLVLDDVWTENHQLWEQLKSILSCGAVGSRILVTTRNENVVEMMRT 323

Query: 122 THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLR 181
           T++ S+  LSE +   +F  +A SGK   K E+L++IG +I  KCKGLPLA KT+ +L+R
Sbjct: 324 TYMHSLGKLSEDKSRELFYQIAFSGKNREKMEDLKEIGEKIADKCKGLPLAIKTLGNLMR 383

Query: 182 SKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKH 241
           SK+  +EW+N+L +E+W+L+     +   LLLSY++LP +++RCFS+CAVFPKD  I   
Sbjct: 384 SKHNREEWENVLCSEVWKLDVFGIYISPALLLSYHDLPPEIQRCFSFCAVFPKDSVIWSD 443

Query: 242 KLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDF 301
           +LI+LWMAQ YL+   +KEME +G  YF  LA+RSFFQDF K DDG I  CKMHDIVHDF
Sbjct: 444 ELIKLWMAQSYLNSDRSKEMEMVGRTYFEYLAARSFFQDFEKDDDGNIICCKMHDIVHDF 503

Query: 302 AQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSL 361
           AQ+L  NEC  VE+ + ++ ++  F + KI H  L +R   S P   + +   ++ L +L
Sbjct: 504 AQFLTQNECFIVEVDNQKKGSMDLFFQ-KIRHATLVVRE--STP--NFASTCNMKNLHTL 558

Query: 362 LVKSD-EYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL 420
           L K + + S   E L  L   LTCLRAL+L       RN LI+E+P  + KL+HL+YLNL
Sbjct: 559 LAKEEFBISXVLEALXNLLRHLTCLRALDLS------RNRLIEELPKEVGKLIHLRYLNL 612

Query: 421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG 480
               ++ +LPET+C+LYNL+ LN++ C +L++LP+ +GKL  L +L N +TG L+ LP G
Sbjct: 613 SLCYRLRELPETICDLYNLQTLNIEGCSSLQKLPQAMGKLINLRHLENCNTGSLKGLPKG 672

Query: 481 IGELIRLRRVREFVVGGGYDRACSL 505
           IG L  L+ +  F+V    +  C +
Sbjct: 673 IGRLSSLQTLDVFIVSSHGNDECQI 697

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134406|ref|XP_002321815.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222868811|gb|EEF05942.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  449 bits (1154), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 237/495 (47%), Positives = 334/495 (67%), Gaps = 15/495 (3%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
           MGG+GKTTLAQ AYN  +++  FEKR WVCVS PFDE  +A+AIIE L+ G+A +LVE +
Sbjct: 231 MGGLGKTTLAQLAYNADEIKTYFEKRIWVCVSHPFDENTVAKAIIEDLS-GAAPNLVELE 289

Query: 61  SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
            L + I E + GKKFLLVLDDVW ++  KWEP  + LK     S+IL+TTRK+TVA++M 
Sbjct: 290 PLCKRISESIEGKKFLLVLDDVWEDNPRKWEPLKESLKCGAPGSRILVTTRKDTVAKMME 349

Query: 121 STHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           S + + +  L++ ECWSVF  +A  G++    E   +IGR+IV +CKGLPLAAKT+  L+
Sbjct: 350 SDYSLLLGKLTDEECWSVFSQVAFYGRSQDACEMFTEIGRQIVYRCKGLPLAAKTLGGLM 409

Query: 181 RSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
           +SK T ++W NIL NE+WE+E +EKG+  PLLLSY +LP  ++ CF+YCA+FPKD+ + +
Sbjct: 410 QSKTTTEDWDNILSNELWEIEEVEKGIFPPLLLSYYDLPVAIRSCFTYCAMFPKDHVMER 469

Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHD 300
            KLI++WMAQGYL    +KEME +G+ YF ILA+R+FFQDF + D+  I K KMHDIVHD
Sbjct: 470 GKLIKMWMAQGYLKASPSKEMELVGKGYFEILATRAFFQDFQETDEDSI-KFKMHDIVHD 528

Query: 301 FAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRS 360
           FAQ+L  +EC  VE    +     SF E+   H ++T+   A  P SI+        LRS
Sbjct: 529 FAQFLMKDECFTVETDVLKRQKTESFYERA-RHAIMTVSNWARFPQSIYKA----GKLRS 583

Query: 361 LLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL 420
           LL++S   +  S+ L +L  KLT LR  +L   +       I+EIP+++ KLLHL+YL+ 
Sbjct: 584 LLIRSFNDTAISKPLLELLRKLTYLRLFDLSASQ-------IEEIPSDVGKLLHLRYLDF 636

Query: 421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG 480
              K +++LPET+ +LYNL+ L++  C  L++LP+ + KL +L +L    +G + +LP G
Sbjct: 637 SYCKWLKELPETISDLYNLQSLDLTWCVALKKLPQKMRKLIRLRHLEIFGSG-VAFLPRG 695

Query: 481 IGELIRLRRVREFVV 495
           I EL  LR +  F+V
Sbjct: 696 IEELTSLRTLTNFIV 710

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482769|ref|XP_003632834.1| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  441 bits (1135), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 233/505 (46%), Positives = 335/505 (66%), Gaps = 18/505 (3%)

Query: 2   GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQS 61
           GG+GKTTLA+ AYN+  V+ +F++R WVCVS+PFD FR+ RAI+E+L  G    L + ++
Sbjct: 185 GGMGKTTLARLAYNHRQVKAHFDERIWVCVSDPFDPFRVCRAIVEALQKGPCH-LHDLEA 243

Query: 62  LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGS 121
           + Q I  C+AGKKFLLVLDDVW E++  WE     L +    S+IL+TTRKE+V ++MG+
Sbjct: 244 VQQEIRTCIAGKKFLLVLDDVWTENHQLWEQLRNTLTSGAVGSRILVTTRKESVVKMMGT 303

Query: 122 THVISVNVLSEMECWSVFQSLAI-SGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL 180
           T++ S+  LS  +  ++F  +A    ++  K E L++IG +I  KCKGLPLA KT+ +LL
Sbjct: 304 TYMHSLGELSLEQSRALFHQIAFFEKRSWEKEEELKEIGEKIADKCKGLPLAIKTLGNLL 363

Query: 181 RSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
           R KN+E+EW+N+L +E+W+L+  E+ +   LLLSY +LP  ++RCFS+CAVFPKD  I +
Sbjct: 364 RIKNSEEEWKNVLNSEVWQLDEFERDISPALLLSYYDLPPAIQRCFSFCAVFPKDSVIVR 423

Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHD 300
            +LI+LWMAQ YL   G KEME +G  YF  LA+RSFFQDF K  DG I +C+MHDIVHD
Sbjct: 424 AELIKLWMAQSYLKSDGRKEMEMVGRTYFEYLAARSFFQDFEKDTDGNIIRCEMHDIVHD 483

Query: 301 FAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRS 360
           FAQ+L  NEC  VE+ + ++ ++  F + KI H  L +R   S P   + +   ++ L +
Sbjct: 484 FAQFLTQNECFIVEVDNQKKGSMDLFFQ-KIRHATLVVRE--STP--NFASTCNMKNLHT 538

Query: 361 LLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL 420
           LL K    ++ S VL  L   LTCLRAL+L        N+ I+E+P  + KL+HL+YLNL
Sbjct: 539 LLAKE---AFDSRVLEAL-GNLTCLRALDLS------SNDWIEELPKEVGKLIHLRYLNL 588

Query: 421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG 480
              + + +LPET+C+LYNL+ LN++ C +L++LP  +GKL  L +L N  T  L+ LP G
Sbjct: 589 SWCESLRELPETICDLYNLQTLNIEGCSSLQKLPHAMGKLINLRHLENY-TRSLKGLPKG 647

Query: 481 IGELIRLRRVREFVVGGGYDRACSL 505
           IG L  L+ +  F+V    +  C +
Sbjct: 648 IGRLSSLQTLDVFIVSSHGNDECQI 672

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482790|ref|XP_002268671.2| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  440 bits (1132), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 236/509 (46%), Positives = 334/509 (65%), Gaps = 25/509 (4%)

Query: 2   GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQS 61
           GG+GKTTLAQ AY++ +V+ +F++R WVCVS+P+D  R+ RAI+E+L       L + ++
Sbjct: 205 GGMGKTTLAQLAYSHSEVKVHFDERIWVCVSDPYDPIRVCRAIVEALQKKPCH-LHDLEA 263

Query: 62  LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLH----ESKILITTRKETVAR 117
           + Q I+ C+AG+KFLLVLDDVW ED   WE     LKN+LH     S+IL TTRKE+V +
Sbjct: 264 VQQEIQTCIAGQKFLLVLDDVWTEDNQLWEQ----LKNTLHCGAAGSRILATTRKESVVK 319

Query: 118 IMGSTHVISVNVLSEMECWSVFQSLAISGK-TIGKRENLEKIGREIVKKCKGLPLAAKTI 176
           +M +T+   +  LS  +  ++F  +A   + T  K E L++IG +I  KCKGLPLA KT+
Sbjct: 320 MMRATYKHPLGELSSEQSRALFHQIAFYERSTWEKEEELKEIGEKIADKCKGLPLAIKTL 379

Query: 177 ASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDY 236
            +LLR KN+E+EW+N+L +E+W+L+  E+ +   LLLSY +LP  ++RCFS+CAVFPKD 
Sbjct: 380 GNLLRIKNSEEEWKNVLNSEVWQLDEFERDISPALLLSYYDLPPAIQRCFSFCAVFPKDS 439

Query: 237 GIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHD 296
            I + +LI+LWMAQ YL   G+KEME +G  YF  LA+RSFFQDF K DDG I  CKMHD
Sbjct: 440 VIERDELIKLWMAQSYLKSDGSKEMEMVGRTYFEYLAARSFFQDFEKDDDGNIIHCKMHD 499

Query: 297 IVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLR 356
           IVHDFAQ+L  NEC  VE+ + ++ ++  F + KI H  L +R   S P   + +   ++
Sbjct: 500 IVHDFAQFLTLNECFIVEVDNQKKGSMDLFFQ-KIRHATLVVRE--STP--NFASTCNMK 554

Query: 357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLK 416
            L +LL K    ++ S VL  L   LTCLRAL+L+       N LI+E+P  + KL+HL+
Sbjct: 555 NLHTLLAKR---AFDSRVLEALGH-LTCLRALDLR------SNQLIEELPKEVGKLIHLR 604

Query: 417 YLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRY 476
           YLNL     + +LPET+C+LYNL+ LN+  C  L++LP+ +GKL  L +L N D   L+ 
Sbjct: 605 YLNLSYCDSLRELPETICDLYNLQTLNIQACSRLQKLPQAMGKLINLRHLENYDADDLQG 664

Query: 477 LPAGIGELIRLRRVREFVVGGGYDRACSL 505
           LP GIG L  L+ +  F+V    +  C +
Sbjct: 665 LPKGIGRLSSLQTLDVFIVSSHGNDECQI 693

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482784|ref|XP_002269044.2| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  439 bits (1128), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 234/504 (46%), Positives = 333/504 (66%), Gaps = 17/504 (3%)

Query: 2   GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQS 61
           GG+GKTTLAQ AYN+ +V+ +F++R WVCVS+PFD  RI R I+E L   S  +L   ++
Sbjct: 205 GGMGKTTLAQLAYNHPEVKAHFDERIWVCVSDPFDPIRIFREIVEILQRESP-NLHSLEA 263

Query: 62  LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGS 121
           L Q I+ C+AGKKFLLVLDDVW E++  WE     L      S+IL+TTRKE+V  +M +
Sbjct: 264 LQQKIQTCIAGKKFLLVLDDVWTENHQLWEQLNSTLSCGGVGSRILVTTRKESVVEMMRT 323

Query: 122 THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLR 181
           T++ S+  LSE +  ++F  +A  GK   K E+ ++IG +I  KCKGLPLA KT+ +L+R
Sbjct: 324 TYMHSLGKLSEDKSRALFYQIAFYGKNREKMEDFQEIGEKIADKCKGLPLAIKTLGNLMR 383

Query: 182 SKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRKH 241
           SK+  +EW+N+L +E+W+L+   + +   LLLSY +LP  +KRCFS+CAVFPKD  I + 
Sbjct: 384 SKHNREEWENVLCSEVWKLDVFGRDISPALLLSYYDLPPTIKRCFSFCAVFPKDSVIERD 443

Query: 242 KLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDF 301
           +LI+LWMAQ YL   G+KEME +G EYF  LA+RSFFQDF K  D +I +CKMHDIVHDF
Sbjct: 444 ELIKLWMAQSYLKSDGSKEMEMVGREYFEYLAARSFFQDFEKDGDDDIIRCKMHDIVHDF 503

Query: 302 AQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSL 361
           AQ+L  NEC  VE+ + ++ ++  F + KI H  L ++         + +   ++ L +L
Sbjct: 504 AQFLTQNECFVVEVDNQKKGSMDLFFQ-KICHATLVVQESTLN----FASTCNMKNLHTL 558

Query: 362 LVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLK 421
           L KS   ++ S VL  L   LTCLRAL+L    SW  N LI+E+P  + KL+HL+YL+L 
Sbjct: 559 LAKS---AFDSRVLEALGH-LTCLRALDL----SW--NQLIEELPKEVGKLIHLRYLDLS 608

Query: 422 GQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGI 481
             + + +LPET+C+LYNL+ LN+  C +L++LP+ +GKL  L +L N  T  L+ LP GI
Sbjct: 609 RCQSLRELPETICDLYNLQTLNIQYCISLQKLPQAMGKLINLRHLENY-TRSLKGLPKGI 667

Query: 482 GELIRLRRVREFVVGGGYDRACSL 505
           G L  L+ +  F+V    +  C +
Sbjct: 668 GRLSSLQTLDVFIVSSHGNDECQI 691

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	505
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.875	0.419	0.355	1e-69
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.932	0.330	0.313	2.2e-57
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.899	0.532	0.314	4.4e-51
UNIPROTKB|O48647	1802	O48647 "XA1" [Oryza sativa (ta	0.958	0.268	0.292	8.7e-51
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.835	0.455	0.322	4.5e-49
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.895	0.533	0.297	1.8e-46
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.887	0.493	0.287	5.4e-45
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.643	0.389	0.320	5.1e-44
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.885	0.492	0.291	2.2e-42
TAIR|locus:2037623	899	AT1G58410 [Arabidopsis thalian	0.881	0.494	0.298	4.9e-42

TAIR|locus:2091672 AT3G14470 [Arabidopsis thaliana (taxid:3702)]

 Score = 681 (244.8 bits), Expect = 1.0e-69, Sum P(2) = 1.0e-69
 Identities = 169/475 (35%), Positives = 262/475 (55%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
             +GG+GKTTL+Q  YN+  V   F  + W  VSE FD F+I + + ES+T     +  +  
Sbjct:   204 IGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRPC-EFTDLD 262

Query:    61 SLMQHIEECVAGK--KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI 118
              L   ++E + G    FLLVLDD+WNE++  W+   +   ++   S+IL+TTR + VA I
Sbjct:   263 VLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPFIHAAQGSQILVTTRSQRVASI 322

Query:   119 MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS 178
             M + HV ++  LS+ +CWS+F       +       +  +   IV KC+GLPLA KT+  
Sbjct:   323 MCAVHVHNLQPLSDGDCWSLFMKTVFGNQEPCLNREIGDLAERIVHKCRGLPLAVKTLGG 382

Query:   179 LLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGI 238
             +LR +    EW+ +L + IW+L A +  LL  L +SY  LP+ +KRCF+YC++FPK +  
Sbjct:   383 VLRFEGKVIEWERVLSSRIWDLPADKSNLLPVLRVSYYYLPAHLKRCFAYCSIFPKGHAF 442

Query:   239 RKHKLIELWMAQGYLSE-KGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDI 297
              K K++ LWMA+G+L + + +K +E++G EYF+ L SRS  Q   K     I    MHD 
Sbjct:   443 EKDKVVLLWMAEGFLQQTRSSKNLEELGNEYFSELESRSLLQ---KTKTRYI----MHDF 495

Query:   298 VHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRG 357
             +++ AQ+  S E  + +   G +L +S   E+     L  LR   + P+     +  ++ 
Sbjct:   496 INELAQF-ASGE-FSSKFEDGCKLQVS---ERT--RYLSYLRDNYAEPMEFEA-LREVKF 547

Query:   358 LRSLLVKSDEYSWSSEVLPQLF-EKL----TCLRALELQVRESWPRNNLIKEIPTNIEK- 411
             LR+ L  S   S  S  L Q+  EKL    T LR L L        +  I  +P +  K 
Sbjct:   548 LRTFLPLSLTNSSRSCCLDQMVSEKLLPTLTRLRVLSLS-------HYKIARLPPDFFKN 600

Query:   412 LLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL 466
             + H ++L+L  + ++EKLP++LC +YNL+ L +  C +L+ELP  I  L  L YL
Sbjct:   601 ISHARFLDLS-RTELEKLPKSLCYMYNLQTLLLSYCSSLKELPTDISNLINLRYL 654

GO:0005576 "extracellular region" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

TAIR|locus:2091662 AT3G14460 [Arabidopsis thaliana (taxid:3702)]

 Score = 602 (217.0 bits), Expect = 2.2e-57, P = 2.2e-57
 Identities = 161/514 (31%), Positives = 270/514 (52%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
             M G+GKTTL +  +N+  V  +FE + W+     F+ F + +A+++ +T  SA +  +  
Sbjct:   201 MPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTVTKAVLQDIT-SSAVNTEDLP 259

Query:    61 SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG 120
             SL   +++ ++GK+FLLVLDD W+E   +WE F     ++   SKI++TTR E V+ +  
Sbjct:   260 SLQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAFTDAEEGSKIVLTTRSEIVSTVAK 319

Query:   121 STHVISVNVLSEMECWSVFQSLAISGKTIGK-RENLEKIGREIVKKCKGLPLAAKTIASL 179
             +  +  + +++  ECW +    A    ++G   + LE IG+ I ++CKGLPLAA+ IAS 
Sbjct:   320 AEKIYQMKLMTNEECWELISRFAFGNISVGSINQELEGIGKRIAEQCKGLPLAARAIASH 379

Query:   180 LRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIR 239
             LRSK    +W  + +N      +    +L  L LSY+ LP ++KRCF+ C++FPK +   
Sbjct:   380 LRSKPNPDDWYAVSKN----FSSYTNSILPVLKLSYDSLPPQLKRCFALCSIFPKGHVFD 435

Query:   240 KHKLIELWMAQGYLSE-KGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIV 298
             + +L+ LWMA   L + + ++ +EDIG +Y   L ++SFFQ      D  +    MHD++
Sbjct:   436 REELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQSFFQRL----DITMTSFVMHDLM 491

Query:   299 HDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGL 358
             +D A+ +  + C  +E  +  E+  ++       H   + R      ++ + ++ G   L
Sbjct:   492 NDLAKAVSGDFCFRLEDDNIPEIPSTT------RHFSFS-RSQCDASVA-FRSICGAEFL 543

Query:   359 RSLLVKSDEYSWSS-----EVLPQLFEKLTCLRALELQVRE--SWPRN----------NL 401
             R++L  +   S  S     +VL  L   L+ LR L L   +  + P++          +L
Sbjct:   544 RTILPFNSPTSLESLQLTEKVLNPLLNALSGLRILSLSHYQITNLPKSLKGLKLLRYLDL 603

Query:   402 ----IKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGI 457
                 IKE+P  +  L +L+ L L   + +  LP+++ EL NL  L++     L E+P GI
Sbjct:   604 SSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKSIAELINLRLLDLVGTP-LVEMPPGI 662

Query:   458 GKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVR 491
              KLR L  L N   G  R   AG+ EL  L  +R
Sbjct:   663 KKLRSLQKLSNFVIG--RLSGAGLHELKELSHLR 694

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 536 (193.7 bits), Expect = 4.4e-51, P = 4.4e-51
 Identities = 153/486 (31%), Positives = 256/486 (52%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
             MGG+GKTT+AQ  +N+ ++E  FE+R WV VS+ F E +I R+I+ +L   S  D  +  
Sbjct:   190 MGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRNLGDASVGD--DIG 247

Query:    61 SLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVA-RIM 119
             +L++ I++ + GK++L+V+DDVW+++   W+  Y+ L      S +++TTR E+VA R+ 
Sbjct:   248 TLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRGQGGS-VIVTTRSESVAKRVQ 306

Query:   120 G---STHVISVNVLSEMECWSVFQSLAISGKT-IGKRENLEKIGREIVKKCKGLPLAAKT 175
                  TH     +LS    W +F ++A +      +R  LE +G+EIV KCKGLPL  K 
Sbjct:   307 ARDDKTH--RPELLSPDNSWLLFCNVAFAANDGTCERPELEDVGKEIVTKCKGLPLTIKA 364

Query:   176 IASLLRSKN-TEKEWQNILENEIWELEAIEK---GLLAPLLLSYNELPSKVKRCFSYCAV 231
             +  LL  K+    EW+ I E+   EL         +++ L LSY+ELPS +K C    ++
Sbjct:   365 VGGLLLCKDHVYHEWRRIAEHFQDELRGNTSETDNVMSSLQLSYDELPSHLKSCILTLSL 424

Query:   232 FPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYK 291
             +P+D  I K +L+  W+ +G++  +  +   + GE+ F+ L +R   +  +K   G I  
Sbjct:   425 YPEDCVIPKQQLVHGWIGEGFVMWRNGRSATESGEDCFSGLTNRCLIEVVDKTYSGTIIT 484

Query:   292 CKMHDIVHDFAQYLCSNECLA-VEIHSGEELAIS-SFVEK--KILHLLL----TLRRGAS 343
             CK+HD+V D    +   +  +  E  +   L IS +F EK  K+ H L     T + G  
Sbjct:   485 CKIHDMVRDLVIDIAKKDSFSNPEGLNCRHLGISGNFDEKQIKVNHKLRGVVSTTKTGEV 544

Query:   344 VPIS--IWGNVTGLRGLRSLLVKSDEYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNN 400
               ++  +    T  + LR L +    +    SE+L ++   L  L  L L    + P   
Sbjct:   545 NKLNSDLAKKFTDCKYLRVLDISKSIFDAPLSEILDEI-ASLQHLACLSLS--NTHP--- 598

Query:   401 LIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKL 460
             LI + P ++E L +L+ L+    + +++L   +     L  L++ +C +L   P+GIG L
Sbjct:   599 LI-QFPRSMEDLHNLQILDASYCQNLKQLQPCIVLFKKLLVLDMTNCGSLECFPKGIGSL 657

Query:   461 RKLMYL 466
              KL  L
Sbjct:   658 VKLEVL 663

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

UNIPROTKB|O48647 O48647 "XA1" [Oryza sativa (taxid:4530)]

 Score = 542 (195.9 bits), Expect = 8.7e-51, P = 8.7e-51
 Identities = 149/509 (29%), Positives = 249/509 (48%)

Query:     2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQS 61
             GGIGKTTLAQ    +  ++  F  + WV VS+ FD  +I R I++ ++  S + +    +
Sbjct:   328 GGIGKTTLAQLVCKDLVIKSQFNVKIWVYVSDKFDVVKITRQILDHVSNQSHEGISNLDT 387

Query:    62 LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLK-----NSLHE----SKILITTRK 112
             L Q +EE +  KKFL+VLDDVW      W+     L+     NS  E    + I++TTR 
Sbjct:   388 LQQDLEEQMKSKKFLIVLDDVWEIRTDDWKKLLAPLRPNDQVNSSQEEATGNMIILTTRI 447

Query:   113 ETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLA 172
             +++A+ +G+   I +  L + + WS+F+  A           L+ +G++I  + KG PLA
Sbjct:   448 QSIAKSLGTVQSIKLEALKDDDIWSLFKVHAFGNDKHDSSPGLQVLGKQIASELKGNPLA 507

Query:   173 AKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVF 232
             AKT+ SLL +  T   W +I+++E W+      G++  L LSY+ L + +++C SYC++F
Sbjct:   508 AKTVGSLLGTNLTIDHWDSIIKSEEWKSLQQAYGIMQALKLSYDHLSNPLQQCVSYCSLF 567

Query:   233 PKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKC 292
             PK Y   K +LI++W+AQG++ E   K +E  G +Y   L +  F Q          Y  
Sbjct:   568 PKGYSFSKAQLIQIWIAQGFVEESSEK-LEQKGWKYLAELVNSGFLQQVESTRFSSEYFV 626

Query:   293 KMHDIVHDFAQYLCSNECLAVEIHSGEELAIS----SFVEKKILHL--LLTLRRGASVPI 346
              MHD++HD AQ +   E   ++     ELA S    S V            + R      
Sbjct:   627 -MHDLMHDLAQKVSQTEYATIDGSECTELAPSIRHLSIVTDSAYRKEKYRNISRNEVFEK 685

Query:   347 SIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP 406
              +   V     LRSL++     S   +     F++   LR L  Q+  ++  ++      
Sbjct:   686 RLM-KVKSRSKLRSLVLIGQYDSHFFKYFKDAFKEAQHLRLL--QITATYADSD---SFL 739

Query:   407 TNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL 466
             +++    HL+YL +  ++    LP +L + Y+L+ L++     +  +   I  L  L +L
Sbjct:   740 SSLVNSTHLRYLKIVTEESGRTLPRSLRKYYHLQVLDIGYRFGIPRISNDINNLLSLRHL 799

Query:   467 HNEDTGCLRYLPAGIGELIRLRRVREFVV 495
                D  C     A IG++  L+ +  F+V
Sbjct:   800 VAYDEVCSSI--ANIGKMTSLQELGNFIV 826

GO:0006915 "apoptotic process" evidence=IGI

GO:0006952 "defense response" evidence=IGI

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 479 (173.7 bits), Expect = 4.5e-49, Sum P(2) = 4.5e-49
 Identities = 153/475 (32%), Positives = 236/475 (49%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF---DEFR--IARAIIESLT--PGSA 53
             MGG GKTTL+   + +  V R+FE   WV +S+ +   D FR  I     E+ T  P   
Sbjct:   201 MGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADTQIPAEL 260

Query:    54 KDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE 113
               L  ++ L++ + E +  K++++VLDDVW      W      L + ++ S++++TTR  
Sbjct:   261 YSL-GYRELVEKLVEYLQSKRYIVVLDDVWTTGL--WREISIALPDGIYGSRVMMTTRDM 317

Query:   114 TVARI---MGST-HVISVNVLSEMECWSVFQSLAISGKTIGKR-ENLEKIGREIVKKCKG 168
              VA     +GST H   + +L E E W +F + A        R +NLE I R++V++C+G
Sbjct:   318 NVASFPYGIGSTKH--EIELLKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVERCQG 375

Query:   169 LPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIE--KGLLAPLLLSYNELPSKVKRCF 226
             LPLA  ++ S++ +K  E EW+ +     WEL      K + + + LS+N+LP  +KRCF
Sbjct:   376 LPLAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLPYPLKRCF 435

Query:   227 SYCAVFPKDYGIRKHKLIELWMAQGYLSE-KGAKEMEDIGEEYFNILASRSFFQDFNKYD 285
              YC++FP +Y +++ +LI +WMAQ ++   +G K  E++ + Y N L  R+  Q      
Sbjct:   436 LYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKA-EEVADSYLNELVYRNMLQVILWNP 494

Query:   286 DGEIYKCKMHDIVHDFAQYLCSNE--CLAVEIHSGEELAISSFVEKKILHLLLTLRRGAS 343
              G     KMHD++ + A  +   E  C      S  + A  +       HL +   +   
Sbjct:   495 FGRPKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAETMENYGSRHLCI---QKEM 551

Query:   344 VPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRE--SWPR--- 398
              P SI    T L    SLLV S       E+LP L      LRAL+L+       P    
Sbjct:   552 TPDSI--RATNLH---SLLVCSSA-KHKMELLPSL----NLLRALDLEDSSISKLPDCLV 601

Query:   399 ---N----NL----IKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERL 442
                N    NL    +KE+P N  KL++L+ LN K   KIE+LP  + +L  L  L
Sbjct:   602 TMFNLKYLNLSKTQVKELPKNFHKLVNLETLNTK-HSKIEELPLGMWKLKKLRYL 655

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

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

TAIR|locus:504956483 AT3G46730 [Arabidopsis thaliana (taxid:3702)]

 Score = 494 (179.0 bits), Expect = 1.8e-46, P = 1.8e-46
 Identities = 144/484 (29%), Positives = 242/484 (50%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLV--- 57
             MGG+GKT LA+  YN+GDV+R F+ R W  VS+ +    I   II SL   SA+++    
Sbjct:   193 MGGLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTRDILIRIIRSLGIVSAEEMEKIK 252

Query:    58 ---EFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET 114
                E + L  ++   + GK +++V+DDVW+ D   WE   + L      SK++ITTR   
Sbjct:   253 MFEEDEELEVYLYGLLEGKNYMVVVDDVWDPD--AWESLKRALPCDHRGSKVIITTRIRA 310

Query:   115 VAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGK-RENLEKIGREIVKKCKGLPLA 172
             +A  + G+ +   +  L+  E W++F+  A S   I K  E+L++ G+E+VKKC GLPLA
Sbjct:   311 IAEGVEGTVYAHKLRFLTFEESWTLFERKAFSN--IEKVDEDLQRTGKEMVKKCGGLPLA 368

Query:   173 AKTIASLLRSKNTEKEWQNILENEIWE-LEAIEKGLLAPLLLSYNELPSKVKRCFSYCAV 231
                ++ LL  K T  EW  +  + +W  L+     +     LS+ E+  ++K CF Y +V
Sbjct:   369 IVVLSGLLSRKRTN-EWHEVCAS-LWRRLKDNSIHISTVFDLSFKEMRHELKLCFLYFSV 426

Query:   232 FPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYK 291
             FP+DY I+  KLI L +A+G++ E     MED+   Y + L  RS  +   + + G++  
Sbjct:   427 FPEDYEIKVEKLIHLLVAEGFIQEDEEMMMEDVARCYIDELVDRSLVKA-ERIERGKVMS 485

Query:   292 CKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGN 351
             C++HD++ D A    + E   V +++ E+   S    ++++H L+           +   
Sbjct:   486 CRIHDLLRDLA-IKKAKELNFVNVYN-EKQHSSDICRREVVHHLMN-------DYYLCDR 536

Query:   352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEK 411
                 R +RS L   +   +       L  KL  LR L ++    +   N+   +P  I +
Sbjct:   537 RVNKR-MRSFLFIGERRGFGYVNTTNL--KLKLLRVLNMEGL-LFVSKNISNTLPDVIGE 592

Query:   412 LLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDT 471
             L+HL+YL +     +  LP ++  L  L+ L+        +    + KL  L ++  +  
Sbjct:   593 LIHLRYLGI-ADTYVSILPASISNLRFLQTLDASGNDPF-QYTTDLSKLTSLRHVIGKFV 650

Query:   472 G-CL 474
             G CL
Sbjct:   651 GECL 654

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 445 (161.7 bits), Expect = 5.4e-45, Sum P(2) = 5.4e-45
 Identities = 138/480 (28%), Positives = 234/480 (48%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTP--GSAKDLVE 58
             MGGIGKTTLA+  +++  V R+F+   WVCVS+ F +  + + I++ L P  G    + E
Sbjct:   193 MGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELQPHDGDILQMDE 252

Query:    59 FQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI 118
             + +L + + + +   ++L+VLDDVW ++   W+   K +       K+L+T+R E V   
Sbjct:   253 Y-ALQRKLFQLLEAGRYLVVLDDVWKKE--DWDVI-KAVFPRKRGWKMLLTSRNEGVGIH 308

Query:   119 MGSTHV-ISVNVLSEMECWSVFQSLAISGKT---IGKRENLEKIGREIVKKCKGLPLAAK 174
                T +    ++L+  E W + + +    +    +   E +E +G+E+V  C GLPLA K
Sbjct:   309 ADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRLDEEMEAMGKEMVTHCGGLPLAVK 368

Query:   175 TIASLLRSKNTEKEWQNILEN---EI----WELEAIEKGLLAPLLLSYNELPSKVKRCFS 227
              +  LL +K+T  EW+ + +N   +I    W  +     +   L LSY +LP+ +K CF 
Sbjct:   369 ALGGLLANKHTVPEWKRVFDNIGSQIVGGSWLDDNSLNSVYRILSLSYEDLPTHLKHCFL 428

Query:   228 YCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDG 287
               A FP+D  I  + L   W A+G     G+  +ED GE Y   L  R+     + Y   
Sbjct:   429 NLAHFPEDSEISTYSLFYYWAAEGIYD--GST-IEDSGEYYLEELVRRNLVIADDNYLSW 485

Query:   288 EIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPIS 347
             +   C+MHD++ +        E   ++I        +   +       L++  G +  I 
Sbjct:   486 QSKYCQMHDMMREVCLSKAKEENF-LQIIIDPTCTSTINAQSPSRSRRLSIHSGKAFHIL 544

Query:   348 IWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT 407
                N T +R L  ++ + +E  W       +F  LT LR L+L    SW +    K +P 
Sbjct:   545 GHKNKTKVRSL--IVPRFEEDYWIRSA--SVFHNLTLLRVLDL----SWVKFEGGK-LPC 595

Query:   408 NIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVD-DCQNLRELPRGIGKLRKLMYL 466
             +I  L+HL+YL+L  + K+  LP T+  L  L  LN+  D +    +P  + ++ +L YL
Sbjct:   596 SIGGLIHLRYLSLY-EAKVSHLPSTMRNLKLLLYLNLRVDTEEPIHVPNVLKEMIQLRYL 654

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:2075170 RPP13 "RECOGNITION OF PERONOSPORA PARASITICA 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 455 (165.2 bits), Expect = 5.1e-44, Sum P(2) = 5.1e-44
 Identities = 110/343 (32%), Positives = 185/343 (53%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
             MGG+GKT LA+  YN+ DV+  FE R W  VS+ +    I   II SL   S ++L + +
Sbjct:   193 MGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGEELEKIR 252

Query:    61 SLMQ-----HIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETV 115
                +     ++   + GKK+L+V+DD+W  +   W+   + L  +   S+++ITTR + V
Sbjct:   253 KFAEEELEVYLYGLLEGKKYLVVVDDIWERE--AWDSLKRALPCNHEGSRVIITTRIKAV 310

Query:   116 AR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKR-ENLEKIGREIVKKCKGLPLAA 173
             A  + G  +   +  L+  E W +F+  A   + I ++ E+L K G+E+V+KC+GLPL  
Sbjct:   311 AEGVDGRFYAHKLRFLTFEESWELFEQRAF--RNIQRKDEDLLKTGKEMVQKCRGLPLCI 368

Query:   174 KTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLL--LSYNELPSKVKRCFSYCAV 231
               +A LL S+ T  EW ++  N +W     +   +AP++  LS+ EL  + K CF Y ++
Sbjct:   369 VVLAGLL-SRKTPSEWNDVC-NSLWRRLKDDSIHVAPIVFDLSFKELRHESKLCFLYLSI 426

Query:   232 FPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYK 291
             FP+DY I   KLI L +A+G++       MED+   Y   L  RS  +   + + G++  
Sbjct:   427 FPEDYEIDLEKLIHLLVAEGFIQGDEEMMMEDVARYYIEELIDRSLLEAVRR-ERGKVMS 485

Query:   292 CKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFV-EKKILH 333
             C++HD++ D A    S E   V +++      SS    ++++H
Sbjct:   486 CRIHDLLRDVA-IKKSKELNFVNVYNDHVAQHSSTTCRREVVH 527

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

GO:0009814 "defense response, incompatible interaction" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

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

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

 Score = 423 (154.0 bits), Expect = 2.2e-42, Sum P(2) = 2.2e-42
 Identities = 140/481 (29%), Positives = 232/481 (48%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
             MGGIGKTTLA+  +++  V R+F+   WVCVS+ F    + + I++ L P     L   +
Sbjct:   193 MGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTLKHVWQRILQELQPHDGNILQMDE 252

Query:    61 SLMQ-HIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIM 119
             S +Q  + + +   ++LLVLDDVW ++   W+   K +       K+L+T+R E V    
Sbjct:   253 SALQPKLFQLLETGRYLLVLDDVWKKE--DWDRI-KAVFPRKRGWKMLLTSRNEGVGIHA 309

Query:   120 GSTHV-ISVNVLSEMECWSVFQSLAISGKT---IGKRENLEKIGREIVKKCKGLPLAAKT 175
               T +    ++L+  E W + + +    +    +   E +E +G+E+V  C GLPLA K 
Sbjct:   310 DPTCLTFRASILNPEESWKLCERIVFPRRDETEVRLDEEMEAMGKEMVTHCGGLPLAVKA 369

Query:   176 IASLLRSKNTEKEWQNILEN---EIWELEAIEKGLLAP----LLLSYNELPSKVKRCFSY 228
             +  LL +K+T  EW+ + +N   +I     ++   L      L LSY +LP+ +K  F Y
Sbjct:   370 LGGLLANKHTVPEWKRVSDNIGSQIVGGSCLDDNSLNSVNRILSLSYEDLPTHLKHRFLY 429

Query:   229 CAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGE 288
              A FP+D  I    L   W A+G     G+  ++D GE Y   L  R+     N+Y   E
Sbjct:   430 LAHFPEDSKIYTQDLFNYWAAEGIYD--GST-IQDSGEYYLEELVRRNLVIADNRYLSLE 486

Query:   289 IYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISI 348
                C+MHD++ +        E   ++I        +   +        ++  G +    I
Sbjct:   487 FNFCQMHDMMREVCLSKAKEENF-LQIIKDPTSTSTINAQSPSRSRRFSIHSGKA--FHI 543

Query:   349 WGNVTGLRGLRSLLV-KSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT 407
              G+    + +RSL+V + +E  W       +F  LT LR L+L  R  +    L    P+
Sbjct:   544 LGHRNNPK-VRSLIVSRFEEDFWIRSA--SVFHNLTLLRVLDLS-RVKFEGGKL----PS 595

Query:   408 NIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLN--VDDCQNLRELPRGIGKLRKLMY 465
             +I  L+HL+YL+L G   +  LP T+  L  L  LN  VD+ + +  +P  + ++ +L Y
Sbjct:   596 SIGGLIHLRYLSLYGAV-VSHLPSTMRNLKLLLFLNLRVDNKEPIH-VPNVLKEMLELRY 653

Query:   466 L 466
             L
Sbjct:   654 L 654

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

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

 Score = 454 (164.9 bits), Expect = 4.9e-42, P = 4.9e-42
 Identities = 145/486 (29%), Positives = 240/486 (49%)

Query:     1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ 60
             MGG+GKTTLA+  +N+  V+  F+   WV VS+ F    + + I+++LT    KD ++  
Sbjct:   190 MGGLGKTTLARQVFNHDVVKDRFDGFAWVSVSQEFTRISVWQTILQNLTSKERKDEIQNM 249

Query:    61 S---LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVAR 117
                 L   +   +   K L+VLDD+W E+   W+   K +       K+L+T+R E++A 
Sbjct:   250 KEADLHDDLFRLLESSKTLIVLDDIWKEE--DWD-LIKPIFPPKKGWKVLLTSRTESIA- 305

Query:   118 IMGSTHVISVN--VLSEMECWSVFQSLAISGKTIGK---RENLEKIGREIVKKCKGLPLA 172
             + G T  IS     LS  + W++FQS+A+  K   +    E +E +G++++K C GL LA
Sbjct:   306 MRGDTTYISFKPKCLSIPDSWTLFQSIAMPRKDTSEFKVDEEMENMGKKMIKHCGGLSLA 365

Query:   173 AKTIASLLRSKNTEKEWQNILEN---EIWELEAIEKGLLAPLL-LSYNELPSKVKRCFSY 228
              K +  LL +K T  +W+ + EN    I E  +     +  +L +S+ ELP+ +K CF Y
Sbjct:   366 VKVLGGLLAAKYTLHDWKRLSENIGSHIVERTSGNNSSIDHVLSVSFEELPNYLKHCFLY 425

Query:   229 CAVFPKDYGIRKHKLIELWMAQGYLSEK---GAKEMEDIGEEYFNILASRSFFQDFNKYD 285
              A FP+D+ I   KL   W A+G +SE+     + + D G+ Y   L  R+         
Sbjct:   426 LAHFPEDHEIDVEKLHYYWAAEG-ISERRRYDGETIRDTGDSYIEELVRRNMVISERDVM 484

Query:   286 DGEIYKCKMHDIVHDFAQYLCSNECLA--VEIHSGEELAISSFVEKK-ILHLLLTLRRGA 342
                   C++HD++ +   +    E     V  HS      +    ++ +LH   TL    
Sbjct:   485 TSRFETCRLHDMMREICLFKAKEENFLQIVSNHSPTSNPQTLGASRRFVLHNPTTLH--- 541

Query:   343 SVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLP-QLFEKLTCLRALELQVRESWPRNNL 401
                +  + N   LR   SL+V  D+      +L   +F ++  LR L+L V+  +    L
Sbjct:   542 ---VERYKNNPKLR---SLVVVYDDIGNRRWMLSGSIFTRVKLLRVLDL-VQAKFKGGKL 594

Query:   402 IKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNV-DDCQNLRELPRGIGKL 460
                 P++I KL+HL+YL+LK   K+  LP +L  L  L  L++  D  ++  +P     +
Sbjct:   595 ----PSDIGKLIHLRYLSLK-DAKVSHLPSSLRNLVLLIYLDIRTDFTDIF-VPNVFMGM 648

Query:   461 RKLMYL 466
             R+L YL
Sbjct:   649 RELRYL 654

GO:0005634 "nucleus" evidence=ISM

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: fgenesh4_pg.C_scaffold_223000010 cc-nbs-lrr resistance protein (941 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	505
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	1e-68
PLN03210	1153	PLN03210, PLN03210, Resistant to P	9e-07
COG4886	394	COG4886, COG4886, Leucine-rich repeat (LRR) protei	6e-05
PLN00113	968	PLN00113, PLN00113, leucine-rich repeat receptor-l	1e-04
PLN03210	1153	PLN03210, PLN03210, Resistant to P	2e-04
PLN00113	968	PLN00113, PLN00113, leucine-rich repeat receptor-l	0.002

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

 Score =  221 bits (565), Expect = 1e-68
 Identities = 103/257 (40%), Positives = 152/257 (59%), Gaps = 7/257 (2%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESL-TPGSAKDLVEF 59
           MGG+GKTTLA+  YN+  V  +F+   WV VS+ + EFR+ + I++ L    S       
Sbjct: 27  MGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLDDSDWVEKNE 86

Query: 60  QSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIM 119
             L   I+E +  K+FLLVLDDVW  +   W+       +  + S++++TTR E+VA  M
Sbjct: 87  SELAVKIKEALLRKRFLLVLDDVW--EKNDWDKIGVPFPDGENGSRVIVTTRSESVAGRM 144

Query: 120 GSTH-VISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS 178
           G T     V  L   E W +F +     K +     LE++ +EIV+KCKGLPLA K +  
Sbjct: 145 GGTSKPHEVESLEPEESWELFSNKVFE-KELPPCPELEEVAKEIVEKCKGLPLALKVLGG 203

Query: 179 LLRSKNTEKEWQNILENEIWELEAIE--KGLLAPLLLSYNELPSKVKRCFSYCAVFPKDY 236
           LL  K+T +EW+++LE    EL   +    +L+ L LSY+ LP  +KRCF Y A+FP+DY
Sbjct: 204 LLAFKSTVQEWEHVLEQLNNELAGRDGLNEVLSILSLSYDNLPMHLKRCFLYLALFPEDY 263

Query: 237 GIRKHKLIELWMAQGYL 253
            IRK +LI+LW+A+G++
Sbjct: 264 NIRKEQLIKLWIAEGFV 280

Length = 285

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score = 51.4 bits (123), Expect = 9e-07
 Identities = 115/460 (25%), Positives = 194/460 (42%), Gaps = 91/460 (19%)

Query: 66  IEECVAGKKFLLVLDDVWNEDYY-------KWEPFYKCLKNSLHESKILITTRKETVARI 118
           +EE +  +K L+ +DD+ ++D         +W   +         S+I++ T+ +   R 
Sbjct: 289 MEERLKHRKVLIFIDDLDDQDVLDALAGQTQW---FGS------GSRIIVITKDKHFLRA 339

Query: 119 MGSTHVISVNVLS-----EMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAA 173
            G  H+  V + S     EM C S F       K     +   ++  E+  +   LPL  
Sbjct: 340 HGIDHIYEVCLPSNELALEMFCRSAF-------KKNSPPDGFMELASEVALRAGNLPLGL 392

Query: 174 KTIASLLRSKNTEKEWQNILENEIWELEA-IEKGLLAPLLLSYNELPS-KVKRCFSYCAV 231
             + S LR ++ E +W ++L      L+  IEK     L +SY+ L + K K  F + A 
Sbjct: 393 NVLGSYLRGRDKE-DWMDMLPRLRNGLDGKIEK----TLRVSYDGLNNKKDKAIFRHIAC 447

Query: 232 FPKDYGIRKHKLIELWMAQGYLSEK-GAKEMED--IGEEYFNILASRSFFQDFNKYDDGE 288
               +   K   I+L +A   L    G K + D  +     +I+   S  Q+  K    E
Sbjct: 448 L---FNGEKVNDIKLLLANSDLDVNIGLKNLVDKSLIHVREDIVEMHSLLQEMGK----E 500

Query: 289 IYKCKMHDI-VHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLRRGASVPIS 347
           I + + ++    +F      + C  +E ++G          KK+L + L +     + I 
Sbjct: 501 IVRAQSNEPGEREFLVDA-KDICDVLEDNTGT---------KKVLGITLDIDEIDELHI- 549

Query: 348 IWGNVTGLRGLRSLLV---------KSDEYSWSSEVLPQLFE----KLTCLRALELQVRE 394
              +    +G+R+LL          +  E  W    LP+ F+    KL  LR  +     
Sbjct: 550 ---HENAFKGMRNLLFLKFYTKKWDQKKEVRWH---LPEGFDYLPPKLRLLR-WDKYPLR 602

Query: 395 SWPRN----NLIK-EIP-TNIEKL---LH----LKYLNLKGQKKIEKLPETLCELYNLER 441
             P N    NL+K ++  + +EKL   +H    L+ ++L+G K ++++P+ L    NLE 
Sbjct: 603 CMPSNFRPENLVKLQMQGSKLEKLWDGVHSLTGLRNIDLRGSKNLKEIPD-LSMATNLET 661

Query: 442 LNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGI 481
           L + DC +L ELP  I  L KL  L       L  LP GI
Sbjct: 662 LKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGI 701

syringae 6; Provisional. Length = 1153

>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function unknown]

 Score = 45.0 bits (106), Expect = 6e-05
 Identities = 32/94 (34%), Positives = 43/94 (45%), Gaps = 4/94 (4%)

Query: 398 RNNLIKEIPTNIEKL-LHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG 456
            NN I +IP  I  L  +LK L+L    KIE LP  L  L NL+ L++     L +LP+ 
Sbjct: 124 DNNNITDIPPLIGLLKSNLKELDL-SDNKIESLPSPLRNLPNLKNLDLSFND-LSDLPKL 181

Query: 457 IGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRV 490
           +  L  L  L       +  LP  I  L  L  +
Sbjct: 182 LSNLSNLNNLDLSGNK-ISDLPPEIELLSALEEL 214

Length = 394

>gnl|CDD|215061 PLN00113, PLN00113, leucine-rich repeat receptor-like protein kinase; Provisional

 Score = 44.5 bits (105), Expect = 1e-04
 Identities = 35/110 (31%), Positives = 57/110 (51%), Gaps = 14/110 (12%)

Query: 382 LTCLRALELQVRESWPRNNLIK-EIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLE 440
           +  L  L+L        NN++  EIP +I     LK L+L G   + K+P +L  L +LE
Sbjct: 139 IPNLETLDLS-------NNMLSGEIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLE 191

Query: 441 RLNVDDCQNLRELPRGIGKLR--KLMYL-HNEDTGCLRYLPAGIGELIRL 487
            L +   Q + ++PR +G+++  K +YL +N  +G    +P  IG L  L
Sbjct: 192 FLTLASNQLVGQIPRELGQMKSLKWIYLGYNNLSG---EIPYEIGGLTSL 238

Length = 968

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 31/119 (26%), Positives = 51/119 (42%), Gaps = 18/119 (15%)

Query: 351 NVTGLRGLRSLLVKSDEYSW------SSEVLPQ--LFEKLTCLRALELQVRESW----PR 398
           N++G   L+S    S   SW      + E  P     E L  L   E++  + W    P 
Sbjct: 710 NLSGCSRLKSFPDISTNISWLDLDETAIEEFPSNLRLENLDELILCEMKSEKLWERVQPL 769

Query: 399 NNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGI 457
             L+  +  ++ +L       L     + +LP ++  L+ LE L +++C NL  LP GI
Sbjct: 770 TPLMTMLSPSLTRLF------LSDIPSLVELPSSIQNLHKLEHLEIENCINLETLPTGI 822

syringae 6; Provisional. Length = 1153

>gnl|CDD|215061 PLN00113, PLN00113, leucine-rich repeat receptor-like protein kinase; Provisional

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 35/117 (29%), Positives = 54/117 (46%), Gaps = 12/117 (10%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           +P     LT L  L+L        NNL   IP+++  L +L+YL L   K    +P ++ 
Sbjct: 228 IPYEIGGLTSLNHLDLVY------NNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIF 281

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLH---NEDTGCLRYLPAGIGELIRLR 488
            L  L  L++ D     E+P  + +L+ L  LH   N  TG    +P  +  L RL+
Sbjct: 282 SLQKLISLDLSDNSLSGEIPELVIQLQNLEILHLFSNNFTG---KIPVALTSLPRLQ 335

Length = 968

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	505
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PRK04841	903	transcriptional regulator MalT; Provisional	99.47
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.35
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.33
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.28
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.25
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.24
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.07
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.05
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.01
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.0
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.99
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	98.97
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.91
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.85
PF05729	166	NACHT: NACHT domain	98.82
KOG0472	565	consensus Leucine-rich repeat protein [Function un	98.76
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	98.75
COG3903	414	Predicted ATPase [General function prediction only	98.7
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.7
PLN03150	623	hypothetical protein; Provisional	98.67
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.58
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.56
PLN03150	623	hypothetical protein; Provisional	98.55
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.54
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.53
PRK06893	229	DNA replication initiation factor; Validated	98.53
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.52
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.5
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.49
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	98.47
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.46
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.44
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.43
COG3899	849	Predicted ATPase [General function prediction only	98.42
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.38
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.37
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.35
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.34
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.32
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.29
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.29
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.28
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.2
PF13173	128	AAA_14: AAA domain	98.2
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.17
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.16
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.15
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.09
PRK13342	413	recombination factor protein RarA; Reviewed	98.06
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.05
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.05
PRK08084	235	DNA replication initiation factor; Provisional	98.04
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.04
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.04
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.03
PRK08727	233	hypothetical protein; Validated	98.03
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	98.03
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.02
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.0
cd01128	249	rho_factor Transcription termination factor rho is	97.98
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.96
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	97.96
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.93
PRK05642	234	DNA replication initiation factor; Validated	97.93
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.92
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.92
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.88
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.87
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	97.84
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.84
PF14516	331	AAA_35: AAA-like domain	97.83
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.79
PRK09087	226	hypothetical protein; Validated	97.78
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.78
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.78
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.77
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.77
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.76
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.74
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.74
PRK12402	337	replication factor C small subunit 2; Reviewed	97.74
PRK09376	416	rho transcription termination factor Rho; Provisio	97.73
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.73
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.72
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.7
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.67
PRK15386	426	type III secretion protein GogB; Provisional	97.66
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.65
PLN03025	319	replication factor C subunit; Provisional	97.65
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.64
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.61
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.61
PRK15386	426	type III secretion protein GogB; Provisional	97.59
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.59
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.58
KOG2028	554	consensus ATPase related to the helicase subunit o	97.55
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.54
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.54
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.54
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.52
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.51
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.51
PRK06620	214	hypothetical protein; Validated	97.5
PRK13341	725	recombination factor protein RarA/unknown domain f	97.45
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.44
TIGR00767	415	rho transcription termination factor Rho. Members	97.43
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.42
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.4
PRK04195	482	replication factor C large subunit; Provisional	97.4
KOG4237	498	consensus Extracellular matrix protein slit, conta	97.38
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.36
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.36
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.32
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.31
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.3
PRK12422	445	chromosomal replication initiation protein; Provis	97.25
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.24
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.24
CHL00181	287	cbbX CbbX; Provisional	97.22
PRK08116	268	hypothetical protein; Validated	97.21
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.2
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.2
smart00382	148	AAA ATPases associated with a variety of cellular	97.19
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.19
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.17
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.16
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.16
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.16
PF00004	132	AAA: ATPase family associated with various cellula	97.15
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.15
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.13
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.13
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.12
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.08
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.07
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.06
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.0
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.99
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.97
PHA02544	316	44 clamp loader, small subunit; Provisional	96.97
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.93
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.91
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.89
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.88
PRK04132	846	replication factor C small subunit; Provisional	96.88
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.85
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.85
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.82
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.8
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.79
PRK08181	269	transposase; Validated	96.73
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.71
PRK03992	389	proteasome-activating nucleotidase; Provisional	96.71
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	96.7
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.67
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.66
PRK07952	244	DNA replication protein DnaC; Validated	96.65
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.64
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.63
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.63
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	96.62
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.61
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.61
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.59
PRK12377	248	putative replication protein; Provisional	96.57
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.56
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.52
PRK08939	306	primosomal protein DnaI; Reviewed	96.42
PRK06835	329	DNA replication protein DnaC; Validated	96.41
PRK06921	266	hypothetical protein; Provisional	96.41
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.39
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.39
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.36
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.36
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.29
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.27
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.26
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.24
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	96.22
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.22
PRK09183	259	transposase/IS protein; Provisional	96.2
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.2
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.18
PRK12608	380	transcription termination factor Rho; Provisional	96.18
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.18
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.18
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.0
CHL00176	638	ftsH cell division protein; Validated	95.94
PRK06526	254	transposase; Provisional	95.93
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.92
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	95.92
CHL00095	821	clpC Clp protease ATP binding subunit	95.85
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.8
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	95.76
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.7
KOG2123	388	consensus Uncharacterized conserved protein [Funct	95.65
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.65
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.57
PTZ00202	550	tuzin; Provisional	95.52
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.49
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.47
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.44
PRK04296	190	thymidine kinase; Provisional	95.43
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.43
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.42
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.39
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	95.3
CHL00195	489	ycf46 Ycf46; Provisional	95.29
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.27
PRK07276	290	DNA polymerase III subunit delta'; Validated	95.23
PRK07132	299	DNA polymerase III subunit delta'; Validated	95.23
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.23
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.16
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.14
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.14
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.09
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.07
PRK08118	167	topology modulation protein; Reviewed	95.07
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.89
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	94.89
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	94.88
PRK10536	262	hypothetical protein; Provisional	94.63
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.61
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	94.58
PRK07261	171	topology modulation protein; Provisional	94.57
PRK05541	176	adenylylsulfate kinase; Provisional	94.52
CHL00095	821	clpC Clp protease ATP binding subunit	94.49
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.49
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	94.47
PRK10865	857	protein disaggregation chaperone; Provisional	94.47
PRK10865	857	protein disaggregation chaperone; Provisional	94.43
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.41
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	94.37
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.37
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.37
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	94.35
KOG2982	418	consensus Uncharacterized conserved protein [Funct	94.28
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	94.23
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	94.14
PRK09354	349	recA recombinase A; Provisional	94.12
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	94.06
PRK06067	234	flagellar accessory protein FlaH; Validated	94.06
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	94.0
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	93.98
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	93.95
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.9
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	93.9
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	93.9
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	93.82
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	93.78
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.76
KOG2982	418	consensus Uncharacterized conserved protein [Funct	93.7
PRK05973	237	replicative DNA helicase; Provisional	93.66
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.61
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	93.61
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	93.6
PRK04301	317	radA DNA repair and recombination protein RadA; Va	93.54
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	93.45
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.4
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	93.4
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	93.33
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	93.26
KOG1514	767	consensus Origin recognition complex, subunit 1, a	93.25
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	93.09
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	93.07
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.05
KOG0473	326	consensus Leucine-rich repeat protein [Function un	93.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	92.92
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	92.9
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	92.86
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.73
cd03216	163	ABC_Carb_Monos_I This family represents the domain	92.66
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	92.65
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.64
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.62
PRK04328	249	hypothetical protein; Provisional	92.56
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	92.54
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	92.54
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	92.45
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	92.39
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	92.22
cd03115	173	SRP The signal recognition particle (SRP) mediates	92.21
PRK08233	182	hypothetical protein; Provisional	92.14
KOG0473	326	consensus Leucine-rich repeat protein [Function un	92.07
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	91.98
PRK08533	230	flagellar accessory protein FlaH; Reviewed	91.89
cd03246	173	ABCC_Protease_Secretion This family represents the	91.79
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	91.75
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	91.74
KOG1969	877	consensus DNA replication checkpoint protein CHL12	91.73
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	91.62
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	91.6
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	91.57
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	91.56
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	91.39
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	91.23
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	91.21
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	91.09
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	91.0
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	90.92
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	90.87
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	90.84
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	90.68
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	90.62
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	90.54
PF00154	322	RecA: recA bacterial DNA recombination protein; In	90.5
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	90.47
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	90.46
KOG0736	953	consensus Peroxisome assembly factor 2 containing	90.36
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	90.35
PRK14974	336	cell division protein FtsY; Provisional	90.28
PF07726	131	AAA_3: ATPase family associated with various cellu	90.12
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	90.1
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	90.0
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	89.9
PRK13849	231	putative crown gall tumor protein VirC1; Provision	89.86
COG2884	223	FtsE Predicted ATPase involved in cell division [C	89.76
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	89.75
PRK00771	437	signal recognition particle protein Srp54; Provisi	89.69
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	89.62
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	89.6
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	89.43
PRK05917	290	DNA polymerase III subunit delta'; Validated	89.38
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	89.35
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	89.32
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	89.31
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	89.25
PRK11823	446	DNA repair protein RadA; Provisional	89.22
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	89.21
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	89.1
smart00370	26	LRR Leucine-rich repeats, outliers.	89.09
smart00369	26	LRR_TYP Leucine-rich repeats, typical (most popula	89.09
PHA02244	383	ATPase-like protein	89.09
PF01656	195	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domai	89.08
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	89.04
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	89.03
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	89.01
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	88.96
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	88.94
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	88.83
PRK13531	498	regulatory ATPase RavA; Provisional	88.8
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	88.78
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	88.68
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	88.52
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	88.5
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	88.47
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	88.45
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	88.41
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	88.38
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	88.34
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	88.32
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	88.32
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	88.3
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	88.28
PRK03839	180	putative kinase; Provisional	88.26
TIGR00064	272	ftsY signal recognition particle-docking protein F	88.21
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	88.2
PRK12678	672	transcription termination factor Rho; Provisional	88.19
PTZ00035	337	Rad51 protein; Provisional	88.19
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	88.12
PRK06217	183	hypothetical protein; Validated	88.11
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	88.11
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	88.08
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	88.07
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	88.02
COG1192	259	Soj ATPases involved in chromosome partitioning [C	88.0
PRK09519	790	recA DNA recombination protein RecA; Reviewed	87.99
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	87.89
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	87.77
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	87.67
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	87.57
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	87.57
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	87.49
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	87.4
PHA02518	211	ParA-like protein; Provisional	87.37
PRK00625	173	shikimate kinase; Provisional	87.37
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	87.2
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	87.15
cd03215	182	ABC_Carb_Monos_II This family represents domain II	87.14
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	87.03
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	86.96
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	86.95
PRK05818	261	DNA polymerase III subunit delta'; Validated	86.91
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	86.86
CHL00206	2281	ycf2 Ycf2; Provisional	86.85
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	86.8
PRK10867	433	signal recognition particle protein; Provisional	86.78
KOG3864	221	consensus Uncharacterized conserved protein [Funct	86.73
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	86.7
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	86.63
PRK06762	166	hypothetical protein; Provisional	86.58
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	86.49
COG0488	530	Uup ATPase components of ABC transporters with dup	86.32
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	86.31
PF07015	231	VirC1: VirC1 protein; InterPro: IPR009744 This fam	86.29
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	86.28
PTZ00185	574	ATPase alpha subunit; Provisional	86.28
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	86.18
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	86.16
TIGR00959	428	ffh signal recognition particle protein. This mode	86.1
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	86.05
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	86.02
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	85.97
PRK11608	326	pspF phage shock protein operon transcriptional ac	85.74
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	85.59
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	85.55
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	85.54
PRK13947	171	shikimate kinase; Provisional	85.42
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	85.38
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	85.32
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	85.3
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	85.25
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	85.19
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	85.17
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	85.14
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	85.08
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	85.06
PRK00889	175	adenylylsulfate kinase; Provisional	85.04
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	85.02
cd02042	104	ParA ParA and ParB of Caulobacter crescentus belon	84.99
PRK00131	175	aroK shikimate kinase; Reviewed	84.94
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	84.81
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	84.68
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	84.64
COG1157	441	FliI Flagellar biosynthesis/type III secretory pat	84.56
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	84.52
PTZ00301	210	uridine kinase; Provisional	84.51
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	84.44
PTZ00088	229	adenylate kinase 1; Provisional	84.37
PRK08006	471	replicative DNA helicase; Provisional	84.34
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	84.32
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	84.31
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	84.3
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	84.29
PRK09099	441	type III secretion system ATPase; Provisional	84.28
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	84.2
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	84.19
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	84.13
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	84.12
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	84.0
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	83.99
PRK06547	172	hypothetical protein; Provisional	83.97
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	83.77
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	83.74
PRK00279	215	adk adenylate kinase; Reviewed	83.72
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	83.65
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	83.55
cd02036	179	MinD Bacterial cell division requires the formatio	83.51
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	83.5
cd02034	116	CooC The accessory protein CooC, which contains a	83.39
smart00487	201	DEXDc DEAD-like helicases superfamily.	83.38
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	83.33
PRK05922	434	type III secretion system ATPase; Validated	83.33
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	83.23
PRK14269	246	phosphate ABC transporter ATP-binding protein; Pro	83.17
cd02037	169	MRP-like MRP (Multiple Resistance and pH adaptatio	83.07
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	82.99
PRK03846	198	adenylylsulfate kinase; Provisional	82.97
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	82.93
PLN03211	659	ABC transporter G-25; Provisional	82.91
PRK08506	472	replicative DNA helicase; Provisional	82.9
COG0488	530	Uup ATPase components of ABC transporters with dup	82.89
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	82.87
PRK04040	188	adenylate kinase; Provisional	82.8
PRK05022	509	anaerobic nitric oxide reductase transcription reg	82.76
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	82.73
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	82.73
cd02040	270	NifH NifH gene encodes component II (iron protein)	82.67
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	82.57
COG3265	161	GntK Gluconate kinase [Carbohydrate transport and	82.55
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	82.44
PRK09580	248	sufC cysteine desulfurase ATPase component; Review	82.4
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	82.38
PRK13949	169	shikimate kinase; Provisional	82.3
COG1149	284	MinD superfamily P-loop ATPase containing an inser	82.22
PHA00729	226	NTP-binding motif containing protein	82.2
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	82.16
PRK06696	223	uridine kinase; Validated	82.11
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	82.07
PRK13231	264	nitrogenase reductase-like protein; Reviewed	82.05
PRK06761	282	hypothetical protein; Provisional	82.04
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	81.96
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	81.91
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	81.82
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	81.81
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	81.78
PRK07594	433	type III secretion system ATPase SsaN; Validated	81.64
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	81.53
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	81.52
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	81.48
TIGR00235	207	udk uridine kinase. Model contains a number of lon	81.41
PRK11545	163	gntK gluconate kinase 1; Provisional	81.36
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	81.32
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	81.25
PRK05480	209	uridine/cytidine kinase; Provisional	81.22
CHL00060	494	atpB ATP synthase CF1 beta subunit	81.18
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	81.15

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.9e-60  Score=496.68  Aligned_cols=476  Identities=33%  Similarity=0.542  Sum_probs=395.1

Q ss_pred             CCCCcHHHHHHHHhcCcc-cccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCCh-hcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGD-VERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDL-VEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~-~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      |||+||||||++++++.. +.++|+.++||.+++.++...++.+|+..++....... ...++....+.+.|+++|++||
T Consensus       187 MGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllv  266 (889)
T KOG4658|consen  187 MGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRFLLV  266 (889)
T ss_pred             CCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCceEEE
Confidence            899999999999999876 88999999999999999999999999999986444333 2346778889999999999999


Q ss_pred             EeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHH
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEK  157 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~  157 (505)
                      +||||+..  .|+.+...+|...+||+|++|||+..++.. ++....+++..|+.+|||+||++.++.... ..++..++
T Consensus       267 LDDIW~~~--dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~-~~~~~i~~  343 (889)
T KOG4658|consen  267 LDDIWEEV--DWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTL-GSHPDIEE  343 (889)
T ss_pred             Eecccccc--cHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccc-cccccHHH
Confidence            99999987  599999999999999999999999999987 666778999999999999999999976543 34455899


Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhh----hhcccCchhhHhhccccCChhhhhhhhhhccCC
Q 046115          158 IGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWEL----EAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFP  233 (505)
Q Consensus       158 ~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l----~~~~~~~~~~l~~s~~~L~~~~~~~ll~la~f~  233 (505)
                      +|++++++|+|+|||++++|+.|+.+.+..+|.++++......    ......++.++..||+.|+++.|.||+|||.||
T Consensus       344 lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~lK~CFLycalFP  423 (889)
T KOG4658|consen  344 LAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLSYDNLPEELKSCFLYCALFP  423 (889)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhccHhhhhHHHHHHHHhhccCC
Confidence            9999999999999999999999999999999999998765442    223467889999999999999999999999999


Q ss_pred             CCCCCChHHHHHHHHHcCCCCC-CCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehHHHHHHHHHhhc-----
Q 046115          234 KDYGIRKHKLIELWMAQGYLSE-KGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCS-----  307 (505)
Q Consensus       234 ~~~~i~~~~l~~~w~~~~~~~~-~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~lv~~~~~~~~~-----  307 (505)
                      +++.++.+.++.+|+++|++.. .....+++.+++++.+|++++|+......  ++...|.|||+||++|..++.     
T Consensus       424 ED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~--~~~~~~kmHDvvRe~al~ias~~~~~  501 (889)
T KOG4658|consen  424 EDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDE--GRKETVKMHDVVREMALWIASDFGKQ  501 (889)
T ss_pred             cccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcccc--cceeEEEeeHHHHHHHHHHhcccccc
Confidence            9999999999999999999877 44678999999999999999999876644  455589999999999999999     


Q ss_pred             cceEEeecc-cCcccccccccccceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccc
Q 046115          308 NECLAVEIH-SGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLR  386 (505)
Q Consensus       308 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~  386 (505)
                      .+....... ......-...+ ...++.++..+....++...     .++.|++|.+.+|.. +.....+.+|..|+.|+
T Consensus       502 ~e~~iv~~~~~~~~~~~~~~~-~~~rr~s~~~~~~~~~~~~~-----~~~~L~tLll~~n~~-~l~~is~~ff~~m~~Lr  574 (889)
T KOG4658|consen  502 EENQIVSDGVGLSEIPQVKSW-NSVRRMSLMNNKIEHIAGSS-----ENPKLRTLLLQRNSD-WLLEISGEFFRSLPLLR  574 (889)
T ss_pred             ccceEEECCcCccccccccch-hheeEEEEeccchhhccCCC-----CCCccceEEEeecch-hhhhcCHHHHhhCcceE
Confidence            555333322 11111111222 37899999999888777766     566899999999963 22233566788999999


Q ss_pred             eEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCcee
Q 046115          387 ALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL  466 (505)
Q Consensus       387 ~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L  466 (505)
                      +|||+      .+....++|..++.|-+|+||+++++. +..+|..+++|..|.+|++..+.....+|.....|++|++|
T Consensus       575 VLDLs------~~~~l~~LP~~I~~Li~LryL~L~~t~-I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L  647 (889)
T KOG4658|consen  575 VLDLS------GNSSLSKLPSSIGELVHLRYLDLSDTG-ISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLRVL  647 (889)
T ss_pred             EEECC------CCCccCcCChHHhhhhhhhcccccCCC-ccccchHHHHHHhhheeccccccccccccchhhhcccccEE
Confidence            99999      467789999999999999999999999 99999999999999999999988777887777779999999


Q ss_pred             ecCCCcccccccccccCCccCCccceeEec
Q 046115          467 HNEDTGCLRYLPAGIGELIRLRRVREFVVG  496 (505)
Q Consensus       467 ~l~~~~~~~~~p~~i~~l~~L~~L~~~~~~  496 (505)
                      .+.... ...-...++++.+|+.|....+.
T Consensus       648 ~l~~s~-~~~~~~~l~el~~Le~L~~ls~~  676 (889)
T KOG4658|consen  648 RLPRSA-LSNDKLLLKELENLEHLENLSIT  676 (889)
T ss_pred             Eeeccc-cccchhhHHhhhcccchhhheee
Confidence            987653 11111224445555555544443

>PLN03210 Resistant to P

Probab=100.00  E-value=4.1e-46  Score=412.14  Aligned_cols=446  Identities=22%  Similarity=0.335  Sum_probs=315.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEe---CCCC------------CHHHHHHHHHHHcCCCCCCChhcHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCV---SEPF------------DEFRIARAIIESLTPGSAKDLVEFQSLMQH   65 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~---~~~~------------~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~   65 (505)
                      |||+||||||+++|+  ++..+|++.+|++.   ....            ....++..++.++...........    ..
T Consensus       215 ~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~----~~  288 (1153)
T PLN03210        215 SSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHL----GA  288 (1153)
T ss_pred             CCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCH----HH
Confidence            799999999999999  78889999888753   1110            012344455555432211111111    35


Q ss_pred             HHHHcCCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCcceEeCCCCChhhHHHHHHHhhhC
Q 046115           66 IEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAIS  145 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~  145 (505)
                      +++.++++|+||||||||+..  +|+.+.....++++|++||||||++.++..++..++|+++.++.+||++||+..||.
T Consensus       289 ~~~~L~~krvLLVLDdv~~~~--~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~  366 (1153)
T PLN03210        289 MEERLKHRKVLIFIDDLDDQD--VLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFK  366 (1153)
T ss_pred             HHHHHhCCeEEEEEeCCCCHH--HHHHHHhhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcC
Confidence            677789999999999997654  677777766777899999999999999877666789999999999999999999986


Q ss_pred             CCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhhcccCchhhHhhccccCCh-hhhh
Q 046115          146 GKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPS-KVKR  224 (505)
Q Consensus       146 ~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~L~~-~~~~  224 (505)
                      ...  ++++..+++++|+++|+|+||||+++|++|+++ +..+|...+++....   .+..+..++.+||+.|++ ..|.
T Consensus       367 ~~~--~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k-~~~~W~~~l~~L~~~---~~~~I~~~L~~SYd~L~~~~~k~  440 (1153)
T PLN03210        367 KNS--PPDGFMELASEVALRAGNLPLGLNVLGSYLRGR-DKEDWMDMLPRLRNG---LDGKIEKTLRVSYDGLNNKKDKA  440 (1153)
T ss_pred             CCC--CcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCC-CHHHHHHHHHHHHhC---ccHHHHHHHHHhhhccCccchhh
Confidence            543  345678899999999999999999999999876 789999999875443   345799999999999986 6999


Q ss_pred             hhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehHHHHHHHHH
Q 046115          225 CFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQY  304 (505)
Q Consensus       225 ~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~lv~~~~~~  304 (505)
                      +|+++|+|+.+..++   .+..|.+.+...          ++..++.|++++|++....       .+.||+++|+++++
T Consensus       441 ~Fl~ia~ff~~~~~~---~v~~~l~~~~~~----------~~~~l~~L~~ksLi~~~~~-------~~~MHdLl~~~~r~  500 (1153)
T PLN03210        441 IFRHIACLFNGEKVN---DIKLLLANSDLD----------VNIGLKNLVDKSLIHVRED-------IVEMHSLLQEMGKE  500 (1153)
T ss_pred             hhheehhhcCCCCHH---HHHHHHHhcCCC----------chhChHHHHhcCCEEEcCC-------eEEhhhHHHHHHHH
Confidence            999999999875543   244455544332          2234889999999975321       58999999999999


Q ss_pred             hhccceE-------EeecccCcccccccccccceeEEEEEecCCCccccccccCCCCCCCceEE----------------
Q 046115          305 LCSNECL-------AVEIHSGEELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSL----------------  361 (505)
Q Consensus       305 ~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L----------------  361 (505)
                      ++..+..       ...................++++.+.......+.. ....|.+|.+|+.|                
T Consensus       501 i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i-~~~aF~~m~~L~~L~~~~~~~~~~~~~~~~  579 (1153)
T PLN03210        501 IVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHI-HENAFKGMRNLLFLKFYTKKWDQKKEVRWH  579 (1153)
T ss_pred             HHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeee-cHHHHhcCccccEEEEecccccccccceee
Confidence            9876531       11100000000000011133333333222221111 01123344444444                


Q ss_pred             ---------------EecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccc
Q 046115          362 ---------------LVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKI  426 (505)
Q Consensus       362 ---------------~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~  426 (505)
                                     .+.++.+..    +|..+ .+.+|+.|++.       ++.+..+|..++.+++|++|+|++|..+
T Consensus       580 lp~~~~~lp~~Lr~L~~~~~~l~~----lP~~f-~~~~L~~L~L~-------~s~l~~L~~~~~~l~~Lk~L~Ls~~~~l  647 (1153)
T PLN03210        580 LPEGFDYLPPKLRLLRWDKYPLRC----MPSNF-RPENLVKLQMQ-------GSKLEKLWDGVHSLTGLRNIDLRGSKNL  647 (1153)
T ss_pred             cCcchhhcCcccEEEEecCCCCCC----CCCcC-CccCCcEEECc-------CccccccccccccCCCCCEEECCCCCCc
Confidence                           444443322    33333 35677777777       6667788888888899999999988778


Q ss_pred             cccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccceeEe
Q 046115          427 EKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVV  495 (505)
Q Consensus       427 ~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~~~  495 (505)
                      ..+|. ++.+++|+.|+|++|..+..+|..++++++|+.|++++|..+..+|..+ ++++|+.|++..|
T Consensus       648 ~~ip~-ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i-~l~sL~~L~Lsgc  714 (1153)
T PLN03210        648 KEIPD-LSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGI-NLKSLYRLNLSGC  714 (1153)
T ss_pred             CcCCc-cccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcC-CCCCCCEEeCCCC
Confidence            88886 8888999999999988888899888889999999999888788888766 6777777776544

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=100.00  E-value=3.3e-38  Score=300.62  Aligned_cols=252  Identities=38%  Similarity=0.635  Sum_probs=199.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC--ChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK--DLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~--~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      |||+||||||++++++..+..+|++++|++++...+...++..|+.+++.....  ...+.++....+.+.++++++|||
T Consensus        27 ~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~~~~LlV  106 (287)
T PF00931_consen   27 MGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLKDKRCLLV  106 (287)
T ss_dssp             STTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHCCTSEEEE
T ss_pred             CCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhccccceee
Confidence            799999999999999555889999999999999999999999999999866432  567778899999999999999999


Q ss_pred             EeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCC-cceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHH
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGS-THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEK  157 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~-~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~  157 (505)
                      |||||+..  .|+.+...++.+..+|+||||||++.+...... ...+++++|+.+||++||.+.++... .......++
T Consensus       107 lDdv~~~~--~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~-~~~~~~~~~  183 (287)
T PF00931_consen  107 LDDVWDEE--DLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKE-SESPEDLED  183 (287)
T ss_dssp             EEEE-SHH--HH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS-----TTSCT
T ss_pred             eeeecccc--cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccc
Confidence            99998765  677777777777789999999999887665543 66899999999999999999986554 122334456


Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhh---cccCchhhHhhccccCChhhhhhhhhhccCCC
Q 046115          158 IGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEA---IEKGLLAPLLLSYNELPSKVKRCFSYCAVFPK  234 (505)
Q Consensus       158 ~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~---~~~~~~~~l~~s~~~L~~~~~~~ll~la~f~~  234 (505)
                      .+++|++.|+|+||||+++|++++.+.+...|+..++........   ....+..++..||+.|+++.|.||+++|+||.
T Consensus       184 ~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~f~~L~~f~~  263 (287)
T PF00931_consen  184 LAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFSALELSYDSLPDELRRCFLYLSIFPE  263 (287)
T ss_dssp             HHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHHHHHHHHHSSHTCCHHHHHHGGGSGT
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccceechhcCCccHHHHHhhCcCCCC
Confidence            789999999999999999999996654567888888765544432   34678899999999999999999999999999


Q ss_pred             CCCCChHHHHHHHHHcCCCCC
Q 046115          235 DYGIRKHKLIELWMAQGYLSE  255 (505)
Q Consensus       235 ~~~i~~~~l~~~w~~~~~~~~  255 (505)
                      ++.++.+.++.+|.+++++..
T Consensus       264 ~~~i~~~~li~lW~~e~~i~~  284 (287)
T PF00931_consen  264 GVPIPRERLIRLWVAEGFISS  284 (287)
T ss_dssp             TS-EEHHHHHHHHTT-HHTC-
T ss_pred             CceECHHHHHHHHHHCCCCcc
Confidence            999999999999999988765

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.47  E-value=6.1e-12  Score=139.29  Aligned_cols=268  Identities=17%  Similarity=0.219  Sum_probs=166.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCC-CCCHHHHHHHHHHHcCCCCCC------------ChhcHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE-PFDEFRIARAIIESLTPGSAK------------DLVEFQSLMQHIE   67 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~-~~~~~~~~~~l~~~l~~~~~~------------~~~~~~~~~~~l~   67 (505)
                      ++|.||||++.+++.  ..    +.++|+++.. ..+...+...++..+......            ...+.......+.
T Consensus        40 paG~GKTtl~~~~~~--~~----~~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (903)
T PRK04841         40 PAGYGKTTLISQWAA--GK----NNLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLF  113 (903)
T ss_pred             CCCCCHHHHHHHHHH--hC----CCeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHH
Confidence            589999999999886  22    2688999864 446666666666666311111            1122233334444


Q ss_pred             HHcC--CceEEEEEeCCCCCCccChhHHHHhhcC-CCCCcEEEEEeCchH-H--HHHhCCcceEeCC----CCChhhHHH
Q 046115           68 ECVA--GKKFLLVLDDVWNEDYYKWEPFYKCLKN-SLHESKILITTRKET-V--ARIMGSTHVISVN----VLSEMECWS  137 (505)
Q Consensus        68 ~~l~--~~r~LlvlDdv~~~~~~~~~~~~~~~~~-~~~~~~iLiTtr~~~-~--~~~~~~~~~~~l~----~l~~~ea~~  137 (505)
                      ..+.  +.+++||+||+.+.+.......+..+.. ...+.+++||||... +  ..........++.    +|+.+|+.+
T Consensus       114 ~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~  193 (903)
T PRK04841        114 IELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQ  193 (903)
T ss_pred             HHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHH
Confidence            4443  5789999999987654455544444444 456678889999831 1  1111112245555    999999999


Q ss_pred             HHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCC-HHHHHHHHhhhhhhhhhc-ccCchhhHh-hc
Q 046115          138 VFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNT-EKEWQNILENEIWELEAI-EKGLLAPLL-LS  214 (505)
Q Consensus       138 Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~-~~~~~~~l~~~~~~l~~~-~~~~~~~l~-~s  214 (505)
                      +|.......       -..+.+.++.+.|+|+|+++..++..++.... ....   .    ..+... ...+...+. ..
T Consensus       194 ll~~~~~~~-------~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~~~~~---~----~~~~~~~~~~~~~~l~~~v  259 (903)
T PRK04841        194 FFDQRLSSP-------IEAAESSRLCDDVEGWATALQLIALSARQNNSSLHDS---A----RRLAGINASHLSDYLVEEV  259 (903)
T ss_pred             HHHhccCCC-------CCHHHHHHHHHHhCChHHHHHHHHHHHhhCCCchhhh---h----HhhcCCCchhHHHHHHHHH
Confidence            997654211       12455788999999999999999988755431 1111   1    111111 223455443 44


Q ss_pred             cccCChhhhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeee
Q 046115          215 YNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKM  294 (505)
Q Consensus       215 ~~~L~~~~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~  294 (505)
                      ++.|+++.+..++..|+++   .+..+.+....   +          .+...+.+++|.+.+++....+.. +  .+|++
T Consensus       260 ~~~l~~~~~~~l~~~a~~~---~~~~~l~~~l~---~----------~~~~~~~L~~l~~~~l~~~~~~~~-~--~~yr~  320 (903)
T PRK04841        260 LDNVDLETRHFLLRCSVLR---SMNDALIVRVT---G----------EENGQMRLEELERQGLFIQRMDDS-G--EWFRY  320 (903)
T ss_pred             HhcCCHHHHHHHHHhcccc---cCCHHHHHHHc---C----------CCcHHHHHHHHHHCCCeeEeecCC-C--CEEeh
Confidence            8899999999999999986   34433332211   1          112467799999999964322111 1  26889


Q ss_pred             hHHHHHHHHHhhc
Q 046115          295 HDIVHDFAQYLCS  307 (505)
Q Consensus       295 H~lv~~~~~~~~~  307 (505)
                      |++++++++....
T Consensus       321 H~L~r~~l~~~l~  333 (903)
T PRK04841        321 HPLFASFLRHRCQ  333 (903)
T ss_pred             hHHHHHHHHHHHH
Confidence            9999999998763

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

Probab=99.35  E-value=4.1e-14  Score=115.89  Aligned_cols=146  Identities=29%  Similarity=0.401  Sum_probs=96.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+.++.++.+....+|+++.    ++.+|+.|++.+|++..    +|..++++.+|+.|++.       -+.+..+|.+|
T Consensus        34 ~ITrLtLSHNKl~~vppnia----~l~nlevln~~nnqie~----lp~~issl~klr~lnvg-------mnrl~~lprgf   98 (264)
T KOG0617|consen   34 NITRLTLSHNKLTVVPPNIA----ELKNLEVLNLSNNQIEE----LPTSISSLPKLRILNVG-------MNRLNILPRGF   98 (264)
T ss_pred             hhhhhhcccCceeecCCcHH----Hhhhhhhhhcccchhhh----cChhhhhchhhhheecc-------hhhhhcCcccc
Confidence            55666666666665655554    66667777776666432    45556666677777666       55566666667


Q ss_pred             cCCCCcceeeccCCccc-cccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          410 EKLLHLKYLNLKGQKKI-EKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~-~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      +.++-|+.|||..|... ..+|..+..+.-|+.|.++.|- .+.+|+.++++++|+.|.+..|. +-++|..++.++.|+
T Consensus        99 gs~p~levldltynnl~e~~lpgnff~m~tlralyl~dnd-fe~lp~dvg~lt~lqil~lrdnd-ll~lpkeig~lt~lr  176 (264)
T KOG0617|consen   99 GSFPALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGDND-FEILPPDVGKLTNLQILSLRDND-LLSLPKEIGDLTRLR  176 (264)
T ss_pred             CCCchhhhhhccccccccccCCcchhHHHHHHHHHhcCCC-cccCChhhhhhcceeEEeeccCc-hhhCcHHHHHHHHHH
Confidence            77777777777666632 2566666666666666666666 67777777777777777777776 446777777777776


Q ss_pred             ccce
Q 046115          489 RVRE  492 (505)
Q Consensus       489 ~L~~  492 (505)
                      .|++
T Consensus       177 elhi  180 (264)
T KOG0617|consen  177 ELHI  180 (264)
T ss_pred             HHhc
Confidence            6654

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

Probab=99.33  E-value=3.1e-14  Score=116.60  Aligned_cols=135  Identities=33%  Similarity=0.434  Sum_probs=67.7

Q ss_pred             eEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccc-ccccCcccc
Q 046115          332 LHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNL-IKEIPTNIE  410 (505)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~-~~~~p~~~~  410 (505)
                      ..+.++++.++.+|.++.    .++.|+.|++.-|.+..    +|.-|+.++-|++|||.      .++. -..+|.+|.
T Consensus        59 evln~~nnqie~lp~~is----sl~klr~lnvgmnrl~~----lprgfgs~p~levldlt------ynnl~e~~lpgnff  124 (264)
T KOG0617|consen   59 EVLNLSNNQIEELPTSIS----SLPKLRILNVGMNRLNI----LPRGFGSFPALEVLDLT------YNNLNENSLPGNFF  124 (264)
T ss_pred             hhhhcccchhhhcChhhh----hchhhhheecchhhhhc----CccccCCCchhhhhhcc------ccccccccCCcchh
Confidence            344444444444444332    45555555555444322    44445555555555555      1221 123455555


Q ss_pred             CCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccC
Q 046115          411 KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGE  483 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~  483 (505)
                      .+..|+-|.|+.|. ..-+|+.++++.+||.|.++.|. +-.+|.+++.+..|+.|++.+|. +..+|+.+++
T Consensus       125 ~m~tlralyl~dnd-fe~lp~dvg~lt~lqil~lrdnd-ll~lpkeig~lt~lrelhiqgnr-l~vlppel~~  194 (264)
T KOG0617|consen  125 YMTTLRALYLGDND-FEILPPDVGKLTNLQILSLRDND-LLSLPKEIGDLTRLRELHIQGNR-LTVLPPELAN  194 (264)
T ss_pred             HHHHHHHHHhcCCC-cccCChhhhhhcceeEEeeccCc-hhhCcHHHHHHHHHHHHhcccce-eeecChhhhh
Confidence            55555555555555 45555555555555555555554 55555555555555555555554 4445554444

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.28  E-value=2.4e-10  Score=116.31  Aligned_cols=273  Identities=16%  Similarity=0.192  Sum_probs=174.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCC-CCCHHHHHHHHHHHcCCCCCC------------ChhcHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE-PFDEFRIARAIIESLTPGSAK------------DLVEFQSLMQHIE   67 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~-~~~~~~~~~~l~~~l~~~~~~------------~~~~~~~~~~~l~   67 (505)
                      ++|.|||||+.+.+.  .. ..=..+.|+++.+ ..++..+..-++..+..-.+.            ...+.....+.+.
T Consensus        45 PAGfGKttl~aq~~~--~~-~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~  121 (894)
T COG2909          45 PAGFGKTTLLAQWRE--LA-ADGAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLL  121 (894)
T ss_pred             CCCCcHHHHHHHHHH--hc-CcccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHH
Confidence            589999999999986  22 2335788999766 557888888888888632222            2233344455555


Q ss_pred             HHcCC--ceEEEEEeCCCCCCccChhHHHHhhc-CCCCCcEEEEEeCchHHHHHhC---CcceEeC----CCCChhhHHH
Q 046115           68 ECVAG--KKFLLVLDDVWNEDYYKWEPFYKCLK-NSLHESKILITTRKETVARIMG---STHVISV----NVLSEMECWS  137 (505)
Q Consensus        68 ~~l~~--~r~LlvlDdv~~~~~~~~~~~~~~~~-~~~~~~~iLiTtr~~~~~~~~~---~~~~~~l----~~l~~~ea~~  137 (505)
                      ..+.+  ++..+||||..-........=..++. ...++..++||||.+--.....   .....++    -.|+.+|+.+
T Consensus       122 ~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~  201 (894)
T COG2909         122 NELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAA  201 (894)
T ss_pred             HHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHHHH
Confidence            55533  68999999975544444444344433 4457889999999852211100   0112222    3489999999


Q ss_pred             HHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhhcccCchhh-Hhhccc
Q 046115          138 VFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAP-LLLSYN  216 (505)
Q Consensus       138 Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~-l~~s~~  216 (505)
                      +|.....       .+-....++.+++..+|++-|+..++-.++.+.+.+.-...+.       ...+-+... ..-.++
T Consensus       202 fl~~~~~-------l~Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~Ls-------G~~~~l~dYL~eeVld  267 (894)
T COG2909         202 FLNDRGS-------LPLDAADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGLS-------GAASHLSDYLVEEVLD  267 (894)
T ss_pred             HHHHcCC-------CCCChHHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhcc-------chHHHHHHHHHHHHHh
Confidence            9977531       1112344789999999999999999999985544433222221       111222222 336789


Q ss_pred             cCChhhhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehH
Q 046115          217 ELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHD  296 (505)
Q Consensus       217 ~L~~~~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~  296 (505)
                      .||++.|..++.+++++.   +.. .+......            ++....++++|..+++.-.--++.   -.+|+.|.
T Consensus       268 ~Lp~~l~~FLl~~svl~~---f~~-eL~~~Ltg------------~~ng~amLe~L~~~gLFl~~Ldd~---~~WfryH~  328 (894)
T COG2909         268 RLPPELRDFLLQTSVLSR---FND-ELCNALTG------------EENGQAMLEELERRGLFLQRLDDE---GQWFRYHH  328 (894)
T ss_pred             cCCHHHHHHHHHHHhHHH---hhH-HHHHHHhc------------CCcHHHHHHHHHhCCCceeeecCC---CceeehhH
Confidence            999999999999999865   222 22222211            234667799999999965322211   12899999


Q ss_pred             HHHHHHHHhhccc
Q 046115          297 IVHDFAQYLCSNE  309 (505)
Q Consensus       297 lv~~~~~~~~~~~  309 (505)
                      ++.+|.+.....+
T Consensus       329 LFaeFL~~r~~~~  341 (894)
T COG2909         329 LFAEFLRQRLQRE  341 (894)
T ss_pred             HHHHHHHhhhccc
Confidence            9999999887764

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

Probab=99.25  E-value=1.4e-11  Score=137.36  Aligned_cols=136  Identities=21%  Similarity=0.305  Sum_probs=97.2

Q ss_pred             ccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccc
Q 046115          349 WGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEK  428 (505)
Q Consensus       349 ~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~  428 (505)
                      +..+..+++|++|++.+|.+.+.   +|..+.++++|++|+|+      ++...+.+|..++.+++|++|++++|...+.
T Consensus       157 p~~~~~l~~L~~L~L~~n~l~~~---~p~~~~~l~~L~~L~L~------~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~  227 (968)
T PLN00113        157 PNDIGSFSSLKVLDLGGNVLVGK---IPNSLTNLTSLEFLTLA------SNQLVGQIPRELGQMKSLKWIYLGYNNLSGE  227 (968)
T ss_pred             ChHHhcCCCCCEEECccCccccc---CChhhhhCcCCCeeecc------CCCCcCcCChHHcCcCCccEEECcCCccCCc
Confidence            33455677777777777765543   66667777777777776      3444456677777777788888777775557


Q ss_pred             cchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          429 LPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       429 lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      +|..++.+++|+.|++++|.....+|..++++++|++|++++|...+.+|..+.++++|+.|++.
T Consensus       228 ~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls  292 (968)
T PLN00113        228 IPYEIGGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLS  292 (968)
T ss_pred             CChhHhcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEECc
Confidence            77777777788888887777556777777777788888887777666777777777777777654

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

Probab=99.24  E-value=1.3e-11  Score=137.45  Aligned_cols=152  Identities=26%  Similarity=0.247  Sum_probs=122.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      +++.+.+..+...   ...+..+.++++|++|++.+|.+.+.   +|..+.++.+|+.|+|+      ++...+.+|..+
T Consensus       165 ~L~~L~L~~n~l~---~~~p~~~~~l~~L~~L~L~~n~l~~~---~p~~l~~l~~L~~L~L~------~n~l~~~~p~~l  232 (968)
T PLN00113        165 SLKVLDLGGNVLV---GKIPNSLTNLTSLEFLTLASNQLVGQ---IPRELGQMKSLKWIYLG------YNNLSGEIPYEI  232 (968)
T ss_pred             CCCEEECccCccc---ccCChhhhhCcCCCeeeccCCCCcCc---CChHHcCcCCccEEECc------CCccCCcCChhH
Confidence            4555555554432   23344556899999999999987654   77788999999999998      344556788889


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|...+.+|..++.+++|+.|++++|.....+|..+..+++|++|++++|...+.+|..+.++++|+.
T Consensus       233 ~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~  312 (968)
T PLN00113        233 GGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLSDNSLSGEIPELVIQLQNLEI  312 (968)
T ss_pred             hcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEECcCCeeccCCChhHcCCCCCcE
Confidence            99999999999999866688888999999999999999866788888999999999999999877788888888898888


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       313 L~l~  316 (968)
T PLN00113        313 LHLF  316 (968)
T ss_pred             EECC
Confidence            8764

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

Probab=99.07  E-value=9.6e-12  Score=115.38  Aligned_cols=146  Identities=25%  Similarity=0.432  Sum_probs=120.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceE-EEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRS-LLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~-L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .+..+.++.+....+|....    .++.+.+ +.++.|..++    +|.+++.+.+|..|+|+       ++.+..+|..
T Consensus       389 ~Vt~VnfskNqL~elPk~L~----~lkelvT~l~lsnn~isf----v~~~l~~l~kLt~L~L~-------NN~Ln~LP~e  453 (565)
T KOG0472|consen  389 IVTSVNFSKNQLCELPKRLV----ELKELVTDLVLSNNKISF----VPLELSQLQKLTFLDLS-------NNLLNDLPEE  453 (565)
T ss_pred             ceEEEecccchHhhhhhhhH----HHHHHHHHHHhhcCcccc----chHHHHhhhcceeeecc-------cchhhhcchh
Confidence            36777777777777766554    5555544 4455555544    78889999999999998       9999999999


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCccC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      ++.+..|+.|+++.|+ ...+|..+..+.-|+++-.++|+ ++.+|+. +++|.+|.+|++.+|. +.++|+.+++|++|
T Consensus       454 ~~~lv~Lq~LnlS~Nr-Fr~lP~~~y~lq~lEtllas~nq-i~~vd~~~l~nm~nL~tLDL~nNd-lq~IPp~LgnmtnL  530 (565)
T KOG0472|consen  454 MGSLVRLQTLNLSFNR-FRMLPECLYELQTLETLLASNNQ-IGSVDPSGLKNMRNLTTLDLQNND-LQQIPPILGNMTNL  530 (565)
T ss_pred             hhhhhhhheecccccc-cccchHHHhhHHHHHHHHhcccc-ccccChHHhhhhhhcceeccCCCc-hhhCChhhccccce
Confidence            9999999999999998 88999988888888888778777 7877765 9999999999999887 78899999999999


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      ++|.+.
T Consensus       531 ~hLeL~  536 (565)
T KOG0472|consen  531 RHLELD  536 (565)
T ss_pred             eEEEec
Confidence            988764

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

Probab=99.05  E-value=3.8e-11  Score=117.37  Aligned_cols=147  Identities=23%  Similarity=0.265  Sum_probs=74.8

Q ss_pred             eeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcccc
Q 046115          331 ILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIE  410 (505)
Q Consensus       331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~  410 (505)
                      +..+.++.+.....|.++.    .-+++-+|+|++|++...   +.+.|-++..|-+|||+       ++.++.+|+.+.
T Consensus       105 Lt~lDLShNqL~EvP~~LE----~AKn~iVLNLS~N~IetI---Pn~lfinLtDLLfLDLS-------~NrLe~LPPQ~R  170 (1255)
T KOG0444|consen  105 LTILDLSHNQLREVPTNLE----YAKNSIVLNLSYNNIETI---PNSLFINLTDLLFLDLS-------NNRLEMLPPQIR  170 (1255)
T ss_pred             ceeeecchhhhhhcchhhh----hhcCcEEEEcccCccccC---CchHHHhhHhHhhhccc-------cchhhhcCHHHH
Confidence            3444444444444444443    445555666666654322   22234455556666665       555666666665


Q ss_pred             CCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcC-ccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          411 KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQN-LRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~-~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      .|.+|++|.|++|+..-.--.++-.+.+|++|.+++++. +..+|.++-.|.+|+.++++.|. +..+|..+.++.+|+.
T Consensus       171 RL~~LqtL~Ls~NPL~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~N~-Lp~vPecly~l~~Lrr  249 (1255)
T KOG0444|consen  171 RLSMLQTLKLSNNPLNHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDLHNLRDVDLSENN-LPIVPECLYKLRNLRR  249 (1255)
T ss_pred             HHhhhhhhhcCCChhhHHHHhcCccchhhhhhhcccccchhhcCCCchhhhhhhhhccccccC-CCcchHHHhhhhhhhe
Confidence            666666666665552110001111223333444443321 23456666666666666666665 5566666666666666


Q ss_pred             cce
Q 046115          490 VRE  492 (505)
Q Consensus       490 L~~  492 (505)
                      |++
T Consensus       250 LNL  252 (1255)
T KOG0444|consen  250 LNL  252 (1255)
T ss_pred             ecc
Confidence            664

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

Probab=99.01  E-value=3.9e-08  Score=92.59  Aligned_cols=173  Identities=17%  Similarity=0.134  Sum_probs=106.0

Q ss_pred             CCCCcHHHHHHHHhcCcccc-cCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHH----HHHHHHHHc-CCce
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-RNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQS----LMQHIEECV-AGKK   74 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~----~~~~l~~~l-~~~r   74 (505)
                      ++|+||||+++.+++  ... +.+ ..+|+ +....+..+++..++..++.+...  .+...    ..+.+.... .+++
T Consensus        51 ~~G~GKTtl~~~l~~--~l~~~~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~--~~~~~~~~~l~~~l~~~~~~~~~  124 (269)
T TIGR03015        51 EVGAGKTTLIRNLLK--RLDQERV-VAAKL-VNTRVDAEDLLRMVAADFGLETEG--RDKAALLRELEDFLIEQFAAGKR  124 (269)
T ss_pred             CCCCCHHHHHHHHHH--hcCCCCe-EEeee-eCCCCCHHHHHHHHHHHcCCCCCC--CCHHHHHHHHHHHHHHHHhCCCC
Confidence            479999999999998  333 211 12233 333456778888999888754332  22222    222333322 5678


Q ss_pred             EEEEEeCCCCCCccChhHHHHhhc---CCCCCcEEEEEeCchHHHHHh----------CCcceEeCCCCChhhHHHHHHH
Q 046115           75 FLLVLDDVWNEDYYKWEPFYKCLK---NSLHESKILITTRKETVARIM----------GSTHVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        75 ~LlvlDdv~~~~~~~~~~~~~~~~---~~~~~~~iLiTtr~~~~~~~~----------~~~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      .+||+|+++......++.+.....   .......|++|.... .....          .....+.+++++.+|..+++..
T Consensus       125 ~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~l~~  203 (269)
T TIGR03015       125 ALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLDREETREYIEH  203 (269)
T ss_pred             eEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHHHHH
Confidence            999999998866444554433221   112233455555432 21111          1133678999999999999977


Q ss_pred             hhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          142 LAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      .....+......-.++++..|++.++|.|..|+.++..+
T Consensus       204 ~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       204 RLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            653222111122345789999999999999999998876

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.00  E-value=1.3e-07  Score=94.25  Aligned_cols=278  Identities=13%  Similarity=0.078  Sum_probs=156.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC--CceEEEEeCCCCCHHHHHHHHHHHcCC-CCCCChhcHHHHHHHHHHHcC--CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEPFDEFRIARAIIESLTP-GSAKDLVEFQSLMQHIEECVA--GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f--~~~~wv~~~~~~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~l~~~l~--~~r~   75 (505)
                      ++|+|||++++.+++  +.....  -..+++++....+...++..++.++.. .......+.++..+.+.+.+.  +++.
T Consensus        63 ~~GtGKT~l~~~v~~--~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  140 (394)
T PRK00411         63 PPGTGKTTTVKKVFE--ELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVL  140 (394)
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEE
Confidence            479999999999998  444333  345678888778888999999999874 222223345666666666664  4578


Q ss_pred             EEEEeCCCCCC----ccChhHHHHhhcCCC-CCcEEEEEeCchHHHHHhC-------CcceEeCCCCChhhHHHHHHHhh
Q 046115           76 LLVLDDVWNED----YYKWEPFYKCLKNSL-HESKILITTRKETVARIMG-------STHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        76 LlvlDdv~~~~----~~~~~~~~~~~~~~~-~~~~iLiTtr~~~~~~~~~-------~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +||+|+++.-.    ...+..+...+.... ....+|.++.+........       ....+.+++++.++..+++...+
T Consensus       141 viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~  220 (394)
T PRK00411        141 IVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRV  220 (394)
T ss_pred             EEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHH
Confidence            99999996632    122333333322221 1233566665543322111       13467899999999999998765


Q ss_pred             hCCCCCCCCchHHHHHHHHHHH----cCCChHHHHHHHHHhc----cC---CCHHHHHHHHhhhhhhhhhcccCchhhHh
Q 046115          144 ISGKTIGKRENLEKIGREIVKK----CKGLPLAAKTIASLLR----SK---NTEKEWQNILENEIWELEAIEKGLLAPLL  212 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~----~~g~Plal~~~~~~l~----~~---~~~~~~~~~l~~~~~~l~~~~~~~~~~l~  212 (505)
                      ...-.  ...-.++++..+++.    .|..+.|+.++-....    +.   -+.+.....++..          ....+.
T Consensus       221 ~~~~~--~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~----------~~~~~~  288 (394)
T PRK00411        221 EEGFY--PGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS----------EIVHLS  288 (394)
T ss_pred             Hhhcc--cCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH----------HHHHHH
Confidence            32110  011112333444443    4557777776654321    11   1444444444432          112234


Q ss_pred             hccccCChhhhhhhhhhccCCC--CCCCChHHHHHHHH--HcCCCCCCCCCCHHHHHHHHHHHHHHccccccccc--CCC
Q 046115          213 LSYNELPSKVKRCFSYCAVFPK--DYGIRKHKLIELWM--AQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNK--YDD  286 (505)
Q Consensus       213 ~s~~~L~~~~~~~ll~la~f~~--~~~i~~~~l~~~w~--~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~--~~~  286 (505)
                      -.+..|+.+++..+..++....  ...+....+.....  +.....   .........++++.|...|++.....  +..
T Consensus       289 ~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~---~~~~~~~~~~~l~~L~~~glI~~~~~~~g~~  365 (394)
T PRK00411        289 EVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGY---EPRTHTRFYEYINKLDMLGIINTRYSGKGGR  365 (394)
T ss_pred             HHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCC---CcCcHHHHHHHHHHHHhcCCeEEEEecCCCC
Confidence            5678899988888877664432  12345555443221  111110   11123456779999999999986543  223


Q ss_pred             CCeeEeeeh
Q 046115          287 GEIYKCKMH  295 (505)
Q Consensus       287 ~~~~~~~~H  295 (505)
                      ++...+..+
T Consensus       366 g~~~~~~~~  374 (394)
T PRK00411        366 GRTRLISLS  374 (394)
T ss_pred             CCeEEEEec
Confidence            444445443

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

Probab=98.99  E-value=4.8e-10  Score=96.13  Aligned_cols=130  Identities=25%  Similarity=0.275  Sum_probs=58.1

Q ss_pred             CCCCceEEEecCCCccccccchhHHhh-cCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFE-KLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~-~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~  432 (505)
                      +...++.|++.+|.++....     +. .+.+|+.|+|+       ++.+..++ .+..+++|+.|++++|. ++.++..
T Consensus        17 n~~~~~~L~L~~n~I~~Ie~-----L~~~l~~L~~L~Ls-------~N~I~~l~-~l~~L~~L~~L~L~~N~-I~~i~~~   82 (175)
T PF14580_consen   17 NPVKLRELNLRGNQISTIEN-----LGATLDKLEVLDLS-------NNQITKLE-GLPGLPRLKTLDLSNNR-ISSISEG   82 (175)
T ss_dssp             -------------------S-------TT-TT--EEE-T-------TS--S--T-T----TT--EEE--SS----S-CHH
T ss_pred             cccccccccccccccccccc-----hhhhhcCCCEEECC-------CCCCcccc-CccChhhhhhcccCCCC-CCccccc
Confidence            56678999999998765322     44 57899999999       88888886 47889999999999999 8888655


Q ss_pred             h-hcCCCCcEEecCCCcCccccch--hccccccCceeecCCCcccccccc----cccCCccCCccceeEecCcC
Q 046115          433 L-CELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCLRYLPA----GIGELIRLRRVREFVVGGGY  499 (505)
Q Consensus       433 ~-~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~~p~----~i~~l~~L~~L~~~~~~~~~  499 (505)
                      + ..+++|+.|.+++|. +..+-.  .+..+++|++|++.+|+.. ..+.    .|..+++|+.|+...|...-
T Consensus        83 l~~~lp~L~~L~L~~N~-I~~l~~l~~L~~l~~L~~L~L~~NPv~-~~~~YR~~vi~~lP~Lk~LD~~~V~~~E  154 (175)
T PF14580_consen   83 LDKNLPNLQELYLSNNK-ISDLNELEPLSSLPKLRVLSLEGNPVC-EKKNYRLFVIYKLPSLKVLDGQDVTEEE  154 (175)
T ss_dssp             HHHH-TT--EEE-TTS----SCCCCGGGGG-TT--EEE-TT-GGG-GSTTHHHHHHHH-TT-SEETTEETTS-B
T ss_pred             hHHhCCcCCEEECcCCc-CCChHHhHHHHcCCCcceeeccCCccc-chhhHHHHHHHHcChhheeCCEEccHHH
Confidence            5 469999999999998 666543  4788999999999999854 3333    36889999999999888743

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

Probab=98.97  E-value=3.2e-11  Score=117.94  Aligned_cols=147  Identities=24%  Similarity=0.300  Sum_probs=116.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .++.+.++.+....+|.-+.    ++.+|+.|+|++|+++...    -..+.+.+|+.|+|+       .+.+..+|..+
T Consensus       223 NL~dvDlS~N~Lp~vPecly----~l~~LrrLNLS~N~iteL~----~~~~~W~~lEtLNlS-------rNQLt~LP~av  287 (1255)
T KOG0444|consen  223 NLRDVDLSENNLPIVPECLY----KLRNLRRLNLSGNKITELN----MTEGEWENLETLNLS-------RNQLTVLPDAV  287 (1255)
T ss_pred             hhhhccccccCCCcchHHHh----hhhhhheeccCcCceeeee----ccHHHHhhhhhhccc-------cchhccchHHH
Confidence            56666667776666665554    7788888888888776542    224567778888887       77888889889


Q ss_pred             cCCCCcceeeccCCcc-ccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          410 EKLLHLKYLNLKGQKK-IEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~-~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      ++|+.|+.|.+.+|+. ...+|+.|++|.+|+.+...+|. ++-+|+++..+++|+.|.++.|. +-.+|..|.-++.|.
T Consensus       288 cKL~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aanN~-LElVPEglcRC~kL~kL~L~~Nr-LiTLPeaIHlL~~l~  365 (1255)
T KOG0444|consen  288 CKLTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAANNK-LELVPEGLCRCVKLQKLKLDHNR-LITLPEAIHLLPDLK  365 (1255)
T ss_pred             hhhHHHHHHHhccCcccccCCccchhhhhhhHHHHhhccc-cccCchhhhhhHHHHHhcccccc-eeechhhhhhcCCcc
Confidence            9999999999888884 34788899999999999888887 89999999999999999999887 567898888888888


Q ss_pred             cccee
Q 046115          489 RVREF  493 (505)
Q Consensus       489 ~L~~~  493 (505)
                      .|++.
T Consensus       366 vLDlr  370 (1255)
T KOG0444|consen  366 VLDLR  370 (1255)
T ss_pred             eeecc
Confidence            88765

>PLN03210 Resistant to P

Probab=98.91  E-value=4.6e-09  Score=117.90  Aligned_cols=133  Identities=27%  Similarity=0.383  Sum_probs=102.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      +++.+.+..+....+|..+     .+.+|+.|.+.++.+..    +|..+..+.+|+.|+|+      .++.++.+|. +
T Consensus       590 ~Lr~L~~~~~~l~~lP~~f-----~~~~L~~L~L~~s~l~~----L~~~~~~l~~Lk~L~Ls------~~~~l~~ip~-l  653 (1153)
T PLN03210        590 KLRLLRWDKYPLRCMPSNF-----RPENLVKLQMQGSKLEK----LWDGVHSLTGLRNIDLR------GSKNLKEIPD-L  653 (1153)
T ss_pred             ccEEEEecCCCCCCCCCcC-----CccCCcEEECcCccccc----cccccccCCCCCEEECC------CCCCcCcCCc-c
Confidence            3455555555555555444     46789999999987653    55556788999999998      3555677774 7


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPA  479 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~  479 (505)
                      +.+++|+.|++++|..+..+|..++.+++|+.|++++|..+..+|..+ ++++|++|++++|..+..+|.
T Consensus       654 s~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i-~l~sL~~L~Lsgc~~L~~~p~  722 (1153)
T PLN03210        654 SMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGI-NLKSLYRLNLSGCSRLKSFPD  722 (1153)
T ss_pred             ccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcC-CCCCCCEEeCCCCCCcccccc
Confidence            888999999999998888999989999999999999998888998876 688888888888876666654

syringae 6; Provisional

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.85  E-value=1.1e-06  Score=86.68  Aligned_cols=269  Identities=12%  Similarity=0.072  Sum_probs=146.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC------CceEEEEeCCCCCHHHHHHHHHHHcC---CCCCCChhcHHHHHHHHHHHc-
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF------EKRTWVCVSEPFDEFRIARAIIESLT---PGSAKDLVEFQSLMQHIEECV-   70 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f------~~~~wv~~~~~~~~~~~~~~l~~~l~---~~~~~~~~~~~~~~~~l~~~l-   70 (505)
                      ++|+|||++++.+++  +.....      -..+|+++....+...++..++.++.   ........+.++....+...+ 
T Consensus        48 ~~GtGKT~l~~~~~~--~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~  125 (365)
T TIGR02928        48 KTGTGKTAVTKYVMK--ELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELN  125 (365)
T ss_pred             CCCCCHHHHHHHHHH--HHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHH
Confidence            589999999999997  332221      13568888887788889999999883   222222233445555555555 


Q ss_pred             -CCceEEEEEeCCCCCC---ccChhHHHHhh--cCC-CCCcEEEEEeCchHHHHHh----C-C--cceEeCCCCChhhHH
Q 046115           71 -AGKKFLLVLDDVWNED---YYKWEPFYKCL--KNS-LHESKILITTRKETVARIM----G-S--THVISVNVLSEMECW  136 (505)
Q Consensus        71 -~~~r~LlvlDdv~~~~---~~~~~~~~~~~--~~~-~~~~~iLiTtr~~~~~~~~----~-~--~~~~~l~~l~~~ea~  136 (505)
                       .+++++||||+++.-.   ...+..+....  ... +....++.+++........    . .  ...+.+++.+.++..
T Consensus       126 ~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~  205 (365)
T TIGR02928       126 ERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELR  205 (365)
T ss_pred             hcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHH
Confidence             3568899999996642   11122222211  111 1334455555544332211    1 1  246889999999999


Q ss_pred             HHHHHhhhCC-CCCCCCchHHHHHHHHHHHcCCChH-HHHHHHHHh----ccC---CCHHHHHHHHhhhhhhhhhcccCc
Q 046115          137 SVFQSLAISG-KTIGKRENLEKIGREIVKKCKGLPL-AAKTIASLL----RSK---NTEKEWQNILENEIWELEAIEKGL  207 (505)
Q Consensus       137 ~Lf~~~~~~~-~~~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~~l----~~~---~~~~~~~~~l~~~~~~l~~~~~~~  207 (505)
                      +++...+... ....-.++..+.+..++....|.|- |+.++-...    ..+   -+.+.....++..          -
T Consensus       206 ~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~----------~  275 (365)
T TIGR02928       206 DILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI----------E  275 (365)
T ss_pred             HHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH----------H
Confidence            9998776311 1111122333445566777778884 333322211    111   1333333333321          0


Q ss_pred             hhhHhhccccCChhhhhhhhhhccCC--CCCCCChHHHHHHHHHc-CCCCCCCCCCHHHHHHHHHHHHHHccccccccc
Q 046115          208 LAPLLLSYNELPSKVKRCFSYCAVFP--KDYGIRKHKLIELWMAQ-GYLSEKGAKEMEDIGEEYFNILASRSFFQDFNK  283 (505)
Q Consensus       208 ~~~l~~s~~~L~~~~~~~ll~la~f~--~~~~i~~~~l~~~w~~~-~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~  283 (505)
                      .....-.+..|+.+++.++..++...  .+..+....+...+... ..+.  ........+.++++.|...|++.....
T Consensus       276 ~~~~~~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~~--~~~~~~~~~~~~l~~l~~~gli~~~~~  352 (365)
T TIGR02928       276 KDRLLELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDIG--VDPLTQRRISDLLNELDMLGLVEAEER  352 (365)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhcC--CCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence            12233466788888877766655322  22335555554422211 1111  112334667888999999999987543

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.

>PF05729 NACHT: NACHT domain

Probab=98.82  E-value=2.6e-08  Score=86.32  Aligned_cols=135  Identities=19%  Similarity=0.241  Sum_probs=81.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccC------CCceEEEEeCCCCCHH---HHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN------FEKRTWVCVSEPFDEF---RIARAIIESLTPGSAKDLVEFQSLMQHIEECVA   71 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~------f~~~~wv~~~~~~~~~---~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~   71 (505)
                      .+|+||||+++.++..  ....      +...+|++.+......   .+...+..+... ..   ........  .....
T Consensus         8 ~~G~GKStll~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-~~---~~~~~~~~--~~~~~   79 (166)
T PF05729_consen    8 EPGSGKSTLLRKLAQQ--LAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPE-SI---APIEELLQ--ELLEK   79 (166)
T ss_pred             CCCCChHHHHHHHHHH--HHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhcc-ch---hhhHHHHH--HHHHc
Confidence            3899999999999873  3222      3456677766544332   333444344331 11   11111111  11225


Q ss_pred             CceEEEEEeCCCCCCcc-------ChhHHHHhhcC--CCCCcEEEEEeCchHH---HHHhCCcceEeCCCCChhhHHHHH
Q 046115           72 GKKFLLVLDDVWNEDYY-------KWEPFYKCLKN--SLHESKILITTRKETV---ARIMGSTHVISVNVLSEMECWSVF  139 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~-------~~~~~~~~~~~--~~~~~~iLiTtr~~~~---~~~~~~~~~~~l~~l~~~ea~~Lf  139 (505)
                      .++++||+|+++.-...       .+..+...+..  ..++++++||+|....   .........+++.+|++++..+++
T Consensus        80 ~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  159 (166)
T PF05729_consen   80 NKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYL  159 (166)
T ss_pred             CCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHH
Confidence            68999999999553321       12233333333  2568999999999665   333344568999999999999999


Q ss_pred             HHhh
Q 046115          140 QSLA  143 (505)
Q Consensus       140 ~~~~  143 (505)
                      .++.
T Consensus       160 ~~~f  163 (166)
T PF05729_consen  160 RKYF  163 (166)
T ss_pred             HHHh
Confidence            7653

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

Probab=98.76  E-value=4e-10  Score=104.80  Aligned_cols=119  Identities=29%  Similarity=0.539  Sum_probs=92.4

Q ss_pred             ccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcccc-CCCCcceeeccCCcc
Q 046115          347 SIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIE-KLLHLKYLNLKGQKK  425 (505)
Q Consensus       347 ~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~-~l~~L~~L~l~~~~~  425 (505)
                      .+|+++++|..|..|++..|++..    +|+ |..+..|..|++.       .+.++.+|...+ .+.++..||++.|+ 
T Consensus       197 tlP~~lg~l~~L~~LyL~~Nki~~----lPe-f~gcs~L~Elh~g-------~N~i~~lpae~~~~L~~l~vLDLRdNk-  263 (565)
T KOG0472|consen  197 TLPPELGGLESLELLYLRRNKIRF----LPE-FPGCSLLKELHVG-------ENQIEMLPAEHLKHLNSLLVLDLRDNK-  263 (565)
T ss_pred             cCChhhcchhhhHHHHhhhccccc----CCC-CCccHHHHHHHhc-------ccHHHhhHHHHhcccccceeeeccccc-
Confidence            345556688888888888888754    553 6777888888887       777888887766 78888888888888 


Q ss_pred             ccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccc
Q 046115          426 IEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGI  481 (505)
Q Consensus       426 ~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i  481 (505)
                      ++++|..++.+++|+.||+|+|. +..+|.+++++ .|+.|-+.||+ +..+-+.|
T Consensus       264 lke~Pde~clLrsL~rLDlSNN~-is~Lp~sLgnl-hL~~L~leGNP-lrTiRr~i  316 (565)
T KOG0472|consen  264 LKEVPDEICLLRSLERLDLSNND-ISSLPYSLGNL-HLKFLALEGNP-LRTIRREI  316 (565)
T ss_pred             cccCchHHHHhhhhhhhcccCCc-cccCCcccccc-eeeehhhcCCc-hHHHHHHH
Confidence            88888888888888888888888 88888888888 78888888887 33343333

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=98.75  E-value=1.5e-09  Score=105.61  Aligned_cols=126  Identities=21%  Similarity=0.278  Sum_probs=55.8

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceeeccCCccccccch-
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLPE-  431 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp~-  431 (505)
                      +++.|+.|+++.|.+..+   .++.+.-..+|.+|+|+       ++.+..+++ .+..|..|+.|+|+.|. +..+.. 
T Consensus       291 gLt~L~~L~lS~NaI~ri---h~d~WsftqkL~~LdLs-------~N~i~~l~~~sf~~L~~Le~LnLs~Ns-i~~l~e~  359 (873)
T KOG4194|consen  291 GLTSLEQLDLSYNAIQRI---HIDSWSFTQKLKELDLS-------SNRITRLDEGSFRVLSQLEELNLSHNS-IDHLAEG  359 (873)
T ss_pred             ccchhhhhccchhhhhee---ecchhhhcccceeEecc-------ccccccCChhHHHHHHHhhhhcccccc-hHHHHhh
Confidence            555555555555554433   23334444455555555       444444432 23344444444444444 333322 


Q ss_pred             hhhcCCCCcEEecCCCcCccccch---hccccccCceeecCCCcccccccc-cccCCccCCccc
Q 046115          432 TLCELYNLERLNVDDCQNLRELPR---GIGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVR  491 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~lp~---~~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~  491 (505)
                      .+..+.+|+.|||++|.....+.+   .+..|++|+.|++.||+ +.++|. .|..+++|++|+
T Consensus       360 af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~l~gNq-lk~I~krAfsgl~~LE~Ld  422 (873)
T KOG4194|consen  360 AFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLRLTGNQ-LKSIPKRAFSGLEALEHLD  422 (873)
T ss_pred             HHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhheeecCce-eeecchhhhccCcccceec
Confidence            233444444444444443333322   13344444444444444 233332 244444444444

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.70  E-value=5.2e-08  Score=92.15  Aligned_cols=286  Identities=19%  Similarity=0.163  Sum_probs=185.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .|||||||++-.+..   +...|. +++++++....+.......+...++.+..+.....    ..+.....++|.++|+
T Consensus        22 ~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~g~~~~----~~~~~~~~~rr~llvl   94 (414)
T COG3903          22 AGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQPGDSAV----DTLVRRIGDRRALLVL   94 (414)
T ss_pred             cCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhcccccccchHHH----HHHHHHHhhhhHHHHh
Confidence            489999999988886   556675 45567777777777777777777876655433333    3455566788999999


Q ss_pred             eCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCcceEeCCCCChh-hHHHHHHHhhhCCCC-CCCCchHHH
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEM-ECWSVFQSLAISGKT-IGKRENLEK  157 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~~~~~l~~l~~~-ea~~Lf~~~~~~~~~-~~~~~~~~~  157 (505)
                      ||...-- ..-......+......-.++.|+|+....   .....+.++.++.. ++.++|...+.-... ..-......
T Consensus        95 dncehl~-~~~a~~i~all~~~~~~~~~atsre~~l~---~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~a  170 (414)
T COG3903          95 DNCEHLL-DACAALIVALLGACPRLAILATSREAILV---AGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLTDDNAA  170 (414)
T ss_pred             cCcHHHH-HHHHHHHHHHHccchhhhhHHHhHhhhcc---cccccccCCccccCCchhHHHHHHHHHhccceeecCCchH
Confidence            9984322 13334455566666667799999976543   34556777777766 788888655422111 122233456


Q ss_pred             HHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhhc-------ccCchhhHhhccccCChhhhhhhhhhc
Q 046115          158 IGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAI-------EKGLLAPLLLSYNELPSKVKRCFSYCA  230 (505)
Q Consensus       158 ~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~-------~~~~~~~l~~s~~~L~~~~~~~ll~la  230 (505)
                      .+..|++..+|.|++|..+++..+.-. ...-...+......+...       +......+..||.-|....+-.+..++
T Consensus       171 ~v~~icr~ldg~~laielaaarv~sl~-~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe~~~~~rLa  249 (414)
T COG3903         171 AVAEICRRLDGIPLAIELAAARVRSLS-PDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWERALFGRLA  249 (414)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcC-HHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHHHHHhcchh
Confidence            789999999999999999999887653 333333333322222222       246777899999999999999999999


Q ss_pred             cCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehHHHHHHHHHhhccc
Q 046115          231 VFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDFAQYLCSNE  309 (505)
Q Consensus       231 ~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~lv~~~~~~~~~~~  309 (505)
                      .|...+......    |.+.+-..    ....-.....+..+++.+++.-.....   ...|+.-+.++.|+..+..+.
T Consensus       250 ~~~g~f~~~l~~----~~a~g~~~----~~~~y~~~~a~~ll~~kslv~a~~~~~---~a~~Rl~eT~r~YalaeL~r~  317 (414)
T COG3903         250 VFVGGFDLGLAL----AVAAGADV----DVPRYLVLLALTLLVDKSLVVALDLLG---RARYRLLETGRRYALAELHRS  317 (414)
T ss_pred             hhhhhhcccHHH----HHhcCCcc----ccchHHHHHHHHHHhhccchhhhhhhh---HHHHHHHHHHHHHHHHHHHhh
Confidence            998866554322    22221111    011223444567788888875433221   114777788888887766543

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

Probab=98.70  E-value=1.8e-09  Score=104.92  Aligned_cols=123  Identities=29%  Similarity=0.418  Sum_probs=87.6

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .+..|+.|+++.|+++-    +|..++.+ -|++|-++       ++.++.+|..++.+.+|..|+.+.|. +..+|+++
T Consensus       119 ~L~~lt~l~ls~NqlS~----lp~~lC~l-pLkvli~s-------NNkl~~lp~~ig~~~tl~~ld~s~ne-i~slpsql  185 (722)
T KOG0532|consen  119 NLEALTFLDLSSNQLSH----LPDGLCDL-PLKVLIVS-------NNKLTSLPEEIGLLPTLAHLDVSKNE-IQSLPSQL  185 (722)
T ss_pred             hhhHHHHhhhccchhhc----CChhhhcC-cceeEEEe-------cCccccCCcccccchhHHHhhhhhhh-hhhchHHh
Confidence            66777777777777654    44434433 46777777       77777777777777777777777777 77777777


Q ss_pred             hcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          434 CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      +.+.+|+.|+++.|+ +..+|+++..|+ |..|+++.|+ +..+|-.|.+|..|++|.+
T Consensus       186 ~~l~slr~l~vrRn~-l~~lp~El~~Lp-Li~lDfScNk-is~iPv~fr~m~~Lq~l~L  241 (722)
T KOG0532|consen  186 GYLTSLRDLNVRRNH-LEDLPEELCSLP-LIRLDFSCNK-ISYLPVDFRKMRHLQVLQL  241 (722)
T ss_pred             hhHHHHHHHHHhhhh-hhhCCHHHhCCc-eeeeecccCc-eeecchhhhhhhhheeeee
Confidence            777777777777777 777777776554 7777777776 5677777777777777654

>PLN03150 hypothetical protein; Provisional

Probab=98.67  E-value=5.3e-08  Score=102.00  Aligned_cols=113  Identities=21%  Similarity=0.285  Sum_probs=90.0

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcC
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCEL  436 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l  436 (505)
                      .++.|.|.+|.+.+.   +|..+..+.+|+.|+|+      ++...+.+|..++.+++|++|+|++|...+.+|..++++
T Consensus       419 ~v~~L~L~~n~L~g~---ip~~i~~L~~L~~L~Ls------~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L  489 (623)
T PLN03150        419 FIDGLGLDNQGLRGF---IPNDISKLRHLQSINLS------GNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQL  489 (623)
T ss_pred             EEEEEECCCCCcccc---CCHHHhCCCCCCEEECC------CCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcC
Confidence            477888888887654   77778889999999998      344456788888899999999999998667888888999


Q ss_pred             CCCcEEecCCCcCccccchhcccc-ccCceeecCCCccccccc
Q 046115          437 YNLERLNVDDCQNLRELPRGIGKL-RKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~~~~l-~~L~~L~l~~~~~~~~~p  478 (505)
                      ++|+.|+|++|.....+|..++.+ .++..+++.+|..+...|
T Consensus       490 ~~L~~L~Ls~N~l~g~iP~~l~~~~~~~~~l~~~~N~~lc~~p  532 (623)
T PLN03150        490 TSLRILNLNGNSLSGRVPAALGGRLLHRASFNFTDNAGLCGIP  532 (623)
T ss_pred             CCCCEEECcCCcccccCChHHhhccccCceEEecCCccccCCC
Confidence            999999999988777888887654 467788888887555443

>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=98.58  E-value=3.3e-07  Score=84.24  Aligned_cols=169  Identities=19%  Similarity=0.130  Sum_probs=81.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHH-------------HHHHcCCCCC-----CChhcHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARA-------------IIESLTPGSA-----KDLVEFQSL   62 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~-------------l~~~l~~~~~-----~~~~~~~~~   62 (505)
                      +.|+|||+|++++.+  .....-..++|+...+..........             +...+.....     .........
T Consensus        28 ~rg~GKTsLl~~~~~--~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (234)
T PF01637_consen   28 PRGSGKTSLLKEFIN--ELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLSEDSFSA  105 (234)
T ss_dssp             STTSSHHHHHHHHHH--HCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--
T ss_pred             CCcCCHHHHHHHHHH--HhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcchhhHHHH
Confidence            479999999999998  45332224555555444322211111             1111111000     111222333


Q ss_pred             HHHHHHHcC--CceEEEEEeCCCCCC------ccChhHHHHhhcC---CCCCcEEEEEeCchHHHHH--------hCCcc
Q 046115           63 MQHIEECVA--GKKFLLVLDDVWNED------YYKWEPFYKCLKN---SLHESKILITTRKETVARI--------MGSTH  123 (505)
Q Consensus        63 ~~~l~~~l~--~~r~LlvlDdv~~~~------~~~~~~~~~~~~~---~~~~~~iLiTtr~~~~~~~--------~~~~~  123 (505)
                      ...+.+.+.  +++++||+|++....      ..-...+...+..   ..+.+.| ++.....+...        .+...
T Consensus       106 l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v-~~~S~~~~~~~~~~~~~~~~~~~~  184 (234)
T PF01637_consen  106 LERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIV-ITGSSDSLMEEFLDDKSPLFGRFS  184 (234)
T ss_dssp             HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEE-EEESSHHHHHHTT-TTSTTTT---
T ss_pred             HHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEE-EECCchHHHHHhhcccCccccccc
Confidence            333333332  345999999996544      1111223333333   3344444 44444433322        23344


Q ss_pred             eEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          124 VISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       124 ~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                      .+.+++|+.+++++++.......  ..- +..++...+|++.+||+|..|..
T Consensus       185 ~~~l~~l~~~e~~~~~~~~~~~~--~~~-~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  185 HIELKPLSKEEAREFLKELFKEL--IKL-PFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             EEEE----HHHHHHHHHHHHHCC---------HHHHHHHHHHHTT-HHHHHH
T ss_pred             eEEEeeCCHHHHHHHHHHHHHHh--hcc-cCCHHHHHHHHHHhCCCHHHHhc
Confidence            69999999999999998865332  111 22356679999999999988764

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

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

Probab=98.56  E-value=8.9e-08  Score=82.20  Aligned_cols=123  Identities=27%  Similarity=0.273  Sum_probs=54.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      +.+.+.+..+.+..+..-..    .+.+|+.|++++|.++....     +..++.|+.|+++       ++.+..++..+
T Consensus        20 ~~~~L~L~~n~I~~Ie~L~~----~l~~L~~L~Ls~N~I~~l~~-----l~~L~~L~~L~L~-------~N~I~~i~~~l   83 (175)
T PF14580_consen   20 KLRELNLRGNQISTIENLGA----TLDKLEVLDLSNNQITKLEG-----LPGLPRLKTLDLS-------NNRISSISEGL   83 (175)
T ss_dssp             ----------------S--T----T-TT--EEE-TTS--S--TT---------TT--EEE---------SS---S-CHHH
T ss_pred             ccccccccccccccccchhh----hhcCCCEEECCCCCCccccC-----ccChhhhhhcccC-------CCCCCccccch
Confidence            44666777776665432111    47899999999999876432     6678999999999       88888886655


Q ss_pred             -cCCCCcceeeccCCccccccc--hhhhcCCCCcEEecCCCcCccccchh----ccccccCceeecCC
Q 046115          410 -EKLLHLKYLNLKGQKKIEKLP--ETLCELYNLERLNVDDCQNLRELPRG----IGKLRKLMYLHNED  470 (505)
Q Consensus       410 -~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~lp~~----~~~l~~L~~L~l~~  470 (505)
                       ..+++|+.|++++|+ +..+.  ..++.+++|+.|++.+|+ +...+.+    +..+|+|+.||-..
T Consensus        84 ~~~lp~L~~L~L~~N~-I~~l~~l~~L~~l~~L~~L~L~~NP-v~~~~~YR~~vi~~lP~Lk~LD~~~  149 (175)
T PF14580_consen   84 DKNLPNLQELYLSNNK-ISDLNELEPLSSLPKLRVLSLEGNP-VCEKKNYRLFVIYKLPSLKVLDGQD  149 (175)
T ss_dssp             HHH-TT--EEE-TTS----SCCCCGGGGG-TT--EEE-TT-G-GGGSTTHHHHHHHH-TT-SEETTEE
T ss_pred             HHhCCcCCEEECcCCc-CCChHHhHHHHcCCCcceeeccCCc-ccchhhHHHHHHHHcChhheeCCEE
Confidence             468999999999998 54432  247889999999999999 6655653    78899999998543

>PLN03150 hypothetical protein; Provisional

Probab=98.55  E-value=1.1e-07  Score=99.72  Aligned_cols=94  Identities=28%  Similarity=0.420  Sum_probs=83.7

Q ss_pred             cceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCc
Q 046115          385 LRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLM  464 (505)
Q Consensus       385 L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~  464 (505)
                      ++.|+|.      ++...+.+|..++.+++|+.|+|++|...+.+|..++.+++|+.|+|++|.....+|..++++++|+
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~  493 (623)
T PLN03150        420 IDGLGLD------NQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLR  493 (623)
T ss_pred             EEEEECC------CCCccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCC
Confidence            6778887      4555567899999999999999999996679999999999999999999997779999999999999


Q ss_pred             eeecCCCcccccccccccCC
Q 046115          465 YLHNEDTGCLRYLPAGIGEL  484 (505)
Q Consensus       465 ~L~l~~~~~~~~~p~~i~~l  484 (505)
                      +|++++|.+.+.+|..++.+
T Consensus       494 ~L~Ls~N~l~g~iP~~l~~~  513 (623)
T PLN03150        494 ILNLNGNSLSGRVPAALGGR  513 (623)
T ss_pred             EEECcCCcccccCChHHhhc
Confidence            99999999889999887653

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

Probab=98.54  E-value=2.9e-06  Score=80.03  Aligned_cols=143  Identities=17%  Similarity=0.265  Sum_probs=87.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHH-HHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIE-ECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~-~~l~~~r~Llvl   79 (505)
                      ++|+||||||+.++.  .....|     ..++...+-                  ..+..+..+.-+ ....+++.+|++
T Consensus        56 PPG~GKTTlA~liA~--~~~~~f-----~~~sAv~~g------------------vkdlr~i~e~a~~~~~~gr~tiLfl  110 (436)
T COG2256          56 PPGTGKTTLARLIAG--TTNAAF-----EALSAVTSG------------------VKDLREIIEEARKNRLLGRRTILFL  110 (436)
T ss_pred             CCCCCHHHHHHHHHH--hhCCce-----EEecccccc------------------HHHHHHHHHHHHHHHhcCCceEEEE
Confidence            589999999999998  555554     333322222                  222333333332 233478999999


Q ss_pred             eCCCCCCccChhHHHHhhcCCCCCcEEEE--EeCchHHH---HHhCCcceEeCCCCChhhHHHHHHHhhhCC-CCCC--C
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSLHESKILI--TTRKETVA---RIMGSTHVISVNVLSEMECWSVFQSLAISG-KTIG--K  151 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~~~~~iLi--Ttr~~~~~---~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~-~~~~--~  151 (505)
                      |.|.+-...+-+.++..+.   +|.-|+|  ||.++...   .......++.+++|+.+|..+++.+..... ....  .
T Consensus       111 DEIHRfnK~QQD~lLp~vE---~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~  187 (436)
T COG2256         111 DEIHRFNKAQQDALLPHVE---NGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQI  187 (436)
T ss_pred             ehhhhcChhhhhhhhhhhc---CCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCccc
Confidence            9998866545455544443   5666666  77775321   112345699999999999999998843222 2211  0


Q ss_pred             CchHHHHHHHHHHHcCCChH
Q 046115          152 RENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       152 ~~~~~~~~~~i~~~~~g~Pl  171 (505)
                      ..-.+++...++..++|---
T Consensus       188 ~~i~~~a~~~l~~~s~GD~R  207 (436)
T COG2256         188 IVLDEEALDYLVRLSNGDAR  207 (436)
T ss_pred             ccCCHHHHHHHHHhcCchHH
Confidence            11234577788888888664

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.53  E-value=8.3e-06  Score=78.26  Aligned_cols=234  Identities=17%  Similarity=0.144  Sum_probs=123.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcH----HHHHHHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEF----QSLMQHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~----~~~~~~l~~~l~~~r~L   76 (505)
                      ++|+|||+||+.+++  +....+   ..+... .......+...+..+....---.++.    ....+.+...+.+.+..
T Consensus        38 p~G~GKT~la~~ia~--~~~~~~---~~~~~~-~~~~~~~l~~~l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~  111 (305)
T TIGR00635        38 PPGLGKTTLAHIIAN--EMGVNL---KITSGP-ALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLD  111 (305)
T ss_pred             CCCCCHHHHHHHHHH--HhCCCE---EEeccc-hhcCchhHHHHHHhcccCCEEEEehHhhhCHHHHHHhhHHHhhhhee
Confidence            589999999999998  443332   112111 11111222233333332210000000    11223344455555566


Q ss_pred             EEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHh-CC-cceEeCCCCChhhHHHHHHHhhhCCCCCCCCch
Q 046115           77 LVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIM-GS-THVISVNVLSEMECWSVFQSLAISGKTIGKREN  154 (505)
Q Consensus        77 lvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~-~~-~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~  154 (505)
                      +|+|+......  +   .   ....+.+-|..||+...+.... .. ...+.+++++.+|..+++...+...+.    .-
T Consensus       112 ~v~~~~~~~~~--~---~---~~~~~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~----~~  179 (305)
T TIGR00635       112 IVIGKGPSARS--V---R---LDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNV----EI  179 (305)
T ss_pred             eeeccCccccc--e---e---ecCCCeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCC----Cc
Confidence            66666543321  0   0   0112356677777765443322 11 346789999999999999887753322    22


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHhcc------CC--CHHHHHHHHhhhhhhhhhcccCchhhHhhccccCChhhhhhh
Q 046115          155 LEKIGREIVKKCKGLPLAAKTIASLLRS------KN--TEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCF  226 (505)
Q Consensus       155 ~~~~~~~i~~~~~g~Plal~~~~~~l~~------~~--~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~L~~~~~~~l  226 (505)
                      .++++..|++.|+|.|-.+..++..+..      ..  +.+.....               ...+...+..+++..+.++
T Consensus       180 ~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~---------------l~~l~~~~~~l~~~~~~~L  244 (305)
T TIGR00635       180 EPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKA---------------LEMLMIDELGLDEIDRKLL  244 (305)
T ss_pred             CHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHH---------------HHHhCCCCCCCCHHHHHHH
Confidence            3567889999999999766555543310      00  11111111               1114556788888888877


Q ss_pred             hhh-ccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHH-HHHHccccc
Q 046115          227 SYC-AVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFN-ILASRSFFQ  279 (505)
Q Consensus       227 l~l-a~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~-~L~~~~Ll~  279 (505)
                      ..+ +.+..+ .+....+....   |.        ....+..+++ .|++.+++.
T Consensus       245 ~al~~~~~~~-~~~~~~ia~~l---g~--------~~~~~~~~~e~~Li~~~li~  287 (305)
T TIGR00635       245 SVLIEQFQGG-PVGLKTLAAAL---GE--------DADTIEDVYEPYLLQIGFLQ  287 (305)
T ss_pred             HHHHHHhCCC-cccHHHHHHHh---CC--------CcchHHHhhhHHHHHcCCcc
Confidence            734 555433 45444433322   11        1234666678 699999996

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=98.53  E-value=1e-06  Score=80.33  Aligned_cols=148  Identities=16%  Similarity=0.141  Sum_probs=90.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||.||..+++  +...+...+.|++......   ...                      ...+.+. +.-+||+|
T Consensus        47 ~~G~GKThL~~ai~~--~~~~~~~~~~y~~~~~~~~---~~~----------------------~~~~~~~-~~dlLilD   98 (229)
T PRK06893         47 GKSSGKSHLLKAVSN--HYLLNQRTAIYIPLSKSQY---FSP----------------------AVLENLE-QQDLVCLD   98 (229)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCCeEEeeHHHhhh---hhH----------------------HHHhhcc-cCCEEEEe
Confidence            479999999999998  5554555667887642100   000                      1111222 23489999


Q ss_pred             CCCCCC-ccChh-HHHHhhcCC-CCCcEEEE-EeCc---------hHHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           81 DVWNED-YYKWE-PFYKCLKNS-LHESKILI-TTRK---------ETVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        81 dv~~~~-~~~~~-~~~~~~~~~-~~~~~iLi-Ttr~---------~~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      |++... ...|+ .+...+... ..+..++| |++.         +.+...+.....+++++++.++.++++++.+...+
T Consensus        99 Di~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~  178 (229)
T PRK06893         99 DLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRG  178 (229)
T ss_pred             ChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcC
Confidence            997642 22343 233333322 23455654 4443         34455555566899999999999999998876443


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      . .   -.++++..|++.+.|..-.+..+-..+
T Consensus       179 l-~---l~~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        179 I-E---LSDEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             C-C---CCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            2 1   224677889999988776665555444

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.52  E-value=2e-06  Score=83.18  Aligned_cols=242  Identities=17%  Similarity=0.142  Sum_probs=125.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHH----HHHHHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ----SLMQHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~----~~~~~l~~~l~~~r~L   76 (505)
                      ++|+|||+||+.+++  +....+   .++. +........+..++..+.....--.++.+    ...+.+...+.+.+..
T Consensus        59 ppG~GKT~la~~ia~--~l~~~~---~~~~-~~~~~~~~~l~~~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~  132 (328)
T PRK00080         59 PPGLGKTTLANIIAN--EMGVNI---RITS-GPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLD  132 (328)
T ss_pred             CCCccHHHHHHHHHH--HhCCCe---EEEe-cccccChHHHHHHHHhcccCCEEEEecHhhcchHHHHHHHHHHHhccee
Confidence            589999999999998  444332   1222 11122222333444444322110001111    1122334444455555


Q ss_pred             EEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhC-C-cceEeCCCCChhhHHHHHHHhhhCCCCCCCCch
Q 046115           77 LVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG-S-THVISVNVLSEMECWSVFQSLAISGKTIGKREN  154 (505)
Q Consensus        77 lvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~-~-~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~  154 (505)
                      +++|+..+....     ...+   .+.+-|..|++...+..... . ...+.+++++.++..+++.+.+...+.    .-
T Consensus       133 ~~l~~~~~~~~~-----~~~l---~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~----~~  200 (328)
T PRK00080        133 IMIGKGPAARSI-----RLDL---PPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGV----EI  200 (328)
T ss_pred             eeeccCccccce-----eecC---CCceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCC----Cc
Confidence            666655332210     0011   12456677777544433221 1 246889999999999999987754332    22


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhhcccCchhhHhhccccCChhhhhhhh-hhccCC
Q 046115          155 LEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFS-YCAVFP  233 (505)
Q Consensus       155 ~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~L~~~~~~~ll-~la~f~  233 (505)
                      .++++..|++.|+|.|-.+..+...+.      .|...-.... -....-......+...+..|++..+.++. .+..|.
T Consensus       201 ~~~~~~~ia~~~~G~pR~a~~~l~~~~------~~a~~~~~~~-I~~~~v~~~l~~~~~~~~~l~~~~~~~l~~~~~~~~  273 (328)
T PRK00080        201 DEEGALEIARRSRGTPRIANRLLRRVR------DFAQVKGDGV-ITKEIADKALDMLGVDELGLDEMDRKYLRTIIEKFG  273 (328)
T ss_pred             CHHHHHHHHHHcCCCchHHHHHHHHHH------HHHHHcCCCC-CCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHcC
Confidence            346788999999999965544444321      1111000000 00000011223345677788888888886 555565


Q ss_pred             CCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHH-HHHHccccc
Q 046115          234 KDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFN-ILASRSFFQ  279 (505)
Q Consensus       234 ~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~-~L~~~~Ll~  279 (505)
                      .+ .+..+.+....           ....+.+++.++ .|++.++++
T Consensus       274 ~~-~~~~~~~a~~l-----------g~~~~~~~~~~e~~Li~~~li~  308 (328)
T PRK00080        274 GG-PVGLDTLAAAL-----------GEERDTIEDVYEPYLIQQGFIQ  308 (328)
T ss_pred             CC-ceeHHHHHHHH-----------CCCcchHHHHhhHHHHHcCCcc
Confidence            44 56655554332           111234566677 899999996

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.50  E-value=9.8e-08  Score=102.35  Aligned_cols=131  Identities=32%  Similarity=0.484  Sum_probs=104.3

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccc-cccccCcc-ccCCCCcceeeccCCccccccch
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNN-LIKEIPTN-IEKLLHLKYLNLKGQKKIEKLPE  431 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~-~~~~~p~~-~~~l~~L~~L~l~~~~~~~~lp~  431 (505)
                      .....|.+.+.+|....    ++.. .....|+.|-+.      .+. .+...+.. |..++.|++|||++|..++.+|.
T Consensus       521 ~~~~~rr~s~~~~~~~~----~~~~-~~~~~L~tLll~------~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~  589 (889)
T KOG4658|consen  521 SWNSVRRMSLMNNKIEH----IAGS-SENPKLRTLLLQ------RNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPS  589 (889)
T ss_pred             chhheeEEEEeccchhh----ccCC-CCCCccceEEEe------ecchhhhhcCHHHHhhCcceEEEECCCCCccCcCCh
Confidence            44677888888887532    2221 223368888776      122 14455444 67899999999999998999999


Q ss_pred             hhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccceeEec
Q 046115          432 TLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVVG  496 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~~~~  496 (505)
                      .|+.|-+|++|+++++. +..+|.++++|++|.+|++..+..+..+|..+..|++|++|.++...
T Consensus       590 ~I~~Li~LryL~L~~t~-I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~  653 (889)
T KOG4658|consen  590 SIGELVHLRYLDLSDTG-ISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLPRSA  653 (889)
T ss_pred             HHhhhhhhhcccccCCC-ccccchHHHHHHhhheeccccccccccccchhhhcccccEEEeeccc
Confidence            99999999999999988 89999999999999999999998777776666779999999998765

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

Probab=98.49  E-value=2.2e-08  Score=90.00  Aligned_cols=129  Identities=28%  Similarity=0.280  Sum_probs=99.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.++.+.+.++..+..    -.+.++.|++++|.+.-    +.+ +..+.+|+.|||+       +|.+.++-.+-
T Consensus       285 ~LtelDLS~N~I~~iDESvK----L~Pkir~L~lS~N~i~~----v~n-La~L~~L~~LDLS-------~N~Ls~~~Gwh  348 (490)
T KOG1259|consen  285 ELTELDLSGNLITQIDESVK----LAPKLRRLILSQNRIRT----VQN-LAELPQLQLLDLS-------GNLLAECVGWH  348 (490)
T ss_pred             hhhhccccccchhhhhhhhh----hccceeEEeccccceee----ehh-hhhcccceEeecc-------cchhHhhhhhH
Confidence            55666666676666655543    56889999999998653    333 6778899999998       67677766555


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccc--hhccccccCceeecCCCccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELP--RGIGKLRKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~~p  478 (505)
                      -+|.+++.|.|++|. +..+.. +++|.+|..||+++|+ ++.+.  .+|+++|.|+++.+.+|+ +..+|
T Consensus       349 ~KLGNIKtL~La~N~-iE~LSG-L~KLYSLvnLDl~~N~-Ie~ldeV~~IG~LPCLE~l~L~~NP-l~~~v  415 (490)
T KOG1259|consen  349 LKLGNIKTLKLAQNK-IETLSG-LRKLYSLVNLDLSSNQ-IEELDEVNHIGNLPCLETLRLTGNP-LAGSV  415 (490)
T ss_pred             hhhcCEeeeehhhhh-Hhhhhh-hHhhhhheeccccccc-hhhHHHhcccccccHHHHHhhcCCC-ccccc
Confidence            678899999999988 777766 8899999999999988 77664  368999999999999998 44444

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=98.47  E-value=1.3e-07  Score=92.49  Aligned_cols=165  Identities=21%  Similarity=0.219  Sum_probs=110.3

Q ss_pred             cccccccc-cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEeccccc----
Q 046115          321 LAISSFVE-KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRES----  395 (505)
Q Consensus       321 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~----  395 (505)
                      .....++. ..+.++.+..+.+..+..+   .|.++.+|.+|.|+.|.++..   ++..|.++.+|+.|+|..+..    
T Consensus       164 i~~~sfp~~~ni~~L~La~N~It~l~~~---~F~~lnsL~tlkLsrNrittL---p~r~Fk~L~~L~~LdLnrN~irive  237 (873)
T KOG4194|consen  164 IPKPSFPAKVNIKKLNLASNRITTLETG---HFDSLNSLLTLKLSRNRITTL---PQRSFKRLPKLESLDLNRNRIRIVE  237 (873)
T ss_pred             ccCCCCCCCCCceEEeeccccccccccc---cccccchheeeecccCccccc---CHHHhhhcchhhhhhccccceeeeh
Confidence            33334444 5788888888887766543   345777999999999988765   566677799999999873210    


Q ss_pred             ------CC-------ccccccccCc-cccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchhcccc
Q 046115          396 ------WP-------RNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRGIGKL  460 (505)
Q Consensus       396 ------~~-------~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~~~~l  460 (505)
                            ++       ..+.+..+-. .|-.|.++++|+|..|+ ++.+-. .+..|..|+.|++|+|.+-+.-+.++...
T Consensus       238 ~ltFqgL~Sl~nlklqrN~I~kL~DG~Fy~l~kme~l~L~~N~-l~~vn~g~lfgLt~L~~L~lS~NaI~rih~d~Wsft  316 (873)
T KOG4194|consen  238 GLTFQGLPSLQNLKLQRNDISKLDDGAFYGLEKMEHLNLETNR-LQAVNEGWLFGLTSLEQLDLSYNAIQRIHIDSWSFT  316 (873)
T ss_pred             hhhhcCchhhhhhhhhhcCcccccCcceeeecccceeecccch-hhhhhcccccccchhhhhccchhhhheeecchhhhc
Confidence                  00       0111222211 23456678888888888 655543 45788889999999988334445667777


Q ss_pred             ccCceeecCCCcccccccc-cccCCccCCcccee
Q 046115          461 RKLMYLHNEDTGCLRYLPA-GIGELIRLRRVREF  493 (505)
Q Consensus       461 ~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~~  493 (505)
                      ++|+.|++++|. +..+++ .|..|..|++|++-
T Consensus       317 qkL~~LdLs~N~-i~~l~~~sf~~L~~Le~LnLs  349 (873)
T KOG4194|consen  317 QKLKELDLSSNR-ITRLDEGSFRVLSQLEELNLS  349 (873)
T ss_pred             ccceeEeccccc-cccCChhHHHHHHHhhhhccc
Confidence            899999999987 445554 47777777777754

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.46  E-value=4.7e-07  Score=95.62  Aligned_cols=102  Identities=29%  Similarity=0.432  Sum_probs=64.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....+|..+.      .+|++|++++|.++.    +|..+.  .+|+.|+|+       ++.+..+|..+
T Consensus       200 ~L~~L~Ls~N~LtsLP~~l~------~nL~~L~Ls~N~Lts----LP~~l~--~~L~~L~Ls-------~N~L~~LP~~l  260 (754)
T PRK15370        200 QITTLILDNNELKSLPENLQ------GNIKTLYANSNQLTS----IPATLP--DTIQEMELS-------INRITELPERL  260 (754)
T ss_pred             CCcEEEecCCCCCcCChhhc------cCCCEEECCCCcccc----CChhhh--ccccEEECc-------CCccCcCChhH
Confidence            66777777777776665442      478888888887664    333222  357777776       55566666554


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchh
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG  456 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~  456 (505)
                      .  .+|++|++++|. +..+|..+.  .+|+.|++++|. +..+|..
T Consensus       261 ~--s~L~~L~Ls~N~-L~~LP~~l~--~sL~~L~Ls~N~-Lt~LP~~  301 (754)
T PRK15370        261 P--SALQSLDLFHNK-ISCLPENLP--EELRYLSVYDNS-IRTLPAH  301 (754)
T ss_pred             h--CCCCEEECcCCc-cCccccccC--CCCcEEECCCCc-cccCccc
Confidence            2  467777777666 556665443  367777777765 5555543

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

Probab=98.44  E-value=1e-08  Score=99.79  Aligned_cols=131  Identities=27%  Similarity=0.385  Sum_probs=85.2

Q ss_pred             EEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCC
Q 046115          335 LLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLH  414 (505)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~  414 (505)
                      .++.+....+|....    .+..|..+.++.|.+..    +|..++++..|++|+|+       .+.+..+|..+|.|+ 
T Consensus        81 DlsrNR~~elp~~~~----~f~~Le~liLy~n~~r~----ip~~i~~L~~lt~l~ls-------~NqlS~lp~~lC~lp-  144 (722)
T KOG0532|consen   81 DLSRNRFSELPEEAC----AFVSLESLILYHNCIRT----IPEAICNLEALTFLDLS-------SNQLSHLPDGLCDLP-  144 (722)
T ss_pred             hccccccccCchHHH----HHHHHHHHHHHhcccee----cchhhhhhhHHHHhhhc-------cchhhcCChhhhcCc-
Confidence            334444444444443    45566666666665532    55566777777777776       666666777676666 


Q ss_pred             cceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCC
Q 046115          415 LKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGEL  484 (505)
Q Consensus       415 L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l  484 (505)
                      |+.|-+++|+ ++.+|..++.+..|..||.+.|. +..+|..++++.+|+.|++..|. +..+|..+..|
T Consensus       145 Lkvli~sNNk-l~~lp~~ig~~~tl~~ld~s~ne-i~slpsql~~l~slr~l~vrRn~-l~~lp~El~~L  211 (722)
T KOG0532|consen  145 LKVLIVSNNK-LTSLPEEIGLLPTLAHLDVSKNE-IQSLPSQLGYLTSLRDLNVRRNH-LEDLPEELCSL  211 (722)
T ss_pred             ceeEEEecCc-cccCCcccccchhHHHhhhhhhh-hhhchHHhhhHHHHHHHHHhhhh-hhhCCHHHhCC
Confidence            7777777776 77777777766777777777766 77777777777777777777665 45666665543

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.43  E-value=6.1e-07  Score=94.81  Aligned_cols=124  Identities=24%  Similarity=0.393  Sum_probs=95.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      ....+.+.......+|..++      ++|+.|++.+|.++.    +|..+.  .+|+.|+++       ++.+..+|..+
T Consensus       179 ~~~~L~L~~~~LtsLP~~Ip------~~L~~L~Ls~N~Lts----LP~~l~--~nL~~L~Ls-------~N~LtsLP~~l  239 (754)
T PRK15370        179 NKTELRLKILGLTTIPACIP------EQITTLILDNNELKS----LPENLQ--GNIKTLYAN-------SNQLTSIPATL  239 (754)
T ss_pred             CceEEEeCCCCcCcCCcccc------cCCcEEEecCCCCCc----CChhhc--cCCCEEECC-------CCccccCChhh
Confidence            44566666666676776554      579999999998875    444333  589999998       66778888755


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGI  481 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i  481 (505)
                        ..+|+.|+|++|. +..+|..+.  .+|+.|++++|. +..+|..+.  ++|++|++++|. +..+|..+
T Consensus       240 --~~~L~~L~Ls~N~-L~~LP~~l~--s~L~~L~Ls~N~-L~~LP~~l~--~sL~~L~Ls~N~-Lt~LP~~l  302 (754)
T PRK15370        240 --PDTIQEMELSINR-ITELPERLP--SALQSLDLFHNK-ISCLPENLP--EELRYLSVYDNS-IRTLPAHL  302 (754)
T ss_pred             --hccccEEECcCCc-cCcCChhHh--CCCCEEECcCCc-cCccccccC--CCCcEEECCCCc-cccCcccc
Confidence              3589999999999 789998764  589999999988 788998764  589999999997 45666543

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.42  E-value=6.2e-06  Score=88.91  Aligned_cols=219  Identities=15%  Similarity=0.144  Sum_probs=137.3

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCC------CCcEEEEEeCch--HHHHHhCCcceEeCCCCChhhHHHHHHHh
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSL------HESKILITTRKE--TVARIMGSTHVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~------~~~~iLiTtr~~--~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      +.++.++|+||+.|.+.....-+...+..-.      +....+.|.+..  .+.........+.+.+|+..+...+....
T Consensus       152 ~~~plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~  231 (849)
T COG3899         152 EEHPLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAAT  231 (849)
T ss_pred             ccCCeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHH
Confidence            4469999999998877655544443333221      122333344432  22222344568999999999999999876


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCC------CHHHHHHHHhhhhhhhhhcccCchhhHhhccc
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKN------TEKEWQNILENEIWELEAIEKGLLAPLLLSYN  216 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~------~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~  216 (505)
                      ......     ........|+++..|+|+.+..+-+.+....      +...|+.-+... .... ....+...+....+
T Consensus       232 l~~~~~-----~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i-~~~~-~~~~vv~~l~~rl~  304 (849)
T COG3899         232 LGCTKL-----LPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASL-GILA-TTDAVVEFLAARLQ  304 (849)
T ss_pred             hCCccc-----ccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhc-CCch-hhHHHHHHHHHHHh
Confidence            532122     2234578899999999999999999887742      334444332211 1111 11224556888999


Q ss_pred             cCChhhhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCC-CCCeeEe---
Q 046115          217 ELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYD-DGEIYKC---  292 (505)
Q Consensus       217 ~L~~~~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~-~~~~~~~---  292 (505)
                      .|+...|+.+...||+..  .|+...+...+-          ......+.+.++.|....++...+... .......   
T Consensus       305 kL~~~t~~Vl~~AA~iG~--~F~l~~La~l~~----------~~~~~~a~~l~~al~e~lI~~~~~~yr~~~~~~~~~Y~  372 (849)
T COG3899         305 KLPGTTREVLKAAACIGN--RFDLDTLAALAE----------DSPALEAAALLDALQEGLILPLSETYRFGSNVDIATYK  372 (849)
T ss_pred             cCCHHHHHHHHHHHHhCc--cCCHHHHHHHHh----------hchHHHHHHHHHHhHhhceeccccccccccccchhhHH
Confidence            999999999999999976  455666655441          134566777788887777765432111 1111122   


Q ss_pred             eehHHHHHHHHHhhcc
Q 046115          293 KMHDIVHDFAQYLCSN  308 (505)
Q Consensus       293 ~~H~lv~~~~~~~~~~  308 (505)
                      ..|+.|++.+-....+
T Consensus       373 F~H~~vqqaaY~~i~~  388 (849)
T COG3899         373 FLHDRVQQAAYNLIPE  388 (849)
T ss_pred             hhHHHHHHHHhccCch
Confidence            6899999988665543

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

Probab=98.38  E-value=8.1e-08  Score=86.38  Aligned_cols=124  Identities=23%  Similarity=0.287  Sum_probs=99.9

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .-..|+.|++++|.++.    +.....-.++++.|+++       .|.+....+ +..|++|..|||++|. ++++...=
T Consensus       282 TWq~LtelDLS~N~I~~----iDESvKL~Pkir~L~lS-------~N~i~~v~n-La~L~~L~~LDLS~N~-Ls~~~Gwh  348 (490)
T KOG1259|consen  282 TWQELTELDLSGNLITQ----IDESVKLAPKLRRLILS-------QNRIRTVQN-LAELPQLQLLDLSGNL-LAECVGWH  348 (490)
T ss_pred             hHhhhhhccccccchhh----hhhhhhhccceeEEecc-------ccceeeehh-hhhcccceEeecccch-hHhhhhhH
Confidence            34679999999998876    44445667899999999       666666554 7889999999999999 88887744


Q ss_pred             hcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccc--cccccCCccCCcccee
Q 046115          434 CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYL--PAGIGELIRLRRVREF  493 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~--p~~i~~l~~L~~L~~~  493 (505)
                      -+|.|.++|+|++|. ++.+ .+++++.+|..|++++|+ +..+  ...|++++-|+++.+.
T Consensus       349 ~KLGNIKtL~La~N~-iE~L-SGL~KLYSLvnLDl~~N~-Ie~ldeV~~IG~LPCLE~l~L~  407 (490)
T KOG1259|consen  349 LKLGNIKTLKLAQNK-IETL-SGLRKLYSLVNLDLSSNQ-IEELDEVNHIGNLPCLETLRLT  407 (490)
T ss_pred             hhhcCEeeeehhhhh-Hhhh-hhhHhhhhheeccccccc-hhhHHHhcccccccHHHHHhhc
Confidence            689999999999988 7877 478999999999999997 4444  2468888888877654

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

Probab=98.37  E-value=4.5e-08  Score=100.58  Aligned_cols=110  Identities=28%  Similarity=0.431  Sum_probs=71.6

Q ss_pred             CCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhh
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC  434 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~  434 (505)
                      ...|.+|++++|..+.    .|..+..+.+|+.|+++       .+.+.+.|.+++.+.+|++|.|.+|. ++.+|.+++
T Consensus        44 ~v~L~~l~lsnn~~~~----fp~~it~l~~L~~ln~s-------~n~i~~vp~s~~~~~~l~~lnL~~n~-l~~lP~~~~  111 (1081)
T KOG0618|consen   44 RVKLKSLDLSNNQISS----FPIQITLLSHLRQLNLS-------RNYIRSVPSSCSNMRNLQYLNLKNNR-LQSLPASIS  111 (1081)
T ss_pred             eeeeEEeecccccccc----CCchhhhHHHHhhcccc-------hhhHhhCchhhhhhhcchhheeccch-hhcCchhHH
Confidence            4446677777766554    34446666667777776       66666667666677777777777666 667777677


Q ss_pred             cCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccc
Q 046115          435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYL  477 (505)
Q Consensus       435 ~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~  477 (505)
                      .+.+|+.|++++|. ...+|.-+..+..+..+..++|..+.++
T Consensus       112 ~lknl~~LdlS~N~-f~~~Pl~i~~lt~~~~~~~s~N~~~~~l  153 (1081)
T KOG0618|consen  112 ELKNLQYLDLSFNH-FGPIPLVIEVLTAEEELAASNNEKIQRL  153 (1081)
T ss_pred             hhhcccccccchhc-cCCCchhHHhhhHHHHHhhhcchhhhhh
Confidence            77777777777766 6666666666666666666666333333

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

Probab=98.35  E-value=1.3e-07  Score=97.23  Aligned_cols=110  Identities=20%  Similarity=0.296  Sum_probs=57.6

Q ss_pred             cCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCcccccc
Q 046115          350 GNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL  429 (505)
Q Consensus       350 ~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~l  429 (505)
                      +-+.++++|+.|.|++|.+..+   +...+.++..|+.|+|+       ++.++.+|..+..++.|++|-..+|. +..+
T Consensus       377 p~l~~~~hLKVLhLsyNrL~~f---pas~~~kle~LeeL~LS-------GNkL~~Lp~tva~~~~L~tL~ahsN~-l~~f  445 (1081)
T KOG0618|consen  377 PVLVNFKHLKVLHLSYNRLNSF---PASKLRKLEELEELNLS-------GNKLTTLPDTVANLGRLHTLRAHSNQ-LLSF  445 (1081)
T ss_pred             hhhccccceeeeeecccccccC---CHHHHhchHHhHHHhcc-------cchhhhhhHHHHhhhhhHHHhhcCCc-eeec
Confidence            3344555555555555554432   33344555555555555       55555555555555555555555555 5555


Q ss_pred             chhhhcCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCc
Q 046115          430 PETLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~  472 (505)
                      | ++.+++.|+.+|++.|.... .+|..... ++|++|+++||.
T Consensus       446 P-e~~~l~qL~~lDlS~N~L~~~~l~~~~p~-p~LkyLdlSGN~  487 (1081)
T KOG0618|consen  446 P-ELAQLPQLKVLDLSCNNLSEVTLPEALPS-PNLKYLDLSGNT  487 (1081)
T ss_pred             h-hhhhcCcceEEecccchhhhhhhhhhCCC-cccceeeccCCc
Confidence            5 35566666666666555221 22222211 566666666664

>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=98.34  E-value=4.9e-07  Score=63.51  Aligned_cols=58  Identities=28%  Similarity=0.528  Sum_probs=40.3

Q ss_pred             CCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCc
Q 046115          413 LHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       413 ~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~  472 (505)
                      ++|++|++++|. +..+|. .+..+++|++|++++|. +..+|+ .+..+++|++|++++|+
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 PNLESLDLSNNK-LTEIPPDSFSNLPNLETLDLSNNN-LTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TTESEEEETSST-ESEECTTTTTTGTTESEEEETSSS-ESEEETTTTTTSTTESEEEETSSS
T ss_pred             CcCcEEECCCCC-CCccCHHHHcCCCCCCEeEccCCc-cCccCHHHHcCCCCCCEEeCcCCc
Confidence            357777777776 666664 45677777777777777 566654 46777777777777775

...

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.32  E-value=3.6e-06  Score=88.68  Aligned_cols=34  Identities=24%  Similarity=0.240  Sum_probs=17.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSW  370 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~  370 (505)
                      .+..+.+..+....+|.       .+++|++|++.+|.++.
T Consensus       223 ~L~~L~L~~N~Lt~LP~-------lp~~Lk~LdLs~N~Lts  256 (788)
T PRK15387        223 HITTLVIPDNNLTSLPA-------LPPELRTLEVSGNQLTS  256 (788)
T ss_pred             CCCEEEccCCcCCCCCC-------CCCCCcEEEecCCccCc
Confidence            45555555555554432       23456666666665543

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.29  E-value=7e-07  Score=93.94  Aligned_cols=86  Identities=23%  Similarity=0.251  Sum_probs=61.0

Q ss_pred             cccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhcccccc
Q 046115          383 TCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRK  462 (505)
Q Consensus       383 ~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~  462 (505)
                      .+|+.|+++       ++.+..+|..   .++|+.|++++|+ +..+|..   +.+|+.|++++|. +..+|..+.++++
T Consensus       382 ~~L~~LdLs-------~N~Lt~LP~l---~s~L~~LdLS~N~-LssIP~l---~~~L~~L~Ls~Nq-Lt~LP~sl~~L~~  446 (788)
T PRK15387        382 SGLKELIVS-------GNRLTSLPVL---PSELKELMVSGNR-LTSLPML---PSGLLSLSVYRNQ-LTRLPESLIHLSS  446 (788)
T ss_pred             cccceEEec-------CCcccCCCCc---ccCCCEEEccCCc-CCCCCcc---hhhhhhhhhccCc-ccccChHHhhccC
Confidence            356777776       5556666643   3567788888887 6677753   3457778888887 7788888888888


Q ss_pred             CceeecCCCcccccccccccC
Q 046115          463 LMYLHNEDTGCLRYLPAGIGE  483 (505)
Q Consensus       463 L~~L~l~~~~~~~~~p~~i~~  483 (505)
                      |+.|++++|++.+..|..+.+
T Consensus       447 L~~LdLs~N~Ls~~~~~~L~~  467 (788)
T PRK15387        447 ETTVNLEGNPLSERTLQALRE  467 (788)
T ss_pred             CCeEECCCCCCCchHHHHHHH
Confidence            888888888876666555533

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

Probab=98.29  E-value=9.8e-07  Score=73.03  Aligned_cols=107  Identities=19%  Similarity=0.141  Sum_probs=73.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-----CCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCc-e
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-----FEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGK-K   74 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-----f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-r   74 (505)
                      .+|+|||++++++++  .....     -..++|+++....+...+...++.+++..... ..+..+..+.+.+.+.+. .
T Consensus        12 ~~G~GKT~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~~~l~~~~~~~l~~~~~   88 (131)
T PF13401_consen   12 PPGSGKTTLIKRLAR--QLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKS-RQTSDELRSLLIDALDRRRV   88 (131)
T ss_dssp             -TTSSHHHHHHHHHH--HHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS-TS-HHHHHHHHHHHHHHCTE
T ss_pred             CCCCCHHHHHHHHHH--HhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccc-cCCHHHHHHHHHHHHHhcCC
Confidence            379999999999998  33322     34567999888889999999999999855544 445555667777777554 4


Q ss_pred             EEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCc
Q 046115           75 FLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRK  112 (505)
Q Consensus        75 ~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~  112 (505)
                      .+||+|+++.- ....++.+.. +.+ ..+.++++..+.
T Consensus        89 ~~lviDe~~~l~~~~~l~~l~~-l~~-~~~~~vvl~G~~  125 (131)
T PF13401_consen   89 VLLVIDEADHLFSDEFLEFLRS-LLN-ESNIKVVLVGTP  125 (131)
T ss_dssp             EEEEEETTHHHHTHHHHHHHHH-HTC-SCBEEEEEEESS
T ss_pred             eEEEEeChHhcCCHHHHHHHHH-HHh-CCCCeEEEEECh
Confidence            69999999665 4333344433 333 566777777664

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.28  E-value=9.9e-06  Score=74.06  Aligned_cols=148  Identities=18%  Similarity=0.124  Sum_probs=86.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||+.+++  +........+++++..-.+..   .                      .+...+.+ .-+||+|
T Consensus        46 ~~G~GKT~la~~~~~--~~~~~~~~~~~i~~~~~~~~~---~----------------------~~~~~~~~-~~lLvID   97 (226)
T TIGR03420        46 ESGSGKSHLLQAACA--AAEERGKSAIYLPLAELAQAD---P----------------------EVLEGLEQ-ADLVCLD   97 (226)
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCcEEEEeHHHHHHhH---H----------------------HHHhhccc-CCEEEEe
Confidence            479999999999998  443334455677654321100   0                      01111222 2389999


Q ss_pred             CCCCCCccC--hhHHHHhhcCC-CCCcEEEEEeCchH---------HHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           81 DVWNEDYYK--WEPFYKCLKNS-LHESKILITTRKET---------VARIMGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        81 dv~~~~~~~--~~~~~~~~~~~-~~~~~iLiTtr~~~---------~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      |++......  ...+...+... ..+..+++||+...         +...+.....+.+++++.++...++.........
T Consensus        98 di~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~  177 (226)
T TIGR03420        98 DVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAARRGL  177 (226)
T ss_pred             ChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHHcCC
Confidence            997643221  33344433321 23347888887532         2222222457899999999989988765432111


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                          .-.++++..+++.+.|.|..+..+...+
T Consensus       178 ----~~~~~~l~~L~~~~~gn~r~L~~~l~~~  205 (226)
T TIGR03420       178 ----QLPDEVADYLLRHGSRDMGSLMALLDAL  205 (226)
T ss_pred             ----CCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence                1234667888888999998776665443

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.20  E-value=2.7e-05  Score=68.86  Aligned_cols=90  Identities=13%  Similarity=0.155  Sum_probs=64.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +.+-++|+||+..........+...+.+....+.++++|++. .+...+ .....+.+.+++.++..+.+....     .
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~g-----i  169 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQG-----I  169 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHcC-----C
Confidence            456789999997766556777888887766666676666653 332222 234589999999999999887751     1


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                           .++.+..+++.++|.|.
T Consensus       170 -----~~~~~~~i~~~~~g~~r  186 (188)
T TIGR00678       170 -----SEEAAELLLALAGGSPG  186 (188)
T ss_pred             -----CHHHHHHHHHHcCCCcc
Confidence                 14668899999999885

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.

>PF13173 AAA_14: AAA domain

Probab=98.20  E-value=5.4e-06  Score=68.17  Aligned_cols=111  Identities=23%  Similarity=0.260  Sum_probs=72.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      +.|+|||||+++++.+  .. .-..++++++...........+                  ..+.+.+....++.++++|
T Consensus        10 ~R~vGKTtll~~~~~~--~~-~~~~~~yi~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~i~iD   68 (128)
T PF13173_consen   10 PRGVGKTTLLKQLAKD--LL-PPENILYINFDDPRDRRLADPD------------------LLEYFLELIKPGKKYIFID   68 (128)
T ss_pred             CCCCCHHHHHHHHHHH--hc-ccccceeeccCCHHHHHHhhhh------------------hHHHHHHhhccCCcEEEEe
Confidence            3699999999999973  22 3356777876653221100000                  1222333333477899999


Q ss_pred             CCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHH-----h-CCcceEeCCCCChhh
Q 046115           81 DVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI-----M-GSTHVISVNVLSEME  134 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~-----~-~~~~~~~l~~l~~~e  134 (505)
                      +++...  .|...+..+.+..+..+|++|+........     . +....+++.+|+..|
T Consensus        69 Eiq~~~--~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E  126 (128)
T PF13173_consen   69 EIQYLP--DWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFRE  126 (128)
T ss_pred             hhhhhc--cHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHH
Confidence            996653  788888888887777899999998665532     1 224577899998877

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=98.17  E-value=1.7e-06  Score=83.72  Aligned_cols=157  Identities=19%  Similarity=0.139  Sum_probs=98.4

Q ss_pred             ceeEEEEEecCCCc-cccccccCCCCCCCceEEEecCCCcccc-ccchhHHhhcC-cccceEEecccccCCcccccc---
Q 046115          330 KILHLLLTLRRGAS-VPISIWGNVTGLRGLRSLLVKSDEYSWS-SEVLPQLFEKL-TCLRALELQVRESWPRNNLIK---  403 (505)
Q Consensus       330 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~L~~L~l~~~~~~~~-~~~~~~~~~~l-~~L~~L~l~~~~~~~~~~~~~---  403 (505)
                      ++..+.+..+.... .+..+..-... ++|+.|.+++|.++.. ...+...+..+ .+|+.|+++       ++.+.   
T Consensus        82 ~L~~L~l~~~~~~~~~~~~~~~l~~~-~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~-------~n~l~~~~  153 (319)
T cd00116          82 GLQELDLSDNALGPDGCGVLESLLRS-SSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLG-------RNRLEGAS  153 (319)
T ss_pred             ceeEEEccCCCCChhHHHHHHHHhcc-CcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcC-------CCcCCchH
Confidence            66777776665542 12222111112 4599999999987631 11234446666 889999998       33333   


Q ss_pred             --ccCccccCCCCcceeeccCCcccc----ccchhhhcCCCCcEEecCCCcCc----cccchhccccccCceeecCCCcc
Q 046115          404 --EIPTNIEKLLHLKYLNLKGQKKIE----KLPETLCELYNLERLNVDDCQNL----RELPRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       404 --~~p~~~~~l~~L~~L~l~~~~~~~----~lp~~~~~l~~L~~L~l~~~~~~----~~lp~~~~~l~~L~~L~l~~~~~  473 (505)
                        .++..+..+++|++|++++|....    .++..+..+++|+.|++++|...    ..++..+..+++|++|++++|..
T Consensus       154 ~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~l  233 (319)
T cd00116         154 CEALAKALRANRDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNNL  233 (319)
T ss_pred             HHHHHHHHHhCCCcCEEECcCCCCchHHHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCCCcC
Confidence              344456778899999999998331    34455666789999999998732    23444567788999999999975


Q ss_pred             ccccccccc-----CCccCCccceeE
Q 046115          474 LRYLPAGIG-----ELIRLRRVREFV  494 (505)
Q Consensus       474 ~~~~p~~i~-----~l~~L~~L~~~~  494 (505)
                      ...-+..+.     ..+.|+.|++..
T Consensus       234 ~~~~~~~l~~~~~~~~~~L~~L~l~~  259 (319)
T cd00116         234 TDAGAAALASALLSPNISLLTLSLSC  259 (319)
T ss_pred             chHHHHHHHHHHhccCCCceEEEccC
Confidence            432222221     135666666543

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).

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=98.16  E-value=1.2e-06  Score=84.61  Aligned_cols=156  Identities=21%  Similarity=0.186  Sum_probs=100.4

Q ss_pred             ceeEEEEEecCCCcccc-ccccCCCCC-CCceEEEecCCCccccc-cchhHHhhcCcccceEEecccccCCcccccc---
Q 046115          330 KILHLLLTLRRGASVPI-SIWGNVTGL-RGLRSLLVKSDEYSWSS-EVLPQLFEKLTCLRALELQVRESWPRNNLIK---  403 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~-~~~~~~~~~-~~L~~L~l~~~~~~~~~-~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~---  403 (505)
                      .+..+.+..+....... .+...+..+ ++|+.|++.+|.+++.. ..++..+..+++|+.|+++       ++.+.   
T Consensus       109 ~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~~~~~~~~~~~L~~L~l~-------~n~l~~~~  181 (319)
T cd00116         109 SLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCEALAKALRANRDLKELNLA-------NNGIGDAG  181 (319)
T ss_pred             cccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHHHHHHHHHhCCCcCEEECc-------CCCCchHH
Confidence            37777777766542111 112223356 89999999999987421 1255567778899999998       33333   


Q ss_pred             --ccCccccCCCCcceeeccCCccc----cccchhhhcCCCCcEEecCCCcCccccchhc-c----ccccCceeecCCCc
Q 046115          404 --EIPTNIEKLLHLKYLNLKGQKKI----EKLPETLCELYNLERLNVDDCQNLRELPRGI-G----KLRKLMYLHNEDTG  472 (505)
Q Consensus       404 --~~p~~~~~l~~L~~L~l~~~~~~----~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~-~----~l~~L~~L~l~~~~  472 (505)
                        .++..+..+++|++|++++|...    ..++..+..+++|+.|++++|.....-+..+ .    ..++|++|++++|.
T Consensus       182 ~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~l~~~~~~~l~~~~~~~~~~L~~L~l~~n~  261 (319)
T cd00116         182 IRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNNLTDAGAAALASALLSPNISLLTLSLSCND  261 (319)
T ss_pred             HHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCCCcCchHHHHHHHHHHhccCCCceEEEccCCC
Confidence              34445566789999999999832    2345556788999999999998332112222 1    23799999999997


Q ss_pred             cc----ccccccccCCccCCccce
Q 046115          473 CL----RYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       473 ~~----~~~p~~i~~l~~L~~L~~  492 (505)
                      +.    ..++..+..+++|+.+++
T Consensus       262 i~~~~~~~l~~~~~~~~~L~~l~l  285 (319)
T cd00116         262 ITDDGAKDLAEVLAEKESLLELDL  285 (319)
T ss_pred             CCcHHHHHHHHHHhcCCCccEEEC
Confidence            54    223334445555555543

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).

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.15  E-value=0.00014  Score=75.93  Aligned_cols=178  Identities=9%  Similarity=0.030  Sum_probs=95.9

Q ss_pred             CCCCcHHHHHHHHhcCcccc-----cCCC--ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC--
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-----RNFE--KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA--   71 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-----~~f~--~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~--   71 (505)
                      ++|.|||+.++.+++  ++.     ....  .+++|++....+...++..|..++............+....+...+.  
T Consensus       789 ~PGTGKTATVK~VLr--ELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~  866 (1164)
T PTZ00112        789 MPGTGKTATVYSVIQ--LLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKD  866 (1164)
T ss_pred             CCCCCHHHHHHHHHH--HHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcc
Confidence            489999999999987  332     1222  35688888888888899999998853333333334445555555442  


Q ss_pred             -CceEEEEEeCCCCCCccChhHHHHhhcCC-CCCcEEEE--EeCchH----HHHHhCC---cceEeCCCCChhhHHHHHH
Q 046115           72 -GKKFLLVLDDVWNEDYYKWEPFYKCLKNS-LHESKILI--TTRKET----VARIMGS---THVISVNVLSEMECWSVFQ  140 (505)
Q Consensus        72 -~~r~LlvlDdv~~~~~~~~~~~~~~~~~~-~~~~~iLi--Ttr~~~----~~~~~~~---~~~~~l~~l~~~ea~~Lf~  140 (505)
                       +...+||||+++.-....-+.+...+.+. ..+++|+|  +|.+.+    +...+..   ...+...+.+.++-.+++.
T Consensus       867 ~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk  946 (1164)
T PTZ00112        867 NRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIK  946 (1164)
T ss_pred             cccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHH
Confidence             23468999999653211112222222221 23444444  343311    1122111   2246679999999999998


Q ss_pred             HhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          141 SLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      ..+.........+..+-+|+.++..-|-.=.||.++-.+.
T Consensus       947 ~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAg  986 (1164)
T PTZ00112        947 ERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAF  986 (1164)
T ss_pred             HHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHH
Confidence            8775322212222222333333333344445555554443

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=98.09  E-value=2.3e-06  Score=85.41  Aligned_cols=123  Identities=32%  Similarity=0.512  Sum_probs=58.6

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .+++|+.|.+..|.++.    +|........|+.|+++       ++.+..+|..+..+..|++|.+++|. ....+..+
T Consensus       161 ~l~~L~~L~l~~N~l~~----l~~~~~~~~~L~~L~ls-------~N~i~~l~~~~~~~~~L~~l~~~~N~-~~~~~~~~  228 (394)
T COG4886         161 NLPNLKNLDLSFNDLSD----LPKLLSNLSNLNNLDLS-------GNKISDLPPEIELLSALEELDLSNNS-IIELLSSL  228 (394)
T ss_pred             ccccccccccCCchhhh----hhhhhhhhhhhhheecc-------CCccccCchhhhhhhhhhhhhhcCCc-ceecchhh
Confidence            44444444444444332    22212234444444444       44444444444444445555555554 33333334


Q ss_pred             hcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccc
Q 046115          434 CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVR  491 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~  491 (505)
                      .++.++..+.+.+|+ +..+|..++.+++|+.|++++|. +..++. ++.+.+|+.|.
T Consensus       229 ~~~~~l~~l~l~~n~-~~~~~~~~~~l~~l~~L~~s~n~-i~~i~~-~~~~~~l~~L~  283 (394)
T COG4886         229 SNLKNLSGLELSNNK-LEDLPESIGNLSNLETLDLSNNQ-ISSISS-LGSLTNLRELD  283 (394)
T ss_pred             hhcccccccccCCce-eeeccchhccccccceecccccc-cccccc-ccccCccCEEe
Confidence            555555555555544 44445555666666666666665 334443 44555554444

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.06  E-value=6.6e-05  Score=75.00  Aligned_cols=149  Identities=19%  Similarity=0.254  Sum_probs=85.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHH-cCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEEC-VAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~-l~~~r~Llvl   79 (505)
                      ++|+||||||+.+++  .....|     +.++........++.++..                  .... ..+++.+|++
T Consensus        44 ppGtGKTtLA~~ia~--~~~~~~-----~~l~a~~~~~~~ir~ii~~------------------~~~~~~~g~~~vL~I   98 (413)
T PRK13342         44 PPGTGKTTLARIIAG--ATDAPF-----EALSAVTSGVKDLREVIEE------------------ARQRRSAGRRTILFI   98 (413)
T ss_pred             CCCCCHHHHHHHHHH--HhCCCE-----EEEecccccHHHHHHHHHH------------------HHHhhhcCCceEEEE
Confidence            489999999999998  333332     3222211111112222221                  1111 1357789999


Q ss_pred             eCCCCCCccChhHHHHhhcCCCCCcEEEE--EeCchH--HHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCch
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSLHESKILI--TTRKET--VAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKREN  154 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~~~~~iLi--Ttr~~~--~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~  154 (505)
                      |+++.......+.+...+..   +..++|  ||.++.  +.. .......+.+.+++.++...++.+....... ....-
T Consensus        99 DEi~~l~~~~q~~LL~~le~---~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~-~~i~i  174 (413)
T PRK13342         99 DEIHRFNKAQQDALLPHVED---GTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKER-GLVEL  174 (413)
T ss_pred             echhhhCHHHHHHHHHHhhc---CcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhc-CCCCC
Confidence            99987654455555555443   444444  344432  111 1223468899999999999999875432111 00122


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHH
Q 046115          155 LEKIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       155 ~~~~~~~i~~~~~g~Plal~~~~~  178 (505)
                      .+++...+++.|+|.+..+..+..
T Consensus       175 ~~~al~~l~~~s~Gd~R~aln~Le  198 (413)
T PRK13342        175 DDEALDALARLANGDARRALNLLE  198 (413)
T ss_pred             CHHHHHHHHHhCCCCHHHHHHHHH
Confidence            356788899999999876544443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.05  E-value=8.6e-05  Score=78.39  Aligned_cols=101  Identities=13%  Similarity=0.139  Sum_probs=71.1

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|++.......+..+++.+......+++|++|.+ ..+... ......+.+.+++.++....+.......+.
T Consensus       117 ~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI  196 (944)
T PRK14949        117 RGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQL  196 (944)
T ss_pred             cCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCC
Confidence            456789999999887777788888888876666666655544 444322 223468999999999999998876533221


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH-HHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL-AAKT  175 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl-al~~  175 (505)
                          ...++.+..|++.++|.|- |+.+
T Consensus       197 ----~~edeAL~lIA~~S~Gd~R~ALnL  220 (944)
T PRK14949        197 ----PFEAEALTLLAKAANGSMRDALSL  220 (944)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHH
Confidence                2235678899999999885 4433

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=98.05  E-value=1.4e-06  Score=82.60  Aligned_cols=155  Identities=19%  Similarity=0.134  Sum_probs=98.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      +++.+++.+...+..+..  .....|++++.|+|++|-++.... +-....++++|+.|+|+       .+.+....++ 
T Consensus       122 kL~~IsLdn~~V~~~~~~--~~~k~~~~v~~LdLS~NL~~nw~~-v~~i~eqLp~Le~LNls-------~Nrl~~~~~s~  191 (505)
T KOG3207|consen  122 KLREISLDNYRVEDAGIE--EYSKILPNVRDLDLSRNLFHNWFP-VLKIAEQLPSLENLNLS-------SNRLSNFISSN  191 (505)
T ss_pred             hhhheeecCccccccchh--hhhhhCCcceeecchhhhHHhHHH-HHHHHHhcccchhcccc-------cccccCCcccc
Confidence            555566555554433321  223378999999999998876633 66678899999999998       4444333322 


Q ss_pred             -ccCCCCcceeeccCCcccc-ccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccc--ccccCC
Q 046115          409 -IEKLLHLKYLNLKGQKKIE-KLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP--AGIGEL  484 (505)
Q Consensus       409 -~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p--~~i~~l  484 (505)
                       -..+++|+.|.|+.|.... ++-...-.+++|+.|.|.+|..+...-.....+..|+.|++++|+.. .++  ..++.+
T Consensus       192 ~~~~l~~lK~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~li-~~~~~~~~~~l  270 (505)
T KOG3207|consen  192 TTLLLSHLKQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNNLI-DFDQGYKVGTL  270 (505)
T ss_pred             chhhhhhhheEEeccCCCCHHHHHHHHHhCCcHHHhhhhcccccceecchhhhhhHHhhccccCCccc-ccccccccccc
Confidence             2367889999999998433 34444456788888888877433322223344567778888877743 444  235666


Q ss_pred             ccCCccceeEe
Q 046115          485 IRLRRVREFVV  495 (505)
Q Consensus       485 ~~L~~L~~~~~  495 (505)
                      +.|+.|++..+
T Consensus       271 ~~L~~Lnls~t  281 (505)
T KOG3207|consen  271 PGLNQLNLSST  281 (505)
T ss_pred             cchhhhhcccc
Confidence            66666665433

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.04  E-value=8.7e-05  Score=67.94  Aligned_cols=148  Identities=16%  Similarity=0.135  Sum_probs=85.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||..+++  .....-..+.++++.....   .                  ..+..+    .+.+ --+|++|
T Consensus        53 p~G~GKThLl~a~~~--~~~~~~~~v~y~~~~~~~~---~------------------~~~~~~----~~~~-~dlliiD  104 (235)
T PRK08084         53 REGAGRSHLLHAACA--ELSQRGRAVGYVPLDKRAW---F------------------VPEVLE----GMEQ-LSLVCID  104 (235)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCeEEEEEHHHHhh---h------------------hHHHHH----Hhhh-CCEEEEe
Confidence            479999999999988  4443334456776543100   0                  011111    1111 1378999


Q ss_pred             CCCCCCc-cChhHHH-HhhcCC--CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           81 DVWNEDY-YKWEPFY-KCLKNS--LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        81 dv~~~~~-~~~~~~~-~~~~~~--~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      |++.... ..|+... ..+...  ..+.++|+||+.+         ++...+....++++.+++.++-.+++.+.+...+
T Consensus       105 di~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~  184 (235)
T PRK08084        105 NIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRARLRG  184 (235)
T ss_pred             ChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcC
Confidence            9965321 2333222 222221  1224799999763         3333445557999999999999999877554322


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      .    .-.++++..|++.+.|..-.+..+-..+
T Consensus       185 ~----~l~~~v~~~L~~~~~~d~r~l~~~l~~l  213 (235)
T PRK08084        185 F----ELPEDVGRFLLKRLDREMRTLFMTLDQL  213 (235)
T ss_pred             C----CCCHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            1    1235677888888887776555544443

>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=98.04  E-value=6.3e-06  Score=57.78  Aligned_cols=57  Identities=30%  Similarity=0.543  Sum_probs=38.9

Q ss_pred             ccceEEecccccCCccccccccCc-cccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCc
Q 046115          384 CLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQ  448 (505)
Q Consensus       384 ~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~  448 (505)
                      +|++|+++       ++.+..+|. .+..+++|++|++++|. +..+|+ .+..+++|+.|++++|+
T Consensus         2 ~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    2 NLESLDLS-------NNKLTEIPPDSFSNLPNLETLDLSNNN-LTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TESEEEET-------SSTESEECTTTTTTGTTESEEEETSSS-ESEEETTTTTTSTTESEEEETSSS
T ss_pred             cCcEEECC-------CCCCCccCHHHHcCCCCCCEeEccCCc-cCccCHHHHcCCCCCCEEeCcCCc
Confidence            56677776       555666653 45677777777777777 566654 55777777777777775

...

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.04  E-value=5.4e-05  Score=78.32  Aligned_cols=103  Identities=10%  Similarity=0.087  Sum_probs=71.9

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++.-++|||+++......+..+++.+.......++|+||.+. .+... ......+.+..++.++..+.+.......+. 
T Consensus       118 gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI-  196 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERI-  196 (830)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCC-
Confidence            455688899998877666788888887776677777777764 33221 233468899999999999999876643322 


Q ss_pred             CCCchHHHHHHHHHHHcCCCh-HHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLP-LAAKTIAS  178 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~P-lal~~~~~  178 (505)
                         .-.++.+..|++.++|.. -++..+-.
T Consensus       197 ---~id~eAL~lIA~~A~GsmRdALsLLdQ  223 (830)
T PRK07003        197 ---AFEPQALRLLARAAQGSMRDALSLTDQ  223 (830)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence               123567888999998865 45555433

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.03  E-value=0.00015  Score=70.97  Aligned_cols=96  Identities=13%  Similarity=0.199  Sum_probs=66.2

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++......+..+...+......+.+|++|.+. .+...+ .....+++.+++.++..+.+...+...+. 
T Consensus       118 ~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~-  196 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESI-  196 (363)
T ss_pred             CCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCC-
Confidence            356699999997766555677888777766666666666553 333322 23468899999999999888776533221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                         .-.++++..|++.++|.|-
T Consensus       197 ---~i~~~al~~ia~~s~G~~R  215 (363)
T PRK14961        197 ---DTDEYALKLIAYHAHGSMR  215 (363)
T ss_pred             ---CCCHHHHHHHHHHcCCCHH
Confidence               1234667889999999885

>PRK08727 hypothetical protein; Validated

Probab=98.03  E-value=0.00011  Score=67.13  Aligned_cols=141  Identities=16%  Similarity=0.107  Sum_probs=82.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||.||..+++  +..++...+++++..+.      ...+.               ...    +.+ ...-+||+|
T Consensus        49 ~~G~GKThL~~a~~~--~~~~~~~~~~y~~~~~~------~~~~~---------------~~~----~~l-~~~dlLiID  100 (233)
T PRK08727         49 PAGTGKTHLALALCA--AAEQAGRSSAYLPLQAA------AGRLR---------------DAL----EAL-EGRSLVALD  100 (233)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEEeHHHh------hhhHH---------------HHH----HHH-hcCCEEEEe
Confidence            379999999999988  44444445667764321      11110               011    111 123489999


Q ss_pred             CCCCCCc-cChh-HHHHhhcCC-CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           81 DVWNEDY-YKWE-PFYKCLKNS-LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        81 dv~~~~~-~~~~-~~~~~~~~~-~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      |+..... ..+. .+...+... ..+..+|+|++..         ++.........+++++++.++-.+++.+.+...+.
T Consensus       101 Di~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l  180 (233)
T PRK08727        101 GLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRGL  180 (233)
T ss_pred             CcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHHHcCC
Confidence            9964321 1222 233322221 2456799999862         22223334568899999999999999986644322


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                          .-.++++..|++.+.|..-.+
T Consensus       181 ----~l~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        181 ----ALDEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             ----CCCHHHHHHHHHhCCCCHHHH
Confidence                122466778888887665444

>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=98.03  E-value=6.2e-06  Score=53.03  Aligned_cols=34  Identities=38%  Similarity=0.583  Sum_probs=15.8

Q ss_pred             CcceeeccCCccccccchhhhcCCCCcEEecCCCc
Q 046115          414 HLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQ  448 (505)
Q Consensus       414 ~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~  448 (505)
                      +|++|++++|+ ++.+|+.+++|++|++|++++|+
T Consensus         2 ~L~~L~l~~N~-i~~l~~~l~~l~~L~~L~l~~N~   35 (44)
T PF12799_consen    2 NLEELDLSNNQ-ITDLPPELSNLPNLETLNLSNNP   35 (44)
T ss_dssp             T-SEEEETSSS--SSHGGHGTTCTTSSEEEETSSC
T ss_pred             cceEEEccCCC-CcccCchHhCCCCCCEEEecCCC
Confidence            34455555554 44444444555555555555544

...

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=98.02  E-value=7.7e-07  Score=83.24  Aligned_cols=136  Identities=24%  Similarity=0.292  Sum_probs=96.7

Q ss_pred             CCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCccee
Q 046115          340 RGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYL  418 (505)
Q Consensus       340 ~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L  418 (505)
                      ...++|.++|      .....+.|..|.++..   +|..|+.+.+||.|+|+       +|.+..+ |..|.++..|..|
T Consensus        57 GL~eVP~~LP------~~tveirLdqN~I~~i---P~~aF~~l~~LRrLdLS-------~N~Is~I~p~AF~GL~~l~~L  120 (498)
T KOG4237|consen   57 GLTEVPANLP------PETVEIRLDQNQISSI---PPGAFKTLHRLRRLDLS-------KNNISFIAPDAFKGLASLLSL  120 (498)
T ss_pred             CcccCcccCC------CcceEEEeccCCcccC---Chhhccchhhhceeccc-------ccchhhcChHhhhhhHhhhHH
Confidence            3455666655      4566777888877654   67778888888888888       5555554 6778888887777


Q ss_pred             eccCCccccccch-hhhcCCCCcEEecCCCcCccccc-hhccccccCceeecCCCcccccccc-cccCCccCCcccee
Q 046115          419 NLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELP-RGIGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVREF  493 (505)
Q Consensus       419 ~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~~  493 (505)
                      -+-++..++.+|+ .+..|..|+.|.+.-|+ +.-++ ..++.|++|..|.+-.|. +.+++. .|..+.+++++++-
T Consensus       121 vlyg~NkI~~l~k~~F~gL~slqrLllNan~-i~Cir~~al~dL~~l~lLslyDn~-~q~i~~~tf~~l~~i~tlhlA  196 (498)
T KOG4237|consen  121 VLYGNNKITDLPKGAFGGLSSLQRLLLNANH-INCIRQDALRDLPSLSLLSLYDNK-IQSICKGTFQGLAAIKTLHLA  196 (498)
T ss_pred             HhhcCCchhhhhhhHhhhHHHHHHHhcChhh-hcchhHHHHHHhhhcchhcccchh-hhhhccccccchhccchHhhh
Confidence            7666444888886 45788888888888887 55444 457888888888887776 556665 57777777777654

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.00  E-value=0.00013  Score=74.60  Aligned_cols=96  Identities=13%  Similarity=0.146  Sum_probs=67.4

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHH-HHhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVA-RIMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~-~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+...+.....+..+|++|.+. .+. +.......+++.+++.++..+.+.......+. 
T Consensus       117 gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI-  195 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQI-  195 (702)
T ss_pred             CCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCC-
Confidence            466789999998766556777888777766666777766653 222 22234568999999999999998876643322 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                         .-..+++..|++.++|.+.
T Consensus       196 ---~id~eAL~~IA~~S~GdLR  214 (702)
T PRK14960        196 ---AADQDAIWQIAESAQGSLR  214 (702)
T ss_pred             ---CCCHHHHHHHHHHcCCCHH
Confidence               2235668889999999774

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

Probab=97.98  E-value=1.4e-05  Score=73.13  Aligned_cols=83  Identities=17%  Similarity=0.135  Sum_probs=52.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC--CCHHHHHHHHHHHcCCCCCCCh--h---cHHHHHHHHHHH-cCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP--FDEFRIARAIIESLTPGSAKDL--V---EFQSLMQHIEEC-VAG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~--~~~~~~~~~l~~~l~~~~~~~~--~---~~~~~~~~l~~~-l~~   72 (505)
                      .+|+|||||++.+++.... .+|+.++|+.+...  .+..++++.+...+-......+  .   -.....+..... -.+
T Consensus        24 ~~G~GKTTLlr~I~n~l~~-~~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~~~~~~G  102 (249)
T cd01128          24 PPKAGKTTLLQSIANAITK-NHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHG  102 (249)
T ss_pred             CCCCCHHHHHHHHHhcccc-ccCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence            4799999999999985322 37899999986665  7888999998333321111111  1   111222222222 247


Q ss_pred             ceEEEEEeCCCC
Q 046115           73 KKFLLVLDDVWN   84 (505)
Q Consensus        73 ~r~LlvlDdv~~   84 (505)
                      +++++++|++.+
T Consensus       103 ~~vll~iDei~r  114 (249)
T cd01128         103 KDVVILLDSITR  114 (249)
T ss_pred             CCEEEEEECHHH
Confidence            899999999954

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.96  E-value=4.7e-05  Score=77.23  Aligned_cols=98  Identities=15%  Similarity=0.178  Sum_probs=67.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++......+..+...+......+.+|+++.. ..+...+ .....+++.+++.++..+.+...+...+. 
T Consensus       115 ~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi-  193 (504)
T PRK14963        115 GGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGR-  193 (504)
T ss_pred             CCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            45668999999776655677788887776555555555543 3333222 23568999999999999999887643332 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                         .-.++++..|++.++|.+--+
T Consensus       194 ---~i~~~Al~~ia~~s~GdlR~a  214 (504)
T PRK14963        194 ---EAEPEALQLVARLADGAMRDA  214 (504)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHH
Confidence               113567889999999998544

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=97.96  E-value=4.5e-06  Score=83.30  Aligned_cols=145  Identities=28%  Similarity=0.397  Sum_probs=99.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCC-CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLR-GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      ....+.+..+....++....    .+. +|+.|++..|.+..    +|..+..+++|+.|+++       .+.+..+|..
T Consensus       117 ~l~~L~l~~n~i~~i~~~~~----~~~~nL~~L~l~~N~i~~----l~~~~~~l~~L~~L~l~-------~N~l~~l~~~  181 (394)
T COG4886         117 NLTSLDLDNNNITDIPPLIG----LLKSNLKELDLSDNKIES----LPSPLRNLPNLKNLDLS-------FNDLSDLPKL  181 (394)
T ss_pred             ceeEEecCCcccccCccccc----cchhhcccccccccchhh----hhhhhhccccccccccC-------Cchhhhhhhh
Confidence            45666666666666655442    342 78888888887643    43446777888888887       7777777776


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      .+.++.|+.|++++|+ +..+|..+..+.+|+++.+++|+ ....|..+.+++++..+.+.+|. ...+|..++.+++|+
T Consensus       182 ~~~~~~L~~L~ls~N~-i~~l~~~~~~~~~L~~l~~~~N~-~~~~~~~~~~~~~l~~l~l~~n~-~~~~~~~~~~l~~l~  258 (394)
T COG4886         182 LSNLSNLNNLDLSGNK-ISDLPPEIELLSALEELDLSNNS-IIELLSSLSNLKNLSGLELSNNK-LEDLPESIGNLSNLE  258 (394)
T ss_pred             hhhhhhhhheeccCCc-cccCchhhhhhhhhhhhhhcCCc-ceecchhhhhcccccccccCCce-eeeccchhccccccc
Confidence            6677888888888888 77787766677778888888876 55666667777777777777776 334455566666666


Q ss_pred             ccce
Q 046115          489 RVRE  492 (505)
Q Consensus       489 ~L~~  492 (505)
                      .|++
T Consensus       259 ~L~~  262 (394)
T COG4886         259 TLDL  262 (394)
T ss_pred             eecc
Confidence            6554

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.93  E-value=0.00024  Score=72.33  Aligned_cols=104  Identities=13%  Similarity=0.134  Sum_probs=69.7

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|++..........++..+......+.+| +||....+... ......+++.+++.++....+.......+.
T Consensus       117 ~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi  196 (546)
T PRK14957        117 QGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENI  196 (546)
T ss_pred             cCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCC
Confidence            3566799999997776667778888888765555555 55544434322 233568999999999988888765432221


Q ss_pred             CCCCchHHHHHHHHHHHcCCCh-HHHHHHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLP-LAAKTIAS  178 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~P-lal~~~~~  178 (505)
                          .-.++++..|++.++|.+ .|+..+-.
T Consensus       197 ----~~e~~Al~~Ia~~s~GdlR~alnlLek  223 (546)
T PRK14957        197 ----NSDEQSLEYIAYHAKGSLRDALSLLDQ  223 (546)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence                223566788999999966 45555543

>PRK05642 DNA replication initiation factor; Validated

Probab=97.93  E-value=0.00015  Score=66.38  Aligned_cols=147  Identities=17%  Similarity=0.189  Sum_probs=86.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      +|+|||.||+.+++  +...+-..++|++..+      +...               ..    .+.+.+.+-. +||+||
T Consensus        54 ~G~GKTHLl~a~~~--~~~~~~~~v~y~~~~~------~~~~---------------~~----~~~~~~~~~d-~LiiDD  105 (234)
T PRK05642         54 DGVGRSHLLQAACL--RFEQRGEPAVYLPLAE------LLDR---------------GP----ELLDNLEQYE-LVCLDD  105 (234)
T ss_pred             CCCCHHHHHHHHHH--HHHhCCCcEEEeeHHH------HHhh---------------hH----HHHHhhhhCC-EEEEec
Confidence            69999999999987  4443334567777532      1110               01    1222222222 688999


Q ss_pred             CCCCC-ccChhH-HHHhhcCC-CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           82 VWNED-YYKWEP-FYKCLKNS-LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        82 v~~~~-~~~~~~-~~~~~~~~-~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +.... ...|+. +...+... ..|.++|+|++..         ++...+....++++.+++.++-.++++..+...+. 
T Consensus       106 i~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~~~~-  184 (234)
T PRK05642        106 LDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASRRGL-  184 (234)
T ss_pred             hhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCC-
Confidence            96432 123333 33333322 3466799988752         22223334468899999999999999865543221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      .   -.++++..|++.+.+..-.+..+-..|
T Consensus       185 ~---l~~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        185 H---LTDEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             C---CCHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            1   124677888888888776555554444

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.92  E-value=0.00025  Score=68.15  Aligned_cols=147  Identities=15%  Similarity=0.113  Sum_probs=89.8

Q ss_pred             CCCCcHHHHHHHHhcCc----ccccCCCceEEEEe-CCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceE
Q 046115            1 MGGIGKTTLAQFAYNNG----DVERNFEKRTWVCV-SEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~----~~~~~f~~~~wv~~-~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~   75 (505)
                      +.|+|||++|+.++..-    ....+.|...|... +......+ .+++.+.+..                 .-..+++-
T Consensus        34 ~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~-ir~~~~~~~~-----------------~p~~~~~k   95 (313)
T PRK05564         34 EDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDD-IRNIIEEVNK-----------------KPYEGDKK   95 (313)
T ss_pred             CCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHH-HHHHHHHHhc-----------------CcccCCce
Confidence            46999999999998721    11223343344331 22222212 3333333321                 01124556


Q ss_pred             EEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHH-HHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCc
Q 046115           76 LLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETV-ARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRE  153 (505)
Q Consensus        76 LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~-~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~  153 (505)
                      ++|+|+++......+..+.+.+.+...++.+|++|.+.+- .+. ......+.+.+++.++....+.....   .     
T Consensus        96 v~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~---~-----  167 (313)
T PRK05564         96 VIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYN---D-----  167 (313)
T ss_pred             EEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhc---C-----
Confidence            7778888666666788899999988888888888876532 221 12245889999999999888865431   1     


Q ss_pred             hHHHHHHHHHHHcCCChHHH
Q 046115          154 NLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       154 ~~~~~~~~i~~~~~g~Plal  173 (505)
                      ..++.+..++..++|.|.-.
T Consensus       168 ~~~~~~~~l~~~~~g~~~~a  187 (313)
T PRK05564        168 IKEEEKKSAIAFSDGIPGKV  187 (313)
T ss_pred             CCHHHHHHHHHHcCCCHHHH
Confidence            11344678899999988643

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=0.00014  Score=74.29  Aligned_cols=104  Identities=13%  Similarity=0.120  Sum_probs=69.6

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEE-EeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILI-TTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLi-Ttr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .++.-++|+|+++......+..+++.+.....++.+|+ ||....+...+ .....+.+..++.++..+.+.......+.
T Consensus       122 ~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi  201 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGI  201 (700)
T ss_pred             cCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCC
Confidence            34667999999988776677888888877655555554 55444443322 22458899999999999988876533222


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                          ....+.+..|++.++|.|. ++..+-.
T Consensus       202 ----~~d~eAL~~IA~~A~Gs~RdALsLLdQ  228 (700)
T PRK12323        202 ----AHEVNALRLLAQAAQGSMRDALSLTDQ  228 (700)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence                1224567889999999985 3433333

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.88  E-value=0.00039  Score=69.76  Aligned_cols=96  Identities=13%  Similarity=0.146  Sum_probs=67.7

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++.-++|+|++..........+.+.+.+....+.+|++| ....+...+ .....+++.+++.++..+.+...+...+. 
T Consensus       115 ~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi-  193 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENI-  193 (491)
T ss_pred             CCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCC-
Confidence            456689999997766656778888888766666665555 434444332 33568899999999999999887643332 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                         .-.++++..|++.++|.+-
T Consensus       194 ---~i~~eAL~lIa~~s~GslR  212 (491)
T PRK14964        194 ---EHDEESLKLIAENSSGSMR  212 (491)
T ss_pred             ---CCCHHHHHHHHHHcCCCHH
Confidence               1235668889999999875

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.87  E-value=7.3e-05  Score=75.55  Aligned_cols=97  Identities=15%  Similarity=0.174  Sum_probs=68.3

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|+++......+..+...+......+.+| +||+...+...+ .....+++.+++.++....+...+...+.
T Consensus       126 ~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi  205 (507)
T PRK06645        126 QGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENL  205 (507)
T ss_pred             cCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCC
Confidence            3567789999998766667788888887766666655 455555554433 23457899999999999999877643332


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                          .-.++++..|++.++|.+-
T Consensus       206 ----~ie~eAL~~Ia~~s~GslR  224 (507)
T PRK06645        206 ----KTDIEALRIIAYKSEGSAR  224 (507)
T ss_pred             ----CCCHHHHHHHHHHcCCCHH
Confidence                1234667889999999774

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=97.84  E-value=8.3e-06  Score=77.53  Aligned_cols=114  Identities=24%  Similarity=0.317  Sum_probs=82.0

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccc--h
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP--E  431 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp--~  431 (505)
                      .+++|..|.+++|.++|.  .+......+++|.+|+|+      .|+.+........-++.|+.|+|++|.++. ++  .
T Consensus       195 ~l~~lK~L~l~~CGls~k--~V~~~~~~fPsl~~L~L~------~N~~~~~~~~~~~i~~~L~~LdLs~N~li~-~~~~~  265 (505)
T KOG3207|consen  195 LLSHLKQLVLNSCGLSWK--DVQWILLTFPSLEVLYLE------ANEIILIKATSTKILQTLQELDLSNNNLID-FDQGY  265 (505)
T ss_pred             hhhhhheEEeccCCCCHH--HHHHHHHhCCcHHHhhhh------cccccceecchhhhhhHHhhccccCCcccc-ccccc
Confidence            567899999999998864  366677888999999998      233333333334567889999999998443 33  3


Q ss_pred             hhhcCCCCcEEecCCCcCccc--cchh-----ccccccCceeecCCCccccccc
Q 046115          432 TLCELYNLERLNVDDCQNLRE--LPRG-----IGKLRKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~--lp~~-----~~~l~~L~~L~l~~~~~~~~~p  478 (505)
                      .++.++.|+.|+++.|. +.+  +|+.     ...+++|+.|++..|+ +..++
T Consensus       266 ~~~~l~~L~~Lnls~tg-i~si~~~d~~s~~kt~~f~kL~~L~i~~N~-I~~w~  317 (505)
T KOG3207|consen  266 KVGTLPGLNQLNLSSTG-IASIAEPDVESLDKTHTFPKLEYLNISENN-IRDWR  317 (505)
T ss_pred             ccccccchhhhhccccC-cchhcCCCccchhhhcccccceeeecccCc-ccccc
Confidence            47888999999999888 443  3443     4667889999999987 44454

>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=97.84  E-value=2.1e-05  Score=50.60  Aligned_cols=40  Identities=25%  Similarity=0.426  Sum_probs=33.2

Q ss_pred             CCCcEEecCCCcCccccchhccccccCceeecCCCccccccc
Q 046115          437 YNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p  478 (505)
                      ++|++|++++|. +..+|+.+++|++|+.|++++|+ +..+|
T Consensus         1 ~~L~~L~l~~N~-i~~l~~~l~~l~~L~~L~l~~N~-i~~i~   40 (44)
T PF12799_consen    1 KNLEELDLSNNQ-ITDLPPELSNLPNLETLNLSNNP-ISDIS   40 (44)
T ss_dssp             TT-SEEEETSSS--SSHGGHGTTCTTSSEEEETSSC-CSBEG
T ss_pred             CcceEEEccCCC-CcccCchHhCCCCCCEEEecCCC-CCCCc
Confidence            479999999998 88999989999999999999997 44443

...

>PF14516 AAA_35: AAA-like domain

Probab=97.83  E-value=0.0017  Score=62.81  Aligned_cols=171  Identities=13%  Similarity=0.112  Sum_probs=94.9

Q ss_pred             CCCcHHHHHHHHhcCccccc-CCCceEEEEeCCC-----CCHHHHHHHH----HHHcCCCCCC------ChhcHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEP-----FDEFRIARAI----IESLTPGSAK------DLVEFQSLMQH   65 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~-----~~~~~~~~~l----~~~l~~~~~~------~~~~~~~~~~~   65 (505)
                      -.+|||+|..++.+  .... .| .++++++...     .+....++.+    .++++.....      ...........
T Consensus        40 Rq~GKTSll~~l~~--~l~~~~~-~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~  116 (331)
T PF14516_consen   40 RQMGKTSLLLRLLE--RLQQQGY-RCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEY  116 (331)
T ss_pred             ccCCHHHHHHHHHH--HHHHCCC-EEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHH
Confidence            36899999999887  4433 34 4447876652     2344444444    4454432210      01111122233


Q ss_pred             HHHHc---CCceEEEEEeCCCCCCc-c-----ChhHHHHhhcCCC----CCcE--EEEEeCchHHHHH-----hCCcceE
Q 046115           66 IEECV---AGKKFLLVLDDVWNEDY-Y-----KWEPFYKCLKNSL----HESK--ILITTRKETVARI-----MGSTHVI  125 (505)
Q Consensus        66 l~~~l---~~~r~LlvlDdv~~~~~-~-----~~~~~~~~~~~~~----~~~~--iLiTtr~~~~~~~-----~~~~~~~  125 (505)
                      +.+.+   .+++.+|++|+++..-. .     -+..+........    ...-  |++.+........     ......+
T Consensus       117 ~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i  196 (331)
T PF14516_consen  117 FEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPI  196 (331)
T ss_pred             HHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCcccccce
Confidence            33322   25899999999954221 1     1122222222111    1112  2333222111111     1224478


Q ss_pred             eCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccC
Q 046115          126 SVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSK  183 (505)
Q Consensus       126 ~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~  183 (505)
                      .+++|+.+|...|...+...     .   ....+.+|...++|||..+..++..+...
T Consensus       197 ~L~~Ft~~ev~~L~~~~~~~-----~---~~~~~~~l~~~tgGhP~Lv~~~~~~l~~~  246 (331)
T PF14516_consen  197 ELPDFTPEEVQELAQRYGLE-----F---SQEQLEQLMDWTGGHPYLVQKACYLLVEE  246 (331)
T ss_pred             eCCCCCHHHHHHHHHhhhcc-----C---CHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            89999999999999876421     1   12338899999999999999999999765

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.79  E-value=0.00035  Score=72.22  Aligned_cols=103  Identities=13%  Similarity=0.116  Sum_probs=67.3

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+++.+......+++|++|.+ ..+... ......+.+..++.++....+.......+. 
T Consensus       118 gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi-  196 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKI-  196 (709)
T ss_pred             CCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            45668999999766554566677777765555666666654 322211 223346788899999999999876643332 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                         .-.++.+..|++.++|.+. ++..+-.
T Consensus       197 ---~id~eAL~~Ia~~A~GslRdAlnLLDq  223 (709)
T PRK08691        197 ---AYEPPALQLLGRAAAGSMRDALSLLDQ  223 (709)
T ss_pred             ---CcCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence               1235678899999999884 4444433

>PRK09087 hypothetical protein; Validated

Probab=97.78  E-value=0.00042  Score=62.84  Aligned_cols=100  Identities=13%  Similarity=0.146  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCccChhHHHHhhcCC-CCCcEEEEEeCc---------hHHHHHhCCcceEeCCCCChhhHHHHHHHhhhC
Q 046115           76 LLVLDDVWNEDYYKWEPFYKCLKNS-LHESKILITTRK---------ETVARIMGSTHVISVNVLSEMECWSVFQSLAIS  145 (505)
Q Consensus        76 LlvlDdv~~~~~~~~~~~~~~~~~~-~~~~~iLiTtr~---------~~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~  145 (505)
                      +|++||+..... .-+.+...+... ..|..+|+|++.         +++...+....++++++++.++-.+++++.+..
T Consensus        90 ~l~iDDi~~~~~-~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~  168 (226)
T PRK09087         90 PVLIEDIDAGGF-DETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFAD  168 (226)
T ss_pred             eEEEECCCCCCC-CHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHH
Confidence            788899954321 122333333322 236789999874         344445556679999999999999999887744


Q ss_pred             CCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          146 GKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       146 ~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      .+. .   -.++++..|++.+.|..-++..+-..+
T Consensus       169 ~~~-~---l~~ev~~~La~~~~r~~~~l~~~l~~L  199 (226)
T PRK09087        169 RQL-Y---VDPHVVYYLVSRMERSLFAAQTIVDRL  199 (226)
T ss_pred             cCC-C---CCHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            322 1   225677888888888777666544433

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.78  E-value=0.00041  Score=71.89  Aligned_cols=102  Identities=11%  Similarity=0.131  Sum_probs=69.7

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|+++.........+++.+......+++|.+|.+ ..+... ......+.+.+++.++....+.......+.
T Consensus       117 ~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i  196 (647)
T PRK07994        117 RGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQI  196 (647)
T ss_pred             cCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcCC
Confidence            456679999999887776788888888876666555554444 444322 223568899999999999988776532221


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH-HHHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL-AAKTI  176 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl-al~~~  176 (505)
                          ...++.+..|++.++|.+- |+..+
T Consensus       197 ----~~e~~aL~~Ia~~s~Gs~R~Al~ll  221 (647)
T PRK07994        197 ----PFEPRALQLLARAADGSMRDALSLT  221 (647)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                1234667889999999875 44443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.78  E-value=0.00031  Score=64.15  Aligned_cols=144  Identities=13%  Similarity=0.152  Sum_probs=83.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||+.+++  +....=..+++++......          .+                   ... ...-+||+|
T Consensus        50 ~~G~GKT~La~ai~~--~~~~~~~~~~~i~~~~~~~----------~~-------------------~~~-~~~~~liiD   97 (227)
T PRK08903         50 EAGSGRSHLLQALVA--DASYGGRNARYLDAASPLL----------AF-------------------DFD-PEAELYAVD   97 (227)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCcEEEEehHHhHH----------HH-------------------hhc-ccCCEEEEe
Confidence            379999999999998  3322222445666443110          00                   011 123478899


Q ss_pred             CCCCCCccChhHHHHhhcCC-CCCc-EEEEEeCchHH--------HHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           81 DVWNEDYYKWEPFYKCLKNS-LHES-KILITTRKETV--------ARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~-~~~~-~iLiTtr~~~~--------~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      |+..........+...+... ..+. .+++|++....        ...+.....+.+++++.++-..++...+-..+.  
T Consensus        98 di~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v--  175 (227)
T PRK08903         98 DVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAAAERGL--  175 (227)
T ss_pred             ChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHHHHcCC--
Confidence            99654433334444444332 1233 46666664321        112223368899999998877777654322221  


Q ss_pred             CCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          151 KRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                        .-.++++..+++.+.|.+..+..+-..+
T Consensus       176 --~l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        176 --QLADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             --CCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence              1234678888889999998877776665

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

Probab=97.77  E-value=0.0057  Score=59.55  Aligned_cols=263  Identities=13%  Similarity=0.140  Sum_probs=140.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC-c-eEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC--CceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE-K-RTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA--GKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~-~-~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~--~~r~L   76 (505)
                      .+|+|||+.++.+++  ++..... . +++|++....+...++..|+++++ ..........+....+.+.+.  ++.++
T Consensus        50 ~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~-~~p~~g~~~~~~~~~l~~~~~~~~~~~I  126 (366)
T COG1474          50 PTGTGKTATVKFVME--ELEESSANVEVVYINCLELRTPYQVLSKILNKLG-KVPLTGDSSLEILKRLYDNLSKKGKTVI  126 (366)
T ss_pred             CCCCCHhHHHHHHHH--HHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcC-CCCCCCCchHHHHHHHHHHHHhcCCeEE
Confidence            379999999999998  5555432 2 689999999999999999999998 444445566667777777774  47899


Q ss_pred             EEEeCCCCCCccChhHHHHhhcCCCC-CcE--EEEEeCchHHHHHh----C---CcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           77 LVLDDVWNEDYYKWEPFYKCLKNSLH-ESK--ILITTRKETVARIM----G---STHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        77 lvlDdv~~~~~~~~~~~~~~~~~~~~-~~~--iLiTtr~~~~~~~~----~---~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +|||+++.-....-+.+...+..... .++  ++..+.+-......    .   ....+..++-+.+|-.+++...+...
T Consensus       127 vvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~  206 (366)
T COG1474         127 VILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEG  206 (366)
T ss_pred             EEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhh
Confidence            99999955322111222222222222 233  34444443322211    1   12347788888999888887766321


Q ss_pred             -CCCCCCchHHHHHHHHHHHcCC-ChHHHHHHHH--HhccCC-----CHHHHHHHHhhhhhhhhhcccCchhhHhhcccc
Q 046115          147 -KTIGKRENLEKIGREIVKKCKG-LPLAAKTIAS--LLRSKN-----TEKEWQNILENEIWELEAIEKGLLAPLLLSYNE  217 (505)
Q Consensus       147 -~~~~~~~~~~~~~~~i~~~~~g-~Plal~~~~~--~l~~~~-----~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~  217 (505)
                       .....++..-+.+..++..-+| -=.|+..+..  .+++..     +...-....+          ..-...+.-.+..
T Consensus       207 ~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~----------~~~~~~~~~~~~~  276 (366)
T COG1474         207 FSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQE----------EIERDVLEEVLKT  276 (366)
T ss_pred             ccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHH----------HhhHHHHHHHHHc
Confidence             1112223333334444444443 3344433332  222210     1111111100          0111223344677


Q ss_pred             CChhhhhhhhhhccCCCCCCCChHHHHHHH--HHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccC
Q 046115          218 LPSKVKRCFSYCAVFPKDYGIRKHKLIELW--MAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKY  284 (505)
Q Consensus       218 L~~~~~~~ll~la~f~~~~~i~~~~l~~~w--~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~  284 (505)
                      |+.+++..++.++...  ..+....+-...  +...+-.      ......+++.+|...|++.....+
T Consensus       277 L~~~~ki~L~~i~~~~--~~~~~~~~y~~y~~~~~~~~~------~~~~~~~ii~~L~~lgiv~~~~~~  337 (366)
T COG1474         277 LPLHQKIVLLAIVELT--VEISTGELYDVYESLCERLRT------SQRRFSDIISELEGLGIVSASLIS  337 (366)
T ss_pred             CCHhHHHHHHHHHHhc--CCCChHHHHHHHHHHHhhhCc------hHHHHHHHHHHHHhcCeEEeeecc
Confidence            7777776665555443  233333322221  1111111      334566778888888888754443

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=0.0011  Score=66.78  Aligned_cols=118  Identities=19%  Similarity=0.184  Sum_probs=72.1

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.-.......+...+......+.++++|.+ ..+...+ .....+.+.+++.++....+...+...+. 
T Consensus       116 ~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi-  194 (472)
T PRK14962        116 GKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGI-  194 (472)
T ss_pred             CCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCC-
Confidence            46679999999665544556677776665444554444433 3333322 33568899999999999988876643222 


Q ss_pred             CCCchHHHHHHHHHHHcCC-ChHHHHHHHHHhcc---CCCHHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKG-LPLAAKTIASLLRS---KNTEKEWQNIL  193 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g-~Plal~~~~~~l~~---~~~~~~~~~~l  193 (505)
                         .-.++++..|++.++| .+.++..+-.....   .-+.+.....+
T Consensus       195 ---~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~~~It~e~V~~~l  239 (472)
T PRK14962        195 ---EIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITLETVHEAL  239 (472)
T ss_pred             ---CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence               1224667888887865 46677766554322   12444444444

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.76  E-value=0.00054  Score=67.30  Aligned_cols=92  Identities=11%  Similarity=0.053  Sum_probs=63.7

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+.+.+.....++.+|++|.+. .+...+ .....+.+.+++.++..+.+.....     
T Consensus       116 ~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~-----  190 (394)
T PRK07940        116 GRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDG-----  190 (394)
T ss_pred             CCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcC-----
Confidence            455588889998876656677888777766667666666663 333222 2346889999999999988874321     


Q ss_pred             CCCchHHHHHHHHHHHcCCChHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                       -   .++.+..++..++|.|..
T Consensus       191 -~---~~~~a~~la~~s~G~~~~  209 (394)
T PRK07940        191 -V---DPETARRAARASQGHIGR  209 (394)
T ss_pred             -C---CHHHHHHHHHHcCCCHHH
Confidence             1   135577899999999953

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.74  E-value=0.0005  Score=70.04  Aligned_cols=101  Identities=13%  Similarity=0.129  Sum_probs=66.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++.-++|+|+++.........+.+.+......+++|++|.+ ..+...+ .....+++.+++.++....+.......+. 
T Consensus       118 ~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi-  196 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENV-  196 (509)
T ss_pred             CCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            45668899999877666777788887776566666655544 3333221 22457889999999988877666533222 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKTI  176 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~~  176 (505)
                         .-.++.+..|++.++|.+. |+..+
T Consensus       197 ---~~~~~al~~ia~~s~GslR~al~lL  221 (509)
T PRK14958        197 ---EFENAALDLLARAANGSVRDALSLL  221 (509)
T ss_pred             ---CCCHHHHHHHHHHcCCcHHHHHHHH
Confidence               1234567889999999884 43334

>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=97.74  E-value=0.00014  Score=61.13  Aligned_cols=99  Identities=17%  Similarity=0.133  Sum_probs=53.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||++|+++++  .....-..+++++..+..........+...             ............++.+||+|
T Consensus        27 ~~G~GKT~l~~~i~~--~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~lilD   91 (151)
T cd00009          27 PPGTGKTTLARAIAN--ELFRPGAPFLYLNASDLLEGLVVAELFGHF-------------LVRLLFELAEKAKPGVLFID   91 (151)
T ss_pred             CCCCCHHHHHHHHHH--HhhcCCCCeEEEehhhhhhhhHHHHHhhhh-------------hHhHHHHhhccCCCeEEEEe
Confidence            479999999999998  443333456677665533322211111100             01111122334567899999


Q ss_pred             CCCCCCccChhHHHHhhcCC------CCCcEEEEEeCchH
Q 046115           81 DVWNEDYYKWEPFYKCLKNS------LHESKILITTRKET  114 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~------~~~~~iLiTtr~~~  114 (505)
                      |++.........+...+...      ..++.+++||....
T Consensus        92 e~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          92 EIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             ChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence            99754222223333333332      36788888888653

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.74  E-value=0.00088  Score=65.29  Aligned_cols=99  Identities=12%  Similarity=0.012  Sum_probs=62.7

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      .+-+||+||+..........+...+......+++++|+..+ .+.... .....+.+.+++.++...++...+...+.. 
T Consensus       125 ~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~-  203 (337)
T PRK12402        125 DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVD-  203 (337)
T ss_pred             CCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCC-
Confidence            34589999996554333445555555555557777777543 222222 224578889999999999998765432221 


Q ss_pred             CCchHHHHHHHHHHHcCCChHHHHH
Q 046115          151 KRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                         -.++++..+++.++|.+-.+..
T Consensus       204 ---~~~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        204 ---YDDDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             ---CCHHHHHHHHHHcCCCHHHHHH
Confidence               2356788899999887755443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.73  E-value=5.4e-05  Score=72.55  Aligned_cols=83  Identities=17%  Similarity=0.173  Sum_probs=53.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC--CHHHHHHHHHHHcCCCCCCChhcHH-----HHHHHHHHH-cCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF--DEFRIARAIIESLTPGSAKDLVEFQ-----SLMQHIEEC-VAG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~--~~~~~~~~l~~~l~~~~~~~~~~~~-----~~~~~l~~~-l~~   72 (505)
                      ++|+||||||+++++... .++|+..+||.+.+..  +..++++.+...+-....+......     ...+.-... ..+
T Consensus       177 ppGvGKTTLaK~Ian~I~-~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~~e~G  255 (416)
T PRK09376        177 PPKAGKTVLLQNIANSIT-TNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVEHG  255 (416)
T ss_pred             CCCCChhHHHHHHHHHHH-hhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence            489999999999998422 2379999999888776  7777777776433222222221111     111111121 257


Q ss_pred             ceEEEEEeCCCC
Q 046115           73 KKFLLVLDDVWN   84 (505)
Q Consensus        73 ~r~LlvlDdv~~   84 (505)
                      ++++|++|++..
T Consensus       256 ~dVlL~iDsItR  267 (416)
T PRK09376        256 KDVVILLDSITR  267 (416)
T ss_pred             CCEEEEEEChHH
Confidence            899999999944

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.73  E-value=0.00013  Score=72.45  Aligned_cols=97  Identities=13%  Similarity=0.050  Sum_probs=66.9

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .++.-++|+|+++......+..++..+......+.+| .||....+...+ .....|.+.+++.++..+.+.......+.
T Consensus       119 ~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi  198 (484)
T PRK14956        119 GGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENV  198 (484)
T ss_pred             cCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCC
Confidence            4566799999998877667888888887655555544 444434443222 23457999999999998888776543222


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                          .-.++++..|++.++|.+.
T Consensus       199 ----~~e~eAL~~Ia~~S~Gd~R  217 (484)
T PRK14956        199 ----QYDQEGLFWIAKKGDGSVR  217 (484)
T ss_pred             ----CCCHHHHHHHHHHcCChHH
Confidence                1235678899999999983

>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=97.72  E-value=0.00033  Score=63.24  Aligned_cols=156  Identities=13%  Similarity=0.186  Sum_probs=88.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCC--ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFE--KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~--~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .|+|||.|..++++  +..+...  .+++++..      +....+...+..      ...    ..+...+. .-=+|++
T Consensus        43 ~G~GKTHLL~Ai~~--~~~~~~~~~~v~y~~~~------~f~~~~~~~~~~------~~~----~~~~~~~~-~~DlL~i  103 (219)
T PF00308_consen   43 SGLGKTHLLQAIAN--EAQKQHPGKRVVYLSAE------EFIREFADALRD------GEI----EEFKDRLR-SADLLII  103 (219)
T ss_dssp             TTSSHHHHHHHHHH--HHHHHCTTS-EEEEEHH------HHHHHHHHHHHT------TSH----HHHHHHHC-TSSEEEE
T ss_pred             CCCCHHHHHHHHHH--HHHhccccccceeecHH------HHHHHHHHHHHc------ccc----hhhhhhhh-cCCEEEE
Confidence            69999999999998  5554432  35566633      444455554441      111    22333333 2348899


Q ss_pred             eCCCCCCcc-Ch-hHHHHhhcCC-CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           80 DDVWNEDYY-KW-EPFYKCLKNS-LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        80 Ddv~~~~~~-~~-~~~~~~~~~~-~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      ||++.-... .| +.+...+... ..|.++|+|++..         ++...+.+...+++.+.+.++-.+++.+.+...+
T Consensus       104 DDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~  183 (219)
T PF00308_consen  104 DDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAKERG  183 (219)
T ss_dssp             ETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT
T ss_pred             ecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhC
Confidence            999653321 12 2233323222 3466899999652         2334445566899999999999999998875433


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      ..    -.++++.-|++.+.+..-.|..+-..+
T Consensus       184 ~~----l~~~v~~~l~~~~~~~~r~L~~~l~~l  212 (219)
T PF00308_consen  184 IE----LPEEVIEYLARRFRRDVRELEGALNRL  212 (219)
T ss_dssp             ------S-HHHHHHHHHHTTSSHHHHHHHHHHH
T ss_pred             CC----CcHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            32    235677788888877766655554433

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.0008  Score=69.60  Aligned_cols=98  Identities=11%  Similarity=0.160  Sum_probs=67.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++.-++|+|+++......+..+++.+......+.+|++| ....+.. .......+.+..++.++..+.+.......+. 
T Consensus       123 g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi-  201 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENV-  201 (618)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCC-
Confidence            345688999998877667777888877765565555554 4333332 2233568999999999999999876543322 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                         .-.++.+..|++.++|.+-.+
T Consensus       202 ---~ie~~AL~~La~~s~GslR~a  222 (618)
T PRK14951        202 ---PAEPQALRLLARAARGSMRDA  222 (618)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHH
Confidence               123466888999999977443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.67  E-value=0.00064  Score=68.29  Aligned_cols=160  Identities=20%  Similarity=0.222  Sum_probs=95.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCC--CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f--~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .|+|||.|++.+++  .+....  ..+++++.      .++...+...+....        .....+.+.+++ .-+||+
T Consensus       150 ~G~GKTHLl~Ai~~--~l~~~~~~~~v~yv~~------~~f~~~~~~~l~~~~--------~~~~~~~~~~~~-~dvLiI  212 (450)
T PRK14087        150 SGMGKTHLLKAAKN--YIESNFSDLKVSYMSG------DEFARKAVDILQKTH--------KEIEQFKNEICQ-NDVLII  212 (450)
T ss_pred             CCCcHHHHHHHHHH--HHHHhCCCCeEEEEEH------HHHHHHHHHHHHHhh--------hHHHHHHHHhcc-CCEEEE
Confidence            69999999999988  544322  23345543      355666666554110        122333444433 347889


Q ss_pred             eCCCCCCc--cChhHHHHhhcCC-CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           80 DDVWNEDY--YKWEPFYKCLKNS-LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        80 Ddv~~~~~--~~~~~~~~~~~~~-~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      ||++....  ...+.+...+... ..+..|++|+...         .+...+....++.+.+++.++-.+++.+.+...+
T Consensus       213 DDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~g  292 (450)
T PRK14087        213 DDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQN  292 (450)
T ss_pred             eccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHhcC
Confidence            99965431  1122333333321 3445788887642         1222334455888999999999999988774322


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      .  ...-.++++..|++.+.|.|-.+..+...+
T Consensus       293 l--~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l  323 (450)
T PRK14087        293 I--KQEVTEEAINFISNYYSDDVRKIKGSVSRL  323 (450)
T ss_pred             C--CCCCCHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            1  012335788999999999998877776544

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.66  E-value=5.9e-05  Score=73.04  Aligned_cols=115  Identities=20%  Similarity=0.277  Sum_probs=65.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      +..++.+.......+| .+      ..+|++|.+.++..-   ..+|..+.  .+|+.|.++      .+..+..+|+. 
T Consensus        53 ~l~~L~Is~c~L~sLP-~L------P~sLtsL~Lsnc~nL---tsLP~~LP--~nLe~L~Ls------~Cs~L~sLP~s-  113 (426)
T PRK15386         53 ASGRLYIKDCDIESLP-VL------PNELTEITIENCNNL---TTLPGSIP--EGLEKLTVC------HCPEISGLPES-  113 (426)
T ss_pred             CCCEEEeCCCCCcccC-CC------CCCCcEEEccCCCCc---ccCCchhh--hhhhheEcc------Ccccccccccc-
Confidence            5567777766666555 22      246888888774321   11343332  468888887      23355566653 


Q ss_pred             cCCCCcceeeccCCc--cccccchhhhcC------------------CCCcEEecCCCcCccccchhccccccCceeecC
Q 046115          410 EKLLHLKYLNLKGQK--KIEKLPETLCEL------------------YNLERLNVDDCQNLRELPRGIGKLRKLMYLHNE  469 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~--~~~~lp~~~~~l------------------~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~  469 (505)
                           |+.|++.++.  .+..+|+++..|                  .+|++|++++|. ...+|..+.  .+|++|.++
T Consensus       114 -----Le~L~L~~n~~~~L~~LPssLk~L~I~~~n~~~~~~lp~~LPsSLk~L~Is~c~-~i~LP~~LP--~SLk~L~ls  185 (426)
T PRK15386        114 -----VRSLEIKGSATDSIKNVPNGLTSLSINSYNPENQARIDNLISPSLKTLSLTGCS-NIILPEKLP--ESLQSITLH  185 (426)
T ss_pred             -----cceEEeCCCCCcccccCcchHhheeccccccccccccccccCCcccEEEecCCC-cccCccccc--ccCcEEEec
Confidence                 4445555433  256677655443                  257778888777 334554433  367777776


Q ss_pred             CC
Q 046115          470 DT  471 (505)
Q Consensus       470 ~~  471 (505)
                      .+
T Consensus       186 ~n  187 (426)
T PRK15386        186 IE  187 (426)
T ss_pred             cc
Confidence            54

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.65  E-value=0.0012  Score=64.23  Aligned_cols=97  Identities=9%  Similarity=0.094  Sum_probs=68.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++..+......+.+.+.....++.+|++|.+.. +...+ .....+.+.+++.++..+++.....     
T Consensus       140 ~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~-----  214 (365)
T PRK07471        140 GGWRVVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGP-----  214 (365)
T ss_pred             CCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcc-----
Confidence            4567899999988877777888888887766677777776643 32222 3356899999999999999977531     


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                       ...  .+.+..++..++|.|.....+
T Consensus       215 -~~~--~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        215 -DLP--DDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             -cCC--HHHHHHHHHHcCCCHHHHHHH
Confidence             111  122367899999999754333

>PLN03025 replication factor C subunit; Provisional

Probab=97.65  E-value=0.0007  Score=65.21  Aligned_cols=96  Identities=9%  Similarity=0.114  Sum_probs=62.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++.-++|+|+++.........+...+......+++++++... .+...+ .....+++.+++.++....+...+...+..
T Consensus        98 ~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~  177 (319)
T PLN03025         98 GRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVP  177 (319)
T ss_pred             CCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCC
Confidence            346799999997765544555666565555566676666442 222211 123478999999999999888776433321


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                          -.++.+..|++.++|..-
T Consensus       178 ----i~~~~l~~i~~~~~gDlR  195 (319)
T PLN03025        178 ----YVPEGLEAIIFTADGDMR  195 (319)
T ss_pred             ----CCHHHHHHHHHHcCCCHH
Confidence                124567889999988763

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.64  E-value=0.0016  Score=63.16  Aligned_cols=97  Identities=14%  Similarity=0.179  Sum_probs=65.7

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+++.+......+.+|++|.. ..+...+ .....+.+.+++.++..+++......    
T Consensus       140 g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~----  215 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSS----  215 (351)
T ss_pred             CCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcc----
Confidence            45678999999887766677788888766555554444443 3332222 23458999999999999999874311    


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAK  174 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~  174 (505)
                       .. -.++.+..+++.++|.|....
T Consensus       216 -~~-~~~~~~~~i~~~s~G~pr~Al  238 (351)
T PRK09112        216 -QG-SDGEITEALLQRSKGSVRKAL  238 (351)
T ss_pred             -cC-CCHHHHHHHHHHcCCCHHHHH
Confidence             11 123457789999999997543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.61  E-value=0.0022  Score=62.99  Aligned_cols=102  Identities=10%  Similarity=0.120  Sum_probs=66.9

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+...+......+.+|++|.+.. +...+ .....++..+++.++..+++...+...+. 
T Consensus       116 ~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~-  194 (355)
T TIGR02397       116 GKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGI-  194 (355)
T ss_pred             CCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCC-
Confidence            3556888999866554456677777766556666666665543 33222 23457888999999998888876533221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIA  177 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~  177 (505)
                         .-.++++..+++.++|.|..+....
T Consensus       195 ---~i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       195 ---KIEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             ---CCCHHHHHHHHHHcCCChHHHHHHH
Confidence               1124678889999999886554443

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.61  E-value=0.0014  Score=62.85  Aligned_cols=92  Identities=13%  Similarity=0.150  Sum_probs=64.2

Q ss_pred             eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCCC
Q 046115           74 KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTIGK  151 (505)
Q Consensus        74 r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~  151 (505)
                      +-++|+|+++.........+.+.+.....++.+|+||.+.. +... ......+.+.+++.+++.+.+.....   .   
T Consensus       107 ~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~---~---  180 (328)
T PRK05707        107 RKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALP---E---  180 (328)
T ss_pred             CeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhcc---c---
Confidence            33446799988777778888888888767777777777643 3322 23355789999999999998876420   1   


Q ss_pred             CchHHHHHHHHHHHcCCChHHH
Q 046115          152 RENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       152 ~~~~~~~~~~i~~~~~g~Plal  173 (505)
                        ...+.+..++..++|.|...
T Consensus       181 --~~~~~~~~~l~la~Gsp~~A  200 (328)
T PRK05707        181 --SDERERIELLTLAGGSPLRA  200 (328)
T ss_pred             --CChHHHHHHHHHcCCCHHHH
Confidence              11233567788999999643

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.59  E-value=7.1e-05  Score=72.53  Aligned_cols=85  Identities=20%  Similarity=0.333  Sum_probs=57.0

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .+.+++.|.+++|.+..+    |.   -..+|+.|.+.      ++..+..+|..+  ..+|++|++++|..+..+|.+ 
T Consensus        50 ~~~~l~~L~Is~c~L~sL----P~---LP~sLtsL~Ls------nc~nLtsLP~~L--P~nLe~L~Ls~Cs~L~sLP~s-  113 (426)
T PRK15386         50 EARASGRLYIKDCDIESL----PV---LPNELTEITIE------NCNNLTTLPGSI--PEGLEKLTVCHCPEISGLPES-  113 (426)
T ss_pred             HhcCCCEEEeCCCCCccc----CC---CCCCCcEEEcc------CCCCcccCCchh--hhhhhheEccCcccccccccc-
Confidence            568899999998876543    32   12368889887      456667777644  468999999998667777764 


Q ss_pred             hcCCCCcEEecCCC--cCccccchhccc
Q 046115          434 CELYNLERLNVDDC--QNLRELPRGIGK  459 (505)
Q Consensus       434 ~~l~~L~~L~l~~~--~~~~~lp~~~~~  459 (505)
                           |+.|+++++  ..+..+|+++..
T Consensus       114 -----Le~L~L~~n~~~~L~~LPssLk~  136 (426)
T PRK15386        114 -----VRSLEIKGSATDSIKNVPNGLTS  136 (426)
T ss_pred             -----cceEEeCCCCCcccccCcchHhh
Confidence                 455555543  335667765443

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.59  E-value=1.3e-05  Score=64.01  Aligned_cols=88  Identities=19%  Similarity=0.292  Sum_probs=39.6

Q ss_pred             CCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhh
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC  434 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~  434 (505)
                      ...|....+++|.+..+   ++.+-..++..+.|+|+       ++.+...|..+..++.|+.|+++.|+ +...|.-+.
T Consensus        52 ~~el~~i~ls~N~fk~f---p~kft~kf~t~t~lNl~-------~neisdvPeE~Aam~aLr~lNl~~N~-l~~~p~vi~  120 (177)
T KOG4579|consen   52 GYELTKISLSDNGFKKF---PKKFTIKFPTATTLNLA-------NNEISDVPEELAAMPALRSLNLRFNP-LNAEPRVIA  120 (177)
T ss_pred             CceEEEEecccchhhhC---CHHHhhccchhhhhhcc-------hhhhhhchHHHhhhHHhhhcccccCc-cccchHHHH
Confidence            33444444555443322   33333333444445554       44444444444445555555555444 444444444


Q ss_pred             cCCCCcEEecCCCcCccccc
Q 046115          435 ELYNLERLNVDDCQNLRELP  454 (505)
Q Consensus       435 ~l~~L~~L~l~~~~~~~~lp  454 (505)
                      +|.+|-.|+..+|. ...+|
T Consensus       121 ~L~~l~~Lds~~na-~~eid  139 (177)
T KOG4579|consen  121 PLIKLDMLDSPENA-RAEID  139 (177)
T ss_pred             HHHhHHHhcCCCCc-cccCc
Confidence            44444444444444 33343

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.58  E-value=0.0009  Score=68.64  Aligned_cols=104  Identities=11%  Similarity=0.107  Sum_probs=67.5

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|+++.........+.+.+......+.+|.+|.+ +.+... ......+++..++.++....+.......+.
T Consensus       117 ~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi  196 (527)
T PRK14969        117 RGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENI  196 (527)
T ss_pred             cCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCC
Confidence            346679999999776655567788888776555555554443 333211 122458889999999999888766532221


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                          ...++.+..|++.++|.+- |+..+-.
T Consensus       197 ----~~~~~al~~la~~s~Gslr~al~lldq  223 (527)
T PRK14969        197 ----PFDATALQLLARAAAGSMRDALSLLDQ  223 (527)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence                1234667889999999774 4444443

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

Probab=97.55  E-value=0.0014  Score=61.32  Aligned_cols=147  Identities=18%  Similarity=0.198  Sum_probs=88.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+||||||+-++..  -+.+  ...||..+.......-++.++++-.                -...+.++|.+|.+|
T Consensus       170 ppG~GKTtlArlia~t--sk~~--SyrfvelSAt~a~t~dvR~ife~aq----------------~~~~l~krkTilFiD  229 (554)
T KOG2028|consen  170 PPGTGKTTLARLIAST--SKKH--SYRFVELSATNAKTNDVRDIFEQAQ----------------NEKSLTKRKTILFID  229 (554)
T ss_pred             CCCCchHHHHHHHHhh--cCCC--ceEEEEEeccccchHHHHHHHHHHH----------------HHHhhhcceeEEEeH
Confidence            4899999999999984  2222  1456776665444444455444332                122456789999999


Q ss_pred             CCCCCCccChhHHHHhhcCCCCCcEEEE--EeCchHH---HHHhCCcceEeCCCCChhhHHHHHHHhhh---C-CCCCC-
Q 046115           81 DVWNEDYYKWEPFYKCLKNSLHESKILI--TTRKETV---ARIMGSTHVISVNVLSEMECWSVFQSLAI---S-GKTIG-  150 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~~~~~iLi--Ttr~~~~---~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~---~-~~~~~-  150 (505)
                      .|.+....+-+.++   |--.+|.-++|  ||.++..   ...+..-.++.++.|+.++-..++.+..-   . .+.+. 
T Consensus       230 EiHRFNksQQD~fL---P~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~  306 (554)
T KOG2028|consen  230 EIHRFNKSQQDTFL---PHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDP  306 (554)
T ss_pred             Hhhhhhhhhhhccc---ceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCC
Confidence            99775443333333   22235665665  7777532   22233456889999999999888876321   1 11111 


Q ss_pred             -CC---chHHHHHHHHHHHcCCCh
Q 046115          151 -KR---ENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       151 -~~---~~~~~~~~~i~~~~~g~P  170 (505)
                       +.   .-...++..++..|+|-.
T Consensus       307 l~n~s~~ve~siidyla~lsdGDa  330 (554)
T KOG2028|consen  307 LPNSSMFVEDSIIDYLAYLSDGDA  330 (554)
T ss_pred             CCCcchhhhHHHHHHHHHhcCchH
Confidence             11   134566777788888865

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.54  E-value=0.0014  Score=65.15  Aligned_cols=98  Identities=13%  Similarity=0.144  Sum_probs=65.9

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++.......+..+...+.+..+.+.+|++| +...+.+.+ .....+++.+++.++....+....-..+. 
T Consensus       126 ~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~-  204 (397)
T PRK14955        126 GRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGI-  204 (397)
T ss_pred             CCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            456688999997766556778888887766666665555 434443322 12347889999999998888776532221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                         .-.++.+..+++.++|.+--+
T Consensus       205 ---~i~~~al~~l~~~s~g~lr~a  225 (397)
T PRK14955        205 ---SVDADALQLIGRKAQGSMRDA  225 (397)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHH
Confidence               123567889999999977533

>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=97.54  E-value=0.00068  Score=59.95  Aligned_cols=138  Identities=21%  Similarity=0.231  Sum_probs=72.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+||||||.-+++  +....|.   +.+. ...+...-+..++..                      ++ ++-+|.+|
T Consensus        58 PPG~GKTTLA~IIA~--e~~~~~~---~~sg-~~i~k~~dl~~il~~----------------------l~-~~~ILFID  108 (233)
T PF05496_consen   58 PPGLGKTTLARIIAN--ELGVNFK---ITSG-PAIEKAGDLAAILTN----------------------LK-EGDILFID  108 (233)
T ss_dssp             STTSSHHHHHHHHHH--HCT--EE---EEEC-CC--SCHHHHHHHHT-------------------------TT-EEEEC
T ss_pred             CCccchhHHHHHHHh--ccCCCeE---eccc-hhhhhHHHHHHHHHh----------------------cC-CCcEEEEe
Confidence            589999999999999  5655542   2221 111111111222222                      22 33466678


Q ss_pred             CCCCCCccChhHHHHhhcCCC-------------------CCcEEEEEeCchHHHHHhCC-cce-EeCCCCChhhHHHHH
Q 046115           81 DVWNEDYYKWEPFYKCLKNSL-------------------HESKILITTRKETVARIMGS-THV-ISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~-------------------~~~~iLiTtr~~~~~~~~~~-~~~-~~l~~l~~~ea~~Lf  139 (505)
                      .+..-...+-+.+...+.++.                   +-+-|=.|||.-.+...... ..+ ..++..+.+|-.++.
T Consensus       109 EIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv  188 (233)
T PF05496_consen  109 EIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIV  188 (233)
T ss_dssp             TCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHH
T ss_pred             chhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHH
Confidence            886655444444444444321                   12234458887554433322 333 468999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCChH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                      .+.+..-+    -+-.++.+.+|++.+.|-|-
T Consensus       189 ~r~a~~l~----i~i~~~~~~~Ia~rsrGtPR  216 (233)
T PF05496_consen  189 KRSARILN----IEIDEDAAEEIARRSRGTPR  216 (233)
T ss_dssp             HHCCHCTT-----EE-HHHHHHHHHCTTTSHH
T ss_pred             HHHHHHhC----CCcCHHHHHHHHHhcCCChH
Confidence            87664322    23346789999999999995

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.54  E-value=0.0024  Score=65.79  Aligned_cols=106  Identities=11%  Similarity=0.131  Sum_probs=70.5

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|+++.........++..+........+|++|.+ ..+... ......+++..++.++....+...+.....
T Consensus       117 ~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi  196 (624)
T PRK14959        117 EGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGV  196 (624)
T ss_pred             cCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCC
Confidence            345679999999776655677788877765445555554444 444322 223457889999999999888776543221


Q ss_pred             CCCCchHHHHHHHHHHHcCCCh-HHHHHHHHHh
Q 046115          149 IGKRENLEKIGREIVKKCKGLP-LAAKTIASLL  180 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~P-lal~~~~~~l  180 (505)
                          .-..+.+..|++.++|.+ .|+..+...+
T Consensus       197 ----~id~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        197 ----DYDPAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence                123467888999999965 6777776544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.52  E-value=0.0025  Score=66.02  Aligned_cols=100  Identities=11%  Similarity=0.104  Sum_probs=67.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+.+.+......+.+|++| ....+...+ .....+++..++.++....+...+...+. 
T Consensus       131 a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi-  209 (598)
T PRK09111        131 ARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGV-  209 (598)
T ss_pred             CCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            355678999997766556777888877766666665544 434433222 23458899999999999999876643322 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                         .-.++.+..|++.++|.+..+..
T Consensus       210 ---~i~~eAl~lIa~~a~Gdlr~al~  232 (598)
T PRK09111        210 ---EVEDEALALIARAAEGSVRDGLS  232 (598)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHH
Confidence               12246788899999999865443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.51  E-value=0.0023  Score=65.60  Aligned_cols=102  Identities=13%  Similarity=0.167  Sum_probs=65.8

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      ++-++|+|+++......+..+...+......+.+|++| ....+... ......+++.+++.++....+...+...+.  
T Consensus       119 ~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi--  196 (605)
T PRK05896        119 KYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKI--  196 (605)
T ss_pred             CcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCC--
Confidence            34469999997766556677888777665555555444 43344322 233558899999999999888876533221  


Q ss_pred             CCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          151 KRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                        .-.++++..+++.++|.+- |+..+-.
T Consensus       197 --~Is~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        197 --KIEDNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             --CCCHHHHHHHHHHcCCcHHHHHHHHHH
Confidence              1124567889999999664 4444443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.51  E-value=0.0022  Score=68.92  Aligned_cols=104  Identities=8%  Similarity=0.117  Sum_probs=69.4

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .++.-++|||+++.........+++.+.+....+.+|++| ....+...+ .....|++..++.++..+++.......+.
T Consensus       118 ~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv  197 (824)
T PRK07764        118 ESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGV  197 (824)
T ss_pred             cCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCC
Confidence            3456678899998877777788888888776666655555 444444332 33568899999999988888775432222


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                          .-.++.+..|++.++|.+. ++..+-+
T Consensus       198 ----~id~eal~lLa~~sgGdlR~Al~eLEK  224 (824)
T PRK07764        198 ----PVEPGVLPLVIRAGGGSVRDSLSVLDQ  224 (824)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence                1234567789999999884 3333333

>PRK06620 hypothetical protein; Validated

Probab=97.50  E-value=0.0026  Score=57.18  Aligned_cols=96  Identities=9%  Similarity=0.002  Sum_probs=57.4

Q ss_pred             EEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           75 FLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        75 ~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      -++++||++......+-.+...+..  .|..+|+|++.+       ++...+....++++++++.++-..++.+.+...+
T Consensus        87 d~lliDdi~~~~~~~lf~l~N~~~e--~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~  164 (214)
T PRK06620         87 NAFIIEDIENWQEPALLHIFNIINE--KQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS  164 (214)
T ss_pred             CEEEEeccccchHHHHHHHHHHHHh--cCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC
Confidence            4788999964321122222222223  456899998752       2333344455899999999998888877654222


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHH
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                      . .   -.++++..|++.+.|.--.+.-+
T Consensus       165 l-~---l~~ev~~~L~~~~~~d~r~l~~~  189 (214)
T PRK06620        165 V-T---ISRQIIDFLLVNLPREYSKIIEI  189 (214)
T ss_pred             C-C---CCHHHHHHHHHHccCCHHHHHHH
Confidence            1 1   22466777888777665444433

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

Probab=97.45  E-value=0.0014  Score=69.42  Aligned_cols=97  Identities=14%  Similarity=0.212  Sum_probs=57.3

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEE--eCchH--HHHH-hCCcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILIT--TRKET--VARI-MGSTHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiT--tr~~~--~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +++.+|++|+++.-.....+.+...+.   .+..++|+  |.++.  +... ......+.+++++.++...++.+.....
T Consensus       108 ~~~~IL~IDEIh~Ln~~qQdaLL~~lE---~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~  184 (725)
T PRK13341        108 GKRTILFIDEVHRFNKAQQDALLPWVE---NGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDK  184 (725)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHHHhc---CceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHH
Confidence            457799999997655434445554333   34555553  44432  2111 1224578999999999999998765310


Q ss_pred             CC---CCCCchHHHHHHHHHHHcCCChH
Q 046115          147 KT---IGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       147 ~~---~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                      ..   .....-.++++..|++.+.|..-
T Consensus       185 ~~~~g~~~v~I~deaL~~La~~s~GD~R  212 (725)
T PRK13341        185 ERGYGDRKVDLEPEAEKHLVDVANGDAR  212 (725)
T ss_pred             HhhcCCcccCCCHHHHHHHHHhCCCCHH
Confidence            00   01112235677888888888653

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.0055  Score=63.23  Aligned_cols=105  Identities=12%  Similarity=0.170  Sum_probs=70.2

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........++..+......+.+| +||....+...+ .....++...++.++..+.+.......+. 
T Consensus       117 ~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi-  195 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGV-  195 (584)
T ss_pred             CCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCC-
Confidence            455688999998777667778888888765555555 455444444332 33568999999999998888776543322 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHHHHHHh
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKTIASLL  180 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~~l  180 (505)
                         .-.++.+..|++.++|.+- ++..+-..+
T Consensus       196 ---~i~~~al~~Ia~~s~GdlR~aln~Ldql~  224 (584)
T PRK14952        196 ---VVDDAVYPLVIRAGGGSPRDTLSVLDQLL  224 (584)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence               1124567888999999774 555554433

>TIGR00767 rho transcription termination factor Rho

Probab=97.43  E-value=0.00032  Score=67.72  Aligned_cols=82  Identities=15%  Similarity=0.159  Sum_probs=53.8

Q ss_pred             CCCCcHHHHHHHHhcCccccc-CCCceEEEEeCCC--CCHHHHHHHHHHHcCCCCCCChhcH-----HHHHHHHHHH-cC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEP--FDEFRIARAIIESLTPGSAKDLVEF-----QSLMQHIEEC-VA   71 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~--~~~~~~~~~l~~~l~~~~~~~~~~~-----~~~~~~l~~~-l~   71 (505)
                      .+|+|||||++.+++  .+.. +|+..+|+.+.+.  .+..++++.+...+-..........     ....+..... -.
T Consensus       176 ~~g~GKTtL~~~i~~--~I~~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae~~~~~  253 (415)
T TIGR00767       176 PPKAGKTVLLQKIAQ--AITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEH  253 (415)
T ss_pred             CCCCChhHHHHHHHH--hhcccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHHHHHHc
Confidence            479999999999998  4433 5998899987755  6888999988654432222221111     1112222222 25


Q ss_pred             CceEEEEEeCCCC
Q 046115           72 GKKFLLVLDDVWN   84 (505)
Q Consensus        72 ~~r~LlvlDdv~~   84 (505)
                      +++++|++|.+..
T Consensus       254 GkdVVLlIDEitR  266 (415)
T TIGR00767       254 KKDVVILLDSITR  266 (415)
T ss_pred             CCCeEEEEEChhH
Confidence            7899999999955

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

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.42  E-value=0.0053  Score=59.26  Aligned_cols=96  Identities=9%  Similarity=0.036  Sum_probs=61.8

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      .+-++++|+++.-.......+...+......+.+++++..+ .+... ......+.+.+++.++....+...+...+.  
T Consensus       102 ~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~--  179 (319)
T PRK00440        102 PFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGI--  179 (319)
T ss_pred             CceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCC--
Confidence            35689999986554334455666666555556777766432 22111 122447899999999999988877643322  


Q ss_pred             CCchHHHHHHHHHHHcCCChHH
Q 046115          151 KRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                        .-.++++..+++.++|.+.-
T Consensus       180 --~i~~~al~~l~~~~~gd~r~  199 (319)
T PRK00440        180 --EITDDALEAIYYVSEGDMRK  199 (319)
T ss_pred             --CCCHHHHHHHHHHcCCCHHH
Confidence              12256788899999998765

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.40  E-value=0.0042  Score=64.91  Aligned_cols=102  Identities=11%  Similarity=0.111  Sum_probs=68.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.......+.+...+......+.+|+++.+ ..+...+ .....+.+..++..+....+...+...+..
T Consensus       119 ~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~  198 (585)
T PRK14950        119 ARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGIN  198 (585)
T ss_pred             CCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            45678999999766555677788777776566666665544 3333322 234578899999999988887765432221


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIA  177 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~  177 (505)
                          -.++.+..+++.++|.+..+...-
T Consensus       199 ----i~~eal~~La~~s~Gdlr~al~~L  222 (585)
T PRK14950        199 ----LEPGALEAIARAATGSMRDAENLL  222 (585)
T ss_pred             ----CCHHHHHHHHHHcCCCHHHHHHHH
Confidence                224678899999999886544433

>PRK04195 replication factor C large subunit; Provisional

Probab=97.40  E-value=0.0046  Score=63.15  Aligned_cols=153  Identities=16%  Similarity=0.147  Sum_probs=86.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+||||+|+.+++  +..  |+ ++-++.+..... .....++.......               .....++-+||+|
T Consensus        47 ppG~GKTtla~ala~--el~--~~-~ielnasd~r~~-~~i~~~i~~~~~~~---------------sl~~~~~kvIiID  105 (482)
T PRK04195         47 PPGVGKTSLAHALAN--DYG--WE-VIELNASDQRTA-DVIERVAGEAATSG---------------SLFGARRKLILLD  105 (482)
T ss_pred             CCCCCHHHHHHHHHH--HcC--CC-EEEEcccccccH-HHHHHHHHHhhccC---------------cccCCCCeEEEEe
Confidence            489999999999998  432  22 233444433222 22222222221000               0111357799999


Q ss_pred             CCCCCCc----cChhHHHHhhcCCCCCcEEEEEeCchH-HHH-Hh-CCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCc
Q 046115           81 DVWNEDY----YKWEPFYKCLKNSLHESKILITTRKET-VAR-IM-GSTHVISVNVLSEMECWSVFQSLAISGKTIGKRE  153 (505)
Q Consensus        81 dv~~~~~----~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~-~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~  153 (505)
                      +++....    ..+..+...+..  .++.||+|+.+.. ... .. .....+.+.+++..+....+.......+..    
T Consensus       106 EaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~----  179 (482)
T PRK04195        106 EVDGIHGNEDRGGARAILELIKK--AKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIE----  179 (482)
T ss_pred             cCcccccccchhHHHHHHHHHHc--CCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCC----
Confidence            9966432    234556555553  2345666665432 111 11 234578899999999988887766433321    


Q ss_pred             hHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          154 NLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       154 ~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      -.++++..|++.++|..-.+......+
T Consensus       180 i~~eaL~~Ia~~s~GDlR~ain~Lq~~  206 (482)
T PRK04195        180 CDDEALKEIAERSGGDLRSAINDLQAI  206 (482)
T ss_pred             CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            125678899999998775554433333

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=97.38  E-value=2.1e-05  Score=73.90  Aligned_cols=103  Identities=21%  Similarity=0.270  Sum_probs=85.2

Q ss_pred             ccceEEecccccCCccccccccCcc-ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchh-ccccc
Q 046115          384 CLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG-IGKLR  461 (505)
Q Consensus       384 ~L~~L~l~~~~~~~~~~~~~~~p~~-~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~  461 (505)
                      .-..++|.       .|.+..+|+. |+.+++|+.|||+.|....--|..+..+..|.+|-+.++..++.+|.. ++.|.
T Consensus        68 ~tveirLd-------qN~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~  140 (498)
T KOG4237|consen   68 ETVEIRLD-------QNQISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLS  140 (498)
T ss_pred             cceEEEec-------cCCcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHH
Confidence            56778888       8889998764 789999999999999933344788999999988888775559999975 89999


Q ss_pred             cCceeecCCCcccccccccccCCccCCcccee
Q 046115          462 KLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       462 ~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      +|+.|.+.-|.........|.+|++|..|.+|
T Consensus       141 slqrLllNan~i~Cir~~al~dL~~l~lLsly  172 (498)
T KOG4237|consen  141 SLQRLLLNANHINCIRQDALRDLPSLSLLSLY  172 (498)
T ss_pred             HHHHHhcChhhhcchhHHHHHHhhhcchhccc
Confidence            99999999998555555668999999888887

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

Probab=97.36  E-value=0.0042  Score=57.65  Aligned_cols=167  Identities=17%  Similarity=0.121  Sum_probs=96.6

Q ss_pred             CCCcHHHHHHHHhcCcccccC----CCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCC-ceEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERN----FEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAG-KKFL   76 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~----f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~r~L   76 (505)
                      +|+|||++++++.+.+-....    --.|+.|..-..++...+...|+.+++.+.... ....+........++. +--+
T Consensus        70 snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~-~~~~~~~~~~~~llr~~~vrm  148 (302)
T PF05621_consen   70 SNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPR-DRVAKLEQQVLRLLRRLGVRM  148 (302)
T ss_pred             CCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCC-CCHHHHHHHHHHHHHHcCCcE
Confidence            689999999999874211111    114666777788899999999999999665332 2333333333333322 3348


Q ss_pred             EEEeCCCCC------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH-----hCCcceEeCCCCChhhH-HHHHHHhh-
Q 046115           77 LVLDDVWNE------DYYKWEPFYKCLKNSLHESKILITTRKETVARI-----MGSTHVISVNVLSEMEC-WSVFQSLA-  143 (505)
Q Consensus        77 lvlDdv~~~------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~-----~~~~~~~~l~~l~~~ea-~~Lf~~~~-  143 (505)
                      ||+|.+.+-      .+...-..++.+.+.-.=+-|.+-|++-..+-.     ...+..+.++....++- ..|+.... 
T Consensus       149 LIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~  228 (302)
T PF05621_consen  149 LIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLASRFEPFELPRWELDEEFRRLLASFER  228 (302)
T ss_pred             EEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHHhccCCccCCCCCCCcHHHHHHHHHHH
Confidence            999998652      122233334444443344557777776322111     12355677777776654 44443332 


Q ss_pred             -hCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          144 -ISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       144 -~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                       .+-+. ...-..++.++.|.+.++|+.
T Consensus       229 ~LPLr~-~S~l~~~~la~~i~~~s~G~i  255 (302)
T PF05621_consen  229 ALPLRK-PSNLASPELARRIHERSEGLI  255 (302)
T ss_pred             hCCCCC-CCCCCCHHHHHHHHHHcCCch
Confidence             11111 112234678999999999987

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.36  E-value=0.0085  Score=60.80  Aligned_cols=102  Identities=12%  Similarity=0.132  Sum_probs=65.3

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEe-CchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITT-RKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTt-r~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|+++.........+...+........+|++| +...+... ......+.+.+++.++....+...+-..+.
T Consensus       117 ~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi  196 (486)
T PRK14953        117 KGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKI  196 (486)
T ss_pred             cCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCC
Confidence            3466799999997665545667777777655455555444 43333322 223458899999999998888776533221


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHHHHHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                          ...++++..+++.++|.+..+...
T Consensus       197 ----~id~~al~~La~~s~G~lr~al~~  220 (486)
T PRK14953        197 ----EYEEKALDLLAQASEGGMRDAASL  220 (486)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHHHH
Confidence                123466788999999977544333

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.32  E-value=0.0038  Score=62.42  Aligned_cols=154  Identities=16%  Similarity=0.150  Sum_probs=87.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC--ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE--KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~--~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+|||.||+.+++  +..++..  .+++++..      ++...+...+...      ..+.    +.+.+++ .-+||
T Consensus       144 ~~G~GKThL~~ai~~--~l~~~~~~~~v~yi~~~------~~~~~~~~~~~~~------~~~~----~~~~~~~-~dlLi  204 (405)
T TIGR00362       144 GVGLGKTHLLHAIGN--EILENNPNAKVVYVSSE------KFTNDFVNALRNN------KMEE----FKEKYRS-VDLLL  204 (405)
T ss_pred             CCCCcHHHHHHHHHH--HHHHhCCCCcEEEEEHH------HHHHHHHHHHHcC------CHHH----HHHHHHh-CCEEE
Confidence            379999999999998  5555442  34566532      3344455544311      1222    2223322 23889


Q ss_pred             EeCCCCCCccC--hhHHHHhhcCC-CCCcEEEEEeCc-hHHH--------HHhCCcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           79 LDDVWNEDYYK--WEPFYKCLKNS-LHESKILITTRK-ETVA--------RIMGSTHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        79 lDdv~~~~~~~--~~~~~~~~~~~-~~~~~iLiTtr~-~~~~--------~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +||++......  .+.+...+... ..+..+++|+.. +...        ..+.....+.+++.+.++-..++...+...
T Consensus       205 iDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~  284 (405)
T TIGR00362       205 IDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEEE  284 (405)
T ss_pred             EehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHHc
Confidence            99996532111  12233323221 234568888764 2211        112223468899999999999998877443


Q ss_pred             CCCCCCchHHHHHHHHHHHcCCChHHHHHHH
Q 046115          147 KTIGKRENLEKIGREIVKKCKGLPLAAKTIA  177 (505)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~  177 (505)
                      +.    .-.++++..|++.+.+..-.+..+-
T Consensus       285 ~~----~l~~e~l~~ia~~~~~~~r~l~~~l  311 (405)
T TIGR00362       285 GL----ELPDEVLEFIAKNIRSNVRELEGAL  311 (405)
T ss_pred             CC----CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            22    1125677888888888776554443

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).

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.31  E-value=0.0074  Score=62.78  Aligned_cols=100  Identities=15%  Similarity=0.138  Sum_probs=66.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +.+-++|+|+++.........+...+......+.+| +|++...+... ......+++.+++.++....+...+...+. 
T Consensus       126 ~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi-  204 (620)
T PRK14954        126 GRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGI-  204 (620)
T ss_pred             CCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCC-
Confidence            345578999997766556777888887765555544 45444444432 234568999999999988888765532221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKT  175 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~  175 (505)
                         .-.++.+..+++.++|..- |+..
T Consensus       205 ---~I~~eal~~La~~s~Gdlr~al~e  228 (620)
T PRK14954        205 ---QIDADALQLIARKAQGSMRDAQSI  228 (620)
T ss_pred             ---CCCHHHHHHHHHHhCCCHHHHHHH
Confidence               1134668889999999654 4443

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.30  E-value=0.013  Score=52.65  Aligned_cols=174  Identities=15%  Similarity=0.166  Sum_probs=101.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChh-cHHHHHHHHHHHc-CCce-EEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLV-EFQSLMQHIEECV-AGKK-FLLV   78 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~-~~~~~~~~l~~~l-~~~r-~Llv   78 (505)
                      -|+|||.+++.+...  ..++=..+ -+......+...+...++..+......... ..++.-..+.... +++| ..++
T Consensus        60 vGsGKTv~~Ral~~s--~~~d~~~~-v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~l~  136 (269)
T COG3267          60 VGSGKTVLRRALLAS--LNEDQVAV-VVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVVLM  136 (269)
T ss_pred             CCCchhHHHHHHHHh--cCCCceEE-EEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCeEEe
Confidence            389999999955442  22221122 233445566778888888888742222222 2233333444444 4566 9999


Q ss_pred             EeCCCCCCccChhHHHHhhcC---CCCCcEEEEEeCc--------hHHHHHhCCcce-EeCCCCChhhHHHHHHHhhhCC
Q 046115           79 LDDVWNEDYYKWEPFYKCLKN---SLHESKILITTRK--------ETVARIMGSTHV-ISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~---~~~~~~iLiTtr~--------~~~~~~~~~~~~-~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +|+..+.....++.+.-...-   .+..-+|+..-..        ......-....+ |++.+++.++...++.......
T Consensus       137 vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~t~~yl~~~Le~a  216 (269)
T COG3267         137 VDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHRLEGA  216 (269)
T ss_pred             ehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChHHHHHHHHHHHhcc
Confidence            999977665555555544332   2111223332221        111111122334 8999999999999987765443


Q ss_pred             CCCCCCchHHHHHHHHHHHcCCChHHHHHHHHH
Q 046115          147 KTIGKRENLEKIGREIVKKCKGLPLAAKTIASL  179 (505)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~  179 (505)
                       ....+--..+++..|.+...|.|.+++.++..
T Consensus       217 -~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~  248 (269)
T COG3267         217 -GLPEPLFSDDALLLIHEASQGIPRLINNLATL  248 (269)
T ss_pred             -CCCcccCChhHHHHHHHHhccchHHHHHHHHH
Confidence             22233334577888999999999999988763

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.25  E-value=0.0089  Score=59.98  Aligned_cols=147  Identities=16%  Similarity=0.097  Sum_probs=81.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ..|+|||+||+.+++  ++...-..+++++.      ..+...+...+..+      .    ...+....+ ..-+|++|
T Consensus       149 ~~G~GKTHLl~Ai~~--~l~~~~~~v~yi~~------~~f~~~~~~~l~~~------~----~~~f~~~~~-~~dvLiID  209 (445)
T PRK12422        149 PEGSGKTHLMQAAVH--ALRESGGKILYVRS------ELFTEHLVSAIRSG------E----MQRFRQFYR-NVDALFIE  209 (445)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCCEEEeeH------HHHHHHHHHHHhcc------h----HHHHHHHcc-cCCEEEEc
Confidence            479999999999998  55433334556653      23444555554311      1    122333333 33488889


Q ss_pred             CCCCCCcc--ChhHHHHhhcCC-CCCcEEEEEeCc-hHH--------HHHhCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           81 DVWNEDYY--KWEPFYKCLKNS-LHESKILITTRK-ETV--------ARIMGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        81 dv~~~~~~--~~~~~~~~~~~~-~~~~~iLiTtr~-~~~--------~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      |++.....  ..+.+...+... ..|..||+||.. +..        ...+.....+++.+++.++-..++.+.+...+.
T Consensus       210 Diq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~  289 (445)
T PRK12422        210 DIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAEALSI  289 (445)
T ss_pred             chhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHHHcCC
Confidence            98553211  112222222211 235578888854 221        222333458889999999999999887643322


Q ss_pred             CCCCchHHHHHHHHHHHcCCCh
Q 046115          149 IGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                       .   -.++++..|++.+.+.-
T Consensus       290 -~---l~~evl~~la~~~~~di  307 (445)
T PRK12422        290 -R---IEETALDFLIEALSSNV  307 (445)
T ss_pred             -C---CCHHHHHHHHHhcCCCH
Confidence             1   12455666777776544

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.24  E-value=0.0089  Score=58.92  Aligned_cols=96  Identities=14%  Similarity=0.196  Sum_probs=60.6

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeC-chHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTR-KETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr-~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++++|+++......+..+...+......+.+++++. ...+... .....+++..+++.++....+...+...+..
T Consensus       107 ~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~  186 (367)
T PRK14970        107 GKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIK  186 (367)
T ss_pred             CCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCCC
Confidence            3455899999966544446667666655444555555553 3333222 2234588999999999988887766433221


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                          -.++++..+++.++|.+-
T Consensus       187 ----i~~~al~~l~~~~~gdlr  204 (367)
T PRK14970        187 ----FEDDALHIIAQKADGALR  204 (367)
T ss_pred             ----CCHHHHHHHHHhCCCCHH
Confidence                124678888899998664

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.24  E-value=0.0085  Score=62.85  Aligned_cols=102  Identities=17%  Similarity=0.123  Sum_probs=67.2

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcE-EEEEeCchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESK-ILITTRKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~-iLiTtr~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++.......+..++..+......+. |++|++...+... ......+++.+++.++....+...+...+. 
T Consensus       117 g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI-  195 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENI-  195 (725)
T ss_pred             CCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCC-
Confidence            4666889999977665567778877776554444 5555554444432 233468999999999999888765432222 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKTIA  177 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~~~  177 (505)
                         ....+++..+++.++|.+- |+..+-
T Consensus       196 ---~id~eAl~~LA~lS~GslR~AlslLe  221 (725)
T PRK07133        196 ---SYEKNALKLIAKLSSGSLRDALSIAE  221 (725)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence               1124568889999999764 444433

>CHL00181 cbbX CbbX; Provisional

Probab=97.22  E-value=0.011  Score=55.73  Aligned_cols=126  Identities=12%  Similarity=0.171  Sum_probs=67.4

Q ss_pred             CCCCcHHHHHHHHhcCccccc-CC-CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVER-NF-EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~-~f-~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+|||++|+.++.  .... .+ ...-|+.++.        ..+...+. +..     .......+...   ..-+|+
T Consensus        67 ~pGtGKT~lAr~la~--~~~~~g~~~~~~~~~v~~--------~~l~~~~~-g~~-----~~~~~~~l~~a---~ggVLf  127 (287)
T CHL00181         67 SPGTGKTTVALKMAD--ILYKLGYIKKGHLLTVTR--------DDLVGQYI-GHT-----APKTKEVLKKA---MGGVLF  127 (287)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCCCCCceEEecH--------HHHHHHHh-ccc-----hHHHHHHHHHc---cCCEEE
Confidence            489999999999987  3211 11 1112444431        12222221 111     01111222222   224999


Q ss_pred             EeCCCCC---------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHHh--------CCcceEeCCCCChhhHHHHHHH
Q 046115           79 LDDVWNE---------DYYKWEPFYKCLKNSLHESKILITTRKETVARIM--------GSTHVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        79 lDdv~~~---------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~--------~~~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      +|++...         .......+...+.+...+..||.++....+....        .-...+..++++.+|..+++..
T Consensus       128 IDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~  207 (287)
T CHL00181        128 IDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKI  207 (287)
T ss_pred             EEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHH
Confidence            9999542         1112344555555555667777777644332111        1134789999999999999987


Q ss_pred             hhhC
Q 046115          142 LAIS  145 (505)
Q Consensus       142 ~~~~  145 (505)
                      ....
T Consensus       208 ~l~~  211 (287)
T CHL00181        208 MLEE  211 (287)
T ss_pred             HHHH
Confidence            7643

>PRK08116 hypothetical protein; Validated

Probab=97.21  E-value=0.0013  Score=61.44  Aligned_cols=95  Identities=22%  Similarity=0.273  Sum_probs=53.3

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      +|+|||.||..+++  ....+...++++++      .+++..+...+....   ...    ...+.+.+.+-. ||||||
T Consensus       123 ~GtGKThLa~aia~--~l~~~~~~v~~~~~------~~ll~~i~~~~~~~~---~~~----~~~~~~~l~~~d-lLviDD  186 (268)
T PRK08116        123 VGTGKTYLAACIAN--ELIEKGVPVIFVNF------PQLLNRIKSTYKSSG---KED----ENEIIRSLVNAD-LLILDD  186 (268)
T ss_pred             CCCCHHHHHHHHHH--HHHHcCCeEEEEEH------HHHHHHHHHHHhccc---ccc----HHHHHHHhcCCC-EEEEec
Confidence            69999999999999  55444445667763      234444444443111   111    112333344333 899999


Q ss_pred             CCCCCccCh--hHHHHhhcCC-CCCcEEEEEeCc
Q 046115           82 VWNEDYYKW--EPFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~--~~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      +..+....|  ..+...+... ..+..+||||..
T Consensus       187 lg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        187 LGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            965433334  3344333322 345679999975

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=97.20  E-value=0.00013  Score=73.07  Aligned_cols=104  Identities=24%  Similarity=0.315  Sum_probs=59.4

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .+++|..|++.+|.+...    ...+..+.+|++|+++       .+.+..+.. +..++.|+.|++++|. +..++. +
T Consensus        93 ~~~~l~~l~l~~n~i~~i----~~~l~~~~~L~~L~ls-------~N~I~~i~~-l~~l~~L~~L~l~~N~-i~~~~~-~  158 (414)
T KOG0531|consen   93 KLKSLEALDLYDNKIEKI----ENLLSSLVNLQVLDLS-------FNKITKLEG-LSTLTLLKELNLSGNL-ISDISG-L  158 (414)
T ss_pred             cccceeeeeccccchhhc----ccchhhhhcchheecc-------ccccccccc-hhhccchhhheeccCc-chhccC-C
Confidence            556666666666665432    1114456666666666       555555543 4555556666666666 555554 4


Q ss_pred             hcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCc
Q 046115          434 CELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTG  472 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~  472 (505)
                      ..+.+|+.+++++|+ +..++.. ...+.+|+.+.+.+|.
T Consensus       159 ~~l~~L~~l~l~~n~-i~~ie~~~~~~~~~l~~l~l~~n~  197 (414)
T KOG0531|consen  159 ESLKSLKLLDLSYNR-IVDIENDELSELISLEELDLGGNS  197 (414)
T ss_pred             ccchhhhcccCCcch-hhhhhhhhhhhccchHHHhccCCc
Confidence            446666666666666 4444432 3555666666666654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.20  E-value=0.0026  Score=62.60  Aligned_cols=143  Identities=15%  Similarity=0.162  Sum_probs=74.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHH-HHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIE-ECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~-~~l~~~r~Llvl   79 (505)
                      ++|+|||++|+.+++  +....|     +.+..        ..+.....       .........+. ..-...+.+|++
T Consensus       164 ppGtGKT~lakaia~--~l~~~~-----~~v~~--------~~l~~~~~-------g~~~~~i~~~f~~a~~~~p~il~i  221 (364)
T TIGR01242       164 PPGTGKTLLAKAVAH--ETNATF-----IRVVG--------SELVRKYI-------GEGARLVREIFELAKEKAPSIIFI  221 (364)
T ss_pred             CCCCCHHHHHHHHHH--hCCCCE-----Eecch--------HHHHHHhh-------hHHHHHHHHHHHHHHhcCCcEEEh
Confidence            479999999999998  454443     22211        11111110       00111111222 222345789999


Q ss_pred             eCCCCCC-----------c---cChhHHHHhhcC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNED-----------Y---YKWEPFYKCLKN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~-----------~---~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |+++...           .   ..+..+...+..  ...+..|+.||....... ..   +. ...+.++..+.++..++
T Consensus       222 DEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~I  301 (364)
T TIGR01242       222 DEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEI  301 (364)
T ss_pred             hhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHH
Confidence            9985421           0   012222222222  134677888887643221 11   11 35788999999999999


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |..+...... ....+    ...+++.+.|..
T Consensus       302 l~~~~~~~~l-~~~~~----~~~la~~t~g~s  328 (364)
T TIGR01242       302 LKIHTRKMKL-AEDVD----LEAIAKMTEGAS  328 (364)
T ss_pred             HHHHHhcCCC-CccCC----HHHHHHHcCCCC
Confidence            9887643222 11122    446777776654

Many proteins may score above the trusted cutoff because an internal

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.19  E-value=0.0018  Score=53.80  Aligned_cols=107  Identities=17%  Similarity=0.062  Sum_probs=53.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCc-eEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGK-KFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-r~Llvl   79 (505)
                      .+|+||||+|+.++.  ........+++++.............  .... ....................... ..+|++
T Consensus        10 ~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~viii   84 (148)
T smart00382       10 PPGSGKTTLARALAR--ELGPPGGGVIYIDGEDILEEVLDQLL--LIIV-GGKKASGSGELRLRLALALARKLKPDVLIL   84 (148)
T ss_pred             CCCCcHHHHHHHHHh--ccCCCCCCEEEECCEEccccCHHHHH--hhhh-hccCCCCCHHHHHHHHHHHHHhcCCCEEEE
Confidence            479999999999998  44444345666765554332222221  1111 11111222222223333333333 489999


Q ss_pred             eCCCCCCccChhHHHH--------hhcCCCCCcEEEEEeCc
Q 046115           80 DDVWNEDYYKWEPFYK--------CLKNSLHESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~--------~~~~~~~~~~iLiTtr~  112 (505)
                      |++.............        .......+..++.|+..
T Consensus        85 Dei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       85 DEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             ECCcccCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence            9997754322222111        11122345667777773

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.19  E-value=0.0098  Score=59.91  Aligned_cols=102  Identities=12%  Similarity=0.153  Sum_probs=66.1

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+...+.+....+.+|++|.+ ..+... ......+++.+++.++....+...+...+. 
T Consensus       120 ~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~-  198 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGI-  198 (451)
T ss_pred             CCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCC-
Confidence            45678899999665544556677777776556666655543 333322 223458899999999999888776532221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKTIA  177 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~~~  177 (505)
                         .-.++++..|++.++|.+- |+..+-
T Consensus       199 ---~i~~~al~~L~~~s~gdlr~a~~~Le  224 (451)
T PRK06305        199 ---ETSREALLPIARAAQGSLRDAESLYD  224 (451)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence               1235678889999999764 444433

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=97.17  E-value=9.3e-05  Score=74.18  Aligned_cols=106  Identities=27%  Similarity=0.391  Sum_probs=85.2

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .+..+..+.+..|.+..    +-..++.+++|..|++.       ++.+..+...+..+.+|++|++++|. ++.+.. +
T Consensus        70 ~l~~l~~l~l~~n~i~~----~~~~l~~~~~l~~l~l~-------~n~i~~i~~~l~~~~~L~~L~ls~N~-I~~i~~-l  136 (414)
T KOG0531|consen   70 SLTSLKELNLRQNLIAK----ILNHLSKLKSLEALDLY-------DNKIEKIENLLSSLVNLQVLDLSFNK-ITKLEG-L  136 (414)
T ss_pred             HhHhHHhhccchhhhhh----hhcccccccceeeeecc-------ccchhhcccchhhhhcchheeccccc-cccccc-h
Confidence            45556666666666543    22236788999999998       77788877668899999999999999 888887 8


Q ss_pred             hcCCCCcEEecCCCcCccccchhccccccCceeecCCCccc
Q 046115          434 CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~  474 (505)
                      ..+..|+.|++++|. +..++ .+..+++|+.+++++|...
T Consensus       137 ~~l~~L~~L~l~~N~-i~~~~-~~~~l~~L~~l~l~~n~i~  175 (414)
T KOG0531|consen  137 STLTLLKELNLSGNL-ISDIS-GLESLKSLKLLDLSYNRIV  175 (414)
T ss_pred             hhccchhhheeccCc-chhcc-CCccchhhhcccCCcchhh
Confidence            889999999999999 88875 4566899999999999844

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.16  E-value=0.0084  Score=60.27  Aligned_cols=173  Identities=15%  Similarity=0.085  Sum_probs=96.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-C-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-E-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+|||.||..+++  ++...+ . .++|++.      .++...+...+...      ..++    .........-+|+
T Consensus       138 ~~G~GKTHLl~ai~~--~l~~~~~~~~v~yi~~------~~f~~~~~~~~~~~------~~~~----f~~~~~~~~dvLl  199 (440)
T PRK14088        138 GVGLGKTHLLQSIGN--YVVQNEPDLRVMYITS------EKFLNDLVDSMKEG------KLNE----FREKYRKKVDVLL  199 (440)
T ss_pred             CCCCcHHHHHHHHHH--HHHHhCCCCeEEEEEH------HHHHHHHHHHHhcc------cHHH----HHHHHHhcCCEEE
Confidence            379999999999998  555543 2 3557764      34555665555411      1122    2223323345899


Q ss_pred             EeCCCCCCc-cCh-hHHHHhhcCC-CCCcEEEEEeC-chHHH----H----HhCCcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           79 LDDVWNEDY-YKW-EPFYKCLKNS-LHESKILITTR-KETVA----R----IMGSTHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        79 lDdv~~~~~-~~~-~~~~~~~~~~-~~~~~iLiTtr-~~~~~----~----~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +||++.... ... +.+...+... ..+..|++||. .+.-.    .    .+.....+.+++.+.++-..++++.+...
T Consensus       200 IDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~  279 (440)
T PRK14088        200 IDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIE  279 (440)
T ss_pred             EechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhc
Confidence            999964311 011 1222222211 23457888874 33221    1    22334478899999999999998876432


Q ss_pred             CCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh------cc-CCCHHHHHHHHhh
Q 046115          147 KTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL------RS-KNTEKEWQNILEN  195 (505)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l------~~-~~~~~~~~~~l~~  195 (505)
                      +. .   -.++++..|++.+.|.--.|..+-..+      .+ ..+....++.+..
T Consensus       280 ~~-~---l~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~~~~it~~~a~~~L~~  331 (440)
T PRK14088        280 HG-E---LPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGEEVDLKEAILLLKD  331 (440)
T ss_pred             CC-C---CCHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            22 1   124678888888887665554443332      11 1255555555553

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.016  Score=60.67  Aligned_cols=100  Identities=10%  Similarity=0.081  Sum_probs=64.6

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........++..+......+.+|++|.+ ..+...+ .....+++..++.++....+...+...+. 
T Consensus       120 ~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi-  198 (620)
T PRK14948        120 ARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESI-  198 (620)
T ss_pred             CCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCC-
Confidence            45568899999776655677788888776555555444444 3333222 23457888899999988888765533221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                         .-.++++..+++.++|.+.....
T Consensus       199 ---~is~~al~~La~~s~G~lr~A~~  221 (620)
T PRK14948        199 ---EIEPEALTLVAQRSQGGLRDAES  221 (620)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHH
Confidence               11245688899999998754433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.16  E-value=0.0085  Score=61.58  Aligned_cols=154  Identities=12%  Similarity=0.136  Sum_probs=88.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCC--CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f--~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .|+|||.|+..+++  +....+  ..+++++..      ++...+...+...      .    ...+.+.+.+ -=+|||
T Consensus       323 sGsGKTHLL~AIa~--~a~~~~~g~~V~Yitae------ef~~el~~al~~~------~----~~~f~~~y~~-~DLLlI  383 (617)
T PRK14086        323 SGLGKTHLLHAIGH--YARRLYPGTRVRYVSSE------EFTNEFINSIRDG------K----GDSFRRRYRE-MDILLV  383 (617)
T ss_pred             CCCCHHHHHHHHHH--HHHHhCCCCeEEEeeHH------HHHHHHHHHHHhc------c----HHHHHHHhhc-CCEEEE
Confidence            69999999999998  554433  234566643      3444444444310      1    1122233332 247889


Q ss_pred             eCCCCCCcc-Ch-hHHHHhhcCC-CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           80 DDVWNEDYY-KW-EPFYKCLKNS-LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        80 Ddv~~~~~~-~~-~~~~~~~~~~-~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      ||++..... .+ +.+...+... ..+..|||||+..         .+...+....++.+...+.+.-..++.+.+....
T Consensus       384 DDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~~r~  463 (617)
T PRK14086        384 DDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAVQEQ  463 (617)
T ss_pred             ehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHHhcC
Confidence            999653221 11 2233333222 2356788888762         2333344566889999999999999988775433


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHH
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~  178 (505)
                      . ..   .++++..|++.+.+..-.|..+-.
T Consensus       464 l-~l---~~eVi~yLa~r~~rnvR~LegaL~  490 (617)
T PRK14086        464 L-NA---PPEVLEFIASRISRNIRELEGALI  490 (617)
T ss_pred             C-CC---CHHHHHHHHHhccCCHHHHHHHHH
Confidence            2 11   246777788887766555544433

>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=97.15  E-value=0.0013  Score=54.08  Aligned_cols=92  Identities=18%  Similarity=0.078  Sum_probs=50.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCC-ceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAG-KKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~r~Llvl   79 (505)
                      .+|+|||++|+.+++  ...   ...+.++...-.             .   .............+.+.-.. ++.+|++
T Consensus         6 ~~G~GKT~l~~~la~--~l~---~~~~~i~~~~~~-------------~---~~~~~~~~~i~~~~~~~~~~~~~~vl~i   64 (132)
T PF00004_consen    6 PPGTGKTTLARALAQ--YLG---FPFIEIDGSELI-------------S---SYAGDSEQKIRDFFKKAKKSAKPCVLFI   64 (132)
T ss_dssp             STTSSHHHHHHHHHH--HTT---SEEEEEETTHHH-------------T---SSTTHHHHHHHHHHHHHHHTSTSEEEEE
T ss_pred             cCCCCeeHHHHHHHh--hcc---cccccccccccc-------------c---ccccccccccccccccccccccceeeee
Confidence            479999999999998  432   123455543210             0   01112222223333332223 4799999


Q ss_pred             eCCCCCCccC-----------hhHHHHhhcCCC---CCcEEEEEeCch
Q 046115           80 DDVWNEDYYK-----------WEPFYKCLKNSL---HESKILITTRKE  113 (505)
Q Consensus        80 Ddv~~~~~~~-----------~~~~~~~~~~~~---~~~~iLiTtr~~  113 (505)
                      ||++.-....           ...+...+....   .+..|+.||...
T Consensus        65 De~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~  112 (132)
T PF00004_consen   65 DEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSP  112 (132)
T ss_dssp             ETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSG
T ss_pred             ccchhcccccccccccccccccceeeecccccccccccceeEEeeCCh
Confidence            9996543333           445555555443   346777777763

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 ....

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.15  E-value=0.0076  Score=61.07  Aligned_cols=153  Identities=13%  Similarity=0.110  Sum_probs=87.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC--ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE--KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~--~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+|||.||+.+++  +...++.  .+++++..      ++...+...+...      ..    ..+.+.++ ..-+||
T Consensus       156 ~~G~GKThL~~ai~~--~~~~~~~~~~v~yi~~~------~~~~~~~~~~~~~------~~----~~~~~~~~-~~dlLi  216 (450)
T PRK00149        156 GVGLGKTHLLHAIGN--YILEKNPNAKVVYVTSE------KFTNDFVNALRNN------TM----EEFKEKYR-SVDVLL  216 (450)
T ss_pred             CCCCCHHHHHHHHHH--HHHHhCCCCeEEEEEHH------HHHHHHHHHHHcC------cH----HHHHHHHh-cCCEEE
Confidence            379999999999999  6655543  34466543      2334444444311      11    22233333 234899


Q ss_pred             EeCCCCCCcc--ChhHHHHhhcCC-CCCcEEEEEeCch-H----H----HHHhCCcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           79 LDDVWNEDYY--KWEPFYKCLKNS-LHESKILITTRKE-T----V----ARIMGSTHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        79 lDdv~~~~~~--~~~~~~~~~~~~-~~~~~iLiTtr~~-~----~----~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +||++.....  ..+.+...+... ..+..+++||... .    +    ...+.....+++++.+.++-..++...+...
T Consensus       217 iDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~  296 (450)
T PRK00149        217 IDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKAEEE  296 (450)
T ss_pred             EehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHHHc
Confidence            9999653211  112222222211 2345688887653 1    1    2223334578999999999999998877432


Q ss_pred             CCCCCCchHHHHHHHHHHHcCCChHHHHHH
Q 046115          147 KTIGKRENLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                      +.    .-.++++..|++.+.|..-.+..+
T Consensus       297 ~~----~l~~e~l~~ia~~~~~~~R~l~~~  322 (450)
T PRK00149        297 GI----DLPDEVLEFIAKNITSNVRELEGA  322 (450)
T ss_pred             CC----CCCHHHHHHHHcCcCCCHHHHHHH
Confidence            21    123567888999998887655444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.13  E-value=0.0097  Score=56.12  Aligned_cols=70  Identities=13%  Similarity=0.161  Sum_probs=43.4

Q ss_pred             EEEEEeCCCCC---------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH--hC------CcceEeCCCCChhhHHH
Q 046115           75 FLLVLDDVWNE---------DYYKWEPFYKCLKNSLHESKILITTRKETVARI--MG------STHVISVNVLSEMECWS  137 (505)
Q Consensus        75 ~LlvlDdv~~~---------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~--~~------~~~~~~l~~l~~~ea~~  137 (505)
                      -+|++|++..-         .......+...+.....+.+||.++........  ..      -...+.+++++.+|-.+
T Consensus       123 gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~  202 (284)
T TIGR02880       123 GVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLV  202 (284)
T ss_pred             cEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHH
Confidence            58899999532         111234555666555566677777654322111  11      13478899999999999


Q ss_pred             HHHHhhh
Q 046115          138 VFQSLAI  144 (505)
Q Consensus       138 Lf~~~~~  144 (505)
                      ++....-
T Consensus       203 I~~~~l~  209 (284)
T TIGR02880       203 IAGLMLK  209 (284)
T ss_pred             HHHHHHH
Confidence            9887753

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.13  E-value=0.007  Score=57.65  Aligned_cols=92  Identities=11%  Similarity=0.148  Sum_probs=65.2

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+++.+.....++.+|++|.++ .+... ......+.+.+++.+++.+.+....      
T Consensus       112 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~~------  185 (319)
T PRK08769        112 GIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQG------  185 (319)
T ss_pred             CCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHcC------
Confidence            356789999998777667778888888877777777777653 33322 2335578899999999998886531      


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                       .+   ++.+..++..++|.|+..
T Consensus       186 -~~---~~~a~~~~~l~~G~p~~A  205 (319)
T PRK08769        186 -VS---ERAAQEALDAARGHPGLA  205 (319)
T ss_pred             -CC---hHHHHHHHHHcCCCHHHH
Confidence             11   223667899999999754

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.12  E-value=0.0034  Score=63.79  Aligned_cols=99  Identities=9%  Similarity=0.102  Sum_probs=68.1

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........++..+......+++|++|.++ .+... ......+++.+++.++....+...+...+. 
T Consensus       116 ~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi-  194 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGV-  194 (535)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCC-
Confidence            456688999998777666777888887766667766666553 22221 123468899999999999988766533222 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAK  174 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~  174 (505)
                         .-.++++..|++.++|.+.-+.
T Consensus       195 ---~i~~~Al~~Ia~~s~GdlR~al  216 (535)
T PRK08451        195 ---SYEPEALEILARSGNGSLRDTL  216 (535)
T ss_pred             ---CCCHHHHHHHHHHcCCcHHHHH
Confidence               1235678899999999884433

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.08  E-value=0.006  Score=63.92  Aligned_cols=113  Identities=12%  Similarity=0.014  Sum_probs=64.2

Q ss_pred             HHHHHHHHcCCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEE--EeCchHH-HHHh-CCcceEeCCCCChhhHHH
Q 046115           62 LMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILI--TTRKETV-ARIM-GSTHVISVNVLSEMECWS  137 (505)
Q Consensus        62 ~~~~l~~~l~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLi--Ttr~~~~-~~~~-~~~~~~~l~~l~~~ea~~  137 (505)
                      .+..+.+.+.++++.++-|+.|..+...|..+...+....+...++|  ||+++.. ...+ .....+.+.+++.+|...
T Consensus       281 ~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~  360 (615)
T TIGR02903       281 LQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIAL  360 (615)
T ss_pred             HHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHH
Confidence            34566667777777777666666555556666555555555555666  6665431 1111 223467789999999999


Q ss_pred             HHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHH
Q 046115          138 VFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       138 Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~  178 (505)
                      ++...+.....    .-.+++...|.+.+..-+-++..++.
T Consensus       361 Il~~~a~~~~v----~ls~eal~~L~~ys~~gRraln~L~~  397 (615)
T TIGR02903       361 IVLNAAEKINV----HLAAGVEELIARYTIEGRKAVNILAD  397 (615)
T ss_pred             HHHHHHHHcCC----CCCHHHHHHHHHCCCcHHHHHHHHHH
Confidence            99886642211    11134455555544433455554443

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.

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.07  E-value=3.8e-05  Score=77.69  Aligned_cols=124  Identities=22%  Similarity=0.247  Sum_probs=90.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      ++..++++.+.......++    .-++.|+.|+|++|++...    . ++..+++|+.|||+       .|.+...|.--
T Consensus       165 ~L~~a~fsyN~L~~mD~SL----qll~ale~LnLshNk~~~v----~-~Lr~l~~LkhLDls-------yN~L~~vp~l~  228 (1096)
T KOG1859|consen  165 KLATASFSYNRLVLMDESL----QLLPALESLNLSHNKFTKV----D-NLRRLPKLKHLDLS-------YNCLRHVPQLS  228 (1096)
T ss_pred             hHhhhhcchhhHHhHHHHH----HHHHHhhhhccchhhhhhh----H-HHHhcccccccccc-------cchhccccccc
Confidence            4444555444443333333    2568999999999998653    2 47889999999998       67777777522


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccch--hccccccCceeecCCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~  472 (505)
                      ..=.+|..|.++||. ++.+-. +.+|.+|+.||++.|- +.....  -++.|..|+.|.+.||+
T Consensus       229 ~~gc~L~~L~lrnN~-l~tL~g-ie~LksL~~LDlsyNl-l~~hseL~pLwsLs~L~~L~LeGNP  290 (1096)
T KOG1859|consen  229 MVGCKLQLLNLRNNA-LTTLRG-IENLKSLYGLDLSYNL-LSEHSELEPLWSLSSLIVLWLEGNP  290 (1096)
T ss_pred             hhhhhheeeeecccH-HHhhhh-HHhhhhhhccchhHhh-hhcchhhhHHHHHHHHHHHhhcCCc
Confidence            222349999999998 888877 8899999999999987 544432  25778889999999998

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.06  E-value=0.00012  Score=58.60  Aligned_cols=85  Identities=28%  Similarity=0.351  Sum_probs=49.3

Q ss_pred             hhcCcccceEEecccccCCccccccccCccccC-CCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhc
Q 046115          379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEK-LLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGI  457 (505)
Q Consensus       379 ~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~-l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~  457 (505)
                      +.....|...+|+       +|.++.+|+.+.. .+.++.|++++|. +..+|..+..++.|+.|+++.|+ +...|.-+
T Consensus        49 l~~~~el~~i~ls-------~N~fk~fp~kft~kf~t~t~lNl~~ne-isdvPeE~Aam~aLr~lNl~~N~-l~~~p~vi  119 (177)
T KOG4579|consen   49 LSKGYELTKISLS-------DNGFKKFPKKFTIKFPTATTLNLANNE-ISDVPEELAAMPALRSLNLRFNP-LNAEPRVI  119 (177)
T ss_pred             HhCCceEEEEecc-------cchhhhCCHHHhhccchhhhhhcchhh-hhhchHHHhhhHHhhhcccccCc-cccchHHH
Confidence            3444455555665       5555556555542 3356666666666 66666666666666666666666 55555555


Q ss_pred             cccccCceeecCCCc
Q 046115          458 GKLRKLMYLHNEDTG  472 (505)
Q Consensus       458 ~~l~~L~~L~l~~~~  472 (505)
                      ..|.+|-.|+..+|.
T Consensus       120 ~~L~~l~~Lds~~na  134 (177)
T KOG4579|consen  120 APLIKLDMLDSPENA  134 (177)
T ss_pred             HHHHhHHHhcCCCCc
Confidence            556666666655554

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

Probab=97.00  E-value=0.0081  Score=58.56  Aligned_cols=130  Identities=17%  Similarity=0.177  Sum_probs=75.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|.|||-|+.++++  ...........+.+..    +......+..+..          ...+...+..  .-=++++||
T Consensus       122 ~GlGKTHLl~Aign--~~~~~~~~a~v~y~~s----e~f~~~~v~a~~~----------~~~~~Fk~~y--~~dlllIDD  183 (408)
T COG0593         122 VGLGKTHLLQAIGN--EALANGPNARVVYLTS----EDFTNDFVKALRD----------NEMEKFKEKY--SLDLLLIDD  183 (408)
T ss_pred             CCCCHHHHHHHHHH--HHHhhCCCceEEeccH----HHHHHHHHHHHHh----------hhHHHHHHhh--ccCeeeech
Confidence            59999999999999  6666655333333322    2344444444441          1222333333  223889999


Q ss_pred             CCCCCc--cChhHHHHhhcCC-CCCcEEEEEeCc---------hHHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           82 VWNEDY--YKWEPFYKCLKNS-LHESKILITTRK---------ETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        82 v~~~~~--~~~~~~~~~~~~~-~~~~~iLiTtr~---------~~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++-..-  ..-+.+...+..- ..|-+|++|++.         +.+.....+...+++.+.+.+....++...+...+..
T Consensus       184 iq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~  263 (408)
T COG0593         184 IQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAEDRGIE  263 (408)
T ss_pred             HhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHHhcCCC
Confidence            855221  1122233323221 233489998865         2334445566789999999999999998876544443

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

Probab=96.99  E-value=0.0091  Score=59.13  Aligned_cols=141  Identities=20%  Similarity=0.185  Sum_probs=83.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      -++||||+++.+..  ...+.   .++++.-+......-+.+.....                  ...-..++..|+||.
T Consensus        46 R~~GKTtll~~l~~--~~~~~---~iy~~~~d~~~~~~~l~d~~~~~------------------~~~~~~~~~yifLDE  102 (398)
T COG1373          46 RQVGKTTLLKLLIK--GLLEE---IIYINFDDLRLDRIELLDLLRAY------------------IELKEREKSYIFLDE  102 (398)
T ss_pred             ccccHHHHHHHHHh--hCCcc---eEEEEecchhcchhhHHHHHHHH------------------HHhhccCCceEEEec
Confidence            47999999977766  33333   55665443222211111111111                  111112788999999


Q ss_pred             CCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHH-----H-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchH
Q 046115           82 VWNEDYYKWEPFYKCLKNSLHESKILITTRKETVAR-----I-MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENL  155 (505)
Q Consensus        82 v~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-----~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~  155 (505)
                      |+...  .|...+..+.+.++. +|++|+.+..+..     . .+....+.+.||+..|-..+-.      ...... ..
T Consensus       103 Iq~v~--~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~~~------~~~~~~-~~  172 (398)
T COG1373         103 IQNVP--DWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKLKG------EEIEPS-KL  172 (398)
T ss_pred             ccCch--hHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhhcc------cccchh-HH
Confidence            97654  899999999988877 8899888754432     2 2346688999999999655432      000000 11


Q ss_pred             HHHHHHHHHHcCCChHHHHHH
Q 046115          156 EKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       156 ~~~~~~i~~~~~g~Plal~~~  176 (505)
                      .. .-+-.-..||.|.++..-
T Consensus       173 ~~-~f~~Yl~~GGfP~~v~~~  192 (398)
T COG1373         173 EL-LFEKYLETGGFPESVKAD  192 (398)
T ss_pred             HH-HHHHHHHhCCCcHHHhCc
Confidence            11 333445679999876543

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.97  E-value=0.027  Score=58.97  Aligned_cols=97  Identities=16%  Similarity=0.187  Sum_probs=66.4

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEE-EeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILI-TTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLi-Ttr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+...+......+.+|+ |++...+...+ ....++++.+++.++....+...+...+. 
T Consensus       120 ~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi-  198 (614)
T PRK14971        120 GKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGI-  198 (614)
T ss_pred             CCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCC-
Confidence            3455889999977766667788888887655565544 54544444332 33568999999999999988876543322 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                         .-.++++..|++.++|..--
T Consensus       199 ---~i~~~al~~La~~s~gdlr~  218 (614)
T PRK14971        199 ---TAEPEALNVIAQKADGGMRD  218 (614)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHH
Confidence               12245688899999997643

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.97  E-value=0.0077  Score=58.08  Aligned_cols=117  Identities=16%  Similarity=0.200  Sum_probs=61.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHH-HcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEE-CVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~-~l~~~r~Llvl   79 (505)
                      .+|+|||++|+.+++  +...   ....++... .. ....+..+..+.                 .. ...+.+-++|+
T Consensus        51 ~~G~GKT~la~~l~~--~~~~---~~~~i~~~~-~~-~~~i~~~l~~~~-----------------~~~~~~~~~~vlii  106 (316)
T PHA02544         51 SPGTGKTTVAKALCN--EVGA---EVLFVNGSD-CR-IDFVRNRLTRFA-----------------STVSLTGGGKVIII  106 (316)
T ss_pred             cCCCCHHHHHHHHHH--HhCc---cceEeccCc-cc-HHHHHHHHHHHH-----------------HhhcccCCCeEEEE
Confidence            479999999999998  4322   223444443 11 111111111110                 00 01234567899


Q ss_pred             eCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchH-HHHH-hCCcceEeCCCCChhhHHHHHHH
Q 046115           80 DDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKET-VARI-MGSTHVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        80 Ddv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~-~~~~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      |++... .......+...+.....++.+++||.... +... ......+.++..+.++..+++..
T Consensus       107 De~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~  171 (316)
T PHA02544        107 DEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQ  171 (316)
T ss_pred             ECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHH
Confidence            999654 22222334444555566788888887542 1111 12234677777788887766543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.93  E-value=0.033  Score=58.02  Aligned_cols=103  Identities=12%  Similarity=0.105  Sum_probs=66.8

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+...+......+.+| +||....+...+ .....+++..++.++....+.......+. 
T Consensus       118 ~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi-  196 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGI-  196 (576)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCC-
Confidence            355678899997766556777888887765555555 455444444332 23457889999999988888765432221 


Q ss_pred             CCCchHHHHHHHHHHHcCCCh-HHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLP-LAAKTIAS  178 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~P-lal~~~~~  178 (505)
                         .-..+.+..|++.++|.. .|+..+-.
T Consensus       197 ---~i~~~al~~la~~a~G~lr~al~~Ldq  223 (576)
T PRK14965        197 ---SISDAALALVARKGDGSMRDSLSTLDQ  223 (576)
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence               122466788999999866 55555433

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

Probab=96.91  E-value=0.0012  Score=69.65  Aligned_cols=114  Identities=21%  Similarity=0.278  Sum_probs=82.6

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCcccc-ccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIE-KLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~-~lp~~  432 (505)
                      -+++|++|.+.+-.+....  .-..+.++++|++||++       ++.+..+ .+++.|++|+.|.+.+-.... ..-..
T Consensus       146 ~LPsL~sL~i~~~~~~~~d--F~~lc~sFpNL~sLDIS-------~TnI~nl-~GIS~LknLq~L~mrnLe~e~~~~l~~  215 (699)
T KOG3665|consen  146 MLPSLRSLVISGRQFDNDD--FSQLCASFPNLRSLDIS-------GTNISNL-SGISRLKNLQVLSMRNLEFESYQDLID  215 (699)
T ss_pred             hCcccceEEecCceecchh--HHHHhhccCccceeecC-------CCCccCc-HHHhccccHHHHhccCCCCCchhhHHH
Confidence            3589999999987764321  44557789999999999       7777777 678999999999999877332 22234


Q ss_pred             hhcCCCCcEEecCCCcCccc--cch----hccccccCceeecCCCcccccc
Q 046115          433 LCELYNLERLNVDDCQNLRE--LPR----GIGKLRKLMYLHNEDTGCLRYL  477 (505)
Q Consensus       433 ~~~l~~L~~L~l~~~~~~~~--lp~----~~~~l~~L~~L~l~~~~~~~~~  477 (505)
                      +..|.+|+.||+|.......  +..    --..||.|+.|+.+++.+...+
T Consensus       216 LF~L~~L~vLDIS~~~~~~~~~ii~qYlec~~~LpeLrfLDcSgTdi~~~~  266 (699)
T KOG3665|consen  216 LFNLKKLRVLDISRDKNNDDTKIIEQYLECGMVLPELRFLDCSGTDINEEI  266 (699)
T ss_pred             HhcccCCCeeeccccccccchHHHHHHHHhcccCccccEEecCCcchhHHH
Confidence            78899999999998653321  111    1255899999999988754433

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.89  E-value=0.026  Score=53.91  Aligned_cols=97  Identities=20%  Similarity=0.194  Sum_probs=64.1

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      +++-++|+|++..........+++.+....+..-||+|++...+.+.+ .....+.+.+++.++..+.+........   
T Consensus       123 ~~~kVvII~~ae~m~~~aaNaLLK~LEEPp~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~---  199 (314)
T PRK07399        123 APRKVVVIEDAETMNEAAANALLKTLEEPGNGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI---  199 (314)
T ss_pred             CCceEEEEEchhhcCHHHHHHHHHHHhCCCCCeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc---
Confidence            466789999997776666777888887766444444554444443332 3356899999999999999987542111   


Q ss_pred             CCchHHHHHHHHHHHcCCChHHHHH
Q 046115          151 KRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                          .+.....++..++|.|.....
T Consensus       200 ----~~~~~~~l~~~a~Gs~~~al~  220 (314)
T PRK07399        200 ----LNINFPELLALAQGSPGAAIA  220 (314)
T ss_pred             ----chhHHHHHHHHcCCCHHHHHH
Confidence                111135788899999965433

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.88  E-value=0.019  Score=56.77  Aligned_cols=139  Identities=19%  Similarity=0.220  Sum_probs=81.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||.+++.+    ..|..+--++-..-             .+   -.+............+..+..=-.||+|
T Consensus       546 p~~sGKTaLAA~iA~~----S~FPFvKiiSpe~m-------------iG---~sEsaKc~~i~k~F~DAYkS~lsiivvD  605 (744)
T KOG0741|consen  546 PPGSGKTALAAKIALS----SDFPFVKIISPEDM-------------IG---LSESAKCAHIKKIFEDAYKSPLSIIVVD  605 (744)
T ss_pred             CCCCChHHHHHHHHhh----cCCCeEEEeChHHc-------------cC---ccHHHHHHHHHHHHHHhhcCcceEEEEc
Confidence            4799999999999973    56766554432211             01   1112222333444555667777899999


Q ss_pred             CCCCCCccCh------------hH---HHHhhcCCCCCcEEEEEeCchHHHHHhCC----cceEeCCCCCh-hhHHHHHH
Q 046115           81 DVWNEDYYKW------------EP---FYKCLKNSLHESKILITTRKETVARIMGS----THVISVNVLSE-MECWSVFQ  140 (505)
Q Consensus        81 dv~~~~~~~~------------~~---~~~~~~~~~~~~~iLiTtr~~~~~~~~~~----~~~~~l~~l~~-~ea~~Lf~  140 (505)
                      |+..  ..+|            +.   +++..|+.++..-|+-||..+.+...++-    ...+.++.++. ++..+.++
T Consensus       606 diEr--LiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~  683 (744)
T KOG0741|consen  606 DIER--LLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLLEVLE  683 (744)
T ss_pred             chhh--hhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHHHHHH
Confidence            9933  2232            22   22333444455567778888888887654    34778888887 66667666


Q ss_pred             HhhhCCCCCCCCchHHHHHHHHHHHc
Q 046115          141 SLAISGKTIGKRENLEKIGREIVKKC  166 (505)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~i~~~~  166 (505)
                      ..-     ...+.+.+.++.+....|
T Consensus       684 ~~n-----~fsd~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  684 ELN-----IFSDDEVRAIAEQLLSKK  704 (744)
T ss_pred             Hcc-----CCCcchhHHHHHHHhccc
Confidence            542     122333444555555555

>PRK04132 replication factor C small subunit; Provisional

Probab=96.88  E-value=0.034  Score=59.68  Aligned_cols=149  Identities=9%  Similarity=0.013  Sum_probs=94.5

Q ss_pred             CCCCcHHHHHHHHhcCccc-ccCCC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDV-ERNFE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~-~~~f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      +.++||||+|..+++  +. .+.++ .++-++.+...... ..++++..+......               -..+.-++|
T Consensus       574 Ph~lGKTT~A~ala~--~l~g~~~~~~~lElNASd~rgid-~IR~iIk~~a~~~~~---------------~~~~~KVvI  635 (846)
T PRK04132        574 PTVLHNTTAALALAR--ELFGENWRHNFLELNASDERGIN-VIREKVKEFARTKPI---------------GGASFKIIF  635 (846)
T ss_pred             CCcccHHHHHHHHHH--hhhcccccCeEEEEeCCCcccHH-HHHHHHHHHHhcCCc---------------CCCCCEEEE
Confidence            457999999999999  44 22332 35567766644443 334444333211110               012457999


Q ss_pred             EeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHH
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLE  156 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~  156 (505)
                      +|+++.........+...+......++++.++.+. .+...+ .....+.+.+++.++....+...+...+. .   -.+
T Consensus       636 IDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi-~---i~~  711 (846)
T PRK04132        636 LDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL-E---LTE  711 (846)
T ss_pred             EECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCC-C---CCH
Confidence            99998877667777888887766667777666653 333222 23568899999999988888766532221 1   124


Q ss_pred             HHHHHHHHHcCCChH
Q 046115          157 KIGREIVKKCKGLPL  171 (505)
Q Consensus       157 ~~~~~i~~~~~g~Pl  171 (505)
                      +.+..|++.++|.+.
T Consensus       712 e~L~~Ia~~s~GDlR  726 (846)
T PRK04132        712 EGLQAILYIAEGDMR  726 (846)
T ss_pred             HHHHHHHHHcCCCHH
Confidence            578899999999884

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.85  E-value=0.017  Score=53.84  Aligned_cols=70  Identities=9%  Similarity=0.109  Sum_probs=40.9

Q ss_pred             EEEEEeCCCCCC--------ccChhHHHHhhcCCCCCcEEEEEeCchHHHH------Hh-CC-cceEeCCCCChhhHHHH
Q 046115           75 FLLVLDDVWNED--------YYKWEPFYKCLKNSLHESKILITTRKETVAR------IM-GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        75 ~LlvlDdv~~~~--------~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~------~~-~~-~~~~~l~~l~~~ea~~L  138 (505)
                      .+|++|++..-.        ......+...+........+++++....+..      .. .. ...+.+++++.+|-.++
T Consensus       107 ~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~I  186 (261)
T TIGR02881       107 GVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEI  186 (261)
T ss_pred             CEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHH
Confidence            488999996421        1123445555555444445555554432211      11 11 24688999999999999


Q ss_pred             HHHhhh
Q 046115          139 FQSLAI  144 (505)
Q Consensus       139 f~~~~~  144 (505)
                      +.+...
T Consensus       187 l~~~~~  192 (261)
T TIGR02881       187 AERMVK  192 (261)
T ss_pred             HHHHHH
Confidence            987764

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.

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.85  E-value=0.0013  Score=56.50  Aligned_cols=62  Identities=26%  Similarity=0.298  Sum_probs=26.6

Q ss_pred             ccCCCCcceeeccCCccccccchhhh-cCCCCcEEecCCCcCccccch--hccccccCceeecCCCc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLC-ELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~-~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~  472 (505)
                      +..++.|.+|.+.+|+ ++.+-+.+. .+++|..|.|.+|+ +..+-+  .+..+|+|++|.+-+|+
T Consensus        60 lp~l~rL~tLll~nNr-It~I~p~L~~~~p~l~~L~LtnNs-i~~l~dl~pLa~~p~L~~Ltll~Np  124 (233)
T KOG1644|consen   60 LPHLPRLHTLLLNNNR-ITRIDPDLDTFLPNLKTLILTNNS-IQELGDLDPLASCPKLEYLTLLGNP  124 (233)
T ss_pred             CCCccccceEEecCCc-ceeeccchhhhccccceEEecCcc-hhhhhhcchhccCCccceeeecCCc
Confidence            3444445555555444 433333232 33445555555544 333321  12334445555544444

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.82  E-value=0.051  Score=56.25  Aligned_cols=98  Identities=9%  Similarity=0.162  Sum_probs=65.9

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|++.......+..+...+......+.+|.+|.+ ..+...+ .....++..+++.++....+...+...+.
T Consensus       117 ~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi  196 (563)
T PRK06647        117 SSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQI  196 (563)
T ss_pred             cCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcCC
Confidence            356668999999776665677788887766566666555543 3443322 23457889999999998888776533222


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                          .-.++++..|++.++|.+-.
T Consensus       197 ----~id~eAl~lLa~~s~GdlR~  216 (563)
T PRK06647        197 ----KYEDEALKWIAYKSTGSVRD  216 (563)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHH
Confidence                12356788899999998743

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.80  E-value=0.032  Score=53.31  Aligned_cols=91  Identities=11%  Similarity=0.062  Sum_probs=66.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+++.+.....++.+|++|.++ .+... ...-..+.+.+++.+++.+.+.....     
T Consensus       106 g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~~-----  180 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSS-----  180 (325)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHhc-----
Confidence            456688899998887777888999998887777877777764 33322 23356889999999999998876531     


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                        .+  ...+...+..++|.|.
T Consensus       181 --~~--~~~~~~~~~l~~g~p~  198 (325)
T PRK06871        181 --AE--ISEILTALRINYGRPL  198 (325)
T ss_pred             --cC--hHHHHHHHHHcCCCHH
Confidence              11  1225567889999995

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=96.79  E-value=0.00063  Score=60.91  Aligned_cols=85  Identities=25%  Similarity=0.227  Sum_probs=41.5

Q ss_pred             CCCCcceeeccCC--ccccccchhhhcCCCCcEEecCCCcCccccc--hhccccccCceeecCCCcccccccc----ccc
Q 046115          411 KLLHLKYLNLKGQ--KKIEKLPETLCELYNLERLNVDDCQNLRELP--RGIGKLRKLMYLHNEDTGCLRYLPA----GIG  482 (505)
Q Consensus       411 ~l~~L~~L~l~~~--~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~~p~----~i~  482 (505)
                      .|++|++|.++.|  .....++-..-++++|++|++++|+ ++.+-  +.+..+.+|..|++..|.... +-.    .|.
T Consensus        63 ~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nk-i~~lstl~pl~~l~nL~~Ldl~n~~~~~-l~dyre~vf~  140 (260)
T KOG2739|consen   63 KLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNK-IKDLSTLRPLKELENLKSLDLFNCSVTN-LDDYREKVFL  140 (260)
T ss_pred             CcchhhhhcccCCcccccccceehhhhCCceeEEeecCCc-cccccccchhhhhcchhhhhcccCCccc-cccHHHHHHH
Confidence            3455555555555  3334444434444566666666655 33211  123444555556655554322 211    244


Q ss_pred             CCccCCccceeEecC
Q 046115          483 ELIRLRRVREFVVGG  497 (505)
Q Consensus       483 ~l~~L~~L~~~~~~~  497 (505)
                      -+++|++|+.+.|.+
T Consensus       141 ll~~L~~LD~~dv~~  155 (260)
T KOG2739|consen  141 LLPSLKYLDGCDVDG  155 (260)
T ss_pred             HhhhhccccccccCC
Confidence            556666666665554

>PRK08181 transposase; Validated

Probab=96.73  E-value=0.0039  Score=57.92  Aligned_cols=94  Identities=18%  Similarity=0.136  Sum_probs=50.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||.||..+++  +...+...++|++.      .+++..+.....      ....++..    ..+. +-=|||+|
T Consensus       114 p~GtGKTHLa~Aia~--~a~~~g~~v~f~~~------~~L~~~l~~a~~------~~~~~~~l----~~l~-~~dLLIID  174 (269)
T PRK08181        114 PPGGGKSHLAAAIGL--ALIENGWRVLFTRT------TDLVQKLQVARR------ELQLESAI----AKLD-KFDLLILD  174 (269)
T ss_pred             cCCCcHHHHHHHHHH--HHHHcCCceeeeeH------HHHHHHHHHHHh------CCcHHHHH----HHHh-cCCEEEEe
Confidence            479999999999988  44444445566653      234444432211      11122222    2222 23499999


Q ss_pred             CCCCCCccCh--hHHHHhhcCCCCCcEEEEEeCch
Q 046115           81 DVWNEDYYKW--EPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        81 dv~~~~~~~~--~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      |+.......+  ..+...+........+||||+-+
T Consensus       175 Dlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        175 DLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             ccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            9965432222  23444444332234689998853

>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=96.71  E-value=0.0039  Score=56.38  Aligned_cols=29  Identities=24%  Similarity=0.283  Sum_probs=24.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCV   31 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~   31 (505)
                      .+|+|||+|+..+..  .....|.++++++-
T Consensus        21 ~sGSGKT~li~~lL~--~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   21 KSGSGKTTLIKSLLY--YLRHKFDHIFLITP   49 (241)
T ss_pred             CCCCCHHHHHHHHHH--hhcccCCEEEEEec
Confidence            379999999999998  67888988887754

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

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=96.71  E-value=0.013  Score=58.06  Aligned_cols=143  Identities=15%  Similarity=0.210  Sum_probs=72.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHH-HHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQH-IEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~-l~~~l~~~r~Llvl   79 (505)
                      ++|+|||++|+.+++  +....     |+.+..        ..+..... +      +....... +...-...+.+|+|
T Consensus       173 ppGtGKT~lAkaia~--~~~~~-----~i~v~~--------~~l~~~~~-g------~~~~~i~~~f~~a~~~~p~Ilfi  230 (389)
T PRK03992        173 PPGTGKTLLAKAVAH--ETNAT-----FIRVVG--------SELVQKFI-G------EGARLVRELFELAREKAPSIIFI  230 (389)
T ss_pred             CCCCChHHHHHHHHH--HhCCC-----EEEeeh--------HHHhHhhc-c------chHHHHHHHHHHHHhcCCeEEEE
Confidence            489999999999998  44333     232221        11111111 0      01111122 22222345789999


Q ss_pred             eCCCCCC----------ccCh-hHHHHhh---cC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNED----------YYKW-EPFYKCL---KN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~----------~~~~-~~~~~~~---~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |+++.-.          ...+ ..+...+   ..  ...+..||.||...+... ..   +. ...+.++..+.++-.++
T Consensus       231 DEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~I  310 (389)
T PRK03992        231 DEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEI  310 (389)
T ss_pred             echhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHH
Confidence            9985420          0011 1122222   21  123566777887643322 11   11 35789999999999999


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |+.+...... ....+    ...+++.+.|+-
T Consensus       311 l~~~~~~~~~-~~~~~----~~~la~~t~g~s  337 (389)
T PRK03992        311 LKIHTRKMNL-ADDVD----LEELAELTEGAS  337 (389)
T ss_pred             HHHHhccCCC-CCcCC----HHHHHHHcCCCC
Confidence            9877532221 22222    345666666644

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=96.70  E-value=0.00032  Score=63.78  Aligned_cols=134  Identities=19%  Similarity=0.141  Sum_probs=59.8

Q ss_pred             ccCCCCCCCceEEEecCCCcccccc-chhHHhhcCcccceEEecccccCCccccccc-cCc-ccc-CCCCcceeeccCCc
Q 046115          349 WGNVTGLRGLRSLLVKSDEYSWSSE-VLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPT-NIE-KLLHLKYLNLKGQK  424 (505)
Q Consensus       349 ~~~~~~~~~L~~L~l~~~~~~~~~~-~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~-~~~-~l~~L~~L~l~~~~  424 (505)
                      ...+.+-.+|+.|+++.+.  |+++ .+.-.+.+++.|..|+|+       .+.... .-. .+. -=.+|..|+|+|+.
T Consensus       227 ~~~iAkN~~L~~lnlsm~s--G~t~n~~~ll~~scs~L~~LNls-------Wc~l~~~~Vtv~V~hise~l~~LNlsG~r  297 (419)
T KOG2120|consen  227 VNTIAKNSNLVRLNLSMCS--GFTENALQLLLSSCSRLDELNLS-------WCFLFTEKVTVAVAHISETLTQLNLSGYR  297 (419)
T ss_pred             HHHHhccccceeecccccc--ccchhHHHHHHHhhhhHhhcCch-------HhhccchhhhHHHhhhchhhhhhhhhhhH
Confidence            3344466777777777664  2221 122235566666666665       111100 000 000 01234455555553


Q ss_pred             cc---cccchhhhcCCCCcEEecCCCcCccc-cchhccccccCceeecCCCccccccccc---ccCCccCCcccee
Q 046115          425 KI---EKLPETLCELYNLERLNVDDCQNLRE-LPRGIGKLRKLMYLHNEDTGCLRYLPAG---IGELIRLRRVREF  493 (505)
Q Consensus       425 ~~---~~lp~~~~~l~~L~~L~l~~~~~~~~-lp~~~~~l~~L~~L~l~~~~~~~~~p~~---i~~l~~L~~L~~~  493 (505)
                      ..   ..+..-..++++|..|||+.|-.++. .-..+.+++.|++|.++-|.  +..|..   +...++|.+|+.+
T Consensus       298 rnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSlsRCY--~i~p~~~~~l~s~psl~yLdv~  371 (419)
T KOG2120|consen  298 RNLQKSHLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLSRCY--DIIPETLLELNSKPSLVYLDVF  371 (419)
T ss_pred             hhhhhhHHHHHHHhCCceeeeccccccccCchHHHHHHhcchheeeehhhhc--CCChHHeeeeccCcceEEEEec
Confidence            21   12222223556666666666544332 11234555566666666554  233332   3444555555544

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.67  E-value=0.00012  Score=65.76  Aligned_cols=61  Identities=25%  Similarity=0.287  Sum_probs=27.6

Q ss_pred             CCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccch--hccccccCceeecCCCccc
Q 046115          411 KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~  474 (505)
                      +++.|++|.|+-|. ++.+.+ +..|.+|++|.|+.|. +..+-+  .+.++|+|++|-+..|+..
T Consensus        39 kMp~lEVLsLSvNk-IssL~p-l~rCtrLkElYLRkN~-I~sldEL~YLknlpsLr~LWL~ENPCc  101 (388)
T KOG2123|consen   39 KMPLLEVLSLSVNK-ISSLAP-LQRCTRLKELYLRKNC-IESLDELEYLKNLPSLRTLWLDENPCC  101 (388)
T ss_pred             hcccceeEEeeccc-cccchh-HHHHHHHHHHHHHhcc-cccHHHHHHHhcCchhhhHhhccCCcc
Confidence            44444444444444 444443 4444444444444444 333322  2444444444444444433

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

Probab=96.66  E-value=0.00097  Score=70.28  Aligned_cols=108  Identities=20%  Similarity=0.253  Sum_probs=74.6

Q ss_pred             CCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhc
Q 046115          356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCE  435 (505)
Q Consensus       356 ~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~  435 (505)
                      .+|+.|++.|.... ....+...-..+++|+.|.+.++..     ....+-.-+.++++|..||++++. ++.+ ..++.
T Consensus       122 ~nL~~LdI~G~~~~-s~~W~~kig~~LPsL~sL~i~~~~~-----~~~dF~~lc~sFpNL~sLDIS~Tn-I~nl-~GIS~  193 (699)
T KOG3665|consen  122 QNLQHLDISGSELF-SNGWPKKIGTMLPSLRSLVISGRQF-----DNDDFSQLCASFPNLRSLDISGTN-ISNL-SGISR  193 (699)
T ss_pred             HhhhhcCccccchh-hccHHHHHhhhCcccceEEecCcee-----cchhHHHHhhccCccceeecCCCC-ccCc-HHHhc
Confidence            57788888776532 1122333334688999999984321     111223335689999999999999 8888 45999


Q ss_pred             CCCCcEEecCCCcCccccc--hhccccccCceeecCCCc
Q 046115          436 LYNLERLNVDDCQNLRELP--RGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       436 l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~  472 (505)
                      |+|||.|.+.+=. ....+  ..+-+|++|+.||++...
T Consensus       194 LknLq~L~mrnLe-~e~~~~l~~LF~L~~L~vLDIS~~~  231 (699)
T KOG3665|consen  194 LKNLQVLSMRNLE-FESYQDLIDLFNLKKLRVLDISRDK  231 (699)
T ss_pred             cccHHHHhccCCC-CCchhhHHHHhcccCCCeeeccccc
Confidence            9999999988733 33322  247889999999998775

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.65  E-value=0.0028  Score=57.89  Aligned_cols=94  Identities=16%  Similarity=0.165  Sum_probs=51.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      +|+|||+||..+++  .....-..++++++      .+++..+-.... .   ......    .+.+.+. +.=+||+||
T Consensus       108 ~GtGKThLa~aia~--~l~~~g~~v~~it~------~~l~~~l~~~~~-~---~~~~~~----~~l~~l~-~~dlLvIDD  170 (244)
T PRK07952        108 PGTGKNHLAAAICN--ELLLRGKSVLIITV------ADIMSAMKDTFS-N---SETSEE----QLLNDLS-NVDLLVIDE  170 (244)
T ss_pred             CCCCHHHHHHHHHH--HHHhcCCeEEEEEH------HHHHHHHHHHHh-h---ccccHH----HHHHHhc-cCCEEEEeC
Confidence            79999999999998  55444445566643      334443333321 0   111111    2333344 334888899


Q ss_pred             CCCCCccChhH--HHHhhcCC-CCCcEEEEEeCc
Q 046115           82 VWNEDYYKWEP--FYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~~--~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      +.......|+.  +...+... .....+||||.-
T Consensus       171 ig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl  204 (244)
T PRK07952        171 IGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNS  204 (244)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence            97765555543  33333322 234568888874

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.64  E-value=0.019  Score=55.51  Aligned_cols=70  Identities=10%  Similarity=0.128  Sum_probs=50.9

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHHH
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      +.+-++|+|++..........+++.+.+...++.+|.+|.++ .+.+.+ .....+++.+++.++..+.+..
T Consensus       109 ~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        109 SNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             cCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHH
Confidence            455679999997777666778888888877777777777653 233222 3356899999999999888865

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

Probab=96.63  E-value=0.0021  Score=55.93  Aligned_cols=93  Identities=22%  Similarity=0.340  Sum_probs=45.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ..|+|||.||..+++  +...+=..+.|++.          .+++..+......  ....+...    .+.+ -=|||||
T Consensus        55 ~~G~GKThLa~ai~~--~~~~~g~~v~f~~~----------~~L~~~l~~~~~~--~~~~~~~~----~l~~-~dlLilD  115 (178)
T PF01695_consen   55 PPGTGKTHLAVAIAN--EAIRKGYSVLFITA----------SDLLDELKQSRSD--GSYEELLK----RLKR-VDLLILD  115 (178)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTT--EEEEEH----------HHHHHHHHCCHCC--TTHCHHHH----HHHT-SSCEEEE
T ss_pred             hHhHHHHHHHHHHHH--HhccCCcceeEeec----------Cceeccccccccc--cchhhhcC----cccc-ccEeccc
Confidence            379999999999988  44333234567763          2344444322111  11222222    2222 2388899


Q ss_pred             CCCCCCccCh--hHHHHhhcCCCCCcEEEEEeCc
Q 046115           81 DVWNEDYYKW--EPFYKCLKNSLHESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~--~~~~~~~~~~~~~~~iLiTtr~  112 (505)
                      |+.......|  ..+...+........+||||.-
T Consensus       116 DlG~~~~~~~~~~~l~~ii~~R~~~~~tIiTSN~  149 (178)
T PF01695_consen  116 DLGYEPLSEWEAELLFEIIDERYERKPTIITSNL  149 (178)
T ss_dssp             TCTSS---HHHHHCTHHHHHHHHHT-EEEEEESS
T ss_pred             ccceeeecccccccchhhhhHhhcccCeEeeCCC
Confidence            9966543332  2222222222122368888884

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.63  E-value=0.08  Score=54.97  Aligned_cols=98  Identities=12%  Similarity=0.099  Sum_probs=63.3

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEE-EEeCchHHHHHh-CCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKIL-ITTRKETVARIM-GSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iL-iTtr~~~~~~~~-~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .+++-++|+|++.......+..+...+......+.+| +||....+...+ .....++..+++.++....+...+...+.
T Consensus       117 ~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi  196 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGI  196 (559)
T ss_pred             cCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCC
Confidence            3456788999997766556777777776654444444 454443333222 23457889999999998888776533222


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                          .-.++++..|++.++|.+..
T Consensus       197 ----~i~~~al~~ia~~s~G~~R~  216 (559)
T PRK05563        197 ----EYEDEALRLIARAAEGGMRD  216 (559)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHH
Confidence                11246678889999887753

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=96.62  E-value=0.00019  Score=72.75  Aligned_cols=121  Identities=21%  Similarity=0.223  Sum_probs=85.6

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhh-c
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC-E  435 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~-~  435 (505)
                      .|.+-+.++|.+.-    +...+.-+..|+.|+|+       +|.+.+.- .+..|++|++|||+.|. +..+|. ++ .
T Consensus       165 ~L~~a~fsyN~L~~----mD~SLqll~ale~LnLs-------hNk~~~v~-~Lr~l~~LkhLDlsyN~-L~~vp~-l~~~  230 (1096)
T KOG1859|consen  165 KLATASFSYNRLVL----MDESLQLLPALESLNLS-------HNKFTKVD-NLRRLPKLKHLDLSYNC-LRHVPQ-LSMV  230 (1096)
T ss_pred             hHhhhhcchhhHHh----HHHHHHHHHHhhhhccc-------hhhhhhhH-HHHhcccccccccccch-hccccc-cchh
Confidence            35555566666542    55567778889999998       55555544 57889999999999999 888887 43 2


Q ss_pred             CCCCcEEecCCCcCccccchhccccccCceeecCCCccccccc-ccccCCccCCcccee
Q 046115          436 LYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRLRRVREF  493 (505)
Q Consensus       436 l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L~~L~~~  493 (505)
                      -..|+.|+|+||- ++.+. ++.+|++|+.|++++|-..+.-- ..+..|.+|+.|.+.
T Consensus       231 gc~L~~L~lrnN~-l~tL~-gie~LksL~~LDlsyNll~~hseL~pLwsLs~L~~L~Le  287 (1096)
T KOG1859|consen  231 GCKLQLLNLRNNA-LTTLR-GIENLKSLYGLDLSYNLLSEHSELEPLWSLSSLIVLWLE  287 (1096)
T ss_pred             hhhheeeeecccH-HHhhh-hHHhhhhhhccchhHhhhhcchhhhHHHHHHHHHHHhhc
Confidence            2349999999988 77773 78999999999999995332211 113455566655543

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.61  E-value=0.048  Score=51.95  Aligned_cols=91  Identities=13%  Similarity=0.103  Sum_probs=65.3

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+.+.+.....++.+|.+|.++ .+..- ...-..+.+.+++.+++.+.+....    . 
T Consensus       107 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~----~-  181 (319)
T PRK06090        107 NGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQG----I-  181 (319)
T ss_pred             CCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHcC----C-
Confidence            345688999998877777788999988877777777766664 33332 3345688999999999999886531    1 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAK  174 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~  174 (505)
                        .     .+..++..++|.|+...
T Consensus       182 --~-----~~~~~l~l~~G~p~~A~  199 (319)
T PRK06090        182 --T-----VPAYALKLNMGSPLKTL  199 (319)
T ss_pred             --c-----hHHHHHHHcCCCHHHHH
Confidence              1     13467889999998543

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.61  E-value=0.042  Score=52.95  Aligned_cols=91  Identities=10%  Similarity=0.026  Sum_probs=65.3

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+++.+.+...++.+|.+|.++ .+..- ......+.+.+++.+++.+.+....      
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~------  180 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREV------  180 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHcc------
Confidence            466789999998877777788999998877777777777664 34332 2334578899999999988886532      


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                      ..+   .+.+..++..++|.|.
T Consensus       181 ~~~---~~~a~~~~~la~G~~~  199 (334)
T PRK07993        181 TMS---QDALLAALRLSAGAPG  199 (334)
T ss_pred             CCC---HHHHHHHHHHcCCCHH
Confidence            111   2336678999999995

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.59  E-value=0.021  Score=62.16  Aligned_cols=98  Identities=11%  Similarity=0.010  Sum_probs=53.4

Q ss_pred             CceEEEEEeCCCCC-------CccChhHHHHhhcCCCCCcEEEEEeCchHHHH-------HhCCcceEeCCCCChhhHHH
Q 046115           72 GKKFLLVLDDVWNE-------DYYKWEPFYKCLKNSLHESKILITTRKETVAR-------IMGSTHVISVNVLSEMECWS  137 (505)
Q Consensus        72 ~~r~LlvlDdv~~~-------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-------~~~~~~~~~l~~l~~~ea~~  137 (505)
                      +.+++|++|++..-       ...+...++......+. -++|-+|.....-+       .......+.+++++.+++.+
T Consensus       279 ~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~G~-l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~  357 (852)
T TIGR03345       279 PQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALARGE-LRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIR  357 (852)
T ss_pred             CCCeEEEEeChHHhccCCCccccccHHHHhhHHhhCCC-eEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHHH
Confidence            46899999998542       11222334444444443 34444444322111       11345689999999999999


Q ss_pred             HHHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          138 VFQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       138 Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ++....-.-.....-.-.+++...+++.+.++.
T Consensus       358 iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       358 MLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             HHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence            975443111110011123566777777776554

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.

>PRK12377 putative replication protein; Provisional

Probab=96.57  E-value=0.003  Score=57.84  Aligned_cols=93  Identities=20%  Similarity=0.087  Sum_probs=51.2

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      +|+|||.||..+++  ........++++++.      +++..+-.....     .....    .+.+.+ .+--|||+||
T Consensus       110 ~GtGKThLa~AIa~--~l~~~g~~v~~i~~~------~l~~~l~~~~~~-----~~~~~----~~l~~l-~~~dLLiIDD  171 (248)
T PRK12377        110 PGTGKNHLAAAIGN--RLLAKGRSVIVVTVP------DVMSRLHESYDN-----GQSGE----KFLQEL-CKVDLLVLDE  171 (248)
T ss_pred             CCCCHHHHHHHHHH--HHHHcCCCeEEEEHH------HHHHHHHHHHhc-----cchHH----HHHHHh-cCCCEEEEcC
Confidence            69999999999999  555554456677653      334443333321     00111    122223 3456999999


Q ss_pred             CCCCCccChh--HHHHhhcCC-CCCcEEEEEeCc
Q 046115           82 VWNEDYYKWE--PFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~--~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      +.......|.  .+...+... .....+||||.-
T Consensus       172 lg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl  205 (248)
T PRK12377        172 IGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNL  205 (248)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCC
Confidence            9554433343  333333332 233458888874

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

Probab=96.56  E-value=0.0092  Score=54.88  Aligned_cols=92  Identities=12%  Similarity=0.096  Sum_probs=64.7

Q ss_pred             EEEEEeCCCCCCccChhHHHHhhcCCCCCcE-EEEEeCchHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCC
Q 046115           75 FLLVLDDVWNEDYYKWEPFYKCLKNSLHESK-ILITTRKETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTIGKR  152 (505)
Q Consensus        75 ~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~-iLiTtr~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~  152 (505)
                      -.||||+++......|..+...+.+.....+ ||||+--..+-.. ...-.-+..+++..++.+.-++..+..++..   
T Consensus       131 KiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~---  207 (346)
T KOG0989|consen  131 KIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVD---  207 (346)
T ss_pred             eEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhCCC---
Confidence            5789999999888899999999998766555 5555544332221 1223467788999999988888877544432   


Q ss_pred             chHHHHHHHHHHHcCCCh
Q 046115          153 ENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       153 ~~~~~~~~~i~~~~~g~P  170 (505)
                       -.+++.+.|++.++|.-
T Consensus       208 -~d~~al~~I~~~S~GdL  224 (346)
T KOG0989|consen  208 -IDDDALKLIAKISDGDL  224 (346)
T ss_pred             -CCHHHHHHHHHHcCCcH
Confidence             23567888999888854

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

Probab=96.52  E-value=0.086  Score=50.22  Aligned_cols=136  Identities=16%  Similarity=0.205  Sum_probs=81.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCC-CCChhc-----HHHHHHHHHH--Hc--C
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS-AKDLVE-----FQSLMQHIEE--CV--A   71 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~-----~~~~~~~l~~--~l--~   71 (505)
                      +|.|||.+.+++.+.  .   =...+|+++.+.++...++..|+.+....+ +.....     .-.....+.+  ..  +
T Consensus        39 sgTGKT~~~r~~l~~--~---n~~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~  113 (438)
T KOG2543|consen   39 SGTGKTYLVRQLLRK--L---NLENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNR  113 (438)
T ss_pred             CCCchhHHHHHHHhh--c---CCcceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhcc
Confidence            699999999999983  3   224689999999999999999999995222 221111     1122222333  12  2


Q ss_pred             CceEEEEEeCCCCCCccC---hhHHHHhhcCCCCCcEEEEEeCchHHHHH---hCC--cceEeCCCCChhhHHHHHHHh
Q 046115           72 GKKFLLVLDDVWNEDYYK---WEPFYKCLKNSLHESKILITTRKETVARI---MGS--THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~---~~~~~~~~~~~~~~~~iLiTtr~~~~~~~---~~~--~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      ++.++||+||++.-.+..   +..+.+...-.....-+|+++...-....   .+.  ..++..+.-+.+|..+++.+.
T Consensus       114 d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~  192 (438)
T KOG2543|consen  114 DQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEKQYLINTGTLEIVVLHFPQYSVEETQVILSRD  192 (438)
T ss_pred             CceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHHHhhcccCCCCceEEecCCCCHHHHHHHHhcC
Confidence            468999999996543211   22222222222223445666654322222   222  235557888999999888764

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.42  E-value=0.0072  Score=57.45  Aligned_cols=92  Identities=20%  Similarity=0.274  Sum_probs=54.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|+|||.||..+++  +...+-..+.++.+.      .++..+-.....+      ...+.    .+.++ +-=||||||
T Consensus       165 ~G~GKThLa~Aia~--~l~~~g~~v~~~~~~------~l~~~lk~~~~~~------~~~~~----l~~l~-~~dlLiIDD  225 (306)
T PRK08939        165 FGVGKSYLLAAIAN--ELAKKGVSSTLLHFP------EFIRELKNSISDG------SVKEK----IDAVK-EAPVLMLDD  225 (306)
T ss_pred             CCCCHHHHHHHHHH--HHHHcCCCEEEEEHH------HHHHHHHHHHhcC------cHHHH----HHHhc-CCCEEEEec
Confidence            69999999999999  554433345566543      3444444444311      11222    22222 345899999


Q ss_pred             CCCCCccChhH--HHHhhcC-C-CCCcEEEEEeCc
Q 046115           82 VWNEDYYKWEP--FYKCLKN-S-LHESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~~--~~~~~~~-~-~~~~~iLiTtr~  112 (505)
                      +..+....|..  +...+.+ . ..+..+++||.-
T Consensus       226 iG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        226 IGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             CCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence            98776666653  4454432 2 345678889883

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.41  E-value=0.0052  Score=58.91  Aligned_cols=94  Identities=18%  Similarity=0.268  Sum_probs=49.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|+|||.||..+++  +...+-..++++++..      ++..+...-. ..   ..+....    .+.+.+ -=|||+||
T Consensus       192 ~GtGKThLa~aIa~--~l~~~g~~V~y~t~~~------l~~~l~~~~~-~~---~~~~~~~----~~~l~~-~DLLIIDD  254 (329)
T PRK06835        192 TGTGKTFLSNCIAK--ELLDRGKSVIYRTADE------LIEILREIRF-NN---DKELEEV----YDLLIN-CDLLIIDD  254 (329)
T ss_pred             CCCcHHHHHHHHHH--HHHHCCCeEEEEEHHH------HHHHHHHHHh-cc---chhHHHH----HHHhcc-CCEEEEec
Confidence            69999999999998  5544444566776432      2332222111 00   1111111    122222 23899999


Q ss_pred             CCCCCccCh--hHHHHhhcCC-CCCcEEEEEeCc
Q 046115           82 VWNEDYYKW--EPFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~--~~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      +..+....|  ..+...+... ..+..+||||.-
T Consensus       255 lG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl  288 (329)
T PRK06835        255 LGTEKITEFSKSELFNLINKRLLRQKKMIISTNL  288 (329)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            966543333  3344433332 234568888884

>PRK06921 hypothetical protein; Provisional

Probab=96.41  E-value=0.015  Score=54.13  Aligned_cols=90  Identities=22%  Similarity=0.293  Sum_probs=48.0

Q ss_pred             CCCcHHHHHHHHhcCcccccC-CCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            2 GGIGKTTLAQFAYNNGDVERN-FEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~-f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .|+|||.||..+++  +...+ ...+++++..      +++..+...+           +.. ....+.+. .-=|||+|
T Consensus       126 ~G~GKThLa~aia~--~l~~~~g~~v~y~~~~------~l~~~l~~~~-----------~~~-~~~~~~~~-~~dlLiID  184 (266)
T PRK06921        126 PGSGKTHLLTAAAN--ELMRKKGVPVLYFPFV------EGFGDLKDDF-----------DLL-EAKLNRMK-KVEVLFID  184 (266)
T ss_pred             CCCcHHHHHHHHHH--HHhhhcCceEEEEEHH------HHHHHHHHHH-----------HHH-HHHHHHhc-CCCEEEEe
Confidence            69999999999998  55544 4456677742      2223322211           111 11122232 34599999


Q ss_pred             CCCC-----CCccChh--HHHHhhcCC-CCCcEEEEEeCc
Q 046115           81 DVWN-----EDYYKWE--PFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        81 dv~~-----~~~~~~~--~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      |+..     +....|.  .+...+... ..+..+||||..
T Consensus       185 Dl~~~~~g~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~  224 (266)
T PRK06921        185 DLFKPVNGKPRATEWQIEQMYSVLNYRYLNHKPILISSEL  224 (266)
T ss_pred             ccccccCCCccCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            9932     3222333  244433332 234568888874

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.39  E-value=0.0062  Score=52.51  Aligned_cols=80  Identities=29%  Similarity=0.285  Sum_probs=35.6

Q ss_pred             cCcccceEEecccccCCccccccccCcccc-CCCCcceeeccCCccccc---cchhhhcCCCCcEEecCCCcCccccchh
Q 046115          381 KLTCLRALELQVRESWPRNNLIKEIPTNIE-KLLHLKYLNLKGQKKIEK---LPETLCELYNLERLNVDDCQNLRELPRG  456 (505)
Q Consensus       381 ~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~-~l~~L~~L~l~~~~~~~~---lp~~~~~l~~L~~L~l~~~~~~~~lp~~  456 (505)
                      .+..|..|.|.       ++.+..+.+.+. .+++|..|.|.+|. +.+   +-+ +..|+.|+.|.+-+|+ ....+.+
T Consensus        62 ~l~rL~tLll~-------nNrIt~I~p~L~~~~p~l~~L~LtnNs-i~~l~dl~p-La~~p~L~~Ltll~Np-v~~k~~Y  131 (233)
T KOG1644|consen   62 HLPRLHTLLLN-------NNRITRIDPDLDTFLPNLKTLILTNNS-IQELGDLDP-LASCPKLEYLTLLGNP-VEHKKNY  131 (233)
T ss_pred             CccccceEEec-------CCcceeeccchhhhccccceEEecCcc-hhhhhhcch-hccCCccceeeecCCc-hhcccCc
Confidence            34445555554       444444433333 23445555555544 222   222 3344455555555544 3333322


Q ss_pred             ----ccccccCceeecCC
Q 046115          457 ----IGKLRKLMYLHNED  470 (505)
Q Consensus       457 ----~~~l~~L~~L~l~~  470 (505)
                          +..+|+|++|++..
T Consensus       132 R~yvl~klp~l~~LDF~k  149 (233)
T KOG1644|consen  132 RLYVLYKLPSLRTLDFQK  149 (233)
T ss_pred             eeEEEEecCcceEeehhh
Confidence                44555555555443

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

Probab=96.39  E-value=0.021  Score=56.93  Aligned_cols=122  Identities=18%  Similarity=0.178  Sum_probs=64.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  +....|   +.+..+.          +..... +     .........+.......+.+|+||
T Consensus       225 PPGTGKT~LAraIA~--el~~~f---i~V~~se----------L~~k~~-G-----e~~~~vr~lF~~A~~~~P~ILfID  283 (438)
T PTZ00361        225 PPGTGKTLLAKAVAN--ETSATF---LRVVGSE----------LIQKYL-G-----DGPKLVRELFRVAEENAPSIVFID  283 (438)
T ss_pred             CCCCCHHHHHHHHHH--hhCCCE---EEEecch----------hhhhhc-c-----hHHHHHHHHHHHHHhCCCcEEeHH
Confidence            479999999999998  554443   1222111          111111 0     001111222222234567899999


Q ss_pred             CCCCCC------c--------cChhHHHHhhcC--CCCCcEEEEEeCchHHHHH-h---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNED------Y--------YKWEPFYKCLKN--SLHESKILITTRKETVARI-M---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~------~--------~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~~-~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++...      .        ..+..++..+..  ...+..||.||...+.... +   +. ...+.++..+.++..++|
T Consensus       284 EID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il  363 (438)
T PTZ00361        284 EIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIF  363 (438)
T ss_pred             HHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHH
Confidence            973210      0        001122222222  1345678888876544332 1   11 457889999999999999


Q ss_pred             HHhh
Q 046115          140 QSLA  143 (505)
Q Consensus       140 ~~~~  143 (505)
                      ..+.
T Consensus       364 ~~~~  367 (438)
T PTZ00361        364 EIHT  367 (438)
T ss_pred             HHHH
Confidence            8765

>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=96.36  E-value=0.024  Score=48.55  Aligned_cols=59  Identities=17%  Similarity=0.252  Sum_probs=40.1

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-H-HHHhCCcceEeCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-V-ARIMGSTHVISVNVL  130 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~-~~~~~~~~~~~l~~l  130 (505)
                      +++=++|+||++.........+++.+......+.++++|++.. + .+.......+.+.++
T Consensus       101 ~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~~~~l  161 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIRFRPL  161 (162)
T ss_dssp             SSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEEE---
T ss_pred             CCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEecCCC
Confidence            3567899999988887788899999999888899998888754 2 222233445555554

...

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

Probab=96.36  E-value=0.009  Score=58.94  Aligned_cols=83  Identities=13%  Similarity=0.147  Sum_probs=48.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--CCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--AGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~~r~Llv   78 (505)
                      ++|+|||++|+++++.......|+.+.||.+++..+..+.+...    .+....-....+-..+.+.+..  .+++++||
T Consensus       202 ppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~----rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vli  277 (459)
T PRK11331        202 PPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY----RPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFI  277 (459)
T ss_pred             CCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhccc----CCCCCCeEecCchHHHHHHHHHhcccCCcEEE
Confidence            68999999999999843233456777799999887765554322    1111110000111112222222  24689999


Q ss_pred             EeCCCCCCc
Q 046115           79 LDDVWNEDY   87 (505)
Q Consensus        79 lDdv~~~~~   87 (505)
                      +|++.....
T Consensus       278 IDEINRani  286 (459)
T PRK11331        278 IDEINRANL  286 (459)
T ss_pred             EehhhccCH
Confidence            999966543

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.29  E-value=0.089  Score=49.07  Aligned_cols=35  Identities=23%  Similarity=0.230  Sum_probs=22.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRI   40 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~   40 (505)
                      .+|+|||+||+.++.  ....   ..+.+++....+..++
T Consensus        29 ~~GtGKT~lA~~la~--~lg~---~~~~i~~~~~~~~~dl   63 (262)
T TIGR02640        29 PAGTGKTTLAMHVAR--KRDR---PVMLINGDAELTTSDL   63 (262)
T ss_pred             CCCCCHHHHHHHHHH--HhCC---CEEEEeCCccCCHHHH
Confidence            479999999999987  3322   2345566555444443

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

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.27  E-value=0.078  Score=51.10  Aligned_cols=89  Identities=12%  Similarity=0.174  Sum_probs=62.3

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+++.+....+++.+|.+|.+ ..+... ......+.+.+++.++..+.+....    . 
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~----~-  205 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG----V-  205 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC----C-
Confidence            34568889999888777788899999887777766666655 333332 2335688999999999999887642    1 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                        . +    ...++..++|.|..
T Consensus       206 --~-~----~~~~l~~~~Gsp~~  221 (342)
T PRK06964        206 --A-D----ADALLAEAGGAPLA  221 (342)
T ss_pred             --C-h----HHHHHHHcCCCHHH
Confidence              1 1    12356788999964

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.26  E-value=0.045  Score=52.54  Aligned_cols=69  Identities=9%  Similarity=0.106  Sum_probs=46.2

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHHh-CCcceEeCCCCChhhHHHHHHH
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARIM-GSTHVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~~-~~~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      ++-++|+|++...+......+.+.+.....++.+|++|.+.. +...+ .....+.+.+++.+++.+.+..
T Consensus       113 ~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        113 GLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             CceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHh
Confidence            334445688877666666777777766555666777777643 33322 2245788999999999888865

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

Probab=96.24  E-value=0.021  Score=48.27  Aligned_cols=110  Identities=18%  Similarity=0.177  Sum_probs=59.7

Q ss_pred             CCCcHHHHHHHHhcCccccc-CCCceE--EEEeCCCCCHHHHHHHHH--H--HcCCCC----CCChhc---HHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVER-NFEKRT--WVCVSEPFDEFRIARAII--E--SLTPGS----AKDLVE---FQSLMQHIE   67 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~-~f~~~~--wv~~~~~~~~~~~~~~l~--~--~l~~~~----~~~~~~---~~~~~~~l~   67 (505)
                      .|.||||+|...+-  +..+ .+...+  |+...........+..+-  .  +++.+.    .....+   ..+..+...
T Consensus        11 ~G~Gkt~~a~g~~~--ra~~~g~~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~~~~~~a~   88 (159)
T cd00561          11 NGKGKTTAALGLAL--RALGHGYRVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAAEGWAFAK   88 (159)
T ss_pred             CCCCHHHHHHHHHH--HHHHCCCeEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHHHHHHHHH
Confidence            59999999977766  3333 333222  454443344444444431  0  001110    111111   112333344


Q ss_pred             HHcCC-ceEEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           68 ECVAG-KKFLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        68 ~~l~~-~r~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      +.+.. .-=|+|||.+-.   -.....+.+.+.+.....+..+++|.|+.
T Consensus        89 ~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          89 EAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            44433 456999999833   23345667777777777788999999983

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.

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

Probab=96.22  E-value=0.0064  Score=53.35  Aligned_cols=20  Identities=25%  Similarity=0.371  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN   22 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~   22 (505)
                      .+|+|||+|.++++.  .....
T Consensus        32 ~~G~GKT~ll~~~~~--~~~~~   51 (185)
T PF13191_consen   32 ESGSGKTSLLRALLD--RLAER   51 (185)
T ss_dssp             -TTSSHHHHHHHHHH--HHHHH
T ss_pred             CCCCCHHHHHHHHHH--HHHhc
Confidence            479999999999988  55544

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.22  E-value=0.012  Score=53.59  Aligned_cols=36  Identities=19%  Similarity=0.172  Sum_probs=26.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFR   39 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~   39 (505)
                      .+|+|||++|.+++.  .....-..++|++.. ..+...
T Consensus        31 ~~GsGKT~l~~~la~--~~~~~~~~v~yi~~e-~~~~~r   66 (225)
T PRK09361         31 PPGSGKTNICLQLAV--EAAKNGKKVIYIDTE-GLSPER   66 (225)
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCeEEEEECC-CCCHHH
Confidence            479999999999987  444445678899987 444433

>PRK09183 transposase/IS protein; Provisional

Probab=96.20  E-value=0.008  Score=55.82  Aligned_cols=93  Identities=16%  Similarity=0.217  Sum_probs=45.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||..++.  .....-..+.+++..      ++...+......      ....   ..+...+ ...-++|+|
T Consensus       110 p~GtGKThLa~al~~--~a~~~G~~v~~~~~~------~l~~~l~~a~~~------~~~~---~~~~~~~-~~~dlLiiD  171 (259)
T PRK09183        110 PSGVGKTHLAIALGY--EAVRAGIKVRFTTAA------DLLLQLSTAQRQ------GRYK---TTLQRGV-MAPRLLIID  171 (259)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCeEEEEeHH------HHHHHHHHHHHC------CcHH---HHHHHHh-cCCCEEEEc
Confidence            479999999999987  332222234455422      233332222110      0111   1222222 344699999


Q ss_pred             CCCCCCccChh--HHHHhhcCC-CCCcEEEEEeCc
Q 046115           81 DVWNEDYYKWE--PFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~--~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      |+.-.......  .+...+... ..+ .+||||..
T Consensus       172 dlg~~~~~~~~~~~lf~li~~r~~~~-s~iiTsn~  205 (259)
T PRK09183        172 EIGYLPFSQEEANLFFQVIAKRYEKG-SMILTSNL  205 (259)
T ss_pred             ccccCCCChHHHHHHHHHHHHHHhcC-cEEEecCC
Confidence            99653222222  344444332 233 48888885

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.20  E-value=0.023  Score=57.63  Aligned_cols=130  Identities=14%  Similarity=0.232  Sum_probs=68.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-----CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCce
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-----EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKK   74 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-----~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r   74 (505)
                      ++|+|||++|+.+++  +....+     ....|+++..+        +++....   ...........+..+... .+++
T Consensus       224 PPGTGKT~LAKAlA~--eL~~~i~~~~~~~~~fl~v~~~--------eLl~kyv---Gete~~ir~iF~~Ar~~a~~g~p  290 (512)
T TIGR03689       224 PPGCGKTLIAKAVAN--SLAQRIGAETGDKSYFLNIKGP--------ELLNKYV---GETERQIRLIFQRAREKASDGRP  290 (512)
T ss_pred             CCCCcHHHHHHHHHH--hhccccccccCCceeEEeccch--------hhccccc---chHHHHHHHHHHHHHHHhhcCCC
Confidence            589999999999998  444332     23445554431        1111111   000111112222222222 3468


Q ss_pred             EEEEEeCCCCCC-------ccC-----hhHHHHhhcCC--CCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhH
Q 046115           75 FLLVLDDVWNED-------YYK-----WEPFYKCLKNS--LHESKILITTRKETVAR-IM---GS-THVISVNVLSEMEC  135 (505)
Q Consensus        75 ~LlvlDdv~~~~-------~~~-----~~~~~~~~~~~--~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea  135 (505)
                      ++|+||+++...       ...     +..+...+...  ..+..||.||...+... .+   +. ...+.++..+.++.
T Consensus       291 ~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r  370 (512)
T TIGR03689       291 VIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAA  370 (512)
T ss_pred             ceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHH
Confidence            999999995421       001     12333333322  13445666666544322 22   12 34689999999999


Q ss_pred             HHHHHHhh
Q 046115          136 WSVFQSLA  143 (505)
Q Consensus       136 ~~Lf~~~~  143 (505)
                      .++|..+.
T Consensus       371 ~~Il~~~l  378 (512)
T TIGR03689       371 ADIFSKYL  378 (512)
T ss_pred             HHHHHHHh
Confidence            99998875

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.

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

Probab=96.18  E-value=0.041  Score=59.32  Aligned_cols=125  Identities=14%  Similarity=0.156  Sum_probs=63.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-----C-CceEE-EEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-----F-EKRTW-VCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-----f-~~~~w-v~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~   72 (505)
                      .+|+|||++|+.++.  ++...     + +..+| ++.+          .++..    .. ...+.++....+.+.+ ..
T Consensus       211 ~pG~GKT~l~~~la~--~~~~~~~p~~l~~~~~~~~~~~----------~l~a~----~~-~~g~~e~~l~~i~~~~~~~  273 (731)
T TIGR02639       211 EPGVGKTAIAEGLAL--RIAEGKVPENLKNAKIYSLDMG----------SLLAG----TK-YRGDFEERLKAVVSEIEKE  273 (731)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCchhhcCCeEEEecHH----------HHhhh----cc-ccchHHHHHHHHHHHHhcc
Confidence            479999999999998  44221     1 22232 2311          11110    00 1112333333333333 34


Q ss_pred             ceEEEEEeCCCCCC--------ccChhHHHHhhcCCCCCcEEEEEeCchHH------HHH-hCCcceEeCCCCChhhHHH
Q 046115           73 KKFLLVLDDVWNED--------YYKWEPFYKCLKNSLHESKILITTRKETV------ARI-MGSTHVISVNVLSEMECWS  137 (505)
Q Consensus        73 ~r~LlvlDdv~~~~--------~~~~~~~~~~~~~~~~~~~iLiTtr~~~~------~~~-~~~~~~~~l~~l~~~ea~~  137 (505)
                      ++.+|++|++..-.        ......++......+. -++|-+|...+.      ... ......+.++.++.++..+
T Consensus       274 ~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~g~-i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~  352 (731)
T TIGR02639       274 PNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSSGK-LRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVK  352 (731)
T ss_pred             CCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhCCC-eEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHH
Confidence            57899999985321        1122334444443333 334444433221      111 1235688999999999999


Q ss_pred             HHHHhh
Q 046115          138 VFQSLA  143 (505)
Q Consensus       138 Lf~~~~  143 (505)
                      +++...
T Consensus       353 il~~~~  358 (731)
T TIGR02639       353 ILKGLK  358 (731)
T ss_pred             HHHHHH
Confidence            998654

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.18  E-value=0.021  Score=55.01  Aligned_cols=81  Identities=20%  Similarity=0.229  Sum_probs=49.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCC-Cc-eEEEEeCC-CCCHHHHHHHHHHHcCCCCCCChhcH----H-HHHHHHHHHc-CC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF-EK-RTWVCVSE-PFDEFRIARAIIESLTPGSAKDLVEF----Q-SLMQHIEECV-AG   72 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f-~~-~~wv~~~~-~~~~~~~~~~l~~~l~~~~~~~~~~~----~-~~~~~l~~~l-~~   72 (505)
                      +|+|||||++.+++  .+..+. +. ++|+-+++ ..+..++.+.+...+.....+.....    . ...+...... .+
T Consensus       142 pGtGKTTLl~~la~--~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae~f~~~G  219 (380)
T PRK12608        142 PRAGKTVLLQQIAA--AVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAKRLVEQG  219 (380)
T ss_pred             CCCCHHHHHHHHHH--HHHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence            79999999999988  554443 43 35666655 45777888888887764332222111    1 1112222221 57


Q ss_pred             ceEEEEEeCCCC
Q 046115           73 KKFLLVLDDVWN   84 (505)
Q Consensus        73 ~r~LlvlDdv~~   84 (505)
                      ++++||+|++..
T Consensus       220 kdVVLvlDsltr  231 (380)
T PRK12608        220 KDVVILLDSLTR  231 (380)
T ss_pred             CCEEEEEeCcHH
Confidence            899999999943

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

Probab=96.18  E-value=0.075  Score=52.54  Aligned_cols=144  Identities=13%  Similarity=0.173  Sum_probs=73.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  .....|     +.+..        ..+..... +     .......+.+.......+.+|++|
T Consensus       187 ppGTGKT~LAkalA~--~l~~~f-----i~i~~--------s~l~~k~~-g-----e~~~~lr~lf~~A~~~~P~ILfID  245 (398)
T PTZ00454        187 PPGTGKTMLAKAVAH--HTTATF-----IRVVG--------SEFVQKYL-G-----EGPRMVRDVFRLARENAPSIIFID  245 (398)
T ss_pred             CCCCCHHHHHHHHHH--hcCCCE-----EEEeh--------HHHHHHhc-c-----hhHHHHHHHHHHHHhcCCeEEEEE
Confidence            479999999999998  443332     22211        11111111 0     001111222223334568999999


Q ss_pred             CCCCCC----------ccC----hhHHHHhhcC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNED----------YYK----WEPFYKCLKN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~----------~~~----~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++...          ...    +..+...+..  ...+..||.||...+... .+   +. ...+.++..+.++..++|
T Consensus       246 EID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il  325 (398)
T PTZ00454        246 EVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIF  325 (398)
T ss_pred             CHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHH
Confidence            975310          001    1222332322  124567888887654322 11   11 456888888888888888


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      +.+...-.. ....+    ...+++.+.|+.
T Consensus       326 ~~~~~~~~l-~~dvd----~~~la~~t~g~s  351 (398)
T PTZ00454        326 QTITSKMNL-SEEVD----LEDFVSRPEKIS  351 (398)
T ss_pred             HHHHhcCCC-CcccC----HHHHHHHcCCCC
Confidence            866532221 22223    345666665553

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

Probab=96.18  E-value=0.39  Score=47.16  Aligned_cols=163  Identities=16%  Similarity=0.143  Sum_probs=86.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCC--CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCC--ceEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAG--KKFLL   77 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f--~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~--~r~Ll   77 (505)
                      +|.|||.+...++.+  .....  ..++.+++..-....+++..|...+.......... .+....+..+...  +-+++
T Consensus       184 PGtgkt~~l~rvl~~--~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~~~q~~~s~~~~-~~~~~~~~~h~~q~k~~~ll  260 (529)
T KOG2227|consen  184 PGTGKTALLSRVLDS--LSKSSKSPVTVYINCTSLTEASAIFKKIFSSLLQDLVSPGTG-MQHLEKFEKHTKQSKFMLLL  260 (529)
T ss_pred             CCcchHHHHHHHHHh--hhhhcccceeEEEeeccccchHHHHHHHHHHHHHHhcCCchh-HHHHHHHHHHHhcccceEEE
Confidence            699999999988873  33333  24578888776777777887777762111111111 2333444444433  46899


Q ss_pred             EEeCCCCCCccChhHHHHhhcCC-CCCcE-EEEEeCch------HHHHH---h-CCcceEeCCCCChhhHHHHHHHhhhC
Q 046115           78 VLDDVWNEDYYKWEPFYKCLKNS-LHESK-ILITTRKE------TVARI---M-GSTHVISVNVLSEMECWSVFQSLAIS  145 (505)
Q Consensus        78 vlDdv~~~~~~~~~~~~~~~~~~-~~~~~-iLiTtr~~------~~~~~---~-~~~~~~~l~~l~~~ea~~Lf~~~~~~  145 (505)
                      |+|..+.-....-..+...+.|. -++++ |||---+.      .+...   . -....+..++.+.++.+++|....-.
T Consensus       261 VlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~  340 (529)
T KOG2227|consen  261 VLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSE  340 (529)
T ss_pred             EechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhc
Confidence            99998542211222222222222 23344 44432221      11111   1 12447778899999999999877532


Q ss_pred             CCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          146 GKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       146 ~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ...   ......++.-++++|.|..
T Consensus       341 ~~t---~~~~~~Aie~~ArKvaa~S  362 (529)
T KOG2227|consen  341 EST---SIFLNAAIELCARKVAAPS  362 (529)
T ss_pred             ccc---cccchHHHHHHHHHhccCc
Confidence            222   2222334455555554444

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=96.00  E-value=0.0045  Score=55.58  Aligned_cols=86  Identities=17%  Similarity=0.163  Sum_probs=60.2

Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCC--cCccccchhccccccCceeecCCCccccccccc---ccCC
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDC--QNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG---IGEL  484 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~--~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~---i~~l  484 (505)
                      -.+..|+.|++.++. ++.+-. +-.|++|+.|.++.|  +....++....++|+|+++++++|...  .++.   +..+
T Consensus        40 d~~~~le~ls~~n~g-ltt~~~-~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~--~lstl~pl~~l  115 (260)
T KOG2739|consen   40 DEFVELELLSVINVG-LTTLTN-FPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIK--DLSTLRPLKEL  115 (260)
T ss_pred             ccccchhhhhhhccc-eeeccc-CCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccc--cccccchhhhh
Confidence            345566666677666 444433 446789999999999  655567766777799999999999843  2333   4566


Q ss_pred             ccCCccceeEecCcC
Q 046115          485 IRLRRVREFVVGGGY  499 (505)
Q Consensus       485 ~~L~~L~~~~~~~~~  499 (505)
                      .+|..|.++.|+.-+
T Consensus       116 ~nL~~Ldl~n~~~~~  130 (260)
T KOG2739|consen  116 ENLKSLDLFNCSVTN  130 (260)
T ss_pred             cchhhhhcccCCccc
Confidence            777788877776543

>CHL00176 ftsH cell division protein; Validated

Probab=95.94  E-value=0.13  Score=54.15  Aligned_cols=142  Identities=14%  Similarity=0.200  Sum_probs=75.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.++.  +...     -|+.++..    ++    ..... +     .........+.......+++|++|
T Consensus       224 PpGTGKT~LAralA~--e~~~-----p~i~is~s----~f----~~~~~-g-----~~~~~vr~lF~~A~~~~P~ILfID  282 (638)
T CHL00176        224 PPGTGKTLLAKAIAG--EAEV-----PFFSISGS----EF----VEMFV-G-----VGAARVRDLFKKAKENSPCIVFID  282 (638)
T ss_pred             CCCCCHHHHHHHHHH--HhCC-----CeeeccHH----HH----HHHhh-h-----hhHHHHHHHHHHHhcCCCcEEEEe
Confidence            489999999999998  3322     23333211    11    11110 0     011222333444455678999999


Q ss_pred             CCCCCC----------ccC----hhHHHHhhcC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNED----------YYK----WEPFYKCLKN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~----------~~~----~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++.-.          ...    +..++..+..  ...+..|+.||...+... .+   +. ...+.++..+.++-.+++
T Consensus       283 EID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL  362 (638)
T CHL00176        283 EIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDIL  362 (638)
T ss_pred             cchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHH
Confidence            994321          011    2223322222  234556777776654322 11   11 357788888999988888


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCC
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKG  168 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g  168 (505)
                      ..+......     ........+++.+.|
T Consensus       363 ~~~l~~~~~-----~~d~~l~~lA~~t~G  386 (638)
T CHL00176        363 KVHARNKKL-----SPDVSLELIARRTPG  386 (638)
T ss_pred             HHHHhhccc-----chhHHHHHHHhcCCC
Confidence            877643111     112345677888877

>PRK06526 transposase; Provisional

Probab=95.93  E-value=0.015  Score=53.61  Aligned_cols=94  Identities=16%  Similarity=0.168  Sum_probs=45.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||..++.  +....-..+.|++.      .+++..+.....    .  ....   ..+. .+ .+.-+||+|
T Consensus       106 p~GtGKThLa~al~~--~a~~~g~~v~f~t~------~~l~~~l~~~~~----~--~~~~---~~l~-~l-~~~dlLIID  166 (254)
T PRK06526        106 PPGTGKTHLAIGLGI--RACQAGHRVLFATA------AQWVARLAAAHH----A--GRLQ---AELV-KL-GRYPLLIVD  166 (254)
T ss_pred             CCCCchHHHHHHHHH--HHHHCCCchhhhhH------HHHHHHHHHHHh----c--CcHH---HHHH-Hh-ccCCEEEEc
Confidence            479999999999987  33322223334322      233333332211    0  0111   1222 22 234589999


Q ss_pred             CCCCCCccCh--hHHHHhhcCCCCCcEEEEEeCch
Q 046115           81 DVWNEDYYKW--EPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        81 dv~~~~~~~~--~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      |+.......+  ..+...+........+|+||..+
T Consensus       167 D~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~  201 (254)
T PRK06526        167 EVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKP  201 (254)
T ss_pred             ccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCC
Confidence            9965422122  22333333222223488888854

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.92  E-value=0.034  Score=47.39  Aligned_cols=34  Identities=29%  Similarity=0.270  Sum_probs=24.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFD   36 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~   36 (505)
                      .+|+|||++|..++.  ....+-..++|++......
T Consensus         7 ~~G~GKT~l~~~i~~--~~~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           7 PTGSGKTTLALQLAL--NIATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCEEEEEECCcchH
Confidence            379999999999988  4444435677888766543

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.

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=95.92  E-value=0.0049  Score=57.56  Aligned_cols=111  Identities=17%  Similarity=0.135  Sum_probs=55.3

Q ss_pred             CCCCceEEEecCCCcccc-ccchhHHhhcCcccceEEecccccCCccccccccC--------------ccccCCCCccee
Q 046115          354 GLRGLRSLLVKSDEYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP--------------TNIEKLLHLKYL  418 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~-~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p--------------~~~~~l~~L~~L  418 (505)
                      +++.|+.|+|+.|-+..- ...+...+.++..|+.|.|.       |+.++...              ..+..-+.|+++
T Consensus        90 ~~~~L~~ldLSDNA~G~~g~~~l~~ll~s~~~L~eL~L~-------N~Glg~~ag~~l~~al~~l~~~kk~~~~~~Lrv~  162 (382)
T KOG1909|consen   90 GCPKLQKLDLSDNAFGPKGIRGLEELLSSCTDLEELYLN-------NCGLGPEAGGRLGRALFELAVNKKAASKPKLRVF  162 (382)
T ss_pred             cCCceeEeeccccccCccchHHHHHHHHhccCHHHHhhh-------cCCCChhHHHHHHHHHHHHHHHhccCCCcceEEE
Confidence            566777777777765321 11133345566667777776       33332211              113344566666


Q ss_pred             eccCCccccccc-----hhhhcCCCCcEEecCCCcCcc----ccchhccccccCceeecCCCc
Q 046115          419 NLKGQKKIEKLP-----ETLCELYNLERLNVDDCQNLR----ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       419 ~l~~~~~~~~lp-----~~~~~l~~L~~L~l~~~~~~~----~lp~~~~~l~~L~~L~l~~~~  472 (505)
                      ...+|+ +..-+     ..+...+.|+.+.+..|.+-.    .+-.++..++.|+.|++..|.
T Consensus       163 i~~rNr-len~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNt  224 (382)
T KOG1909|consen  163 ICGRNR-LENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNT  224 (382)
T ss_pred             Eeeccc-cccccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccch
Confidence            666666 43333     223444555665555544111    111234555566666666554

>CHL00095 clpC Clp protease ATP binding subunit

Probab=95.85  E-value=0.067  Score=58.49  Aligned_cols=124  Identities=19%  Similarity=0.171  Sum_probs=63.8

Q ss_pred             CCCCcHHHHHHHHhcCccccc-----CC-CceEE-EEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER-----NF-EKRTW-VCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~-----~f-~~~~w-v~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~   72 (505)
                      .+|+|||++|+.++.  ++..     .. +..+| ++.+          .++.    +.. ...+.++....+.+.+ ..
T Consensus       208 ~pGvGKTal~~~la~--~i~~~~vp~~l~~~~i~~l~~~----------~l~a----g~~-~~ge~e~rl~~i~~~~~~~  270 (821)
T CHL00095        208 EPGVGKTAIAEGLAQ--RIVNRDVPDILEDKLVITLDIG----------LLLA----GTK-YRGEFEERLKRIFDEIQEN  270 (821)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCChhhcCCeEEEeeHH----------HHhc----cCC-CccHHHHHHHHHHHHHHhc
Confidence            489999999999988  4421     11 23333 2211          1111    111 1122333333333332 34


Q ss_pred             ceEEEEEeCCCC-------CCccChhHHHHhhcCCCCCcEEEEEeCchHHHH------H-hCCcceEeCCCCChhhHHHH
Q 046115           73 KKFLLVLDDVWN-------EDYYKWEPFYKCLKNSLHESKILITTRKETVAR------I-MGSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        73 ~r~LlvlDdv~~-------~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~------~-~~~~~~~~l~~l~~~ea~~L  138 (505)
                      ++.+|++|++..       ........++......+.=..|-.||.++ ...      . ......+.+...+.++...+
T Consensus       271 ~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~rg~l~~IgaTt~~e-y~~~ie~D~aL~rRf~~I~v~ep~~~e~~aI  349 (821)
T CHL00095        271 NNIILVIDEVHTLIGAGAAEGAIDAANILKPALARGELQCIGATTLDE-YRKHIEKDPALERRFQPVYVGEPSVEETIEI  349 (821)
T ss_pred             CCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhCCCcEEEEeCCHHH-HHHHHhcCHHHHhcceEEecCCCCHHHHHHH
Confidence            689999999842       11113344555444444433344444433 211      1 12345778888999998888


Q ss_pred             HHHh
Q 046115          139 FQSL  142 (505)
Q Consensus       139 f~~~  142 (505)
                      +...
T Consensus       350 Lr~l  353 (821)
T CHL00095        350 LFGL  353 (821)
T ss_pred             HHHH
Confidence            7643

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.80  E-value=0.023  Score=51.06  Aligned_cols=37  Identities=19%  Similarity=0.213  Sum_probs=27.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRI   40 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~   40 (505)
                      .+|+|||++|.+++.  ...+.-..++|++... ++...+
T Consensus        20 ~~GsGKT~l~~~~~~--~~~~~g~~v~yi~~e~-~~~~rl   56 (209)
T TIGR02237        20 PPGSGKTNICMILAV--NAARQGKKVVYIDTEG-LSPERF   56 (209)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCeEEEEECCC-CCHHHH
Confidence            479999999999887  4444456788999876 544433

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

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=95.76  E-value=0.033  Score=51.07  Aligned_cols=46  Identities=22%  Similarity=0.153  Sum_probs=29.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccC----CCceEEEEeCCCCCHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN----FEKRTWVCVSEPFDEFRIARAIIES   47 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~----f~~~~wv~~~~~~~~~~~~~~l~~~   47 (505)
                      .+|+|||+||.+++........    -..++|++....++...+ .+++..
T Consensus        27 ~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl-~~~~~~   76 (235)
T cd01123          27 EFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL-VQIAER   76 (235)
T ss_pred             CCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH-HHHHHH
Confidence            3799999999999752122221    257889998877665433 333443

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 .

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.70  E-value=0.16  Score=52.24  Aligned_cols=150  Identities=13%  Similarity=0.164  Sum_probs=75.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.++.  +....     ++.++..    +    +..... +     .........+.......+.+|++|
T Consensus        96 ppGtGKT~la~alA~--~~~~~-----~~~i~~~----~----~~~~~~-g-----~~~~~l~~~f~~a~~~~p~Il~iD  154 (495)
T TIGR01241        96 PPGTGKTLLAKAVAG--EAGVP-----FFSISGS----D----FVEMFV-G-----VGASRVRDLFEQAKKNAPCIIFID  154 (495)
T ss_pred             CCCCCHHHHHHHHHH--HcCCC-----eeeccHH----H----HHHHHh-c-----ccHHHHHHHHHHHHhcCCCEEEEe
Confidence            589999999999998  33222     2222211    1    111111 0     011122223333334567899999


Q ss_pred             CCCCCC----------ccC----hhHHHHhhcC--CCCCcEEEEEeCchHH-HHHh---C-CcceEeCCCCChhhHHHHH
Q 046115           81 DVWNED----------YYK----WEPFYKCLKN--SLHESKILITTRKETV-ARIM---G-STHVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~----------~~~----~~~~~~~~~~--~~~~~~iLiTtr~~~~-~~~~---~-~~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++.-.          ...    ...+...+..  ...+..||.||..+.. ...+   + -...+.++..+.++-.+++
T Consensus       155 Eid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il  234 (495)
T TIGR01241       155 EIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEIL  234 (495)
T ss_pred             chhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHH
Confidence            984411          001    1122222221  2234556667766432 2211   1 1457888888888888888


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCC-hHHHHHH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGL-PLAAKTI  176 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~-Plal~~~  176 (505)
                      ..+...... ...    .....+++.+.|+ +-.|..+
T Consensus       235 ~~~l~~~~~-~~~----~~l~~la~~t~G~sgadl~~l  267 (495)
T TIGR01241       235 KVHAKNKKL-APD----VDLKAVARRTPGFSGADLANL  267 (495)
T ss_pred             HHHHhcCCC-Ccc----hhHHHHHHhCCCCCHHHHHHH
Confidence            776532211 111    2245777788764 3444443

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.

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.65  E-value=0.0014  Score=59.22  Aligned_cols=99  Identities=26%  Similarity=0.266  Sum_probs=67.0

Q ss_pred             CCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccch--hh
Q 046115          356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE--TL  433 (505)
Q Consensus       356 ~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~--~~  433 (505)
                      .+.+-|+.-|+.++..    . .+.+|+.|++|.|+       -|.+..+.+ +..+++|+.|.|+.|. +..+-.  .+
T Consensus        19 ~~vkKLNcwg~~L~DI----s-ic~kMp~lEVLsLS-------vNkIssL~p-l~rCtrLkElYLRkN~-I~sldEL~YL   84 (388)
T KOG2123|consen   19 ENVKKLNCWGCGLDDI----S-ICEKMPLLEVLSLS-------VNKISSLAP-LQRCTRLKELYLRKNC-IESLDELEYL   84 (388)
T ss_pred             HHhhhhcccCCCccHH----H-HHHhcccceeEEee-------ccccccchh-HHHHHHHHHHHHHhcc-cccHHHHHHH
Confidence            3444455555554432    2 25678888888888       555666544 6788888888888888 555543  35


Q ss_pred             hcCCCCcEEecCCCcCccccchh-----ccccccCceeec
Q 046115          434 CELYNLERLNVDDCQNLRELPRG-----IGKLRKLMYLHN  468 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~-----~~~l~~L~~L~l  468 (505)
                      .++++|+.|.|..|+....-+..     +..||+|+.|+-
T Consensus        85 knlpsLr~LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLDn  124 (388)
T KOG2123|consen   85 KNLPSLRTLWLDENPCCGEAGQNYRRKVLRVLPNLKKLDN  124 (388)
T ss_pred             hcCchhhhHhhccCCcccccchhHHHHHHHHcccchhccC
Confidence            68888999999888866655542     567788888773

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=95.65  E-value=0.071  Score=53.82  Aligned_cols=97  Identities=13%  Similarity=0.159  Sum_probs=66.4

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      .++--..|+|.|.-.....+..+++-+.........|..|.+ ..+.. .....+.|.+..++.++-...+...+...+.
T Consensus       117 ~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I  196 (515)
T COG2812         117 EGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGI  196 (515)
T ss_pred             cccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCC
Confidence            345568899999777767788888888876665655555544 33322 2344568899999999998888887754433


Q ss_pred             CCCCchHHHHHHHHHHHcCCChH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                          ...++++..|++..+|...
T Consensus       197 ----~~e~~aL~~ia~~a~Gs~R  215 (515)
T COG2812         197 ----NIEEDALSLIARAAEGSLR  215 (515)
T ss_pred             ----ccCHHHHHHHHHHcCCChh
Confidence                2335667778888887543

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

Probab=95.57  E-value=0.047  Score=52.75  Aligned_cols=115  Identities=16%  Similarity=0.140  Sum_probs=67.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccC---------------------CCceEEEEeCCCCC---HHHHHHHHHHHcCCCCCCCh
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN---------------------FEKRTWVCVSEPFD---EFRIARAIIESLTPGSAKDL   56 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~---------------------f~~~~wv~~~~~~~---~~~~~~~l~~~l~~~~~~~~   56 (505)
                      ++|+||||+|.++++.  +...                     ...+..++.+....   ..+..+++.+.......   
T Consensus        32 p~G~Gktt~a~~lA~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~~~---  106 (325)
T COG0470          32 PPGVGKTTAALALAKE--LLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSESPL---  106 (325)
T ss_pred             CCCCCHHHHHHHHHHH--HhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhccCCC---
Confidence            4699999999999883  3221                     23444444443333   23333333333321111   


Q ss_pred             hcHHHHHHHHHHHcCCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhh
Q 046115           57 VEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEME  134 (505)
Q Consensus        57 ~~~~~~~~~l~~~l~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~e  134 (505)
                                    .++.-++++|+++.........+...+......+.++++|..+ .+...+ .....+.+.+.+..+
T Consensus       107 --------------~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~~~~  172 (325)
T COG0470         107 --------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRLE  172 (325)
T ss_pred             --------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhhhcceeeecCCchHHH
Confidence                          3567799999998776656677777777777778888888753 222212 223456666633333

>PTZ00202 tuzin; Provisional

Probab=95.52  E-value=0.44  Score=46.98  Aligned_cols=133  Identities=15%  Similarity=0.160  Sum_probs=71.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcH-HHHHHHHHHHc-C-CceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEF-QSLMQHIEECV-A-GKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~-~~~~~~l~~~l-~-~~r~Ll   77 (505)
                      ++|+|||||++.+...  ..   ...++++..   +..+++..++.+|+.+......+. ....+.+.+.- . +++.+|
T Consensus       294 ~~G~GKTTLlR~~~~~--l~---~~qL~vNpr---g~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVL  365 (550)
T PTZ00202        294 FRGCGKSSLCRSAVRK--EG---MPAVFVDVR---GTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKMNGETPLL  365 (550)
T ss_pred             CCCCCHHHHHHHHHhc--CC---ceEEEECCC---CHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEE
Confidence            4799999999999973  22   123344444   679999999999996333222222 33333333332 2 566666


Q ss_pred             EEeCCCCCCcc-ChhHHHHhhcCCCCCcEEEEEeCchHHHH---HhCCcceEeCCCCChhhHHHHHHHh
Q 046115           78 VLDDVWNEDYY-KWEPFYKCLKNSLHESKILITTRKETVAR---IMGSTHVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        78 vlDdv~~~~~~-~~~~~~~~~~~~~~~~~iLiTtr~~~~~~---~~~~~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      |+-==.-.+.. .+.... .+--...-|+|++----+.+..   ..+....|.++.|+.++|..+-+..
T Consensus       366 II~lreg~~l~rvyne~v-~la~drr~ch~v~evpleslt~~~~~lprldf~~vp~fsr~qaf~y~~h~  433 (550)
T PTZ00202        366 VLKLREGSSLQRVYNEVV-ALACDRRLCHVVIEVPLESLTIANTLLPRLDFYLVPNFSRSQAFAYTQHA  433 (550)
T ss_pred             EEEecCCCcHHHHHHHHH-HHHccchhheeeeeehHhhcchhcccCccceeEecCCCCHHHHHHHHhhc
Confidence            65321111100 011111 1111234577776433322211   1234568899999999998877654

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

Probab=95.49  E-value=0.16  Score=48.13  Aligned_cols=153  Identities=16%  Similarity=0.188  Sum_probs=81.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC-CceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA-GKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~-~~r~Llvl   79 (505)
                      ++|.|||-||+++++  +....|     +.+..        .+++++.-.       +-.+.+..+.+.-+ ..+..|.+
T Consensus       193 PPGTGKTLLAkAVA~--~T~AtF-----Irvvg--------SElVqKYiG-------EGaRlVRelF~lArekaPsIIFi  250 (406)
T COG1222         193 PPGTGKTLLAKAVAN--QTDATF-----IRVVG--------SELVQKYIG-------EGARLVRELFELAREKAPSIIFI  250 (406)
T ss_pred             CCCCcHHHHHHHHHh--ccCceE-----EEecc--------HHHHHHHhc-------cchHHHHHHHHHHhhcCCeEEEE
Confidence            589999999999999  555555     44333        223332220       01122333333333 35789999


Q ss_pred             eCCCC--------------CCccChhHHHHhhcCCC--CCcEEEEEeCchHHHHHh----CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWN--------------EDYYKWEPFYKCLKNSL--HESKILITTRKETVARIM----GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~--------------~~~~~~~~~~~~~~~~~--~~~~iLiTtr~~~~~~~~----~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |.++.              +-+-.+-+++..+.-|+  ...+||..|...+++...    +. .+.++++.-+.+--.++
T Consensus       251 DEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~I  330 (406)
T COG1222         251 DEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEI  330 (406)
T ss_pred             echhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHH
Confidence            98833              11112344555555443  467888888766554321    22 45778875555555666


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh----HHHHHHHHHh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP----LAAKTIASLL  180 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P----lal~~~~~~l  180 (505)
                      |.-++-. -.....-+.    ..+++.|.|..    -|+.+=|+++
T Consensus       331 l~IHtrk-M~l~~dvd~----e~la~~~~g~sGAdlkaictEAGm~  371 (406)
T COG1222         331 LKIHTRK-MNLADDVDL----ELLARLTEGFSGADLKAICTEAGMF  371 (406)
T ss_pred             HHHHhhh-ccCccCcCH----HHHHHhcCCCchHHHHHHHHHHhHH
Confidence            6655422 222333343    35666666654    3444445543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.47  E-value=0.13  Score=56.52  Aligned_cols=71  Identities=14%  Similarity=0.050  Sum_probs=39.5

Q ss_pred             CceEEEEEeCCCCCC-------ccChhHHHHhhcCCCCCcEEEEEeCchH---H--HH-HhCCcceEeCCCCChhhHHHH
Q 046115           72 GKKFLLVLDDVWNED-------YYKWEPFYKCLKNSLHESKILITTRKET---V--AR-IMGSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~-------~~~~~~~~~~~~~~~~~~~iLiTtr~~~---~--~~-~~~~~~~~~l~~l~~~ea~~L  138 (505)
                      +++.+|++|++..-.       ..+...++......+.=..|-.||.++.   +  .. .......+.++..+.++...+
T Consensus       265 ~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~g~i~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~~i  344 (852)
T TIGR03346       265 EGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGATTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISI  344 (852)
T ss_pred             CCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhhcCceEEEEeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHHHH
Confidence            468999999985321       0112333443333333333334454432   1  11 112355788999999999998


Q ss_pred             HHHh
Q 046115          139 FQSL  142 (505)
Q Consensus       139 f~~~  142 (505)
                      +...
T Consensus       345 L~~~  348 (852)
T TIGR03346       345 LRGL  348 (852)
T ss_pred             HHHH
Confidence            8755

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.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=95.44  E-value=0.047  Score=50.56  Aligned_cols=48  Identities=23%  Similarity=0.264  Sum_probs=31.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccC---C-CceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN---F-EKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~---f-~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||.+++-...+...   . ..++||+-...+....+. +|+++..
T Consensus        46 ~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~   97 (256)
T PF08423_consen   46 ESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFG   97 (256)
T ss_dssp             STTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTT
T ss_pred             ecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccc
Confidence            3799999999888753233222   2 347799988888876654 4666554

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 ....

>PRK04296 thymidine kinase; Provisional

Probab=95.43  E-value=0.025  Score=49.88  Aligned_cols=105  Identities=12%  Similarity=-0.013  Sum_probs=55.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC-ChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK-DLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .|.||||+|..++.  +...+...++.+.  ..++.......+..+++..... ......+....+.+ ..++.-+||+|
T Consensus        11 ~GsGKTT~~l~~~~--~~~~~g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~~~dvviID   85 (190)
T PRK04296         11 MNSGKSTELLQRAY--NYEERGMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGEKIDCVLID   85 (190)
T ss_pred             CCCHHHHHHHHHHH--HHHHcCCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCCCCCEEEEE
Confidence            59999999988887  4444433444442  1112222233445555422111 12233444444444 33345689999


Q ss_pred             CCCCCCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           81 DVWNEDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      .++--+..++..+...+  ...|..|++|.++.
T Consensus        86 Eaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~  116 (190)
T PRK04296         86 EAQFLDKEQVVQLAEVL--DDLGIPVICYGLDT  116 (190)
T ss_pred             ccccCCHHHHHHHHHHH--HHcCCeEEEEecCc
Confidence            99553322233333333  24577899999874

>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=95.43  E-value=0.0071  Score=32.20  Aligned_cols=9  Identities=33%  Similarity=0.468  Sum_probs=3.6

Q ss_pred             CcEEecCCC
Q 046115          439 LERLNVDDC  447 (505)
Q Consensus       439 L~~L~l~~~  447 (505)
                      |++|+|++|
T Consensus         2 L~~Ldls~n   10 (22)
T PF00560_consen    2 LEYLDLSGN   10 (22)
T ss_dssp             ESEEEETSS
T ss_pred             ccEEECCCC
Confidence            334444444

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 ....

>cd01394 radB RadB

Probab=95.42  E-value=0.039  Score=49.94  Aligned_cols=34  Identities=18%  Similarity=0.089  Sum_probs=24.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFD   36 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~   36 (505)
                      .+|+||||+|.+++.  ....+-..++|++....+.
T Consensus        27 ~~GsGKT~l~~~~a~--~~~~~g~~v~yi~~e~~~~   60 (218)
T cd01394          27 PPGTGKTNIAIQLAV--ETAGQGKKVAYIDTEGLSS   60 (218)
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCeEEEEECCCCCH
Confidence            379999999999987  4444445677887655543

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

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.39  E-value=0.13  Score=53.03  Aligned_cols=153  Identities=14%  Similarity=0.047  Sum_probs=79.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC--CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF--DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~--~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .|+|||+||+++++... +..+-++.+++++.-.  ..+.+++.+-.                  ....++.-.+-+|||
T Consensus       440 ~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~------------------vfse~~~~~PSiIvL  500 (952)
T KOG0735|consen  440 KGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNN------------------VFSEALWYAPSIIVL  500 (952)
T ss_pred             CCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHH------------------HHHHHHhhCCcEEEE
Confidence            69999999999999322 3445556677776532  22333333222                  233456678889999


Q ss_pred             eCCCC------CCccCh-------hHH----HHhhcCCCCCcEEEEEeCchHHHHH-h---CC-cceEeCCCCChhhHHH
Q 046115           80 DDVWN------EDYYKW-------EPF----YKCLKNSLHESKILITTRKETVARI-M---GS-THVISVNVLSEMECWS  137 (505)
Q Consensus        80 Ddv~~------~~~~~~-------~~~----~~~~~~~~~~~~iLiTtr~~~~~~~-~---~~-~~~~~l~~l~~~ea~~  137 (505)
                      ||++-      ..-.+|       ..+    ...+...+..-.+|.|......... .   .. ...+.++.+..++-.+
T Consensus       501 Ddld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~  580 (952)
T KOG0735|consen  501 DDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKE  580 (952)
T ss_pred             cchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHH
Confidence            99832      111111       111    2222223333345556655332211 1   11 3356788888777666


Q ss_pred             HHHHhhhCCCCCCCCchHHHHHHHHHHHcCCC-hHHHHHHH
Q 046115          138 VFQSLAISGKTIGKRENLEKIGREIVKKCKGL-PLAAKTIA  177 (505)
Q Consensus       138 Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~-Plal~~~~  177 (505)
                      +++... ....  ... ..+...-+..+|+|+ |..+.+.-
T Consensus       581 IL~~~~-s~~~--~~~-~~~dLd~ls~~TEGy~~~DL~ifV  617 (952)
T KOG0735|consen  581 ILTTIF-SKNL--SDI-TMDDLDFLSVKTEGYLATDLVIFV  617 (952)
T ss_pred             HHHHHH-Hhhh--hhh-hhHHHHHHHHhcCCccchhHHHHH
Confidence            665532 2121  111 122233488888774 55555443

>TIGR00602 rad24 checkpoint protein rad24

Probab=95.30  E-value=0.11  Score=54.30  Aligned_cols=48  Identities=10%  Similarity=0.037  Sum_probs=28.6

Q ss_pred             ceEeCCCCChhhHHHHHHHhhhCCCCCCCC---chHHHHHHHHHHHcCCCh
Q 046115          123 HVISVNVLSEMECWSVFQSLAISGKTIGKR---ENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       123 ~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~---~~~~~~~~~i~~~~~g~P  170 (505)
                      ..+..++++..+-.+.+.............   -..++++..|+..++|--
T Consensus       267 ~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~GDi  317 (637)
T TIGR00602       267 SNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSGDI  317 (637)
T ss_pred             eEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCChH
Confidence            468899999999777776665332111101   112456777777777744

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

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.29  E-value=0.1  Score=52.94  Aligned_cols=146  Identities=14%  Similarity=0.079  Sum_probs=74.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||.+|+.+++  +....|   +-++.+.          +.....      ........+.+...-...+++|++|
T Consensus       267 PpGTGKTllAkaiA~--e~~~~~---~~l~~~~----------l~~~~v------Gese~~l~~~f~~A~~~~P~IL~ID  325 (489)
T CHL00195        267 IQGTGKSLTAKAIAN--DWQLPL---LRLDVGK----------LFGGIV------GESESRMRQMIRIAEALSPCILWID  325 (489)
T ss_pred             CCCCcHHHHHHHHHH--HhCCCE---EEEEhHH----------hccccc------ChHHHHHHHHHHHHHhcCCcEEEeh
Confidence            589999999999998  432222   1222211          111110      0011112222222223468999999


Q ss_pred             CCCCCC-------cc-----ChhHHHHhhcCCCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHHHHHhh
Q 046115           81 DVWNED-------YY-----KWEPFYKCLKNSLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        81 dv~~~~-------~~-----~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +++.--       ..     ....+...+.....+..|+.||....... .+   +. ...+.++..+.++-.++|..+.
T Consensus       326 EID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l  405 (489)
T CHL00195        326 EIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHL  405 (489)
T ss_pred             hhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHH
Confidence            985310       00     11223333444445556777887654321 11   22 3467788888999899998776


Q ss_pred             hCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          144 ISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      .........   ......+++.+.|+.
T Consensus       406 ~~~~~~~~~---~~dl~~La~~T~GfS  429 (489)
T CHL00195        406 QKFRPKSWK---KYDIKKLSKLSNKFS  429 (489)
T ss_pred             hhcCCCccc---ccCHHHHHhhcCCCC
Confidence            432211100   112456777776655

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

Probab=95.27  E-value=0.067  Score=48.66  Aligned_cols=80  Identities=19%  Similarity=0.139  Sum_probs=44.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC------CceEEEEeCCCCCHHHHHHHHHHHcCCCC--------CCChhcHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF------EKRTWVCVSEPFDEFRIARAIIESLTPGS--------AKDLVEFQSLMQHI   66 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f------~~~~wv~~~~~~~~~~~~~~l~~~l~~~~--------~~~~~~~~~~~~~l   66 (505)
                      .+|+|||+||.+++.  ......      ..++|++....++...+ ..+........        -....+.++....+
T Consensus        27 ~~GsGKT~l~~~ia~--~~~~~~~~~g~~~~v~yi~~e~~~~~~rl-~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l  103 (226)
T cd01393          27 EFGSGKTQLCLQLAV--EAQLPGELGGLEGKVVYIDTEGAFRPERL-VQLAVRFGLDPEEVLDNIYVARPYNGEQQLEIV  103 (226)
T ss_pred             CCCCChhHHHHHHHH--HhhcccccCCCcceEEEEecCCCCCHHHH-HHHHHHhccchhhhhccEEEEeCCCHHHHHHHH
Confidence            379999999999886  333333      56789998776665443 33333322110        01112334444444


Q ss_pred             HHHc----CCceEEEEEeCCC
Q 046115           67 EECV----AGKKFLLVLDDVW   83 (505)
Q Consensus        67 ~~~l----~~~r~LlvlDdv~   83 (505)
                      ....    ..+.-++|+|.+.
T Consensus       104 ~~~~~~~~~~~~~lvVIDsis  124 (226)
T cd01393         104 EELERIMSSGRVDLVVVDSVA  124 (226)
T ss_pred             HHHHHHhhcCCeeEEEEcCcc
Confidence            4333    2345588999974

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.

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=95.23  E-value=0.23  Score=46.64  Aligned_cols=68  Identities=16%  Similarity=0.234  Sum_probs=46.8

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHh-CCcceEeCCCCChhhHHHHHH
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIM-GSTHVISVNVLSEMECWSVFQ  140 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~-~~~~~~~l~~l~~~ea~~Lf~  140 (505)
                      +++-++|+|+++.........+++.+.....++.+|.+|.++ .+..-+ .....+.+.. +.++..+.+.
T Consensus       103 ~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        103 GKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             CCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHH
Confidence            456789999998887777888999999887777777777654 333322 2345667765 6666666664

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=95.23  E-value=0.42  Score=45.28  Aligned_cols=94  Identities=14%  Similarity=0.170  Sum_probs=61.4

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc-hHHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK-ETVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~-~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..........+.+.+......+.+|++|.+ ..+.+. ......+++.+++.++..+.+....      
T Consensus        89 ~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~~~------  162 (299)
T PRK07132         89 SQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLSKN------  162 (299)
T ss_pred             CCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHHcC------
Confidence            46778889998776655667788888887777777765544 444432 2346689999999999888776531      


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                       .+   ++.+..++...+|.--|+..
T Consensus       163 -~~---~~~a~~~a~~~~~~~~a~~~  184 (299)
T PRK07132        163 -KE---KEYNWFYAYIFSNFEQAEKY  184 (299)
T ss_pred             -CC---hhHHHHHHHHcCCHHHHHHH
Confidence             11   23355555566653344444

>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=95.23  E-value=0.01  Score=31.60  Aligned_cols=21  Identities=29%  Similarity=0.801  Sum_probs=15.0

Q ss_pred             CcceeeccCCccccccchhhhc
Q 046115          414 HLKYLNLKGQKKIEKLPETLCE  435 (505)
Q Consensus       414 ~L~~L~l~~~~~~~~lp~~~~~  435 (505)
                      +|++|++++|. ++.+|..+++
T Consensus         1 ~L~~Ldls~n~-l~~ip~~~~~   21 (22)
T PF00560_consen    1 NLEYLDLSGNN-LTSIPSSFSN   21 (22)
T ss_dssp             TESEEEETSSE-ESEEGTTTTT
T ss_pred             CccEEECCCCc-CEeCChhhcC
Confidence            47788888886 6677776554

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=95.16  E-value=0.27  Score=49.86  Aligned_cols=147  Identities=18%  Similarity=0.299  Sum_probs=82.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||-||+++++  +-.-+|     +.+..+        ++++...      ..+.....+..++.-..-++.|.||
T Consensus       553 PPGCGKTLlAKAVAN--Eag~NF-----isVKGP--------ELlNkYV------GESErAVR~vFqRAR~saPCVIFFD  611 (802)
T KOG0733|consen  553 PPGCGKTLLAKAVAN--EAGANF-----ISVKGP--------ELLNKYV------GESERAVRQVFQRARASAPCVIFFD  611 (802)
T ss_pred             CCCccHHHHHHHHhh--hccCce-----EeecCH--------HHHHHHh------hhHHHHHHHHHHHhhcCCCeEEEec
Confidence            589999999999999  666665     655542        3333332      1122233344444445679999999


Q ss_pred             CCCCC-------Ccc----ChhHHHHhhcC--CCCCcEEEEEeCchHHHHH-h---CC-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNE-------DYY----KWEPFYKCLKN--SLHESKILITTRKETVARI-M---GS-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~-------~~~----~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~~-~---~~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      .++.-       ...    .+.+++.-+..  ...|..||-.|..+++-.. +   +. ....-|+.-+.+|-.++++..
T Consensus       612 EiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~  691 (802)
T KOG0733|consen  612 EIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTI  691 (802)
T ss_pred             chhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHH
Confidence            98431       111    12333333332  2346667766666554221 1   11 345667777888888999887


Q ss_pred             hhCCCC-CCCCchHHHHHHHHHHHcCCCh
Q 046115          143 AISGKT-IGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       143 ~~~~~~-~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ....+. ...+-+++++++.  .+|.|+.
T Consensus       692 tkn~k~pl~~dVdl~eia~~--~~c~gft  718 (802)
T KOG0733|consen  692 TKNTKPPLSSDVDLDEIARN--TKCEGFT  718 (802)
T ss_pred             hccCCCCCCcccCHHHHhhc--ccccCCc
Confidence            753221 1333455555542  3566655

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

Probab=95.14  E-value=0.15  Score=54.73  Aligned_cols=71  Identities=14%  Similarity=0.131  Sum_probs=42.1

Q ss_pred             CceEEEEEeCCCCC--------CccChhHHHHhhcCCCCCcEEEEEeCchHHHH-------HhCCcceEeCCCCChhhHH
Q 046115           72 GKKFLLVLDDVWNE--------DYYKWEPFYKCLKNSLHESKILITTRKETVAR-------IMGSTHVISVNVLSEMECW  136 (505)
Q Consensus        72 ~~r~LlvlDdv~~~--------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-------~~~~~~~~~l~~l~~~ea~  136 (505)
                      ..+.+|++|++..-        ...+...+...+...+. -++|-+|......+       .......+.+++.+.+++.
T Consensus       277 ~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~-i~vIgATt~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~~  355 (758)
T PRK11034        277 DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGK-IRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETV  355 (758)
T ss_pred             cCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCC-eEEEecCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHH
Confidence            45789999998531        12233444555554443 34444444333211       1134568999999999999


Q ss_pred             HHHHHhh
Q 046115          137 SVFQSLA  143 (505)
Q Consensus       137 ~Lf~~~~  143 (505)
                      +++....
T Consensus       356 ~IL~~~~  362 (758)
T PRK11034        356 QIINGLK  362 (758)
T ss_pred             HHHHHHH
Confidence            9998653

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

Probab=95.14  E-value=0.027  Score=52.04  Aligned_cols=71  Identities=20%  Similarity=0.228  Sum_probs=40.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      +|+|||.||.++++  ++.+.--.+.++++.      +++.+|......         +.....+.+.++ +-=||||||
T Consensus       114 ~G~GKThLa~Ai~~--~l~~~g~sv~f~~~~------el~~~Lk~~~~~---------~~~~~~l~~~l~-~~dlLIiDD  175 (254)
T COG1484         114 PGVGKTHLAIAIGN--ELLKAGISVLFITAP------DLLSKLKAAFDE---------GRLEEKLLRELK-KVDLLIIDD  175 (254)
T ss_pred             CCCcHHHHHHHHHH--HHHHcCCeEEEEEHH------HHHHHHHHHHhc---------CchHHHHHHHhh-cCCEEEEec
Confidence            79999999999999  665332345566533      455555544441         111222333222 223899999


Q ss_pred             CCCCCccCh
Q 046115           82 VWNEDYYKW   90 (505)
Q Consensus        82 v~~~~~~~~   90 (505)
                      +..+....|
T Consensus       176 lG~~~~~~~  184 (254)
T COG1484         176 IGYEPFSQE  184 (254)
T ss_pred             ccCccCCHH
Confidence            976544443

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.09  E-value=0.074  Score=45.52  Aligned_cols=111  Identities=20%  Similarity=0.128  Sum_probs=60.3

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceE--EEEeCCCCCHHHHHHHHHH---HcCCCC----CCCh---hcHHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRT--WVCVSEPFDEFRIARAIIE---SLTPGS----AKDL---VEFQSLMQHIEEC   69 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~--wv~~~~~~~~~~~~~~l~~---~l~~~~----~~~~---~~~~~~~~~l~~~   69 (505)
                      .|.||||.|..++-. .....+...+  |+.-.........+..+.-   +++.+.    ....   ....+..+...+.
T Consensus        14 ~GkGKtt~a~g~a~r-a~~~g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~a~~~   92 (173)
T TIGR00708        14 NGKGKTTAAFGMALR-ALGHGKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKAAWQHAKEM   92 (173)
T ss_pred             CCCChHHHHHHHHHH-HHHCCCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHHHHHHHHHH
Confidence            589999999777662 2233344322  6655433344444443300   111110    0111   1122334444555


Q ss_pred             cCC-ceEEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           70 VAG-KKFLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        70 l~~-~r~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      +.. .-=|+|||.+-.   -...+.+.+.+.+.....+..|++|-|+.
T Consensus        93 l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        93 LADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            544 445999999832   22345566777777777788999999984

Alternate name: corrinoid adenosyltransferase.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.07  E-value=0.22  Score=53.94  Aligned_cols=144  Identities=15%  Similarity=0.181  Sum_probs=74.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  +....|     +.+..        .+++....      ..............-...+.+|+||
T Consensus       495 ppGtGKT~lakalA~--e~~~~f-----i~v~~--------~~l~~~~v------Gese~~i~~~f~~A~~~~p~iifiD  553 (733)
T TIGR01243       495 PPGTGKTLLAKAVAT--ESGANF-----IAVRG--------PEILSKWV------GESEKAIREIFRKARQAAPAIIFFD  553 (733)
T ss_pred             CCCCCHHHHHHHHHH--hcCCCE-----EEEeh--------HHHhhccc------CcHHHHHHHHHHHHHhcCCEEEEEE
Confidence            479999999999998  443333     33322        11222111      0111112222223334567999999


Q ss_pred             CCCCC--------Cc----cChhHHHHhhcC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHHHHH
Q 046115           81 DVWNE--------DY----YKWEPFYKCLKN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        81 dv~~~--------~~----~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      +++.-        ..    ....+++..+..  ...+..||.||..++... ..   +. ...+.++..+.++-.++|..
T Consensus       554 Eid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~  633 (733)
T TIGR01243       554 EIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKI  633 (733)
T ss_pred             ChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHH
Confidence            98431        00    012233333432  223455666776654322 11   12 45778888888888888876


Q ss_pred             hhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          142 LAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      +...... ....+    ...+++.+.|+.
T Consensus       634 ~~~~~~~-~~~~~----l~~la~~t~g~s  657 (733)
T TIGR01243       634 HTRSMPL-AEDVD----LEELAEMTEGYT  657 (733)
T ss_pred             HhcCCCC-CccCC----HHHHHHHcCCCC
Confidence            5422111 22222    456777777654

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.

>PRK08118 topology modulation protein; Reviewed

Probab=95.07  E-value=0.0093  Score=51.36  Aligned_cols=28  Identities=29%  Similarity=0.500  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHhcCcccc-cCCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-RNFEKRTW   28 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-~~f~~~~w   28 (505)
                      ++|+||||||+.+++...+. -+|+..+|
T Consensus         9 ~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          9 SGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             CCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            58999999999999843222 34666766

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.89  E-value=0.11  Score=48.24  Aligned_cols=82  Identities=21%  Similarity=0.160  Sum_probs=50.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCC---CCCCChhcHHHHHHHHHHHcCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTP---GSAKDLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      +.|+||||+|.+++-  .....-..++||+....++++.+..-....+..   .......+-.+..+.+.+....+--|+
T Consensus        68 ~~gsGKT~lal~~~~--~aq~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~v~~~~~~e~q~~i~~~~~~~~~~~i~Lv  145 (279)
T COG0468          68 PESSGKTTLALQLVA--NAQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLVSQPDTGEQQLEIAEKLARSGAEKIDLL  145 (279)
T ss_pred             CCCcchhhHHHHHHH--HhhcCCCeEEEEeCCCCCCHHHHHHHHHhhhcceeEecCCCHHHHHHHHHHHHHhccCCCCEE
Confidence            469999999988876  344444478899999988886654433332321   222233333344444444444445689


Q ss_pred             EEeCCCC
Q 046115           78 VLDDVWN   84 (505)
Q Consensus        78 vlDdv~~   84 (505)
                      |+|.+..
T Consensus       146 VVDSvaa  152 (279)
T COG0468         146 VVDSVAA  152 (279)
T ss_pred             EEecCcc
Confidence            9999833

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

Probab=94.89  E-value=0.1  Score=48.31  Aligned_cols=43  Identities=21%  Similarity=0.295  Sum_probs=29.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceE-EEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRT-WVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~-wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|.|||+||..+++  .++.+|..++ ++-+++.. +..++..++..
T Consensus        78 ~G~GKTtLa~~i~~--~i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~  122 (274)
T cd01133          78 AGVGKTVLIMELIN--NIAKAHGGYSVFAGVGERTREGNDLYHEMKE  122 (274)
T ss_pred             CCCChhHHHHHHHH--HHHhcCCCEEEEEEeccCcHHHHHHHHHHHh
Confidence            69999999999999  7776775444 55566544 44455555544

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.

>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=94.88  E-value=0.84  Score=44.04  Aligned_cols=53  Identities=11%  Similarity=0.206  Sum_probs=30.5

Q ss_pred             HHHHHc--CCceEEEEEeCCCCCCccChhHHHHhhcCC--CCCcEEEEEeCchHHHH
Q 046115           65 HIEECV--AGKKFLLVLDDVWNEDYYKWEPFYKCLKNS--LHESKILITTRKETVAR  117 (505)
Q Consensus        65 ~l~~~l--~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~  117 (505)
                      .+...+  .++|.++++||+++-.......+...+...  .+++.+|+..-.+.+..
T Consensus       162 ~~~~~l~~~~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~~D~~~l~~  218 (325)
T PF07693_consen  162 KIKKKLKESKKRIVIIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILAFDPEILEK  218 (325)
T ss_pred             HHHHhhhcCCceEEEEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEEecHHHHHH
Confidence            344444  347999999999886554444444443321  25666666655444433

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 [].

>PRK10536 hypothetical protein; Provisional

Probab=94.63  E-value=0.1  Score=47.72  Aligned_cols=37  Identities=11%  Similarity=0.164  Sum_probs=26.3

Q ss_pred             eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           74 KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        74 r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      .-++|+|.+++-+..++..++.   ..+.+|++++|--..
T Consensus       177 ~~~vIvDEaqn~~~~~~k~~lt---R~g~~sk~v~~GD~~  213 (262)
T PRK10536        177 NAVVILDEAQNVTAAQMKMFLT---RLGENVTVIVNGDIT  213 (262)
T ss_pred             CCEEEEechhcCCHHHHHHHHh---hcCCCCEEEEeCChh
Confidence            4599999998877655555554   445789999886643

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.61  E-value=0.098  Score=57.43  Aligned_cols=103  Identities=15%  Similarity=0.165  Sum_probs=53.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC-CChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA-KDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      ++|+|||++|+.++.  ...+.-...+.++++...+... ...+   ++.+.. ....+.+.....++   +....+|+|
T Consensus       603 p~GvGKt~lA~~La~--~l~~~~~~~i~~d~s~~~~~~~-~~~l---~g~~~g~~g~~~~g~l~~~v~---~~p~~vlll  673 (852)
T TIGR03346       603 PTGVGKTELAKALAE--FLFDDEDAMVRIDMSEYMEKHS-VARL---IGAPPGYVGYEEGGQLTEAVR---RKPYSVVLF  673 (852)
T ss_pred             CCCCCHHHHHHHHHH--HhcCCCCcEEEEechhhcccch-HHHh---cCCCCCccCcccccHHHHHHH---cCCCcEEEE
Confidence            479999999999998  4433333445566554332211 1111   221111 11111122222222   233459999


Q ss_pred             eCCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |++.......+..+.+.+....           ..+-||.||.-
T Consensus       674 Deieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       674 DEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             eccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            9998776666677777664331           23446777764

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

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=94.58  E-value=0.045  Score=59.66  Aligned_cols=103  Identities=17%  Similarity=0.130  Sum_probs=52.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCC-CCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS-AKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      ++|+|||.||+.++.  ..-+.....+-++++...+....    ..-++.+. .......+.....++   +....+|+|
T Consensus       604 p~GvGKT~lA~~La~--~l~~~~~~~~~~dmse~~~~~~~----~~l~g~~~gyvg~~~~g~L~~~v~---~~p~svvll  674 (852)
T TIGR03345       604 PSGVGKTETALALAE--LLYGGEQNLITINMSEFQEAHTV----SRLKGSPPGYVGYGEGGVLTEAVR---RKPYSVVLL  674 (852)
T ss_pred             CCCCCHHHHHHHHHH--HHhCCCcceEEEeHHHhhhhhhh----ccccCCCCCcccccccchHHHHHH---hCCCcEEEE
Confidence            479999999999987  44333333344444432211111    11112111 111111112222222   245679999


Q ss_pred             eCCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |++.......+..+.+.+....           ..+-||+||.-
T Consensus       675 DEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNl  718 (852)
T TIGR03345       675 DEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNA  718 (852)
T ss_pred             echhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCC
Confidence            9997666555566666555432           45567777664

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.

>PRK07261 topology modulation protein; Provisional

Probab=94.57  E-value=0.077  Score=45.86  Aligned_cols=15  Identities=40%  Similarity=0.468  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||||++++.
T Consensus         8 ~~GsGKSTla~~l~~   22 (171)
T PRK07261          8 YSGSGKSTLARKLSQ   22 (171)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999986

>PRK05541 adenylylsulfate kinase; Provisional

Probab=94.52  E-value=0.065  Score=46.63  Aligned_cols=28  Identities=25%  Similarity=0.504  Sum_probs=22.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~   30 (505)
                      ++|+||||+|+.++.  .....+..+++++
T Consensus        15 ~~GsGKst~a~~l~~--~l~~~~~~~~~~~   42 (176)
T PRK05541         15 LAGSGKTTIAKALYE--RLKLKYSNVIYLD   42 (176)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEEe
Confidence            579999999999998  6666666677664

>CHL00095 clpC Clp protease ATP binding subunit

Probab=94.49  E-value=0.081  Score=57.84  Aligned_cols=102  Identities=14%  Similarity=0.168  Sum_probs=53.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCC-CCChhcHHHHHHHHHHHcCC-ceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS-AKDLVEFQSLMQHIEECVAG-KKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~l~~~l~~-~r~Llv   78 (505)
                      +.|+|||+||+.+++  ..-+.-...+-++.++..+.... ..+   ++.+. .....+.+    .+...++. ...+++
T Consensus       547 p~GvGKt~lA~~LA~--~l~~~~~~~~~~d~s~~~~~~~~-~~l---~g~~~gyvg~~~~~----~l~~~~~~~p~~Vvl  616 (821)
T CHL00095        547 PTGVGKTELTKALAS--YFFGSEDAMIRLDMSEYMEKHTV-SKL---IGSPPGYVGYNEGG----QLTEAVRKKPYTVVL  616 (821)
T ss_pred             CCCCcHHHHHHHHHH--HhcCCccceEEEEchhccccccH-HHh---cCCCCcccCcCccc----hHHHHHHhCCCeEEE
Confidence            479999999999997  44222234445555543322211 111   22111 11111111    23333433 346899


Q ss_pred             EeCCCCCCccChhHHHHhhcCC-----------CCCcEEEEEeCc
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNS-----------LHESKILITTRK  112 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~-----------~~~~~iLiTtr~  112 (505)
                      ||++.......+..+.+.+...           ...+-||.||.-
T Consensus       617 lDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~  661 (821)
T CHL00095        617 FDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNL  661 (821)
T ss_pred             ECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCc
Confidence            9999776665666667665542           134556666664

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

Probab=94.49  E-value=0.13  Score=44.74  Aligned_cols=111  Identities=18%  Similarity=0.100  Sum_probs=60.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceE--EEEeCCCCCHHHHHHHHH--HH--cCCC----CCCCh---hcHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRT--WVCVSEPFDEFRIARAII--ES--LTPG----SAKDL---VEFQSLMQHIEE   68 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~--wv~~~~~~~~~~~~~~l~--~~--l~~~----~~~~~---~~~~~~~~~l~~   68 (505)
                      .|-||||.|...+-. .....+...+  |+.-.........+..+-  ..  .+.+    .....   ....+..+...+
T Consensus        31 ~GkGKtt~a~g~a~r-a~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~~~~~~~a~~  109 (191)
T PRK05986         31 NGKGKSTAAFGMALR-AVGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAAREGWEEAKR  109 (191)
T ss_pred             CCCChHHHHHHHHHH-HHHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHHHHHHHHHHH
Confidence            589999999777652 2223343322  555443334444444321  11  1111    01111   111223444455


Q ss_pred             HcCC-ceEEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           69 CVAG-KKFLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        69 ~l~~-~r~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      .+.. +-=|+|||.+-.   ....+.+.+.+.+.....+..|++|-|+.
T Consensus       110 ~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986        110 MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence            5544 456999999732   23345667777777777788999999983

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=94.47  E-value=0.15  Score=43.89  Aligned_cols=32  Identities=22%  Similarity=0.260  Sum_probs=23.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEF   38 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~   38 (505)
                      +|+|||++|.+++.  .   ....++++.-.+..+.+
T Consensus         8 ~~sGKS~~a~~~~~--~---~~~~~~y~at~~~~d~e   39 (169)
T cd00544           8 ARSGKSRFAERLAA--E---LGGPVTYIATAEAFDDE   39 (169)
T ss_pred             CCCCHHHHHHHHHH--h---cCCCeEEEEccCcCCHH
Confidence            69999999999987  3   22456677666666553

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.47  E-value=0.11  Score=57.01  Aligned_cols=90  Identities=17%  Similarity=0.177  Sum_probs=45.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC-CceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA-GKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~-~~r~Llvl   79 (505)
                      +.|+|||++|+.+++  ...+.-...+.++++...+. .....+   ++.+  ......++. ..+...++ ...-+|+|
T Consensus       606 p~G~GKT~lA~aLa~--~l~~~~~~~i~id~se~~~~-~~~~~L---iG~~--pgy~g~~~~-g~l~~~v~~~p~~vLll  676 (857)
T PRK10865        606 PTGVGKTELCKALAN--FMFDSDDAMVRIDMSEFMEK-HSVSRL---VGAP--PGYVGYEEG-GYLTEAVRRRPYSVILL  676 (857)
T ss_pred             CCCCCHHHHHHHHHH--HhhcCCCcEEEEEhHHhhhh-hhHHHH---hCCC--Ccccccchh-HHHHHHHHhCCCCeEEE
Confidence            479999999999997  44333233455555442211 111111   2211  111111110 11222222 23469999


Q ss_pred             eCCCCCCccChhHHHHhhcC
Q 046115           80 DDVWNEDYYKWEPFYKCLKN   99 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~   99 (505)
                      |++.......+..+...+..
T Consensus       677 DEieka~~~v~~~Ll~ile~  696 (857)
T PRK10865        677 DEVEKAHPDVFNILLQVLDD  696 (857)
T ss_pred             eehhhCCHHHHHHHHHHHhh
Confidence            99976666566666665543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.43  E-value=0.48  Score=52.04  Aligned_cols=72  Identities=13%  Similarity=-0.012  Sum_probs=39.5

Q ss_pred             CceEEEEEeCCCCCC-------ccChhHHHHhhcCCCCCcEEEEEeCchH-----HHHH-hCCcceEeCCCCChhhHHHH
Q 046115           72 GKKFLLVLDDVWNED-------YYKWEPFYKCLKNSLHESKILITTRKET-----VARI-MGSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~-------~~~~~~~~~~~~~~~~~~~iLiTtr~~~-----~~~~-~~~~~~~~l~~l~~~ea~~L  138 (505)
                      .++++|++|++..-.       ..+...++......+.=..|-.||.++.     .... ......+.+...+.++...+
T Consensus       270 ~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~g~l~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~~i  349 (857)
T PRK10865        270 EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAI  349 (857)
T ss_pred             CCCeEEEEecHHHhccCCCCccchhHHHHhcchhhcCCCeEEEcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHHHH
Confidence            468999999985421       1122344444444443333334555442     1111 12344677888899999888


Q ss_pred             HHHhh
Q 046115          139 FQSLA  143 (505)
Q Consensus       139 f~~~~  143 (505)
                      +....
T Consensus       350 L~~l~  354 (857)
T PRK10865        350 LRGLK  354 (857)
T ss_pred             HHHHh
Confidence            86543

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

Probab=94.41  E-value=0.047  Score=57.55  Aligned_cols=91  Identities=19%  Similarity=0.303  Sum_probs=52.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceE-EEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKF-LLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~-Llvl   79 (505)
                      +.|+|||-||+.++.  ..-+.=+..+-++.++.-....+     ..|- +.++.-...++ -..|-+..++++| +|+|
T Consensus       529 PTGVGKTELAkaLA~--~Lfg~e~aliR~DMSEy~EkHsV-----SrLI-GaPPGYVGyee-GG~LTEaVRr~PySViLl  599 (786)
T COG0542         529 PTGVGKTELAKALAE--ALFGDEQALIRIDMSEYMEKHSV-----SRLI-GAPPGYVGYEE-GGQLTEAVRRKPYSVILL  599 (786)
T ss_pred             CCcccHHHHHHHHHH--HhcCCCccceeechHHHHHHHHH-----HHHh-CCCCCCceecc-ccchhHhhhcCCCeEEEe
Confidence            579999999999998  44322255566666653322221     2222 22222222222 2234445566655 8889


Q ss_pred             eCCCCCCccChhHHHHhhcCC
Q 046115           80 DDVWNEDYYKWEPFYKCLKNS  100 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~  100 (505)
                      |.|.......+..+.+.+.+.
T Consensus       600 DEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         600 DEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             chhhhcCHHHHHHHHHHhcCC
Confidence            999777766777777776654

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

Probab=94.37  E-value=1.9  Score=39.17  Aligned_cols=90  Identities=21%  Similarity=0.302  Sum_probs=47.3

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|.|||++++.+.+  +....=--+  |.+.                    ..+..+.....+.++.  ...|++|.+||
T Consensus        61 rGtGKSSlVkall~--~y~~~GLRl--Iev~--------------------k~~L~~l~~l~~~l~~--~~~kFIlf~DD  114 (249)
T PF05673_consen   61 RGTGKSSLVKALLN--EYADQGLRL--IEVS--------------------KEDLGDLPELLDLLRD--RPYKFILFCDD  114 (249)
T ss_pred             CCCCHHHHHHHHHH--HHhhcCceE--EEEC--------------------HHHhccHHHHHHHHhc--CCCCEEEEecC
Confidence            69999999999988  343321111  2221                    1122333333344432  34699999999


Q ss_pred             CCCC-CccChhHHHHhhcC----CCCCcEEEEEeCchHHHH
Q 046115           82 VWNE-DYYKWEPFYKCLKN----SLHESKILITTRKETVAR  117 (505)
Q Consensus        82 v~~~-~~~~~~~~~~~~~~----~~~~~~iLiTtr~~~~~~  117 (505)
                      +.=+ ....+..+...+.-    ...+..|..||.-+++.+
T Consensus       115 LsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~  155 (249)
T PF05673_consen  115 LSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVP  155 (249)
T ss_pred             CCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccc
Confidence            8322 22344444433321    223455666776666544

>TIGR02012 tigrfam_recA protein RecA

Probab=94.37  E-value=0.084  Score=50.25  Aligned_cols=76  Identities=20%  Similarity=0.175  Sum_probs=46.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  .....-..++||+..+.++..     .+.+++....    ..+...++....+....+ +..-
T Consensus        63 ~~GsGKTtLaL~~~~--~~~~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~~~~~~  135 (321)
T TIGR02012        63 PESSGKTTLALHAIA--EAQKAGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVD  135 (321)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhccCCc
Confidence            479999999999887  444444567799888766653     2344432211    112334455555554443 3567


Q ss_pred             EEEEeCCC
Q 046115           76 LLVLDDVW   83 (505)
Q Consensus        76 LlvlDdv~   83 (505)
                      ++|+|.|.
T Consensus       136 lIVIDSv~  143 (321)
T TIGR02012       136 IIVVDSVA  143 (321)
T ss_pred             EEEEcchh
Confidence            99999984

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.

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

Probab=94.37  E-value=0.08  Score=50.43  Aligned_cols=76  Identities=20%  Similarity=0.160  Sum_probs=47.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCC----CCChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS----AKDLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~----~~~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  ...+.-..++||+....++..     .+..++...    ...+.+.++....+....+ +.--
T Consensus        63 p~GsGKTtLal~~~~--~~~~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~s~~~~  135 (325)
T cd00983          63 PESSGKTTLALHAIA--EAQKLGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIADSLVRSGAVD  135 (325)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHHHHHhccCCC
Confidence            479999999999887  444444567899988777653     233343211    1122234455555554443 3467


Q ss_pred             EEEEeCCC
Q 046115           76 LLVLDDVW   83 (505)
Q Consensus        76 LlvlDdv~   83 (505)
                      ++|+|.|.
T Consensus       136 lIVIDSva  143 (325)
T cd00983         136 LIVVDSVA  143 (325)
T ss_pred             EEEEcchH
Confidence            89999974

RecA couples ATP hydrolysis to DNA strand exchange.

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=94.35  E-value=0.032  Score=52.31  Aligned_cols=133  Identities=12%  Similarity=0.055  Sum_probs=81.3

Q ss_pred             CCCCceEEEecCCCccccccchhHH-------hhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccc
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQL-------FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKI  426 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~-------~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~  426 (505)
                      ..++|+...++..........+|+.       +....+|++|+|+++..  .-+.+..+-.-+.++..|+.|.|.+|. +
T Consensus        56 ~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLSDNA~--G~~g~~~l~~ll~s~~~L~eL~L~N~G-l  132 (382)
T KOG1909|consen   56 SKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLSDNAF--GPKGIRGLEELLSSCTDLEELYLNNCG-L  132 (382)
T ss_pred             hcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeecccccc--CccchHHHHHHHHhccCHHHHhhhcCC-C
Confidence            4557777776665543332223332       34556899999983221  001111122235678889999999988 5


Q ss_pred             cccch--------------hhhcCCCCcEEecCCCcCccccch-----hccccccCceeecCCCcccccccc-------c
Q 046115          427 EKLPE--------------TLCELYNLERLNVDDCQNLRELPR-----GIGKLRKLMYLHNEDTGCLRYLPA-------G  480 (505)
Q Consensus       427 ~~lp~--------------~~~~l~~L~~L~l~~~~~~~~lp~-----~~~~l~~L~~L~l~~~~~~~~~p~-------~  480 (505)
                      +....              .+..-+.|+++....|+ +...+.     .+...+.|+.+.+..|..   -|.       .
T Consensus       133 g~~ag~~l~~al~~l~~~kk~~~~~~Lrv~i~~rNr-len~ga~~~A~~~~~~~~leevr~~qN~I---~~eG~~al~ea  208 (382)
T KOG1909|consen  133 GPEAGGRLGRALFELAVNKKAASKPKLRVFICGRNR-LENGGATALAEAFQSHPTLEEVRLSQNGI---RPEGVTALAEA  208 (382)
T ss_pred             ChhHHHHHHHHHHHHHHHhccCCCcceEEEEeeccc-cccccHHHHHHHHHhccccceEEEecccc---cCchhHHHHHH
Confidence            43322              23345778999888888 776664     367778899999888852   233       3


Q ss_pred             ccCCccCCcccee
Q 046115          481 IGELIRLRRVREF  493 (505)
Q Consensus       481 i~~l~~L~~L~~~  493 (505)
                      +.++++|+.|++.
T Consensus       209 l~~~~~LevLdl~  221 (382)
T KOG1909|consen  209 LEHCPHLEVLDLR  221 (382)
T ss_pred             HHhCCcceeeecc
Confidence            5677777777764

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.28  E-value=0.026  Score=51.71  Aligned_cols=161  Identities=14%  Similarity=0.156  Sum_probs=88.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEeccccc---CCccccccccC
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRES---WPRNNLIKEIP  406 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~---~~~~~~~~~~p  406 (505)
                      .++.+.++.+..+......|   ....+|++|.|+|..++|..  ..+++..++.++.|.++++.-   .-..+.++...
T Consensus        98 ~l~~LNls~N~L~s~I~~lp---~p~~nl~~lVLNgT~L~w~~--~~s~l~~lP~vtelHmS~N~~rq~n~Dd~c~e~~s  172 (418)
T KOG2982|consen   98 ALTTLNLSCNSLSSDIKSLP---LPLKNLRVLVLNGTGLSWTQ--STSSLDDLPKVTELHMSDNSLRQLNLDDNCIEDWS  172 (418)
T ss_pred             cceEeeccCCcCCCccccCc---ccccceEEEEEcCCCCChhh--hhhhhhcchhhhhhhhccchhhhhccccccccccc
Confidence            34445555554443222222   35789999999999988753  566677777777777762100   00011111100


Q ss_pred             cc---cc-----------------CCCCcceeeccCCccccccc--hhhhcCCCCcEEecCCCcCccccc--hhcccccc
Q 046115          407 TN---IE-----------------KLLHLKYLNLKGQKKIEKLP--ETLCELYNLERLNVDDCQNLRELP--RGIGKLRK  462 (505)
Q Consensus       407 ~~---~~-----------------~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~  462 (505)
                      ..   +.                 .++++..+-+-.|+ +....  ...-.++.+..|+|+.++ +.+.-  ..+..++.
T Consensus       173 ~~v~tlh~~~c~~~~w~~~~~l~r~Fpnv~sv~v~e~P-lK~~s~ek~se~~p~~~~LnL~~~~-idswasvD~Ln~f~~  250 (418)
T KOG2982|consen  173 TEVLTLHQLPCLEQLWLNKNKLSRIFPNVNSVFVCEGP-LKTESSEKGSEPFPSLSCLNLGANN-IDSWASVDALNGFPQ  250 (418)
T ss_pred             hhhhhhhcCCcHHHHHHHHHhHHhhcccchheeeecCc-ccchhhcccCCCCCcchhhhhcccc-cccHHHHHHHcCCch
Confidence            00   01                 12233333333333 22111  123345666677777766 44332  35678889


Q ss_pred             CceeecCCCcccccccc------cccCCccCCccceeEecC
Q 046115          463 LMYLHNEDTGCLRYLPA------GIGELIRLRRVREFVVGG  497 (505)
Q Consensus       463 L~~L~l~~~~~~~~~p~------~i~~l~~L~~L~~~~~~~  497 (505)
                      |+.|++++++..+.+-.      -|+.+++++.|+.-.+++
T Consensus       251 l~dlRv~~~Pl~d~l~~~err~llIaRL~~v~vLNGskIss  291 (418)
T KOG2982|consen  251 LVDLRVSENPLSDPLRGGERRFLLIARLTKVQVLNGSKISS  291 (418)
T ss_pred             hheeeccCCcccccccCCcceEEEEeeccceEEecCcccch
Confidence            99999999886665533      267888888888765554

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=94.23  E-value=0.19  Score=43.72  Aligned_cols=55  Identities=11%  Similarity=0.067  Sum_probs=32.4

Q ss_pred             HHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHH
Q 046115           63 MQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVAR  117 (505)
Q Consensus        63 ~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~  117 (505)
                      .-.+.+.+..++=++++|..... +......+...+.....+..||++|.+.....
T Consensus       106 rv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~  161 (178)
T cd03247         106 RLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIE  161 (178)
T ss_pred             HHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHH
Confidence            33455566667788899997542 22223333343333223677888888876654

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.

>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=94.14  E-value=0.39  Score=41.86  Aligned_cols=114  Identities=13%  Similarity=0.101  Sum_probs=59.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCC--CCCHHH------HHHHHHHHcCCCC-----CCChhcHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE--PFDEFR------IARAIIESLTPGS-----AKDLVEFQSLMQHIE   67 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~--~~~~~~------~~~~l~~~l~~~~-----~~~~~~~~~~~~~l~   67 (505)
                      ..|+|||||++.++.  .. .-..+.++++-..  ..+...      ...++++.++...     ....+.-+...-.+.
T Consensus        33 ~nGsGKStLl~~i~G--~~-~~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~~qrl~la  109 (180)
T cd03214          33 PNGAGKSTLLKTLAG--LL-KPSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSGGERQRVLLA  109 (180)
T ss_pred             CCCCCHHHHHHHHhC--CC-CCCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHHHHHHHHH
Confidence            369999999999987  32 2245555543211  111111      1222445444221     112222233334456


Q ss_pred             HHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CC-CcEEEEEeCchHHHH
Q 046115           68 ECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LH-ESKILITTRKETVAR  117 (505)
Q Consensus        68 ~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~-~~~iLiTtr~~~~~~  117 (505)
                      +.+...+-++++|..... +......+...+... .. +..||++|.+.....
T Consensus       110 ral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~  162 (180)
T cd03214         110 RALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAA  162 (180)
T ss_pred             HHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            666677789999997442 222333444444332 12 567888888866543

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.

>PRK09354 recA recombinase A; Provisional

Probab=94.12  E-value=0.11  Score=50.05  Aligned_cols=76  Identities=20%  Similarity=0.180  Sum_probs=47.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  ...+.=..++||+....++..     .+..++....    ..+...++....+...++ +..-
T Consensus        68 ~~GsGKTtLal~~~~--~~~~~G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~s~~~~  140 (349)
T PRK09354         68 PESSGKTTLALHAIA--EAQKAGGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVD  140 (349)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcCCCC
Confidence            479999999999887  444444667899988877763     2344432210    112234455555555443 3566


Q ss_pred             EEEEeCCC
Q 046115           76 LLVLDDVW   83 (505)
Q Consensus        76 LlvlDdv~   83 (505)
                      ++|+|.|.
T Consensus       141 lIVIDSva  148 (349)
T PRK09354        141 LIVVDSVA  148 (349)
T ss_pred             EEEEeChh
Confidence            89999984

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.06  E-value=0.4  Score=43.87  Aligned_cols=136  Identities=16%  Similarity=0.106  Sum_probs=75.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCC-----CCCHHHHHHHHHHHcCCCCC------CChhcHHHHHHHHHHHc
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE-----PFDEFRIARAIIESLTPGSA------KDLVEFQSLMQHIEECV   70 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~-----~~~~~~~~~~l~~~l~~~~~------~~~~~~~~~~~~l~~~l   70 (505)
                      +|.||||+++.+..  -..- -.+.+++....     .....+...+++...+....      .+.+.-+...-.+.+.+
T Consensus        48 SG~GKSTlgr~i~~--L~~p-t~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQRi~IARAL  124 (268)
T COG4608          48 SGCGKSTLGRLILG--LEEP-TSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQRIGIARAL  124 (268)
T ss_pred             CCCCHHHHHHHHHc--CcCC-CCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhhHHHHHHH
Confidence            79999999999998  3322 23444443222     22344556677777664331      22333344445577777


Q ss_pred             CCceEEEEEeCCCCCCccCh-hHHHHhhcC--CCCCcEEEEEeCchHHHHHhCC-cceEeC-CCCChhhHHHHHH
Q 046115           71 AGKKFLLVLDDVWNEDYYKW-EPFYKCLKN--SLHESKILITTRKETVARIMGS-THVISV-NVLSEMECWSVFQ  140 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~-~~~~~~~~~--~~~~~~iLiTtr~~~~~~~~~~-~~~~~l-~~l~~~ea~~Lf~  140 (505)
                      .-++-++|.|...+.-+... .++...+.+  ...|...|..|-+-.+...+.. ..++.+ .-.+...+.++|.
T Consensus       125 al~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~isdri~VMy~G~iVE~g~~~~~~~  199 (268)
T COG4608         125 ALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYISDRIAVMYLGKIVEIGPTEEVFS  199 (268)
T ss_pred             hhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhhcccEEEEecCceeEecCHHHHhh
Confidence            88889999999755322222 334433332  2346677888887666655432 112222 2234445555554

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.06  E-value=0.18  Score=46.18  Aligned_cols=107  Identities=18%  Similarity=0.116  Sum_probs=56.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC-------------------CChhcHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA-------------------KDLVEFQS   61 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~-------------------~~~~~~~~   61 (505)
                      .+|+|||+||.+++.  ....+=..++|++..+.+  .++.+.+ .+++....                   ....+.++
T Consensus        33 ~~GsGKt~l~~~~~~--~~~~~g~~~~y~~~e~~~--~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~~~~~  107 (234)
T PRK06067         33 DHGTGKSVLSQQFVY--GALKQGKKVYVITTENTS--KSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGFEWNSTLANK  107 (234)
T ss_pred             CCCCChHHHHHHHHH--HHHhCCCEEEEEEcCCCH--HHHHHHH-HHCCCChhHHHhCCCceEEeccccccccCcchHHH
Confidence            379999999999976  333333567789886543  3444432 22321110                   01123345


Q ss_pred             HHHHHHHHcCC-ceEEEEEeCCCC----CCccChhHHHHhhcC-CCCCcEEEEEeCc
Q 046115           62 LMQHIEECVAG-KKFLLVLDDVWN----EDYYKWEPFYKCLKN-SLHESKILITTRK  112 (505)
Q Consensus        62 ~~~~l~~~l~~-~r~LlvlDdv~~----~~~~~~~~~~~~~~~-~~~~~~iLiTtr~  112 (505)
                      ..+.+...... +.-++|+|.+..    .+......+...+.. ...+..+++|+..
T Consensus       108 ll~~l~~~i~~~~~~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~  164 (234)
T PRK06067        108 LLELIIEFIKSKREDVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHP  164 (234)
T ss_pred             HHHHHHHHHHhcCCCEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecC
Confidence            55556555543 556899999752    111122333222321 1235567777653

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=94.00  E-value=0.4  Score=44.01  Aligned_cols=135  Identities=18%  Similarity=0.235  Sum_probs=66.1

Q ss_pred             CCCCcHHHHHHHHhcCccccc------------CCCceEEEEeCCCC-CHHHHHHHHHHHcCCCCCC----------C--
Q 046115            1 MGGIGKTTLAQFAYNNGDVER------------NFEKRTWVCVSEPF-DEFRIARAIIESLTPGSAK----------D--   55 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~------------~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~~----------~--   55 (505)
                      ++|+|||+||..++.  .+..            .=..+++++...+. ...+-+..+...+......          .  
T Consensus         9 ~~G~GKS~lal~la~--~va~G~~~~g~~~~~~~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~g~~~~l   86 (239)
T cd01125           9 PGGTGKSSLLLVLAL--AMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDSGRIQPI   86 (239)
T ss_pred             CCCCCHHHHHHHHHH--HHhcCccccCCccccCCCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEeccCCCce
Confidence            589999999988876  2221            11134455555443 3344455555544211000          0  


Q ss_pred             ---h---hcHHHHHHHHHHHc-CCceEEEEEeCCCC------CCccChhHHHHhhcC--CCCCcEEEEEeCchHHHH---
Q 046115           56 ---L---VEFQSLMQHIEECV-AGKKFLLVLDDVWN------EDYYKWEPFYKCLKN--SLHESKILITTRKETVAR---  117 (505)
Q Consensus        56 ---~---~~~~~~~~~l~~~l-~~~r~LlvlDdv~~------~~~~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~---  117 (505)
                         .   .......+.+.+.+ ..+.-++|+|.+..      .+......+...+..  ...++.|++++-......   
T Consensus        87 ~~~~~~~~~~~~~~~~l~~~~~~~~~~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~~~~~  166 (239)
T cd01125          87 SIAREGRIIVVPEFERIIEQLLIRRIDLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGSAKDG  166 (239)
T ss_pred             ecccCCcccccHHHHHHHHHHHhcCCCEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCcccccCc
Confidence               0   01112233333333 34567999997632      122233344444432  134677888776542111   


Q ss_pred             -----------HhC-CcceEeCCCCChhhHHH
Q 046115          118 -----------IMG-STHVISVNVLSEMECWS  137 (505)
Q Consensus       118 -----------~~~-~~~~~~l~~l~~~ea~~  137 (505)
                                 ..+ ....+.+.+++.+|+.+
T Consensus       167 ~~~~~~rGssal~~~~r~~~~l~~~~~~~~~~  198 (239)
T cd01125         167 DTQEAARGASALVDGARWVRALTRMTSEEAEK  198 (239)
T ss_pred             ccccccCcHHHHhcccceEEEEeeCCHHHHHh
Confidence                       001 12366677777777665

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=93.98  E-value=1.4  Score=39.35  Aligned_cols=15  Identities=33%  Similarity=0.189  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||-+..+++
T Consensus        56 pPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   56 PPGTGKTTSILCLAR   70 (333)
T ss_pred             CCCCchhhHHHHHHH
Confidence            689999999888887

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

Probab=93.95  E-value=0.9  Score=43.85  Aligned_cols=64  Identities=13%  Similarity=0.134  Sum_probs=34.9

Q ss_pred             CCCcEEEEEeCchHHHHH-h---CC-cceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHH
Q 046115          101 LHESKILITTRKETVARI-M---GS-THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       101 ~~~~~iLiTtr~~~~~~~-~---~~-~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                      ..+..||+||.++..... +   +. ...|  ..-+.++-.++++.+.-. ..  .+   ...+.+|+....|-|+-
T Consensus       266 ~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~-~~--l~---~~dv~~Lv~~f~gq~~D  334 (413)
T PLN00020        266 IPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRD-DG--VS---REDVVKLVDTFPGQPLD  334 (413)
T ss_pred             CCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhcc-CC--CC---HHHHHHHHHcCCCCCch
Confidence            456778999988664322 1   11 1233  334566666676655422 11  11   23466677777777753

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=93.90  E-value=0.54  Score=44.05  Aligned_cols=43  Identities=26%  Similarity=0.268  Sum_probs=28.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CCceEEEEeCCCCCHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FEKRTWVCVSEPFDEFRIARAIIES   47 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~~~~wv~~~~~~~~~~~~~~l~~~   47 (505)
                      .+|+|||++|.+++.  ....+ =..++|++...+  ..++...+...
T Consensus        38 ~~G~GKT~l~~~~~~--~~~~~~g~~vl~iS~E~~--~~~~~~r~~~~   81 (271)
T cd01122          38 GTGVGKTTFLREYAL--DLITQHGVRVGTISLEEP--VVRTARRLLGQ   81 (271)
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCceEEEEEcccC--HHHHHHHHHHH
Confidence            379999999999987  44333 356778887663  34445554443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=93.90  E-value=0.011  Score=54.13  Aligned_cols=114  Identities=15%  Similarity=0.152  Sum_probs=74.8

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhc-CcccceEEecccccCCccccccccCccccCCCCcceeeccCCcccc-cc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEK-LTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIE-KL  429 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~-l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~-~l  429 (505)
                      +..|+.|..|+++-+.++...  +.-.+.. -.+|..|+|+|+..   +-....+.--...+++|..|||+.|-.++ ..
T Consensus       256 ~~scs~L~~LNlsWc~l~~~~--Vtv~V~hise~l~~LNlsG~rr---nl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~  330 (419)
T KOG2120|consen  256 LSSCSRLDELNLSWCFLFTEK--VTVAVAHISETLTQLNLSGYRR---NLQKSHLSTLVRRCPNLVHLDLSDSVMLKNDC  330 (419)
T ss_pred             HHhhhhHhhcCchHhhccchh--hhHHHhhhchhhhhhhhhhhHh---hhhhhHHHHHHHhCCceeeeccccccccCchH
Confidence            346788888888777653221  2211222 34788888886521   11111222224578999999999987665 33


Q ss_pred             chhhhcCCCCcEEecCCCcCccccch---hccccccCceeecCCCc
Q 046115          430 PETLCELYNLERLNVDDCQNLRELPR---GIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~~~~~lp~---~~~~l~~L~~L~l~~~~  472 (505)
                      ...+.+++.|++|.++.|..  ..|.   .++..|+|.+|++.||-
T Consensus       331 ~~~~~kf~~L~~lSlsRCY~--i~p~~~~~l~s~psl~yLdv~g~v  374 (419)
T KOG2120|consen  331 FQEFFKFNYLQHLSLSRCYD--IIPETLLELNSKPSLVYLDVFGCV  374 (419)
T ss_pred             HHHHHhcchheeeehhhhcC--CChHHeeeeccCcceEEEEecccc
Confidence            44578999999999999883  2333   36888999999998874

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

Probab=93.90  E-value=0.71  Score=42.48  Aligned_cols=161  Identities=19%  Similarity=0.169  Sum_probs=82.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHH----HHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLM----QHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~----~~l~~~l~~~r~L   76 (505)
                      ++|.||||||.-+++  +...++    -+..+...+-..-+..++..+..++.--.++..+..    +.+.-.+.+-+.=
T Consensus        60 PPGlGKTTLA~IIA~--Emgvn~----k~tsGp~leK~gDlaaiLt~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lD  133 (332)
T COG2255          60 PPGLGKTTLAHIIAN--ELGVNL----KITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLD  133 (332)
T ss_pred             CCCCcHHHHHHHHHH--HhcCCe----EecccccccChhhHHHHHhcCCcCCeEEEehhhhcChhHHHHhhhhhhheeEE
Confidence            589999999999999  554443    223333333333344445545433322222222211    2223333333333


Q ss_pred             EEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCC--cceEeCCCCChhhHHHHHHHhhhCCCCCCCCch
Q 046115           77 LVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGS--THVISVNVLSEMECWSVFQSLAISGKTIGKREN  154 (505)
Q Consensus        77 lvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~--~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~  154 (505)
                      |++.-=....     .+.-.++   +-.-|=.|||--.+......  ..+..++-.+.+|-.++..+.+..-..    +-
T Consensus       134 I~IG~gp~Ar-----sv~ldLp---pFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i----~i  201 (332)
T COG2255         134 IIIGKGPAAR-----SIRLDLP---PFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI----EI  201 (332)
T ss_pred             EEEccCCccc-----eEeccCC---CeeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC----CC
Confidence            3333221111     0111222   22335568886544332211  225567778889998888887733222    22


Q ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHhcc
Q 046115          155 LEKIGREIVKKCKGLPLAAKTIASLLRS  182 (505)
Q Consensus       155 ~~~~~~~i~~~~~g~Plal~~~~~~l~~  182 (505)
                      .++.+.+|++...|-|-   ++.+.+++
T Consensus       202 ~~~~a~eIA~rSRGTPR---IAnRLLrR  226 (332)
T COG2255         202 DEEAALEIARRSRGTPR---IANRLLRR  226 (332)
T ss_pred             ChHHHHHHHHhccCCcH---HHHHHHHH
Confidence            34668899999999994   44444443

>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=93.82  E-value=0.088  Score=46.57  Aligned_cols=108  Identities=22%  Similarity=0.174  Sum_probs=49.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEe----CCCC-----CHHH----HHHHHHHHcCCCCCCChhcHHHHHHH--
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCV----SEPF-----DEFR----IARAIIESLTPGSAKDLVEFQSLMQH--   65 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~----~~~~-----~~~~----~~~~l~~~l~~~~~~~~~~~~~~~~~--   65 (505)
                      ++|.|||.||.+.+-+.-..++|+.++++.-    ++..     +..+    .+.-+...+..-.  .....+...+.  
T Consensus        27 ~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~--~~~~~~~~~~~~~  104 (205)
T PF02562_consen   27 PAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELF--GKEKLEELIQNGK  104 (205)
T ss_dssp             -TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS---TTCHHHHHHTTS
T ss_pred             CCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHh--ChHhHHHHhhcCe
Confidence            4799999999888764333578888887641    1111     1111    1112222222100  11112221110  


Q ss_pred             ----HHHHcCC---ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           66 ----IEECVAG---KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        66 ----l~~~l~~---~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                          -...+++   ...++|+|.+++-...++..++.   ..+.+|+++++--..
T Consensus       105 Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilT---R~g~~skii~~GD~~  156 (205)
T PF02562_consen  105 IEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILT---RIGEGSKIIITGDPS  156 (205)
T ss_dssp             EEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHT---TB-TT-EEEEEE---
T ss_pred             EEEEehhhhcCccccceEEEEecccCCCHHHHHHHHc---ccCCCcEEEEecCce
Confidence                0012334   35899999998876555555544   456889999987654

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

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

Probab=93.78  E-value=0.17  Score=48.81  Aligned_cols=74  Identities=20%  Similarity=0.287  Sum_probs=47.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHcCCceEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      +|+|||||..+++.  ..+.+. .+++|+-.++..-   .+--+.+++.+...    ...+++...+.+.+   .+.-++
T Consensus       102 PGIGKSTLLLQva~--~lA~~~-~vLYVsGEES~~Q---iklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~---~~p~lv  172 (456)
T COG1066         102 PGIGKSTLLLQVAA--RLAKRG-KVLYVSGEESLQQ---IKLRADRLGLPTNNLYLLAETNLEDIIAELEQ---EKPDLV  172 (456)
T ss_pred             CCCCHHHHHHHHHH--HHHhcC-cEEEEeCCcCHHH---HHHHHHHhCCCccceEEehhcCHHHHHHHHHh---cCCCEE
Confidence            79999999999998  666665 7888987765433   33334555533322    23444444444443   577899


Q ss_pred             EEeCCCC
Q 046115           78 VLDDVWN   84 (505)
Q Consensus        78 vlDdv~~   84 (505)
                      |+|.++.
T Consensus       173 VIDSIQT  179 (456)
T COG1066         173 VIDSIQT  179 (456)
T ss_pred             EEeccce
Confidence            9999855

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

Probab=93.76  E-value=0.18  Score=54.43  Aligned_cols=87  Identities=14%  Similarity=0.138  Sum_probs=46.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC-CChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA-KDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      ++|+|||.||+.++.  ..   +...+.++.++..+...    +-..++.+.. ......+.....++   .....+++|
T Consensus       492 p~GvGKT~lA~~la~--~l---~~~~~~~d~se~~~~~~----~~~lig~~~gyvg~~~~~~l~~~~~---~~p~~Vvll  559 (731)
T TIGR02639       492 PTGVGKTELAKQLAE--AL---GVHLERFDMSEYMEKHT----VSRLIGAPPGYVGFEQGGLLTEAVR---KHPHCVLLL  559 (731)
T ss_pred             CCCccHHHHHHHHHH--Hh---cCCeEEEeCchhhhccc----HHHHhcCCCCCcccchhhHHHHHHH---hCCCeEEEE
Confidence            479999999999998  44   23445666554322111    1111221111 11111122222222   234579999


Q ss_pred             eCCCCCCccChhHHHHhhcC
Q 046115           80 DDVWNEDYYKWEPFYKCLKN   99 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~   99 (505)
                      |+++......+..+.+.+..
T Consensus       560 DEieka~~~~~~~Ll~~ld~  579 (731)
T TIGR02639       560 DEIEKAHPDIYNILLQVMDY  579 (731)
T ss_pred             echhhcCHHHHHHHHHhhcc
Confidence            99977666566666665553

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.70  E-value=0.036  Score=50.84  Aligned_cols=88  Identities=24%  Similarity=0.298  Sum_probs=59.9

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCcccc-ccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIE-KLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~-~lp~~  432 (505)
                      .++.++.|+|.+|.++..++ +...+.+|+.|++|+|+-+..   ++.++.+|   -.+.+|++|-|.|+...+ ..-+.
T Consensus        69 ~~~~v~elDL~~N~iSdWse-I~~ile~lP~l~~LNls~N~L---~s~I~~lp---~p~~nl~~lVLNgT~L~w~~~~s~  141 (418)
T KOG2982|consen   69 SVTDVKELDLTGNLISDWSE-IGAILEQLPALTTLNLSCNSL---SSDIKSLP---LPLKNLRVLVLNGTGLSWTQSTSS  141 (418)
T ss_pred             HhhhhhhhhcccchhccHHH-HHHHHhcCccceEeeccCCcC---CCccccCc---ccccceEEEEEcCCCCChhhhhhh
Confidence            45788888999998887766 666688899999999881111   22344444   346688888888877432 44444


Q ss_pred             hhcCCCCcEEecCCCc
Q 046115          433 LCELYNLERLNVDDCQ  448 (505)
Q Consensus       433 ~~~l~~L~~L~l~~~~  448 (505)
                      +..++.++.|.++.|.
T Consensus       142 l~~lP~vtelHmS~N~  157 (418)
T KOG2982|consen  142 LDDLPKVTELHMSDNS  157 (418)
T ss_pred             hhcchhhhhhhhccch
Confidence            5677777777777764

>PRK05973 replicative DNA helicase; Provisional

Probab=93.66  E-value=0.39  Score=43.65  Aligned_cols=32  Identities=16%  Similarity=0.073  Sum_probs=23.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      .+|+|||++|.+++.  ....+-..+++++...+
T Consensus        72 ~PG~GKT~lalqfa~--~~a~~Ge~vlyfSlEes  103 (237)
T PRK05973         72 RPGHGKTLLGLELAV--EAMKSGRTGVFFTLEYT  103 (237)
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCeEEEEEEeCC
Confidence            379999999999987  44344456777877665

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

Probab=93.61  E-value=0.48  Score=48.14  Aligned_cols=154  Identities=14%  Similarity=0.164  Sum_probs=77.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||.||+++++  +..     +-|+.++.+        +|+..+.      ....+...+...+.-..-++++++|
T Consensus       231 PPGCGKT~lA~AiAg--el~-----vPf~~isAp--------eivSGvS------GESEkkiRelF~~A~~~aPcivFiD  289 (802)
T KOG0733|consen  231 PPGCGKTSLANAIAG--ELG-----VPFLSISAP--------EIVSGVS------GESEKKIRELFDQAKSNAPCIVFID  289 (802)
T ss_pred             CCCccHHHHHHHHhh--hcC-----CceEeecch--------hhhcccC------cccHHHHHHHHHHHhccCCeEEEee
Confidence            589999999999999  443     334544431        2232222      2223334444444556679999999


Q ss_pred             CCCCCC------cc-----ChhHHHHhhcCC------CCCcEEEE-EeCchHHHHH---hCC-cceEeCCCCChhhHHHH
Q 046115           81 DVWNED------YY-----KWEPFYKCLKNS------LHESKILI-TTRKETVARI---MGS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        81 dv~~~~------~~-----~~~~~~~~~~~~------~~~~~iLi-Ttr~~~~~~~---~~~-~~~~~l~~l~~~ea~~L  138 (505)
                      +++-..      +.     ...+++..+..-      +.+.-||- |+|-..+...   .+. .+.+.+..-+...-.++
T Consensus       290 eIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~I  369 (802)
T KOG0733|consen  290 EIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEI  369 (802)
T ss_pred             cccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHH
Confidence            984411      11     123444444322      12222333 4443333222   222 45677777777776677


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCC----ChHHHHHHHHHh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKG----LPLAAKTIASLL  180 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g----~Plal~~~~~~l  180 (505)
                      +....-+-+. ...-+    .++|++..-|    --.||...|+..
T Consensus       370 L~~~~~~lrl-~g~~d----~~qlA~lTPGfVGADL~AL~~~Aa~v  410 (802)
T KOG0733|consen  370 LRIICRGLRL-SGDFD----FKQLAKLTPGFVGADLMALCREAAFV  410 (802)
T ss_pred             HHHHHhhCCC-CCCcC----HHHHHhcCCCccchhHHHHHHHHHHH
Confidence            7655432222 12223    3345555544    335555555543

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.61  E-value=1.1  Score=46.03  Aligned_cols=144  Identities=13%  Similarity=0.140  Sum_probs=70.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||++|+.+++  +-..+|     +.+..        .+++..+.      ........+..++.-.--.++|.||
T Consensus       476 PPGC~KT~lAkalAn--e~~~nF-----lsvkg--------pEL~sk~v------GeSEr~ir~iF~kAR~~aP~IiFfD  534 (693)
T KOG0730|consen  476 PPGCGKTLLAKALAN--EAGMNF-----LSVKG--------PELFSKYV------GESERAIREVFRKARQVAPCIIFFD  534 (693)
T ss_pred             CCCcchHHHHHHHhh--hhcCCe-----eeccC--------HHHHHHhc------CchHHHHHHHHHHHhhcCCeEEehh
Confidence            589999999999999  555555     33322        12222222      1111112222222223345788888


Q ss_pred             CCCCCC-----------ccChhHHHHhhcCCCCCcEEEE---EeCchHHHHHh-C--C-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNED-----------YYKWEPFYKCLKNSLHESKILI---TTRKETVARIM-G--S-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~~-----------~~~~~~~~~~~~~~~~~~~iLi---Ttr~~~~~~~~-~--~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      .++.-.           .-.+.+++..+.-......|+|   |-|...+...+ .  . ..++-++.-+.+.-.++|+.+
T Consensus       535 EiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~  614 (693)
T KOG0730|consen  535 EIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQC  614 (693)
T ss_pred             hHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHH
Confidence            773311           0112233333332222223333   33333333322 2  2 456777777888888899888


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      +..-.. .+..+    ..+|++..+|+.
T Consensus       615 ~kkmp~-~~~vd----l~~La~~T~g~S  637 (693)
T KOG0730|consen  615 AKKMPF-SEDVD----LEELAQATEGYS  637 (693)
T ss_pred             HhcCCC-Ccccc----HHHHHHHhccCC
Confidence            743332 22233    345555555544

>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=93.60  E-value=0.031  Score=48.21  Aligned_cols=34  Identities=24%  Similarity=0.124  Sum_probs=26.4

Q ss_pred             CCCCcHHHHHHHHhcCcccc-cCCCceEEEEeCCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-RNFEKRTWVCVSEPFD   36 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-~~f~~~~wv~~~~~~~   36 (505)
                      +.|+|||.+|+.++.  ... +.....+-++++...+
T Consensus        11 psGvGKT~la~~la~--~l~~~~~~~~~~~d~s~~~~   45 (171)
T PF07724_consen   11 PSGVGKTELAKALAE--LLFVGSERPLIRIDMSEYSE   45 (171)
T ss_dssp             STTSSHHHHHHHHHH--HHT-SSCCEEEEEEGGGHCS
T ss_pred             CCCCCHHHHHHHHHH--HhccCCccchHHHhhhcccc
Confidence            479999999999998  665 5666777788776444

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 ....

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=93.54  E-value=0.21  Score=48.06  Aligned_cols=48  Identities=23%  Similarity=0.222  Sum_probs=31.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccC----CCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN----FEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~----f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||++|.+++........    =..++||+....++...+. ++++.++
T Consensus       110 ~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g  161 (317)
T PRK04301        110 EFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALG  161 (317)
T ss_pred             CCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcC
Confidence            4799999999998863222111    1368899998887776554 4445544

>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=93.45  E-value=0.032  Score=46.40  Aligned_cols=35  Identities=26%  Similarity=0.143  Sum_probs=23.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCc-eEEEEeCCCCCHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEK-RTWVCVSEPFDEFRIA   41 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~-~~wv~~~~~~~~~~~~   41 (505)
                      .+|+|||+||+.+++  ..    .. ..-+.+....+..++.
T Consensus         7 ~~G~GKt~l~~~la~--~~----~~~~~~i~~~~~~~~~dl~   42 (139)
T PF07728_consen    7 PPGTGKTTLARELAA--LL----GRPVIRINCSSDTTEEDLI   42 (139)
T ss_dssp             SSSSSHHHHHHHHHH--HH----TCEEEEEE-TTTSTHHHHH
T ss_pred             CCCCCHHHHHHHHHH--Hh----hcceEEEEeccccccccce
Confidence            479999999999998  44    22 2235666666665444

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.40  E-value=0.24  Score=47.51  Aligned_cols=48  Identities=21%  Similarity=0.177  Sum_probs=31.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccC----CCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN----FEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~----f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||++|.+++........    =..++||+....++...+. +++..++
T Consensus       103 ~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~g  154 (310)
T TIGR02236       103 EFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARG  154 (310)
T ss_pred             CCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcC
Confidence            3799999999998763222111    1268899998888776544 4455544

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D

Probab=93.40  E-value=0.052  Score=26.75  Aligned_cols=11  Identities=27%  Similarity=0.558  Sum_probs=4.1

Q ss_pred             CCcEEecCCCc
Q 046115          438 NLERLNVDDCQ  448 (505)
Q Consensus       438 ~L~~L~l~~~~  448 (505)
                      +|+.|+|++|+
T Consensus         2 ~L~~L~l~~n~   12 (17)
T PF13504_consen    2 NLRTLDLSNNR   12 (17)
T ss_dssp             T-SEEEETSS-
T ss_pred             ccCEEECCCCC
Confidence            34444444444

...

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=93.33  E-value=0.26  Score=47.06  Aligned_cols=48  Identities=25%  Similarity=0.228  Sum_probs=32.3

Q ss_pred             CCCCcHHHHHHHHhcCccccc----CCCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER----NFEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~----~f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||.+++-..+...    .=..++||+....+..+.+. ++++.++
T Consensus       104 ~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g  155 (313)
T TIGR02238       104 EFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFG  155 (313)
T ss_pred             CCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcC
Confidence            479999999988764222221    12367899998888776654 4566665

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.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.26  E-value=0.81  Score=42.83  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=39.3

Q ss_pred             CCCCcHHHHHHHHhcCc--ccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCce--EE
Q 046115            1 MGGIGKTTLAQFAYNNG--DVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKK--FL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~--~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r--~L   76 (505)
                      ++|.|||+|+++++..-  +...+|....-+.++.        ..+..++...+.   .-.....+.+.+.+.++.  +.
T Consensus       185 PPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins--------hsLFSKWFsESg---KlV~kmF~kI~ELv~d~~~lVf  253 (423)
T KOG0744|consen  185 PPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS--------HSLFSKWFSESG---KLVAKMFQKIQELVEDRGNLVF  253 (423)
T ss_pred             CCCCChhHHHHHHHHhheeeecCccccceEEEEeh--------hHHHHHHHhhhh---hHHHHHHHHHHHHHhCCCcEEE
Confidence            68999999999999863  2335565555555443        223333321111   122334455555555543  45


Q ss_pred             EEEeCC
Q 046115           77 LVLDDV   82 (505)
Q Consensus        77 lvlDdv   82 (505)
                      +.+|.|
T Consensus       254 vLIDEV  259 (423)
T KOG0744|consen  254 VLIDEV  259 (423)
T ss_pred             EEeHHH
Confidence            557887

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

Probab=93.25  E-value=1.4  Score=45.74  Aligned_cols=77  Identities=13%  Similarity=0.129  Sum_probs=50.0

Q ss_pred             CCCcHHHHHHHHhcCcc---cc---cCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-----
Q 046115            2 GGIGKTTLAQFAYNNGD---VE---RNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-----   70 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~---~~---~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-----   70 (505)
                      +|+|||+....|.+.-+   .+   ..|+ -+.|+...-....++...|+.++......    +....+.|..+.     
T Consensus       431 PGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l~~~~~~Y~~I~~~lsg~~~~----~~~al~~L~~~f~~~k~  505 (767)
T KOG1514|consen  431 PGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRLASPREIYEKIWEALSGERVT----WDAALEALNFRFTVPKP  505 (767)
T ss_pred             CCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceeecCHHHHHHHHHHhcccCccc----HHHHHHHHHHhhccCCC
Confidence            69999999999987311   11   2233 33566666677899999999999733333    333344444444     


Q ss_pred             CCceEEEEEeCCC
Q 046115           71 AGKKFLLVLDDVW   83 (505)
Q Consensus        71 ~~~r~LlvlDdv~   83 (505)
                      +.+.+++++|+++
T Consensus       506 ~~~~~VvLiDElD  518 (767)
T KOG1514|consen  506 KRSTTVVLIDELD  518 (767)
T ss_pred             CCCCEEEEeccHH
Confidence            2357899999873

>TIGR00763 lon ATP-dependent protease La

Probab=93.09  E-value=0.42  Score=52.02  Aligned_cols=130  Identities=17%  Similarity=0.175  Sum_probs=62.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  .....|   +-++++...+..+    +...   ...-.....+...+.+.... ..+-+|+||
T Consensus       355 ppG~GKT~lAk~iA~--~l~~~~---~~i~~~~~~~~~~----i~g~---~~~~~g~~~g~i~~~l~~~~-~~~~villD  421 (775)
T TIGR00763       355 PPGVGKTSLGKSIAK--ALNRKF---VRFSLGGVRDEAE----IRGH---RRTYVGAMPGRIIQGLKKAK-TKNPLFLLD  421 (775)
T ss_pred             CCCCCHHHHHHHHHH--HhcCCe---EEEeCCCcccHHH----HcCC---CCceeCCCCchHHHHHHHhC-cCCCEEEEe
Confidence            479999999999998  554443   2223333222211    1110   00000111122233333332 333478999


Q ss_pred             CCCCCCcc----ChhHHHHhhcC--------C------C-CCcEEEEEeCchH-HHH-HhCCcceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDYY----KWEPFYKCLKN--------S------L-HESKILITTRKET-VAR-IMGSTHVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~~----~~~~~~~~~~~--------~------~-~~~~iLiTtr~~~-~~~-~~~~~~~~~l~~l~~~ea~~Lf  139 (505)
                      .++.....    ....+...+.+        .      + .+.-+|.||.... +.. ......++++.+++.++-.+++
T Consensus       422 Eidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~R~~vi~~~~~~~~e~~~I~  501 (775)
T TIGR00763       422 EIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPLLDRMEVIELSGYTEEEKLEIA  501 (775)
T ss_pred             chhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHHHhCCeeEEecCCCCHHHHHHHH
Confidence            98553211    11223332221        0      0 2333444554432 111 1234568899999998888887


Q ss_pred             HHhh
Q 046115          140 QSLA  143 (505)
Q Consensus       140 ~~~~  143 (505)
                      ..+.
T Consensus       502 ~~~l  505 (775)
T TIGR00763       502 KKYL  505 (775)
T ss_pred             HHHH
Confidence            6643

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.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=93.07  E-value=0.6  Score=40.30  Aligned_cols=53  Identities=13%  Similarity=0.183  Sum_probs=31.6

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +.+.+..++-++++|.-... +......+...+.....+..||++|.+......
T Consensus       107 la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~  160 (171)
T cd03228         107 IARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTIRD  160 (171)
T ss_pred             HHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHHHh
Confidence            55556667789999997542 222233344444333235678888888766543

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.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.05  E-value=0.21  Score=48.19  Aligned_cols=48  Identities=23%  Similarity=0.169  Sum_probs=32.7

Q ss_pred             CCCCcHHHHHHHHhcCccccc---C-CCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER---N-FEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~---~-f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+|+.+++-..+...   . -..++||+....+...++.+ +++.++
T Consensus       134 ~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g  185 (344)
T PLN03187        134 EFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFG  185 (344)
T ss_pred             CCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcC
Confidence            379999999988864322221   1 24678999999888766544 566665

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=93.00  E-value=0.005  Score=54.20  Aligned_cols=88  Identities=17%  Similarity=0.188  Sum_probs=63.6

Q ss_pred             hhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhcc
Q 046115          379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIG  458 (505)
Q Consensus       379 ~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~  458 (505)
                      +-.+...++||++       .+..-.+...++.++.|..|+++.|. +..+|..++++..+..+++..|. ....|.+.+
T Consensus        38 i~~~kr~tvld~~-------s~r~vn~~~n~s~~t~~~rl~~sknq-~~~~~~d~~q~~e~~~~~~~~n~-~~~~p~s~~  108 (326)
T KOG0473|consen   38 IASFKRVTVLDLS-------SNRLVNLGKNFSILTRLVRLDLSKNQ-IKFLPKDAKQQRETVNAASHKNN-HSQQPKSQK  108 (326)
T ss_pred             hhccceeeeehhh-------hhHHHhhccchHHHHHHHHHhccHhh-HhhChhhHHHHHHHHHHHhhccc-hhhCCcccc
Confidence            5566777777777       55555666667777777777887777 77777777777777777776665 777777777


Q ss_pred             ccccCceeecCCCcccc
Q 046115          459 KLRKLMYLHNEDTGCLR  475 (505)
Q Consensus       459 ~l~~L~~L~l~~~~~~~  475 (505)
                      +++.+++++..+|.+..
T Consensus       109 k~~~~k~~e~k~~~~~~  125 (326)
T KOG0473|consen  109 KEPHPKKNEQKKTEFFR  125 (326)
T ss_pred             ccCCcchhhhccCcchH
Confidence            77878777777776443

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=92.92  E-value=1.3  Score=46.79  Aligned_cols=145  Identities=12%  Similarity=0.113  Sum_probs=80.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||-||++++..  .     ++-|++++.+        +.++.+.      ........+.....-.+.+++|.+|
T Consensus       352 PPGTGKTLLAKAiAGE--A-----gVPF~svSGS--------EFvE~~~------g~~asrvr~lf~~ar~~aP~iifid  410 (774)
T KOG0731|consen  352 PPGTGKTLLAKAIAGE--A-----GVPFFSVSGS--------EFVEMFV------GVGASRVRDLFPLARKNAPSIIFID  410 (774)
T ss_pred             CCCCcHHHHHHHHhcc--c-----CCceeeechH--------HHHHHhc------ccchHHHHHHHHHhhccCCeEEEec
Confidence            5899999999999983  2     3445666542        2223232      0111122222222334567888888


Q ss_pred             CCCCC---------------CccChhHHHHhhcCCCC--CcEEEEEeCchHHHHHh----CC-cceEeCCCCChhhHHHH
Q 046115           81 DVWNE---------------DYYKWEPFYKCLKNSLH--ESKILITTRKETVARIM----GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        81 dv~~~---------------~~~~~~~~~~~~~~~~~--~~~iLiTtr~~~~~~~~----~~-~~~~~l~~l~~~ea~~L  138 (505)
                      .++..               ....+.+++..+..+..  +.-+|-+|+.+++....    +. .+.+.++.-+...-.++
T Consensus       411 eida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i  490 (774)
T KOG0731|consen  411 EIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASI  490 (774)
T ss_pred             ccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHH
Confidence            87331               11223445555554433  33344566665553321    22 45677777788888899


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |..++-.-..   ..+..++.+ ++...-|++
T Consensus       491 ~~~h~~~~~~---~~e~~dl~~-~a~~t~gf~  518 (774)
T KOG0731|consen  491 LKVHLRKKKL---DDEDVDLSK-LASLTPGFS  518 (774)
T ss_pred             HHHHhhccCC---CcchhhHHH-HHhcCCCCc
Confidence            9888743332   223344455 888888877

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=92.90  E-value=0.15  Score=43.97  Aligned_cols=40  Identities=18%  Similarity=0.284  Sum_probs=23.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIES   47 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~   47 (505)
                      +|+|||++|..++.  ....   .++++.-.... ..+....+...
T Consensus        10 ~~sGKS~~a~~l~~--~~~~---~~~~iat~~~~-~~e~~~ri~~h   49 (170)
T PRK05800         10 ARSGKSRFAERLAA--QSGL---QVLYIATAQPF-DDEMAARIAHH   49 (170)
T ss_pred             CCccHHHHHHHHHH--HcCC---CcEeCcCCCCC-hHHHHHHHHHH
Confidence            69999999999987  3211   23444444333 33555555443

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=92.86  E-value=0.63  Score=40.62  Aligned_cols=21  Identities=29%  Similarity=0.406  Sum_probs=16.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF   23 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f   23 (505)
                      .+|+||||+|++++.  ..+++-
T Consensus         9 yPgsGKTtfakeLak--~L~~~i   29 (261)
T COG4088           9 YPGSGKTTFAKELAK--ELRQEI   29 (261)
T ss_pred             CCCCCchHHHHHHHH--HHHHhh
Confidence            489999999999987  554443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.73  E-value=0.65  Score=50.33  Aligned_cols=144  Identities=13%  Similarity=0.106  Sum_probs=69.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||+.+++  +....|   +.++...          +.....      ..........+.......+.+|++|
T Consensus       220 ppGtGKT~laraia~--~~~~~~---i~i~~~~----------i~~~~~------g~~~~~l~~lf~~a~~~~p~il~iD  278 (733)
T TIGR01243       220 PPGTGKTLLAKAVAN--EAGAYF---ISINGPE----------IMSKYY------GESEERLREIFKEAEENAPSIIFID  278 (733)
T ss_pred             CCCCChHHHHHHHHH--HhCCeE---EEEecHH----------Hhcccc------cHHHHHHHHHHHHHHhcCCcEEEee
Confidence            479999999999998  443322   2232111          111110      0111122223333334567899999


Q ss_pred             CCCCCCc-----------cChhHHHHhhcCC-CCCcEEEE-EeCchH-HHHHhC---C-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNEDY-----------YKWEPFYKCLKNS-LHESKILI-TTRKET-VARIMG---S-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~~~-----------~~~~~~~~~~~~~-~~~~~iLi-Ttr~~~-~~~~~~---~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      +++....           .....+...+... ..+..++| ||.... +.....   . ...+.+...+.++-.+++...
T Consensus       279 Eid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~  358 (733)
T TIGR01243       279 EIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVH  358 (733)
T ss_pred             hhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHH
Confidence            9844210           0122333333322 22333444 554432 222111   1 346777888888888888755


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      .-. ......    .....+++.+.|+.
T Consensus       359 ~~~-~~l~~d----~~l~~la~~t~G~~  381 (733)
T TIGR01243       359 TRN-MPLAED----VDLDKLAEVTHGFV  381 (733)
T ss_pred             hcC-CCCccc----cCHHHHHHhCCCCC
Confidence            421 111111    22556777887765

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.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=92.66  E-value=0.39  Score=41.11  Aligned_cols=109  Identities=16%  Similarity=0.109  Sum_probs=56.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC--CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF--DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~--~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      ..|+|||||.+.++..  . .-..+.++++.....  +.....   ...+.  .....+.-+...-.+.+.+...+-+++
T Consensus        34 ~nGsGKSTLl~~i~G~--~-~~~~G~v~~~g~~~~~~~~~~~~---~~~i~--~~~qLS~G~~qrl~laral~~~p~ill  105 (163)
T cd03216          34 ENGAGKSTLMKILSGL--Y-KPDSGEILVDGKEVSFASPRDAR---RAGIA--MVYQLSVGERQMVEIARALARNARLLI  105 (163)
T ss_pred             CCCCCHHHHHHHHhCC--C-CCCCeEEEECCEECCcCCHHHHH---hcCeE--EEEecCHHHHHHHHHHHHHhcCCCEEE
Confidence            3699999999999873  2 234555655422211  111111   11111  001122333334445566666778888


Q ss_pred             EeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHH
Q 046115           79 LDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVAR  117 (505)
Q Consensus        79 lDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~  117 (505)
                      +|+.... +......+...+... ..+..||++|.+.....
T Consensus       106 lDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~  146 (163)
T cd03216         106 LDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEVF  146 (163)
T ss_pred             EECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            9997442 222333444444332 23667888888876443

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.

>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=92.65  E-value=0.93  Score=37.83  Aligned_cols=96  Identities=17%  Similarity=0.170  Sum_probs=51.9

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|.|||||++.++..  . .-..+.+|++...             .+.  -....+.-+...-.+.+.+..++-++++|+
T Consensus        35 nGsGKStLl~~l~G~--~-~~~~G~i~~~~~~-------------~i~--~~~~lS~G~~~rv~laral~~~p~illlDE   96 (144)
T cd03221          35 NGAGKSTLLKLIAGE--L-EPDEGIVTWGSTV-------------KIG--YFEQLSGGEKMRLALAKLLLENPNLLLLDE   96 (144)
T ss_pred             CCCCHHHHHHHHcCC--C-CCCceEEEECCeE-------------EEE--EEccCCHHHHHHHHHHHHHhcCCCEEEEeC
Confidence            699999999999873  2 2234555553210             000  000022222333345556666777899999


Q ss_pred             CCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHH
Q 046115           82 VWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVAR  117 (505)
Q Consensus        82 v~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~  117 (505)
                      .... +......+...+...  +..||++|.+.....
T Consensus        97 P~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~  131 (144)
T cd03221          97 PTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLD  131 (144)
T ss_pred             CccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHH
Confidence            7442 222334444444433  346888888766554

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.

>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=92.64  E-value=0.068  Score=43.09  Aligned_cols=15  Identities=40%  Similarity=0.359  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.+++
T Consensus         7 ~~gsGKST~a~~La~   21 (121)
T PF13207_consen    7 PPGSGKSTLAKELAE   21 (121)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999998

...

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.62  E-value=0.2  Score=49.06  Aligned_cols=74  Identities=20%  Similarity=0.235  Sum_probs=40.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHcCCceEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      +|+|||||+.+++.  .....-..++|++..+..+   ....-+..++.....    ...+.++..+.+.   ..+.-++
T Consensus        91 pG~GKStLllq~a~--~~a~~g~~VlYvs~EEs~~---qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~---~~~~~lV  162 (372)
T cd01121          91 PGIGKSTLLLQVAA--RLAKRGGKVLYVSGEESPE---QIKLRADRLGISTENLYLLAETNLEDILASIE---ELKPDLV  162 (372)
T ss_pred             CCCCHHHHHHHHHH--HHHhcCCeEEEEECCcCHH---HHHHHHHHcCCCcccEEEEccCcHHHHHHHHH---hcCCcEE
Confidence            79999999999987  4444445677887655422   222223445422211    1123333333332   2245578


Q ss_pred             EEeCCC
Q 046115           78 VLDDVW   83 (505)
Q Consensus        78 vlDdv~   83 (505)
                      |+|.+.
T Consensus       163 VIDSIq  168 (372)
T cd01121         163 IIDSIQ  168 (372)
T ss_pred             EEcchH
Confidence            888873

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.

>PRK04328 hypothetical protein; Provisional

Probab=92.56  E-value=0.39  Score=44.36  Aligned_cols=33  Identities=21%  Similarity=0.101  Sum_probs=24.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF   35 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~   35 (505)
                      .+|+|||+||.+++.  +..++-..++|++..+.+
T Consensus        31 ~pGsGKT~l~~~fl~--~~~~~ge~~lyis~ee~~   63 (249)
T PRK04328         31 GPGTGKSIFSQQFLW--NGLQMGEPGVYVALEEHP   63 (249)
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCcEEEEEeeCCH
Confidence            379999999998876  333444677889877644

>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=92.54  E-value=1.4  Score=37.83  Aligned_cols=110  Identities=14%  Similarity=0.022  Sum_probs=53.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEE-------eCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCc
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVC-------VSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGK   73 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~-------~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~   73 (505)
                      ..|.|||||++.++..  ... ..+.++++       +.+......  ..+.+.+........+.-++..-.+.+.+..+
T Consensus        35 ~nGsGKSTLl~~l~G~--~~~-~~G~i~~~~~~~i~~~~q~~~~~~--~tv~~nl~~~~~~~LS~G~~~rv~laral~~~  109 (166)
T cd03223          35 PSGTGKSSLFRALAGL--WPW-GSGRIGMPEGEDLLFLPQRPYLPL--GTLREQLIYPWDDVLSGGEQQRLAFARLLLHK  109 (166)
T ss_pred             CCCCCHHHHHHHHhcC--CCC-CCceEEECCCceEEEECCCCcccc--ccHHHHhhccCCCCCCHHHHHHHHHHHHHHcC
Confidence            3699999999999874  211 12222221       112111110  01222221111222333334444456666667


Q ss_pred             eEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHH
Q 046115           74 KFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVAR  117 (505)
Q Consensus        74 r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~  117 (505)
                      +-++++|.-... +......+...+...  +..||++|.+.....
T Consensus       110 p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~~  152 (166)
T cd03223         110 PKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLWK  152 (166)
T ss_pred             CCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHHh
Confidence            778889986442 222233344434333  356888888766543

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

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

Probab=92.54  E-value=0.43  Score=51.66  Aligned_cols=130  Identities=17%  Similarity=0.158  Sum_probs=64.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.++.  .....|   +-++++...+..++...-....+       ...+...+.+... ...+-+|+||
T Consensus       357 ppG~GKTtl~~~ia~--~l~~~~---~~i~~~~~~d~~~i~g~~~~~~g-------~~~G~~~~~l~~~-~~~~~villD  423 (784)
T PRK10787        357 PPGVGKTSLGQSIAK--ATGRKY---VRMALGGVRDEAEIRGHRRTYIG-------SMPGKLIQKMAKV-GVKNPLFLLD  423 (784)
T ss_pred             CCCCCHHHHHHHHHH--HhCCCE---EEEEcCCCCCHHHhccchhccCC-------CCCcHHHHHHHhc-CCCCCEEEEE
Confidence            489999999999997  444433   22334443333211111000011       1112223333322 2234578899


Q ss_pred             CCCCCCccC----hhHHHHhhcCC--------------C-CCcEEEEEeCchHHHHH-hCCcceEeCCCCChhhHHHHHH
Q 046115           81 DVWNEDYYK----WEPFYKCLKNS--------------L-HESKILITTRKETVARI-MGSTHVISVNVLSEMECWSVFQ  140 (505)
Q Consensus        81 dv~~~~~~~----~~~~~~~~~~~--------------~-~~~~iLiTtr~~~~~~~-~~~~~~~~l~~l~~~ea~~Lf~  140 (505)
                      .++......    ...+...+.+.              + ...-+|.|+....+... .+...++++.+++.+|-.++..
T Consensus       424 Eidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~  503 (784)
T PRK10787        424 EIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAK  503 (784)
T ss_pred             ChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHH
Confidence            985533211    24444443321              1 23334445544332221 2345688899999999888877


Q ss_pred             Hhh
Q 046115          141 SLA  143 (505)
Q Consensus       141 ~~~  143 (505)
                      .+.
T Consensus       504 ~~L  506 (784)
T PRK10787        504 RHL  506 (784)
T ss_pred             Hhh
Confidence            654

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=92.45  E-value=0.42  Score=46.20  Aligned_cols=48  Identities=19%  Similarity=0.124  Sum_probs=32.2

Q ss_pred             CCCCcHHHHHHHHhcCccccc---CC-CceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER---NF-EKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~---~f-~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||..++-......   .- ..++||+....+..+++ .++++.++
T Consensus       131 ~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~  182 (342)
T PLN03186        131 EFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFG  182 (342)
T ss_pred             CCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcC
Confidence            379999999988874222211   11 25889999998887655 45566654

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

Probab=92.39  E-value=0.62  Score=48.36  Aligned_cols=129  Identities=17%  Similarity=0.168  Sum_probs=71.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC-ChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK-DLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      ++|+|||.|++.+++  ...+.|   +-+.++.-.|..++        ...... -..-.+..++.+.+ .+.++-+++|
T Consensus       358 PPGVGKTSLgkSIA~--al~Rkf---vR~sLGGvrDEAEI--------RGHRRTYIGamPGrIiQ~mkk-a~~~NPv~LL  423 (782)
T COG0466         358 PPGVGKTSLGKSIAK--ALGRKF---VRISLGGVRDEAEI--------RGHRRTYIGAMPGKIIQGMKK-AGVKNPVFLL  423 (782)
T ss_pred             CCCCCchhHHHHHHH--HhCCCE---EEEecCccccHHHh--------ccccccccccCChHHHHHHHH-hCCcCCeEEe
Confidence            689999999999998  666666   33445554443221        101000 11112233333332 2456778999


Q ss_pred             eCCCCCCc----------------cChhHHHHhhcC--CCCCcEEEEEeCch-H-H-HHHhCCcceEeCCCCChhhHHHH
Q 046115           80 DDVWNEDY----------------YKWEPFYKCLKN--SLHESKILITTRKE-T-V-ARIMGSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~~----------------~~~~~~~~~~~~--~~~~~~iLiTtr~~-~-~-~~~~~~~~~~~l~~l~~~ea~~L  138 (505)
                      |.++....                .+-..|.+.+.+  .+-.-.+.|+|-+. + + .+..+...++++.+-+.+|-.++
T Consensus       424 DEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~I  503 (782)
T COG0466         424 DEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEI  503 (782)
T ss_pred             echhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeecCCChHHHHHH
Confidence            99844211                122233333332  12333466666652 2 2 33345667999999999998877


Q ss_pred             HHHhh
Q 046115          139 FQSLA  143 (505)
Q Consensus       139 f~~~~  143 (505)
                      -.++.
T Consensus       504 Ak~~L  508 (782)
T COG0466         504 AKRHL  508 (782)
T ss_pred             HHHhc
Confidence            77665

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=92.22  E-value=0.97  Score=46.95  Aligned_cols=131  Identities=17%  Similarity=0.137  Sum_probs=69.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||.+|+.+++  ...+.|   +-++++.-.|..++-       +.-..--..-.+..++.|.+. +..+-|+.+|
T Consensus       446 PPGVGKTSI~kSIA~--ALnRkF---fRfSvGG~tDvAeIk-------GHRRTYVGAMPGkiIq~LK~v-~t~NPliLiD  512 (906)
T KOG2004|consen  446 PPGVGKTSIAKSIAR--ALNRKF---FRFSVGGMTDVAEIK-------GHRRTYVGAMPGKIIQCLKKV-KTENPLILID  512 (906)
T ss_pred             CCCCCcccHHHHHHH--HhCCce---EEEeccccccHHhhc-------ccceeeeccCChHHHHHHHhh-CCCCceEEee
Confidence            589999999999998  666665   223455544432211       000001112223344444333 3456688888


Q ss_pred             CCCCC----------------CccChhHHHHhhcC--CCCCcEEEEEeCch-H--HHHHhCCcceEeCCCCChhhHHHHH
Q 046115           81 DVWNE----------------DYYKWEPFYKCLKN--SLHESKILITTRKE-T--VARIMGSTHVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~----------------~~~~~~~~~~~~~~--~~~~~~iLiTtr~~-~--~~~~~~~~~~~~l~~l~~~ea~~Lf  139 (505)
                      .|+.-                +..+-..|.+.+.+  .+-.....|.|-+. +  .....+...++++.+...+|-+.+-
T Consensus       513 EvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA  592 (906)
T KOG2004|consen  513 EVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIA  592 (906)
T ss_pred             hhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheEEEEeccccccCChhhhhhhheeeccCccHHHHHHHH
Confidence            88331                11223334444443  12222344555542 1  1222345568999999999977777


Q ss_pred             HHhhh
Q 046115          140 QSLAI  144 (505)
Q Consensus       140 ~~~~~  144 (505)
                      .++..
T Consensus       593 ~~yLi  597 (906)
T KOG2004|consen  593 ERYLI  597 (906)
T ss_pred             HHhhh
Confidence            66553

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=92.21  E-value=0.92  Score=39.18  Aligned_cols=82  Identities=17%  Similarity=0.089  Sum_probs=39.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHHHHcCCCC--CCChhcHHHHH-HHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAIIESLTPGS--AKDLVEFQSLM-QHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~~~l~~~~--~~~~~~~~~~~-~~l~~~l~~~r~L   76 (505)
                      ++|+||||+++.++.  .....=..++.++.... ....+.+.....+.+.+.  .....+..+.. +.+........-+
T Consensus         8 ~~G~GKTt~~~~la~--~~~~~g~~v~~i~~D~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~   85 (173)
T cd03115           8 LQGVGKTTTAAKLAL--YLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHAREENFDV   85 (173)
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCcEEEEEcCCCChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHHHhCCCCE
Confidence            589999999999987  44333123344443322 122333444444443211  11222333332 3333334444445


Q ss_pred             EEEeCCCC
Q 046115           77 LVLDDVWN   84 (505)
Q Consensus        77 lvlDdv~~   84 (505)
                      +|+|-...
T Consensus        86 viiDt~g~   93 (173)
T cd03115          86 VIVDTAGR   93 (173)
T ss_pred             EEEECccc
Confidence            66888744

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.

>PRK08233 hypothetical protein; Provisional

Probab=92.14  E-value=0.4  Score=41.74  Aligned_cols=15  Identities=40%  Similarity=0.448  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||||..++.
T Consensus        11 ~~GsGKtTla~~L~~   25 (182)
T PRK08233         11 VSGGGKTTLTERLTH   25 (182)
T ss_pred             CCCCCHHHHHHHHHh
Confidence            479999999999987

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=92.07  E-value=0.0056  Score=53.90  Aligned_cols=87  Identities=16%  Similarity=0.163  Sum_probs=72.0

Q ss_pred             CCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccc
Q 046115          351 NVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP  430 (505)
Q Consensus       351 ~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp  430 (505)
                      ++......+.|+++.|.+..    +...++.++-|.-|+++       .+.+..+|..++.+..+..+++.+|. ....|
T Consensus        37 ei~~~kr~tvld~~s~r~vn----~~~n~s~~t~~~rl~~s-------knq~~~~~~d~~q~~e~~~~~~~~n~-~~~~p  104 (326)
T KOG0473|consen   37 EIASFKRVTVLDLSSNRLVN----LGKNFSILTRLVRLDLS-------KNQIKFLPKDAKQQRETVNAASHKNN-HSQQP  104 (326)
T ss_pred             hhhccceeeeehhhhhHHHh----hccchHHHHHHHHHhcc-------HhhHhhChhhHHHHHHHHHHHhhccc-hhhCC
Confidence            34467888899999887654    44446667778888888       88899999999999999999999888 89999


Q ss_pred             hhhhcCCCCcEEecCCCcC
Q 046115          431 ETLCELYNLERLNVDDCQN  449 (505)
Q Consensus       431 ~~~~~l~~L~~L~l~~~~~  449 (505)
                      .++++++.++.+++.+|..
T Consensus       105 ~s~~k~~~~k~~e~k~~~~  123 (326)
T KOG0473|consen  105 KSQKKEPHPKKNEQKKTEF  123 (326)
T ss_pred             ccccccCCcchhhhccCcc
Confidence            9999999999999999774

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=91.98  E-value=0.063  Score=47.45  Aligned_cols=34  Identities=26%  Similarity=0.297  Sum_probs=20.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC--------CceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF--------EKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f--------~~~~wv~~~~~   34 (505)
                      .+|+|||+++..++........|        ..++|++...+
T Consensus        40 ~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   40 PPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             CSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             CCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            47999999998887632111122        36778887766

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=91.89  E-value=1  Score=41.04  Aligned_cols=40  Identities=15%  Similarity=0.079  Sum_probs=24.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAI   44 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l   44 (505)
                      .+|+||||+|.+++.  ...++=..+++++...  +..++.+.+
T Consensus        32 ~~G~GKTtl~~~~~~--~~~~~g~~~~yi~~e~--~~~~~~~~~   71 (230)
T PRK08533         32 DESTGKSILSQRLAY--GFLQNGYSVSYVSTQL--TTTEFIKQM   71 (230)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCcEEEEeCCC--CHHHHHHHH
Confidence            379999999977766  2322224566777444  334445544

>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=91.79  E-value=0.87  Score=39.38  Aligned_cols=55  Identities=11%  Similarity=0.131  Sum_probs=30.8

Q ss_pred             HHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHH
Q 046115           63 MQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVAR  117 (505)
Q Consensus        63 ~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~  117 (505)
                      .-.+.+.+..++-++++|+.... +......+...+... ..|..||++|.+.....
T Consensus       104 rv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~  160 (173)
T cd03246         104 RLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPETLA  160 (173)
T ss_pred             HHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            33455556666678899997442 222223333333321 23667888888876554

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

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=91.75  E-value=1.4  Score=38.24  Aligned_cols=107  Identities=14%  Similarity=0.152  Sum_probs=54.0

Q ss_pred             CCCCcHHHHHHHHhcC-ccc--ccC---C--CceEEEEeCCCCCHHHHHHHHHHHcCCCCC------CChhcHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNN-GDV--ERN---F--EKRTWVCVSEPFDEFRIARAIIESLTPGSA------KDLVEFQSLMQHI   66 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~-~~~--~~~---f--~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~------~~~~~~~~~~~~l   66 (505)
                      ..|+|||||.+.+..+ .++  ..+   |  ..+.|+.  +        .+.+..++....      ...+.-+...-.+
T Consensus        29 ~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~~--q--------~~~l~~~~L~~~~~~~~~~~LSgGq~qrl~l   98 (176)
T cd03238          29 VSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFID--Q--------LQFLIDVGLGYLTLGQKLSTLSGGELQRVKL   98 (176)
T ss_pred             CCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEEh--H--------HHHHHHcCCCccccCCCcCcCCHHHHHHHHH
Confidence            4799999999988632 111  111   1  0122321  1        345565553221      1112222333345


Q ss_pred             HHHcCCc--eEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHH
Q 046115           67 EECVAGK--KFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVAR  117 (505)
Q Consensus        67 ~~~l~~~--r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~  117 (505)
                      .+.+..+  +-++++|..... +......+...+... ..|..||++|.+.....
T Consensus        99 aral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~  153 (176)
T cd03238          99 ASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLS  153 (176)
T ss_pred             HHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            5555556  678888987442 222333344433332 24667888888876654

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=91.74  E-value=2.4  Score=38.92  Aligned_cols=120  Identities=10%  Similarity=0.108  Sum_probs=70.5

Q ss_pred             EEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc--hHHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCc
Q 046115           76 LLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK--ETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRE  153 (505)
Q Consensus        76 LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~--~~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~  153 (505)
                      ++|+-.++.-..+.-+.+..-+..-...|++|+.-.+  +.+...-...-.+.+++.+++|....++.....++...+  
T Consensus       130 vvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp--  207 (351)
T KOG2035|consen  130 VVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLP--  207 (351)
T ss_pred             EEEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCc--
Confidence            4445445443333445566666666677887774433  222222122347889999999999999887755554322  


Q ss_pred             hHHHHHHHHHHHcCCCh-HHHHHHHHHhccC---------CCHHHHHHHHhhhhhh
Q 046115          154 NLEKIGREIVKKCKGLP-LAAKTIASLLRSK---------NTEKEWQNILENEIWE  199 (505)
Q Consensus       154 ~~~~~~~~i~~~~~g~P-lal~~~~~~l~~~---------~~~~~~~~~l~~~~~~  199 (505)
                        ++.+.+|+++++|.- .||-+.-..-..+         ....+|+..+.+....
T Consensus       208 --~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~~i~e~a~~  261 (351)
T KOG2035|consen  208 --KELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEIYIQEIARV  261 (351)
T ss_pred             --HHHHHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHHHHHHHHHHH
Confidence              678999999998864 3333222211111         1345888877764433

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=91.73  E-value=0.38  Score=49.90  Aligned_cols=64  Identities=20%  Similarity=0.254  Sum_probs=42.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--CCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--AGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~~r~Llv   78 (505)
                      ++|.||||||..+++.    ..| .++=|+++...+...+-..|...+....                .+  .+++.-||
T Consensus       334 ppGlGKTTLAHViAkq----aGY-sVvEINASDeRt~~~v~~kI~~avq~~s----------------~l~adsrP~CLV  392 (877)
T KOG1969|consen  334 PPGLGKTTLAHVIAKQ----AGY-SVVEINASDERTAPMVKEKIENAVQNHS----------------VLDADSRPVCLV  392 (877)
T ss_pred             CCCCChhHHHHHHHHh----cCc-eEEEecccccccHHHHHHHHHHHHhhcc----------------ccccCCCcceEE
Confidence            5899999999999983    223 4556788877776666666555543111                22  25778888


Q ss_pred             EeCCCCC
Q 046115           79 LDDVWNE   85 (505)
Q Consensus        79 lDdv~~~   85 (505)
                      +|.++-.
T Consensus       393 iDEIDGa  399 (877)
T KOG1969|consen  393 IDEIDGA  399 (877)
T ss_pred             EecccCC
Confidence            8988543

>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=91.62  E-value=0.15  Score=42.99  Aligned_cols=28  Identities=29%  Similarity=0.138  Sum_probs=22.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~   30 (505)
                      ++|+||||||+++..  +....-..+.+++
T Consensus        10 lsGsGKtTlA~~L~~--~L~~~g~~~~~LD   37 (156)
T PF01583_consen   10 LSGSGKTTLARALER--RLFARGIKVYLLD   37 (156)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTS-EEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEec
Confidence            589999999999998  6666666777776

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 ....

>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=91.60  E-value=1.4  Score=38.19  Aligned_cols=102  Identities=13%  Similarity=0.010  Sum_probs=51.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ..|+|||||++.++..  .. -..+.++++.....           .+  ......+.-++..-.+.+.+..++-++++|
T Consensus        33 ~nGsGKSTLl~~l~Gl--~~-p~~G~i~~~g~~i~-----------~~--~q~~~LSgGq~qrv~laral~~~p~lllLD   96 (177)
T cd03222          33 PNGTGKTTAVKILAGQ--LI-PNGDNDEWDGITPV-----------YK--PQYIDLSGGELQRVAIAAALLRNATFYLFD   96 (177)
T ss_pred             CCCChHHHHHHHHHcC--CC-CCCcEEEECCEEEE-----------EE--cccCCCCHHHHHHHHHHHHHhcCCCEEEEE
Confidence            3699999999999873  21 12333333210000           00  000002223334444556666677899999


Q ss_pred             CCCCC-CccChhHHHHhhcCC--CCCcEEEEEeCchHHHHH
Q 046115           81 DVWNE-DYYKWEPFYKCLKNS--LHESKILITTRKETVARI  118 (505)
Q Consensus        81 dv~~~-~~~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~~  118 (505)
                      .-... +......+...+...  ..+..||++|-+......
T Consensus        97 EPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~~~~  137 (177)
T cd03222          97 EPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVLDY  137 (177)
T ss_pred             CCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHHHHHH
Confidence            97442 222233333333322  122568888887665543

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.

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=91.57  E-value=0.2  Score=45.27  Aligned_cols=93  Identities=17%  Similarity=0.181  Sum_probs=48.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCC-ceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAG-KKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~r~Llvl   79 (505)
                      ++|.|||.+|+++++  +.     ..+||.+-.+        +++..-.       .+-.+.+..+.+-.+. |-++|.|
T Consensus       219 ppgtgktl~aravan--rt-----dacfirvigs--------elvqkyv-------gegarmvrelf~martkkaciiff  276 (435)
T KOG0729|consen  219 PPGTGKTLCARAVAN--RT-----DACFIRVIGS--------ELVQKYV-------GEGARMVRELFEMARTKKACIIFF  276 (435)
T ss_pred             CCCCchhHHHHHHhc--cc-----CceEEeehhH--------HHHHHHh-------hhhHHHHHHHHHHhcccceEEEEe
Confidence            589999999999999  33     3345554331        1222111       0011222333333334 5688888


Q ss_pred             eCCCC--------------CCccChhHHHHhhcCCC--CCcEEEEEeCchHH
Q 046115           80 DDVWN--------------EDYYKWEPFYKCLKNSL--HESKILITTRKETV  115 (505)
Q Consensus        80 Ddv~~--------------~~~~~~~~~~~~~~~~~--~~~~iLiTtr~~~~  115 (505)
                      |.++.              +-+..+-.++..+..++  .+-+||..|..++.
T Consensus       277 deidaiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlmatnrpdt  328 (435)
T KOG0729|consen  277 DEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDT  328 (435)
T ss_pred             eccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCC
Confidence            88732              11112333445555443  34678887766554

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

Probab=91.56  E-value=2.1  Score=44.18  Aligned_cols=123  Identities=14%  Similarity=0.120  Sum_probs=69.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||.||+++++  +....|     +.+...        .++....      ...............+..++.|.+|
T Consensus       284 pPGtGKT~lAkava~--~~~~~f-----i~v~~~--------~l~sk~v------Gesek~ir~~F~~A~~~~p~iiFiD  342 (494)
T COG0464         284 PPGTGKTLLAKAVAL--ESRSRF-----ISVKGS--------ELLSKWV------GESEKNIRELFEKARKLAPSIIFID  342 (494)
T ss_pred             CCCCCHHHHHHHHHh--hCCCeE-----EEeeCH--------HHhcccc------chHHHHHHHHHHHHHcCCCcEEEEE
Confidence            589999999999999  444444     333321        1122111      1111222333333445678999999


Q ss_pred             CCCCC------C-----ccChhHHHHhhc--CCCCCcEEEEEeCchHHHHHh----CC-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNE------D-----YYKWEPFYKCLK--NSLHESKILITTRKETVARIM----GS-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~------~-----~~~~~~~~~~~~--~~~~~~~iLiTtr~~~~~~~~----~~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      .++.-      .     .....+++..+.  ....+..||-+|..+......    +. ...+.++.-+.++..+.|..+
T Consensus       343 EiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~  422 (494)
T COG0464         343 EIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIH  422 (494)
T ss_pred             chhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHH
Confidence            98431      1     012344444443  233445566666655443321    12 457888999999999999887


Q ss_pred             hh
Q 046115          143 AI  144 (505)
Q Consensus       143 ~~  144 (505)
                      ..
T Consensus       423 ~~  424 (494)
T COG0464         423 LR  424 (494)
T ss_pred             hc
Confidence            64

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=91.39  E-value=0.46  Score=45.50  Aligned_cols=48  Identities=21%  Similarity=0.083  Sum_probs=30.8

Q ss_pred             CCCCcHHHHHHHHhcCccccc----CCCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER----NFEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~----~f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||..++.......    .-..++|++....+.... +.++++.++
T Consensus       104 ~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~  155 (316)
T TIGR02239       104 EFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYG  155 (316)
T ss_pred             CCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcC
Confidence            379999999998875212211    113568999888777765 444555554

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).

>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=91.23  E-value=0.41  Score=41.18  Aligned_cols=101  Identities=18%  Similarity=0.084  Sum_probs=48.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCC-hhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKD-LVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~-~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .|+||+.+|+.+.+.  -.+.-..-+-|+++.- +.+.+-.++...-....... ....+    .+. .  ...--|+||
T Consensus        31 ~GtGK~~lA~~IH~~--s~r~~~pfi~vnc~~~-~~~~~e~~LFG~~~~~~~~~~~~~~G----~l~-~--A~~GtL~Ld  100 (168)
T PF00158_consen   31 TGTGKELLARAIHNN--SPRKNGPFISVNCAAL-PEELLESELFGHEKGAFTGARSDKKG----LLE-Q--ANGGTLFLD  100 (168)
T ss_dssp             TTSSHHHHHHHHHHC--STTTTS-EEEEETTTS--HHHHHHHHHEBCSSSSTTTSSEBEH----HHH-H--TTTSEEEEE
T ss_pred             CCCcHHHHHHHHHHh--hhcccCCeEEEehhhh-hcchhhhhhhccccccccccccccCC----cee-e--ccceEEeec
Confidence            699999999999882  2222222334455532 22333333333222111111 11111    111 1  123368899


Q ss_pred             CCCCCCccChhHHHHhhcCC-----------CCCcEEEEEeCc
Q 046115           81 DVWNEDYYKWEPFYKCLKNS-----------LHESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~-----------~~~~~iLiTtr~  112 (505)
                      +|.+-....-..+...+...           ...++||.||..
T Consensus       101 ~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~  143 (168)
T PF00158_consen  101 EIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSK  143 (168)
T ss_dssp             TGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS
T ss_pred             chhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCc
Confidence            99776554445555555432           126788888875

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 ....

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

Probab=91.21  E-value=0.39  Score=51.62  Aligned_cols=86  Identities=12%  Similarity=0.117  Sum_probs=44.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC-CceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA-GKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~-~~r~Llvl   79 (505)
                      ++|+|||.+|+.++.  ...   ...+.++++...+... ...+   ++.+......+..   ..+...++ ....+|+|
T Consensus       496 P~GvGKT~lAk~LA~--~l~---~~~i~id~se~~~~~~-~~~L---iG~~~gyvg~~~~---g~L~~~v~~~p~sVlll  563 (758)
T PRK11034        496 PTGVGKTEVTVQLSK--ALG---IELLRFDMSEYMERHT-VSRL---IGAPPGYVGFDQG---GLLTDAVIKHPHAVLLL  563 (758)
T ss_pred             CCCCCHHHHHHHHHH--HhC---CCcEEeechhhccccc-HHHH---cCCCCCccccccc---chHHHHHHhCCCcEEEe
Confidence            479999999999988  442   2334555554322211 1121   2211110011111   11222232 34579999


Q ss_pred             eCCCCCCccChhHHHHhhc
Q 046115           80 DDVWNEDYYKWEPFYKCLK   98 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~   98 (505)
                      |++.......+..+...+.
T Consensus       564 DEieka~~~v~~~LLq~ld  582 (758)
T PRK11034        564 DEIEKAHPDVFNLLLQVMD  582 (758)
T ss_pred             ccHhhhhHHHHHHHHHHHh
Confidence            9997766555666666554

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=91.09  E-value=17  Score=35.97  Aligned_cols=115  Identities=10%  Similarity=0.066  Sum_probs=73.7

Q ss_pred             eEEEEEeCCCCCCc---cChhHHHHhh--cCCCCCcEEEEEeCchHHH----HHhC--CcceEeCCCCChhhHHHHHHHh
Q 046115           74 KFLLVLDDVWNEDY---YKWEPFYKCL--KNSLHESKILITTRKETVA----RIMG--STHVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        74 r~LlvlDdv~~~~~---~~~~~~~~~~--~~~~~~~~iLiTtr~~~~~----~~~~--~~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      |-++|+||......   ..|+.+.+.-  .-..+=.+||+.|-+....    +.++  ..+.+.+...+.+-|..+....
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~  228 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQ  228 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHH
Confidence            67899999854321   1123333221  1123445788888775433    3333  3567889999999999999887


Q ss_pred             hhCCCCC------------CC----CchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHH
Q 046115          143 AISGKTI------------GK----RENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKE  188 (505)
Q Consensus       143 ~~~~~~~------------~~----~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~  188 (505)
                      .......            ..    ...........++.+||=-.-|..+++.++.+.++.+
T Consensus       229 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p~~  290 (431)
T PF10443_consen  229 LDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESPEE  290 (431)
T ss_pred             hcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCHHH
Confidence            6432110            00    0123445677889999999999999999999875543

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=91.00  E-value=1.2  Score=40.49  Aligned_cols=33  Identities=21%  Similarity=0.129  Sum_probs=23.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF   35 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~   35 (505)
                      .+|+|||+||.+++.  .....-..++|++.....
T Consensus        28 ~~G~GKT~l~~~~~~--~~~~~g~~~~~is~e~~~   60 (229)
T TIGR03881        28 EPGTGKTIFCLHFAY--KGLRDGDPVIYVTTEESR   60 (229)
T ss_pred             CCCCChHHHHHHHHH--HHHhcCCeEEEEEccCCH
Confidence            379999999998876  222334577889875543

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.

>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=90.92  E-value=0.28  Score=45.69  Aligned_cols=15  Identities=33%  Similarity=0.169  Sum_probs=13.3

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||+|+++..
T Consensus         9 ~P~SGKTt~a~~L~~   23 (270)
T PF08433_consen    9 LPCSGKTTRAKELKK   23 (270)
T ss_dssp             -TTSSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHH
Confidence            489999999999987

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

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

Probab=90.87  E-value=2.3  Score=38.71  Aligned_cols=143  Identities=15%  Similarity=0.152  Sum_probs=74.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r~Llvl   79 (505)
                      ++|.|||.+|+++++  +.+--|     +.+..       ..-|-+..+        +-.+.+..+.++- +.-+|.+.+
T Consensus       159 ppGTGKTm~Akalan--e~kvp~-----l~vka-------t~liGehVG--------dgar~Ihely~rA~~~aPcivFi  216 (368)
T COG1223         159 PPGTGKTMMAKALAN--EAKVPL-----LLVKA-------TELIGEHVG--------DGARRIHELYERARKAAPCIVFI  216 (368)
T ss_pred             CCCccHHHHHHHHhc--ccCCce-----EEech-------HHHHHHHhh--------hHHHHHHHHHHHHHhcCCeEEEe
Confidence            579999999999999  332222     22221       111111221        2223334444443 335899999


Q ss_pred             eCCCCCC----c----cC----hhHHHHhhc--CCCCCcEEEEEeCchHHHHH-hCC--cceEeCCCCChhhHHHHHHHh
Q 046115           80 DDVWNED----Y----YK----WEPFYKCLK--NSLHESKILITTRKETVARI-MGS--THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        80 Ddv~~~~----~----~~----~~~~~~~~~--~~~~~~~iLiTtr~~~~~~~-~~~--~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      |.++...    .    .+    ...++..+.  ..+.|...|-.|..++++.. +.+  ...++..--+++|-.+++...
T Consensus       217 DE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y  296 (368)
T COG1223         217 DELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYY  296 (368)
T ss_pred             hhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHH
Confidence            9873311    0    11    122222222  23457667777776665442 222  335566666788888888877


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      +..-..   +  .+...+.+++..+|+.
T Consensus       297 ~k~~Pl---p--v~~~~~~~~~~t~g~S  319 (368)
T COG1223         297 AKKFPL---P--VDADLRYLAAKTKGMS  319 (368)
T ss_pred             HHhCCC---c--cccCHHHHHHHhCCCC
Confidence            632221   1  1122556666666654

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=90.84  E-value=0.62  Score=42.70  Aligned_cols=32  Identities=22%  Similarity=0.138  Sum_probs=23.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      .+|+|||+||.+++.  +..++-..++|++...+
T Consensus        29 ~pGsGKT~la~~~l~--~~~~~ge~~lyvs~ee~   60 (237)
T TIGR03877        29 GPGTGKSIFSQQFLW--NGLQMGEPGIYVALEEH   60 (237)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEEEeeCC
Confidence            379999999998876  33344567888887664

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=90.68  E-value=2.8  Score=44.57  Aligned_cols=122  Identities=14%  Similarity=0.159  Sum_probs=62.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.++.  +....|   +.++.+.          +..... +     .......+.+.......+++|++|
T Consensus       193 ~~G~GKt~~~~~~a~--~~~~~f---~~is~~~----------~~~~~~-g-----~~~~~~~~~f~~a~~~~P~IifID  251 (644)
T PRK10733        193 PPGTGKTLLAKAIAG--EAKVPF---FTISGSD----------FVEMFV-G-----VGASRVRDMFEQAKKAAPCIIFID  251 (644)
T ss_pred             CCCCCHHHHHHHHHH--HcCCCE---EEEehHH----------hHHhhh-c-----ccHHHHHHHHHHHHhcCCcEEEeh
Confidence            479999999999998  443332   2222221          011110 0     011122222333334467899999


Q ss_pred             CCCCCC----------ccCh----hHHHHhhcCC--CCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNED----------YYKW----EPFYKCLKNS--LHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~----------~~~~----~~~~~~~~~~--~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++.-.          ....    ..++..+...  ..+.-+|.||..++... ..   +. ...+.++..+.++-.+++
T Consensus       252 EiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il  331 (644)
T PRK10733        252 EIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL  331 (644)
T ss_pred             hHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHH
Confidence            984420          0011    2222222222  23445556777655322 11   12 357778888888888888


Q ss_pred             HHhh
Q 046115          140 QSLA  143 (505)
Q Consensus       140 ~~~~  143 (505)
                      ..+.
T Consensus       332 ~~~~  335 (644)
T PRK10733        332 KVHM  335 (644)
T ss_pred             HHHh
Confidence            7765

>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=90.62  E-value=0.15  Score=41.42  Aligned_cols=15  Identities=40%  Similarity=0.463  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+++..
T Consensus         6 ~~GsGKtTia~~L~~   20 (129)
T PF13238_consen    6 IPGSGKTTIAKELAE   20 (129)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

...

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=90.54  E-value=0.38  Score=41.77  Aligned_cols=16  Identities=38%  Similarity=0.384  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHhcC
Q 046115            1 MGGIGKTTLAQFAYNN   16 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~   16 (505)
                      .+|+||||+|+.++..
T Consensus         8 ~pGaGK~T~A~~La~~   23 (178)
T COG0563           8 PPGAGKSTLAKKLAKK   23 (178)
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            4899999999999983

>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=90.50  E-value=0.32  Score=46.28  Aligned_cols=74  Identities=23%  Similarity=0.178  Sum_probs=41.2

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcC-CceEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVA-GKKFL   76 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~~r~L   76 (505)
                      .|+||||||.++..  +..+.-..++||+....++..     .+..++...+    ..+...++......+.++ +..-+
T Consensus        62 ~ssGKttLaL~~ia--~~q~~g~~~a~ID~e~~ld~~-----~a~~lGvdl~rllv~~P~~~E~al~~~e~lirsg~~~l  134 (322)
T PF00154_consen   62 ESSGKTTLALHAIA--EAQKQGGICAFIDAEHALDPE-----YAESLGVDLDRLLVVQPDTGEQALWIAEQLIRSGAVDL  134 (322)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTT-EEEEEESSS---HH-----HHHHTT--GGGEEEEE-SSHHHHHHHHHHHHHTTSESE
T ss_pred             CCCchhhhHHHHHH--hhhcccceeEEecCcccchhh-----HHHhcCccccceEEecCCcHHHHHHHHHHHhhcccccE
Confidence            68999999998887  454444567799998876653     3344443221    112333444455555443 34568


Q ss_pred             EEEeCC
Q 046115           77 LVLDDV   82 (505)
Q Consensus        77 lvlDdv   82 (505)
                      +|+|.|
T Consensus       135 VVvDSv  140 (322)
T PF00154_consen  135 VVVDSV  140 (322)
T ss_dssp             EEEE-C
T ss_pred             EEEecC
Confidence            899998

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 ....

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.47  E-value=3  Score=37.27  Aligned_cols=61  Identities=13%  Similarity=0.054  Sum_probs=34.6

Q ss_pred             HHHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHHHhCCc
Q 046115           62 LMQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVARIMGST  122 (505)
Q Consensus        62 ~~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~~~~~~  122 (505)
                      -...+.+.+-=++-+.|||..++- +...+..+...+... ..++.+||.|-.+.++..+...
T Consensus       151 KR~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr~~~~~~liITHy~rll~~i~pD  213 (251)
T COG0396         151 KRNEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALREEGRGVLIITHYQRLLDYIKPD  213 (251)
T ss_pred             HHHHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHhcCCCeEEEEecHHHHHhhcCCC
Confidence            334455555556679999998663 222333333333321 3455677777777777766543

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=90.46  E-value=1.2  Score=36.12  Aligned_cols=117  Identities=12%  Similarity=0.231  Sum_probs=55.2

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLP  430 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp  430 (505)
                      |.++++|+.+.+... +...   -...|..+.+|+.+.+.       ++ +..++ ..+..+..++.+.+.+ . +..++
T Consensus         8 F~~~~~l~~i~~~~~-~~~I---~~~~F~~~~~l~~i~~~-------~~-~~~i~~~~F~~~~~l~~i~~~~-~-~~~i~   73 (129)
T PF13306_consen    8 FYNCSNLESITFPNT-IKKI---GENAFSNCTSLKSINFP-------NN-LTSIGDNAFSNCKSLESITFPN-N-LKSIG   73 (129)
T ss_dssp             TTT-TT--EEEETST---EE----TTTTTT-TT-SEEEES-------ST-TSCE-TTTTTT-TT-EEEEETS-T-T-EE-
T ss_pred             HhCCCCCCEEEECCC-eeEe---Chhhccccccccccccc-------cc-ccccceeeeecccccccccccc-c-ccccc
Confidence            457778888887642 2221   33346667788888886       43 44443 3456676788888865 3 44454


Q ss_pred             h-hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccc-cccCCccC
Q 046115          431 E-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPA-GIGELIRL  487 (505)
Q Consensus       431 ~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L  487 (505)
                      . .+..+.+|+.+.+..+  +..++.. +.+. +|+.+.+..+  ...++. .|.++++|
T Consensus        74 ~~~F~~~~~l~~i~~~~~--~~~i~~~~f~~~-~l~~i~~~~~--~~~i~~~~F~~~~~l  128 (129)
T PF13306_consen   74 DNAFSNCTNLKNIDIPSN--ITEIGSSSFSNC-NLKEINIPSN--ITKIEENAFKNCTKL  128 (129)
T ss_dssp             TTTTTT-TTECEEEETTT---BEEHTTTTTT--T--EEE-TTB---SS----GGG-----
T ss_pred             cccccccccccccccCcc--ccEEchhhhcCC-CceEEEECCC--ccEECCccccccccC
Confidence            4 3456888888888653  5555544 5555 7888877653  233333 35666555

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=90.36  E-value=1.8  Score=45.44  Aligned_cols=63  Identities=17%  Similarity=0.267  Sum_probs=39.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||-+|++|+.  +..-.     |+++..+        ++++.--      .++.+...+...+.-...+|.|.||
T Consensus       713 PPGTGKTLlAKAVAT--EcsL~-----FlSVKGP--------ELLNMYV------GqSE~NVR~VFerAR~A~PCVIFFD  771 (953)
T KOG0736|consen  713 PPGTGKTLLAKAVAT--ECSLN-----FLSVKGP--------ELLNMYV------GQSEENVREVFERARSAAPCVIFFD  771 (953)
T ss_pred             CCCCchHHHHHHHHh--hceee-----EEeecCH--------HHHHHHh------cchHHHHHHHHHHhhccCCeEEEec
Confidence            589999999999998  33333     4666552        3333222      1222333444444556689999999


Q ss_pred             CCCC
Q 046115           81 DVWN   84 (505)
Q Consensus        81 dv~~   84 (505)
                      .+++
T Consensus       772 ELDS  775 (953)
T KOG0736|consen  772 ELDS  775 (953)
T ss_pred             cccc
Confidence            9855

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=90.35  E-value=2.2  Score=39.01  Aligned_cols=60  Identities=18%  Similarity=0.164  Sum_probs=37.1

Q ss_pred             hcHHHHHHHHHHHcCCceEEEEEeCCCCC-C---ccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           57 VEFQSLMQHIEECVAGKKFLLVLDDVWNE-D---YYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        57 ~~~~~~~~~l~~~l~~~r~LlvlDdv~~~-~---~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +.-+...-.+.+.|.+.+=||+||.-... +   ...+-.++..+...  |+.||++|-|-.....
T Consensus       141 SGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e--g~tIl~vtHDL~~v~~  204 (254)
T COG1121         141 SGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE--GKTVLMVTHDLGLVMA  204 (254)
T ss_pred             CcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC--CCEEEEEeCCcHHhHh
Confidence            33344455677888888999999985331 2   22223333333333  8899999998665543

>PRK14974 cell division protein FtsY; Provisional

Probab=90.28  E-value=1.4  Score=42.42  Aligned_cols=82  Identities=17%  Similarity=0.058  Sum_probs=41.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CCceEEEEeCCC-CCHHHHHHHHHHHcCCCCCC--ChhcHHH-HHHHHHHHcCCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FEKRTWVCVSEP-FDEFRIARAIIESLTPGSAK--DLVEFQS-LMQHIEECVAGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~~~~wv~~~~~-~~~~~~~~~l~~~l~~~~~~--~~~~~~~-~~~~l~~~l~~~r~   75 (505)
                      ++|+||||++..++.  ....+ + .++.++.... ....+.++.....++.+...  ...+... ..+.+........-
T Consensus       148 ~~GvGKTTtiakLA~--~l~~~g~-~V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~~~~~~~~D  224 (336)
T PRK14974        148 VNGTGKTTTIAKLAY--YLKKNGF-SVVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIEHAKARGID  224 (336)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCC-eEEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHHHHHhCCCC
Confidence            579999999888886  44332 3 2334442211 12334455666666643221  1122222 22333332222233


Q ss_pred             EEEEeCCCCC
Q 046115           76 LLVLDDVWNE   85 (505)
Q Consensus        76 LlvlDdv~~~   85 (505)
                      ++++|-....
T Consensus       225 vVLIDTaGr~  234 (336)
T PRK14974        225 VVLIDTAGRM  234 (336)
T ss_pred             EEEEECCCcc
Confidence            8999998654

>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=90.12  E-value=0.099  Score=42.09  Aligned_cols=21  Identities=38%  Similarity=0.537  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHhcCcccccCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFE   24 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~   24 (505)
                      +|+|||++|+.++.  .+...|.
T Consensus         8 PG~GKT~la~~lA~--~~~~~f~   28 (131)
T PF07726_consen    8 PGVGKTTLAKALAR--SLGLSFK   28 (131)
T ss_dssp             --HHHHHHHHHHHH--HTT--EE
T ss_pred             CccHHHHHHHHHHH--HcCCcee
Confidence            79999999999998  6666664

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.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=90.10  E-value=0.8  Score=39.59  Aligned_cols=54  Identities=19%  Similarity=0.228  Sum_probs=32.0

Q ss_pred             HHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHH
Q 046115           64 QHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVAR  117 (505)
Q Consensus        64 ~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~  117 (505)
                      -.+.+.+..++-++++|+.... +......+.+.+... ..|..||++|.+.....
T Consensus       104 v~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~~~~  159 (173)
T cd03230         104 LALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILEEAE  159 (173)
T ss_pred             HHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHH
Confidence            3466666778889999997442 222223333333322 23567888888876554

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=90.00  E-value=2.4  Score=37.86  Aligned_cols=65  Identities=8%  Similarity=0.074  Sum_probs=37.5

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcC-CCCCcEEEEEeCchHHHHHhCCcceEeCCCCChh
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKN-SLHESKILITTRKETVARIMGSTHVISVNVLSEM  133 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iLiTtr~~~~~~~~~~~~~~~l~~l~~~  133 (505)
                      +.+.+..++-++++|.-... +......+...+.. ...|..||++|.+......   ..++.++.++.+
T Consensus       138 la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~~~~~~---~~~~~~~~~~~~  204 (207)
T PRK13539        138 LARLLVSNRPIWILDEPTAALDAAAVALFAELIRAHLAQGGIVIAATHIPLGLPG---ARELDLGPFAAE  204 (207)
T ss_pred             HHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCchhhcc---CcEEeecCccCC
Confidence            44555566779999997442 22223334444432 1246678999888665443   456777665443

>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=89.90  E-value=0.92  Score=39.43  Aligned_cols=55  Identities=16%  Similarity=0.111  Sum_probs=31.7

Q ss_pred             HHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CC-CcEEEEEeCchHHHH
Q 046115           63 MQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LH-ESKILITTRKETVAR  117 (505)
Q Consensus        63 ~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~-~~~iLiTtr~~~~~~  117 (505)
                      .-.+.+.+..++=++++|.-... +......+...+... .. +..||++|-+.....
T Consensus       108 r~~la~al~~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~~~  165 (178)
T cd03229         108 RVALARALAMDPDVLLLDEPTSALDPITRREVRALLKSLQAQLGITVVLVTHDLDEAA  165 (178)
T ss_pred             HHHHHHHHHCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            33455566667788999997442 222333444444332 12 567888888766554

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.

>PRK13849 putative crown gall tumor protein VirC1; Provisional

Probab=89.86  E-value=1.1  Score=40.74  Aligned_cols=36  Identities=22%  Similarity=0.122  Sum_probs=24.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFR   39 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~   39 (505)
                      ||+||||+|..++.  .....=..++-++...+.+...
T Consensus        11 GGvGKTT~a~nLA~--~la~~G~~VlliD~DpQ~s~~~   46 (231)
T PRK13849         11 GGAGKTTALMGLCA--ALASDGKRVALFEADENRPLTR   46 (231)
T ss_pred             CCccHHHHHHHHHH--HHHhCCCcEEEEeCCCCCCHHH
Confidence            89999999999887  4443323455677666555443

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

Probab=89.76  E-value=3.5  Score=35.73  Aligned_cols=66  Identities=14%  Similarity=0.089  Sum_probs=39.6

Q ss_pred             ChhcHHHHHHHHHHHcCCceEEEEEeCCC-CCCccChhHHHHhhcC-CCCCcEEEEEeCchHHHHHhC
Q 046115           55 DLVEFQSLMQHIEECVAGKKFLLVLDDVW-NEDYYKWEPFYKCLKN-SLHESKILITTRKETVARIMG  120 (505)
Q Consensus        55 ~~~~~~~~~~~l~~~l~~~r~LlvlDdv~-~~~~~~~~~~~~~~~~-~~~~~~iLiTtr~~~~~~~~~  120 (505)
                      +.+.-++..-.+.+.+-+++-+|+-|.-. +-+...-..+...+.. +..|..|++.|-+..+...+.
T Consensus       137 ~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~  204 (223)
T COG2884         137 QLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMR  204 (223)
T ss_pred             ccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhcc
Confidence            34444555556677777888888888641 1111111222333332 346889999999998887654

>cd01131 PilT Pilus retraction ATPase PilT

Probab=89.75  E-value=0.35  Score=42.93  Aligned_cols=101  Identities=10%  Similarity=0.143  Sum_probs=48.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHH-HHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEF-RIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~-~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      ..|+||||++..++.  .........++. +..+.... .-...++.+-.     ...+.....+.+...+....=.|++
T Consensus         9 ptGSGKTTll~~ll~--~~~~~~~~~i~t-~e~~~E~~~~~~~~~i~q~~-----vg~~~~~~~~~i~~aLr~~pd~ii~   80 (198)
T cd01131           9 PTGSGKSTTLAAMID--YINKNKTHHILT-IEDPIEFVHESKRSLINQRE-----VGLDTLSFENALKAALRQDPDVILV   80 (198)
T ss_pred             CCCCCHHHHHHHHHH--HhhhcCCcEEEE-EcCCccccccCccceeeecc-----cCCCccCHHHHHHHHhcCCcCEEEE
Confidence            369999999998887  444343334333 22221110 00000111100     0111122334566666666779999


Q ss_pred             eCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET  114 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~  114 (505)
                      |.+.+..  .+.......   ..|..++.|+-...
T Consensus        81 gEird~e--~~~~~l~~a---~~G~~v~~t~Ha~~  110 (198)
T cd01131          81 GEMRDLE--TIRLALTAA---ETGHLVMSTLHTNS  110 (198)
T ss_pred             cCCCCHH--HHHHHHHHH---HcCCEEEEEecCCc
Confidence            9996543  233323322   24555666665443

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.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=89.69  E-value=1.8  Score=43.40  Aligned_cols=48  Identities=19%  Similarity=0.115  Sum_probs=27.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHHHHcCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAIIESLTP   50 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~~~l~~   50 (505)
                      .+|+||||.|..++.  ....+-..+.-+++... +...+.+..+..+++.
T Consensus       103 ~~GsGKTTtaakLA~--~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gv  151 (437)
T PRK00771        103 LQGSGKTTTAAKLAR--YFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGV  151 (437)
T ss_pred             CCCCcHHHHHHHHHH--HHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCC
Confidence            479999999999987  44433123334443321 1234555666666653

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.62  E-value=1.9  Score=42.17  Aligned_cols=105  Identities=8%  Similarity=0.030  Sum_probs=49.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC-CceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA-GKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~-~~r~Llv   78 (505)
                      .+|+||||++..++.  ....+=..+..++..... ...+.+....+.++.+.. ...+.....+.+...-. .+.=+++
T Consensus       249 ptGvGKTTTiaKLA~--~L~~~GkkVglI~aDt~RiaAvEQLk~yae~lgipv~-v~~d~~~L~~aL~~lk~~~~~DvVL  325 (436)
T PRK11889        249 PTGVGKTTTLAKMAW--QFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVI-AVRDEAAMTRALTYFKEEARVDYIL  325 (436)
T ss_pred             CCCCcHHHHHHHHHH--HHHHcCCcEEEEecCCcchHHHHHHHHHhhhcCCcEE-ecCCHHHHHHHHHHHHhccCCCEEE
Confidence            479999999999987  443332234455543322 233334444444442221 11233333333333221 1235778


Q ss_pred             EeCCCCCC--ccChhHHHHhhcCCCCCcEEEE
Q 046115           79 LDDVWNED--YYKWEPFYKCLKNSLHESKILI  108 (505)
Q Consensus        79 lDdv~~~~--~~~~~~~~~~~~~~~~~~~iLi  108 (505)
                      +|-..+..  ...+..+...+....+...+||
T Consensus       326 IDTaGRs~kd~~lm~EL~~~lk~~~PdevlLV  357 (436)
T PRK11889        326 IDTAGKNYRASETVEEMIETMGQVEPDYICLT  357 (436)
T ss_pred             EeCccccCcCHHHHHHHHHHHhhcCCCeEEEE
Confidence            88875532  2224444444433333333444

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=89.60  E-value=1.8  Score=41.74  Aligned_cols=101  Identities=12%  Similarity=0.057  Sum_probs=48.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHH-HHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARA-IIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~-l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .|+||+++|+.+...  -...-...+-|++....  ...+.. +...-. +........  ....+.   ....--|+||
T Consensus        31 ~GtGK~~lAr~iH~~--s~r~~~pfv~vnc~~~~--~~~l~~~lfG~~~-g~~~ga~~~--~~G~~~---~a~gGtL~Ld  100 (329)
T TIGR02974        31 RGTGKELIAARLHYL--SKRWQGPLVKLNCAALS--ENLLDSELFGHEA-GAFTGAQKR--HQGRFE---RADGGTLFLD  100 (329)
T ss_pred             CCChHHHHHHHHHHh--cCccCCCeEEEeCCCCC--hHHHHHHHhcccc-ccccCcccc--cCCchh---hCCCCEEEeC
Confidence            699999999998762  22121233445665432  222222 211110 000000000  000011   1223468999


Q ss_pred             CCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           81 DVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      +|..-.......+...+....           ...+||.||..
T Consensus       101 ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~  143 (329)
T TIGR02974       101 ELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNA  143 (329)
T ss_pred             ChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEEEEechh
Confidence            997766555556666554321           34577777753

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

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=89.43  E-value=1.8  Score=40.19  Aligned_cols=45  Identities=16%  Similarity=0.119  Sum_probs=28.8

Q ss_pred             CCCcHHHHHHHHhcCccc--ccCCCceEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDV--ERNFEKRTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~--~~~f~~~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|+..+++....  +++-+.++++-+++.. +..++..++..
T Consensus        78 ~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~  125 (276)
T cd01135          78 SGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEE  125 (276)
T ss_pred             CCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhh
Confidence            689999999998874221  1223567788777654 44555555544

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.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=89.38  E-value=4.9  Score=37.75  Aligned_cols=59  Identities=12%  Similarity=0.165  Sum_probs=39.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVL  130 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l  130 (505)
                      +++-++|+|+++.........+++.+.....++.+|++|.++ .+... ......+.+.++
T Consensus        94 ~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~  154 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPME  154 (290)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccch
Confidence            456688999998887778888999888877777766666663 33322 222345556544

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=89.35  E-value=5.3  Score=38.19  Aligned_cols=32  Identities=16%  Similarity=0.136  Sum_probs=20.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      .+|+|||++|+.++.  .....|   +.|.+....+.
T Consensus        72 ~pGtGKTtla~~lA~--~l~~~~---~rV~~~~~l~~  103 (327)
T TIGR01650        72 YHGTGKSTHIEQIAA--RLNWPC---VRVNLDSHVSR  103 (327)
T ss_pred             CCCChHHHHHHHHHH--HHCCCe---EEEEecCCCCh
Confidence            479999999999998  443332   24444444333

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

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=89.32  E-value=0.76  Score=45.77  Aligned_cols=83  Identities=11%  Similarity=0.148  Sum_probs=45.1

Q ss_pred             CCCcHHHHHHHHhcCccc-----c----c--CCCceEEEEeCCCCCHHHHHHHHHHHcC-CCC------CCChhcHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDV-----E----R--NFEKRTWVCVSEPFDEFRIARAIIESLT-PGS------AKDLVEFQSLM   63 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~-----~----~--~f~~~~wv~~~~~~~~~~~~~~l~~~l~-~~~------~~~~~~~~~~~   63 (505)
                      +|+|||+|+..+++....     .    +  .=..+++.-+++..+..+.+...+.+-+ ...      ..+.....+..
T Consensus       150 sGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~atsd~p~~~R~~  229 (466)
T TIGR01040       150 AGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLANDPTIERII  229 (466)
T ss_pred             CCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHH
Confidence            699999999999874321     0    0  0014557777777666665655555443 110      11111111111


Q ss_pred             -----HHHHHHc---CCceEEEEEeCCCC
Q 046115           64 -----QHIEECV---AGKKFLLVLDDVWN   84 (505)
Q Consensus        64 -----~~l~~~l---~~~r~LlvlDdv~~   84 (505)
                           -.+.+.+   +++++|+++||+.+
T Consensus       230 a~~~a~tiAEyfr~~~G~~VLl~~DslTr  258 (466)
T TIGR01040       230 TPRLALTTAEYLAYQCEKHVLVILTDMSS  258 (466)
T ss_pred             HHhhhHHHHHHHHHhcCCcEEEeccChHH
Confidence                 1123333   46899999999833

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=89.31  E-value=0.37  Score=52.88  Aligned_cols=128  Identities=14%  Similarity=0.155  Sum_probs=65.3

Q ss_pred             HHHcCCceEEEEEeCCCCCCccC----hhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCcceEeCCCCChhhHHHHHH--
Q 046115           67 EECVAGKKFLLVLDDVWNEDYYK----WEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVNVLSEMECWSVFQ--  140 (505)
Q Consensus        67 ~~~l~~~r~LlvlDdv~~~~~~~----~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~~~~~l~~l~~~ea~~Lf~--  140 (505)
                      .+.++..++++++|.++......    ...+...++.. +.+++|+|+|.............+++..+.++.-.....  
T Consensus       299 ~e~l~~g~~llLlDGlDe~~~~~~~~~~~~i~~f~~~~-~~~~~iltcR~~~~~~~~~~f~~~ei~~~~~~~i~~~~~~~  377 (824)
T COG5635         299 QELLKTGKLLLLLDGLDELEPKNQRALIREINKFLQEY-PDAQVLLTCRPDTYKEEFKGFAVFEIYKFLDLQINQFILYQ  377 (824)
T ss_pred             HHHHhccchhhHhhccchhhhhhHHHHHHHHHHHhhhc-cCCeEEEEeccchhhhhhhhhhhccchhhhHHHHHHHHHHH
Confidence            56778899999999985533222    22233333333 467899999875444333334455555555554332221  


Q ss_pred             ------HhhhCCCCCC---CCchHHHHHHHHHHHcCCChHHHHHHHHHhccC-----CCHHHHHHHHhh
Q 046115          141 ------SLAISGKTIG---KRENLEKIGREIVKKCKGLPLAAKTIASLLRSK-----NTEKEWQNILEN  195 (505)
Q Consensus       141 ------~~~~~~~~~~---~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~-----~~~~~~~~~l~~  195 (505)
                            ...+......   ....+..-...-++.....|++|.+.+......     ...+.|+..++.
T Consensus       378 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ik~l~~~p~~L~l~c~~~~~~~~lP~~~~~ly~~~~~~  446 (824)
T COG5635         378 WLDAFIEDWFGDSRLLAKKLLERLKLPENRRIKELALTPLLLALECLIWQAQGDLPESRAELYEQAVDA  446 (824)
T ss_pred             HHHHHHHhhhcccchhhHHHHHHhcchhhHHHHHhccCHHHHHHHHHhhhHHhhCCCCcHHHHHHHHHH
Confidence                  1111111100   000011112233344488899999998655421     145556655554

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=89.25  E-value=3.4  Score=42.66  Aligned_cols=144  Identities=13%  Similarity=0.103  Sum_probs=74.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCc-eEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGK-KFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-r~Llvl   79 (505)
                      ++|.|||-+++++++  +...+      +-...       ..+++..+.      .+........+.+..+.+ +..|.+
T Consensus       226 ppg~Gkt~l~~aVa~--e~~a~------~~~i~-------~peli~k~~------gEte~~LR~~f~~a~k~~~psii~I  284 (693)
T KOG0730|consen  226 PPGTGKTFLVRAVAN--EYGAF------LFLIN-------GPELISKFP------GETESNLRKAFAEALKFQVPSIIFI  284 (693)
T ss_pred             CCCCChHHHHHHHHH--HhCce------eEecc-------cHHHHHhcc------cchHHHHHHHHHHHhccCCCeeEeH
Confidence            479999999999999  33321      11111       123333333      122233455556666677 888888


Q ss_pred             eCCCCCC----------ccChhHHHHhhcCCC--CCcEEEEEeCchHHHH-HhC--C-cceEeCCCCChhhHHHHHHHhh
Q 046115           80 DDVWNED----------YYKWEPFYKCLKNSL--HESKILITTRKETVAR-IMG--S-THVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        80 Ddv~~~~----------~~~~~~~~~~~~~~~--~~~~iLiTtr~~~~~~-~~~--~-~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      |++....          .....++...+...+  .+.-||-+|+.++... ...  . .+.+.++..+..+-.++++...
T Consensus       285 dEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~~l~  364 (693)
T KOG0730|consen  285 DELDALCPKREGADDVESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILRVLT  364 (693)
T ss_pred             HhHhhhCCcccccchHHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHHHHHH
Confidence            8874421          111233344333433  3444555676654322 111  2 3467777777777777776654


Q ss_pred             hCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          144 ISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ..-+. ..+.++.    .++..+.|+-
T Consensus       365 k~~~~-~~~~~l~----~iA~~thGyv  386 (693)
T KOG0730|consen  365 KKMNL-LSDVDLE----DIAVSTHGYV  386 (693)
T ss_pred             HhcCC-cchhhHH----HHHHHccchh
Confidence            32222 2234444    4555555544

>PRK11823 DNA repair protein RadA; Provisional

Probab=89.22  E-value=0.4  Score=48.39  Aligned_cols=31  Identities=29%  Similarity=0.238  Sum_probs=23.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      +|+|||||+.+++.  ....+-..++|++..+.
T Consensus        89 pG~GKTtL~lq~a~--~~a~~g~~vlYvs~Ees  119 (446)
T PRK11823         89 PGIGKSTLLLQVAA--RLAAAGGKVLYVSGEES  119 (446)
T ss_pred             CCCCHHHHHHHHHH--HHHhcCCeEEEEEcccc
Confidence            79999999999987  44433346778887654

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=89.21  E-value=0.72  Score=42.64  Aligned_cols=15  Identities=27%  Similarity=0.507  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|++++.
T Consensus         7 ~pGSGKST~a~~La~   21 (249)
T TIGR03574         7 LPGVGKSTFSKELAK   21 (249)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

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

Probab=89.10  E-value=1.7  Score=39.11  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=17.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRT   27 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~   27 (505)
                      -|+|||.|.+++.+  ++....--.+
T Consensus        94 RGtGKSSLVKA~~~--e~~~~glrLV  117 (287)
T COG2607          94 RGTGKSSLVKALLN--EYADEGLRLV  117 (287)
T ss_pred             CCCChHHHHHHHHH--HHHhcCCeEE
Confidence            48999999999988  6666554433

>smart00370 LRR Leucine-rich repeats, outliers

Probab=89.09  E-value=0.34  Score=26.74  Aligned_cols=19  Identities=42%  Similarity=0.674  Sum_probs=11.7

Q ss_pred             CCCcEEecCCCcCccccchh
Q 046115          437 YNLERLNVDDCQNLRELPRG  456 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~  456 (505)
                      .+|+.|+|++|. +..+|++
T Consensus         2 ~~L~~L~L~~N~-l~~lp~~   20 (26)
T smart00370        2 PNLRELDLSNNQ-LSSLPPG   20 (26)
T ss_pred             CCCCEEECCCCc-CCcCCHH
Confidence            456666666665 6666654

>smart00369 LRR_TYP Leucine-rich repeats, typical (most populated) subfamily

Probab=89.09  E-value=0.34  Score=26.74  Aligned_cols=19  Identities=42%  Similarity=0.674  Sum_probs=11.7

Q ss_pred             CCCcEEecCCCcCccccchh
Q 046115          437 YNLERLNVDDCQNLRELPRG  456 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~  456 (505)
                      .+|+.|+|++|. +..+|++
T Consensus         2 ~~L~~L~L~~N~-l~~lp~~   20 (26)
T smart00369        2 PNLRELDLSNNQ-LSSLPPG   20 (26)
T ss_pred             CCCCEEECCCCc-CCcCCHH
Confidence            456666666665 6666654

>PHA02244 ATPase-like protein

Probab=89.09  E-value=1.2  Score=43.17  Aligned_cols=15  Identities=27%  Similarity=0.313  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+|||+||++++.
T Consensus       127 ppGtGKTtLA~aLA~  141 (383)
T PHA02244        127 GAGSGKNHIAEQIAE  141 (383)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases

Probab=89.08  E-value=0.4  Score=42.22  Aligned_cols=35  Identities=26%  Similarity=0.324  Sum_probs=24.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEF   38 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~   38 (505)
                      ||+||||+|..++.  ....+-..++-++........
T Consensus         8 GG~GKTt~a~~la~--~la~~g~~VlliD~D~~~~~~   42 (195)
T PF01656_consen    8 GGVGKTTIAANLAQ--ALARKGKKVLLIDLDPQAPNL   42 (195)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTS-EEEEEESTTSHHH
T ss_pred             CCccHHHHHHHHHh--ccccccccccccccCcccccH
Confidence            89999999999988  565554566667775544433

These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....

>TIGR00416 sms DNA repair protein RadA

Probab=89.04  E-value=0.52  Score=47.60  Aligned_cols=31  Identities=32%  Similarity=0.330  Sum_probs=22.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      +|+|||||+.+++.  ....+-..++|++..++
T Consensus       103 pGsGKTTL~lq~a~--~~a~~g~kvlYvs~EEs  133 (454)
T TIGR00416       103 PGIGKSTLLLQVAC--QLAKNQMKVLYVSGEES  133 (454)
T ss_pred             CCCCHHHHHHHHHH--HHHhcCCcEEEEECcCC
Confidence            79999999999977  44333345778887654

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)).

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=89.03  E-value=0.91  Score=43.72  Aligned_cols=15  Identities=33%  Similarity=0.366  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+++.+..
T Consensus         7 l~GaGKST~~~~l~~   21 (340)
T TIGR03575         7 LPAAGKSTLARSLSA   21 (340)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999986

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=89.01  E-value=15  Score=36.37  Aligned_cols=15  Identities=27%  Similarity=0.321  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|.|||++..++|+
T Consensus       243 PPGTGKSS~IaAmAn  257 (457)
T KOG0743|consen  243 PPGTGKSSFIAAMAN  257 (457)
T ss_pred             CCCCCHHHHHHHHHh
Confidence            689999999999998

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=88.96  E-value=0.3  Score=40.78  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=17.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FE   24 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~   24 (505)
                      |+|+||||++..+++  ..+.+ |.
T Consensus        13 ~PGvGKtTl~~ki~e--~L~~~g~k   35 (179)
T COG1618          13 RPGVGKTTLVLKIAE--KLREKGYK   35 (179)
T ss_pred             CCCccHHHHHHHHHH--HHHhcCce
Confidence            689999999999998  55444 53

>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=88.94  E-value=0.26  Score=41.00  Aligned_cols=15  Identities=40%  Similarity=0.372  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         7 ~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    7 PPGSGKSTLAKRLAK   21 (143)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999986

...

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=88.83  E-value=8.3  Score=34.89  Aligned_cols=26  Identities=35%  Similarity=0.355  Sum_probs=19.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE   33 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~   33 (505)
                      ++|.|||.||+++++       +....|+.++.
T Consensus       189 ppgtGktLlaraVah-------ht~c~firvsg  214 (404)
T KOG0728|consen  189 PPGTGKTLLARAVAH-------HTDCTFIRVSG  214 (404)
T ss_pred             CCCCchhHHHHHHHh-------hcceEEEEech
Confidence            479999999999998       33444666665

>PRK13531 regulatory ATPase RavA; Provisional

Probab=88.80  E-value=1.5  Score=44.22  Aligned_cols=67  Identities=12%  Similarity=0.246  Sum_probs=38.8

Q ss_pred             EEEEeCCCCCCccChhHHHHhhcCCC---------CCcEEEEEeCchHHH------HHhCC-cceEeCCCCChhhH-HHH
Q 046115           76 LLVLDDVWNEDYYKWEPFYKCLKNSL---------HESKILITTRKETVA------RIMGS-THVISVNVLSEMEC-WSV  138 (505)
Q Consensus        76 LlvlDdv~~~~~~~~~~~~~~~~~~~---------~~~~iLiTtr~~~~~------~~~~~-~~~~~l~~l~~~ea-~~L  138 (505)
                      ++++|+++.........+...+....         -..++++++.++...      ..... ...+.+++++.++. .++
T Consensus       110 lLfLDEI~rasp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~DRFliri~vp~l~~~~~e~~l  189 (498)
T PRK13531        110 IVFLDEIWKAGPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSM  189 (498)
T ss_pred             EEeecccccCCHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHhhEEEEEECCCCCchHHHHHH
Confidence            89999998766655666666663221         123466655553221      11222 23577888986554 677


Q ss_pred             HHHh
Q 046115          139 FQSL  142 (505)
Q Consensus       139 f~~~  142 (505)
                      +...
T Consensus       190 L~~~  193 (498)
T PRK13531        190 LTSQ  193 (498)
T ss_pred             HHcc
Confidence            7653

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=88.78  E-value=1.7  Score=45.05  Aligned_cols=71  Identities=15%  Similarity=0.161  Sum_probs=42.2

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCC----------------------------CCCcEEEE-EeCchH-HHHHh-CC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNS----------------------------LHESKILI-TTRKET-VARIM-GS  121 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~----------------------------~~~~~iLi-Ttr~~~-~~~~~-~~  121 (505)
                      ..-.|++|++..........+...+...                            ....++|. ||+++. +.... ..
T Consensus       175 ~gG~L~IdEI~~L~~~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrsR  254 (531)
T TIGR02902       175 HGGVLFIDEIGELHPVQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRSR  254 (531)
T ss_pred             CCcEEEEechhhCCHHHHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhhh
Confidence            4468999999776655566666544321                            11235554 455432 11111 12


Q ss_pred             cceEeCCCCChhhHHHHHHHhh
Q 046115          122 THVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus       122 ~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      ...+.+.+++.+|-.+++...+
T Consensus       255 ~~~I~f~pL~~eei~~Il~~~a  276 (531)
T TIGR02902       255 CVEIFFRPLLDEEIKEIAKNAA  276 (531)
T ss_pred             hheeeCCCCCHHHHHHHHHHHH
Confidence            3467788999998888887765

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

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

Probab=88.68  E-value=0.31  Score=40.34  Aligned_cols=41  Identities=12%  Similarity=0.103  Sum_probs=26.9

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCC-CCCcEEEEEeCch
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNS-LHESKILITTRKE  113 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~-~~~~~iLiTtr~~  113 (505)
                      +.--|+++|++.-.......+...+... ....++|.||+..
T Consensus        69 ~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~  110 (138)
T PF14532_consen   69 KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQD  110 (138)
T ss_dssp             TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-
T ss_pred             CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCC
Confidence            3345779999776655556666666543 5678999998853

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=88.52  E-value=4.3  Score=36.58  Aligned_cols=53  Identities=15%  Similarity=0.177  Sum_probs=29.9

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +.+.+..++-++++|+.... +......+...+.....+..||++|.+......
T Consensus       150 laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~  203 (221)
T cd03244         150 LARALLRKSKILVLDEATASVDPETDALIQKTIREAFKDCTVLTIAHRLDTIID  203 (221)
T ss_pred             HHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHHHHhh
Confidence            44445556678999997542 222233344444433334678888888765543

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=88.50  E-value=3.6  Score=35.51  Aligned_cols=110  Identities=21%  Similarity=0.204  Sum_probs=61.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceE--EEEeCCCCCHHHHHHHH---HHHcCCCC------CC---ChhcHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRT--WVCVSEPFDEFRIARAI---IESLTPGS------AK---DLVEFQSLMQHIE   67 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~--wv~~~~~~~~~~~~~~l---~~~l~~~~------~~---~~~~~~~~~~~l~   67 (505)
                      .|=||||=|--.+-. .+...+...+  |+.-.-.......+..+   +...+.+.      ..   +........+...
T Consensus        37 ~GKGKTTAAlG~alR-a~GhG~rv~vvQFiKg~~~~GE~~~~~~~~~~v~~~~~~~g~tw~~~~~~~d~~aa~~~w~~a~  115 (198)
T COG2109          37 NGKGKTTAALGLALR-ALGHGLRVGVVQFIKGGWKYGEEAALEKFGLGVEFHGMGEGFTWETQDREADIAAAKAGWEHAK  115 (198)
T ss_pred             CCCChhHHHHHHHHH-HhcCCCEEEEEEEeecCcchhHHHHHHhhccceeEEecCCceeCCCcCcHHHHHHHHHHHHHHH
Confidence            488999998544431 3334454332  77665444444444443   11111111      10   1122233444555


Q ss_pred             HHcCCce-EEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCc
Q 046115           68 ECVAGKK-FLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRK  112 (505)
Q Consensus        68 ~~l~~~r-~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~  112 (505)
                      +.+.+.+ =|+|||.+.-   -....++.+...+........|++|-|.
T Consensus       116 ~~l~~~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~  164 (198)
T COG2109         116 EALADGKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRG  164 (198)
T ss_pred             HHHhCCCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCC
Confidence            5666654 4889999722   2334667778877777778899999997

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=88.47  E-value=1.5  Score=43.98  Aligned_cols=81  Identities=17%  Similarity=0.216  Sum_probs=44.4

Q ss_pred             CCCcHHHHHHHHhcCccccc-CCCceEEEEeCCCC-CHHHHHHHHHHHcCCC------CCCChhcHHHH-----HHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEPF-DEFRIARAIIESLTPG------SAKDLVEFQSL-----MQHIEE   68 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~------~~~~~~~~~~~-----~~~l~~   68 (505)
                      +|+|||+|+.++++  ...+ +-+.++++-+++.. +..++...+...-...      ...+.....+.     .-.+.+
T Consensus       152 ~G~GKt~Ll~~~~~--~~~~~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~~a~tiAE  229 (461)
T PRK12597        152 AGVGKTVLMMELIF--NISKQHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVLTGLTIAE  229 (461)
T ss_pred             CCCChhHHHHHHHH--HHHhhCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            69999999999887  4443 33566677666543 4455555554421100      01111111111     111222


Q ss_pred             Hc---CCceEEEEEeCCCC
Q 046115           69 CV---AGKKFLLVLDDVWN   84 (505)
Q Consensus        69 ~l---~~~r~LlvlDdv~~   84 (505)
                      .+   .++++|+++||+.+
T Consensus       230 yfrd~~G~~VLl~~DslTR  248 (461)
T PRK12597        230 YLRDEEKEDVLLFIDNIFR  248 (461)
T ss_pred             HHHHhcCCceEEEeccchH
Confidence            33   37899999999933

>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=88.45  E-value=0.77  Score=41.15  Aligned_cols=75  Identities=19%  Similarity=0.332  Sum_probs=42.3

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHHHH--cC-----CCCCCChhcHH--------HHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAIIES--LT-----PGSAKDLVEFQ--------SLMQH   65 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~~~--l~-----~~~~~~~~~~~--------~~~~~   65 (505)
                      +|+|||+|+.++++  ...  -+.++++-+++. .+..++..++...  +.     ....++.....        ...+.
T Consensus        24 ~g~GKt~Ll~~i~~--~~~--~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~a~t~AEy   99 (215)
T PF00006_consen   24 AGVGKTVLLQEIAN--NQD--ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYTALTIAEY   99 (215)
T ss_dssp             TTSSHHHHHHHHHH--HCT--TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred             cccccchhhHHHHh--ccc--ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhccchhhhHH
Confidence            69999999999988  332  244577777765 3455555555432  10     01111111111        11122


Q ss_pred             HHHHcCCceEEEEEeCC
Q 046115           66 IEECVAGKKFLLVLDDV   82 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv   82 (505)
                      ++.  .++++|+++||+
T Consensus       100 frd--~G~dVlli~Dsl  114 (215)
T PF00006_consen  100 FRD--QGKDVLLIIDSL  114 (215)
T ss_dssp             HHH--TTSEEEEEEETH
T ss_pred             Hhh--cCCceeehhhhh
Confidence            332  689999999998

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 ....

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=88.41  E-value=1.3  Score=37.59  Aligned_cols=110  Identities=15%  Similarity=0.083  Sum_probs=55.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|.|||||++.++.  ... ...+.++++........  .......+....+  .+.-+...-.+...+...+-++++|.
T Consensus        34 nGsGKStll~~l~g--~~~-~~~G~i~~~~~~~~~~~--~~~~~~~i~~~~q--lS~G~~~r~~l~~~l~~~~~i~ilDE  106 (157)
T cd00267          34 NGSGKSTLLRAIAG--LLK-PTSGEILIDGKDIAKLP--LEELRRRIGYVPQ--LSGGQRQRVALARALLLNPDLLLLDE  106 (157)
T ss_pred             CCCCHHHHHHHHhC--CCC-CCccEEEECCEEcccCC--HHHHHhceEEEee--CCHHHHHHHHHHHHHhcCCCEEEEeC
Confidence            69999999999988  332 24555555432211100  0011111110000  22223333345556666678999999


Q ss_pred             CCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHHH
Q 046115           82 VWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVARI  118 (505)
Q Consensus        82 v~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~~  118 (505)
                      .... +......+...+... ..+..++++|-+......
T Consensus       107 p~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~  145 (157)
T cd00267         107 PTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAEL  145 (157)
T ss_pred             CCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            8542 222233333333321 124678888888766554

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.

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

Probab=88.38  E-value=2.3  Score=42.70  Aligned_cols=16  Identities=38%  Similarity=0.372  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHhcC
Q 046115            1 MGGIGKTTLAQFAYNN   16 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~   16 (505)
                      ++|.|||-||++++..
T Consensus       345 PPGTGKTlLARAvAGE  360 (752)
T KOG0734|consen  345 PPGTGKTLLARAVAGE  360 (752)
T ss_pred             CCCCchhHHHHHhhcc
Confidence            5899999999999983

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=88.34  E-value=0.6  Score=40.92  Aligned_cols=54  Identities=11%  Similarity=0.115  Sum_probs=31.2

Q ss_pred             HHHHHcCC--ceEEEEEeCCCCCCccC-h----hHHHHhhcCCCCCcEEEEEeCchHHHHHh
Q 046115           65 HIEECVAG--KKFLLVLDDVWNEDYYK-W----EPFYKCLKNSLHESKILITTRKETVARIM  119 (505)
Q Consensus        65 ~l~~~l~~--~r~LlvlDdv~~~~~~~-~----~~~~~~~~~~~~~~~iLiTtr~~~~~~~~  119 (505)
                      ++...+..  ++-++++|......+.. -    ..+...+.. ..++.++++|-..++...+
T Consensus        68 ~l~~~l~~~~~~~llllDEp~~g~d~~~~~~~~~~~l~~l~~-~~~~~iii~TH~~~l~~~~  128 (185)
T smart00534       68 ETANILKNATENSLVLLDELGRGTSTYDGVAIAAAVLEYLLE-KIGALTLFATHYHELTKLA  128 (185)
T ss_pred             HHHHHHHhCCCCeEEEEecCCCCCCHHHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHHHHh
Confidence            34444433  78899999985543211 1    222333322 2367899999987766544

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=88.32  E-value=1.6  Score=40.78  Aligned_cols=108  Identities=15%  Similarity=0.010  Sum_probs=52.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCC------CCC-CChhcHHHHHHHHHHHcCCc
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTP------GSA-KDLVEFQSLMQHIEECVAGK   73 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~------~~~-~~~~~~~~~~~~l~~~l~~~   73 (505)
                      ..|+|||||.+.++.  .+. ...+.++++-..-... +...++......      ... ..............-.....
T Consensus       119 ~~g~GKttl~~~l~~--~~~-~~~G~i~~~g~~v~~~-d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k~~~~~~~i~~~~  194 (270)
T TIGR02858       119 PPQCGKTTLLRDLAR--ILS-TGISQLGLRGKKVGIV-DERSEIAGCVNGVPQHDVGIRTDVLDGCPKAEGMMMLIRSMS  194 (270)
T ss_pred             CCCCCHHHHHHHHhC--ccC-CCCceEEECCEEeecc-hhHHHHHHHhcccccccccccccccccchHHHHHHHHHHhCC
Confidence            379999999999998  443 2345555532111100 011222222210      000 00111111111111222246


Q ss_pred             eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHH
Q 046115           74 KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVAR  117 (505)
Q Consensus        74 r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~  117 (505)
                      +-++++|.+....  .+..+...+.   .|..+|+||-+..+..
T Consensus       195 P~villDE~~~~e--~~~~l~~~~~---~G~~vI~ttH~~~~~~  233 (270)
T TIGR02858       195 PDVIVVDEIGREE--DVEALLEALH---AGVSIIATAHGRDVED  233 (270)
T ss_pred             CCEEEEeCCCcHH--HHHHHHHHHh---CCCEEEEEechhHHHH
Confidence            7799999985432  3444555442   4778999998765533

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.

>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

Probab=88.32  E-value=0.91  Score=41.44  Aligned_cols=112  Identities=19%  Similarity=0.156  Sum_probs=57.9

Q ss_pred             CCCCCCceEEEecCCCccc-cccchhHHhhcCcccceEEecccccCCccccccccCc--------------cccCCCCcc
Q 046115          352 VTGLRGLRSLLVKSDEYSW-SSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT--------------NIEKLLHLK  416 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~-~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~--------------~~~~l~~L~  416 (505)
                      +.+|+.|+..+|+.|-+.. .+..+..++.+-+.|..|.|+       |+.++.+..              ....-+.|+
T Consensus        88 Llkcp~l~~v~LSDNAfg~~~~e~L~d~is~~t~l~HL~l~-------NnGlGp~aG~rigkal~~la~nKKaa~kp~Le  160 (388)
T COG5238          88 LLKCPRLQKVDLSDNAFGSEFPEELGDLISSSTDLVHLKLN-------NNGLGPIAGGRIGKALFHLAYNKKAADKPKLE  160 (388)
T ss_pred             HhcCCcceeeeccccccCcccchHHHHHHhcCCCceeEEee-------cCCCCccchhHHHHHHHHHHHHhhhccCCCce
Confidence            3477888888888877643 223344556677778888887       444433221              123445666


Q ss_pred             eeeccCCccccccchh-----hhcCCCCcEEecCCCcCcccc------chhccccccCceeecCCCc
Q 046115          417 YLNLKGQKKIEKLPET-----LCELYNLERLNVDDCQNLREL------PRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       417 ~L~l~~~~~~~~lp~~-----~~~l~~L~~L~l~~~~~~~~l------p~~~~~l~~L~~L~l~~~~  472 (505)
                      +.....|+ +...|..     +..=.+|.++.+..|. ++.-      -.++..+.+|+.|++..|.
T Consensus       161 ~vicgrNR-lengs~~~~a~~l~sh~~lk~vki~qNg-Irpegv~~L~~~gl~y~~~LevLDlqDNt  225 (388)
T COG5238         161 VVICGRNR-LENGSKELSAALLESHENLKEVKIQQNG-IRPEGVTMLAFLGLFYSHSLEVLDLQDNT  225 (388)
T ss_pred             EEEeccch-hccCcHHHHHHHHHhhcCceeEEeeecC-cCcchhHHHHHHHHHHhCcceeeeccccc
Confidence            66666666 4433321     1111355555555544 2110      0123444555555555554

>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=88.30  E-value=0.31  Score=34.72  Aligned_cols=15  Identities=33%  Similarity=0.344  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||+|+.+.+
T Consensus         7 ~~gsGKst~~~~l~~   21 (69)
T cd02019           7 GSGSGKSTVAKKLAE   21 (69)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            379999999999998

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=88.28  E-value=1.4  Score=41.01  Aligned_cols=33  Identities=15%  Similarity=0.131  Sum_probs=23.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF   35 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~   35 (505)
                      .+|+|||++|.+++.  ...++=..+++++...+.
T Consensus        44 ~pGtGKT~l~~qf~~--~~a~~Ge~vlyis~Ee~~   76 (259)
T TIGR03878        44 VSDTGKSLMVEQFAV--TQASRGNPVLFVTVESPA   76 (259)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCcEEEEEecCCc
Confidence            479999999999876  333333467788887543

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK03839 putative kinase; Provisional

Probab=88.26  E-value=0.27  Score=42.83  Aligned_cols=15  Identities=33%  Similarity=0.583  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.+++
T Consensus         8 ~pGsGKsT~~~~La~   22 (180)
T PRK03839          8 TPGVGKTTVSKLLAE   22 (180)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999998

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=88.21  E-value=1.6  Score=40.81  Aligned_cols=82  Identities=13%  Similarity=0.082  Sum_probs=43.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCCC--CChhcHHH-HHHHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGSA--KDLVEFQS-LMQHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~--~~~~~~~~-~~~~l~~~l~~~r~L   76 (505)
                      ++|+||||.+..++.  .....-..+..++..... ...+.+....+..+.+..  ....+... ....+.....+..=+
T Consensus        80 ~~G~GKTTt~akLA~--~l~~~g~~V~li~~D~~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~l~~~~~~~~D~  157 (272)
T TIGR00064        80 VNGVGKTTTIAKLAN--KLKKQGKSVLLAAGDTFRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDAIQKAKARNIDV  157 (272)
T ss_pred             CCCCcHHHHHHHHHH--HHHhcCCEEEEEeCCCCCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHHHHHHHCCCCE
Confidence            489999999999987  444332345566644321 123444555555552211  11122222 223344433444568


Q ss_pred             EEEeCCCC
Q 046115           77 LVLDDVWN   84 (505)
Q Consensus        77 lvlDdv~~   84 (505)
                      +++|-...
T Consensus       158 ViIDT~G~  165 (272)
T TIGR00064       158 VLIDTAGR  165 (272)
T ss_pred             EEEeCCCC
Confidence            88898754

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.

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

Probab=88.20  E-value=2.3  Score=45.38  Aligned_cols=86  Identities=16%  Similarity=0.150  Sum_probs=56.1

Q ss_pred             cHHHHHHHHHHHc-CCceEEEEEeCCCCC----C----ccChhHHHHhhcCCCCCcEEEEEeCchH---HHH---HhCCc
Q 046115           58 EFQSLMQHIEECV-AGKKFLLVLDDVWNE----D----YYKWEPFYKCLKNSLHESKILITTRKET---VAR---IMGST  122 (505)
Q Consensus        58 ~~~~~~~~l~~~l-~~~r~LlvlDdv~~~----~----~~~~~~~~~~~~~~~~~~~iLiTtr~~~---~~~---~~~~~  122 (505)
                      +.++....+.+.+ +.+++.|.+|.+...    .    ..+...++++....+.--.|=.||-++.   +.+   ....+
T Consensus       246 eFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLARGeL~~IGATT~~EYRk~iEKD~AL~RRF  325 (786)
T COG0542         246 EFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIGATTLDEYRKYIEKDAALERRF  325 (786)
T ss_pred             cHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhcCCeEEEEeccHHHHHHHhhhchHHHhcC
Confidence            3444444444444 345899999997331    1    2456677777777776666778887642   222   12347


Q ss_pred             ceEeCCCCChhhHHHHHHHhh
Q 046115          123 HVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus       123 ~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +.+.+...+.++++.++....
T Consensus       326 Q~V~V~EPs~e~ti~ILrGlk  346 (786)
T COG0542         326 QKVLVDEPSVEDTIAILRGLK  346 (786)
T ss_pred             ceeeCCCCCHHHHHHHHHHHH
Confidence            789999999999999997654

>PRK12678 transcription termination factor Rho; Provisional

Probab=88.19  E-value=1.1  Score=45.91  Aligned_cols=82  Identities=21%  Similarity=0.182  Sum_probs=40.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-CceEE-EEeCCCCC-HHHHHHHHHHHcCCCCCCChhcHHH----HHHHHHHHc--C
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-EKRTW-VCVSEPFD-EFRIARAIIESLTPGSAKDLVEFQS----LMQHIEECV--A   71 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-~~~~w-v~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~~~~----~~~~l~~~l--~   71 (505)
                      .+|+|||+|+..+++  .+..+. +..++ +-+++-+. ..++.+.+-.++-............    ..-.+.+.+  .
T Consensus       424 pp~aGKTtLL~~IAn--~i~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~Ae~fre~  501 (672)
T PRK12678        424 PPKAGKTTILQNIAN--AITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIERAKRLVEL  501 (672)
T ss_pred             CCCCCHHHHHHHHHH--HHhhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHHHHHHHHc
Confidence            379999999999998  564433 33333 33444332 3333222211111111222211111    111122333  5


Q ss_pred             CceEEEEEeCCCC
Q 046115           72 GKKFLLVLDDVWN   84 (505)
Q Consensus        72 ~~r~LlvlDdv~~   84 (505)
                      ++.+||++|++..
T Consensus       502 G~dVlillDSlTR  514 (672)
T PRK12678        502 GKDVVVLLDSITR  514 (672)
T ss_pred             CCCEEEEEeCchH
Confidence            7899999999943

>PTZ00035 Rad51 protein; Provisional

Probab=88.19  E-value=1.8  Score=41.82  Aligned_cols=48  Identities=19%  Similarity=0.095  Sum_probs=30.3

Q ss_pred             CCCCcHHHHHHHHhcCcccc----cCCCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVE----RNFEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~----~~f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+|+..++-..+..    +.=..++||+....+.... +.++++.++
T Consensus       126 ~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g  177 (337)
T PTZ00035        126 EFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFG  177 (337)
T ss_pred             CCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhC
Confidence            37999999998887532211    1223566999877776655 444455544

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=88.12  E-value=0.92  Score=40.32  Aligned_cols=19  Identities=32%  Similarity=0.359  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHhcCcccccC
Q 046115            2 GGIGKTTLAQFAYNNGDVERN   22 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~   22 (505)
                      +|+||||+|++++.  .+...
T Consensus        17 SgSGKTTva~~l~~--~~~~~   35 (218)
T COG0572          17 SGSGKTTVAKELSE--QLGVE   35 (218)
T ss_pred             CCCCHHHHHHHHHH--HhCcC
Confidence            69999999999998  55544

>PRK06217 hypothetical protein; Validated

Probab=88.11  E-value=0.68  Score=40.47  Aligned_cols=16  Identities=31%  Similarity=0.335  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhcC
Q 046115            1 MGGIGKTTLAQFAYNN   16 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~   16 (505)
                      ++|+||||+|++++..
T Consensus         9 ~~GsGKSTla~~L~~~   24 (183)
T PRK06217          9 ASGSGTTTLGAALAER   24 (183)
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            4799999999999973

>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=88.11  E-value=1.2  Score=39.35  Aligned_cols=49  Identities=16%  Similarity=0.086  Sum_probs=31.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHHHHcCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAIIESLTPG   51 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~~~l~~~   51 (505)
                      +.|+||||.+.+++.  ....+=..+..++.... ....+.++...+.++.+
T Consensus         9 ptGvGKTTt~aKLAa--~~~~~~~~v~lis~D~~R~ga~eQL~~~a~~l~vp   58 (196)
T PF00448_consen    9 PTGVGKTTTIAKLAA--RLKLKGKKVALISADTYRIGAVEQLKTYAEILGVP   58 (196)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTT--EEEEEESTSSTHHHHHHHHHHHHHTEE
T ss_pred             CCCCchHhHHHHHHH--HHhhccccceeecCCCCCccHHHHHHHHHHHhccc
Confidence            479999999988887  44444334557775543 34456677777777644

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 ....

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=88.08  E-value=1.4  Score=37.05  Aligned_cols=15  Identities=33%  Similarity=0.516  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||+|+.+..
T Consensus         7 ~~GsGKSTla~~L~~   21 (149)
T cd02027           7 LSGSGKSTIARALEE   21 (149)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999988

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=88.07  E-value=2.9  Score=35.58  Aligned_cols=15  Identities=33%  Similarity=0.481  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.+..
T Consensus         6 ~~GsGKSTla~~l~~   20 (163)
T TIGR01313         6 VAGSGKSTIASALAH   20 (163)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

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.

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=88.02  E-value=1.7  Score=47.06  Aligned_cols=85  Identities=16%  Similarity=0.110  Sum_probs=50.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC--CChhcHHHHHHHHHHHcCCc-eEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA--KDLVEFQSLMQHIEECVAGK-KFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~l~~~l~~~-r~Ll   77 (505)
                      +.|+|||-||++++.  .+-+..+.-+-++.++.-+        ..++.....  ..-.    ....|-..++++ -..|
T Consensus       599 pdgvGKt~lAkaLA~--~~Fgse~~~IriDmse~~e--------vskligsp~gyvG~e----~gg~LteavrrrP~sVV  664 (898)
T KOG1051|consen  599 PDGVGKTELAKALAE--YVFGSEENFIRLDMSEFQE--------VSKLIGSPPGYVGKE----EGGQLTEAVKRRPYSVV  664 (898)
T ss_pred             CCchhHHHHHHHHHH--HHcCCccceEEechhhhhh--------hhhccCCCcccccch----hHHHHHHHHhcCCceEE
Confidence            469999999999998  6656666666677665211        333321111  1122    223556666665 5678


Q ss_pred             EEeCCCCCCccChhHHHHhhcC
Q 046115           78 VLDDVWNEDYYKWEPFYKCLKN   99 (505)
Q Consensus        78 vlDdv~~~~~~~~~~~~~~~~~   99 (505)
                      +||||...+......+.+.+..
T Consensus       665 LfdeIEkAh~~v~n~llq~lD~  686 (898)
T KOG1051|consen  665 LFEEIEKAHPDVLNILLQLLDR  686 (898)
T ss_pred             EEechhhcCHHHHHHHHHHHhc
Confidence            8999977665444444444443

>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=88.00  E-value=0.45  Score=44.27  Aligned_cols=31  Identities=26%  Similarity=0.272  Sum_probs=23.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCC-CceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF-EKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f-~~~~wv~~~~~   34 (505)
                      ||+||||+|..++.  ..+..- ..++-|+...+
T Consensus        12 GGvGKTT~a~nLa~--~La~~~~~kVLliDlDpQ   43 (259)
T COG1192          12 GGVGKTTTAVNLAA--ALAKRGGKKVLLIDLDPQ   43 (259)
T ss_pred             CCccHHHHHHHHHH--HHHHhcCCcEEEEeCCCc
Confidence            89999999999998  666333 56777876654

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=87.99  E-value=1.2  Score=47.66  Aligned_cols=76  Identities=16%  Similarity=0.122  Sum_probs=47.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  .....=..++|++..+.++..     .++.++....    ......++....+...+. ++--
T Consensus        68 ~~GsGKTtLal~~~~--~a~~~G~~v~yId~E~t~~~~-----~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~~~~~~  140 (790)
T PRK09519         68 PESSGKTTVALHAVA--NAQAAGGVAAFIDAEHALDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALD  140 (790)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEECCccchhHH-----HHHHcCCChhHeEEecCCCHHHHHHHHHHHhhcCCCe
Confidence            379999999988776  333333567899988877742     5555653321    112233444455555443 3567


Q ss_pred             EEEEeCCC
Q 046115           76 LLVLDDVW   83 (505)
Q Consensus        76 LlvlDdv~   83 (505)
                      |+|+|.+.
T Consensus       141 LVVIDSI~  148 (790)
T PRK09519        141 IVVIDSVA  148 (790)
T ss_pred             EEEEcchh
Confidence            89999984

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=87.89  E-value=0.95  Score=37.32  Aligned_cols=60  Identities=17%  Similarity=0.247  Sum_probs=34.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAG   72 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~   72 (505)
                      +|+||||+|.+++..  .     +.-|++++.-....+    +.......-.--..+.+...+.|...+..
T Consensus        16 PG~GKstl~~~lae~--~-----~~~~i~isd~vkEn~----l~~gyDE~y~c~i~DEdkv~D~Le~~m~~   75 (176)
T KOG3347|consen   16 PGTGKSTLAERLAEK--T-----GLEYIEISDLVKENN----LYEGYDEEYKCHILDEDKVLDELEPLMIE   75 (176)
T ss_pred             CCCCchhHHHHHHHH--h-----CCceEehhhHHhhhc----chhcccccccCccccHHHHHHHHHHHHhc
Confidence            799999999999972  2     334666665322222    22223222233345566666776666644

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

Probab=87.77  E-value=2.1  Score=36.87  Aligned_cols=111  Identities=11%  Similarity=-0.071  Sum_probs=58.9

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceE--EEEeCCCCCHHHHHHHHH----HHcCCCC---CCC-----hhcHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRT--WVCVSEPFDEFRIARAII----ESLTPGS---AKD-----LVEFQSLMQHIE   67 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~--wv~~~~~~~~~~~~~~l~----~~l~~~~---~~~-----~~~~~~~~~~l~   67 (505)
                      .|=||||-|.-.+-. .....+...+  |+.-.........+..+-    .+++.+.   ..+     .....+..+..+
T Consensus        30 dGKGKTTAAlGlalR-AaG~G~rV~iiQFlKg~~~~GE~~~l~~~~~v~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~a~  108 (178)
T PRK07414         30 SQRNFFTSVMAQALR-IAGQGTPVLIVQFLKGGIQQGPDRPIQLGQNLDWVRCDLPRCLDTPHLDESEKKALQELWQYTQ  108 (178)
T ss_pred             CCCCchHHHHHHHHH-HhcCCCEEEEEEEecCCCcchHHHHHHhCCCcEEEECCCCCeeeCCCcCHHHHHHHHHHHHHHH
Confidence            478999999555431 2233343322  555443334434433321    1111110   011     111123344455


Q ss_pred             HHcCC-ceEEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           68 ECVAG-KKFLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        68 ~~l~~-~r~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      +.+.. .-=|+|||.+-.   -...+.+.+...+.....+..|++|-|+.
T Consensus       109 ~~l~~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~  158 (178)
T PRK07414        109 AVVDEGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEM  158 (178)
T ss_pred             HHHhCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCC
Confidence            55544 456999999732   23345667777777777888999999983

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=87.67  E-value=5.1  Score=35.62  Aligned_cols=57  Identities=12%  Similarity=0.102  Sum_probs=32.3

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHHHhCC
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVARIMGS  121 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~~~~~  121 (505)
                      .+...+...+-++++|.-... +......+...+... ..+..||++|.+......++.
T Consensus       139 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~i~~~~~  197 (204)
T PRK13538        139 ALARLWLTRAPLWILDEPFTAIDKQGVARLEALLAQHAEQGGMVILTTHQDLPVASDKV  197 (204)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecChhhhccCCc
Confidence            345555566778899997442 222233333333321 235678888888766655444

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=87.57  E-value=1.2  Score=43.41  Aligned_cols=80  Identities=15%  Similarity=0.104  Sum_probs=42.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC--CceEEEEeCCC-CCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEP-FDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f--~~~~wv~~~~~-~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      +.|+||||++.+++.  .....+  ..+..++.... ....+.++...+.++.+... ..+..+....+ ..+.++ -++
T Consensus       145 ptGvGKTTtiakLA~--~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~-~~~~~~l~~~l-~~l~~~-DlV  219 (374)
T PRK14722        145 PTGVGKTTTTAKLAA--RCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHA-VKDGGDLQLAL-AELRNK-HMV  219 (374)
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEe-cCCcccHHHHH-HHhcCC-CEE
Confidence            479999999999987  433333  34556654332 23455666666666643321 11111122222 334444 456


Q ss_pred             EEeCCCCC
Q 046115           78 VLDDVWNE   85 (505)
Q Consensus        78 vlDdv~~~   85 (505)
                      ++|.....
T Consensus       220 LIDTaG~~  227 (374)
T PRK14722        220 LIDTIGMS  227 (374)
T ss_pred             EEcCCCCC
Confidence            69998543

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=87.57  E-value=1.8  Score=43.13  Aligned_cols=79  Identities=19%  Similarity=0.201  Sum_probs=41.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCC------CCChhcHHHH-----HHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGS------AKDLVEFQSL-----MQHIEEC   69 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~------~~~~~~~~~~-----~~~l~~~   69 (505)
                      .|+|||||++.+++  ...  .+.++..-+++.. +..++...++..-....      ..+.....+.     .-.+.+.
T Consensus       171 sG~GKSTLL~~I~~--~~~--~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~A~tiAEy  246 (444)
T PRK08972        171 SGVGKSVLLGMMTR--GTT--ADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCETATTIAEY  246 (444)
T ss_pred             CCCChhHHHHHhcc--CCC--CCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            69999999999987  222  2455566666544 34445555444311110      1111111111     0112222


Q ss_pred             c--CCceEEEEEeCCCC
Q 046115           70 V--AGKKFLLVLDDVWN   84 (505)
Q Consensus        70 l--~~~r~LlvlDdv~~   84 (505)
                      +  .++++|+++||+.+
T Consensus       247 frd~G~~VLl~~DslTR  263 (444)
T PRK08972        247 FRDQGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHcCCCEEEEEcChHH
Confidence            2  57899999999843

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=87.49  E-value=4.4  Score=36.48  Aligned_cols=53  Identities=17%  Similarity=0.201  Sum_probs=30.7

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +...+..++-++++|..... +......+...+.....+..||++|.+......
T Consensus       144 la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~~~~~~  197 (220)
T cd03263         144 LAIALIGGPSVLLLDEPTSGLDPASRRAIWDLILEVRKGRSIILTTHSMDEAEA  197 (220)
T ss_pred             HHHHHhcCCCEEEECCCCCCCCHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHH
Confidence            44555667789999997542 222233344433332234678888888765543

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=87.40  E-value=2  Score=42.87  Aligned_cols=80  Identities=20%  Similarity=0.180  Sum_probs=42.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCC-------CCCChhcHHH----HHHHHHHHc
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPG-------SAKDLVEFQS----LMQHIEECV   70 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~-------~~~~~~~~~~----~~~~l~~~l   70 (505)
                      +|+|||||+..++..  ... ..+++.+.-.+..+..+.....+..-+..       ...+..-...    ....+.+.+
T Consensus       165 sG~GKTtLl~~Ia~~--~~~-~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~~~a~~iAEyf  241 (432)
T PRK06793        165 SGVGKSTLLGMIAKN--AKA-DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAAKLATSIAEYF  241 (432)
T ss_pred             CCCChHHHHHHHhcc--CCC-CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            699999999999873  321 22344433334456666666555442211       1111111111    111122222


Q ss_pred             --CCceEEEEEeCCCC
Q 046115           71 --AGKKFLLVLDDVWN   84 (505)
Q Consensus        71 --~~~r~LlvlDdv~~   84 (505)
                        .++++||++|++.+
T Consensus       242 r~~G~~VLlilDslTr  257 (432)
T PRK06793        242 RDQGNNVLLMMDSVTR  257 (432)
T ss_pred             HHcCCcEEEEecchHH
Confidence              47899999999955

>PHA02518 ParA-like protein; Provisional

Probab=87.37  E-value=0.7  Score=41.32  Aligned_cols=35  Identities=26%  Similarity=0.135  Sum_probs=23.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEF   38 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~   38 (505)
                      ||+||||+|..++.  ..+.+=..++-|+...+.+..
T Consensus        10 GGvGKTT~a~~la~--~la~~g~~vlliD~D~q~~~~   44 (211)
T PHA02518         10 GGAGKTTVATNLAS--WLHADGHKVLLVDLDPQGSST   44 (211)
T ss_pred             CCCCHHHHHHHHHH--HHHhCCCeEEEEeCCCCCChH
Confidence            89999999998877  444332345567766555443

>PRK00625 shikimate kinase; Provisional

Probab=87.37  E-value=0.33  Score=41.91  Aligned_cols=15  Identities=20%  Similarity=0.359  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.++.
T Consensus         8 ~pGsGKTT~~k~La~   22 (173)
T PRK00625          8 LPTVGKTSFGKALAK   22 (173)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999987

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=87.20  E-value=2.4  Score=42.54  Aligned_cols=81  Identities=21%  Similarity=0.270  Sum_probs=43.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCC-CceEEEEeCCCC-CHHHHHHHHHHHcCCCC------CCChhcHHHH-----HHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF-EKRTWVCVSEPF-DEFRIARAIIESLTPGS------AKDLVEFQSL-----MQHIEE   68 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f-~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~------~~~~~~~~~~-----~~~l~~   68 (505)
                      +|+|||+|+..++.  ....+. +.++++-+++.. +..++..++...=....      ..+.....+.     .-.+.+
T Consensus       153 ~GvGKt~Ll~~i~~--~~~~~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~a~tiAE  230 (463)
T PRK09280        153 AGVGKTVLIQELIN--NIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALTGLTMAE  230 (463)
T ss_pred             CCCChhHHHHHHHH--HHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            69999999998876  343332 345566666543 45566666554321100      0111111111     111223


Q ss_pred             Hc---CCceEEEEEeCCCC
Q 046115           69 CV---AGKKFLLVLDDVWN   84 (505)
Q Consensus        69 ~l---~~~r~LlvlDdv~~   84 (505)
                      .+   .++++||++|++.+
T Consensus       231 yfrd~~G~~VLll~DslTR  249 (463)
T PRK09280        231 YFRDVEGQDVLLFIDNIFR  249 (463)
T ss_pred             HHHHhcCCceEEEecchHH
Confidence            33   67899999999943

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=87.15  E-value=1.2  Score=47.88  Aligned_cols=102  Identities=16%  Similarity=0.132  Sum_probs=51.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|+|||.+|+.+.+.  -...-...+.+++....+ ..+...+...-. +.....  .......+.   ....-.|+||+
T Consensus       408 ~GTGK~~lA~~ih~~--s~r~~~~~v~i~c~~~~~-~~~~~~lfg~~~-~~~~g~--~~~~~g~le---~a~~GtL~Lde  478 (686)
T PRK15429        408 TGTGKELIARAIHNL--SGRNNRRMVKMNCAAMPA-GLLESDLFGHER-GAFTGA--SAQRIGRFE---LADKSSLFLDE  478 (686)
T ss_pred             CCcCHHHHHHHHHHh--cCCCCCCeEEEecccCCh-hHhhhhhcCccc-cccccc--ccchhhHHH---hcCCCeEEEec
Confidence            699999999999873  222223445566665321 112222222111 000000  001111121   12235799999


Q ss_pred             CCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           82 VWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |..-......++...+....           .+.+||.||..
T Consensus       479 i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~  520 (686)
T PRK15429        479 VGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNR  520 (686)
T ss_pred             hhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCC
Confidence            97765555556666554321           34578888764

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=87.14  E-value=7.9  Score=33.64  Aligned_cols=54  Identities=13%  Similarity=0.110  Sum_probs=30.9

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHHH
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVARI  118 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~~  118 (505)
                      .+.+.+..++-++++|+-... +......+.+.+... ..+..||++|.+......
T Consensus       114 ~la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~~  169 (182)
T cd03215         114 VLARWLARDPRVLILDEPTRGVDVGAKAEIYRLIRELADAGKAVLLISSELDELLG  169 (182)
T ss_pred             HHHHHHccCCCEEEECCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            355556667789999997442 222233333333322 236678999888654443

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. In members of 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.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=87.03  E-value=0.88  Score=40.89  Aligned_cols=49  Identities=10%  Similarity=0.089  Sum_probs=29.8

Q ss_pred             CCceEEEEEeCCCCCCcc-C----hhHHHHhhcCCC-CCcEEEEEeCchHHHHHh
Q 046115           71 AGKKFLLVLDDVWNEDYY-K----WEPFYKCLKNSL-HESKILITTRKETVARIM  119 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~-~----~~~~~~~~~~~~-~~~~iLiTtr~~~~~~~~  119 (505)
                      ...+-|+++|......+. +    ...+...+...+ .+..+|+||-...+....
T Consensus       106 ~~~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~~~  160 (213)
T cd03281         106 ATRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRS  160 (213)
T ss_pred             CCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHHhh
Confidence            467899999998664321 1    123344443332 245799999987766543

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

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=86.96  E-value=2.7  Score=41.59  Aligned_cols=15  Identities=33%  Similarity=0.135  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||+|..++.
T Consensus       231 ptGvGKTTtaaKLA~  245 (432)
T PRK12724        231 PTGSGKTTSIAKLAA  245 (432)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999986

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=86.95  E-value=14  Score=38.81  Aligned_cols=144  Identities=19%  Similarity=0.204  Sum_probs=78.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||-||.+++..  -     ..-+|++..+        +++.+.-      ..+.+...+...+.-.-++|.|.||
T Consensus       709 ppGcGKT~la~a~a~~--~-----~~~fisvKGP--------ElL~KyI------GaSEq~vR~lF~rA~~a~PCiLFFD  767 (952)
T KOG0735|consen  709 PPGCGKTLLASAIASN--S-----NLRFISVKGP--------ELLSKYI------GASEQNVRDLFERAQSAKPCILFFD  767 (952)
T ss_pred             CCCCcHHHHHHHHHhh--C-----CeeEEEecCH--------HHHHHHh------cccHHHHHHHHHHhhccCCeEEEec
Confidence            5899999999999872  1     2235776653        3333322      1122333444445556689999999


Q ss_pred             CCCCCC-----------ccChhHHHHhhcCC--CCCcEEEE-EeCchHHHHHh---CC-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNED-----------YYKWEPFYKCLKNS--LHESKILI-TTRKETVARIM---GS-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~~-----------~~~~~~~~~~~~~~--~~~~~iLi-Ttr~~~~~~~~---~~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      ..++..           +....+++..+...  -.|.-|+. |||-.-+....   +. .+.+.-+.-++.|-.++|+..
T Consensus       768 EfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~l  847 (952)
T KOG0735|consen  768 EFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVL  847 (952)
T ss_pred             cccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHH
Confidence            985421           12234444444422  13555555 55543332221   22 456666777888888888776


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      .-.-.. ...    -..+.++...+|+.
T Consensus       848 s~s~~~-~~~----vdl~~~a~~T~g~t  870 (952)
T KOG0735|consen  848 SNSLLK-DTD----VDLECLAQKTDGFT  870 (952)
T ss_pred             hhccCC-ccc----cchHHHhhhcCCCc
Confidence            521111 111    22556777777766

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=86.91  E-value=8.5  Score=35.45  Aligned_cols=58  Identities=14%  Similarity=0.076  Sum_probs=38.9

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHhCC-cceEeCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIMGS-THVISVNVL  130 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~~~-~~~~~l~~l  130 (505)
                      ++-++|+|+++.........+++.+.....++.+|.+|.++ .+..-+.+ ...+.+...
T Consensus        88 ~~KV~II~~ae~m~~~AaNaLLK~LEEPp~~t~fiLit~~~~~lLpTI~SRCq~~~~~~~  147 (261)
T PRK05818         88 GKKIYIIYGIEKLNKQSANSLLKLIEEPPKNTYGIFTTRNENNILNTILSRCVQYVVLSK  147 (261)
T ss_pred             CCEEEEeccHhhhCHHHHHHHHHhhcCCCCCeEEEEEECChHhCchHhhhheeeeecCCh
Confidence            45677899998877778888999998887777777777664 33332222 235555554

>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=86.86  E-value=0.59  Score=40.90  Aligned_cols=32  Identities=28%  Similarity=0.148  Sum_probs=23.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      .+|+|||+||.+++.  ...++=..++|++...+
T Consensus         7 ~~G~GKT~l~~~~~~--~~~~~g~~v~~~s~e~~   38 (187)
T cd01124           7 GPGTGKTTFALQFLY--AGLARGEPGLYVTLEES   38 (187)
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCcEEEEECCCC
Confidence            479999999999887  33333356778887654

A related protein is found in archaea.

>CHL00206 ycf2 Ycf2; Provisional

Probab=86.85  E-value=8.8  Score=45.23  Aligned_cols=70  Identities=9%  Similarity=0.085  Sum_probs=38.6

Q ss_pred             CCceEEEEEeCCCCCCc-----cChhHHHHhhcCC-----CCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhH
Q 046115           71 AGKKFLLVLDDVWNEDY-----YKWEPFYKCLKNS-----LHESKILITTRKETVAR-IM---GS-THVISVNVLSEMEC  135 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~-----~~~~~~~~~~~~~-----~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea  135 (505)
                      +..+++|.+|+++.-..     ..+..++..+...     ..+.-||.+|..++... +.   +. .+.+.++.++..+-
T Consensus      1730 k~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R 1809 (2281)
T CHL00206       1730 AMSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQ 1809 (2281)
T ss_pred             HCCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhH
Confidence            45689999999865321     1245666555532     23444566665554422 21   22 45777776666555


Q ss_pred             HHHHH
Q 046115          136 WSVFQ  140 (505)
Q Consensus       136 ~~Lf~  140 (505)
                      .+.|.
T Consensus      1810 ~kiL~ 1814 (2281)
T CHL00206       1810 RKHFF 1814 (2281)
T ss_pred             HHHHH
Confidence            55443

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=86.80  E-value=8.4  Score=35.90  Aligned_cols=94  Identities=12%  Similarity=0.110  Sum_probs=56.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+-++++++.      .+..+-+..+..++...++..+...........   .-.....+..++.+..-+++.|
T Consensus       102 ~~g~gKt~a~~~y~~s------~p~~~l~~~~p~~~a~~~i~~i~~~~~~~~~~~---~~d~~~~~~~~l~~~~~~iivD  172 (297)
T COG2842         102 YAGLGKTQAAKNYAPS------NPNALLIEADPSYTALVLILIICAAAFGATDGT---INDLTERLMIRLRDTVRLIIVD  172 (297)
T ss_pred             cccchhHHHHHhhccc------CccceeecCChhhHHHHHHHHHHHHHhcccchh---HHHHHHHHHHHHccCcceeeee
Confidence            4799999999999983      223333456666666566665555544222221   2223334444557777889999


Q ss_pred             CCCCCCccChhHHHHhhcCCCCC
Q 046115           81 DVWNEDYYKWEPFYKCLKNSLHE  103 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~~~  103 (505)
                      +.+.-....++.+.......+-+
T Consensus       173 EA~~L~~~ale~lr~i~d~~Gi~  195 (297)
T COG2842         173 EADRLPYRALEELRRIHDKTGIG  195 (297)
T ss_pred             hhhccChHHHHHHHHHHHhhCce
Confidence            98775555566666555544444

>PRK10867 signal recognition particle protein; Provisional

Probab=86.78  E-value=1.7  Score=43.53  Aligned_cols=15  Identities=40%  Similarity=0.370  Sum_probs=12.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||.|..++.
T Consensus       108 ~~GsGKTTtaakLA~  122 (433)
T PRK10867        108 LQGAGKTTTAGKLAK  122 (433)
T ss_pred             CCCCcHHHHHHHHHH
Confidence            479999998888876

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.73  E-value=0.14  Score=44.35  Aligned_cols=83  Identities=18%  Similarity=0.223  Sum_probs=39.2

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccc-hhhhc
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP-ETLCE  435 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~  435 (505)
                      .+..++-++..+...   --..+..++.++.|.+.+++.+.+. .++.+.   +..++|+.|++++|+.+++-. ..+.+
T Consensus       102 ~IeaVDAsds~I~~e---Gle~L~~l~~i~~l~l~~ck~~dD~-~L~~l~---~~~~~L~~L~lsgC~rIT~~GL~~L~~  174 (221)
T KOG3864|consen  102 KIEAVDASDSSIMYE---GLEHLRDLRSIKSLSLANCKYFDDW-CLERLG---GLAPSLQDLDLSGCPRITDGGLACLLK  174 (221)
T ss_pred             eEEEEecCCchHHHH---HHHHHhccchhhhheeccccchhhH-HHHHhc---ccccchheeeccCCCeechhHHHHHHH
Confidence            355555555544321   2222555556666666532211100 011111   134566677777666655432 23456


Q ss_pred             CCCCcEEecCC
Q 046115          436 LYNLERLNVDD  446 (505)
Q Consensus       436 l~~L~~L~l~~  446 (505)
                      +++|+.|.|++
T Consensus       175 lknLr~L~l~~  185 (221)
T KOG3864|consen  175 LKNLRRLHLYD  185 (221)
T ss_pred             hhhhHHHHhcC
Confidence            66666666555

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=86.70  E-value=2.3  Score=39.44  Aligned_cols=41  Identities=17%  Similarity=0.227  Sum_probs=23.7

Q ss_pred             CCCcHHHHH-HHHhcCcccccCCCce-EEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLA-QFAYNNGDVERNFEKR-TWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA-~~~~~~~~~~~~f~~~-~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|| ..+++  +.  +-+.+ +++-+++.. +..++..++..
T Consensus        78 ~g~GKt~L~l~~i~~--~~--~~~v~~V~~~iGer~~ev~e~~~~~~~  121 (274)
T cd01132          78 RQTGKTAIAIDTIIN--QK--GKKVYCIYVAIGQKASTVAQVVKTLEE  121 (274)
T ss_pred             CCCCccHHHHHHHHH--hc--CCCeEEEEEecccchHHHHHHHHHHHh
Confidence            579999996 55555  22  23444 455566643 44555555553

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.

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=86.63  E-value=1.9  Score=43.57  Aligned_cols=41  Identities=15%  Similarity=0.174  Sum_probs=25.9

Q ss_pred             CCCcHHHHH-HHHhcCcccccCCCc-eEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLA-QFAYNNGDVERNFEK-RTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA-~~~~~~~~~~~~f~~-~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|| ..+++  +.  .-+. ++++-+++.. +..++...+..
T Consensus       171 ~g~GKT~Lal~~I~~--q~--~~dv~~V~~~IGeR~rev~e~i~~l~~  214 (497)
T TIGR03324       171 RQTGKTAIAIDTILN--QK--GRNVLCIYCAIGQRASAVAKVVANLRE  214 (497)
T ss_pred             CCCCHHHHHHHHHHH--hc--CCCcEEEEEEeccCcHHHHHHHHHhhh
Confidence            499999997 57777  32  3344 5677777754 44555555544

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, 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 alpha subunit of this apparent second ATP synthase.

>PRK06762 hypothetical protein; Provisional

Probab=86.58  E-value=0.4  Score=41.14  Aligned_cols=15  Identities=40%  Similarity=0.443  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        10 ~~GsGKST~A~~L~~   24 (166)
T PRK06762         10 NSGSGKTTIAKQLQE   24 (166)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

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

Probab=86.49  E-value=0.52  Score=43.90  Aligned_cols=31  Identities=29%  Similarity=0.259  Sum_probs=27.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      +|+|||++|.+++.  +..++...++||+..+.
T Consensus        32 pGsGKT~f~~qfl~--~~~~~ge~vlyvs~~e~   62 (260)
T COG0467          32 PGTGKTIFALQFLY--EGAREGEPVLYVSTEES   62 (260)
T ss_pred             CCCcHHHHHHHHHH--HHHhcCCcEEEEEecCC
Confidence            79999999999998  66777888999998875

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=86.32  E-value=2.2  Score=43.92  Aligned_cols=89  Identities=16%  Similarity=0.106  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHcCCCCCCC------hhcHHHHHHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEe
Q 046115           38 FRIARAIIESLTPGSAKD------LVEFQSLMQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITT  110 (505)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~------~~~~~~~~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTt  110 (505)
                      ....+..+..++.+....      .+.-+...-.+...+..+.-+||||.-.+. +....+.+...+..+. | .||+.|
T Consensus       416 e~~~r~~L~~f~F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f~-G-tvl~VS  493 (530)
T COG0488         416 EQEVRAYLGRFGFTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDFE-G-TVLLVS  493 (530)
T ss_pred             HHHHHHHHHHcCCChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhCC-C-eEEEEe
Confidence            344555555555443322      222233444566666778899999997553 4445566666666553 4 488889


Q ss_pred             CchHHHHHhCCcceEeCCC
Q 046115          111 RKETVARIMGSTHVISVNV  129 (505)
Q Consensus       111 r~~~~~~~~~~~~~~~l~~  129 (505)
                      -++.....+. ..++.+.+
T Consensus       494 HDr~Fl~~va-~~i~~~~~  511 (530)
T COG0488         494 HDRYFLDRVA-TRIWLVED  511 (530)
T ss_pred             CCHHHHHhhc-ceEEEEcC
Confidence            9988777655 34666654

>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=86.31  E-value=0.34  Score=45.35  Aligned_cols=72  Identities=24%  Similarity=0.234  Sum_probs=34.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .+|+|||++++.+..  ..... . .+.-++++...+... ++.+++.-.......          ...--.+|+.++.+
T Consensus        41 ~~GtGKT~li~~~l~--~l~~~-~~~~~~~~~s~~Tts~~-~q~~ie~~l~k~~~~----------~~gP~~~k~lv~fi  106 (272)
T PF12775_consen   41 PSGTGKTSLIQNFLS--SLDSD-KYLVITINFSAQTTSNQ-LQKIIESKLEKRRGR----------VYGPPGGKKLVLFI  106 (272)
T ss_dssp             STTSSHHHHHHHHHH--CSTTC-CEEEEEEES-TTHHHHH-HHHCCCTTECECTTE----------EEEEESSSEEEEEE
T ss_pred             CCCCchhHHHHhhhc--cCCcc-ccceeEeeccCCCCHHH-HHHHHhhcEEcCCCC----------CCCCCCCcEEEEEe
Confidence            479999999999886  33221 2 123455554433322 222222111000000          00012468899999


Q ss_pred             eCCCCCC
Q 046115           80 DDVWNED   86 (505)
Q Consensus        80 Ddv~~~~   86 (505)
                      ||+.-+.
T Consensus       107 DDlN~p~  113 (272)
T PF12775_consen  107 DDLNMPQ  113 (272)
T ss_dssp             ETTT-S-
T ss_pred             cccCCCC
Confidence            9995544

>PF07015 VirC1: VirC1 protein; InterPro: IPR009744 This family consists of several bacterial VirC1 proteins

Probab=86.29  E-value=0.81  Score=41.06  Aligned_cols=31  Identities=23%  Similarity=0.231  Sum_probs=22.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      ||.||||++..++.  ....+=..+.-|+...+
T Consensus        11 GGaGKTT~~~~LAs--~la~~G~~V~lIDaDpn   41 (231)
T PF07015_consen   11 GGAGKTTAAMALAS--ELAARGARVALIDADPN   41 (231)
T ss_pred             CCCcHHHHHHHHHH--HHHHCCCeEEEEeCCCC
Confidence            89999999999998  66555455556665443

In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [].

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=86.28  E-value=3.5  Score=36.58  Aligned_cols=57  Identities=14%  Similarity=0.069  Sum_probs=33.2

Q ss_pred             HHHHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchHHHH
Q 046115           61 SLMQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKETVAR  117 (505)
Q Consensus        61 ~~~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~~~~  117 (505)
                      ...-.+.+.+...+-++++|+.... +......+...+... ..+..||++|.+.....
T Consensus       110 ~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~L~~~~~~~~tiii~sh~~~~~~  168 (200)
T cd03217         110 KKRNEILQLLLLEPDLAILDEPDSGLDIDALRLVAEVINKLREEGKSVLIITHYQRLLD  168 (200)
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecCHHHHH
Confidence            3344456666667789999997442 222233333333322 23667888888876655

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PTZ00185 ATPase alpha subunit; Provisional

Probab=86.28  E-value=3.8  Score=41.56  Aligned_cols=81  Identities=19%  Similarity=0.263  Sum_probs=43.4

Q ss_pred             CCCcHHHHH-HHHhcCcccc-----cCCCceEEEEeCCCCCHHHHHHHHHHHcCC---C-----CCCChhcHH-------
Q 046115            2 GGIGKTTLA-QFAYNNGDVE-----RNFEKRTWVCVSEPFDEFRIARAIIESLTP---G-----SAKDLVEFQ-------   60 (505)
Q Consensus         2 ~G~GKT~LA-~~~~~~~~~~-----~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~---~-----~~~~~~~~~-------   60 (505)
                      .|+|||+|| ..+++...+.     ++-..++++-+++......-+...+++-+.   .     ...+..-..       
T Consensus       198 ~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~r~~Apy~a  277 (574)
T PTZ00185        198 RQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGLQYLAPYSG  277 (574)
T ss_pred             CCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHHHHHHHHHH
Confidence            599999998 5666632111     233456688888866554444444444331   0     011111111       


Q ss_pred             -HHHHHHHHHcCCceEEEEEeCCCC
Q 046115           61 -SLMQHIEECVAGKKFLLVLDDVWN   84 (505)
Q Consensus        61 -~~~~~l~~~l~~~r~LlvlDdv~~   84 (505)
                       ...+.+++  .++.+|+|+||+.+
T Consensus       278 ~tiAEYFrd--~GkdVLiv~DDLTr  300 (574)
T PTZ00185        278 VTMGEYFMN--RGRHCLCVYDDLSK  300 (574)
T ss_pred             HHHHHHHHH--cCCCEEEEEcCchH
Confidence             11222332  47899999999843

>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=86.18  E-value=3.1  Score=37.61  Aligned_cols=15  Identities=27%  Similarity=0.273  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||+|+.++.
T Consensus         7 ~sGSGKTTla~~L~~   21 (220)
T cd02025           7 SVAVGKSTTARVLQA   21 (220)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            379999999999987

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

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=86.16  E-value=4.6  Score=40.49  Aligned_cols=79  Identities=11%  Similarity=0.060  Sum_probs=40.3

Q ss_pred             CCCCcHHHHHHHHhcCcccc--cCCCceEEEEeCCCCC-HHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVE--RNFEKRTWVCVSEPFD-EFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~--~~f~~~~wv~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      ++|+||||++..++.  ...  ..-..+..|+...... ..+.+....+.++.+... ..+..+....+.+ +. ..=++
T Consensus       229 ptGvGKTTt~~kLA~--~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~-~~~~~~l~~~l~~-~~-~~DlV  303 (424)
T PRK05703        229 PTGVGKTTTLAKLAA--RYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEV-VYDPKELAKALEQ-LR-DCDVI  303 (424)
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEc-cCCHHhHHHHHHH-hC-CCCEE
Confidence            479999999988876  333  2223555676543221 123333334444432211 1222333333333 23 35688


Q ss_pred             EEeCCCC
Q 046115           78 VLDDVWN   84 (505)
Q Consensus        78 vlDdv~~   84 (505)
                      ++|....
T Consensus       304 lIDt~G~  310 (424)
T PRK05703        304 LIDTAGR  310 (424)
T ss_pred             EEeCCCC
Confidence            8997644

>TIGR00959 ffh signal recognition particle protein

Probab=86.10  E-value=1.6  Score=43.60  Aligned_cols=15  Identities=33%  Similarity=0.257  Sum_probs=13.2

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||.|..++.
T Consensus       107 ~~GsGKTTtaakLA~  121 (428)
T TIGR00959       107 LQGSGKTTTCGKLAY  121 (428)
T ss_pred             CCCCcHHHHHHHHHH
Confidence            479999999988887

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.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=86.05  E-value=3.1  Score=41.58  Aligned_cols=78  Identities=14%  Similarity=0.127  Sum_probs=39.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCC-----CCCChhcHHH---------HHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPG-----SAKDLVEFQS---------LMQHIE   67 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~-----~~~~~~~~~~---------~~~~l~   67 (505)
                      +|+|||||++.++..  . ....+++++......+..++....+......     ...+.....+         ..+.++
T Consensus       174 SGsGKTTLL~~Ia~l--~-~pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~a~~iAEyfr  250 (450)
T PRK06002        174 SGVGKSTLLAMLARA--D-AFDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLTATAIAEYFR  250 (450)
T ss_pred             CCCCHHHHHHHHhCC--C-CCCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            799999999988862  2 2223455554334445544444333322110     1111111111         112222


Q ss_pred             HHcCCceEEEEEeCCCC
Q 046115           68 ECVAGKKFLLVLDDVWN   84 (505)
Q Consensus        68 ~~l~~~r~LlvlDdv~~   84 (505)
                      .  .++++|+++||+.+
T Consensus       251 d--~G~~Vll~~DslTr  265 (450)
T PRK06002        251 D--RGENVLLIVDSVTR  265 (450)
T ss_pred             H--cCCCEEEeccchHH
Confidence            2  47899999999843

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=86.02  E-value=2.5  Score=39.83  Aligned_cols=77  Identities=14%  Similarity=0.069  Sum_probs=37.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-C-CceEEEEeCCCC-CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-F-EKRTWVCVSEPF-DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f-~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      .+|+||||++..++.  ....+ - ..+..|+..... ...+.+....+.++.+.. ...+.......+. .+.+ .=++
T Consensus       202 ptGvGKTTt~~kLa~--~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~-~~~~~~~l~~~l~-~~~~-~d~v  276 (282)
T TIGR03499       202 PTGVGKTTTLAKLAA--RFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVK-VARDPKELRKALD-RLRD-KDLI  276 (282)
T ss_pred             CCCCCHHHHHHHHHH--HHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCcee-ccCCHHHHHHHHH-HccC-CCEE
Confidence            479999999999887  44332 1 345566654322 223334444444442221 1122233333333 3333 3477


Q ss_pred             EEeCC
Q 046115           78 VLDDV   82 (505)
Q Consensus        78 vlDdv   82 (505)
                      ++|..
T Consensus       277 liDt~  281 (282)
T TIGR03499       277 LIDTA  281 (282)
T ss_pred             EEeCC
Confidence            77753

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=85.97  E-value=3.8  Score=39.29  Aligned_cols=42  Identities=12%  Similarity=0.143  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeC-CCCCHHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVS-EPFDEFRIARAIIES   47 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~-~~~~~~~~~~~l~~~   47 (505)
                      .|.|||||++.++.  ....  +.++..-++ ...+..++.......
T Consensus        78 sG~GKTtLl~~Ia~--~~~~--~~~vi~~iGer~~ev~~~~~~~~~~  120 (326)
T cd01136          78 SGVGKSTLLGMIAR--GTTA--DVNVIALIGERGREVREFIEKDLGE  120 (326)
T ss_pred             CCCChHHHHHHHhC--CCCC--CEEEEEEEecCCccHHHHHHHHHhc
Confidence            69999999999987  3322  233333333 334555555555443

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=85.74  E-value=1.9  Score=41.56  Aligned_cols=102  Identities=12%  Similarity=0.047  Sum_probs=49.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|+||+++|+.+...  -...-...+.|++....+ ..+...+...-. +.......  .....+.   ....-.|+||+
T Consensus        38 ~GtGK~~lA~~iH~~--s~r~~~pfv~v~c~~~~~-~~~~~~lfg~~~-~~~~g~~~--~~~g~l~---~a~gGtL~l~~  108 (326)
T PRK11608         38 RGTGKELIASRLHYL--SSRWQGPFISLNCAALNE-NLLDSELFGHEA-GAFTGAQK--RHPGRFE---RADGGTLFLDE  108 (326)
T ss_pred             CCCcHHHHHHHHHHh--CCccCCCeEEEeCCCCCH-HHHHHHHccccc-cccCCccc--ccCCchh---ccCCCeEEeCC
Confidence            699999999998762  211112344566665332 222222221111 00000000  0011111   11233588999


Q ss_pred             CCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           82 VWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |..-.......+...+....           ..++||.||..
T Consensus       109 i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~  150 (326)
T PRK11608        109 LATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNA  150 (326)
T ss_pred             hhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCch
Confidence            97766555566666554321           13678887754

>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=85.59  E-value=0.7  Score=45.07  Aligned_cols=94  Identities=17%  Similarity=0.214  Sum_probs=46.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      -|.|||.|.-.+++.-.++.+          .-....+...++-..+.... ...    .....+.+.+.++..||+||.
T Consensus        71 vG~GKT~Lmd~f~~~lp~~~k----------~R~HFh~Fm~~vh~~l~~~~-~~~----~~l~~va~~l~~~~~lLcfDE  135 (362)
T PF03969_consen   71 VGRGKTMLMDLFYDSLPIKRK----------RRVHFHEFMLDVHSRLHQLR-GQD----DPLPQVADELAKESRLLCFDE  135 (362)
T ss_pred             CCCchhHHHHHHHHhCCcccc----------ccccccHHHHHHHHHHHHHh-CCC----ccHHHHHHHHHhcCCEEEEee
Confidence            499999999999885222111          01111233333333332100 111    123344556667777999999


Q ss_pred             CCCCCccCh---hHHHHhhcCCCCCcEEEEEeCch
Q 046115           82 VWNEDYYKW---EPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        82 v~~~~~~~~---~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      ..-.+..+.   ..+...+.  ..|. |||+|.|.
T Consensus       136 F~V~DiaDAmil~rLf~~l~--~~gv-vlVaTSN~  167 (362)
T PF03969_consen  136 FQVTDIADAMILKRLFEALF--KRGV-VLVATSNR  167 (362)
T ss_pred             eeccchhHHHHHHHHHHHHH--HCCC-EEEecCCC
Confidence            754443222   22333332  3554 66666664

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

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=85.55  E-value=2.4  Score=42.47  Aligned_cols=81  Identities=20%  Similarity=0.259  Sum_probs=44.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCC-CceEEEEeCCC-CCHHHHHHHHHHHcCCCC------CCChhcHHHH-----HHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF-EKRTWVCVSEP-FDEFRIARAIIESLTPGS------AKDLVEFQSL-----MQHIEE   68 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f-~~~~wv~~~~~-~~~~~~~~~l~~~l~~~~------~~~~~~~~~~-----~~~l~~   68 (505)
                      +|+|||+|+.+++.  ....+. ..++++-+++. .+..++...+...=....      ..+.....+.     .-.+.+
T Consensus       152 ~G~GKt~L~~~~~~--~~~~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~a~tiAE  229 (461)
T TIGR01039       152 AGVGKTVLIQELIN--NIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVALTGLTMAE  229 (461)
T ss_pred             CCCChHHHHHHHHH--HHHhcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            69999999999887  443332 34557767654 345566666544211110      1111111111     111223


Q ss_pred             Hc---CCceEEEEEeCCCC
Q 046115           69 CV---AGKKFLLVLDDVWN   84 (505)
Q Consensus        69 ~l---~~~r~LlvlDdv~~   84 (505)
                      .+   +++++||++||+.+
T Consensus       230 yfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       230 YFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHhcCCeeEEEecchhH
Confidence            33   56899999999944

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.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=85.54  E-value=0.52  Score=40.89  Aligned_cols=15  Identities=20%  Similarity=0.262  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|++++.
T Consensus        10 ~~gsGKst~a~~l~~   24 (175)
T cd00227          10 GSSAGKSSIARALQS   24 (175)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK13947 shikimate kinase; Provisional

Probab=85.42  E-value=0.47  Score=40.88  Aligned_cols=15  Identities=33%  Similarity=0.399  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.+++
T Consensus         9 ~~GsGKst~a~~La~   23 (171)
T PRK13947          9 FMGTGKTTVGKRVAT   23 (171)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999998

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=85.38  E-value=0.52  Score=39.61  Aligned_cols=15  Identities=27%  Similarity=0.437  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.+..
T Consensus         7 ~~GsGKST~a~~l~~   21 (150)
T cd02021           7 VSGSGKSTVGKALAE   21 (150)
T ss_pred             CCCCCHHHHHHHHHh
Confidence            589999999999988

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=85.32  E-value=1.7  Score=38.74  Aligned_cols=48  Identities=23%  Similarity=0.367  Sum_probs=30.2

Q ss_pred             CCceEEEEEeCCCCCCcc-C----hhHHHHhhcCCCCCcEEEEEeCchHHHHHhC
Q 046115           71 AGKKFLLVLDDVWNEDYY-K----WEPFYKCLKNSLHESKILITTRKETVARIMG  120 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~-~----~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~  120 (505)
                      ..++-|+++|........ +    ...+...+...  ++.+|++|-+..+.....
T Consensus       106 ~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~~~--~~~~i~~TH~~~l~~~~~  158 (204)
T cd03282         106 ADGDSLVLIDELGRGTSSADGFAISLAILECLIKK--ESTVFFATHFRDIAAILG  158 (204)
T ss_pred             cCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhc--CCEEEEECChHHHHHHhh
Confidence            356789999998553321 1    22334444433  778999999887766543

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

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

Probab=85.30  E-value=0.55  Score=41.56  Aligned_cols=37  Identities=16%  Similarity=0.237  Sum_probs=21.0

Q ss_pred             eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc
Q 046115           74 KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK  112 (505)
Q Consensus        74 r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~  112 (505)
                      +-+||+|.+.-.+...+..+......  .++++++.--.
T Consensus        94 ~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~  130 (196)
T PF13604_consen   94 KDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDP  130 (196)
T ss_dssp             TSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-T
T ss_pred             ccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCc
Confidence            35999999966555556666665554  35666665443

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=85.25  E-value=9.7  Score=33.86  Aligned_cols=53  Identities=19%  Similarity=0.230  Sum_probs=30.5

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +.+.+..++=++++|+.... +......+...+.....+..+|++|.+......
T Consensus       136 laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~th~~~~~~~  189 (207)
T cd03369         136 LARALLKRPRVLVLDEATASIDYATDALIQKTIREEFTNSTILTIAHRLRTIID  189 (207)
T ss_pred             HHHHHhhCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHHHHhh
Confidence            44455556678889997542 222233344444433346678888888766543

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.19  E-value=6.8  Score=38.30  Aligned_cols=81  Identities=11%  Similarity=0.001  Sum_probs=44.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r~Llv   78 (505)
                      +.|+||||++..++.  ....+-..+.+++..... ...+.++...+.++.+.. ...+..+..+.+...- .+..=+++
T Consensus       214 ptGvGKTTt~akLA~--~l~~~g~~V~lItaDtyR~gAveQLk~yae~lgvpv~-~~~dp~dL~~al~~l~~~~~~D~VL  290 (407)
T PRK12726        214 QTGVGKTTTLVKLGW--QLLKQNRTVGFITTDTFRSGAVEQFQGYADKLDVELI-VATSPAELEEAVQYMTYVNCVDHIL  290 (407)
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCeEEEEeCCccCccHHHHHHHHhhcCCCCEE-ecCCHHHHHHHHHHHHhcCCCCEEE
Confidence            369999999999887  333332345677765433 234455555666653322 1223344433333322 13456888


Q ss_pred             EeCCCC
Q 046115           79 LDDVWN   84 (505)
Q Consensus        79 lDdv~~   84 (505)
                      +|-...
T Consensus       291 IDTAGr  296 (407)
T PRK12726        291 IDTVGR  296 (407)
T ss_pred             EECCCC
Confidence            898855

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=85.17  E-value=1.1  Score=39.87  Aligned_cols=47  Identities=13%  Similarity=0.118  Sum_probs=28.1

Q ss_pred             CceEEEEEeCCCCCCccCh-h----HHHHhhcCCCCCcEEEEEeCchHHHHHhC
Q 046115           72 GKKFLLVLDDVWNEDYYKW-E----PFYKCLKNSLHESKILITTRKETVARIMG  120 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~-~----~~~~~~~~~~~~~~iLiTtr~~~~~~~~~  120 (505)
                      ..+-++++|.....-+... .    .+...+..  .++.+|++|-+.++...+.
T Consensus       107 ~~~~llllDEp~~gld~~~~~~l~~~ll~~l~~--~~~~vi~~tH~~~~~~~~~  158 (202)
T cd03243         107 TPRSLVLIDELGRGTSTAEGLAIAYAVLEHLLE--KGCRTLFATHFHELADLPE  158 (202)
T ss_pred             cCCeEEEEecCCCCCCHHHHHHHHHHHHHHHHh--cCCeEEEECChHHHHHHhh
Confidence            4788999999855322211 1    22232322  3667899998877766544

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

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

Probab=85.14  E-value=0.51  Score=41.70  Aligned_cols=74  Identities=16%  Similarity=0.226  Sum_probs=37.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CC---ceEEEEeCCCCCHHHHHHHHHHHcCC---CCCCChhcHHHHHHHHHHHcCCc
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FE---KRTWVCVSEPFDEFRIARAIIESLTP---GSAKDLVEFQSLMQHIEECVAGK   73 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~---~~~wv~~~~~~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~l~~~l~~~   73 (505)
                      .+|+||||+|++++.  ..... ..   ....+.............. -.....   -......+.+...+.+.....++
T Consensus         7 ~sgSGKTTla~~L~~--~L~~~~~~~~~~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~~p~a~d~~~l~~~l~~L~~g~   83 (194)
T PF00485_consen    7 PSGSGKTTLAKRLAQ--ILNKRGIPAMEMDIILSLDDFYDDYHLRDR-KGRGENRYNFDHPDAFDFDLLKEDLKALKNGG   83 (194)
T ss_dssp             STTSSHHHHHHHHHH--HHTTCTTTCCCSEEEEEGGGGBHHHHHHHH-HHHCTTTSSTTSGGGBSHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHH--HhCccCcCccceeEEEeecccccccchhhH-hhccccccCCCCccccCHHHHHHHHHHHhCCC
Confidence            479999999999987  45432 32   1333333322222221111 121110   12234566666667676655555


Q ss_pred             eEEE
Q 046115           74 KFLL   77 (505)
Q Consensus        74 r~Ll   77 (505)
                      .+-+
T Consensus        84 ~i~~   87 (194)
T PF00485_consen   84 SIEI   87 (194)
T ss_dssp             CEEE
T ss_pred             cccc
Confidence            5433

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 ....

>TIGR01817 nifA Nif-specific regulatory protein

Probab=85.08  E-value=4.3  Score=42.28  Aligned_cols=101  Identities=11%  Similarity=0.044  Sum_probs=48.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcH-HHHHHHHHHHcCCceEEEEEe
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEF-QSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~-~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .|+|||++|+.+.+.  -...-...+.|++....+  ..+...+  ++ ......... ......   ......-.|+||
T Consensus       228 ~GtGK~~lA~~ih~~--s~r~~~pfv~i~c~~~~~--~~~~~~l--fg-~~~~~~~~~~~~~~g~---~~~a~~GtL~ld  297 (534)
T TIGR01817       228 SGTGKELIAKAIHYL--SPRAKRPFVKVNCAALSE--TLLESEL--FG-HEKGAFTGAIAQRKGR---FELADGGTLFLD  297 (534)
T ss_pred             CCccHHHHHHHHHHh--CCCCCCCeEEeecCCCCH--HHHHHHH--cC-CCCCccCCCCcCCCCc---ccccCCCeEEEe
Confidence            699999999999873  222222344566665422  2222211  11 110000000 000000   001223468899


Q ss_pred             CCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           81 DVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      +|..-.......+...+....           ...+||.||..
T Consensus       298 ei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~  340 (534)
T TIGR01817       298 EIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNR  340 (534)
T ss_pred             chhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCC
Confidence            997766555566666654321           13577777654

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.

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=85.06  E-value=7.7  Score=35.14  Aligned_cols=21  Identities=38%  Similarity=0.436  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF   23 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f   23 (505)
                      ++|.|||.||+++++  .....|
T Consensus       197 ppg~gktml~kava~--~t~a~f  217 (408)
T KOG0727|consen  197 PPGTGKTMLAKAVAN--HTTAAF  217 (408)
T ss_pred             CCCCcHHHHHHHHhh--ccchhe
Confidence            589999999999999  344444

>PRK00889 adenylylsulfate kinase; Provisional

Probab=85.04  E-value=0.65  Score=40.23  Aligned_cols=15  Identities=40%  Similarity=0.572  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~~GsGKST~a~~la~   26 (175)
T PRK00889         12 LSGAGKTTIARALAE   26 (175)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

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

Probab=85.02  E-value=0.4  Score=37.71  Aligned_cols=15  Identities=47%  Similarity=0.485  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+|||++|..++.
T Consensus         6 ~~G~GKS~l~~~l~~   20 (107)
T PF00910_consen    6 PPGIGKSTLAKELAK   20 (107)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            379999999999887

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

>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation

Probab=84.99  E-value=0.55  Score=36.52  Aligned_cols=14  Identities=50%  Similarity=0.570  Sum_probs=13.0

Q ss_pred             CCCcHHHHHHHHhc
Q 046115            2 GGIGKTTLAQFAYN   15 (505)
Q Consensus         2 ~G~GKT~LA~~~~~   15 (505)
                      ||+||||+|..++.
T Consensus         9 gG~Gkst~~~~la~   22 (104)
T cd02042           9 GGVGKTTTAVNLAA   22 (104)
T ss_pred             CCcCHHHHHHHHHH
Confidence            89999999999887

ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=84.94  E-value=0.51  Score=40.71  Aligned_cols=15  Identities=27%  Similarity=0.488  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~~GsGKstla~~La~   26 (175)
T PRK00131         12 FMGAGKSTIGRLLAK   26 (175)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999998

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=84.81  E-value=9.4  Score=34.77  Aligned_cols=55  Identities=11%  Similarity=0.125  Sum_probs=32.6

Q ss_pred             HHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           64 QHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        64 ~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      -.+.+.+..++-++++|..... +......+...+.....|..||++|.+......
T Consensus       146 l~la~aL~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sh~~~~~~~  201 (236)
T cd03253         146 VAIARAILKNPPILLLDEATSALDTHTEREIQAALRDVSKGRTTIVIAHRLSTIVN  201 (236)
T ss_pred             HHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHHHHHh
Confidence            3355556667789999997542 222333444444433226678888888766544

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. 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.

>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=84.68  E-value=1.6  Score=38.04  Aligned_cols=15  Identities=47%  Similarity=0.465  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||||..++.
T Consensus         7 ~sgsGKttla~~l~~   21 (179)
T cd02028           7 PSGSGKTTFAKKLSN   21 (179)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            379999999999987

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=84.64  E-value=2.8  Score=33.79  Aligned_cols=99  Identities=14%  Similarity=0.295  Sum_probs=55.8

Q ss_pred             HhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch
Q 046115          378 LFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR  455 (505)
Q Consensus       378 ~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~  455 (505)
                      .|..+.+|+.+.+.       .. +..++ ..+..+.+|+.+.+..+  +..++. .+..+.+|+.+.+.+ . +..++.
T Consensus         7 ~F~~~~~l~~i~~~-------~~-~~~I~~~~F~~~~~l~~i~~~~~--~~~i~~~~F~~~~~l~~i~~~~-~-~~~i~~   74 (129)
T PF13306_consen    7 AFYNCSNLESITFP-------NT-IKKIGENAFSNCTSLKSINFPNN--LTSIGDNAFSNCKSLESITFPN-N-LKSIGD   74 (129)
T ss_dssp             TTTT-TT--EEEET-------ST---EE-TTTTTT-TT-SEEEESST--TSCE-TTTTTT-TT-EEEEETS-T-T-EE-T
T ss_pred             HHhCCCCCCEEEEC-------CC-eeEeChhhccccccccccccccc--ccccceeeeecccccccccccc-c-cccccc
Confidence            36677789999886       33 44444 34677888999999874  666655 457777899999976 3 566665


Q ss_pred             h-ccccccCceeecCCCcccccccc-cccCCccCCccc
Q 046115          456 G-IGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVR  491 (505)
Q Consensus       456 ~-~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~  491 (505)
                      . +..+++|+.+.+..+  ...++. .|.++ .|+.+.
T Consensus        75 ~~F~~~~~l~~i~~~~~--~~~i~~~~f~~~-~l~~i~  109 (129)
T PF13306_consen   75 NAFSNCTNLKNIDIPSN--ITEIGSSSFSNC-NLKEIN  109 (129)
T ss_dssp             TTTTT-TTECEEEETTT---BEEHTTTTTT--T--EEE
T ss_pred             ccccccccccccccCcc--ccEEchhhhcCC-CceEEE
Confidence            4 667899999999765  234433 46665 666554

>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=84.56  E-value=5.3  Score=39.05  Aligned_cols=78  Identities=19%  Similarity=0.235  Sum_probs=45.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEe-CCCCCHHHHHHHHHHHcCCCC------CCChhcHHHHH-----HHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCV-SEPFDEFRIARAIIESLTPGS------AKDLVEFQSLM-----QHIEEC   69 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~-~~~~~~~~~~~~l~~~l~~~~------~~~~~~~~~~~-----~~l~~~   69 (505)
                      +|+|||||.-.+++.    ..+|.++-.-+ .+-.+..+.....+..-+...      ..+.+...+..     ..+.+.
T Consensus       172 sGVGKStLLgMiar~----t~aDv~ViaLIGERGREVrEFIE~~Lg~egl~rsViVvATSD~s~l~R~~aa~~At~IAEy  247 (441)
T COG1157         172 SGVGKSTLLGMIARN----TEADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESALMRLKAAFTATTIAEY  247 (441)
T ss_pred             CCCcHHHHHHHHhcc----ccCCEEEEEEeeccchhHHHHHHHhcchhhccceEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            699999999999982    44565553333 334566666666655443221      12222332222     223444


Q ss_pred             c--CCceEEEEEeCCC
Q 046115           70 V--AGKKFLLVLDDVW   83 (505)
Q Consensus        70 l--~~~r~LlvlDdv~   83 (505)
                      .  +++++||++|.+.
T Consensus       248 FRDqG~~VLL~mDSlT  263 (441)
T COG1157         248 FRDQGKRVLLIMDSLT  263 (441)
T ss_pred             HHhCCCeEEEEeecHH
Confidence            4  4689999999983

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=84.52  E-value=0.57  Score=37.71  Aligned_cols=14  Identities=36%  Similarity=0.373  Sum_probs=12.6

Q ss_pred             CCcHHHHHHHHhcC
Q 046115            3 GIGKTTLAQFAYNN   16 (505)
Q Consensus         3 G~GKT~LA~~~~~~   16 (505)
                      |+||||+++.+++.
T Consensus        25 GaGKTtf~r~l~~~   38 (123)
T PF02367_consen   25 GAGKTTFVRGLARA   38 (123)
T ss_dssp             TSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            89999999999864

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>PTZ00301 uridine kinase; Provisional

Probab=84.51  E-value=0.87  Score=40.71  Aligned_cols=15  Identities=27%  Similarity=0.408  Sum_probs=13.2

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||||+.+..
T Consensus        11 ~SgSGKTTla~~l~~   25 (210)
T PTZ00301         11 ASGSGKSSLSTNIVS   25 (210)
T ss_pred             CCcCCHHHHHHHHHH
Confidence            379999999998876

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=84.44  E-value=15  Score=33.20  Aligned_cols=65  Identities=14%  Similarity=0.109  Sum_probs=39.9

Q ss_pred             hcHHHHHHHHHHHcCCceEEEEEeCCC-CCCccChhHHHHhhcCC--CCCcEEEEEeCchHHHHHhCC
Q 046115           57 VEFQSLMQHIEECVAGKKFLLVLDDVW-NEDYYKWEPFYKCLKNS--LHESKILITTRKETVARIMGS  121 (505)
Q Consensus        57 ~~~~~~~~~l~~~l~~~r~LlvlDdv~-~~~~~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~~~~~  121 (505)
                      +.-++..-.+.+.+...+-+|+.|.-. +-+...-..+...+...  ..|..||+.|-++.++..++.
T Consensus       144 SGGqqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~~~dr  211 (226)
T COG1136         144 SGGQQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAKYADR  211 (226)
T ss_pred             CHHHHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHhCCE
Confidence            444455556777777777888888742 22222333444444432  346789999999998876543

>PTZ00088 adenylate kinase 1; Provisional

Probab=84.37  E-value=1.3  Score=40.19  Aligned_cols=15  Identities=33%  Similarity=0.521  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        14 ~PGsGK~T~a~~La~   28 (229)
T PTZ00088         14 APGVGKGTFAEILSK   28 (229)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>PRK08006 replicative DNA helicase; Provisional

Probab=84.34  E-value=6.2  Score=40.16  Aligned_cols=43  Identities=19%  Similarity=0.159  Sum_probs=26.4

Q ss_pred             CCCcHHHHHHHHhcCccccc-CCCceEEEEeCCCCCHHHHHHHHHHHc
Q 046115            2 GGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEPFDEFRIARAIIESL   48 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~~~~~~~~~~l~~~l   48 (505)
                      +|+|||++|..++.  .... +-..+++++..  -+..++...++...
T Consensus       233 PgmGKTafalnia~--~~a~~~g~~V~~fSlE--M~~~ql~~Rlla~~  276 (471)
T PRK08006        233 PSMGKTTFAMNLCE--NAAMLQDKPVLIFSLE--MPGEQIMMRMLASL  276 (471)
T ss_pred             CCCCHHHHHHHHHH--HHHHhcCCeEEEEecc--CCHHHHHHHHHHHh
Confidence            79999999999887  3332 21234455443  44556666666544

>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=84.32  E-value=0.89  Score=41.60  Aligned_cols=29  Identities=28%  Similarity=0.134  Sum_probs=18.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCV   31 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~   31 (505)
                      |+|+||||+++.+.+  -...+-..++-|+.
T Consensus         4 paGSGKTT~~~~~~~--~~~~~~~~~~~vNL   32 (238)
T PF03029_consen    4 PAGSGKTTFCKGLSE--WLESNGRDVYIVNL   32 (238)
T ss_dssp             STTSSHHHHHHHHHH--HHTTT-S-EEEEE-
T ss_pred             CCCCCHHHHHHHHHH--HHHhccCCceEEEc
Confidence            689999999999877  33333233444543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=84.31  E-value=8  Score=38.17  Aligned_cols=82  Identities=12%  Similarity=0.071  Sum_probs=42.3

Q ss_pred             CCCCcHHHHHHHHhcCcccc--cCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVE--RNFEKRTWVCVSEPF-DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~--~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      ..|+||||.+..++......  .+-..+..++..... .....++...+.++.+.. .....++....+.. + +..-++
T Consensus       182 ptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~-~~~~~~~l~~~L~~-~-~~~DlV  258 (388)
T PRK12723        182 PTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVK-AIESFKDLKEEITQ-S-KDFDLV  258 (388)
T ss_pred             CCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceE-eeCcHHHHHHHHHH-h-CCCCEE
Confidence            36999999999888631111  111234455544322 223345555665654321 11222333333333 2 345688


Q ss_pred             EEeCCCCC
Q 046115           78 VLDDVWNE   85 (505)
Q Consensus        78 vlDdv~~~   85 (505)
                      ++|-....
T Consensus       259 LIDTaGr~  266 (388)
T PRK12723        259 LVDTIGKS  266 (388)
T ss_pred             EEcCCCCC
Confidence            99998554

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=84.30  E-value=3.2  Score=41.28  Aligned_cols=40  Identities=20%  Similarity=0.192  Sum_probs=23.3

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAII   45 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~   45 (505)
                      +|+|||||+..+++  ...  .+..+...+++. .+..++...+.
T Consensus       146 sG~GKTtLl~~I~~--~~~--~~~~vi~~iGer~~ev~e~~~~~~  186 (411)
T TIGR03496       146 SGVGKSTLLGMMAR--YTE--ADVVVVGLIGERGREVKEFIEDIL  186 (411)
T ss_pred             CCCCHHHHHHHHhc--CCC--CCEEEEEEEecChHHHHHHHHHHh
Confidence            69999999999987  222  233444445443 33444444443

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.

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=84.29  E-value=5.1  Score=38.02  Aligned_cols=53  Identities=21%  Similarity=0.172  Sum_probs=29.3

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCC-cEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHE-SKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~-~~iLiTtr~~~~~~~  118 (505)
                      +...|..++=+++||.-.+. +...-..+.+.+... ..| ..|++||-.......
T Consensus       147 ia~aL~~~P~lliLDEPt~GLDp~~~~~~~~~l~~l~~~g~~tvlissH~l~e~~~  202 (293)
T COG1131         147 IALALLHDPELLILDEPTSGLDPESRREIWELLRELAKEGGVTILLSTHILEEAEE  202 (293)
T ss_pred             HHHHHhcCCCEEEECCCCcCCCHHHHHHHHHHHHHHHhCCCcEEEEeCCcHHHHHH
Confidence            45556667789999997442 222222233333322 223 679999987554443

>PRK09099 type III secretion system ATPase; Provisional

Probab=84.28  E-value=3.1  Score=41.69  Aligned_cols=42  Identities=14%  Similarity=0.122  Sum_probs=25.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~   46 (505)
                      +|+|||||++.++..  .... .++++..-.+..+..++...+..
T Consensus       172 sG~GKTtLl~~ia~~--~~~d-~~vi~~iGer~~ev~ef~~~~~~  213 (441)
T PRK09099        172 AGVGKSTLMGMFARG--TQCD-VNVIALIGERGREVREFIELILG  213 (441)
T ss_pred             CCCCHHHHHHHHhCC--CCCC-eEEEEEEccChHHHHHHHHHHhh
Confidence            699999999999873  2221 24444444444455555555544

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=84.20  E-value=6.3  Score=39.62  Aligned_cols=44  Identities=20%  Similarity=0.214  Sum_probs=27.9

Q ss_pred             CCCCcHHHHHHHHhcCcccc-cCCCceEEEEeCCCCCHHHHHHHHHHHc
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-RNFEKRTWVCVSEPFDEFRIARAIIESL   48 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-~~f~~~~wv~~~~~~~~~~~~~~l~~~l   48 (505)
                      .+|+|||++|..++.  ... .+=..++|++..-  +...+...++...
T Consensus       202 ~pg~GKT~~al~ia~--~~a~~~g~~v~~fSlEm--~~~~l~~Rl~~~~  246 (421)
T TIGR03600       202 RPSMGKTTLALNIAE--NVALREGKPVLFFSLEM--SAEQLGERLLASK  246 (421)
T ss_pred             CCCCCHHHHHHHHHH--HHHHhCCCcEEEEECCC--CHHHHHHHHHHHH
Confidence            379999999999986  332 2223566776543  4556666665543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=84.19  E-value=2.7  Score=41.82  Aligned_cols=80  Identities=18%  Similarity=0.136  Sum_probs=39.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCC------CCChhcHHHH-----HHHHHHHc
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS------AKDLVEFQSL-----MQHIEECV   70 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~------~~~~~~~~~~-----~~~l~~~l   70 (505)
                      +|+|||||++.++.  .... ..+++.....+..+..++....+..-+...      ..+.....+.     .-.+.+.+
T Consensus       149 sG~GKTtLl~~I~~--~~~~-~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~~a~~iAEyf  225 (418)
T TIGR03498       149 SGVGKSTLLSMLAR--NTDA-DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAYTATAIAEYF  225 (418)
T ss_pred             CCCChHHHHHHHhC--CCCC-CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            69999999999887  3322 223333333334444455554443321110      1111111111     11122222


Q ss_pred             --CCceEEEEEeCCCC
Q 046115           71 --AGKKFLLVLDDVWN   84 (505)
Q Consensus        71 --~~~r~LlvlDdv~~   84 (505)
                        .++++||++||+.+
T Consensus       226 rd~G~~Vll~~DslTr  241 (418)
T TIGR03498       226 RDQGKDVLLLMDSVTR  241 (418)
T ss_pred             HHcCCCEEEeccchhH
Confidence              57899999999844

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.

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=84.13  E-value=3  Score=41.53  Aligned_cols=14  Identities=36%  Similarity=0.586  Sum_probs=12.9

Q ss_pred             CCCcHHHHHHHHhc
Q 046115            2 GGIGKTTLAQFAYN   15 (505)
Q Consensus         2 ~G~GKT~LA~~~~~   15 (505)
                      +|+|||||+..+++
T Consensus       146 sG~GKTtLl~~i~~  159 (413)
T TIGR03497       146 SGVGKSTLLGMIAR  159 (413)
T ss_pred             CCCCHHHHHHHHhC
Confidence            69999999998887

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.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=84.12  E-value=14  Score=33.06  Aligned_cols=54  Identities=15%  Similarity=0.084  Sum_probs=29.6

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcC-CCCCcEEEEEeCchHHHHH
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKN-SLHESKILITTRKETVARI  118 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iLiTtr~~~~~~~  118 (505)
                      .+.+.+-.++-++++|...+. +......+...+.. ...+..||++|.+......
T Consensus       147 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~~~~~~  202 (214)
T PRK13543        147 ALARLWLSPAPLWLLDEPYANLDLEGITLVNRMISAHLRGGGAALVTTHGAYAAPP  202 (214)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEecChhhhhh
Confidence            344455556668899997442 22222333333322 1235678888888765543

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=84.00  E-value=12  Score=35.72  Aligned_cols=139  Identities=16%  Similarity=0.133  Sum_probs=70.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC-ceEEEEeCCCCC-HHHHHHHHHHHc----CCCCCCChhcHHHHHHHHHHHcCC--
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE-KRTWVCVSEPFD-EFRIARAIIESL----TPGSAKDLVEFQSLMQHIEECVAG--   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~-~~~wv~~~~~~~-~~~~~~~l~~~l----~~~~~~~~~~~~~~~~~l~~~l~~--   72 (505)
                      +.|+|||+|......+   .+.|. ...-|....... ..-.++.|.+++    .... ....+..+....+...|+.  
T Consensus        57 prgsgkT~li~~~Ls~---~q~~~E~~l~v~Lng~~~~dk~al~~I~rql~~e~~~~~-k~~gsfte~l~~lL~~L~~~~  132 (408)
T KOG2228|consen   57 PRGSGKTILIDTRLSD---IQENGENFLLVRLNGELQTDKIALKGITRQLALELNRIV-KSFGSFTENLSKLLEALKKGD  132 (408)
T ss_pred             cCCCCceEeeHHHHhh---HHhcCCeEEEEEECccchhhHHHHHHHHHHHHHHHhhhh-eeecccchhHHHHHHHHhcCC
Confidence            4799999999777763   23332 223333333222 222444555444    3221 1122223334444444432  


Q ss_pred             ----ceEEEEEeCCCCCCccChhHHHHhhcC-----CCCCcEEEEEeCchH---HHHHhCC----cceEeCCCCChhhHH
Q 046115           73 ----KKFLLVLDDVWNEDYYKWEPFYKCLKN-----SLHESKILITTRKET---VARIMGS----THVISVNVLSEMECW  136 (505)
Q Consensus        73 ----~r~LlvlDdv~~~~~~~~~~~~~~~~~-----~~~~~~iLiTtr~~~---~~~~~~~----~~~~~l~~l~~~ea~  136 (505)
                          -++++|+|.++-...-.-+.+...+.+     ..+-|-|-+|||-..   +.+.+..    ..++-++.+...+-+
T Consensus       133 ~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv  212 (408)
T KOG2228|consen  133 ETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLEKRVKSRFSHRVIFMLPSLPLGDYV  212 (408)
T ss_pred             CCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHhhcccceeeccCCCChHHHH
Confidence                368899988754332222223332222     345677888998632   2233322    235556777777877


Q ss_pred             HHHHHhh
Q 046115          137 SVFQSLA  143 (505)
Q Consensus       137 ~Lf~~~~  143 (505)
                      ++++...
T Consensus       213 ~l~r~ll  219 (408)
T KOG2228|consen  213 DLYRKLL  219 (408)
T ss_pred             HHHHHHh
Confidence            7776654

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=83.99  E-value=0.79  Score=39.02  Aligned_cols=20  Identities=25%  Similarity=0.351  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN   22 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~   22 (505)
                      ++|+||||+|.++..  ....+
T Consensus        31 LSGsGKSTiA~ale~--~L~~~   50 (197)
T COG0529          31 LSGSGKSTIANALEE--KLFAK   50 (197)
T ss_pred             CCCCCHHHHHHHHHH--HHHHc
Confidence            589999999999988  55444

>PRK06547 hypothetical protein; Provisional

Probab=83.97  E-value=0.63  Score=40.16  Aligned_cols=15  Identities=47%  Similarity=0.395  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||+|+.++.
T Consensus        23 ~~GsGKTt~a~~l~~   37 (172)
T PRK06547         23 RSGSGKTTLAGALAA   37 (172)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=83.77  E-value=2.6  Score=38.15  Aligned_cols=44  Identities=20%  Similarity=0.192  Sum_probs=24.7

Q ss_pred             HHHHHHHHHcCCCCC-----CChhcHHHHHHHHHHHcCCceEEEEEeCC
Q 046115           39 RIARAIIESLTPGSA-----KDLVEFQSLMQHIEECVAGKKFLLVLDDV   82 (505)
Q Consensus        39 ~~~~~l~~~l~~~~~-----~~~~~~~~~~~~l~~~l~~~r~LlvlDdv   82 (505)
                      +...++++..+....     .+.+.-.+..-.+.+.+..++=+|++|.-
T Consensus       109 ~~a~~~L~~VgL~~~~~~~P~qLSGGMrQRVaiARAL~~~P~lLLlDEP  157 (248)
T COG1116         109 ERAKELLELVGLAGFEDKYPHQLSGGMRQRVAIARALATRPKLLLLDEP  157 (248)
T ss_pred             HHHHHHHHHcCCcchhhcCccccChHHHHHHHHHHHHhcCCCEEEEcCC
Confidence            455666666654332     22233333444466667677778888875

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=83.74  E-value=3.6  Score=41.17  Aligned_cols=43  Identities=21%  Similarity=0.282  Sum_probs=28.6

Q ss_pred             CCCcHHHHHHHHhcCcccc-cCCCceEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVE-RNFEKRTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~-~~f~~~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|+.++++.  .. .+-+.++++-+++.. +..++..++..
T Consensus       147 ~G~GKt~l~~~~~~~--~~~~~~~v~V~~~iGeR~rEv~e~~~~~~~  191 (449)
T TIGR03305       147 AGVGKTVLLTEMIHN--MVGQHQGVSIFCGIGERCREGEELYREMKE  191 (449)
T ss_pred             CCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHhh
Confidence            699999999998873  32 223567788776654 44455555544

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.

>PRK00279 adk adenylate kinase; Reviewed

Probab=83.72  E-value=3.8  Score=36.82  Aligned_cols=15  Identities=40%  Similarity=0.450  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         8 ~pGsGKsT~a~~la~   22 (215)
T PRK00279          8 PPGAGKGTQAKFIAE   22 (215)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            489999999999987

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=83.65  E-value=4.8  Score=37.36  Aligned_cols=43  Identities=21%  Similarity=0.200  Sum_probs=28.5

Q ss_pred             CCCcHHHHHHHHhcCcccccC-CCceEEEEeCCCCCHHHHHHHHHHHc
Q 046115            2 GGIGKTTLAQFAYNNGDVERN-FEKRTWVCVSEPFDEFRIARAIIESL   48 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~-f~~~~wv~~~~~~~~~~~~~~l~~~l   48 (505)
                      +|+|||++|..++.  ....+ -..++|++..-+  ..++...++...
T Consensus        28 pg~GKT~~~l~ia~--~~a~~~~~~vly~SlEm~--~~~l~~R~la~~   71 (259)
T PF03796_consen   28 PGVGKTAFALQIAL--NAALNGGYPVLYFSLEMS--EEELAARLLARL   71 (259)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTSSEEEEEESSS---HHHHHHHHHHHH
T ss_pred             ccCCchHHHHHHHH--HHHHhcCCeEEEEcCCCC--HHHHHHHHHHHh
Confidence            79999999999998  44443 267777776543  345555555544

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=83.55  E-value=4.5  Score=41.27  Aligned_cols=102  Identities=11%  Similarity=0.082  Sum_probs=49.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|+||+++|+.+...  -.+.....+-+++...  ..+.+...+  ++. ..........  ...........-.|+||+
T Consensus       166 ~GtGK~~~A~~ih~~--~~~~~~~~~~~~c~~~--~~~~~~~~l--fg~-~~~~~~~~~~--~~~g~~~~a~~gtl~l~e  236 (463)
T TIGR01818       166 SGTGKELVARALHRH--SPRANGPFIALNMAAI--PKDLIESEL--FGH-EKGAFTGANT--RRQGRFEQADGGTLFLDE  236 (463)
T ss_pred             CCCCHHHHHHHHHHh--CCCCCCCeEEEeCCCC--CHHHHHHHh--cCC-CCCCCCCccc--CCCCcEEECCCCeEEEEc
Confidence            699999999999872  2222233344555543  223333322  221 0000000000  000001111234588999


Q ss_pred             CCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           82 VWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |..-.......+...+....           .+++||.||..
T Consensus       237 i~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~  278 (463)
T TIGR01818       237 IGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQ  278 (463)
T ss_pred             hhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCC
Confidence            97766555566666554321           24578887764

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

>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell

Probab=83.51  E-value=0.87  Score=39.41  Aligned_cols=31  Identities=23%  Similarity=0.124  Sum_probs=21.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE   33 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~   33 (505)
                      -||+||||+|..++.  ..+++=..++-|+...
T Consensus         8 kgG~GKtt~a~~la~--~l~~~g~~vllvD~D~   38 (179)
T cd02036           8 KGGVGKTTTTANLGT--ALAQLGYKVVLIDADL   38 (179)
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCeEEEEeCCC
Confidence            389999999999987  5544433455565443

The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=83.50  E-value=7.9  Score=34.37  Aligned_cols=15  Identities=33%  Similarity=0.306  Sum_probs=13.4

Q ss_pred             CCCcHHHHHHHHhcC
Q 046115            2 GGIGKTTLAQFAYNN   16 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~   16 (505)
                      .|+|||||++.++..
T Consensus        42 nGsGKSTLl~~l~G~   56 (202)
T cd03233          42 PGSGCSTLLKALANR   56 (202)
T ss_pred             CCCCHHHHHHHhccc
Confidence            699999999999873

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including 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.

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=83.39  E-value=3.4  Score=32.94  Aligned_cols=28  Identities=25%  Similarity=0.266  Sum_probs=18.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~   30 (505)
                      .||+|||+++..++.  ....+-..+.-++
T Consensus         7 kgG~GKTt~a~~la~--~l~~~g~~V~~id   34 (116)
T cd02034           7 KGGVGKTTIAALLAR--YLAEKGKPVLAID   34 (116)
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCcEEEEE
Confidence            389999999999987  4443322344454

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=83.38  E-value=3.9  Score=35.53  Aligned_cols=38  Identities=18%  Similarity=0.117  Sum_probs=18.6

Q ss_pred             EEEEeCCCCCCc-cChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           76 LLVLDDVWNEDY-YKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        76 LlvlDdv~~~~~-~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      ++|+|++..... .....+...+.....+.++++.|-.+
T Consensus       132 ~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~~v~~saT~  170 (201)
T smart00487      132 LVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATP  170 (201)
T ss_pred             EEEEECHHHHhcCCcHHHHHHHHHhCCccceEEEEecCC
Confidence            899999866432 12222222222223445566655543

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=83.33  E-value=11  Score=34.82  Aligned_cols=54  Identities=15%  Similarity=0.208  Sum_probs=29.9

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC--CCCcEEEEEeCchHHHHH
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS--LHESKILITTRKETVARI  118 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~~  118 (505)
                      .+...+..++-++++|...+. +......+...+...  ..+..||++|-+......
T Consensus       130 ~laral~~~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~g~tiiivsH~~~~i~~  186 (251)
T PRK09544        130 LLARALLNRPQLLVLDEPTQGVDVNGQVALYDLIDQLRRELDCAVLMVSHDLHLVMA  186 (251)
T ss_pred             HHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHhcCCEEEEEecCHHHHHH
Confidence            345555566779999997543 222223333333321  125678888888765543

>PRK05922 type III secretion system ATPase; Validated

Probab=83.33  E-value=2.4  Score=42.25  Aligned_cols=79  Identities=15%  Similarity=0.155  Sum_probs=39.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHHHHcCCCC------CCChhcHHHH-----HHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAIIESLTPGS------AKDLVEFQSL-----MQHIEEC   69 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~~~l~~~~------~~~~~~~~~~-----~~~l~~~   69 (505)
                      .|+|||||++.++.  ..  +.+..+.+-+++. .+..+.+.+.........      ..+.....+.     .-.+.+.
T Consensus       166 nG~GKSTLL~~Ia~--~~--~~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~~~a~tiAEy  241 (434)
T PRK05922        166 PGSGKSSLLSTIAK--GS--KSTINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAGRAAMTIAEY  241 (434)
T ss_pred             CCCChHHHHHHHhc--cC--CCCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            69999999999997  32  2233333334442 333455545444332111      0111111111     1112222


Q ss_pred             c--CCceEEEEEeCCCC
Q 046115           70 V--AGKKFLLVLDDVWN   84 (505)
Q Consensus        70 l--~~~r~LlvlDdv~~   84 (505)
                      +  .++++|+++||+.+
T Consensus       242 frd~G~~VLl~~DslTR  258 (434)
T PRK05922        242 FRDQGHRVLFIMDSLSR  258 (434)
T ss_pred             HHHcCCCEEEeccchhH
Confidence            2  47899999999944

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=83.23  E-value=4.5  Score=37.12  Aligned_cols=76  Identities=17%  Similarity=0.237  Sum_probs=42.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC--CceEEE-------EeCCCCCHHH--HHHHHHHHcCCCCCCCh--------hcHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF--EKRTWV-------CVSEPFDEFR--IARAIIESLTPGSAKDL--------VEFQS   61 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f--~~~~wv-------~~~~~~~~~~--~~~~l~~~l~~~~~~~~--------~~~~~   61 (505)
                      |+|+||||+.+++...  ...++  ..++=+       ...-..++++  -.++.+.+...+.+...        ...++
T Consensus        27 MAGSGKTTF~QrL~~h--l~~~~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPNGgI~TsLNLF~tk~dq  104 (366)
T KOG1532|consen   27 MAGSGKTTFMQRLNSH--LHAKKTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPNGGIVTSLNLFATKFDQ  104 (366)
T ss_pred             cCCCCchhHHHHHHHH--HhhccCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCCcchhhhHHHHHHHHHH
Confidence            8999999999888763  32332  223222       2233345554  34577777665554432        34455


Q ss_pred             HHHHHHHHcCCceEEEE
Q 046115           62 LMQHIEECVAGKKFLLV   78 (505)
Q Consensus        62 ~~~~l~~~l~~~r~Llv   78 (505)
                      .+..+.+.-....|.||
T Consensus       105 v~~~iek~~~~~~~~li  121 (366)
T KOG1532|consen  105 VIELIEKRAEEFDYVLI  121 (366)
T ss_pred             HHHHHHHhhcccCEEEE
Confidence            55566655544455443

>PRK14269 phosphate ABC transporter ATP-binding protein; Provisional

Probab=83.17  E-value=11  Score=34.68  Aligned_cols=55  Identities=22%  Similarity=0.180  Sum_probs=31.6

Q ss_pred             HHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHH
Q 046115           63 MQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVAR  117 (505)
Q Consensus        63 ~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~  117 (505)
                      .-.+.+.+..++-++++|..... +......+...+.....+..||++|.+.....
T Consensus       150 rv~laral~~~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~tH~~~~~~  205 (246)
T PRK14269        150 RLCIARALAIKPKLLLLDEPTSALDPISSGVIEELLKELSHNLSMIMVTHNMQQGK  205 (246)
T ss_pred             HHHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHhCCCEEEEEecCHHHHH
Confidence            34455566667779999997442 22223334444433223667888888866543

>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily

Probab=83.07  E-value=2.8  Score=35.98  Aligned_cols=29  Identities=24%  Similarity=0.177  Sum_probs=18.8

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVS   32 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~   32 (505)
                      ||+||||+|..++.  ..+..=..++-|+..
T Consensus         9 gG~GKTt~a~~LA~--~la~~g~~vllvD~D   37 (169)
T cd02037           9 GGVGKSTVAVNLAL--ALAKLGYKVGLLDAD   37 (169)
T ss_pred             CcCChhHHHHHHHH--HHHHcCCcEEEEeCC
Confidence            89999999988887  443322234445543

Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=82.99  E-value=1.5  Score=39.31  Aligned_cols=35  Identities=23%  Similarity=0.214  Sum_probs=21.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      ||+||||+|..++.. -.+++=..+.=|+...+++.
T Consensus         9 GG~GKTtiaalll~~-l~~~~~~~VLvVDaDpd~nL   43 (255)
T COG3640           9 GGVGKTTIAALLLKR-LLSKGGYNVLVVDADPDSNL   43 (255)
T ss_pred             CCccHHHHHHHHHHH-HHhcCCceEEEEeCCCCCCh
Confidence            899999999885541 23333123445676665554

>PRK03846 adenylylsulfate kinase; Provisional

Probab=82.97  E-value=1  Score=40.00  Aligned_cols=15  Identities=33%  Similarity=0.439  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||||+.+..
T Consensus        32 ~~GsGKSTla~~l~~   46 (198)
T PRK03846         32 LSGSGKSTVAGALEE   46 (198)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            469999999999988

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=82.93  E-value=1.3  Score=42.23  Aligned_cols=35  Identities=26%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      .||+||||+|.+.+-  ..+.....++=|+.....+.
T Consensus        10 KGGVGKTT~aaA~A~--~lA~~g~kvLlvStDPAhsL   44 (322)
T COG0003          10 KGGVGKTTIAAATAV--KLAESGKKVLLVSTDPAHSL   44 (322)
T ss_pred             CCcccHHHHHHHHHH--HHHHcCCcEEEEEeCCCCch
Confidence            389999999988765  34444344555554444333

>PLN03211 ABC transporter G-25; Provisional

Probab=82.91  E-value=9.5  Score=40.79  Aligned_cols=79  Identities=15%  Similarity=0.120  Sum_probs=40.4

Q ss_pred             HHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchH--HHHHhCC------cceEeCCCCChhhHH
Q 046115           67 EECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKET--VARIMGS------THVISVNVLSEMECW  136 (505)
Q Consensus        67 ~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~--~~~~~~~------~~~~~l~~l~~~ea~  136 (505)
                      ...+-.++-++++|.-... +......+.+.+... ..|..||+||-+..  +...++.      .+++.-  =+.+++.
T Consensus       218 a~aL~~~P~iLlLDEPtsgLD~~~~~~l~~~L~~l~~~g~TvI~~sH~~~~~i~~~~D~iilL~~G~iv~~--G~~~~~~  295 (659)
T PLN03211        218 AHEMLINPSLLILDEPTSGLDATAAYRLVLTLGSLAQKGKTIVTSMHQPSSRVYQMFDSVLVLSEGRCLFF--GKGSDAM  295 (659)
T ss_pred             HHHHHhCCCEEEEeCCCCCcCHHHHHHHHHHHHHHHhCCCEEEEEecCCCHHHHHhhceEEEecCCcEEEE--CCHHHHH
Confidence            3334445568999997442 222222333333321 13567888887754  3332222      112222  2567888


Q ss_pred             HHHHHhhhCCC
Q 046115          137 SVFQSLAISGK  147 (505)
Q Consensus       137 ~Lf~~~~~~~~  147 (505)
                      +.|....+...
T Consensus       296 ~~f~~~G~~~P  306 (659)
T PLN03211        296 AYFESVGFSPS  306 (659)
T ss_pred             HHHHHCCCCCC
Confidence            88887654433

>PRK08506 replicative DNA helicase; Provisional

Probab=82.90  E-value=8.5  Score=39.29  Aligned_cols=44  Identities=11%  Similarity=0.076  Sum_probs=28.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHc
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESL   48 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l   48 (505)
                      .+|+|||++|..++..  ...+=..+++++..  -+..++...++...
T Consensus       200 rpg~GKT~fal~ia~~--~~~~g~~V~~fSlE--Ms~~ql~~Rlla~~  243 (472)
T PRK08506        200 RPSMGKTTLCLNMALK--ALNQDKGVAFFSLE--MPAEQLMLRMLSAK  243 (472)
T ss_pred             CCCCChHHHHHHHHHH--HHhcCCcEEEEeCc--CCHHHHHHHHHHHh
Confidence            3799999999999873  33222345566544  35566666666544

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=82.89  E-value=10  Score=39.20  Aligned_cols=64  Identities=14%  Similarity=0.190  Sum_probs=37.8

Q ss_pred             HHHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCcceEeCC
Q 046115           62 LMQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVN  128 (505)
Q Consensus        62 ~~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~~~~~l~  128 (505)
                      ..-.|.+.|-.++=+|+||.-.+. +.....-+..++. ..+| .+||.|-++..+..+... ++++.
T Consensus       160 ~Rv~LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~-~~~g-tviiVSHDR~FLd~V~t~-I~~ld  224 (530)
T COG0488         160 RRVALARALLEEPDLLLLDEPTNHLDLESIEWLEDYLK-RYPG-TVIVVSHDRYFLDNVATH-ILELD  224 (530)
T ss_pred             HHHHHHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHH-hCCC-cEEEEeCCHHHHHHHhhh-eEEec
Confidence            334466666667779999987553 2222233333333 3445 799999999887765432 44443

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=82.87  E-value=0.71  Score=38.66  Aligned_cols=37  Identities=24%  Similarity=0.245  Sum_probs=25.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTP   50 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~   50 (505)
                      ++|+||||+|+.+++.  ..-.     +++.+      .++++++++.+.
T Consensus         8 ~pGsG~TTva~~lAe~--~gl~-----~vsaG------~iFR~~A~e~gm   44 (179)
T COG1102           8 LPGSGKTTVARELAEH--LGLK-----LVSAG------TIFREMARERGM   44 (179)
T ss_pred             CCCCChhHHHHHHHHH--hCCc-----eeecc------HHHHHHHHHcCC
Confidence            4899999999999982  2111     23333      567888888874

>PRK04040 adenylate kinase; Provisional

Probab=82.80  E-value=0.83  Score=40.09  Aligned_cols=15  Identities=40%  Similarity=0.574  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+++.++.
T Consensus        10 ~pG~GKtt~~~~l~~   24 (188)
T PRK04040         10 VPGVGKTTVLNKALE   24 (188)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999988

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=82.76  E-value=3.3  Score=42.80  Aligned_cols=102  Identities=13%  Similarity=0.147  Sum_probs=51.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLDD   81 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlDd   81 (505)
                      .|+|||++|+.+.+.  -...-...+.|++...++ ..+..++..... +.......  .....+.  ..+ .--|+||+
T Consensus       219 ~GtGK~~~A~~ih~~--s~r~~~p~v~v~c~~~~~-~~~e~~lfG~~~-g~~~ga~~--~~~g~~~--~a~-gGtL~lde  289 (509)
T PRK05022        219 TGVGKELVARAIHAA--SPRADKPLVYLNCAALPE-SLAESELFGHVK-GAFTGAIS--NRSGKFE--LAD-GGTLFLDE  289 (509)
T ss_pred             CCccHHHHHHHHHHh--CCcCCCCeEEEEcccCCh-HHHHHHhcCccc-cccCCCcc--cCCcchh--hcC-CCEEEecC
Confidence            699999999999873  222223445677776543 112222221111 00000000  0000111  112 23478999


Q ss_pred             CCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           82 VWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        82 v~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |..-......++...+....           ...+||.||..
T Consensus       290 I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~  331 (509)
T PRK05022        290 IGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNR  331 (509)
T ss_pred             hhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCC
Confidence            97766555666666654322           24578887764

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=82.73  E-value=9.6  Score=39.67  Aligned_cols=46  Identities=15%  Similarity=0.191  Sum_probs=25.9

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEe
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITT  110 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTt  110 (505)
                      .+.+.+-+++=++|||+..+. |...-..+.+.+....++..+|+.|
T Consensus       480 aiARall~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiIt  526 (529)
T TIGR02868       480 ALARALLADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVIT  526 (529)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence            355555556678899998553 3233444555555544444555444

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=82.73  E-value=4.5  Score=40.45  Aligned_cols=79  Identities=16%  Similarity=0.168  Sum_probs=41.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCC------CCChhcHHHH-----HHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGS------AKDLVEFQSL-----MQHIEEC   69 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~------~~~~~~~~~~-----~~~l~~~   69 (505)
                      +|+|||||++.+++  ...  .+.++++-+++.. +..++....+..-+...      ..+.....+.     .-.+.+.
T Consensus       167 sG~GKTtLL~~I~~--~~~--~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~~~a~tiAEy  242 (442)
T PRK08927        167 SGVGKSVLLSMLAR--NAD--ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAAYLTLAIAEY  242 (442)
T ss_pred             CCCCHHHHHHHHHh--ccC--CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            69999999999987  222  2345555555543 44455544444321100      1111111111     1112222


Q ss_pred             c--CCceEEEEEeCCCC
Q 046115           70 V--AGKKFLLVLDDVWN   84 (505)
Q Consensus        70 l--~~~r~LlvlDdv~~   84 (505)
                      +  .++++|+++||+.+
T Consensus       243 frd~G~~Vll~~DslTr  259 (442)
T PRK08927        243 FRDQGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHCCCcEEEEEeCcHH
Confidence            2  47899999999944

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=82.67  E-value=1.2  Score=41.57  Aligned_cols=34  Identities=29%  Similarity=0.241  Sum_probs=22.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      ||+||||+|..++.  .....=..++=|++..+.+.
T Consensus        10 GGvGKTT~~~nLA~--~La~~G~kVlliD~Dpq~n~   43 (270)
T cd02040          10 GGIGKSTTTQNLSA--ALAEMGKKVMIVGCDPKADS   43 (270)
T ss_pred             CcCCHHHHHHHHHH--HHHhCCCeEEEEEcCCCCCc
Confidence            89999999988877  44432124556776655443

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.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=82.57  E-value=0.75  Score=40.10  Aligned_cols=15  Identities=27%  Similarity=0.120  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         7 ~pGsGKst~a~~la~   21 (183)
T TIGR01359         7 GPGSGKGTQCAKIVE   21 (183)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

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.

>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]

Probab=82.55  E-value=4  Score=33.75  Aligned_cols=17  Identities=24%  Similarity=0.343  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHhcCcccc
Q 046115            2 GGIGKTTLAQFAYNNGDVE   20 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~   20 (505)
                      +|+||||++.+++.  +..
T Consensus         4 sG~GKStvg~~lA~--~lg   20 (161)
T COG3265           4 SGSGKSTVGSALAE--RLG   20 (161)
T ss_pred             CccCHHHHHHHHHH--HcC
Confidence            69999999999998  554

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=82.44  E-value=0.93  Score=37.45  Aligned_cols=15  Identities=33%  Similarity=0.496  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||++.++.
T Consensus         7 psGsGKstl~~~L~~   21 (137)
T cd00071           7 PSGVGKSTLLKRLLE   21 (137)
T ss_pred             CCCCCHHHHHHHHHh
Confidence            479999999999998

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.

>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed

Probab=82.40  E-value=10  Score=34.79  Aligned_cols=54  Identities=13%  Similarity=0.071  Sum_probs=30.1

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcC-CCCCcEEEEEeCchHHHHH
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKN-SLHESKILITTRKETVARI  118 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iLiTtr~~~~~~~  118 (505)
                      .+.+.+...+-++++|..... +......+...+.. ...+..||++|-+......
T Consensus       155 ~laral~~~p~illLDEPt~~LD~~~~~~l~~~l~~l~~~~~tiii~sH~~~~~~~  210 (248)
T PRK09580        155 DILQMAVLEPELCILDESDSGLDIDALKIVADGVNSLRDGKRSFIIVTHYQRILDY  210 (248)
T ss_pred             HHHHHHHcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHh
Confidence            344555556778899997442 22222333332222 1235678899988766554

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=82.38  E-value=11  Score=35.80  Aligned_cols=52  Identities=15%  Similarity=0.196  Sum_probs=29.9

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVAR  117 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~  117 (505)
                      +.+.+-.++-++++|.-.+. +......+...+.....+..||+||.+.....
T Consensus       144 la~al~~~p~lliLDEPt~gLD~~~~~~l~~~l~~~~~~~tiii~sH~l~~~~  196 (301)
T TIGR03522       144 LAQALIHDPKVLILDEPTTGLDPNQLVEIRNVIKNIGKDKTIILSTHIMQEVE  196 (301)
T ss_pred             HHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHHHHH
Confidence            44555567789999997442 22222333333333223567999998876443

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK13949 shikimate kinase; Provisional

Probab=82.30  E-value=0.81  Score=39.39  Aligned_cols=15  Identities=40%  Similarity=0.390  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+++.++.
T Consensus         9 ~~GsGKstl~~~La~   23 (169)
T PRK13949          9 YMGAGKTTLGKALAR   23 (169)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999998

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=82.22  E-value=1  Score=41.19  Aligned_cols=31  Identities=29%  Similarity=0.282  Sum_probs=23.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      ||+||||+|..++.  .....|..++.-..-+.
T Consensus        11 GGtGKTTva~~la~--~l~~~~~~~l~DcDVe~   41 (284)
T COG1149          11 GGTGKTTVAANLAV--LLGDKYKLVLADCDVEA   41 (284)
T ss_pred             CCCChhhHHHHHHH--HhccccceEEEecCCCC
Confidence            89999999999988  77777877665433333

>PHA00729 NTP-binding motif containing protein

Probab=82.20  E-value=0.77  Score=41.24  Aligned_cols=15  Identities=40%  Similarity=0.288  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+|||+||..+++
T Consensus        25 ~pGvGKT~LA~aLa~   39 (226)
T PHA00729         25 KQGSGKTTYALKVAR   39 (226)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            379999999999988

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=82.16  E-value=7.5  Score=34.17  Aligned_cols=52  Identities=23%  Similarity=0.132  Sum_probs=28.6

Q ss_pred             HHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCC-CCCcEEEEEeCchH
Q 046115           63 MQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNS-LHESKILITTRKET  114 (505)
Q Consensus        63 ~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iLiTtr~~~  114 (505)
                      .-.+.+.+..++-++++|..... +......+...+... ..+..||++|.+..
T Consensus       116 rv~la~al~~~p~vlllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiiivtH~~~  169 (192)
T cd03232         116 RLTIGVELAAKPSILFLDEPTSGLDSQAAYNIVRFLKKLADSGQAILCTIHQPS  169 (192)
T ss_pred             HHHHHHHHhcCCcEEEEeCCCcCCCHHHHHHHHHHHHHHHHcCCEEEEEEcCCh
Confidence            33455556666778889986442 222223333333321 23567888888764

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including 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.

>PRK06696 uridine kinase; Validated

Probab=82.11  E-value=0.79  Score=41.54  Aligned_cols=15  Identities=33%  Similarity=0.308  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||||+.++.
T Consensus        30 ~sgsGKSTlA~~L~~   44 (223)
T PRK06696         30 ITASGKTTFADELAE   44 (223)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999997

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=82.07  E-value=8  Score=36.06  Aligned_cols=80  Identities=8%  Similarity=0.086  Sum_probs=39.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC--CceEEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA--GKKFLLV   78 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~--~~r~Llv   78 (505)
                      +|+||||+++.++.  ....+=..+.+++..... .....+......++.+... ..+.....+.+.. ++  ++.=+++
T Consensus        84 ~g~GKTtl~~~l~~--~l~~~~~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~-~~~~~~l~~~l~~-l~~~~~~D~Vi  159 (270)
T PRK06731         84 TGVGKTTTLAKMAW--QFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIA-VRDEAAMTRALTY-FKEEARVDYIL  159 (270)
T ss_pred             CCCcHHHHHHHHHH--HHHHcCCeEEEEecCCCCHHHHHHHHHHhhhcCceEEe-cCCHHHHHHHHHH-HHhcCCCCEEE
Confidence            79999999998877  333322234456554332 2222333333333322111 1223333333322 22  2457889


Q ss_pred             EeCCCCC
Q 046115           79 LDDVWNE   85 (505)
Q Consensus        79 lDdv~~~   85 (505)
                      +|-....
T Consensus       160 IDt~Gr~  166 (270)
T PRK06731        160 IDTAGKN  166 (270)
T ss_pred             EECCCCC
Confidence            9998554

>PRK13231 nitrogenase reductase-like protein; Reviewed

Probab=82.05  E-value=1.6  Score=40.68  Aligned_cols=30  Identities=20%  Similarity=0.248  Sum_probs=21.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      ||+||||+|..++.  ...+.= .++=++.-.+
T Consensus        11 GGvGKTT~a~nLA~--~La~~G-rVLliD~Dpq   40 (264)
T PRK13231         11 GGIGKSTTVSNMAA--AYSNDH-RVLVIGCDPK   40 (264)
T ss_pred             CCCcHHHHHHHHhc--ccCCCC-EEEEEeEccC
Confidence            89999999999988  444332 4555665544

>PRK06761 hypothetical protein; Provisional

Probab=82.04  E-value=1.7  Score=40.70  Aligned_cols=15  Identities=33%  Similarity=0.587  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ~~GsGKTTla~~L~~   25 (282)
T PRK06761         11 LPGFGKSTTAKMLND   25 (282)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=81.96  E-value=0.8  Score=40.05  Aligned_cols=14  Identities=43%  Similarity=0.468  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHhc
Q 046115            2 GGIGKTTLAQFAYN   15 (505)
Q Consensus         2 ~G~GKT~LA~~~~~   15 (505)
                      +|+||||+|+.++.
T Consensus         8 sgsGKTtla~~l~~   21 (187)
T cd02024           8 TNSGKTTLAKLLQR   21 (187)
T ss_pred             CCCCHHHHHHHHHH
Confidence            79999999999988

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.

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=81.91  E-value=1.8  Score=36.60  Aligned_cols=43  Identities=23%  Similarity=0.210  Sum_probs=24.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHc
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESL   48 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l   48 (505)
                      -|.||||+|..+.+-  .. ++.++-==++... ....+.+.+++.+
T Consensus         8 iGCGKTTva~aL~~L--Fg-~wgHvQnDnI~~k-~~~~f~~~~l~~L   50 (168)
T PF08303_consen    8 IGCGKTTVALALSNL--FG-EWGHVQNDNITGK-RKPKFIKAVLELL   50 (168)
T ss_pred             CCcCHHHHHHHHHHH--cC-CCCccccCCCCCC-CHHHHHHHHHHHH
Confidence            599999999999882  21 1211111123223 4556666666666

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=81.82  E-value=6.2  Score=34.95  Aligned_cols=46  Identities=22%  Similarity=0.385  Sum_probs=27.2

Q ss_pred             CceEEEEEeCCCCCCccC-h----hHHHHhhcCCCCCcEEEEEeCchHHHHHh
Q 046115           72 GKKFLLVLDDVWNEDYYK-W----EPFYKCLKNSLHESKILITTRKETVARIM  119 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~-~----~~~~~~~~~~~~~~~iLiTtr~~~~~~~~  119 (505)
                      .++-++++|......+.. .    ..+...+.  ..+..+|++|-+.+.....
T Consensus       104 ~~p~llllDEp~~glD~~~~~~l~~~ll~~l~--~~~~tiiivTH~~~~~~~~  154 (199)
T cd03283         104 GEPVLFLLDEIFKGTNSRERQAASAAVLKFLK--NKNTIGIISTHDLELADLL  154 (199)
T ss_pred             CCCeEEEEecccCCCCHHHHHHHHHHHHHHHH--HCCCEEEEEcCcHHHHHhh
Confidence            378899999974422111 1    12233333  2367899999987766554

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

>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=81.81  E-value=1.4  Score=42.10  Aligned_cols=14  Identities=50%  Similarity=0.629  Sum_probs=12.5

Q ss_pred             CCCcHHHHHHHHhc
Q 046115            2 GGIGKTTLAQFAYN   15 (505)
Q Consensus         2 ~G~GKT~LA~~~~~   15 (505)
                      ||+||||+|..++-
T Consensus        10 GGVGKTT~aaA~A~   23 (305)
T PF02374_consen   10 GGVGKTTVAAALAL   23 (305)
T ss_dssp             TTSSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHH
Confidence            89999999988776

...

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=81.78  E-value=0.86  Score=39.59  Aligned_cols=15  Identities=40%  Similarity=0.561  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||||+.++.
T Consensus         9 ~sGsGKttl~~~l~~   23 (179)
T TIGR02322         9 PSGAGKDTLLDYARA   23 (179)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

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.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=81.64  E-value=4.9  Score=40.12  Aligned_cols=40  Identities=20%  Similarity=0.255  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCC-CCCHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE-PFDEFRIARAII   45 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~-~~~~~~~~~~l~   45 (505)
                      +|+|||||++.+++  ..  +.+..++.-+++ .....+.+.+..
T Consensus       164 sG~GKSTLL~~I~~--~~--~~d~~vi~~iGeRgrEv~efl~~~~  204 (433)
T PRK07594        164 PGVGKSTLLAMLCN--AP--DADSNVLVLIGERGREVREFIDFTL  204 (433)
T ss_pred             CCCCccHHHHHhcC--CC--CCCEEEEEEECCCchHHHHHHHHhh
Confidence            69999999999987  32  233445555554 344445555543

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=81.53  E-value=5.3  Score=37.47  Aligned_cols=54  Identities=17%  Similarity=0.274  Sum_probs=30.0

Q ss_pred             HHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           65 HIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        65 ~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      .+.+.+-.++=++++|+.... +......+...+.....++.||++|-+......
T Consensus       148 ~LaRall~~p~illlDEpts~LD~~~~~~l~~~l~~~~~~~tii~isH~~~~i~~  202 (275)
T cd03289         148 CLARSVLSKAKILLLDEPSAHLDPITYQVIRKTLKQAFADCTVILSEHRIEAMLE  202 (275)
T ss_pred             HHHHHHhcCCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEECCHHHHHh
Confidence            344455556678999997542 222223333334433346778887777655443

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=81.52  E-value=17  Score=33.18  Aligned_cols=53  Identities=17%  Similarity=0.110  Sum_probs=29.9

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +.+.+..++-++++|+.... +......+...+.....+..||++|.+......
T Consensus       154 laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~~~~~~  207 (242)
T TIGR03411       154 IGMLLMQDPKLLLLDEPVAGMTDEETEKTAELLKSLAGKHSVVVVEHDMEFVRS  207 (242)
T ss_pred             HHHHHhcCCCEEEecCCccCCCHHHHHHHHHHHHHHhcCCEEEEEECCHHHHHH
Confidence            44455556679999997442 222233333333332224578888888765543

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

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

Probab=81.48  E-value=0.92  Score=38.90  Aligned_cols=53  Identities=17%  Similarity=0.247  Sum_probs=32.2

Q ss_pred             HHHHHHHHHcCC-ceEEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           61 SLMQHIEECVAG-KKFLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        61 ~~~~~l~~~l~~-~r~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      +..+...+.+.. .-=|+|||.+-.   ....+.+.+...+........+++|-|+.
T Consensus        83 ~~~~~a~~~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~  139 (172)
T PF02572_consen   83 EGLEEAKEAISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNA  139 (172)
T ss_dssp             HHHHHHHHHTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS-
T ss_pred             HHHHHHHHHHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCC
Confidence            344555666654 455999999722   23345677777777777889999999984

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

>TIGR00235 udk uridine kinase

Probab=81.41  E-value=0.88  Score=40.69  Aligned_cols=15  Identities=47%  Similarity=0.596  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||||+.++.
T Consensus        14 ~sGsGKSTl~~~l~~   28 (207)
T TIGR00235        14 GSGSGKTTVARKIYE   28 (207)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

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

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=81.36  E-value=0.91  Score=38.83  Aligned_cols=15  Identities=27%  Similarity=0.408  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         3 ~sGsGKSTla~~la~   17 (163)
T PRK11545          3 VSGSGKSAVASEVAH   17 (163)
T ss_pred             CCCCcHHHHHHHHHH
Confidence            479999999999987

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=81.32  E-value=0.93  Score=39.65  Aligned_cols=15  Identities=27%  Similarity=0.162  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ~~GsGKsTl~~~l~~   25 (188)
T TIGR01360        11 GPGSGKGTQCEKIVE   25 (188)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999986

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.

>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=81.25  E-value=0.92  Score=38.16  Aligned_cols=15  Identities=40%  Similarity=0.547  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         7 ~~GsGKstla~~la~   21 (154)
T cd00464           7 MMGAGKTTVGRLLAK   21 (154)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

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.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=81.22  E-value=0.9  Score=40.67  Aligned_cols=15  Identities=47%  Similarity=0.592  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||||+.++.
T Consensus        14 ~sGsGKTTl~~~l~~   28 (209)
T PRK05480         14 GSGSGKTTVASTIYE   28 (209)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=81.18  E-value=4.1  Score=41.17  Aligned_cols=43  Identities=21%  Similarity=0.207  Sum_probs=28.8

Q ss_pred             CCCcHHHHHHHHhcCcccccC-CCceEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERN-FEKRTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~-f~~~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|+..++.  .+.+. =+.++++-+++.. +..++...+..
T Consensus       170 ~GvGKs~L~~~~~~--~~~~~~~dv~V~~lIGERgrEv~efi~~~~~  214 (494)
T CHL00060        170 AGVGKTVLIMELIN--NIAKAHGGVSVFGGVGERTREGNDLYMEMKE  214 (494)
T ss_pred             CCCChhHHHHHHHH--HHHHhcCCeEEEEEeccCchHHHHHHHHHHh
Confidence            69999999998887  32221 1566777777643 45666666655

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

Probab=81.15  E-value=3.7  Score=40.14  Aligned_cols=32  Identities=28%  Similarity=0.411  Sum_probs=24.5

Q ss_pred             CCCCcHHHHHHHHhcCccc--ccCCCceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDV--ERNFEKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~--~~~f~~~~wv~~~~~   34 (505)
                      .+|+|||.||..++.  +.  ......+++++.+..
T Consensus         9 ~aGTGKTvla~~l~~--~l~~~~~~~~~~~l~~n~~   42 (352)
T PF09848_consen    9 GAGTGKTVLALNLAK--ELQNSEEGKKVLYLCGNHP   42 (352)
T ss_pred             cCCcCHHHHHHHHHH--HhhccccCCceEEEEecch
Confidence            389999999999998  55  556667777776653

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	505
1z6t_A	591	Structure Of The Apoptotic Protease-activating Fact		1e-09
3sfz_A	1249	Crystal Structure Of Full-Length Murine Apaf-1 Leng		3e-09
3iza_B	1263	Structure Of An Apoptosome-Procaspase-9 Card Comple		6e-09
3shf_A	1256	Crystal Structure Of The R265s Mutant Of Full-Lengt		2e-08

>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1 Bound To Adp Length = 591

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 111/241 (46%), Gaps = 50/241 (20%)
Query: 76  LLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVA-RIMGSTHVISVNVL---- 130
           LL+LDDVW+     W      LK    + +IL+TTR ++V   +MG  +V+ V       
Sbjct: 239 LLILDDVWDS----W-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKE 289
Query: 131 SEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRS-------- 182
             +E  S+F ++        K+ +L +    I+K+CKG PL    I +LLR         
Sbjct: 290 KGLEILSLFVNM--------KKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYY 341
Query: 183 --KNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
             +   K+++ I ++  ++ EA+++     + +S   L   +K  ++  ++  KD  +  
Sbjct: 342 LKQLQNKQFKRIRKSSSYDYEALDEA----MSISVEMLREDIKDYYTDLSILQKDVKVPT 397
Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHD 300
             L  LW       +   +E+EDI +E+ N       F D N    G+ ++  +HD+  D
Sbjct: 398 KVLCILW-------DMETEEVEDILQEFVN---KSLLFCDRN----GKSFRYYLHDLQVD 443
Query: 301 F 301
           F
Sbjct: 444 F 444

>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1 Length = 1249

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 100/210 (47%), Gaps = 43/210 (20%)
Query: 76  LLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVA-RIMGSTHVISVNV----L 130
           LL+LDDVW       +P+   LK   ++ +IL+TTR ++V   +MG  HV+ V       
Sbjct: 239 LLILDDVW-------DPWV--LKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGRE 289
Query: 131 SEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRS-------- 182
             +E  S+F ++        K+E+L      I+K+CKG PL    I +LLR         
Sbjct: 290 KGLEILSLFVNM--------KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYY 341
Query: 183 --KNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
             +   K+++ I ++  ++ EA+++     + +S   L   +K  ++  ++  KD  +  
Sbjct: 342 LRQLQNKQFKRIRKSSSYDYEALDEA----MSISVEMLREDIKDYYTDLSILQKDVKVPT 397
Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFN 270
             L  LW  +        +E+EDI +E+ N
Sbjct: 398 KVLCVLWDLE-------TEEVEDILQEFVN 420

>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length Murine Apaf-1 Length = 1256

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/210 (26%), Positives = 98/210 (46%), Gaps = 43/210 (20%)
Query: 76  LLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVA-RIMGSTHVISVNV----L 130
           LL+LDDVW+     W      LK   ++ +IL+TT  ++V   +MG  HV+ V       
Sbjct: 246 LLILDDVWD----PW-----VLKAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGRE 296
Query: 131 SEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRS-------- 182
             +E  S+F ++        K+E+L      I+K+CKG PL    I +LLR         
Sbjct: 297 KGLEILSLFVNM--------KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYY 348
Query: 183 --KNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYGIRK 240
             +   K+++ I ++  ++ EA+++     + +S   L   +K  ++  ++  KD  +  
Sbjct: 349 LRQLQNKQFKRIRKSSSYDYEALDEA----MSISVEMLREDIKDYYTDLSILQKDVKVPT 404
Query: 241 HKLIELWMAQGYLSEKGAKEMEDIGEEYFN 270
             L  LW  +        +E+EDI +E+ N
Sbjct: 405 KVLCVLWDLE-------TEEVEDILQEFVN 427

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	505
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	1e-95
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-89
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-46
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	1e-21
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	4e-19
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	1e-17
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	5e-16
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	1e-14
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-05
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	2e-21
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-18
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	4e-18
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	4e-16
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-11
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	9e-11
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-10
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	3e-10
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-10
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-09
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	6e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-06
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	3e-10
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	8e-10
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	8e-09
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	4e-08
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	8e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	7e-10
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-09
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-09
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	5e-09
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	6e-09
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-07
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-07
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	1e-09
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	1e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	7e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	3e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-04
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	2e-08
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	3e-06
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	3e-05
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	3e-08
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	2e-06
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	2e-06
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	6e-08
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	4e-07
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	2e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	4e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	7e-04
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	1e-07
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	3e-05
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	1e-07
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	1e-07
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	2e-07
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	7e-04
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	3e-07
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	5e-06
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	4e-07
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	4e-06
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-04
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	4e-07
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	7e-06
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	1e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-07
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	4e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	3e-04
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-04
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	9e-07
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	3e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	3e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	4e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-04
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	2e-06
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	5e-06
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	1e-04
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	2e-06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-04
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	3e-04
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	3e-04
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	5e-06
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	4e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-04
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	2e-04
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	5e-06
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	7e-06
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	2e-04
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	6e-06
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	2e-05
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	3e-05
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	4e-05
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	7e-06
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	5e-05
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	8e-06
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	1e-05
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	7e-05
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	1e-04
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	2e-05
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	9e-05
3e6j_A	229	Variable lymphocyte receptor diversity region; var	3e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	6e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-04
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-04
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	5e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	4e-05
1o6v_A	466	Internalin A; bacterial infection, extracellular r	9e-05
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	3e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	5e-04
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	5e-05
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	6e-05
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	9e-05
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-04
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-04
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	7e-05
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	1e-04
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	1e-04
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	8e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	5e-04
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	2e-04
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	7e-04
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	2e-04
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	7e-04
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	8e-04
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	3e-04

>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 =  300 bits (770), Expect = 1e-95
 Identities = 59/320 (18%), Positives = 116/320 (36%), Gaps = 45/320 (14%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEPFDEFRIA--RAIIESLT---PGSA 53
           M G GK+ LA  A  +  +          WV V +      +   + +   L      S 
Sbjct: 155 MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQ 214

Query: 54  KDLVEFQSLMQHIEECVAGK--KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTR 111
           +  +  +     +   +  K  + LL+LDDVW+    K         +     +IL+TTR
Sbjct: 215 RLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKA------FDSQ---CQILLTTR 265

Query: 112 KETVARIMGSTHVISV--NVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGL 169
            ++V   +     +    + L + +   +            K+ +L +    I+K+CKG 
Sbjct: 266 DKSVTDSVMGPKYVVPVESSLGKEKGLEILSL-----FVNMKKADLPEQAHSIIKECKGS 320

Query: 170 PLAAKTIASLLRSKNTE-KEWQNILENEIWELEAIEK-----GLLAPLLLSYNELPSKVK 223
           PL    I +LLR      + +   L+N+ ++            L   + +S   L   +K
Sbjct: 321 PLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIK 380

Query: 224 RCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNK 283
             ++  ++  KD  +    L  LW  +            +  E+      ++S       
Sbjct: 381 DYYTDLSILQKDVKVPTKVLCILWDME-----------TEEVEDILQEFVNKSLLF---C 426

Query: 284 YDDGEIYKCKMHDIVHDFAQ 303
             +G+ ++  +HD+  DF  
Sbjct: 427 DRNGKSFRYYLHDLQVDFLT 446

>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 =  283 bits (724), Expect = 2e-89
 Identities = 56/362 (15%), Positives = 112/362 (30%), Gaps = 38/362 (10%)

Query: 1   MGGIGKTTLAQFAYNNGD--VERNFEKRTWVCVSEPFDE---------FRIARAIIESLT 49
             G GK+ +A  A +  D  +  N++   W+  S    +           + ++  + L 
Sbjct: 160 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLN 219

Query: 50  PGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILIT 109
             S + +             +     L V DDV  E+  +W    +         + L+T
Sbjct: 220 FPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRL--------RCLVT 271

Query: 110 TRKETVARIMGST-HVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKG 168
           TR   ++     T   I V  L   EC+   ++  +        E  E +  + ++   G
Sbjct: 272 TRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVG---EKEEDVLNKTIELSSG 328

Query: 169 LPLAAKTIASLLRSKNTEKEWQ-------NILENEIWELEAIEKGLLAPLLLSYNELPSK 221
            P            K  EK  Q         L           K L   L      L  +
Sbjct: 329 NPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDE 388

Query: 222 VKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDF 281
            +   ++  V P    I       +      +     ++++D   +    L+ R      
Sbjct: 389 DRSALAFAVVMPPGVDIPVKLWSCVIPVD--ICSNEEEQLDDEVADRLKRLSKRGALLSG 446

Query: 282 NKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEEL---AISSFVEKKILHLLLTL 338
                  +   K+  I+H F +++   + +A  I   E+      ++ V     H+    
Sbjct: 447 ---KRMPVLTFKIDHIIHMFLKHVVDAQTIANGISILEQRLLEIGNNNVSVPERHIPSHF 503

Query: 339 RR 340
           ++
Sbjct: 504 QK 505

>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 =  172 bits (437), Expect = 3e-46
 Identities = 81/474 (17%), Positives = 155/474 (32%), Gaps = 118/474 (24%)

Query: 1   MGGIGKTTLAQFAYNNGDVERNFEKRT-WV---CVSEPFDEFRIARAIIESLTP------ 50
           + G GKT +A     +  V+   + +  W+     + P     + + ++  + P      
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS 217

Query: 51  -GSAKDLVEFQSLMQHIEECVAGKKF---LLVLDDVWNEDYYKWEPF-YKCLKNSLHESK 105
             S+   +   S+   +   +  K +   LLVL +V N     W  F   C        K
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA--WNAFNLSC--------K 267

Query: 106 ILITTRKETVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKK 165
           IL+TTR + V   + +     +++       +  +  ++  K +  R   + + RE+   
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP--QDLPREV--- 322

Query: 166 CKGLPLAAKTIASLLRS-KNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNEL-PSKVK 223
               P     IA  +R    T   W N       +L  I +        S N L P++ +
Sbjct: 323 LTTNPRRLSIIAESIRDGLAT---WDNWKHVNCDKLTTIIE-------SSLNVLEPAEYR 372

Query: 224 RCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNK 283
           + F   +VFP    I    L  +W       +    ++  +  +    L   S  +   K
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIW------FDVIKSDVMVVVNK----LHKYSLVEKQPK 422

Query: 284 YDDGEIY------KCK------MHDIVHD---FAQYLCSNECLAVEI----------H-- 316
                I       K K      +H  + D     +   S++ +   +          H  
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLK 482

Query: 317 ---SGEELAISS-------FVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSD 366
                E + +         F+E+KI H         +   SI   +  L+  +  +  +D
Sbjct: 483 NIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW----NASGSILNTLQQLKFYKPYICDND 538

Query: 367 EYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL 420
                       +E+L                N ++  +P   E L+  KY +L
Sbjct: 539 PK----------YERLV---------------NAILDFLPKIEENLICSKYTDL 567

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.4 bits (135), Expect = 2e-08
 Identities = 57/345 (16%), Positives = 105/345 (30%), Gaps = 77/345 (22%)

Query: 123 HVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRS 182
            V     +   +C  V        K+I  +E ++     I+   K        +   L S
Sbjct: 23  SVFEDAFVDNFDCKDVQDMP----KSILSKEEID----HIIMS-KDAVSGTLRLFWTLLS 73

Query: 183 KNTEKEWQNILENEI-----WELEAIEKGLLAPLLLSYNELPSKVKRCFSYCAVFPKDYG 237
           K  E+  Q  +E  +     + +  I+     P +        +  R ++   VF K   
Sbjct: 74  KQ-EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSM-MTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 238 IRKHKLIELWMA------QGYLSEKGAKEMEDIGEEYFNILASRSF-FQDFNKYDDGEIY 290
            R    ++L  A         +   G   +   G+ +  +    S+  Q      D +I+
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDG---VLGSGKTWVALDVCLSYKVQCKM---DFKIF 185

Query: 291 -----KCKMHDIVHDFAQYLC----SNECLAVEIHSGEELAISSFVEKKILHLLLTLRRG 341
                 C   + V +  Q L      N     +  S  +L I S   +  L  LL  +  
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE--LRRLLKSKPY 243

Query: 342 ASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTC-----------LRALEL 390
                              LLV  +    +++     F  L+C              L  
Sbjct: 244 E----------------NCLLVLLN--VQNAKAW-NAFN-LSCKILLTTRFKQVTDFLSA 283

Query: 391 QVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
                   ++    + P  ++ LL LKYL+     + + LP  + 
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLL-LKYLDC----RPQDLPREVL 323

>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} Length = 328

 Score = 95.0 bits (237), Expect = 1e-21
 Identities = 32/114 (28%), Positives = 49/114 (42%), Gaps = 7/114 (6%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           LP     L  L++L++       RN+ +  +   I  L  L+ L+L+G   +   P    
Sbjct: 198 LPASIANLQNLKSLKI-------RNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFG 250

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
               L+RL + DC NL  LP  I +L +L  L       L  LP+ I +L    
Sbjct: 251 GRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANC 304

>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} Length = 328

 Score = 87.3 bits (217), Expect = 4e-19
 Identities = 30/115 (26%), Positives = 46/115 (40%), Gaps = 8/115 (6%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
                + L  L++L L           I+ +P +I  L +LK L ++    +  L   + 
Sbjct: 175 ASGEHQGLVNLQSLRL-------EWTGIRSLPASIANLQNLKSLKIRN-SPLSALGPAIH 226

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR 489
            L  LE L++  C  LR  P   G    L  L  +D   L  LP  I  L +L +
Sbjct: 227 HLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEK 281

>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} Length = 328

 Score = 83.1 bits (206), Expect = 1e-17
 Identities = 25/109 (22%), Positives = 39/109 (35%), Gaps = 9/109 (8%)

Query: 373 EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET 432
             L      L  L  L+L+          ++  P        LK L LK    +  LP  
Sbjct: 219 SALGPAIHHLPKLEELDLR------GCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLD 272

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL---HNEDTGCLRYLP 478
           +  L  LE+L++  C NL  LP  I +L     +    +      ++ P
Sbjct: 273 IHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILVPPHLQAQLDQHRP 321

>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} Length = 328

 Score = 78.1 bits (193), Expect = 5e-16
 Identities = 31/126 (24%), Positives = 50/126 (39%), Gaps = 18/126 (14%)

Query: 373 EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET 432
              P    +L+ L+ + +           + E+P  +++   L+ L L     +  LP +
Sbjct: 94  PQFPDQAFRLSHLQHMTI-------DAAGLMELPDTMQQFAGLETLTLARNP-LRALPAS 145

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGK---------LRKLMYLHNEDTGCLRYLPAGIGE 483
           +  L  L  L++  C  L ELP  +           L  L  L  E TG +R LPA I  
Sbjct: 146 IASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTG-IRSLPASIAN 204

Query: 484 LIRLRR 489
           L  L+ 
Sbjct: 205 LQNLKS 210

>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} Length = 328

 Score = 73.8 bits (182), Expect = 1e-14
 Identities = 30/142 (21%), Positives = 50/142 (35%), Gaps = 15/142 (10%)

Query: 353 TGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKL 412
           T LR    +L +   +  +         +       +++ R        +K     +E  
Sbjct: 23  TALRPYHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETR----TGRALKATADLLEDA 78

Query: 413 --LHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL---H 467
                  L L+    + + P+    L +L+ + +D    L ELP  + +   L  L    
Sbjct: 79  TQPGRVALELRSVP-LPQFPDQAFRLSHLQHMTIDAAG-LMELPDTMQQFAGLETLTLAR 136

Query: 468 NEDTGCLRYLPAGIGELIRLRR 489
           N     LR LPA I  L RLR 
Sbjct: 137 NP----LRALPASIASLNRLRE 154

>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} Length = 328

 Score = 45.3 bits (108), Expect = 3e-05
 Identities = 9/96 (9%), Positives = 21/96 (21%), Gaps = 22/96 (22%)

Query: 415 LKYLNLKGQKKIEKLPETLCELYNLERLNVD-------------------DCQNLRELPR 455
            + L  +G   +    + L +       + +                     + L+    
Sbjct: 14  RENLYFQGSTALRPYHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRALKATAD 73

Query: 456 GIGKLR--KLMYLHNEDTGCLRYLPAGIGELIRLRR 489
            +        + L       L   P     L  L+ 
Sbjct: 74  LLEDATQPGRVALELRSVP-LPQFPDQAFRLSHLQH 108

>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* Length = 1249

 Score = 97.6 bits (243), Expect = 2e-21
 Identities = 71/358 (19%), Positives = 126/358 (35%), Gaps = 54/358 (15%)

Query: 1   MGGIGKTTLAQ-FAYNNGDVERNFEKRT-WVCVSEPFDEFRIARAIIESLTPGSAKDLVE 58
           M G GK+ LA     ++  +E  F     WV + +      + +  +++L     ++   
Sbjct: 155 MAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMK--LQNLCMRLDQEESF 212

Query: 59  FQSLMQHIEECVA---------GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILIT 109
            Q L  +IEE              + LL+LDDVW+            LK   ++ +IL+T
Sbjct: 213 SQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP---------WVLKAFDNQCQILLT 263

Query: 110 TR-KETVARIMGSTHVISVNV-LSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCK 167
           TR K     +MG  HV+ V   L   +   +            K+E+L      I+K+CK
Sbjct: 264 TRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLF-----VNMKKEDLPAEAHSIIKECK 318

Query: 168 GLPLAAKTIASLLRSKNT------EKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSK 221
           G PL    I +LLR           +      +          + L   + +S   L   
Sbjct: 319 GSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLRED 378

Query: 222 VKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDF 281
           +K  ++  ++  KD  +    L  LW               +  E+      ++S     
Sbjct: 379 IKDYYTDLSILQKDVKVPTKVLCVLW-----------DLETEEVEDILQEFVNKSL---L 424

Query: 282 NKYDDGEIYKCKMHDIVHDFAQYLCSNECLAVEIHSGEELAISSFVEKKILHLLLTLR 339
               +G+ +   +HD+  DF       E    ++       ++ F      H L   +
Sbjct: 425 FCNRNGKSFCYYLHDLQVDFLT-----EKNRSQLQDLHRKMVTQFQRYYQPHTLSPDQ 477

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 65.3 bits (159), Expect = 2e-11
 Identities = 35/160 (21%), Positives = 53/160 (33%), Gaps = 40/160 (25%)

Query: 343 SVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLI 402
           ++P  +  ++T L               +   LP L  +L  L              N +
Sbjct: 54  TLPDCLPAHITTL----------VIPDNNLTSLPALPPELRTLEV----------SGNQL 93

Query: 403 KEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELY--------------NLERLNVDDCQ 448
             +P     LL L   +      +  LP  LC+L+               L+ L+V D Q
Sbjct: 94  TSLPVLPPGLLELSIFSNPLT-HLPALPSGLCKLWIFGNQLTSLPVLPPGLQELSVSDNQ 152

Query: 449 NLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
            L  LP    +L KL   +N+    L  LP     L  L 
Sbjct: 153 -LASLPALPSELCKLWAYNNQ----LTSLPMLPSGLQELS 187

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 63.4 bits (154), Expect = 9e-11
 Identities = 28/113 (24%), Positives = 40/113 (35%), Gaps = 22/113 (19%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           LP L   L  L             +N +  +PT   +L  L   N +    +  LP    
Sbjct: 176 LPMLPSGLQELSV----------SDNQLASLPTLPSELYKLWAYNNR----LTSLPALPS 221

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL 487
               L+ L V   + L  LP    +L++LM   N     L  LP     L+ L
Sbjct: 222 ---GLKELIVSGNR-LTSLPVLPSELKELMVSGNR----LTSLPMLPSGLLSL 266

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 62.6 bits (152), Expect = 2e-10
 Identities = 30/113 (26%), Positives = 40/113 (35%), Gaps = 22/113 (19%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           LP L   L  L             +N +  +P    +L  L   N +    +  LP    
Sbjct: 136 LPVLPPGLQELSV----------SDNQLASLPALPSELCKLWAYNNQ----LTSLPM--- 178

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL 487
               L+ L+V D Q L  LP    +L KL   +N     L  LPA    L  L
Sbjct: 179 LPSGLQELSVSDNQ-LASLPTLPSELYKLWAYNNR----LTSLPALPSGLKEL 226

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 61.4 bits (149), Expect = 3e-10
 Identities = 27/128 (21%), Positives = 42/128 (32%), Gaps = 30/128 (23%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLL--------------HLKYLNL 420
           LP L   L  L                +  +P+ + KL                L+ L++
Sbjct: 96  LPVLPPGLLELSIFSNP-------LTHLPALPSGLCKLWIFGNQLTSLPVLPPGLQELSV 148

Query: 421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG 480
              + +  LP        L +L   + Q L  LP     L++L    N+    L  LP  
Sbjct: 149 SDNQ-LASLPALPS---ELCKLWAYNNQ-LTSLPMLPSGLQELSVSDNQ----LASLPTL 199

Query: 481 IGELIRLR 488
             EL +L 
Sbjct: 200 PSELYKLW 207

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 62.6 bits (152), Expect = 2e-10
 Identities = 20/167 (11%), Positives = 49/167 (29%), Gaps = 31/167 (18%)

Query: 350 GNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQ-------------VRESW 396
             +     +     +    +     + +  ++LT L+ +                   + 
Sbjct: 415 KPIKKDSRISLKDTQIGNLTNRITFISKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANS 474

Query: 397 PRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQ-------- 448
                 +    +   L  L  + L     + +LP+ L +L  L+ LN+   +        
Sbjct: 475 DYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQSLNIACNRGISAAQLK 534

Query: 449 -NLRELPRGIGKLRKLMYL---HNEDTGCLRYLPA--GIGELIRLRR 489
            +   L        K+      +N     L   PA   + ++++L  
Sbjct: 535 ADWTRLADDEDTGPKIQIFYMGYNN----LEEFPASASLQKMVKLGL 577

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 59.1 bits (143), Expect = 2e-09
 Identities = 27/162 (16%), Positives = 57/162 (35%), Gaps = 32/162 (19%)

Query: 343 SVPISIWGNVTGLRGLRSL------LVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESW 396
            +P  ++     L  L+SL       + + +       L    +    ++   +      
Sbjct: 506 QLPDFLYD----LPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYM------ 555

Query: 397 PRNNLIKEIPTN--IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELP 454
              N ++E P +  ++K++ L  L+     K+  L         L  L +D  Q + E+P
Sbjct: 556 -GYNNLEEFPASASLQKMVKLGLLDC-VHNKVRHLEA-FGTNVKLTDLKLDYNQ-IEEIP 611

Query: 455 RGIGK-LRKLMYL---HNEDTGCLRYLP--AGIGELIRLRRV 490
                   ++  L   HN+    L+Y+P       +  +  V
Sbjct: 612 EDFCAFTDQVEGLGFSHNK----LKYIPNIFNAKSVYVMGSV 649

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 52.2 bits (125), Expect = 3e-07
 Identities = 14/97 (14%), Positives = 32/97 (32%), Gaps = 16/97 (16%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKI------EKLPET 432
              L  L  +++         N     PT       LK   ++ Q+         + P  
Sbjct: 749 ATTLPYLSNMDV-------SYNCFSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTG 801

Query: 433 LCELYNLERLNVDDCQNLRELPRGIG-KLRKLMYLHN 468
           +    +L +L +     +R++   +  +L  L  + +
Sbjct: 802 ITTCPSLIQLQIGSND-IRKVDEKLTPQLYIL-DIAD 836

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 51.4 bits (123), Expect = 6e-07
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 4/93 (4%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
            P      + L+A  ++ +     N ++++ PT I     L  L + G   I K+ E L 
Sbjct: 768 FPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQI-GSNDIRKVDEKLT 826

Query: 435 ELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYL 466
               L  L++ D  N+  ++      +   MY+
Sbjct: 827 P--QLYILDIADNPNISIDVTSVCPYIEAGMYV 857

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 49.9 bits (119), Expect = 2e-06
 Identities = 18/156 (11%), Positives = 44/156 (28%), Gaps = 23/156 (14%)

Query: 346 ISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI 405
           I    N   +  + S+    ++       +    +    + A  + +       N I++ 
Sbjct: 634 IPNIFNAKSVYVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLS-----YNEIQKF 688

Query: 406 PTNI-EKLLHLKYLNLKG-------QKKIEKLPETLCELYNLERLNVDDCQNLRELPRGI 457
           PT +      +  + L         +  ++         Y L  +++   + L  L    
Sbjct: 689 PTELFATGSPISTIILSNNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNK-LTSLSDDF 747

Query: 458 --GKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
               L  L  +   +N         P       +L+
Sbjct: 748 RATTLPYLSNMDVSYNC----FSSFPTQPLNSSQLK 779

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 61.1 bits (148), Expect = 3e-10
 Identities = 31/126 (24%), Positives = 45/126 (35%), Gaps = 24/126 (19%)

Query: 375 LPQLFEKLTCLRALELQVRESWP-----------RNNLIKEIPTNIEKLLHLKYLNLKGQ 423
           LP+L   L  L A + ++  + P            NN +  +P     L   +Y+N    
Sbjct: 95  LPELPASLEYLDACDNRL-STLPELPASLKHLDVDNNQLTMLPELPALL---EYINA-DN 149

Query: 424 KKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGE 483
            ++  LPE      +LE L+V + Q L  LP     L  L    N     L  LPA    
Sbjct: 150 NQLTMLPELPT---SLEVLSVRNNQ-LTFLPELPESLEALDVSTNL----LESLPAVPVR 201

Query: 484 LIRLRR 489
                 
Sbjct: 202 NHHSEE 207

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 60.0 bits (145), Expect = 8e-10
 Identities = 21/119 (17%), Positives = 32/119 (26%), Gaps = 11/119 (9%)

Query: 371 SSEVLPQLFEKL-TCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL 429
               +   +    +     E Q      RN  +  +      +     L L  +  +  L
Sbjct: 18  FYNTISGTYADYFSAWDKWEKQALPGENRNEAVSLLK--ECLINQFSELQL-NRLNLSSL 74

Query: 430 PETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           P+ L     +  L +     L  LP     L  L    N     L  LP     L  L 
Sbjct: 75  PDNLPP--QITVLEITQNA-LISLPELPASLEYLDACDNR----LSTLPELPASLKHLD 126

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 56.9 bits (137), Expect = 8e-09
 Identities = 25/125 (20%), Positives = 42/125 (33%), Gaps = 29/125 (23%)

Query: 373 EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET 432
            +LP+L   L  + A           NN +  +P   E    L+ L++    ++  LPE 
Sbjct: 133 TMLPELPALLEYINA----------DNNQLTMLP---ELPTSLEVLSV-RNNQLTFLPE- 177

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL-------HNEDTGCLRYLPAGIGELI 485
                +LE L+V     L  LP    +               N     + ++P  I  L 
Sbjct: 178 --LPESLEALDVSTNL-LESLPAVPVRNHHSEETEIFFRCRENR----ITHIPENILSLD 230

Query: 486 RLRRV 490
               +
Sbjct: 231 PTCTI 235

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 55.0 bits (132), Expect = 4e-08
 Identities = 24/104 (23%), Positives = 39/104 (37%), Gaps = 19/104 (18%)

Query: 385 LRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNV 444
           +  LE+         N +  +P     L +L   + +    +  LPE      +L+ L+V
Sbjct: 82  ITVLEI-------TQNALISLPELPASLEYLDACDNR----LSTLPELPA---SLKHLDV 127

Query: 445 DDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           D+ Q L  LP     L  +   +N+    L  LP     L  L 
Sbjct: 128 DNNQ-LTMLPELPALLEYINADNNQ----LTMLPELPTSLEVLS 166

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 47.3 bits (112), Expect = 8e-06
 Identities = 22/119 (18%), Positives = 39/119 (32%), Gaps = 16/119 (13%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLK----YLNLKGQKKIEKLP 430
           L  L E    L AL++         NL++ +P    +  H +    +   +   +I  +P
Sbjct: 172 LTFLPELPESLEALDV-------STNLLESLPAVPVRNHHSEETEIFFRCREN-RITHIP 223

Query: 431 ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR 489
           E +  L     + ++D   L    R             +  G   Y     G+   L R
Sbjct: 224 ENILSLDPTCTIILEDNP-LSSRIRESL---SQQTAQPDYHGPRIYFSMSDGQQNTLHR 278

>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 Length = 454

 Score = 60.0 bits (146), Expect = 7e-10
 Identities = 32/124 (25%), Positives = 46/124 (37%), Gaps = 22/124 (17%)

Query: 375 LPQLFEKLTCLRALELQVRE--SWPRN--------NLIKEIPTNIEKLLHLKYLNLKGQK 424
           LP+L + LT L   E         P N        N I+ +    +    L+ LN+    
Sbjct: 272 LPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLC---DLPPSLEELNV-SNN 327

Query: 425 KIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGEL 484
           K+ +LP        LERL       L E+P     L++L   +N     LR  P     +
Sbjct: 328 KLIELPALPP---RLERLIASFNH-LAEVPELPQNLKQLHVEYNP----LREFPDIPESV 379

Query: 485 IRLR 488
             LR
Sbjct: 380 EDLR 383

>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 Length = 454

 Score = 58.5 bits (142), Expect = 3e-09
 Identities = 32/115 (27%), Positives = 46/115 (40%), Gaps = 18/115 (15%)

Query: 373 EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET 432
           E LP+  + L  L A+          NN +K++P   +  L L+ +   G   +E+LPE 
Sbjct: 186 EELPE-LQNLPFLTAIYA-------DNNSLKKLP---DLPLSLESIVA-GNNILEELPE- 232

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL 487
           L  L  L  +  D+   L+ LP     L  L    N     L  LP     L  L
Sbjct: 233 LQNLPFLTTIYADNNL-LKTLPDLPPSLEALNVRDNY----LTDLPELPQSLTFL 282

>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 Length = 454

 Score = 57.7 bits (140), Expect = 3e-09
 Identities = 30/127 (23%), Positives = 47/127 (37%), Gaps = 27/127 (21%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           L  L +    L AL +       R+N + ++P   + L  L          + +LP  L 
Sbjct: 249 LKTLPDLPPSLEALNV-------RDNYLTDLPELPQSLTFLDVSENIFSG-LSELPPNLY 300

Query: 435 ELY--------------NLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG 480
            L               +LE LNV + + L ELP    +L +L+   N     L  +P  
Sbjct: 301 YLNASSNEIRSLCDLPPSLEELNVSNNK-LIELPALPPRLERLIASFNH----LAEVPEL 355

Query: 481 IGELIRL 487
              L +L
Sbjct: 356 PQNLKQL 362

>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 Length = 454

 Score = 57.3 bits (139), Expect = 5e-09
 Identities = 27/113 (23%), Positives = 44/113 (38%), Gaps = 17/113 (15%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           L +L +    L ++          NN+++E+P  ++ L  L  +       ++ LP+   
Sbjct: 207 LKKLPDLPLSLESIVA-------GNNILEELP-ELQNLPFLTTIYADN-NLLKTLPDLPP 257

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL 487
              +LE LNV D   L +LP     L  L    N  +G    L      L  L
Sbjct: 258 ---SLEALNVRDNY-LTDLPELPQSLTFLDVSENIFSG----LSELPPNLYYL 302

>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 Length = 454

 Score = 56.9 bits (138), Expect = 6e-09
 Identities = 25/110 (22%), Positives = 49/110 (44%), Gaps = 18/110 (16%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            +  + L+ +++        NN +K++P   +    L+++   G  ++E+LPE L  L  
Sbjct: 149 LQNSSFLKIIDV-------DNNSLKKLP---DLPPSLEFIAA-GNNQLEELPE-LQNLPF 196

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           L  +  D+   L++LP     L  ++  +N     L  LP  +  L  L 
Sbjct: 197 LTAIYADNNS-LKKLPDLPLSLESIVAGNNI----LEELPE-LQNLPFLT 240

>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 Length = 454

 Score = 53.1 bits (128), Expect = 1e-07
 Identities = 22/123 (17%), Positives = 33/123 (26%), Gaps = 25/123 (20%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLL-------------HLKYLNLK 421
           +P   E +                +   +  P    +                   L L 
Sbjct: 26  MPVEAENVKSKTEYYNA------WSEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELN 79

Query: 422 GQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGI 481
               +  LPE      +LE L       L ELP     L+ L+  +N     L  LP  +
Sbjct: 80  NLG-LSSLPE---LPPHLESLVASCNS-LTELPELPQSLKSLLVDNNNLK-ALSDLPPLL 133

Query: 482 GEL 484
             L
Sbjct: 134 EYL 136

>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 Length = 454

 Score = 52.7 bits (127), Expect = 2e-07
 Identities = 19/111 (17%), Positives = 30/111 (27%), Gaps = 16/111 (14%)

Query: 390 LQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDC-- 447
             ++E    ++ + E+P   E +           +     P    E   +    + DC  
Sbjct: 11  TFLQEPLRHSSNLTEMPVEAENVKSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLD 70

Query: 448 ----------QNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
                       L  LP     L  L+   N     L  LP     L  L 
Sbjct: 71  RQAHELELNNLGLSSLPELPPHLESLVASCNS----LTELPELPQSLKSLL 117

>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 Length = 454

 Score = 48.8 bits (117), Expect = 3e-06
 Identities = 21/110 (19%), Positives = 40/110 (36%), Gaps = 16/110 (14%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           L ++ E    L+ L +         N ++E P   E +  L+  +      + ++PE   
Sbjct: 349 LAEVPELPQNLKQLHV-------EYNPLREFPDIPESVEDLRMNS-----HLAEVPELPQ 396

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGEL 484
              NL++L+V+    LRE P     +  L            +      +L
Sbjct: 397 ---NLKQLHVETNP-LREFPDIPESVEDLRMNSERVVDPYEFAHETTDKL 442

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 59.3 bits (144), Expect = 1e-09
 Identities = 21/127 (16%), Positives = 42/127 (33%), Gaps = 19/127 (14%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           +    +K+  L  LE          N ++         + L  LNL    +I ++P   C
Sbjct: 322 VETSLQKMKKLGMLECL-------YNQLEGKLPAFGSEIKLASLNLAYN-QITEIPANFC 373

Query: 435 E-LYNLERLNVDDCQNLRELPR--GIGKLRKLMYL---HNE----DTGCLRYLPAGIGEL 484
                +E L+    + L+ +P       +  +  +   +NE    D      L     + 
Sbjct: 374 GFTEQVENLSFAHNK-LKYIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKG 432

Query: 485 IRLRRVR 491
           I +  + 
Sbjct: 433 INVSSIN 439

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 56.6 bits (137), Expect = 1e-08
 Identities = 19/126 (15%), Positives = 36/126 (28%), Gaps = 23/126 (18%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKG-------QKKIE 427
           L     K   + ++ L        N + K           L  +NL G       +  ++
Sbjct: 425 LDPTPFKGINVSSINLS------NNQISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLK 478

Query: 428 KLPETLCELYNLERLNVDDCQNLRELPRGI--GKLRKLMYL---HNEDTGCLRYLPAGIG 482
              E     Y L  +++   + L +L        L  L+ +   +N         P    
Sbjct: 479 DENENFKNTYLLTSIDLRFNK-LTKLSDDFRATTLPYLVGIDLSYNS----FSKFPTQPL 533

Query: 483 ELIRLR 488
               L+
Sbjct: 534 NSSTLK 539

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 55.0 bits (133), Expect = 4e-08
 Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 3/93 (3%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
            P      + L+   ++ +     N  ++E P  I     L  L + G   I K+ E + 
Sbjct: 528 FPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQI-GSNDIRKVNEKIT 586

Query: 435 ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLH 467
              N+  L++ D  N+      +    +     
Sbjct: 587 P--NISVLDIKDNPNISIDLSYVCPYIEAGMYM 617

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 53.9 bits (130), Expect = 7e-08
 Identities = 26/189 (13%), Positives = 53/189 (28%), Gaps = 53/189 (28%)

Query: 350 GNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRAL-------------ELQVRESW 396
            ++     +     +  + S +   + +   +LT LR               E    E+ 
Sbjct: 173 KSIKKSSRITLKDTQIGQLSNNITFVSKAVMRLTKLRQFYMGNSPFVAENICEAWENENS 232

Query: 397 PRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDD---------- 446
                 K      + L  L  + +     + KLP  L  L  ++ +NV            
Sbjct: 233 EYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLK 292

Query: 447 -----------CQNLREL------------PRGIGKLRKLMYL---HNEDTGCLRYLPAG 480
                       + ++ +               + K++KL  L   +N+    L      
Sbjct: 293 DDWQALADAPVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGMLECLYNQ----LEGKLPA 348

Query: 481 IGELIRLRR 489
            G  I+L  
Sbjct: 349 FGSEIKLAS 357

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 48.9 bits (117), Expect = 3e-06
 Identities = 23/172 (13%), Positives = 51/172 (29%), Gaps = 46/172 (26%)

Query: 343 SVPISIWGNVTGLRGLRSLLVKSDEYSWSS---EVLPQLFE--KLTCLRALELQVRESWP 397
            +P +  G       + +L         +    + +P +F+   ++ + A++        
Sbjct: 367 EIPANFCGF---TEQVENLSF-------AHNKLKYIPNIFDAKSVSVMSAIDFS------ 410

Query: 398 RNNL-------IKEIPTNIEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQ- 448
            N +          +     K +++  +NL    +I K P E       L  +N+     
Sbjct: 411 YNEIGSVDGKNFDPLDPTPFKGINVSSINL-SNNQISKFPKELFSTGSPLSSINLMGNML 469

Query: 449 ------NLRELPRGIGKLRKLMYL---HNEDTGCLRYLPAGI--GELIRLRR 489
                 +L++          L  +    N+    L  L        L  L  
Sbjct: 470 TEIPKNSLKDENENFKNTYLLTSIDLRFNK----LTKLSDDFRATTLPYLVG 517

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 48.1 bits (115), Expect = 4e-06
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 9/75 (12%)

Query: 399 NNLIKEIPTNIEKLLHLKYLNLKGQ------KKIEKLPETLCELYNLERLNVDDCQNLRE 452
            N   + PT       LK   ++ Q      + + + PE +    +L +L +     +R+
Sbjct: 522 YNSFSKFPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQIGSND-IRK 580

Query: 453 LPRGIGKLRKLMYLH 467
           +   I     +  L 
Sbjct: 581 VNEKI--TPNISVLD 593

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 12/107 (11%), Positives = 28/107 (26%), Gaps = 12/107 (11%)

Query: 385 LRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKG----QKKIEKLPETLCELYNLE 440
           +  L L+             +P  I +L  L+ L L        +    P+ +    + E
Sbjct: 83  VTGLSLE------GFGASGRVPDAIGQLTELEVLALGSHGEKVNERLFGPKGISANMSDE 136

Query: 441 RLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL 487
           +         +       +      + +            I +  R+
Sbjct: 137 QKQKMRMHYQKTFVDYDPREDFSDLIKDCINSD--PQQKSIKKSSRI 181

>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} Length = 477

 Score = 55.9 bits (135), Expect = 2e-08
 Identities = 26/126 (20%), Positives = 49/126 (38%), Gaps = 18/126 (14%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP 430
           + +  +    L  L  L L       R+  I  I     ++L  LK L +     ++ + 
Sbjct: 165 TSIPTEALSHLHGLIVLRL-------RHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMT 217

Query: 431 ETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYL---HNEDTGCLRYLPAGI-GELI 485
                  NL  L++  C NL  +P   +  L  L +L   +N     +  +   +  EL+
Sbjct: 218 PNCLYGLNLTSLSITHC-NLTAVPYLAVRHLVYLRFLNLSYNP----ISTIEGSMLHELL 272

Query: 486 RLRRVR 491
           RL+ ++
Sbjct: 273 RLQEIQ 278

>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} Length = 477

 Score = 48.9 bits (117), Expect = 3e-06
 Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 12/99 (12%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP 430
             +   +F  L+ L  L++         N I  +   + + L +LK L +     +  + 
Sbjct: 93  KLIPLGVFTGLSNLTKLDIS-------ENKIVILLDYMFQDLYNLKSLEVGDN-DLVYIS 144

Query: 431 E-TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
                 L +LE+L ++ C NL  +P      L  L+ L 
Sbjct: 145 HRAFSGLNSLEQLTLEKC-NLTSIPTEALSHLHGLIVLR 182

>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} Length = 477

 Score = 45.5 bits (108), Expect = 3e-05
 Identities = 23/120 (19%), Positives = 43/120 (35%), Gaps = 12/120 (10%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP 430
             +L  +F+ L  L++LE+        +N +  I       L  L+ L L+    +  +P
Sbjct: 117 VILLDYMFQDLYNLKSLEVG-------DNDLVYISHRAFSGLNSLEQLTLEKC-NLTSIP 168

Query: 431 -ETLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
            E L  L+ L  L +     +  +      +L +L  L       L  +       + L 
Sbjct: 169 TEALSHLHGLIVLRLRHLN-INAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLT 227

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 55.1 bits (133), Expect = 3e-08
 Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 11/115 (9%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
            +++   F K+  L  L +        NN +  +    + +  LK L+L     +  +  
Sbjct: 261 EKIMYHPFVKMQRLERLYIS-------NNRLVALNLYGQPIPTLKVLDLSHN-HLLHVER 312

Query: 432 TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNE-DTGCLRYLPAGIGEL 484
              +   LE L +D    +  L       L+ L   HN+ D   LR L   +   
Sbjct: 313 NQPQFDRLENLYLDHNS-IVTLKLSTHHTLKNLTLSHNDWDCNSLRALFRNVARP 366

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 49.3 bits (118), Expect = 2e-06
 Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 12/101 (11%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP 430
             + P +F+ +  L  L L+        N +  +P  I      L  L++     +E++ 
Sbjct: 106 RYLPPHVFQNVPLLTVLVLE-------RNDLSSLPRGIFHNTPKLTTLSMSNN-NLERIE 157

Query: 431 -ETLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNE 469
            +T     +L+ L +   + L  +   +   L      +N 
Sbjct: 158 DDTFQATTSLQNLQLSSNR-LTHVDLSLIPSLFHANVSYNL 197

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 48.9 bits (117), Expect = 2e-06
 Identities = 20/103 (19%), Positives = 38/103 (36%), Gaps = 18/103 (17%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           L    + +  L+ L+L        +N +  +  N  +   L+ L L     I  L  +  
Sbjct: 287 LNLYGQPIPTLKVLDLS-------HNHLLHVERNQPQFDRLENLYLDHN-SIVTLKLST- 337

Query: 435 ELYNLERLNVDD----CQNLRELPRGIGKLRKLMYLHNEDTGC 473
             + L+ L +      C +LR L R + +      + + D  C
Sbjct: 338 -HHTLKNLTLSHNDWDCNSLRALFRNVARPA----VDDADQHC 375

>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* Length = 768

 Score = 54.5 bits (132), Expect = 6e-08
 Identities = 32/121 (26%), Positives = 54/121 (44%), Gaps = 14/121 (11%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           +P     L+ LR L+L        N L  EIP  +  +  L+ L L       ++P  L 
Sbjct: 434 IPSSLGSLSKLRDLKLW------LNMLEGEIPQELMYVKTLETLILDFNDLTGEIPSGLS 487

Query: 435 ELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLRRV 490
              NL  +++ + + L  E+P+ IG+L  L  L   +N  +G    +PA +G+   L  +
Sbjct: 488 NCTNLNWISLSNNR-LTGEIPKWIGRLENLAILKLSNNSFSG---NIPAELGDCRSLIWL 543

Query: 491 R 491
            
Sbjct: 544 D 544

>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* Length = 768

 Score = 51.8 bits (125), Expect = 4e-07
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIE-KLPETL 433
           +P      + L +L L        N L   IP+++  L  L+ L L     +E ++P+ L
Sbjct: 410 IPPTLSNCSELVSLHLS------FNYLSGTIPSSLGSLSKLRDLKL-WLNMLEGEIPQEL 462

Query: 434 CELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
             +  LE L +D   +L  E+P G+     L ++   +N  TG    +P  IG L  L 
Sbjct: 463 MYVKTLETLILDFN-DLTGEIPSGLSNCTNLNWISLSNNRLTGE---IPKWIGRLENLA 517

>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* Length = 768

 Score = 46.1 bits (110), Expect = 2e-05
 Identities = 23/115 (20%), Positives = 37/115 (32%), Gaps = 12/115 (10%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           +P      T L  + L        N L  EIP  I +L +L  L L        +P  L 
Sbjct: 482 IPSGLSNCTNLNWISLS------NNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELG 535

Query: 435 ELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           +  +L  L+++        +P  + K    +   N   G        I      +
Sbjct: 536 DCRSLIWLDLNT-NLFNGTIPAAMFKQSGKI-AANFIAG---KRYVYIKNDGMKK 585

>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* Length = 768

 Score = 45.3 bits (108), Expect = 4e-05
 Identities = 27/119 (22%), Positives = 43/119 (36%), Gaps = 24/119 (20%)

Query: 382 LTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYL-----NLKGQKKIEKLPETLCEL 436
              L+ L LQ       N    +IP  +     L  L      L G      +P +L  L
Sbjct: 393 KNTLQELYLQ------NNGFTGKIPPTLSNCSELVSLHLSFNYLSGT-----IPSSLGSL 441

Query: 437 YNLERLNVDDCQNLR-ELPRGIGKLRKLMYLH---NEDTGCLRYLPAGIGELIRLRRVR 491
             L  L +     L  E+P+ +  ++ L  L    N+ TG    +P+G+     L  + 
Sbjct: 442 SKLRDLKLWLN-MLEGEIPQELMYVKTLETLILDFNDLTG---EIPSGLSNCTNLNWIS 496

>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* Length = 768

 Score = 41.4 bits (98), Expect = 7e-04
 Identities = 24/124 (19%), Positives = 40/124 (32%), Gaps = 28/124 (22%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYL-----NLKGQKKIEKL 429
           +P L    + L+ L++        N L  +    I     LK L        G      +
Sbjct: 216 IPFLG-DCSALQHLDIS------GNKLSGDFSRAISTCTELKLLNISSNQFVGP-----I 263

Query: 430 PETLCELYNLERLNVDDCQNLR-ELPRGI-GKLRKLMYLH---NEDTGCLRYLPAGIGEL 484
           P    +  +L+ L++ +      E+P  + G    L  L    N   G    +P   G  
Sbjct: 264 PPLPLK--SLQYLSLAEN-KFTGEIPDFLSGACDTLTGLDLSGNHFYGA---VPPFFGSC 317

Query: 485 IRLR 488
             L 
Sbjct: 318 SLLE 321

>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* Length = 567

 Score = 53.2 bits (127), Expect = 1e-07
 Identities = 27/148 (18%), Positives = 52/148 (35%), Gaps = 9/148 (6%)

Query: 320 ELAISSFVEKKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLF 379
           EL   +      + LL+                + L+ +  +     +   S  +L    
Sbjct: 376 ELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSV 435

Query: 380 EKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNL 439
            K+       L +      +  +  +  ++E+LL + +L+L    ++  LP  L  L  L
Sbjct: 436 LKMEYADVRVLHLA-----HKDLTVLC-HLEQLLLVTHLDL-SHNRLRALPPALAALRCL 488

Query: 440 ERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           E L   D   L  +  G+  L +L  L 
Sbjct: 489 EVLQASDNA-LENVD-GVANLPRLQELL 514

>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* Length = 567

 Score = 45.5 bits (107), Expect = 3e-05
 Identities = 15/91 (16%), Positives = 36/91 (39%), Gaps = 12/91 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            E+L  +  L+L        +N ++ +P  +  L  L+ L       +E +   +  L  
Sbjct: 459 LEQLLLVTHLDLS-------HNRLRALPPALAALRCLEVLQASDN-ALENVDG-VANLPR 509

Query: 439 LERLNVDDCQ--NLRELPRGIGKLRKLMYLH 467
           L+ L + + +      +   +    +L+ L+
Sbjct: 510 LQELLLCNNRLQQSAAIQP-LVSCPRLVLLN 539

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 52.2 bits (126), Expect = 1e-07
 Identities = 30/123 (24%), Positives = 44/123 (35%), Gaps = 13/123 (10%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
              +P     L  L  L +        NNL+  IP  I KL  L YL +        +P+
Sbjct: 65  PYPIPSSLANLPYLNFLYI-----GGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPD 119

Query: 432 TLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRL 487
            L ++  L  L+      L   LP  I  L  L+ +    N  +G    +P   G   +L
Sbjct: 120 FLSQIKTLVTLDFSYN-ALSGTLPPSISSLPNLVGITFDGNRISG---AIPDSYGSFSKL 175

Query: 488 RRV 490
              
Sbjct: 176 FTS 178

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 52.8 bits (127), Expect = 1e-07
 Identities = 32/124 (25%), Positives = 46/124 (37%), Gaps = 19/124 (15%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP 430
             +    F  L  L  LEL        +N +  IP      L  LK L L+    IE +P
Sbjct: 101 RTIEIGAFNGLANLNTLELF-------DNRLTTIPNGAFVYLSKLKELWLRNNP-IESIP 152

Query: 431 E-TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYL---HNEDTGCLRYLPAGIGELI 485
                 + +L RL++ + + L  +  G    L  L YL          LR +P     LI
Sbjct: 153 SYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCN----LREIPNLTP-LI 207

Query: 486 RLRR 489
           +L  
Sbjct: 208 KLDE 211

>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* Length = 276

 Score = 51.9 bits (125), Expect = 2e-07
 Identities = 21/121 (17%), Positives = 41/121 (33%), Gaps = 16/121 (13%)

Query: 376 PQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLPE--T 432
              F  L+ L+ L             +  +       L  LK LN+     I+       
Sbjct: 93  LGAFSGLSSLQKLVAV-------ETNLASLENFPIGHLKTLKELNV-AHNLIQSFKLPEY 144

Query: 433 LCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNE---DTGCLRYLPAGIGELIRLR 488
              L NLE L++   + ++ +       L ++  L+         + ++  G  + IRL+
Sbjct: 145 FSNLTNLEHLDLSSNK-IQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLK 203

Query: 489 R 489
            
Sbjct: 204 E 204

>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* Length = 276

 Score = 40.7 bits (96), Expect = 7e-04
 Identities = 27/102 (26%), Positives = 42/102 (41%), Gaps = 17/102 (16%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLK---GQKKIEKLP 430
           LP+ F  LT L  L+L        +N I+ I       L  +  LNL        +  + 
Sbjct: 141 LPEYFSNLTNLEHLDLS-------SNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQ 193

Query: 431 ETLCELYNLERLNVDDCQNLRELPRGI----GKLRKLMYLHN 468
               +   L+ L +D  Q L+ +P GI      L+K+ +LH 
Sbjct: 194 PGAFKEIRLKELALDTNQ-LKSVPDGIFDRLTSLQKI-WLHT 233

>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 Length = 290

 Score = 51.3 bits (123), Expect = 3e-07
 Identities = 31/123 (25%), Positives = 46/123 (37%), Gaps = 19/123 (15%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLPETL 433
           LP L + L  L  L++         N +  +P      L  L+ L L    +++ LP  L
Sbjct: 92  LPLLGQTLPALTVLDVS-------FNRLTSLPLGALRGLGELQELYL-KGNELKTLPPGL 143

Query: 434 CE-LYNLERLNVDDCQNLRELPRGI-GKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
                 LE+L++ +   L ELP G+   L  L  L    N     L  +P G      L 
Sbjct: 144 LTPTPKLEKLSLANNN-LTELPAGLLNGLENLDTLLLQENS----LYTIPKGFFGSHLLP 198

Query: 489 RVR 491
              
Sbjct: 199 FAF 201

>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 Length = 290

 Score = 47.4 bits (113), Expect = 5e-06
 Identities = 29/110 (26%), Positives = 47/110 (42%), Gaps = 18/110 (16%)

Query: 377 QLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE-TLCE 435
           Q+   L  L  L+L        +N ++ +P   + L  L  L++    ++  LP   L  
Sbjct: 71  QVDGTLPVLGTLDLS-------HNQLQSLPLLGQTLPALTVLDV-SFNRLTSLPLGALRG 122

Query: 436 LYNLERLNVDDCQNLRELPRGI-GKLRKLMYL---HNEDTGCLRYLPAGI 481
           L  L+ L +   + L+ LP G+     KL  L   +N     L  LPAG+
Sbjct: 123 LGELQELYLKGNE-LKTLPPGLLTPTPKLEKLSLANNN----LTELPAGL 167

>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* Length = 549

 Score = 51.6 bits (124), Expect = 4e-07
 Identities = 22/109 (20%), Positives = 44/109 (40%), Gaps = 17/109 (15%)

Query: 373 EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET 432
           +   ++   L  L +L++         N    +P + +    +++LNL     I  +   
Sbjct: 377 QKTGEILLTLKNLTSLDIS-------RNTFHPMPDSCQWPEKMRFLNLSS-TGIRVVKT- 427

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL-HNEDTGCLRYLPAG 480
            C    LE L+V +   L      + +L++L Y+  N+    L+ LP  
Sbjct: 428 -CIPQTLEVLDVSNNN-LDSFSLFLPRLQEL-YISRNK----LKTLPDA 469

>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* Length = 549

 Score = 48.2 bits (115), Expect = 4e-06
 Identities = 17/100 (17%), Positives = 34/100 (34%), Gaps = 12/100 (12%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN--IEKLLHLKYLNLKGQKKIEKL 429
           S +    F  L+ L+ L L         N  + +        L +L+ L +   +   ++
Sbjct: 87  SSLSSSWFGPLSSLKYLNLM-------GNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEI 139

Query: 430 PE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLH 467
                  L +L  L +     LR      +  +R + +L 
Sbjct: 140 RRIDFAGLTSLNELEIKALS-LRNYQSQSLKSIRDIHHLT 178

>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* Length = 549

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 23/170 (13%), Positives = 57/170 (33%), Gaps = 11/170 (6%)

Query: 329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSS----EVLPQLFEKLTC 384
             + +L L     A    S          ++ L  +    +  S      L +   +L+ 
Sbjct: 196 SSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKLLRYILELSE 255

Query: 385 LRALELQVRESWPRNNLIKEIPTNIEKL--LHLKYLNLKGQKKIEKLPETLCELYNLERL 442
           +   +  +      N    ++ + + K+  + ++ L++        L      L  ++R+
Sbjct: 256 VEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRI 315

Query: 443 NVDDCQNLRELPRGIGK-LRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
            V++ + +  +P    + L+ L +L    N          A  G    L+
Sbjct: 316 TVENSK-VFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQ 364

>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} Length = 597

 Score = 51.5 bits (123), Expect = 4e-07
 Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 11/115 (9%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
            +++   F K+  L  L +        NN +  +    + +  LK L+L     +  +  
Sbjct: 267 EKIMYHPFVKMQRLERLYIS-------NNRLVALNLYGQPIPTLKVLDLSHN-HLLHVER 318

Query: 432 TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNE-DTGCLRYLPAGIGEL 484
              +   LE L +D    +  L       L+ L   HN+ D   LR L   +   
Sbjct: 319 NQPQFDRLENLYLDHNS-IVTLKLSTHHTLKNLTLSHNDWDCNSLRALFRNVARP 372

>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} Length = 597

 Score = 47.6 bits (113), Expect = 7e-06
 Identities = 16/98 (16%), Positives = 38/98 (38%), Gaps = 13/98 (13%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP 430
             + P +F+ +  L  L L+        N +  +P  I      L  L++     +E++ 
Sbjct: 112 RYLPPHVFQNVPLLTVLVLE-------RNDLSSLPRGIFHNTPKLTTLSMSNN-NLERIE 163

Query: 431 -ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLH 467
            +T     +L+ L +   + L  +   +  +  L + +
Sbjct: 164 DDTFQATTSLQNLQLSSNR-LTHVDLSL--IPSLFHAN 198

>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} Length = 597

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 14/91 (15%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLC 434
           L    + +  L+ L+L        +N +  +  N  +   L+ L L     I  L  +  
Sbjct: 293 LNLYGQPIPTLKVLDLS-------HNHLLHVERNQPQFDRLENLYLDHN-SIVTLKLST- 343

Query: 435 ELYNLERLNVDD----CQNLRELPRGIGKLR 461
             + L+ L +      C +LR L R + +  
Sbjct: 344 -HHTLKNLTLSHNDWDCNSLRALFRNVARPA 373

>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* Length = 606

 Score = 51.2 bits (123), Expect = 6e-07
 Identities = 25/126 (19%), Positives = 45/126 (35%), Gaps = 17/126 (13%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
             +    F   + L+ L+L           + E+P+ +  L  LK L L    K E L +
Sbjct: 267 FNISSNTFHCFSGLQELDLT-------ATHLSELPSGLVGLSTLKKLVLSAN-KFENLCQ 318

Query: 432 -TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYL---HNEDTGCLRYLPAGIGELIR 486
            +     +L  L++       EL  G +  L  L  L   H++    +        +L  
Sbjct: 319 ISASNFPSLTHLSIKGNTKRLELGTGCLENLENLRELDLSHDD----IETSDCCNLQLRN 374

Query: 487 LRRVRE 492
           L  ++ 
Sbjct: 375 LSHLQS 380

>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* Length = 606

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 22/125 (17%), Positives = 41/125 (32%), Gaps = 16/125 (12%)

Query: 371 SSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKL 429
           +S+        L+ L++L L         N    + T   ++   L+ L+L    +++  
Sbjct: 364 TSDCCNLQLRNLSHLQSLNLS-------YNEPLSLKTEAFKECPQLELLDLAFT-RLKVK 415

Query: 430 PE--TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYL---HNEDTGCLRYLPAGIGE 483
                   L+ L+ LN+     L      +   L  L +L    N            +  
Sbjct: 416 DAQSPFQNLHLLKVLNLSHSL-LDISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQT 474

Query: 484 LIRLR 488
           L RL 
Sbjct: 475 LGRLE 479

>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* Length = 606

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 18/100 (18%), Positives = 33/100 (33%), Gaps = 11/100 (11%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQK--KIEK 428
             +          L  L ++       N    E+ T  +E L +L+ L+L        + 
Sbjct: 314 ENLCQISASNFPSLTHLSIK------GNTKRLELGTGCLENLENLRELDLSHDDIETSDC 367

Query: 429 LPETLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
               L  L +L+ LN+   +    L      +  +L  L 
Sbjct: 368 CNLQLRNLSHLQSLNLSYNE-PLSLKTEAFKECPQLELLD 406

>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* Length = 606

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 13/98 (13%), Positives = 30/98 (30%), Gaps = 8/98 (8%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
             +  +    L     L L +       N I  I          + LN  G + +  + +
Sbjct: 166 HYLSKEDMSSLQQATNLSLNLN-----GNDIAGIEPGAFDSAVFQSLNFGGTQNLLVIFK 220

Query: 432 TL--CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLH 467
            L    + +L     +D  +  ++   + +    M + 
Sbjct: 221 GLKNSTIQSLWLGTFEDM-DDEDISPAVFEGLCEMSVE 257

>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* Length = 606

 Score = 41.2 bits (97), Expect = 6e-04
 Identities = 16/98 (16%), Positives = 29/98 (29%), Gaps = 9/98 (9%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL-P 430
           S +          L +L L        N++             LK L+ +    I  L  
Sbjct: 118 SSIDFIPLHNQKTLESLYLG------SNHISSIKLPKGFPTEKLKVLDFQNN-AIHYLSK 170

Query: 431 ETLCELYNLERLNVDDCQN-LRELPRGIGKLRKLMYLH 467
           E +  L     L+++   N +  +  G         L+
Sbjct: 171 EDMSSLQQATNLSLNLNGNDIAGIEPGAFDSAVFQSLN 208

>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* Length = 285

 Score = 49.6 bits (119), Expect = 9e-07
 Identities = 32/123 (26%), Positives = 52/123 (42%), Gaps = 20/123 (16%)

Query: 376 PQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLPE-TL 433
           P LF  L  L+ L LQ       +N ++ +P +    L +L +L L    +I  +PE   
Sbjct: 122 PGLFRGLAALQYLYLQ-------DNALQALPDDTFRDLGNLTHLFL-HGNRISSVPERAF 173

Query: 434 CELYNLERLNVDDCQNLRELPRGI-GKLRKLMYL---HNEDTGCLRYLPAGI-GELIRLR 488
             L++L+RL +   + +  +       L +LM L    N     L  LP      L  L+
Sbjct: 174 RGLHSLDRLLLHQNR-VAHVHPHAFRDLGRLMTLYLFANN----LSALPTEALAPLRALQ 228

Query: 489 RVR 491
            +R
Sbjct: 229 YLR 231

>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} Length = 347

 Score = 49.5 bits (119), Expect = 1e-06
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 11/89 (12%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            + LT LR L L         + I +I   +  L  +  LNL     +      L  +  
Sbjct: 106 LQNLTNLRELYL-------NEDNISDIS-PLANLTKMYSLNLGANHNL-SDLSPLSNMTG 156

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L  L V + + ++++   I  L  L  L 
Sbjct: 157 LNYLTVTESK-VKDVT-PIANLTDLYSLS 183

>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} Length = 347

 Score = 48.3 bits (116), Expect = 3e-06
 Identities = 23/113 (20%), Positives = 39/113 (34%), Gaps = 19/113 (16%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  L  L +         N I +I   ++ L +L+ L L     I  +   L  L  
Sbjct: 84  LSNLVKLTNLYI-------GTNKITDIS-ALQNLTNLRELYLNED-NISDISP-LANLTK 133

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
           +  LN+    NL      +  +  L YL    ++    ++ +   I  L  L 
Sbjct: 134 MYSLNLGANHNL-SDLSPLSNMTGLNYLTVTESK----VKDVTP-IANLTDLY 180

>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} Length = 347

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 25/114 (21%), Positives = 42/114 (36%), Gaps = 19/114 (16%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            E LT L  L L         N I +I   +  L+ L  L + G  KI  +   L  L N
Sbjct: 62  IEYLTNLEYLNL-------NGNQITDIS-PLSNLVKLTNLYI-GTNKITDISA-LQNLTN 111

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLRR 489
           L  L +++   + ++   +  L K+  L    N +        + +  +  L  
Sbjct: 112 LRELYLNEDN-ISDIS-PLANLTKMYSLNLGANHNLS----DLSPLSNMTGLNY 159

>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} Length = 347

 Score = 45.6 bits (109), Expect = 2e-05
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 10/88 (11%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            + LT L+ L +        +N I +I   +  L  L  L L   +   +  E +  L N
Sbjct: 261 VKDLTKLKMLNVG-------SNQISDIS-VLNNLSQLNSLFLNNNQLGNEDMEVIGGLTN 312

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL 466
           L  L +     + ++   +  L K+   
Sbjct: 313 LTTLFLSQNH-ITDIR-PLASLSKMDSA 338

>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} Length = 347

 Score = 45.2 bits (108), Expect = 3e-05
 Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 11/89 (12%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              LT + +L L         N      + +  +  L YL +  + K++ +   +  L +
Sbjct: 128 LANLTKMYSLNL-------GANHNLSDLSPLSNMTGLNYLTV-TESKVKDVTP-IANLTD 178

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L  L+++  Q + ++   +  L  L Y  
Sbjct: 179 LYSLSLNYNQ-IEDIS-PLASLTSLHYFT 205

>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} Length = 347

 Score = 44.5 bits (106), Expect = 4e-05
 Identities = 20/110 (18%), Positives = 42/110 (38%), Gaps = 14/110 (12%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              LT L +L L         N I++I   +  L  L Y       +I  +   +  +  
Sbjct: 173 IANLTDLYSLSLN-------YNQIEDIS-PLASLTSLHYFTA-YVNQITDITP-VANMTR 222

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           L  L + + + + +L   +  L +L +L       +  +   + +L +L+
Sbjct: 223 LNSLKIGNNK-ITDLS-PLANLSQLTWLEIGTNQ-ISDIN-AVKDLTKLK 268

>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} Length = 347

 Score = 42.9 bits (102), Expect = 1e-04
 Identities = 23/112 (20%), Positives = 44/112 (39%), Gaps = 12/112 (10%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              +T L +L++        NN I ++   +  L  L +L +   + I  +   + +L  
Sbjct: 217 VANMTRLNSLKIG-------NNKITDLS-PLANLSQLTWLEIGTNQ-ISDINA-VKDLTK 266

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRV 490
           L+ LNV   Q + ++   +  L +L  L   +          IG L  L  +
Sbjct: 267 LKMLNVGSNQ-ISDIS-VLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTL 316

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 47.6 bits (114), Expect = 2e-06
 Identities = 28/122 (22%), Positives = 49/122 (40%), Gaps = 12/122 (9%)

Query: 346 ISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI 405
            + +  ++GL  L  L +   +   +S+ +P L   LT L  L++        +     I
Sbjct: 78  ATNYNPISGLSNLERLRIMGKD--VTSDKIPNL-SGLTSLTLLDIS------HSAHDDSI 128

Query: 406 PTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMY 465
            T I  L  +  ++L     I  +   L  L  L+ LN+     + +  RGI    KL  
Sbjct: 129 LTKINTLPKVNSIDLSYNGAITDI-MPLKTLPELKSLNIQFDG-VHDY-RGIEDFPKLNQ 185

Query: 466 LH 467
           L+
Sbjct: 186 LY 187

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 46.1 bits (110), Expect = 5e-06
 Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            E    ++ L +        N         I  L +L+ L + G+         L  L +
Sbjct: 62  IEYAHNIKDLTI-------NNIHATNY-NPISGLSNLERLRIMGKDVTSDKIPNLSGLTS 113

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL 466
           L  L++    +   +   I  L K+  +
Sbjct: 114 LTLLDISHSAHDDSILTKINTLPKVNSI 141

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 19/110 (17%), Positives = 36/110 (32%), Gaps = 10/110 (9%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
             ++  L  + L        N  + ++ T IE   ++K L +            +  L N
Sbjct: 40  EAQMNSLTYITL-------ANINVTDL-TGIEYAHNIKDLTI-NNIHATNY-NPISGLSN 89

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           LERL +       +    +  L  L  L    +     +   I  L ++ 
Sbjct: 90  LERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVN 139

>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} Length = 306

 Score = 48.5 bits (116), Expect = 2e-06
 Identities = 30/141 (21%), Positives = 47/141 (33%), Gaps = 14/141 (9%)

Query: 353 TGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKL 412
             L  L  L + S+  S       Q     T L+ L+L         N +  + +N   L
Sbjct: 49  DKLTQLTKLSLSSNGLS-FKGCCSQSDFGTTSLKYLDLS-------FNGVITMSSNFLGL 100

Query: 413 LHLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNE 469
             L++L+ +    ++++ E      L NL  L++      R    GI   L  L  L   
Sbjct: 101 EQLEHLDFQHS-NLKQMSEFSVFLSLRNLIYLDISHTH-TRVAFNGIFNGLSSLEVLKMA 158

Query: 470 DTGCLRYLPAGI-GELIRLRR 489
                      I  EL  L  
Sbjct: 159 GNSFQENFLPDIFTELRNLTF 179

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 48.9 bits (117), Expect = 2e-06
 Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 12/100 (12%)

Query: 371 SSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP 430
                 Q     T L+ L+L         N +  + +N   L  L++L+ +    ++++ 
Sbjct: 361 FKGCCSQSDFGTTSLKYLDLS-------FNGVITMSSNFLGLEQLEHLDFQHS-NLKQMS 412

Query: 431 E--TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
           E      L NL  L++      R    GI   L  L  L 
Sbjct: 413 EFSVFLSLRNLIYLDISHTH-TRVAFNGIFNGLSSLEVLK 451

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 16/93 (17%)

Query: 371 SSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKL 429
               LP +F +L  L  L+L           ++++       L  L+ LN+    +++ +
Sbjct: 458 QENFLPDIFTELRNLTFLDLS-------QCQLEQLSPTAFNSLSSLQVLNMASN-QLKSV 509

Query: 430 PE-TLCELYNLERLNVD------DCQNLRELPR 455
           P+     L +L+++ +        C  +  L R
Sbjct: 510 PDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSR 542

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 7/95 (7%)

Query: 399 NNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLPETLCE-LYNLERLNVDDCQNLRELPRG 456
            N ++ + +        L+ L+L   + I+ + +   + L +L  L +     ++ L  G
Sbjct: 37  FNPLRHLGSYSFFSFPELQVLDLSRCE-IQTIEDGAYQSLSHLSTLILTGNP-IQSLALG 94

Query: 457 I-GKLRKLMYLHNEDTGCLRYLPAG-IGELIRLRR 489
               L  L  L   +T  L  L    IG L  L+ 
Sbjct: 95  AFSGLSSLQKLVAVETN-LASLENFPIGHLKTLKE 128

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 26/123 (21%), Positives = 45/123 (36%), Gaps = 22/123 (17%)

Query: 376 PQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKG-QKKIEKLPETL 433
              F  L+ L+ L             +  +    I  L  LK LN+     +  KLPE  
Sbjct: 93  LGAFSGLSSLQKLVAV-------ETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYF 145

Query: 434 CELYNLERLNVDDCQNLRELPRG-IGKLRKLMYL-------HNEDTGCLRYLPAGIGELI 485
             L NLE L++   + ++ +    +  L ++  L        N     + ++  G  + I
Sbjct: 146 SNLTNLEHLDLSSNK-IQSIYCTDLRVLHQMPLLNLSLDLSLNP----MNFIQPGAFKEI 200

Query: 486 RLR 488
           RL 
Sbjct: 201 RLH 203

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 48.1 bits (115), Expect = 5e-06
 Identities = 26/122 (21%), Positives = 38/122 (31%), Gaps = 15/122 (12%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKG-QKKIEKLP 430
                Q     T L+ L+L         N +  + +N   L  L++L+ +    K     
Sbjct: 362 KGCCSQSDFGTTSLKYLDLS-------FNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEF 414

Query: 431 ETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYL---HNEDTGCLRYLPAGIGELIR 486
                L NL  L++    + R    G    L  L  L    N        LP    EL  
Sbjct: 415 SVFLSLRNLIYLDISHT-HTRVAFNGIFNGLSSLEVLKMAGNSFQENF--LPDIFTELRN 471

Query: 487 LR 488
           L 
Sbjct: 472 LT 473

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 45.0 bits (107), Expect = 4e-05
 Identities = 25/120 (20%), Positives = 35/120 (29%), Gaps = 11/120 (9%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
             +    F     L+ L+L       R  +        + L HL  L L G         
Sbjct: 41  RHLGSYSFFSFPELQVLDLS------RCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALG 94

Query: 432 TLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
               L +L++L   +          IG L+ L  L   HN        LP     L  L 
Sbjct: 95  AFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFK--LPEYFSNLTNLE 152

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 23/113 (20%), Positives = 35/113 (30%), Gaps = 9/113 (7%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  L  L+L    S    +       +      LKYL+L     +  +      L  
Sbjct: 343 EVDLPSLEFLDL----SRNGLSFKGCCSQSDFGTTSLKYLDLSFN-GVITMSSNFLGLEQ 397

Query: 439 LERLNVDDCQNLRELPRGI-GKLRKLMYL---HNEDTGCLRYLPAGIGELIRL 487
           LE L+       +     +   LR L+YL   H         +  G+  L  L
Sbjct: 398 LEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVL 450

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 12/70 (17%), Positives = 20/70 (28%), Gaps = 2/70 (2%)

Query: 399 NNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPRGI 457
           N L      +      L+ L+L   + I+ +       L +L  L +             
Sbjct: 38  NPLRHLGSYSFFSFPELQVLDLSRCE-IQTIEDGAYQSLSHLSTLILTGNPIQSLALGAF 96

Query: 458 GKLRKLMYLH 467
             L  L  L 
Sbjct: 97  SGLSSLQKLV 106

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 47.5 bits (113), Expect = 5e-06
 Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 15/118 (12%)

Query: 376 PQLFEKLTC-LRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE-TL 433
              F  L+     L L         N I+EI  +      L  LNL     +E+LP    
Sbjct: 146 RNSFVGLSFESVILWLN-------KNGIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVF 198

Query: 434 CELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRV 490
                   L++   + +  LP      L+KL      +   L+ LP  + +L+ L   
Sbjct: 199 HGASGPVILDISRTR-IHSLPSYGLENLKKLRARSTYN---LKKLPT-LEKLVALMEA 251

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 47.1 bits (112), Expect = 7e-06
 Identities = 23/131 (17%), Positives = 48/131 (36%), Gaps = 13/131 (9%)

Query: 354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKL 412
            L  L  + +  ++ +    + P+ F+ L  L+ L +        N  IK +P       
Sbjct: 77  NLPKLHEIRI--EKANNLLYINPEAFQNLPNLQYLLIS-------NTGIKHLPDVHKIHS 127

Query: 413 LHLKYLNLKGQKKIEKLPE-TLCEL-YNLERLNVDDCQNLRELPRGIGKLRKLMYLHNED 470
           L    L+++    I  +   +   L +    L ++    ++E+        +L  L+  D
Sbjct: 128 LQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNG-IQEIHNSAFNGTQLDELNLSD 186

Query: 471 TGCLRYLPAGI 481
              L  LP  +
Sbjct: 187 NNNLEELPNDV 197

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 398 RNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLRELPR 455
               ++ I          L+ + +     +E +  +    L  L  + ++   NL  +  
Sbjct: 38  VLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINP 97

Query: 456 GI-GKLRKLMYLHNEDTGCLRYLPAGI 481
                L  L YL   +TG +++LP   
Sbjct: 98  EAFQNLPNLQYLLISNTG-IKHLPDVH 123

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 47.3 bits (113), Expect = 6e-06
 Identities = 14/115 (12%), Positives = 38/115 (33%), Gaps = 9/115 (7%)

Query: 382 LTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLER 441
              L+ L+L        +N +  +    +    + +++L+   K+  + + L    NLE 
Sbjct: 190 FAKLKTLDLS-------SNKLAFMGPEFQSAAGVTWISLRN-NKLVLIEKALRFSQNLEH 241

Query: 442 LNVDDCQ-NLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFVV 495
            ++     +   L     K +++  +  +    L         +  L     +  
Sbjct: 242 FDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGHYGAYCC 296

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 15/95 (15%), Positives = 37/95 (38%), Gaps = 12/95 (12%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLP-ET 432
           + ++ +     +  ++        ++ +K+   ++ +   ++K L+L G   + ++    
Sbjct: 2   IHEIKQNGNRYKIEKVT-------DSSLKQALASLRQSAWNVKELDLSG-NPLSQISAAD 53

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L     LE LN+     L E    +  L  L  L 
Sbjct: 54  LAPFTKLELLNLSSNV-LYETL-DLESLSTLRTLD 86

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 45.0 bits (107), Expect = 3e-05
 Identities = 15/140 (10%), Positives = 37/140 (26%), Gaps = 41/140 (29%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQK------------- 424
             +    + + L        NN I  +          ++YL+LK  +             
Sbjct: 116 CSRGQGKKNIYLA-------NNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASS 168

Query: 425 -----------KIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL---HNED 470
                       I  +   +     L+ L++   + L  +         + ++   +N+ 
Sbjct: 169 DTLEHLNLQYNFIYDVKGQVV-FAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNK- 225

Query: 471 TGCLRYLPAGIGELIRLRRV 490
              L  +   +     L   
Sbjct: 226 ---LVLIEKALRFSQNLEHF 242

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 44.6 bits (106), Expect = 4e-05
 Identities = 16/142 (11%), Positives = 38/142 (26%), Gaps = 39/142 (27%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP------------------TNIEKLL 413
           S++        T L  L L        +N++ E                      +    
Sbjct: 47  SQISAADLAPFTKLELLNLS-------SNVLYETLDLESLSTLRTLDLNNNYVQELLVGP 99

Query: 414 HLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYL---HNE 469
            ++ L+      I ++  +       + + + + + +  L     G   ++ YL    NE
Sbjct: 100 SIETLHAANN-NISRVSCSR--GQGKKNIYLANNK-ITMLRDLDEGCRSRVQYLDLKLNE 155

Query: 470 DTGCLRYLPAG--IGELIRLRR 489
               +  +           L  
Sbjct: 156 ----IDTVNFAELAASSDTLEH 173

>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* Length = 239

 Score = 46.5 bits (111), Expect = 7e-06
 Identities = 16/99 (16%), Positives = 40/99 (40%), Gaps = 11/99 (11%)

Query: 385 LRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERL 442
            + L+L           ++ IP++    L ++  + +     +++L   +   L  +  +
Sbjct: 33  TQTLKLI-------ETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHI 85

Query: 443 NVDDCQNLRELPRGI-GKLRKLMYLHNEDTGCLRYLPAG 480
            + + +NL  +      +L  L +L   +TG L+  P  
Sbjct: 86  EIRNTRNLTYIDPDALKELPLLKFLGIFNTG-LKMFPDL 123

>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* Length = 239

 Score = 43.8 bits (104), Expect = 5e-05
 Identities = 18/123 (14%), Positives = 39/123 (31%), Gaps = 13/123 (10%)

Query: 351 NVTGLRGLRSLLVKSDEYSWSSEVLP-QLFEKLT-CLRALELQVRESWPRNNLIKEIPTN 408
           ++T +       +     +     +P   F+ L      L+L        NN    +   
Sbjct: 122 DLTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLY-------NNGFTSVQGY 174

Query: 409 IEKLLHLKYLNLKGQKKIEKLPE-TLCELYN-LERLNVDDCQNLRELPRGI-GKLRKLMY 465
                 L  + L   K +  + +     +Y+    L+V     +  LP      L++L+ 
Sbjct: 175 AFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLDVSQTS-VTALPSKGLEHLKELIA 233

Query: 466 LHN 468
            + 
Sbjct: 234 RNT 236

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 46.9 bits (112), Expect = 8e-06
 Identities = 31/147 (21%), Positives = 49/147 (33%), Gaps = 39/147 (26%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKE--IPTNIEKLLHLKYLNLKGQK----- 424
            +V   +F  L  +  +E+         N ++           L L YL +   K     
Sbjct: 136 RKVPKGVFSGLRNMNCIEMG-------GNPLENSGFEPGAFDGLKLNYLRISEAKLTGIP 188

Query: 425 ---------------KIEKLPE-TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
                          KI+ +    L     L RL +   Q +R +  G    L  L  LH
Sbjct: 189 KDLPETLNELHLDHNKIQAIELEDLLRYSKLYRLGLGHNQ-IRMIENGSLSFLPTLRELH 247

Query: 468 ---NEDTGCLRYLPAGIGELIRLRRVR 491
              N+    L  +PAG+ +L  L+ V 
Sbjct: 248 LDNNK----LSRVPAGLPDLKLLQVVY 270

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 46.7 bits (111), Expect = 1e-05
 Identities = 18/96 (18%), Positives = 30/96 (31%), Gaps = 12/96 (12%)

Query: 376 PQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI--EKLLHLKYLNLKGQKKIEKLPE-T 432
              F+ L+ L  L L         N  K +        L  L+ L +       K+    
Sbjct: 117 SSWFKPLSSLTFLNL-------LGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKD 169

Query: 433 LCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
              L  LE L +D    L+         ++ + +L 
Sbjct: 170 FAGLTFLEELEIDASD-LQSYEPKSLKSIQNVSHLI 204

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 44.0 bits (104), Expect = 7e-05
 Identities = 20/105 (19%), Positives = 44/105 (41%), Gaps = 13/105 (12%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT----NIEKLLHLKYLNLKGQKKIE 427
             +L    +  + +  LEL  R++        E+ T    ++ K    + + +  +  + 
Sbjct: 211 ILLLEIFVDVTSSVECLEL--RDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDES-LF 267

Query: 428 KLPETLCELYNLERLNVDDCQNLRELPRGI----GKLRKLMYLHN 468
           ++ + L ++  L  L     Q L+ +P GI      L+K+ +LH 
Sbjct: 268 QVMKLLNQISGLLELEFSRNQ-LKSVPDGIFDRLTSLQKI-WLHT 310

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 43.2 bits (102), Expect = 1e-04
 Identities = 24/147 (16%), Positives = 50/147 (34%), Gaps = 18/147 (12%)

Query: 355 LRGLRSLLVKSDEYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKL 412
              L  L +       + +++  + F  LT L  LE+         + ++       + +
Sbjct: 145 FSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEID-------ASDLQSYEPKSLKSI 197

Query: 413 LHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDD----CQNLRELPRGI-GKLRKLMYL 466
            ++ +L L   K+   L E  +    ++E L + D      +  EL  G    L K    
Sbjct: 198 QNVSHLILHM-KQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTF 256

Query: 467 HNEDTGC--LRYLPAGIGELIRLRRVR 491
            N       L  +   + ++  L  + 
Sbjct: 257 RNVKITDESLFQVMKLLNQISGLLELE 283

>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 Length = 291

 Score = 45.4 bits (108), Expect = 2e-05
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 12/88 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            + L  L++L L+       +N I +I   +  L  L+ L L    KI  +   L  L  
Sbjct: 108 LKDLKKLKSLSLE-------HNGISDI-NGLVHLPQLESLYLGNN-KITDI-TVLSRLTK 157

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL 466
           L+ L+++D Q + ++   +  L KL  L
Sbjct: 158 LDTLSLEDNQ-ISDIV-PLAGLTKLQNL 183

>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 Length = 291

 Score = 43.5 bits (103), Expect = 9e-05
 Identities = 27/113 (23%), Positives = 43/113 (38%), Gaps = 12/113 (10%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  L +L L        NN I +I T + +L  L  L+L+   +I  +   L  L  
Sbjct: 130 LVHLPQLESLYL-------GNNKITDI-TVLSRLTKLDTLSLEDN-QISDIVP-LAGLTK 179

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVR 491
           L+ L +     + +L R +  L+ L  L      CL         L+    V+
Sbjct: 180 LQNLYLSKNH-ISDL-RALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVK 230

>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} Length = 229

 Score = 44.3 bits (105), Expect = 3e-05
 Identities = 40/144 (27%), Positives = 66/144 (45%), Gaps = 21/144 (14%)

Query: 339 RRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPR 398
           +R ASVP  I  N   L             +  +++ P +F+ L  L+ L L        
Sbjct: 29  KRHASVPAGIPTNAQILYL---------HDNQITKLEPGVFDSLINLKELYLG------- 72

Query: 399 NNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKLPETLCE-LYNLERLNVDDCQNLRELPRG 456
           +N +  +P  + + L  L  L+L G  ++  LP  + + L +L+ L +   + L ELPRG
Sbjct: 73  SNQLGALPVGVFDSLTQLTVLDL-GTNQLTVLPSAVFDRLVHLKELFMCCNK-LTELPRG 130

Query: 457 IGKLRKLMYLHNEDTGCLRYLPAG 480
           I +L  L +L   D   L+ +P G
Sbjct: 131 IERLTHLTHLA-LDQNQLKSIPHG 153

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 45.8 bits (109), Expect = 3e-05
 Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 17/106 (16%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKG--------Q 423
           + V    F  L  L    L+       NN+      ++  L +++YLNLK          
Sbjct: 261 NVVGNDSFAWLPQLEYFFLE------YNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISL 314

Query: 424 KKIEKL-PETLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
             + K+   +   L  LE LN++D   +  +   +   L  L YL 
Sbjct: 315 ASLPKIDDFSFQWLKCLEHLNMEDND-IPGIKSNMFTGLINLKYLS 359

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 27/123 (21%), Positives = 50/123 (40%), Gaps = 18/123 (14%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
             +    F + + L +L++        N + K  P   +KL  LK LNL    ++ +L +
Sbjct: 38  RRLPAANFTRYSQLTSLDVG------FNTISKLEPELCQKLPMLKVLNL-QHNELSQLSD 90

Query: 432 -TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYL---HNEDTGCLRYLPAG-IGELI 485
            T     NL  L++    +++++      K + L+ L   HN     L     G   +L 
Sbjct: 91  KTFAFCTNLTELHLMSN-SIQKIKNNPFVKQKNLITLDLSHN----GLSSTKLGTQVQLE 145

Query: 486 RLR 488
            L+
Sbjct: 146 NLQ 148

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 25/132 (18%), Positives = 43/132 (32%), Gaps = 26/132 (19%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNL--IKEIPTNIEKLLHLKYLNLKGQKKIEKL 429
            ++    F  +  L+ L L+      R  L  +   P+  + L +L  L+L     I  +
Sbjct: 443 LQLTRNSFALVPSLQRLMLR------RVALKNVDSSPSPFQPLRNLTILDLSNN-NIANI 495

Query: 430 P-ETLCELYNLERLNVDDCQ--------NLRELPRGIGKLRKLMYL---HNEDTGCLRYL 477
             + L  L  LE L++            N       +  L  L  L    N        +
Sbjct: 496 NDDMLEGLEKLEILDLQHNNLARLWKHANPGGPIYFLKGLSHLHILNLESNG----FDEI 551

Query: 478 PAG-IGELIRLR 488
           P     +L  L+
Sbjct: 552 PVEVFKDLFELK 563

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 18/112 (16%)

Query: 385 LRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLN 443
           +  L L        N L +    N  +   L  L++     I KL PE   +L  L+ LN
Sbjct: 27  ITVLNLT------HNQLRRLPAANFTRYSQLTSLDVGFN-TISKLEPELCQKLPMLKVLN 79

Query: 444 VDDCQNLRELPRG-IGKLRKLMYL---HNEDTGCLRYLPAG-IGELIRLRRV 490
           +   + L +L          L  L    N     ++ +      +   L  +
Sbjct: 80  LQHNE-LSQLSDKTFAFCTNLTELHLMSN----SIQKIKNNPFVKQKNLITL 126

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 41.5 bits (98), Expect = 5e-04
 Identities = 28/158 (17%), Positives = 54/158 (34%), Gaps = 40/158 (25%)

Query: 343 SVPISIWGNVTGLRGL---RSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRN 399
            +       +  +R L   RS   +S   +   ++    F+ L CL  L ++       +
Sbjct: 286 HLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNME-------D 338

Query: 400 NLIKEIPTNI-EKLLHLKYLNLKG-----------------QKKIEKL-----------P 430
           N I  I +N+   L++LKYL+L                      +  L            
Sbjct: 339 NDIPGIKSNMFTGLINLKYLSLSNSFTSLRTLTNETFVSLAHSPLHILNLTKNKISKIES 398

Query: 431 ETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLH 467
           +    L +LE L++   +  +EL       L  +  ++
Sbjct: 399 DAFSWLGHLEVLDLGLNEIGQELTGQEWRGLENIFEIY 436

>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 Length = 466

 Score = 45.0 bits (107), Expect = 4e-05
 Identities = 26/110 (23%), Positives = 38/110 (34%), Gaps = 14/110 (12%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              LT L  L L         N +K+I   +  L +L  L+L    +I  L   L  L  
Sbjct: 217 LGILTNLDELSLN-------GNQLKDIG-TLASLTNLTDLDL-ANNQISNLAP-LSGLTK 266

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR 488
           L  L +   Q +  +   +  L  L  L   +   L  +   I  L  L 
Sbjct: 267 LTELKLGANQ-ISNIS-PLAGLTALTNLELNENQ-LEDIS-PISNLKNLT 312

>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 Length = 466

 Score = 43.8 bits (104), Expect = 9e-05
 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 12/89 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              LT L  L++        +N + +I   + KL +L+ L      +I  +   L  L N
Sbjct: 173 LANLTTLERLDIS-------SNKVSDIS-VLAKLTNLESLIA-TNNQISDITP-LGILTN 222

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L+ L+++  Q L+++   +  L  L  L 
Sbjct: 223 LDELSLNGNQ-LKDIG-TLASLTNLTDLD 249

>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 Length = 466

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 12/89 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              LT L  L+L         N I  I   +  L  L  L L   + +E +   +  L N
Sbjct: 261 LSGLTKLTELKLG-------ANQISNIS-PLAGLTALTNLELNENQ-LEDISP-ISNLKN 310

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L  L +     + ++   +  L KL  L 
Sbjct: 311 LTYLTLYFNN-ISDIS-PVSSLTKLQRLF 337

>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 Length = 466

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 19/113 (16%), Positives = 40/113 (35%), Gaps = 20/113 (17%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  +  L+            IK I   +E L +L  +N     ++  +   L  L  
Sbjct: 42  QTDLDQVTTLQAD-------RLGIKSID-GVEYLNNLTQINFSNN-QLTDITP-LKNLTK 91

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
           L  + +++ Q + ++   +  L  L  L   +N+    +  +   +  L  L 
Sbjct: 92  LVDILMNNNQ-IADIT-PLANLTNLTGLTLFNNQ----ITDIDP-LKNLTNLN 137

>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 Length = 466

 Score = 41.5 bits (98), Expect = 5e-04
 Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 13/88 (14%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              LT L  L L        NN I +I   ++ L +L  L L     I  +   L  L +
Sbjct: 108 LANLTNLTGLTL-------FNNQITDID-PLKNLTNLNRLEL-SSNTISDISA-LSGLTS 157

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYL 466
           L++L+  +   + +L   +  L  L  L
Sbjct: 158 LQQLSFGN--QVTDLK-PLANLTTLERL 182

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 44.8 bits (106), Expect = 5e-05
 Identities = 12/90 (13%), Positives = 34/90 (37%), Gaps = 9/90 (10%)

Query: 382 LTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLER 441
              L+ L+L        +N +  +    +    + +++L+   K+  + + L    NLE 
Sbjct: 190 FAKLKTLDLS-------SNKLAFMGPEFQSAAGVTWISLRN-NKLVLIEKALRFSQNLEH 241

Query: 442 LNVDDCQ-NLRELPRGIGKLRKLMYLHNED 470
            ++     +   L     K +++  +  + 
Sbjct: 242 FDLRGNGFHCGTLRDFFSKNQRVQTVAKQT 271

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 44.5 bits (105), Expect = 6e-05
 Identities = 20/114 (17%), Positives = 44/114 (38%), Gaps = 18/114 (15%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIEKLP 430
            + L  L +    ++ L+L         N + +I    +     L+ LNL     + +  
Sbjct: 23  KQALASLRQSAWNVKELDLS-------GNPLSQISAADLAPFTKLELLNLSSN-VLYETL 74

Query: 431 ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYL-HNEDTGCLRYLPAGIGE 483
           + L  L  L  L++++   ++EL  G   +  L +  +N     +  +    G+
Sbjct: 75  D-LESLSTLRTLDLNNNY-VQELLVGP-SIETL-HAANN----NISRVSCSRGQ 120

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 43.7 bits (103), Expect = 9e-05
 Identities = 19/117 (16%), Positives = 38/117 (32%), Gaps = 20/117 (17%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIEKLP--ETLCE 435
             +    + + L        NN I  +          ++YL+LK   +I+ +   E    
Sbjct: 116 CSRGQGKKNIYLA-------NNKITMLRDLDEGCRSRVQYLDLKLN-EIDTVNFAELAAS 167

Query: 436 LYNLERLNVDDCQNLRELPRGIGKLRKLMYL---HNEDTGCLRYLPAGIGELIRLRR 489
              LE LN+     + ++   +    KL  L    N+    L ++         +  
Sbjct: 168 SDTLEHLNLQYNF-IYDVKGQVV-FAKLKTLDLSSNK----LAFMGPEFQSAAGVTW 218

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/95 (15%), Positives = 37/95 (38%), Gaps = 12/95 (12%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKL-PET 432
           + ++ +     +  ++        ++ +K+   ++ +   ++K L+L G   + ++    
Sbjct: 2   IHEIKQNGNRYKIEKVT-------DSSLKQALASLRQSAWNVKELDLSG-NPLSQISAAD 53

Query: 433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L     LE LN+     L E    +  L  L  L 
Sbjct: 54  LAPFTKLELLNLSSNV-LYETL-DLESLSTLRTLD 86

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 21/121 (17%), Positives = 44/121 (36%), Gaps = 12/121 (9%)

Query: 373 EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKG-QKKIEKLPE 431
             +   F+    +  + L       RNN +  I   +    +L++ +L+G       L +
Sbjct: 204 AFMGPEFQSAAGVTWISL-------RNNKLVLIEKALRFSQNLEHFDLRGNGFHCGTLRD 256

Query: 432 TLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG-IGELIRLRRV 490
              +   ++ +     Q +++L     +   +  L +    C   LPA     LI L+R 
Sbjct: 257 FFSKNQRVQTV---AKQTVKKLTGQNEEECTVPTLGHYGAYCCEDLPAPFADRLIALKRK 313

Query: 491 R 491
            
Sbjct: 314 E 314

>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 Length = 347

 Score = 44.0 bits (103), Expect = 7e-05
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 398 RNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLRELPRG 456
           R+  + +   ++    +L  L ++ Q+ ++ L    L  L  L  L +     LR +   
Sbjct: 17  RDGAL-DSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSG-LRFVAPD 74

Query: 457 I-GKLRKLMYLH 467
                 +L  L+
Sbjct: 75  AFHFTPRLSRLN 86

>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 Length = 605

 Score = 43.9 bits (103), Expect = 1e-04
 Identities = 26/113 (23%), Positives = 42/113 (37%), Gaps = 12/113 (10%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  L +L L        NN I +I T + +L  L  L+L+   +I  +   L  L  
Sbjct: 127 LVHLPQLESLYL-------GNNKITDI-TVLSRLTKLDTLSLEDN-QISDIVP-LAGLTK 176

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVR 491
           L+ L +     + +L   +  L+ L  L      CL         L+    V+
Sbjct: 177 LQNLYLSKNH-ISDLR-ALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVK 227

>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* Length = 330

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 26/148 (17%), Positives = 49/148 (33%), Gaps = 40/148 (27%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKE--IPTNI-EKLLHLKYLNLKGQK---- 424
           ++V   +F  L  +  +EL         N +K   I     + +  L Y+ +        
Sbjct: 134 TKVRKSVFNGLNQMIVVELG-------TNPLKSSGIENGAFQGMKKLSYIRIADTNITTI 186

Query: 425 ----------------KIEKLPE-TLCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYL 466
                           KI K+   +L  L NL +L +     +  +  G       L  L
Sbjct: 187 PQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNS-ISAVDNGSLANTPHLREL 245

Query: 467 ---HNEDTGCLRYLPAGIGELIRLRRVR 491
              +N+    L  +P G+ +   ++ V 
Sbjct: 246 HLNNNK----LVKVPGGLADHKYIQVVY 269

>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* Length = 330

 Score = 40.8 bits (96), Expect = 8e-04
 Identities = 24/113 (21%), Positives = 44/113 (38%), Gaps = 14/113 (12%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE 431
           S++ P  F  L  L  L L         N +KE+P  +     L+ L +    +I K+ +
Sbjct: 89  SKISPGAFAPLVKLERLYLS-------KNQLKELPEKM--PKTLQELRVHEN-EITKVRK 138

Query: 432 -TLCELYNLERLNVDDCQ-NLRELPRGI-GKLRKLMYLHNEDTGCLRYLPAGI 481
                L  +  + +         +  G    ++KL Y+   DT  +  +P G+
Sbjct: 139 SVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTN-ITTIPQGL 190

>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* Length = 606

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 27/152 (17%), Positives = 60/152 (39%), Gaps = 9/152 (5%)

Query: 319 EELAISSFVEKKILHLLLTL-RRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQ 377
           + +   +F   K+  L L      +++  +   N+ GL   R +L +  +        P 
Sbjct: 194 DFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPS 253

Query: 378 LFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELY 437
           + E L  +   E ++       N   +       L ++  ++L G   I+ L + + + +
Sbjct: 254 IMEGLCDVTIDEFRLT----YTNDFSDDIVKFHCLANVSAMSLAGV-SIKYLED-VPKHF 307

Query: 438 NLERLNVDDCQNLRELP-RGIGKLRKLMYLHN 468
             + L++  CQ L++ P   +  L+ L    N
Sbjct: 308 KWQSLSIIRCQ-LKQFPTLDLPFLKSLTLTMN 338

>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* Length = 606

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 31/155 (20%), Positives = 45/155 (29%), Gaps = 30/155 (19%)

Query: 346 ISIWGNVTGLRGLRSL------LVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRN 399
            SI      L  L  L      L  S   S+S      L       R L+L         
Sbjct: 340 GSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSL-------RHLDLS-------F 385

Query: 400 NLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELPRGI 457
           N    +  N   L  L++L+ +    ++++ E      L  L  L++    N +    GI
Sbjct: 386 NGAIIMSANFMGLEELQHLDFQH-STLKRVTEFSAFLSLEKLLYLDISYT-NTKIDFDGI 443

Query: 458 -GKLRKLMYL---HNEDTGCLRYLPAGIGELIRLR 488
              L  L  L    N        L         L 
Sbjct: 444 FLGLTSLNTLKMAGNSFKDNT--LSNVFANTTNLT 476

>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* Length = 606

 Score = 41.9 bits (99), Expect = 5e-04
 Identities = 29/130 (22%), Positives = 45/130 (34%), Gaps = 28/130 (21%)

Query: 372 SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIE--K 428
               P  F  LT L  L             +  + +  I +L+ LK LN+     I   K
Sbjct: 93  QSFSPGSFSGLTSLENLVAV-------ETKLASLESFPIGQLITLKKLNV-AHNFIHSCK 144

Query: 429 LPETLCELYNLERLNV----------DDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP 478
           LP     L NL  +++          +D Q LRE P+       L    N     + ++ 
Sbjct: 145 LPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQ---VNLSLDMSLNP----IDFIQ 197

Query: 479 AGIGELIRLR 488
               + I+L 
Sbjct: 198 DQAFQGIKLH 207

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 394 ESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLREL 453
           ES  R   I ++      L +    NL G++ +  L  +  EL  ++  N D+   ++ L
Sbjct: 1   ESIQRPTPINQV-FPDPGLANAVKQNL-GKQSVTDL-VSQKELSGVQNFNGDNSN-IQSL 56

Query: 454 PRGIGKLRKLMYLH 467
             G+     L  LH
Sbjct: 57  A-GMQFFTNLKELH 69

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 40.4 bits (95), Expect = 7e-04
 Identities = 20/108 (18%), Positives = 39/108 (36%), Gaps = 29/108 (26%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            ++L+ ++            N+ I+ +   ++   +LK L+L    +I  L   L +L  
Sbjct: 37  QKELSGVQNFNGD-------NSNIQSL-AGMQFFTNLKELHL-SHNQISDL-SPLKDLTK 86

Query: 439 LERLNVDDCQ----------NLREL---------PRGIGKLRKLMYLH 467
           LE L+V+  +           L  L            +  L+ L  L 
Sbjct: 87  LEELSVNRNRLKNLNGIPSACLSRLFLDNNELRDTDSLIHLKNLEILS 134

>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 Length = 308

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 12/89 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  ++ L+L        +  I ++   +  L +L+ L L    +I  +   L  L N
Sbjct: 103 IAGLQSIKTLDLT-------STQITDVT-PLAGLSNLQVLYL-DLNQITNISP-LAGLTN 152

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           L+ L++ + Q + +L   +  L KL  L 
Sbjct: 153 LQYLSIGNAQ-VSDLT-PLANLSKLTTLK 179

>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 Length = 308

 Score = 40.8 bits (96), Expect = 7e-04
 Identities = 16/89 (17%), Positives = 38/89 (42%), Gaps = 12/89 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
            + L  L  LEL+       +N I ++   ++ L  +  L L     ++ +   +  L +
Sbjct: 59  VQYLNNLIGLELK-------DNQITDLA-PLKNLTKITELEL-SGNPLKNV-SAIAGLQS 108

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           ++ L++   Q + ++   +  L  L  L+
Sbjct: 109 IKTLDLTSTQ-ITDVT-PLAGLSNLQVLY 135

>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 Length = 308

 Score = 40.4 bits (95), Expect = 8e-04
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 12/89 (13%)

Query: 379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN 438
              L  +  L             +  I   ++ L +L  L L    +I  L   L  L  
Sbjct: 37  QADLDGITTLSA-------FGTGVTTIE-GVQYLNNLIGLEL-KDNQITDLAP-LKNLTK 86

Query: 439 LERLNVDDCQNLRELPRGIGKLRKLMYLH 467
           +  L +     L+ +   I  L+ +  L 
Sbjct: 87  ITELELSGNP-LKNVS-AIAGLQSIKTLD 113

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 21/96 (21%), Positives = 32/96 (33%), Gaps = 11/96 (11%)

Query: 375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI-EKLLHLKYLNLKGQKKIEKL-PET 432
           L Q+ + L     L L         N I+ +  +    L  L+ L L  Q     +  E 
Sbjct: 16  LTQVPQVLNTTERLLLS-------FNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEA 68

Query: 433 LCELYNLERLNVDDCQNLRELPRGI-GKLRKLMYLH 467
              L NL  L++   + +  L       L  L  L 
Sbjct: 69  FRNLPNLRILDLGSSK-IYFLHPDAFQGLFHLFELR 103

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	505
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.98
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.97
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.97
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.56
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.55
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.44
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.44
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.44
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.44
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.43
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.4
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.4
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.4
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.4
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.39
2fna_A	357	Conserved hypothetical protein; structural genomic	99.39
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.37
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.37
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.37
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.35
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.34
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.33
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.33
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.33
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.32
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.31
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.31
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.31
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.31
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.3
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.29
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.29
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.28
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.28
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.28
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.28
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.28
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.28
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.28
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.28
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.28
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.28
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.27
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.27
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.26
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.26
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.26
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.26
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.26
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.25
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.25
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.25
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.24
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.24
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.24
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.23
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.23
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.23
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.22
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.22
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.21
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.21
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.21
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.21
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.21
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.2
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.2
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.2
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.2
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.2
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.2
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.19
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.19
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.18
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.18
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.18
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.18
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.18
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.17
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.17
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.17
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.16
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.16
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.16
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.16
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.15
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.15
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.15
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.15
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.15
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.15
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.14
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.14
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.14
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.14
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.14
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.13
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.13
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.13
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.13
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.13
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.12
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.12
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.12
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.12
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.12
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.11
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.1
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.1
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.1
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.09
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.09
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.09
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.08
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.08
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.06
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.03
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.03
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	99.03
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.02
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.01
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.01
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.01
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.0
1o6v_A	466	Internalin A; bacterial infection, extracellular r	98.99
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	98.98
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	98.97
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.96
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	98.96
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	98.95
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	98.94
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.93
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	98.89
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	98.85
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.84
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.83
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.82
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	98.79
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	98.75
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.62
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.62
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.61
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.6
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	98.6
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.53
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	98.5
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	98.42
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	98.39
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.34
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.24
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.23
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.15
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.02
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.02
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.98
3bos_A	242	Putative DNA replication factor; P-loop containing	97.95
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.94
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.91
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.9
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	97.88
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.87
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.87
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.85
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	97.85
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	97.8
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.77
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.76
3pvs_A	447	Replication-associated recombination protein A; ma	97.75
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.64
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.58
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.55
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.53
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.52
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.52
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.51
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.51
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.47
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.47
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.45
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.38
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.35
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.34
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.25
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.2
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.17
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.16
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.13
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	97.11
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.1
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.08
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.97
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.9
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.89
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.86
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.74
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.72
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	96.71
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	96.71
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.69
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.64
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.62
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.51
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.51
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.47
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.36
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.13
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.1
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.07
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.07
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.04
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.98
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.98
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.96
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.87
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.86
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.65
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.55
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	95.55
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.54
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	95.5
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.46
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.45
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.43
2qgz_A	308	Helicase loader, putative primosome component; str	95.36
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	95.23
3co5_A	143	Putative two-component system transcriptional RES	95.13
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	95.11
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	95.04
3io5_A	333	Recombination and repair protein; storage dimer, i	94.82
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	94.76
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	94.66
1xp8_A	366	RECA protein, recombinase A; recombination, radior	94.58
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	94.53
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	94.38
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	94.32
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	94.3
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	94.28
2z43_A	324	DNA repair and recombination protein RADA; archaea	94.27
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	94.26
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	94.15
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	94.13
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.11
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	93.86
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.79
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	93.63
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	93.5
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	93.47
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.39
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.33
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.24
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	93.23
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	92.89
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	92.64
1u94_A	356	RECA protein, recombinase A; homologous recombinat	92.42
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	92.25
2r44_A	331	Uncharacterized protein; putative ATPase, structur	92.11
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	91.89
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	91.8
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	91.09
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	90.43
4a74_A	231	DNA repair and recombination protein RADA; hydrola	90.0
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	89.95
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	89.89
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	89.7
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	89.47
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	89.34
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	89.07
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	87.52
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	87.0
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	86.73
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	86.54
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	86.45
3cwq_A	209	Para family chromosome partitioning protein; alpha	86.36
3ice_A	422	Transcription termination factor RHO; transcriptio	86.01
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	85.65
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	85.45
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	85.35
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	85.32
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	85.31
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	85.26
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	85.14
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	85.13
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	85.05
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	84.75
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	84.7
1via_A	175	Shikimate kinase; structural genomics, transferase	84.61
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	84.28
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	84.08
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	83.88
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	83.79
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	83.61
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	83.51
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	83.19
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	83.08
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	82.96
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	82.88
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	82.67
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	82.57
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	82.46
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	82.46
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	82.29
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	82.27
3l0o_A	427	Transcription termination factor RHO; helicase, RH	82.23
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	82.13
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	82.0
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	81.95
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	81.82
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	81.73
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	81.72
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	81.37
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	81.3
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	81.25
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	81.22
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	81.18
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	81.16
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	80.92
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	80.91
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	80.87
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	80.87
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	80.85
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	80.66
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	80.47
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	80.38
2vli_A	183	Antibiotic resistance protein; transferase, tunica	80.34
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	80.31
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	80.21
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	80.11
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	80.04

>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=100.00  E-value=2.2e-39  Score=334.02  Aligned_cols=288  Identities=19%  Similarity=0.303  Sum_probs=224.7

Q ss_pred             CCCCcHHHHHHHHhc--CcccccCCCceEEEEeCCCC--CHHHHHHHHHHHcCCCCC------CChhcHHHHHHHHHHHc
Q 046115            1 MGGIGKTTLAQFAYN--NGDVERNFEKRTWVCVSEPF--DEFRIARAIIESLTPGSA------KDLVEFQSLMQHIEECV   70 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~--~~~~~~~f~~~~wv~~~~~~--~~~~~~~~l~~~l~~~~~------~~~~~~~~~~~~l~~~l   70 (505)
                      |||+||||||+++|+  +.+++.+|++++||++++.+  +...++..|+.+++....      .+..+.+.....+.+.+
T Consensus       160 ~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L  239 (549)
T 2a5y_B          160 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNAL  239 (549)
T ss_dssp             STTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHH
Confidence            799999999999997  55888999999999999875  789999999999975421      12234566788899999


Q ss_pred             CCc-eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhC-CcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           71 AGK-KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMG-STHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        71 ~~~-r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~-~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      +++ |+||||||||+.+...|       +. .+||+||||||++.++..++ ....+++++|+.+||++||.+.++... 
T Consensus       240 ~~~kr~LlVLDdv~~~~~~~~-------~~-~~gs~ilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~-  310 (549)
T 2a5y_B          240 IDRPNTLFVFDDVVQEETIRW-------AQ-ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMP-  310 (549)
T ss_dssp             TTSTTEEEEEEEECCHHHHHH-------HH-HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC-
T ss_pred             cCCCcEEEEEECCCCchhhcc-------cc-cCCCEEEEEcCCHHHHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCC-
Confidence            996 99999999998653212       11 27899999999998887665 346799999999999999999986543 


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhhcccCchhhHhhccccCChhhhhhhh-
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFS-  227 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~L~~~~~~~ll-  227 (505)
                        ..+...+++.+|+++|+|+||||+++|+.++.+ .. .|...+.......  ....+..++.+||+.|+++.+.||+ 
T Consensus       311 --~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~-~w-~~~~~l~~~l~~~--~~~~i~~~l~~Sy~~L~~~lk~~f~~  384 (549)
T 2a5y_B          311 --VGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK-TF-EKMAQLNNKLESR--GLVGVECITPYSYKSLAMALQRCVEV  384 (549)
T ss_dssp             ----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS-SH-HHHHHHHHHHHHH--CSSTTCCCSSSSSSSHHHHHHHHHHT
T ss_pred             --CchhHHHHHHHHHHHhCCChHHHHHHHHHhccc-hH-HHHHHhHHHhhcc--cHHHHHHHHhcccccccHHHHHHHhc
Confidence              245778899999999999999999999999766 32 3333333322211  2456888899999999999999998 


Q ss_pred             ----------hhccCCCCCCCChHHHHHHHHHc--CCCCCCC-CCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeee
Q 046115          228 ----------YCAVFPKDYGIRKHKLIELWMAQ--GYLSEKG-AKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKM  294 (505)
Q Consensus       228 ----------~la~f~~~~~i~~~~l~~~w~~~--~~~~~~~-~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~  294 (505)
                                +||+||+++.++    +..|+++  |++.... ....++.++ ++++|++++|++....+   ....|+|
T Consensus       385 Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~~~~~~~-~l~~L~~rsLl~~~~~~---~~~~~~m  456 (549)
T 2a5y_B          385 LSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQLDDEVAD-RLKRLSKRGALLSGKRM---PVLTFKI  456 (549)
T ss_dssp             SCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCCTHHHHH-HHHHTTTBSSCSEEECS---SSCEEEC
T ss_pred             cchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCCHHHHHH-HHHHHHHcCCeeEecCC---CceEEEe
Confidence                      999999998888    7789999  8887665 456677666 99999999999876543   2337999


Q ss_pred             hHHHHHHHHHhhccceE
Q 046115          295 HDIVHDFAQYLCSNECL  311 (505)
Q Consensus       295 H~lv~~~~~~~~~~~~~  311 (505)
                      |+++|+||++++.+++.
T Consensus       457 Hdlv~~~a~~~~~~~~~  473 (549)
T 2a5y_B          457 DHIIHMFLKHVVDAQTI  473 (549)
T ss_dssp             CHHHHHHHHTTSCTHHH
T ss_pred             ChHHHHHHHHHHHHHHH
Confidence            99999999998877654

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.98  E-value=1.5e-32  Score=287.52  Aligned_cols=257  Identities=20%  Similarity=0.214  Sum_probs=195.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCc-eEEEEeCCCCCHHHHHHHHHHHcCC---C--CC-----CChhcHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEK-RTWVCVSEPFDEFRIARAIIESLTP---G--SA-----KDLVEFQSLMQHIEEC   69 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~-~~wv~~~~~~~~~~~~~~l~~~l~~---~--~~-----~~~~~~~~~~~~l~~~   69 (505)
                      |||+||||||++++++.+++.+|+. ++|+++++.++...++..++..+..   .  ..     ....+.+...+.++..
T Consensus       158 mGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~l  237 (1221)
T 1vt4_I          158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL  237 (1221)
T ss_dssp             STTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhcCcccccccccccCCCCCHHHHHHHHHHH
Confidence            7999999999999986678889986 8899999999888877777664321   1  00     1123445556666665


Q ss_pred             c---CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCcceEeCC------CCChhhHHHHHH
Q 046115           70 V---AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISVN------VLSEMECWSVFQ  140 (505)
Q Consensus        70 l---~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~~~~~l~------~l~~~ea~~Lf~  140 (505)
                      +   .++|+||||||||+.+  .|+.    ++   +||+||||||++.+...+.....+.++      +|+.+||++||.
T Consensus       238 L~~l~~KRvLLVLDDVwd~e--qLe~----f~---pGSRILVTTRd~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~  308 (1221)
T 1vt4_I          238 LKSKPYENCLLVLLNVQNAK--AWNA----FN---LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL  308 (1221)
T ss_dssp             HHHSTTSSCEEEEESCCCHH--HHHH----HH---SSCCEEEECSCSHHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHH
T ss_pred             HHhhcCCCEEEEEeCcChHH--HHHh----hC---CCeEEEEeccChHHHHhcCCCeEEEecCccccCCcCHHHHHHHHH
Confidence            5   7899999999998843  3333    22   789999999999887544333345555      899999999998


Q ss_pred             HhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCC-CHHHHHHHHhhhhhhhhhcccCchhhHhhccccCC
Q 046115          141 SLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKN-TEKEWQNILENEIWELEAIEKGLLAPLLLSYNELP  219 (505)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~-~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~L~  219 (505)
                      ... ...    .   .++..+   .|+|+||||+++|+.|+.+. ....|...          ....+..++..||+.|+
T Consensus       309 ~~~-g~~----~---eeL~~e---ICgGLPLALkLaGs~Lr~k~~s~eeW~~~----------~~~~I~aaLelSYd~Lp  367 (1221)
T 1vt4_I          309 KYL-DCR----P---QDLPRE---VLTTNPRRLSIIAESIRDGLATWDNWKHV----------NCDKLTTIIESSLNVLE  367 (1221)
T ss_dssp             HHH-CCC----T---TTHHHH---HCCCCHHHHHHHHHHHHHSCSSHHHHHHC----------SCHHHHHHHHHHHHHSC
T ss_pred             HHc-CCC----H---HHHHHH---HhCCCHHHHHHHHHHHhCCCCCHHHHhcC----------ChhHHHHHHHHHHHhCC
Confidence            874 211    1   122333   39999999999999998874 66778642          13568899999999999


Q ss_pred             hhh-hhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehHHH
Q 046115          220 SKV-KRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIV  298 (505)
Q Consensus       220 ~~~-~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~lv  298 (505)
                      ++. |.||+++|+||.++.++.+.+...|.+++          ++.+++++++|++++|++....     ..+|+||+++
T Consensus       368 ~eelK~cFL~LAIFPed~~I~~elLa~LW~aeG----------eedAe~~L~eLvdRSLLq~d~~-----~~rYrMHDLl  432 (1221)
T 1vt4_I          368 PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI----------KSDVMVVVNKLHKYSLVEKQPK-----ESTISIPSIY  432 (1221)
T ss_dssp             TTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC----------SHHHHHHHHHHHTSSSSSBCSS-----SSEEBCCCHH
T ss_pred             HHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC----------HHHHHHHHHHHHhhCCEEEeCC-----CCEEEehHHH
Confidence            999 99999999999999999999999997664          1357889999999999987311     1279999999


Q ss_pred             HHHH
Q 046115          299 HDFA  302 (505)
Q Consensus       299 ~~~~  302 (505)
                      ++++
T Consensus       433 lELr  436 (1221)
T 1vt4_I          433 LELK  436 (1221)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8854

>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=99.97  E-value=1.3e-31  Score=304.15  Aligned_cols=279  Identities=23%  Similarity=0.355  Sum_probs=216.1

Q ss_pred             CCCCcHHHHHHHHhcCccc-ccCC-CceEEEEeCCCCC--HHHHHHHHHHHcCCCC---CCChhcHHHHHHHHHHHcCCc
Q 046115            1 MGGIGKTTLAQFAYNNGDV-ERNF-EKRTWVCVSEPFD--EFRIARAIIESLTPGS---AKDLVEFQSLMQHIEECVAGK   73 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~-~~~f-~~~~wv~~~~~~~--~~~~~~~l~~~l~~~~---~~~~~~~~~~~~~l~~~l~~~   73 (505)
                      |||+||||||++++++.+. ..+| ++++|+++++...  ....+..++..+....   .....+.++..+.++..+.++
T Consensus       155 ~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~  234 (1249)
T 3sfz_A          155 MAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRK  234 (1249)
T ss_dssp             STTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSS
T ss_pred             CCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhcc
Confidence            7999999999999995433 4555 5677999988543  3445666777776432   234567788888999999877


Q ss_pred             --eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHH-hCCcceEeCCC-CChhhHHHHHHHhhhCCCCC
Q 046115           74 --KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARI-MGSTHVISVNV-LSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        74 --r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~-~~~~~~~~l~~-l~~~ea~~Lf~~~~~~~~~~  149 (505)
                        |+||||||||+..         .+....+||+||||||++.+... .+....+.+.. |+.+||++||...+...   
T Consensus       235 ~~~~LlvlDd~~~~~---------~~~~~~~~~~ilvTtR~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~---  302 (1249)
T 3sfz_A          235 HPRSLLILDDVWDPW---------VLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMK---  302 (1249)
T ss_dssp             SCSCEEEEESCCCHH---------HHTTTCSSCEEEEEESSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSC---
T ss_pred             CCCEEEEEecCCCHH---------HHHhhcCCCEEEEEcCCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCC---
Confidence              9999999998743         23334789999999999988743 34567889986 99999999999887432   


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhh----hh----cccCchhhHhhccccCChh
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWEL----EA----IEKGLLAPLLLSYNELPSK  221 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l----~~----~~~~~~~~l~~s~~~L~~~  221 (505)
                        .+..++++.+|+++|+|+||||+++|++|+...  ..|...++......    ..    ....+..++.+||+.|+++
T Consensus       303 --~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~--~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~  378 (1249)
T 3sfz_A          303 --KEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLRED  378 (1249)
T ss_dssp             --STTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS--SCHHHHHHHHHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTT
T ss_pred             --hhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh--hHHHHHHHHHhhhhhhhcccccccchHHHHHHHHHHHHhCCHH
Confidence              223345689999999999999999999998764  24655555432221    00    1135888999999999999


Q ss_pred             hhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehHHHHHH
Q 046115          222 VKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVHDF  301 (505)
Q Consensus       222 ~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~lv~~~  301 (505)
                      .|.||+++|+||+++.++.+.++..|.++           ++.+++++++|++++|++....   ++..+|+||+++|+|
T Consensus       379 ~~~~~~~l~~f~~~~~i~~~~~~~~~~~~-----------~~~~~~~l~~L~~~sl~~~~~~---~~~~~~~~h~l~~~~  444 (1249)
T 3sfz_A          379 IKDYYTDLSILQKDVKVPTKVLCVLWDLE-----------TEEVEDILQEFVNKSLLFCNRN---GKSFCYYLHDLQVDF  444 (1249)
T ss_dssp             THHHHHHGGGSCTTCCEEHHHHHHHHTCC-----------HHHHHHHHHHHHHTTSCEEEES---SSSEEEECCHHHHHH
T ss_pred             HHHHHHHhCccCCCCeeCHHHHHHHhCCC-----------HHHHHHHHHHHHhccceEEecC---CCceEEEecHHHHHH
Confidence            99999999999999999999999999432           5678999999999999985442   333479999999999


Q ss_pred             HHHhhccc
Q 046115          302 AQYLCSNE  309 (505)
Q Consensus       302 ~~~~~~~~  309 (505)
                      +++++.++
T Consensus       445 ~~~~~~~~  452 (1249)
T 3sfz_A          445 LTEKNRSQ  452 (1249)
T ss_dssp             HHHHTGGG
T ss_pred             HHhhhhHH
Confidence            99997765

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.97  E-value=1.4e-29  Score=264.70  Aligned_cols=275  Identities=23%  Similarity=0.337  Sum_probs=202.5

Q ss_pred             CCCCcHHHHHHHHhcCccc-ccCC-CceEEEEeCCCCCHHHHH---HHHHHHcCCC---CCCChhcHHHHHHHHHHHcCC
Q 046115            1 MGGIGKTTLAQFAYNNGDV-ERNF-EKRTWVCVSEPFDEFRIA---RAIIESLTPG---SAKDLVEFQSLMQHIEECVAG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~-~~~f-~~~~wv~~~~~~~~~~~~---~~l~~~l~~~---~~~~~~~~~~~~~~l~~~l~~   72 (505)
                      |||+||||||.+++++..+ ..+| ++++|++++.. +...++   ..++..++..   ......+.+.....+...+.+
T Consensus       155 ~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~  233 (591)
T 1z6t_A          155 MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLR  233 (591)
T ss_dssp             CTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHcc
Confidence            7999999999999986444 6789 57899998875 333333   3334455421   123345666777778777755


Q ss_pred             --ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCcceEeC---CCCChhhHHHHHHHhhhCCC
Q 046115           73 --KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGSTHVISV---NVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        73 --~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~~~~~l---~~l~~~ea~~Lf~~~~~~~~  147 (505)
                        +++||||||+|+..         .+....++++||||||++.+...+.. ..+++   ++|+.+||++||...++.. 
T Consensus       234 ~~~~~LLVLDdv~~~~---------~l~~l~~~~~ilvTsR~~~~~~~~~~-~~~~v~~l~~L~~~ea~~L~~~~~~~~-  302 (591)
T 1z6t_A          234 KHPRSLLILDDVWDSW---------VLKAFDSQCQILLTTRDKSVTDSVMG-PKYVVPVESSLGKEKGLEILSLFVNMK-  302 (591)
T ss_dssp             TCTTCEEEEEEECCHH---------HHHTTCSSCEEEEEESCGGGGTTCCS-CEEEEECCSSCCHHHHHHHHHHHHTSC-
T ss_pred             CCCCeEEEEeCCCCHH---------HHHHhcCCCeEEEECCCcHHHHhcCC-CceEeecCCCCCHHHHHHHHHHHhCCC-
Confidence              78999999997632         12234678999999999887654332 23444   5899999999999887531 


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhh--------hcccCchhhHhhccccCC
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELE--------AIEKGLLAPLLLSYNELP  219 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~--------~~~~~~~~~l~~s~~~L~  219 (505)
                          .....+.+.+|++.|+|+|+||+++|++++....  .|...++.......        .....+..++..||+.|+
T Consensus       303 ----~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~~--~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~  376 (591)
T 1z6t_A          303 ----KADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN--RWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLR  376 (591)
T ss_dssp             ----GGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHSTT--CHHHHHHHHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSC
T ss_pred             ----cccccHHHHHHHHHhCCCcHHHHHHHHHHhcCch--hHHHHHHHHHHhHHHHhhhccccchHHHHHHHHHHHHhCC
Confidence                1222456889999999999999999999987642  56666554332210        112367889999999999


Q ss_pred             hhhhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccccCCCCCeeEeeehHHHH
Q 046115          220 SKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNKYDDGEIYKCKMHDIVH  299 (505)
Q Consensus       220 ~~~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~~~~H~lv~  299 (505)
                      ++.|.||+++|+||.+..++.+.+...|...           .+.+.+++++|++++|+.....   +...+|+||++++
T Consensus       377 ~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~-----------~~~~~~~l~~L~~~~Ll~~~~~---~~~~~~~~H~lv~  442 (591)
T 1z6t_A          377 EDIKDYYTDLSILQKDVKVPTKVLCILWDME-----------TEEVEDILQEFVNKSLLFCDRN---GKSFRYYLHDLQV  442 (591)
T ss_dssp             TTTHHHHHHGGGCCTTCCEEHHHHHHHHTCC-----------HHHHHHHHHHHHHTTSSEEEEE---TTEEEEECCHHHH
T ss_pred             HHHHHHHHHccccCCCCccCHHHHHHHhccC-----------HHHHHHHHHHHHhCcCeEEecC---CCccEEEEcHHHH
Confidence            9999999999999999999999888888432           3457889999999999985432   2334799999999


Q ss_pred             HHHHHhhc
Q 046115          300 DFAQYLCS  307 (505)
Q Consensus       300 ~~~~~~~~  307 (505)
                      +|+++...
T Consensus       443 ~~~~~~~~  450 (591)
T 1z6t_A          443 DFLTEKNC  450 (591)
T ss_dssp             HHHHHHTG
T ss_pred             HHHHhhhh
Confidence            99998844

>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=99.56  E-value=1.8e-14  Score=138.45  Aligned_cols=128  Identities=28%  Similarity=0.369  Sum_probs=102.4

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      ++++|+.|++.+|.++.    +|..+..+++|+.|+++       ++.+..+|+.++.+++|++|++++|...+.+|..+
T Consensus       181 ~l~~L~~L~L~~n~l~~----lp~~l~~l~~L~~L~L~-------~N~l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~  249 (328)
T 4fcg_A          181 GLVNLQSLRLEWTGIRS----LPASIANLQNLKSLKIR-------NSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIF  249 (328)
T ss_dssp             ESTTCCEEEEEEECCCC----CCGGGGGCTTCCEEEEE-------SSCCCCCCGGGGGCTTCCEEECTTCTTCCBCCCCT
T ss_pred             cCCCCCEEECcCCCcCc----chHhhcCCCCCCEEEcc-------CCCCCcCchhhccCCCCCEEECcCCcchhhhHHHh
Confidence            47777777777777652    56667788888888887       66667777778888888888888888777888888


Q ss_pred             hcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          434 CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      +.+++|+.|++++|..+..+|..+..+++|++|++++|...+.+|..++++++|+.+.+
T Consensus       250 ~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~iP~~l~~L~~L~~l~l  308 (328)
T 4fcg_A          250 GGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILV  308 (328)
T ss_dssp             TCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEECTTCTTCCCCCGGGGGSCTTCEEEC
T ss_pred             cCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeCCCCCchhhccHHHhhccCceEEeC
Confidence            88888888888888878888888888888888888888888888888888887776643

>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=99.55  E-value=4.3e-14  Score=135.82  Aligned_cols=152  Identities=26%  Similarity=0.354  Sum_probs=127.6

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhh---------cCcccceEEecccccCCcc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFE---------KLTCLRALELQVRESWPRN  399 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~---------~l~~L~~L~l~~~~~~~~~  399 (505)
                      ..+..+.+..+....+|..    +..+++|++|++++|...+.   +|..+.         .+++|++|+++       +
T Consensus       127 ~~L~~L~Ls~n~l~~lp~~----l~~l~~L~~L~L~~n~~~~~---~p~~~~~~~~~~~~~~l~~L~~L~L~-------~  192 (328)
T 4fcg_A          127 AGLETLTLARNPLRALPAS----IASLNRLRELSIRACPELTE---LPEPLASTDASGEHQGLVNLQSLRLE-------W  192 (328)
T ss_dssp             TTCSEEEEESCCCCCCCGG----GGGCTTCCEEEEEEETTCCC---CCSCSEEEC-CCCEEESTTCCEEEEE-------E
T ss_pred             CCCCEEECCCCccccCcHH----HhcCcCCCEEECCCCCCccc---cChhHhhccchhhhccCCCCCEEECc-------C
Confidence            3678888888877755544    45899999999999765543   554444         48999999998       6


Q ss_pred             ccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccc
Q 046115          400 NLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPA  479 (505)
Q Consensus       400 ~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~  479 (505)
                      +.+..+|..++.+++|++|++++|. +..+|..++.+++|+.|++++|.....+|..++.+++|++|++++|...+.+|.
T Consensus       193 n~l~~lp~~l~~l~~L~~L~L~~N~-l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~  271 (328)
T 4fcg_A          193 TGIRSLPASIANLQNLKSLKIRNSP-LSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPL  271 (328)
T ss_dssp             ECCCCCCGGGGGCTTCCEEEEESSC-CCCCCGGGGGCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCT
T ss_pred             CCcCcchHhhcCCCCCCEEEccCCC-CCcCchhhccCCCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcch
Confidence            6677889889999999999999999 778888899999999999999998889999999999999999999988999999


Q ss_pred             cccCCccCCccceeEe
Q 046115          480 GIGELIRLRRVREFVV  495 (505)
Q Consensus       480 ~i~~l~~L~~L~~~~~  495 (505)
                      .+.++++|+.|++..+
T Consensus       272 ~~~~l~~L~~L~L~~n  287 (328)
T 4fcg_A          272 DIHRLTQLEKLDLRGC  287 (328)
T ss_dssp             TGGGCTTCCEEECTTC
T ss_pred             hhhcCCCCCEEeCCCC
Confidence            9999999988887643

>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=99.44  E-value=9.1e-13  Score=116.71  Aligned_cols=144  Identities=13%  Similarity=0.196  Sum_probs=118.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc-ccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK-EIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-~~p~~  408 (505)
                      .+..+.+..+....++ .    +..+++|++|++.+|.+..    ++ .+..+++|++|+++       ++.+. ..|..
T Consensus        45 ~L~~L~l~~n~i~~l~-~----l~~l~~L~~L~l~~n~~~~----~~-~l~~l~~L~~L~l~-------~n~l~~~~~~~  107 (197)
T 4ezg_A           45 SLTYITLANINVTDLT-G----IEYAHNIKDLTINNIHATN----YN-PISGLSNLERLRIM-------GKDVTSDKIPN  107 (197)
T ss_dssp             TCCEEEEESSCCSCCT-T----GGGCTTCSEEEEESCCCSC----CG-GGTTCTTCCEEEEE-------CTTCBGGGSCC
T ss_pred             CccEEeccCCCccChH-H----HhcCCCCCEEEccCCCCCc----ch-hhhcCCCCCEEEeE-------CCccCcccChh
Confidence            6778888888777655 2    4488999999999997653    33 48889999999999       45554 46788


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      ++.+++|++|++++|......|..++.+++|+.|++++|..+..+| .+..+++|++|++++|. +..++ .+..+++|+
T Consensus       108 l~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n~-i~~~~-~l~~l~~L~  184 (197)
T 4ezg_A          108 LSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFDG-VHDYR-GIEDFPKLN  184 (197)
T ss_dssp             CTTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTBC-CCCCT-TGGGCSSCC
T ss_pred             hcCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCCC-CcChH-HhccCCCCC
Confidence            9999999999999999555678889999999999999998678887 68999999999999998 44565 678888888


Q ss_pred             cccee
Q 046115          489 RVREF  493 (505)
Q Consensus       489 ~L~~~  493 (505)
                      .|++.
T Consensus       185 ~L~l~  189 (197)
T 4ezg_A          185 QLYAF  189 (197)
T ss_dssp             EEEEC
T ss_pred             EEEee
Confidence            87754

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.44  E-value=5.2e-12  Score=122.52  Aligned_cols=265  Identities=11%  Similarity=0.077  Sum_probs=154.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC------CHHHHHHHHHHHcCC-----------------CCCCChh
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF------DEFRIARAIIESLTP-----------------GSAKDLV   57 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~------~~~~~~~~l~~~l~~-----------------~~~~~~~   57 (505)
                      ++|+|||+|++++++  +.     ..+|+++....      +...++..+...+..                 .......
T Consensus        39 ~~G~GKT~Ll~~~~~--~~-----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (350)
T 2qen_A           39 IRRVGKSSLLRAFLN--ER-----PGILIDCRELYAERGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKL  111 (350)
T ss_dssp             CTTSSHHHHHHHHHH--HS-----SEEEEEHHHHHHTTTCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGC
T ss_pred             CCcCCHHHHHHHHHH--Hc-----CcEEEEeecccccccCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccc
Confidence            589999999999998  33     27788865432      555666666665542                 0011123


Q ss_pred             cHHHHHHHHHHHcCC-ceEEEEEeCCCCCCc------cChhHHHHhhcCCCCCcEEEEEeCchHHHHHh-----------
Q 046115           58 EFQSLMQHIEECVAG-KKFLLVLDDVWNEDY------YKWEPFYKCLKNSLHESKILITTRKETVARIM-----------  119 (505)
Q Consensus        58 ~~~~~~~~l~~~l~~-~r~LlvlDdv~~~~~------~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~-----------  119 (505)
                      +..+..+.+...... ++++||+||+++.+.      ..+...+..+.+...+.++++|++........           
T Consensus       112 ~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~  191 (350)
T 2qen_A          112 SLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAYDSLPNLKIILTGSEVGLLHDFLKITDYESPLY  191 (350)
T ss_dssp             CHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHHHHCTTEEEEEEESSHHHHHHHHCTTCTTSTTT
T ss_pred             hHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHHHhcCCeEEEEECCcHHHHHHHHhhcCCCCccc
Confidence            455555666555532 389999999977432      12222333332223568899998876532211           


Q ss_pred             CC-cceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhh
Q 046115          120 GS-THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIW  198 (505)
Q Consensus       120 ~~-~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~  198 (505)
                      +. ...+.+.+|+.+|+.+++.......+. .   ...+.+..+++.++|+|+++..++..+....+...+...+-   .
T Consensus       192 ~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~-~---~~~~~~~~i~~~tgG~P~~l~~~~~~~~~~~~~~~~~~~~~---~  264 (350)
T 2qen_A          192 GRIAGEVLVKPFDKDTSVEFLKRGFREVNL-D---VPENEIEEAVELLDGIPGWLVVFGVEYLRNGDFGRAMKRTL---E  264 (350)
T ss_dssp             TCCCEEEECCCCCHHHHHHHHHHHHHTTTC-C---CCHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCHHHHHHHHH---H
T ss_pred             cCccceeeCCCCCHHHHHHHHHHHHHHcCC-C---CCHHHHHHHHHHhCCCHHHHHHHHHHHhccccHhHHHHHHH---H
Confidence            11 247899999999999999765322111 1   12356789999999999999999876533222222211111   0


Q ss_pred             hhhhcccCchhhHhhccccC---ChhhhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHc
Q 046115          199 ELEAIEKGLLAPLLLSYNEL---PSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASR  275 (505)
Q Consensus       199 ~l~~~~~~~~~~l~~s~~~L---~~~~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~  275 (505)
                      ..       ...+...+..+   ++..+.++..+|+  .  ..+...+.........     + .....+..+++.|.+.
T Consensus       265 ~~-------~~~~~~~l~~l~~~~~~~~~~l~~la~--g--~~~~~~l~~~~~~~~~-----~-~~~~~~~~~l~~L~~~  327 (350)
T 2qen_A          265 VA-------KGLIMGELEELRRRSPRYVDILRAIAL--G--YNRWSLIRDYLAVKGT-----K-IPEPRLYALLENLKKM  327 (350)
T ss_dssp             HH-------HHHHHHHHHHHHHHCHHHHHHHHHHHT--T--CCSHHHHHHHHHHTTC-----C-CCHHHHHHHHHHHHHT
T ss_pred             HH-------HHHHHHHHHHHHhCChhHHHHHHHHHh--C--CCCHHHHHHHHHHHhC-----C-CCHHHHHHHHHHHHhC
Confidence            00       00111111222   6788888888887  2  2344444433322110     1 1234577889999999


Q ss_pred             ccccccccCCCCCeeEe-eehHHHHHHHH
Q 046115          276 SFFQDFNKYDDGEIYKC-KMHDIVHDFAQ  303 (505)
Q Consensus       276 ~Ll~~~~~~~~~~~~~~-~~H~lv~~~~~  303 (505)
                      +++....    +   .| ..|++++++.+
T Consensus       328 gli~~~~----~---~y~~~~p~~~~~~~  349 (350)
T 2qen_A          328 NWIVEED----N---TYKIADPVVATVLR  349 (350)
T ss_dssp             TSEEEET----T---EEEESSHHHHHHHT
T ss_pred             CCEEecC----C---EEEEecHHHHHHHc
Confidence            9997542    1   24 45789988864

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.44  E-value=4.9e-13  Score=127.64  Aligned_cols=128  Identities=14%  Similarity=0.259  Sum_probs=63.7

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc-ccCccccCCCCcceeeccCCccccccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK-EIPTNIEKLLHLKYLNLKGQKKIEKLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-~~p~~~~~l~~L~~L~l~~~~~~~~lp~~  432 (505)
                      .+++|++|++++|.+++.   +|..+..+++|++|+++       ++.+. .+|..++.+++|++|++++|...+.+|..
T Consensus        99 ~l~~L~~L~Ls~n~l~~~---~p~~~~~l~~L~~L~Ls-------~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~  168 (313)
T 1ogq_A           99 KLTQLHYLYITHTNVSGA---IPDFLSQIKTLVTLDFS-------YNALSGTLPPSISSLPNLVGITFDGNRISGAIPDS  168 (313)
T ss_dssp             GCTTCSEEEEEEECCEEE---CCGGGGGCTTCCEEECC-------SSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGG
T ss_pred             cCCCCCEEECcCCeeCCc---CCHHHhCCCCCCEEeCC-------CCccCCcCChHHhcCCCCCeEECcCCcccCcCCHH
Confidence            445555555555544322   34444555555555554       22222 44445555555555555555532345555


Q ss_pred             hhcCC-CCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          433 LCELY-NLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       433 ~~~l~-~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      ++.+. +|+.|++++|.....+|..+..++ |++|++++|...+..|..|..+++|+.|++
T Consensus       169 l~~l~~~L~~L~L~~N~l~~~~~~~~~~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L  228 (313)
T 1ogq_A          169 YGSFSKLFTSMTISRNRLTGKIPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHL  228 (313)
T ss_dssp             GGCCCTTCCEEECCSSEEEEECCGGGGGCC-CSEEECCSSEEEECCGGGCCTTSCCSEEEC
T ss_pred             HhhhhhcCcEEECcCCeeeccCChHHhCCc-ccEEECcCCcccCcCCHHHhcCCCCCEEEC
Confidence            55554 555555555553334555555544 555555555544444555555666655554

>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=99.44  E-value=5.6e-13  Score=121.03  Aligned_cols=130  Identities=25%  Similarity=0.326  Sum_probs=76.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .+..+.+..+....++.   ..+..+++|+.|++.+|.+...   .+..+..+.+|++|+|+       ++.+..+|+. 
T Consensus        41 ~L~~L~Ls~n~i~~~~~---~~~~~l~~L~~L~L~~N~l~~i---~~~~~~~l~~L~~L~Ls-------~N~l~~l~~~~  107 (229)
T 3e6j_A           41 NAQILYLHDNQITKLEP---GVFDSLINLKELYLGSNQLGAL---PVGVFDSLTQLTVLDLG-------TNQLTVLPSAV  107 (229)
T ss_dssp             TCSEEECCSSCCCCCCT---TTTTTCTTCCEEECCSSCCCCC---CTTTTTTCTTCCEEECC-------SSCCCCCCTTT
T ss_pred             CCCEEEcCCCccCccCH---HHhhCccCCcEEECCCCCCCCc---ChhhcccCCCcCEEECC-------CCcCCccChhH
Confidence            45555555555444322   2334566666666666665432   33345566666666666       4455555443 


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCccc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~  474 (505)
                      +..+++|++|++++|. +..+|..+..+++|+.|+|++|. +..+|. .+..+++|++|++.+|...
T Consensus       108 ~~~l~~L~~L~Ls~N~-l~~lp~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~~~  172 (229)
T 3e6j_A          108 FDRLVHLKELFMCCNK-LTELPRGIERLTHLTHLALDQNQ-LKSIPHGAFDRLSSLTHAYLFGNPWD  172 (229)
T ss_dssp             TTTCTTCCEEECCSSC-CCSCCTTGGGCTTCSEEECCSSC-CCCCCTTTTTTCTTCCEEECTTSCBC
T ss_pred             hCcchhhCeEeccCCc-ccccCcccccCCCCCEEECCCCc-CCccCHHHHhCCCCCCEEEeeCCCcc
Confidence            4566666666666666 55666666666666666666665 555553 3566666666666666543

>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=99.43  E-value=4.9e-12  Score=125.67  Aligned_cols=266  Identities=12%  Similarity=0.046  Sum_probs=156.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-----CC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC--C
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-----FE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA--G   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-----f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~--~   72 (505)
                      ++|+|||+||+++++  .....     +. .++|+++....+...++..++.+++........+..+....+...+.  +
T Consensus        60 ~~G~GKT~L~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~  137 (412)
T 1w5s_A           60 RVGIGKTTLAKFTVK--RVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVEN  137 (412)
T ss_dssp             CCSSSHHHHHHHHHH--HHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHH--HHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcC
Confidence            589999999999998  44332     23 35688887778888999999999875433223344455555555553  6


Q ss_pred             ceEEEEEeCCCCCC------ccChhHHHHhhcCC---C--CCcEEEEEeCchHHHHHh--------CC-cceEeCCCCCh
Q 046115           73 KKFLLVLDDVWNED------YYKWEPFYKCLKNS---L--HESKILITTRKETVARIM--------GS-THVISVNVLSE  132 (505)
Q Consensus        73 ~r~LlvlDdv~~~~------~~~~~~~~~~~~~~---~--~~~~iLiTtr~~~~~~~~--------~~-~~~~~l~~l~~  132 (505)
                      ++++||+||+++-.      ...+..+...+...   +  ....+|+||+...+....        .. ...+.+++++.
T Consensus       138 ~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~  217 (412)
T 1w5s_A          138 HYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKS  217 (412)
T ss_dssp             CEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCH
T ss_pred             CeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCH
Confidence            79999999997632      12233333333322   2  445588788765532111        11 22389999999


Q ss_pred             hhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcC------CChHHHHHHHHHh-----ccC---CCHHHHHHHHhhhhh
Q 046115          133 MECWSVFQSLAISGKTIGKRENLEKIGREIVKKCK------GLPLAAKTIASLL-----RSK---NTEKEWQNILENEIW  198 (505)
Q Consensus       133 ~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~------g~Plal~~~~~~l-----~~~---~~~~~~~~~l~~~~~  198 (505)
                      +++.++|.........  .....++.+..+++.++      |.|..+..+....     ...   -+...+...+...  
T Consensus       218 ~e~~~ll~~~~~~~~~--~~~~~~~~~~~i~~~~~~~~~~~G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~--  293 (412)
T 1w5s_A          218 RELYTILEQRAELGLR--DTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSEN--  293 (412)
T ss_dssp             HHHHHHHHHHHHHHBC--TTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHhcCC--CCCCChHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH--
Confidence            9999999755321000  01122466888999999      9997655544321     111   1233333332211  


Q ss_pred             hhhhcccCc-hhhHhhccccCChhhhhhhhhhccCC--CCCCCChHHHHHHHHHcC--CCCCCCCCCHHHHHHHHHHHHH
Q 046115          199 ELEAIEKGL-LAPLLLSYNELPSKVKRCFSYCAVFP--KDYGIRKHKLIELWMAQG--YLSEKGAKEMEDIGEEYFNILA  273 (505)
Q Consensus       199 ~l~~~~~~~-~~~l~~s~~~L~~~~~~~ll~la~f~--~~~~i~~~~l~~~w~~~~--~~~~~~~~~~~~~~~~~l~~L~  273 (505)
                              . ...+...+..|++.++.++..++.+.  .+..++...+...+....  ...  ........+..+++.|.
T Consensus       294 --------~~~~~~~~~l~~l~~~~~~~l~aia~l~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~L~  363 (412)
T 1w5s_A          294 --------EAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYN--VKPRGYTQYHIYLKHLT  363 (412)
T ss_dssp             --------------CCSSSSSCHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHHHHHSC--CCCCCHHHHHHHHHHHH
T ss_pred             --------hccchHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcC--CCCCCHHHHHHHHHHHH
Confidence                    1 23345577889999999998888753  223455544433221100  000  01112345678899999


Q ss_pred             Hcccccccc
Q 046115          274 SRSFFQDFN  282 (505)
Q Consensus       274 ~~~Ll~~~~  282 (505)
                      +.+++....
T Consensus       364 ~~gli~~~~  372 (412)
T 1w5s_A          364 SLGLVDAKP  372 (412)
T ss_dssp             HTTSEEEEC
T ss_pred             hCCCEEeec
Confidence            999997654

>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=99.40  E-value=1e-12  Score=118.43  Aligned_cols=129  Identities=26%  Similarity=0.387  Sum_probs=73.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .+..+.+..+....++.   ..|..+++|+.|++++|.++..   .|..|..+.+|++|+|+       ++.+..+|.. 
T Consensus        33 ~l~~L~l~~n~i~~i~~---~~~~~l~~L~~L~Ls~N~i~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~l~~~~   99 (220)
T 2v9t_B           33 TITEIRLEQNTIKVIPP---GAFSPYKKLRRIDLSNNQISEL---APDAFQGLRSLNSLVLY-------GNKITELPKSL   99 (220)
T ss_dssp             TCCEEECCSSCCCEECT---TSSTTCTTCCEEECCSSCCCEE---CTTTTTTCSSCCEEECC-------SSCCCCCCTTT
T ss_pred             CCCEEECCCCcCCCcCH---hHhhCCCCCCEEECCCCcCCCc---CHHHhhCCcCCCEEECC-------CCcCCccCHhH
Confidence            45555555555544432   2334566666666666665543   44556666666666666       4555555544 


Q ss_pred             ccCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~  473 (505)
                      +..+++|++|+|++|. +..+ |..+..+++|+.|+|++|. +..+|+ .+..+++|++|++++|+.
T Consensus       100 f~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~~  164 (220)
T 2v9t_B          100 FEGLFSLQLLLLNANK-INCLRVDAFQDLHNLNLLSLYDNK-LQTIAKGTFSPLRAIQTMHLAQNPF  164 (220)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCE
T ss_pred             ccCCCCCCEEECCCCC-CCEeCHHHcCCCCCCCEEECCCCc-CCEECHHHHhCCCCCCEEEeCCCCc
Confidence            3556666666666666 4333 4455666666666666666 444443 356666666666666653

>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=99.40  E-value=2.4e-12  Score=118.73  Aligned_cols=149  Identities=24%  Similarity=0.310  Sum_probs=118.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-c
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-N  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~  408 (505)
                      .+..+.+..+....++.   ..+.++++|++|++++|.++..   .+..+..+.+|++|+|+       ++.+..+|+ .
T Consensus        36 ~l~~L~L~~n~l~~~~~---~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~  102 (251)
T 3m19_A           36 DTEKLDLQSTGLATLSD---ATFRGLTKLTWLNLDYNQLQTL---SAGVFDDLTELGTLGLA-------NNQLASLPLGV  102 (251)
T ss_dssp             TCCEEECTTSCCCCCCT---TTTTTCTTCCEEECTTSCCCCC---CTTTTTTCTTCCEEECT-------TSCCCCCCTTT
T ss_pred             CCCEEEccCCCcCccCH---hHhcCcccCCEEECCCCcCCcc---CHhHhccCCcCCEEECC-------CCcccccChhH
Confidence            67777777776655443   3456899999999999988764   56667889999999998       666666664 4


Q ss_pred             ccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      +..+++|++|++++|. ++.+|.. +..+++|+.|+|++|. +..+|+ .++.+++|++|++++|......|..+..+++
T Consensus       103 ~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~  180 (251)
T 3m19_A          103 FDHLTQLDKLYLGGNQ-LKSLPSGVFDRLTKLKELRLNTNQ-LQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGK  180 (251)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTT
T ss_pred             hcccCCCCEEEcCCCc-CCCcChhHhccCCcccEEECcCCc-CCccCHHHcCcCcCCCEEECCCCcCCccCHHHHhCCCC
Confidence            6889999999999998 7777765 5889999999999998 777776 5889999999999999855443446788888


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       181 L~~L~l~  187 (251)
T 3m19_A          181 LQTITLF  187 (251)
T ss_dssp             CCEEECC
T ss_pred             CCEEEee
Confidence            8877754

>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=99.40  E-value=1.5e-12  Score=117.42  Aligned_cols=107  Identities=20%  Similarity=0.247  Sum_probs=52.3

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceeeccCCcccccc-ch
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKL-PE  431 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~l-p~  431 (505)
                      .+++|+.|++.+|.++..   .+..+..+.+|+.|+|+       ++.+..+|+ .+..+++|++|+|++|. +..+ |.
T Consensus        55 ~l~~L~~L~L~~N~i~~i---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~  123 (220)
T 2v70_A           55 KLPQLRKINFSNNKITDI---EEGAFEGASGVNEILLT-------SNRLENVQHKMFKGLESLKTLMLRSNR-ITCVGND  123 (220)
T ss_dssp             GCTTCCEEECCSSCCCEE---CTTTTTTCTTCCEEECC-------SSCCCCCCGGGGTTCSSCCEEECTTSC-CCCBCTT
T ss_pred             cCCCCCEEECCCCcCCEE---CHHHhCCCCCCCEEECC-------CCccCccCHhHhcCCcCCCEEECCCCc-CCeECHh
Confidence            455555555555554432   23334555555555555       333333333 24455555555555555 3322 34


Q ss_pred             hhhcCCCCcEEecCCCcCcccc-chhccccccCceeecCCCc
Q 046115          432 TLCELYNLERLNVDDCQNLREL-PRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~  472 (505)
                      .+..+++|+.|+|++|. +..+ |..+..+++|++|++++|.
T Consensus       124 ~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~  164 (220)
T 2v70_A          124 SFIGLSSVRLLSLYDNQ-ITTVAPGAFDTLHSLSTLNLLANP  164 (220)
T ss_dssp             SSTTCTTCSEEECTTSC-CCCBCTTTTTTCTTCCEEECCSCC
T ss_pred             HcCCCccCCEEECCCCc-CCEECHHHhcCCCCCCEEEecCcC
Confidence            44555555555555555 3333 4445555555555555554

>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=99.40  E-value=9.3e-13  Score=113.44  Aligned_cols=132  Identities=21%  Similarity=0.197  Sum_probs=102.5

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      ..++|+.|++.+|.++.  ..+|..+..+++|++|+++       ++.+..+ ..++.+++|++|++++|.....+|..+
T Consensus        22 ~~~~L~~L~l~~n~l~~--~~i~~~~~~l~~L~~L~l~-------~n~l~~~-~~~~~l~~L~~L~Ls~N~l~~~~~~~~   91 (168)
T 2ell_A           22 TPAAVRELVLDNCKSND--GKIEGLTAEFVNLEFLSLI-------NVGLISV-SNLPKLPKLKKLELSENRIFGGLDMLA   91 (168)
T ss_dssp             CTTSCSEEECCSCBCBT--TBCSSCCGGGGGCCEEEEE-------SSCCCCC-SSCCCCSSCCEEEEESCCCCSCCCHHH
T ss_pred             CcccCCEEECCCCCCCh--hhHHHHHHhCCCCCEEeCc-------CCCCCCh-hhhccCCCCCEEECcCCcCchHHHHHH
Confidence            34789999999988761  1256667888899999998       5556666 668889999999999998333477767


Q ss_pred             hcCCCCcEEecCCCcCccccc--hhccccccCceeecCCCcccccccc----cccCCccCCccceeEecC
Q 046115          434 CELYNLERLNVDDCQNLRELP--RGIGKLRKLMYLHNEDTGCLRYLPA----GIGELIRLRRVREFVVGG  497 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~~p~----~i~~l~~L~~L~~~~~~~  497 (505)
                      ..+++|+.|++++|. +..+|  ..+..+++|++|++++|. +..+|.    .+..+++|+.|++..+..
T Consensus        92 ~~l~~L~~L~Ls~N~-l~~~~~~~~l~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~l~~L~~L~l~~n~~  159 (168)
T 2ell_A           92 EKLPNLTHLNLSGNK-LKDISTLEPLKKLECLKSLDLFNCE-VTNLNDYRESVFKLLPQLTYLDGYDRED  159 (168)
T ss_dssp             HHCTTCCEEECBSSS-CCSSGGGGGGSSCSCCCEEECCSSG-GGTSTTHHHHHHTTCSSCCEETTEETTS
T ss_pred             hhCCCCCEEeccCCc-cCcchhHHHHhcCCCCCEEEeeCCc-CcchHHHHHHHHHhCccCcEecCCCCCh
Confidence            779999999999987 77776  678889999999999997 455665    678888999888876554

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.39  E-value=7.6e-13  Score=126.31  Aligned_cols=148  Identities=16%  Similarity=0.164  Sum_probs=86.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc-ccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK-EIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-~~p~~  408 (505)
                      .++.+.+..+...   ...+..+..+++|++|++++|.+++.   +|..+..+++|++|+++       ++.+. .+|..
T Consensus       102 ~L~~L~Ls~n~l~---~~~p~~~~~l~~L~~L~Ls~N~l~~~---~p~~~~~l~~L~~L~L~-------~N~l~~~~p~~  168 (313)
T 1ogq_A          102 QLHYLYITHTNVS---GAIPDFLSQIKTLVTLDFSYNALSGT---LPPSISSLPNLVGITFD-------GNRISGAIPDS  168 (313)
T ss_dssp             TCSEEEEEEECCE---EECCGGGGGCTTCCEEECCSSEEESC---CCGGGGGCTTCCEEECC-------SSCCEEECCGG
T ss_pred             CCCEEECcCCeeC---CcCCHHHhCCCCCCEEeCCCCccCCc---CChHHhcCCCCCeEECc-------CCcccCcCCHH
Confidence            4555555555443   11222334666667777766665432   55556666667777666       33333 56666


Q ss_pred             ccCCC-CcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccC
Q 046115          409 IEKLL-HLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       409 ~~~l~-~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      ++.++ +|++|++++|...+.+|..+..+. |+.|++++|......|..+..+++|++|++++|...+..| .+..+++|
T Consensus       169 l~~l~~~L~~L~L~~N~l~~~~~~~~~~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~-~~~~l~~L  246 (313)
T 1ogq_A          169 YGSFSKLFTSMTISRNRLTGKIPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLG-KVGLSKNL  246 (313)
T ss_dssp             GGCCCTTCCEEECCSSEEEEECCGGGGGCC-CSEEECCSSEEEECCGGGCCTTSCCSEEECCSSEECCBGG-GCCCCTTC
T ss_pred             HhhhhhcCcEEECcCCeeeccCChHHhCCc-ccEEECcCCcccCcCCHHHhcCCCCCEEECCCCceeeecC-cccccCCC
Confidence            66665 667777766664446666666665 6777776666444555556666667777776666433333 35556666


Q ss_pred             Cccce
Q 046115          488 RRVRE  492 (505)
Q Consensus       488 ~~L~~  492 (505)
                      +.|++
T Consensus       247 ~~L~L  251 (313)
T 1ogq_A          247 NGLDL  251 (313)
T ss_dssp             CEEEC
T ss_pred             CEEEC
Confidence            65554

>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=99.39  E-value=2.9e-11  Score=117.52  Aligned_cols=266  Identities=10%  Similarity=0.068  Sum_probs=151.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-----CCHHHHHHHHHHHcC-------------CCC-----CC---
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-----FDEFRIARAIIESLT-------------PGS-----AK---   54 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-----~~~~~~~~~l~~~l~-------------~~~-----~~---   54 (505)
                      ++|+|||+|++++++  +...   ..+|+++...     .+....+..+...+.             ...     ..   
T Consensus        38 ~~G~GKT~L~~~~~~--~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~  112 (357)
T 2fna_A           38 LRRTGKSSIIKIGIN--ELNL---PYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEI  112 (357)
T ss_dssp             STTSSHHHHHHHHHH--HHTC---CEEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSE
T ss_pred             CCCCCHHHHHHHHHH--hcCC---CEEEEEchhhccccCCCHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEE
Confidence            589999999999998  4332   3578887643     344444444433321             000     00   


Q ss_pred             -------ChhcHHHHHHHHHHHcCCceEEEEEeCCCCCCc---cChhHHHHhhcCCCCCcEEEEEeCchHHHHHh-----
Q 046115           55 -------DLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDY---YKWEPFYKCLKNSLHESKILITTRKETVARIM-----  119 (505)
Q Consensus        55 -------~~~~~~~~~~~l~~~l~~~r~LlvlDdv~~~~~---~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~-----  119 (505)
                             ......+..+.+.+... ++++||+||+++-+.   ..+..++..+.+...+.++++|++........     
T Consensus       113 ~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~  191 (357)
T 2fna_A          113 KFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVED  191 (357)
T ss_dssp             EEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTC
T ss_pred             EeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCchhHHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccC
Confidence                   12234455555554333 489999999977421   23333344333333467899999976532211     


Q ss_pred             -----C-C-cceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHH
Q 046115          120 -----G-S-THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNI  192 (505)
Q Consensus       120 -----~-~-~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~  192 (505)
                           . . ...+.+.+|+.+|+.+++.......+.  ..+.    ...+++.|+|+|+++..++..+........|...
T Consensus       192 ~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~--~~~~----~~~i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~  265 (357)
T 2fna_A          192 PESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADI--DFKD----YEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQ  265 (357)
T ss_dssp             TTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTC--CCCC----HHHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHH
T ss_pred             CCCccccCccceeecCCCCHHHHHHHHHHHHHHcCC--CCCc----HHHHHHHhCCCHHHHHHHHHHHccccchHHHHHH
Confidence                 1 1 257899999999999999875321111  1111    2689999999999999998876433333333221


Q ss_pred             HhhhhhhhhhcccCchhhHh-hcc--ccCChhhhhhhhhhccCCCCCCCChHHHHHHHH-HcCCCCCCCCCCHHHHHHHH
Q 046115          193 LENEIWELEAIEKGLLAPLL-LSY--NELPSKVKRCFSYCAVFPKDYGIRKHKLIELWM-AQGYLSEKGAKEMEDIGEEY  268 (505)
Q Consensus       193 l~~~~~~l~~~~~~~~~~l~-~s~--~~L~~~~~~~ll~la~f~~~~~i~~~~l~~~w~-~~~~~~~~~~~~~~~~~~~~  268 (505)
                      +-.   ..   ...+...+. ..+  ..+++..+.++..+|+  .  . +...+..... ..+.      ......+..+
T Consensus       266 ~~~---~~---~~~~~~~l~~~~~~~~~l~~~~~~~l~~la~--g--~-~~~~l~~~~~~~~g~------~~~~~~~~~~  328 (357)
T 2fna_A          266 TLE---YA---KKLILKEFENFLHGREIARKRYLNIMRTLSK--C--G-KWSDVKRALELEEGI------EISDSEIYNY  328 (357)
T ss_dssp             HHH---HH---HHHHHHHHHHHHTTCGGGHHHHHHHHHHHTT--C--B-CHHHHHHHHHHHHCS------CCCHHHHHHH
T ss_pred             HHH---HH---HHHHHHHHHHHhhccccccHHHHHHHHHHHc--C--C-CHHHHHHHHHHhcCC------CCCHHHHHHH
Confidence            110   00   000111111 111  1677888999999888  2  2 4444433211 1110      0123457788


Q ss_pred             HHHHHHcccccccccCCCCCeeEee-ehHHHHHHH
Q 046115          269 FNILASRSFFQDFNKYDDGEIYKCK-MHDIVHDFA  302 (505)
Q Consensus       269 l~~L~~~~Ll~~~~~~~~~~~~~~~-~H~lv~~~~  302 (505)
                      ++.|.+.+++....    +   .|+ .|++++++.
T Consensus       329 L~~L~~~gli~~~~----~---~y~f~~~~~~~~l  356 (357)
T 2fna_A          329 LTQLTKHSWIIKEG----E---KYCPSEPLISLAF  356 (357)
T ss_dssp             HHHHHHTTSEEESS----S---CEEESSHHHHHHT
T ss_pred             HHHHHhCCCEEecC----C---EEEecCHHHHHhh
Confidence            99999999997543    1   244 688998875

>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=99.37  E-value=1.1e-12  Score=113.91  Aligned_cols=129  Identities=20%  Similarity=0.196  Sum_probs=102.6

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCc-ccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLT-CLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP  430 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~-~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp  430 (505)
                      +..+.+|+.|++.+|.+..    +|. +..+. +|++|+++       ++.+..+ ..++.+++|++|++++|. ++.+|
T Consensus        15 ~~~~~~L~~L~l~~n~l~~----i~~-~~~~~~~L~~L~Ls-------~N~l~~~-~~l~~l~~L~~L~Ls~N~-l~~~~   80 (176)
T 1a9n_A           15 YTNAVRDRELDLRGYKIPV----IEN-LGATLDQFDAIDFS-------DNEIRKL-DGFPLLRRLKTLLVNNNR-ICRIG   80 (176)
T ss_dssp             EECTTSCEEEECTTSCCCS----CCC-GGGGTTCCSEEECC-------SSCCCEE-CCCCCCSSCCEEECCSSC-CCEEC
T ss_pred             cCCcCCceEEEeeCCCCch----hHH-hhhcCCCCCEEECC-------CCCCCcc-cccccCCCCCEEECCCCc-ccccC
Confidence            3467889999999998764    343 44444 89999998       6666666 568889999999999998 77777


Q ss_pred             hhh-hcCCCCcEEecCCCcCccccch--hccccccCceeecCCCccccccccc----ccCCccCCccceeEec
Q 046115          431 ETL-CELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCLRYLPAG----IGELIRLRRVREFVVG  496 (505)
Q Consensus       431 ~~~-~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~~p~~----i~~l~~L~~L~~~~~~  496 (505)
                      +.+ +.+++|+.|++++|. +..+|.  .+..+++|++|++++|. +..+|..    +..+++|+.|++..+.
T Consensus        81 ~~~~~~l~~L~~L~L~~N~-i~~~~~~~~l~~l~~L~~L~l~~N~-i~~~~~~~~~~~~~l~~L~~Ld~~~n~  151 (176)
T 1a9n_A           81 EGLDQALPDLTELILTNNS-LVELGDLDPLASLKSLTYLCILRNP-VTNKKHYRLYVIYKVPQVRVLDFQKVK  151 (176)
T ss_dssp             SCHHHHCTTCCEEECCSCC-CCCGGGGGGGGGCTTCCEEECCSSG-GGGSTTHHHHHHHHCTTCSEETTEECC
T ss_pred             cchhhcCCCCCEEECCCCc-CCcchhhHhhhcCCCCCEEEecCCC-CCCcHhHHHHHHHHCCccceeCCCcCC
Confidence            655 889999999999988 788887  78889999999999998 4567764    7888999988876543

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.37  E-value=7.3e-13  Score=111.63  Aligned_cols=128  Identities=21%  Similarity=0.211  Sum_probs=103.9

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      ..++|+.|++++|.++.  ..+|..+..+++|++|+++       ++.+..+ ..++.+++|++|++++|.....+|..+
T Consensus        15 ~~~~l~~L~l~~n~l~~--~~~~~~~~~l~~L~~L~l~-------~n~l~~~-~~~~~l~~L~~L~Ls~n~i~~~~~~~~   84 (149)
T 2je0_A           15 TPSDVKELVLDNSRSNE--GKLEGLTDEFEELEFLSTI-------NVGLTSI-ANLPKLNKLKKLELSDNRVSGGLEVLA   84 (149)
T ss_dssp             CGGGCSEEECTTCBCBT--TBCCSCCTTCTTCCEEECT-------TSCCCCC-TTCCCCTTCCEEECCSSCCCSCTHHHH
T ss_pred             CCccCeEEEccCCcCCh--hHHHHHHhhcCCCcEEECc-------CCCCCCc-hhhhcCCCCCEEECCCCcccchHHHHh
Confidence            34789999999998762  1266667889999999998       5666666 668899999999999999433488877


Q ss_pred             hcCCCCcEEecCCCcCccccc--hhccccccCceeecCCCcccccccc----cccCCccCCcccee
Q 046115          434 CELYNLERLNVDDCQNLRELP--RGIGKLRKLMYLHNEDTGCLRYLPA----GIGELIRLRRVREF  493 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~~p~----~i~~l~~L~~L~~~  493 (505)
                      +.+++|+.|++++|. +..+|  ..++.+++|++|++++|. +..+|.    .+..+++|+.|++.
T Consensus        85 ~~l~~L~~L~ls~N~-i~~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A           85 EKCPNLTHLNLSGNK-IKDLSTIEPLKKLENLKSLDLFNCE-VTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             HHCTTCCEEECTTSC-CCSHHHHGGGGGCTTCCEEECTTCG-GGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             hhCCCCCEEECCCCc-CCChHHHHHHhhCCCCCEEeCcCCc-ccchHHHHHHHHHHCCCcccccCC
Confidence            889999999999998 77665  779999999999999997 455554    57889999988753

>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=99.37  E-value=2.1e-12  Score=138.76  Aligned_cols=86  Identities=16%  Similarity=0.202  Sum_probs=69.9

Q ss_pred             cccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccC
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      .++.+++|++|++++|...+.+|..++.+++|+.|+|++|.....+|..++.+++|+.|++++|...+.+|..+.++++|
T Consensus       627 ~~~~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~~l~~L  706 (768)
T 3rgz_A          627 TFDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTML  706 (768)
T ss_dssp             SCSSSBCCCEEECCSSCCBSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEECCCGGGGGCCCC
T ss_pred             hhhccccccEEECcCCcccccCCHHHhccccCCEEeCcCCccCCCCChHHhCCCCCCEEECCCCcccCcCChHHhCCCCC
Confidence            34556778888888888666888888888888888888888667888888888888888888888888888888888888


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      +.|++-
T Consensus       707 ~~L~ls  712 (768)
T 3rgz_A          707 TEIDLS  712 (768)
T ss_dssp             SEEECC
T ss_pred             CEEECc
Confidence            877653

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.35  E-value=4.3e-12  Score=118.48  Aligned_cols=147  Identities=26%  Similarity=0.363  Sum_probs=110.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .++.+.+..+....++     .+..+++|++|.+.+|.++..   .+..+..+++|++|+++       ++.+..+|+. 
T Consensus        64 ~L~~L~l~~n~l~~~~-----~l~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~  128 (272)
T 3rfs_A           64 NVRYLALGGNKLHDIS-----ALKELTNLTYLILTGNQLQSL---PNGVFDKLTNLKELVLV-------ENQLQSLPDGV  128 (272)
T ss_dssp             TCCEEECTTSCCCCCG-----GGTTCTTCCEEECTTSCCCCC---CTTTTTTCTTCCEEECT-------TSCCCCCCTTT
T ss_pred             CCcEEECCCCCCCCch-----hhcCCCCCCEEECCCCccCcc---ChhHhcCCcCCCEEECC-------CCcCCccCHHH
Confidence            5677777766655432     455888999999999987654   55557888899999998       5556666554 


Q ss_pred             ccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      ++.+++|++|++++|. ++.+|.. ++.+++|+.|++++|. +..+|+. ++.+++|++|++++|...+..|..+..+++
T Consensus       129 ~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~  206 (272)
T 3rfs_A          129 FDKLTNLTYLNLAHNQ-LQSLPKGVFDKLTNLTELDLSYNQ-LQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTS  206 (272)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTT
T ss_pred             hccCCCCCEEECCCCc-cCccCHHHhccCccCCEEECCCCC-cCccCHHHhcCCccCCEEECCCCcCCccCHHHHhCCcC
Confidence            6788999999999998 6666654 5788999999999988 6666654 688899999999999855544445788888


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       207 L~~L~l~  213 (272)
T 3rfs_A          207 LQYIWLH  213 (272)
T ss_dssp             CCEEECC
T ss_pred             CCEEEcc
Confidence            8877754

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.34  E-value=9.7e-12  Score=115.96  Aligned_cols=126  Identities=25%  Similarity=0.440  Sum_probs=74.9

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceeeccCCccccccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp~~  432 (505)
                      ++++|++|++++|.+...   .+..+..+.+|++|+++       ++.+..+|+ .++.+++|++|++++|. ++.+|..
T Consensus        83 ~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~  151 (270)
T 2o6q_A           83 ELKNLETLWVTDNKLQAL---PIGVFDQLVNLAELRLD-------RNQLKSLPPRVFDSLTKLTYLSLGYNE-LQSLPKG  151 (270)
T ss_dssp             SCTTCCEEECCSSCCCCC---CTTTTTTCSSCCEEECC-------SSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTT
T ss_pred             CCCCCCEEECCCCcCCcC---CHhHcccccCCCEEECC-------CCccCeeCHHHhCcCcCCCEEECCCCc-CCccCHh
Confidence            455555555555554432   33334556666666665       444444433 35667777777777776 5555543


Q ss_pred             -hhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccc-cccCCccCCccce
Q 046115          433 -LCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVRE  492 (505)
Q Consensus       433 -~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~  492 (505)
                       +..+++|+.|++++|. +..+|+ .+..+++|++|++++|.. ..+|. .+..+++|+.|++
T Consensus       152 ~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~N~l-~~~~~~~~~~l~~L~~L~l  212 (270)
T 2o6q_A          152 VFDKLTSLKELRLYNNQ-LKRVPEGAFDKLTELKTLKLDNNQL-KRVPEGAFDSLEKLKMLQL  212 (270)
T ss_dssp             TTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCC-SCCCTTTTTTCTTCCEEEC
T ss_pred             HccCCcccceeEecCCc-CcEeChhHhccCCCcCEEECCCCcC-CcCCHHHhccccCCCEEEe
Confidence             5667777777777776 555554 366677777777777763 34444 3566666666654

>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=99.33  E-value=7.4e-12  Score=117.79  Aligned_cols=128  Identities=27%  Similarity=0.339  Sum_probs=64.2

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-ccCCCCcceeeccCCccccccch-
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIEKLPE-  431 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-~~~l~~L~~L~l~~~~~~~~lp~-  431 (505)
                      .+++|++|.+.+|.++..   .|..+..+++|++|+++       ++.+..+|.. ++.+++|++|++++|. ++.+|. 
T Consensus       103 ~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~  171 (285)
T 1ozn_A          103 GLGRLHTLHLDRCGLQEL---GPGLFRGLAALQYLYLQ-------DNALQALPDDTFRDLGNLTHLFLHGNR-ISSVPER  171 (285)
T ss_dssp             TCTTCCEEECTTSCCCCC---CTTTTTTCTTCCEEECC-------SSCCCCCCTTTTTTCTTCCEEECCSSC-CCEECTT
T ss_pred             CCcCCCEEECCCCcCCEE---CHhHhhCCcCCCEEECC-------CCcccccCHhHhccCCCccEEECCCCc-ccccCHH
Confidence            445555555555544432   33344555555555555       3334444332 4555556666666555 444443 


Q ss_pred             hhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          432 TLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      .+..+++|+.|++++|......|..+..+++|++|++++|...+..+..+..+++|+.|++
T Consensus       172 ~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l  232 (285)
T 1ozn_A          172 AFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQYLRL  232 (285)
T ss_dssp             TTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCCCHHHHTTCTTCCEEEC
T ss_pred             HhcCccccCEEECCCCcccccCHhHccCcccccEeeCCCCcCCcCCHHHcccCcccCEEec
Confidence            2455556666666665533333455555566666666665533222223555555555543

>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=99.33  E-value=4.2e-12  Score=119.43  Aligned_cols=149  Identities=25%  Similarity=0.303  Sum_probs=97.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCC-ccccccchhHHhhcCcccceEEecccccCCcccccccc-Cc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDE-YSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PT  407 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~  407 (505)
                      .++.+.+..+....+.   +..+.++++|++|++.+|. +...   .|..+..+++|+.|+++       ++.+..+ |.
T Consensus        57 ~L~~L~l~~n~l~~~~---~~~~~~l~~L~~L~l~~n~~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~  123 (285)
T 1ozn_A           57 NLTILWLHSNVLARID---AAAFTGLALLEQLDLSDNAQLRSV---DPATFHGLGRLHTLHLD-------RCGLQELGPG  123 (285)
T ss_dssp             TCCEEECCSSCCCEEC---TTTTTTCTTCCEEECCSCTTCCCC---CTTTTTTCTTCCEEECT-------TSCCCCCCTT
T ss_pred             CCCEEECCCCccceeC---HhhcCCccCCCEEeCCCCCCcccc---CHHHhcCCcCCCEEECC-------CCcCCEECHh
Confidence            4566666555544332   2344567778888887775 4432   35556777778888877       4444444 45


Q ss_pred             cccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      .+..+++|++|++++|. ++.+|. .++.+++|+.|++++|. +..+|.. +..+++|++|++++|...+..|..|.+++
T Consensus       124 ~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~  201 (285)
T 1ozn_A          124 LFRGLAALQYLYLQDNA-LQALPDDTFRDLGNLTHLFLHGNR-ISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLG  201 (285)
T ss_dssp             TTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCT
T ss_pred             HhhCCcCCCEEECCCCc-ccccCHhHhccCCCccEEECCCCc-ccccCHHHhcCccccCEEECCCCcccccCHhHccCcc
Confidence            56777778888888777 555554 36777778888888776 5566653 67777788888887775555566777777


Q ss_pred             cCCcccee
Q 046115          486 RLRRVREF  493 (505)
Q Consensus       486 ~L~~L~~~  493 (505)
                      +|+.|++.
T Consensus       202 ~L~~L~l~  209 (285)
T 1ozn_A          202 RLMTLYLF  209 (285)
T ss_dssp             TCCEEECC
T ss_pred             cccEeeCC
Confidence            77766643

>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=99.33  E-value=4e-12  Score=136.53  Aligned_cols=137  Identities=25%  Similarity=0.287  Sum_probs=102.2

Q ss_pred             cccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCcccc
Q 046115          348 IWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIE  427 (505)
Q Consensus       348 ~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~  427 (505)
                      ++..+..+++|+.|++++|.+++.   +|..+..+++|+.|+++      ++...+.+|..++.+++|++|++++|...+
T Consensus       410 ~p~~l~~l~~L~~L~Ls~N~l~~~---~p~~l~~l~~L~~L~L~------~n~l~~~~p~~~~~l~~L~~L~L~~N~l~~  480 (768)
T 3rgz_A          410 IPPTLSNCSELVSLHLSFNYLSGT---IPSSLGSLSKLRDLKLW------LNMLEGEIPQELMYVKTLETLILDFNDLTG  480 (768)
T ss_dssp             CCGGGGGCTTCCEEECCSSEEESC---CCGGGGGCTTCCEEECC------SSCCCSCCCGGGGGCTTCCEEECCSSCCCS
T ss_pred             cCHHHhcCCCCCEEECcCCcccCc---ccHHHhcCCCCCEEECC------CCcccCcCCHHHcCCCCceEEEecCCcccC
Confidence            344455778888888888876643   66667778888888887      344444677777788888888888887555


Q ss_pred             ccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          428 KLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       428 ~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      .+|..++.+++|+.|++++|+....+|.+++.+++|++|++++|...+.+|..++++++|+.|++.
T Consensus       481 ~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~Ls  546 (768)
T 3rgz_A          481 EIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLN  546 (768)
T ss_dssp             CCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCCEEECC
T ss_pred             cCCHHHhcCCCCCEEEccCCccCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCCEEECC
Confidence            777777888888888888888555778778888888888888887777778778877777777654

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.32  E-value=1.1e-11  Score=115.59  Aligned_cols=147  Identities=23%  Similarity=0.354  Sum_probs=83.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-c
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-N  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~  408 (505)
                      .+..+.+..+....++.   ..+.++++|++|.+.+|.++..   .+..+..+++|++|+++       ++.+..+|. .
T Consensus        38 ~l~~L~l~~n~l~~~~~---~~~~~l~~L~~L~l~~n~l~~i---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~  104 (270)
T 2o6q_A           38 DTKKLDLQSNKLSSLPS---KAFHRLTKLRLLYLNDNKLQTL---PAGIFKELKNLETLWVT-------DNKLQALPIGV  104 (270)
T ss_dssp             TCSEEECCSSCCSCCCT---TSSSSCTTCCEEECCSSCCSCC---CTTTTSSCTTCCEEECC-------SSCCCCCCTTT
T ss_pred             CCCEEECcCCCCCeeCH---HHhcCCCCCCEEECCCCccCee---ChhhhcCCCCCCEEECC-------CCcCCcCCHhH
Confidence            45555555555444332   2344666666666666665532   33334556666666666       444555543 3


Q ss_pred             ccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccc-cccCCc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPA-GIGELI  485 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~  485 (505)
                      +..+++|++|++++|. +..+|. .++.+++|+.|++++|. +..+|.. +..+++|++|++++|... .+|. .|.+++
T Consensus       105 ~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~-~~~~~~~~~l~  181 (270)
T 2o6q_A          105 FDQLVNLAELRLDRNQ-LKSLPPRVFDSLTKLTYLSLGYNE-LQSLPKGVFDKLTSLKELRLYNNQLK-RVPEGAFDKLT  181 (270)
T ss_dssp             TTTCSSCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCS-CCCTTTTTTCT
T ss_pred             cccccCCCEEECCCCc-cCeeCHHHhCcCcCCCEEECCCCc-CCccCHhHccCCcccceeEecCCcCc-EeChhHhccCC
Confidence            4566666777776666 444433 34666667777776666 5555544 566666667766666533 3333 355666


Q ss_pred             cCCccce
Q 046115          486 RLRRVRE  492 (505)
Q Consensus       486 ~L~~L~~  492 (505)
                      +|+.|++
T Consensus       182 ~L~~L~L  188 (270)
T 2o6q_A          182 ELKTLKL  188 (270)
T ss_dssp             TCCEEEC
T ss_pred             CcCEEEC
Confidence            6665554

>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=99.31  E-value=7e-12  Score=118.09  Aligned_cols=147  Identities=24%  Similarity=0.274  Sum_probs=119.2

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      ..+..+.+..+....++.   ..+..+++|+.|++++|.++...    . ...+.+|+.|+++       ++.+..+|..
T Consensus        31 ~~l~~L~L~~N~l~~~~~---~~~~~l~~L~~L~L~~n~l~~~~----~-~~~l~~L~~L~Ls-------~N~l~~l~~~   95 (290)
T 1p9a_G           31 KDTTILHLSENLLYTFSL---ATLMPYTRLTQLNLDRAELTKLQ----V-DGTLPVLGTLDLS-------HNQLQSLPLL   95 (290)
T ss_dssp             TTCCEEECTTSCCSEEEG---GGGTTCTTCCEEECTTSCCCEEE----C-CSCCTTCCEEECC-------SSCCSSCCCC
T ss_pred             CCCCEEEcCCCcCCccCH---HHhhcCCCCCEEECCCCccCccc----C-CCCCCcCCEEECC-------CCcCCcCchh
Confidence            367777777776655443   34568999999999999987642    2 3678999999998       7778899998


Q ss_pred             ccCCCCcceeeccCCccccccc-hhhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCccccccccc-ccCCc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAG-IGELI  485 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~-i~~l~  485 (505)
                      +..+++|++|++++|. ++.+| ..+..+++|+.|++++|. +..+|+. +..+++|++|++++|. +..+|.. +..++
T Consensus        96 ~~~l~~L~~L~l~~N~-l~~l~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~~l~  172 (290)
T 1p9a_G           96 GQTLPALTVLDVSFNR-LTSLPLGALRGLGELQELYLKGNE-LKTLPPGLLTPTPKLEKLSLANNN-LTELPAGLLNGLE  172 (290)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCSSTTTTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECTTSC-CSCCCTTTTTTCT
T ss_pred             hccCCCCCEEECCCCc-CcccCHHHHcCCCCCCEEECCCCC-CCccChhhcccccCCCEEECCCCc-CCccCHHHhcCcC
Confidence            9999999999999999 77776 468999999999999998 7777765 6889999999999998 4567665 57888


Q ss_pred             cCCcccee
Q 046115          486 RLRRVREF  493 (505)
Q Consensus       486 ~L~~L~~~  493 (505)
                      +|+.|++.
T Consensus       173 ~L~~L~L~  180 (290)
T 1p9a_G          173 NLDTLLLQ  180 (290)
T ss_dssp             TCCEEECC
T ss_pred             CCCEEECC
Confidence            88888764

>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=99.31  E-value=1e-11  Score=118.08  Aligned_cols=152  Identities=21%  Similarity=0.200  Sum_probs=79.6

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++...   +.++++|+.|++.+|.++.... .+..+..+.+|++|+++       ++.+..+|..+
T Consensus        29 ~l~~L~L~~n~l~~i~~~~---~~~l~~L~~L~L~~n~l~~~~~-~~~~~~~~~~L~~L~Ls-------~n~i~~l~~~~   97 (306)
T 2z66_A           29 SATRLELESNKLQSLPHGV---FDKLTQLTKLSLSSNGLSFKGC-CSQSDFGTTSLKYLDLS-------FNGVITMSSNF   97 (306)
T ss_dssp             TCCEEECCSSCCCCCCTTT---TTTCTTCSEEECCSSCCCEEEE-EEHHHHSCSCCCEEECC-------SCSEEEEEEEE
T ss_pred             CCCEEECCCCccCccCHhH---hhccccCCEEECCCCccCcccC-cccccccccccCEEECC-------CCccccChhhc
Confidence            6677777766666554432   3467777788887777653311 23334556666666666       44444444444


Q ss_pred             cCCCCcceeeccC-------------------------CccccccchhhhcCCCCcEEecCCCcCcc-ccchhccccccC
Q 046115          410 EKLLHLKYLNLKG-------------------------QKKIEKLPETLCELYNLERLNVDDCQNLR-ELPRGIGKLRKL  463 (505)
Q Consensus       410 ~~l~~L~~L~l~~-------------------------~~~~~~lp~~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L  463 (505)
                      ..+++|++|++++                         |......|..+..+++|+.|++++|.... .+|..+..+++|
T Consensus        98 ~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L  177 (306)
T 2z66_A           98 LGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNL  177 (306)
T ss_dssp             ETCTTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTC
T ss_pred             CCCCCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCccchhhcccCcCCCEEECCCCccccccchhHHhhCcCC
Confidence            4445555555544                         44222333334455555555555554222 244455555555


Q ss_pred             ceeecCCCcccccccccccCCccCCccce
Q 046115          464 MYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       464 ~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      ++|++++|...+..|..+..+++|+.|++
T Consensus       178 ~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L  206 (306)
T 2z66_A          178 TFLDLSQCQLEQLSPTAFNSLSSLQVLNM  206 (306)
T ss_dssp             CEEECTTSCCCEECTTTTTTCTTCCEEEC
T ss_pred             CEEECCCCCcCCcCHHHhcCCCCCCEEEC
Confidence            55555555533333444555555555543

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.31  E-value=1.3e-11  Score=110.24  Aligned_cols=131  Identities=27%  Similarity=0.383  Sum_probs=87.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .+..+.+..+....++..   .+..+++|++|++.+|.+...   .+..+..+.+|++|+++       ++.+..+|.. 
T Consensus        29 ~l~~L~l~~n~l~~~~~~---~~~~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~Ls-------~n~l~~~~~~~   95 (208)
T 2o6s_A           29 QTTYLDLETNSLKSLPNG---VFDELTSLTQLYLGGNKLQSL---PNGVFNKLTSLTYLNLS-------TNQLQSLPNGV   95 (208)
T ss_dssp             TCSEEECCSSCCCCCCTT---TTTTCTTCSEEECCSSCCCCC---CTTTTTTCTTCCEEECC-------SSCCCCCCTTT
T ss_pred             CCcEEEcCCCccCcCChh---hhcccccCcEEECCCCccCcc---ChhhcCCCCCcCEEECC-------CCcCCccCHhH
Confidence            566666666665544432   244677788888887776543   44445677778888877       5555565544 


Q ss_pred             ccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLR  475 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~  475 (505)
                      +..+++|++|++++|. ++.+|.. +..+++|+.|++++|. +..+|.. +..+++|++|++++|....
T Consensus        96 ~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~l~~L~~L~l~~N~~~~  162 (208)
T 2o6s_A           96 FDKLTQLKELALNTNQ-LQSLPDGVFDKLTQLKDLRLYQNQ-LKSVPDGVFDRLTSLQYIWLHDNPWDC  162 (208)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSCCBCC
T ss_pred             hcCccCCCEEEcCCCc-CcccCHhHhccCCcCCEEECCCCc-cceeCHHHhccCCCccEEEecCCCeec
Confidence            5677778888888777 5555553 5677778888888777 5555554 6777778888887776443

>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=99.31  E-value=9.8e-12  Score=114.59  Aligned_cols=143  Identities=24%  Similarity=0.286  Sum_probs=114.7

Q ss_pred             eEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-cccc
Q 046115          332 LHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIE  410 (505)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~  410 (505)
                      ..+.........+|..++      ++++.|++.+|.++..   .+..+..+++|++|+|+       ++.+..++ ..+.
T Consensus        17 ~~l~~~~~~l~~~p~~~~------~~l~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~~~   80 (251)
T 3m19_A           17 KEVDCQGKSLDSVPSGIP------ADTEKLDLQSTGLATL---SDATFRGLTKLTWLNLD-------YNQLQTLSAGVFD   80 (251)
T ss_dssp             TEEECTTCCCSSCCSCCC------TTCCEEECTTSCCCCC---CTTTTTTCTTCCEEECT-------TSCCCCCCTTTTT
T ss_pred             eEEecCCCCccccCCCCC------CCCCEEEccCCCcCcc---CHhHhcCcccCCEEECC-------CCcCCccCHhHhc
Confidence            345555666666666553      5899999999998765   56668899999999999       56666654 4578


Q ss_pred             CCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccc-cccCCccC
Q 046115          411 KLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPA-GIGELIRL  487 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L  487 (505)
                      .+++|++|++++|. ++.+|. .+..+++|+.|++++|. +..+|+. +..+++|++|++++|.. ..+|. .|..+++|
T Consensus        81 ~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~Ls~N~l-~~~~~~~~~~l~~L  157 (251)
T 3m19_A           81 DLTELGTLGLANNQ-LASLPLGVFDHLTQLDKLYLGGNQ-LKSLPSGVFDRLTKLKELRLNTNQL-QSIPAGAFDKLTNL  157 (251)
T ss_dssp             TCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCC-CCCCTTTTTTCTTC
T ss_pred             cCCcCCEEECCCCc-ccccChhHhcccCCCCEEEcCCCc-CCCcChhHhccCCcccEEECcCCcC-CccCHHHcCcCcCC
Confidence            99999999999999 667764 56899999999999998 7777775 68899999999999984 45655 68889998


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      +.|++.
T Consensus       158 ~~L~L~  163 (251)
T 3m19_A          158 QTLSLS  163 (251)
T ss_dssp             CEEECC
T ss_pred             CEEECC
Confidence            888764

>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=99.30  E-value=2.2e-11  Score=110.42  Aligned_cols=141  Identities=27%  Similarity=0.395  Sum_probs=114.7

Q ss_pred             EEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-ccCC
Q 046115          334 LLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKL  412 (505)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-~~~l  412 (505)
                      +.........+|..++      ++|+.|++++|.+++.   .|..+..+.+|++|+|+       ++.+..+|.. +..+
T Consensus        24 v~c~~~~l~~ip~~~~------~~L~~L~Ls~n~i~~~---~~~~~~~l~~L~~L~L~-------~N~l~~i~~~~~~~l   87 (229)
T 3e6j_A           24 VDCRSKRHASVPAGIP------TNAQILYLHDNQITKL---EPGVFDSLINLKELYLG-------SNQLGALPVGVFDSL   87 (229)
T ss_dssp             EECTTSCCSSCCSCCC------TTCSEEECCSSCCCCC---CTTTTTTCTTCCEEECC-------SSCCCCCCTTTTTTC
T ss_pred             eEccCCCcCccCCCCC------CCCCEEEcCCCccCcc---CHHHhhCccCCcEEECC-------CCCCCCcChhhcccC
Confidence            3333444555665443      7899999999998765   57778899999999999       6777887754 6899


Q ss_pred             CCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccc-cccCCccCCcc
Q 046115          413 LHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRV  490 (505)
Q Consensus       413 ~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L  490 (505)
                      ++|++|+|++|. ++.+|.. +..+++|+.|++++|. +..+|..+..+++|++|++++|.+ ..+|. .+..+++|+.|
T Consensus        88 ~~L~~L~Ls~N~-l~~l~~~~~~~l~~L~~L~Ls~N~-l~~lp~~~~~l~~L~~L~L~~N~l-~~~~~~~~~~l~~L~~L  164 (229)
T 3e6j_A           88 TQLTVLDLGTNQ-LTVLPSAVFDRLVHLKELFMCCNK-LTELPRGIERLTHLTHLALDQNQL-KSIPHGAFDRLSSLTHA  164 (229)
T ss_dssp             TTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCSCCTTGGGCTTCSEEECCSSCC-CCCCTTTTTTCTTCCEE
T ss_pred             CCcCEEECCCCc-CCccChhHhCcchhhCeEeccCCc-ccccCcccccCCCCCEEECCCCcC-CccCHHHHhCCCCCCEE
Confidence            999999999998 7777764 5899999999999999 889999999999999999999984 45654 57888888877


Q ss_pred             cee
Q 046115          491 REF  493 (505)
Q Consensus       491 ~~~  493 (505)
                      ++.
T Consensus       165 ~l~  167 (229)
T 3e6j_A          165 YLF  167 (229)
T ss_dssp             ECT
T ss_pred             Eee
Confidence            653

>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=99.29  E-value=2.6e-12  Score=124.83  Aligned_cols=150  Identities=19%  Similarity=0.283  Sum_probs=103.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .+..+.+..+....++.   ..+.++++|++|++.+|.++..   .|..+..+++|++|+++       ++.+..+|.. 
T Consensus        53 ~L~~L~l~~n~i~~~~~---~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~Ls-------~n~l~~~~~~~  119 (353)
T 2z80_A           53 AVKSLDLSNNRITYISN---SDLQRCVNLQALVLTSNGINTI---EEDSFSSLGSLEHLDLS-------YNYLSNLSSSW  119 (353)
T ss_dssp             TCCEEECTTSCCCEECT---TTTTTCTTCCEEECTTSCCCEE---CTTTTTTCTTCCEEECC-------SSCCSSCCHHH
T ss_pred             cCcEEECCCCcCcccCH---HHhccCCCCCEEECCCCccCcc---CHhhcCCCCCCCEEECC-------CCcCCcCCHhH
Confidence            66677766666554443   2345778888888888876643   45557777888888887       5666666655 


Q ss_pred             ccCCCCcceeeccCCccccccch--hhhcCCCCcEEecCCCcCccccc-hhccccccCceeecCCCcccccccccccCCc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELP-RGIGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      ++.+++|++|++++|. +..+|.  .+..+++|+.|++++|..+..++ ..+..+++|++|++++|...+..|..+.+++
T Consensus       120 ~~~l~~L~~L~L~~n~-l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~  198 (353)
T 2z80_A          120 FKPLSSLTFLNLLGNP-YKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQ  198 (353)
T ss_dssp             HTTCTTCSEEECTTCC-CSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCS
T ss_pred             hCCCccCCEEECCCCC-CcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCCCCcCccCHHHHhccc
Confidence            6777888888888877 666765  56777888888888775455554 4577777888888887775555566677777


Q ss_pred             cCCcccee
Q 046115          486 RLRRVREF  493 (505)
Q Consensus       486 ~L~~L~~~  493 (505)
                      +|+.|++.
T Consensus       199 ~L~~L~l~  206 (353)
T 2z80_A          199 NVSHLILH  206 (353)
T ss_dssp             EEEEEEEE
T ss_pred             cCCeecCC
Confidence            76666543

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.29  E-value=4.6e-12  Score=132.93  Aligned_cols=87  Identities=16%  Similarity=0.182  Sum_probs=45.4

Q ss_pred             cCcccc--CCCCcceeeccCCccccccchhhhcCCCCcEEecCCCc-Ccc-ccchhcccc------ccCceeecCCCccc
Q 046115          405 IPTNIE--KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQ-NLR-ELPRGIGKL------RKLMYLHNEDTGCL  474 (505)
Q Consensus       405 ~p~~~~--~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~-~~~-~lp~~~~~l------~~L~~L~l~~~~~~  474 (505)
                      +|..++  .+++|++|++++|...+.+|..++++++|+.|++++|. ... .+|..++.+      ++|++|++++|...
T Consensus       239 ip~~l~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~  318 (636)
T 4eco_A          239 KTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLK  318 (636)
T ss_dssp             TTSCCCGGGCTTCCEEEEECCTTCSSCCTTTTTCSSCCEEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSCCS
T ss_pred             CchhhhhcccCCCCEEEecCCcCCccChHHHhcCCCCCEEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCCcCC
Confidence            555555  55555555555555445555555555555555555554 222 455555444      55555555555432


Q ss_pred             ccccc--cccCCccCCccce
Q 046115          475 RYLPA--GIGELIRLRRVRE  492 (505)
Q Consensus       475 ~~~p~--~i~~l~~L~~L~~  492 (505)
                       .+|.  .++++++|+.|++
T Consensus       319 -~ip~~~~l~~l~~L~~L~L  337 (636)
T 4eco_A          319 -TFPVETSLQKMKKLGMLEC  337 (636)
T ss_dssp             -SCCCHHHHTTCTTCCEEEC
T ss_pred             -ccCchhhhccCCCCCEEeC
Confidence             4554  4555555554443

>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=99.28  E-value=3.3e-11  Score=113.55  Aligned_cols=142  Identities=23%  Similarity=0.343  Sum_probs=114.2

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      ..++.+.+..+....++.     +..+++|+.|++++|.++.    +|. +..+++|+.|+++       ++.+..++ .
T Consensus        68 ~~L~~L~L~~n~l~~~~~-----l~~l~~L~~L~l~~n~l~~----~~~-l~~l~~L~~L~L~-------~n~i~~~~-~  129 (291)
T 1h6t_A           68 PNVTKLFLNGNKLTDIKP-----LANLKNLGWLFLDENKVKD----LSS-LKDLKKLKSLSLE-------HNGISDIN-G  129 (291)
T ss_dssp             TTCCEEECCSSCCCCCGG-----GTTCTTCCEEECCSSCCCC----GGG-GTTCTTCCEEECT-------TSCCCCCG-G
T ss_pred             CCCCEEEccCCccCCCcc-----cccCCCCCEEECCCCcCCC----Chh-hccCCCCCEEECC-------CCcCCCCh-h
Confidence            367788887777665544     5589999999999998765    343 7889999999998       66666664 5


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      +..+++|++|++++|. ++.++ .++.+++|+.|++++|. +..+++ +..+++|++|++++|. +..+| .+..+++|+
T Consensus       130 l~~l~~L~~L~l~~n~-l~~~~-~l~~l~~L~~L~L~~N~-l~~~~~-l~~l~~L~~L~L~~N~-i~~l~-~l~~l~~L~  203 (291)
T 1h6t_A          130 LVHLPQLESLYLGNNK-ITDIT-VLSRLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNH-ISDLR-ALAGLKNLD  203 (291)
T ss_dssp             GGGCTTCCEEECCSSC-CCCCG-GGGGCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCBCG-GGTTCTTCS
T ss_pred             hcCCCCCCEEEccCCc-CCcch-hhccCCCCCEEEccCCc-cccchh-hcCCCccCEEECCCCc-CCCCh-hhccCCCCC
Confidence            8889999999999998 77774 48999999999999998 777766 8899999999999997 45565 488888888


Q ss_pred             ccceeE
Q 046115          489 RVREFV  494 (505)
Q Consensus       489 ~L~~~~  494 (505)
                      .|++..
T Consensus       204 ~L~l~~  209 (291)
T 1h6t_A          204 VLELFS  209 (291)
T ss_dssp             EEEEEE
T ss_pred             EEECcC
Confidence            888764

>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=99.28  E-value=7e-12  Score=107.89  Aligned_cols=132  Identities=27%  Similarity=0.316  Sum_probs=107.8

Q ss_pred             ceeEEEEEecCCC--ccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cC
Q 046115          330 KILHLLLTLRRGA--SVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IP  406 (505)
Q Consensus       330 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p  406 (505)
                      .++.+.+..+...  .+|    ..+..+++|+.|++++|.++..     ..+..+++|++|+++       ++.+.. +|
T Consensus        25 ~L~~L~l~~n~l~~~~i~----~~~~~l~~L~~L~l~~n~l~~~-----~~~~~l~~L~~L~Ls-------~N~l~~~~~   88 (168)
T 2ell_A           25 AVRELVLDNCKSNDGKIE----GLTAEFVNLEFLSLINVGLISV-----SNLPKLPKLKKLELS-------ENRIFGGLD   88 (168)
T ss_dssp             SCSEEECCSCBCBTTBCS----SCCGGGGGCCEEEEESSCCCCC-----SSCCCCSSCCEEEEE-------SCCCCSCCC
T ss_pred             cCCEEECCCCCCChhhHH----HHHHhCCCCCEEeCcCCCCCCh-----hhhccCCCCCEEECc-------CCcCchHHH
Confidence            6777777777655  443    3345899999999999998754     347889999999999       555665 67


Q ss_pred             ccccCCCCcceeeccCCccccccc--hhhhcCCCCcEEecCCCcCccccch----hccccccCceeecCCCccccccccc
Q 046115          407 TNIEKLLHLKYLNLKGQKKIEKLP--ETLCELYNLERLNVDDCQNLRELPR----GIGKLRKLMYLHNEDTGCLRYLPAG  480 (505)
Q Consensus       407 ~~~~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~lp~----~~~~l~~L~~L~l~~~~~~~~~p~~  480 (505)
                      ..+..+++|++|++++|. ++.+|  ..+..+++|+.|++++|+ +..+|.    .+..+++|++|++++|. ...+|..
T Consensus        89 ~~~~~l~~L~~L~Ls~N~-l~~~~~~~~l~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~l~~L~~L~l~~n~-~~~~~~~  165 (168)
T 2ell_A           89 MLAEKLPNLTHLNLSGNK-LKDISTLEPLKKLECLKSLDLFNCE-VTNLNDYRESVFKLLPQLTYLDGYDRE-DQEAPDS  165 (168)
T ss_dssp             HHHHHCTTCCEEECBSSS-CCSSGGGGGGSSCSCCCEEECCSSG-GGTSTTHHHHHHTTCSSCCEETTEETT-SCBCCSS
T ss_pred             HHHhhCCCCCEEeccCCc-cCcchhHHHHhcCCCCCEEEeeCCc-CcchHHHHHHHHHhCccCcEecCCCCC-hhhcccc
Confidence            767779999999999998 77776  678999999999999998 777876    68999999999999997 4556643

>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=99.28  E-value=7.8e-12  Score=131.41  Aligned_cols=148  Identities=18%  Similarity=0.136  Sum_probs=110.6

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-c
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-N  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~  408 (505)
                      .++.+.++.+.+..++.   ..|.++++|++|++++|.++..   .|..|..+++|++|+|+       ++.+..+|+ .
T Consensus        53 ~~~~LdLs~N~i~~l~~---~~f~~l~~L~~L~Ls~N~i~~i---~~~~f~~L~~L~~L~Ls-------~N~l~~l~~~~  119 (635)
T 4g8a_A           53 STKNLDLSFNPLRHLGS---YSFFSFPELQVLDLSRCEIQTI---EDGAYQSLSHLSTLILT-------GNPIQSLALGA  119 (635)
T ss_dssp             TCCEEECTTSCCCEECT---TTTTTCTTCCEEECTTCCCCEE---CTTTTTTCTTCCEEECT-------TCCCCEECGGG
T ss_pred             CCCEEEeeCCCCCCCCH---HHHhCCCCCCEEECCCCcCCCc---ChhHhcCCCCCCEEEcc-------CCcCCCCCHHH
Confidence            67788887777766653   3355888899999988887654   45567888889999988       666777765 4


Q ss_pred             ccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      ++.+++|++|++++|. ++.+|. .++.+++|+.|++++|.... .+|..++.+++|++|++++|...+..|..+..+.+
T Consensus       120 f~~L~~L~~L~Ls~N~-l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~l~~L~~  198 (635)
T 4g8a_A          120 FSGLSSLQKLVAVETN-LASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ  198 (635)
T ss_dssp             GTTCTTCCEEECTTSC-CCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSCCCEECGGGGHHHHT
T ss_pred             hcCCCCCCEEECCCCc-CCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhcccCccccccccccccchhh
Confidence            6888899999999888 777765 47888889999998887322 35677888888999999888865555666666666


Q ss_pred             CCccc
Q 046115          487 LRRVR  491 (505)
Q Consensus       487 L~~L~  491 (505)
                      ++.+.
T Consensus       199 l~~~~  203 (635)
T 4g8a_A          199 MPLLN  203 (635)
T ss_dssp             CTTCC
T ss_pred             hhhhh
Confidence            55443

>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=99.28  E-value=8.7e-12  Score=128.30  Aligned_cols=119  Identities=18%  Similarity=0.243  Sum_probs=101.5

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcC
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCEL  436 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l  436 (505)
                      .|+.|++++|.+++    +|. +..+++|+.|+|+       ++.+..+|..++.+++|++|+|++|. ++.+| .++.+
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  507 (567)
T 1dce_A          442 DVRVLHLAHKDLTV----LCH-LEQLLLVTHLDLS-------HNRLRALPPALAALRCLEVLQASDNA-LENVD-GVANL  507 (567)
T ss_dssp             TCSEEECTTSCCSS----CCC-GGGGTTCCEEECC-------SSCCCCCCGGGGGCTTCCEEECCSSC-CCCCG-GGTTC
T ss_pred             CceEEEecCCCCCC----CcC-ccccccCcEeecC-------cccccccchhhhcCCCCCEEECCCCC-CCCCc-ccCCC
Confidence            58899999998876    455 8899999999999       77788999999999999999999999 77788 69999


Q ss_pred             CCCcEEecCCCcCcccc--chhccccccCceeecCCCcccccccccc----cCCccCCccc
Q 046115          437 YNLERLNVDDCQNLREL--PRGIGKLRKLMYLHNEDTGCLRYLPAGI----GELIRLRRVR  491 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~l--p~~~~~l~~L~~L~l~~~~~~~~~p~~i----~~l~~L~~L~  491 (505)
                      ++|+.|+|++|. +..+  |..++.+++|++|++++|. +...|+.+    ..+++|+.|+
T Consensus       508 ~~L~~L~Ls~N~-l~~~~~p~~l~~l~~L~~L~L~~N~-l~~~~~~~~~l~~~lp~L~~L~  566 (567)
T 1dce_A          508 PRLQELLLCNNR-LQQSAAIQPLVSCPRLVLLNLQGNS-LCQEEGIQERLAEMLPSVSSIL  566 (567)
T ss_dssp             SSCCEEECCSSC-CCSSSTTGGGGGCTTCCEEECTTSG-GGGSSSCTTHHHHHCTTCSEEE
T ss_pred             CCCcEEECCCCC-CCCCCCcHHHhcCCCCCEEEecCCc-CCCCccHHHHHHHHCcccCccC
Confidence            999999999998 6666  8899999999999999998 44555543    3467777764

>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=99.28  E-value=7.8e-12  Score=110.64  Aligned_cols=126  Identities=16%  Similarity=0.160  Sum_probs=105.7

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      .+++|+.|.+.+|.+..    +| .+..+++|+.|+++       ++.+..++ .++.+++|++|++++|......|..+
T Consensus        42 ~l~~L~~L~l~~n~i~~----l~-~l~~l~~L~~L~l~-------~n~~~~~~-~l~~l~~L~~L~l~~n~l~~~~~~~l  108 (197)
T 4ezg_A           42 QMNSLTYITLANINVTD----LT-GIEYAHNIKDLTIN-------NIHATNYN-PISGLSNLERLRIMGKDVTSDKIPNL  108 (197)
T ss_dssp             HHHTCCEEEEESSCCSC----CT-TGGGCTTCSEEEEE-------SCCCSCCG-GGTTCTTCCEEEEECTTCBGGGSCCC
T ss_pred             hcCCccEEeccCCCccC----hH-HHhcCCCCCEEEcc-------CCCCCcch-hhhcCCCCCEEEeECCccCcccChhh
Confidence            67899999999998874    44 38889999999999       55555554 68899999999999999544577889


Q ss_pred             hcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          434 CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      +.+++|+.|++++|......|..++.+++|++|++++|..+..+| .+.++++|+.|++.
T Consensus       109 ~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~  167 (197)
T 4ezg_A          109 SGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQ  167 (197)
T ss_dssp             TTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECT
T ss_pred             cCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECC
Confidence            999999999999999555678889999999999999997566776 68888888888764

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.28  E-value=3.5e-12  Score=136.84  Aligned_cols=151  Identities=15%  Similarity=0.177  Sum_probs=109.2

Q ss_pred             ceeEEEEEecCCCcc-------c-------cccccCCC--CCCCceEEEecCCCccccccchhHHhhcCcccceEEeccc
Q 046115          330 KILHLLLTLRRGASV-------P-------ISIWGNVT--GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVR  393 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~-------~-------~~~~~~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~  393 (505)
                      .++.+.+..+.....       +       ..+|..++  ++++|+.|.+++|.+.+.   +|..+.++++|+.|+|+  
T Consensus       449 ~L~~L~Ls~N~Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~N~l~~~---iP~~l~~L~~L~~L~Ls--  523 (876)
T 4ecn_A          449 KLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQ---LPDFLYDLPELQSLNIA--  523 (876)
T ss_dssp             TCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEESCTTCCS---CCGGGGGCSSCCEEECT--
T ss_pred             CCCEEECcCCcCCCCcccccccccccccccccCChhhhhccCCCCCEEECcCCCCCcc---ChHHHhCCCCCCEEECc--
Confidence            567777777765540       0       01455555  788888888888876554   67778888888888887  


Q ss_pred             ccCCcccccc--ccCccccCCC-------CcceeeccCCccccccch--hhhcCCCCcEEecCCCcCccccchhcccccc
Q 046115          394 ESWPRNNLIK--EIPTNIEKLL-------HLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELPRGIGKLRK  462 (505)
Q Consensus       394 ~~~~~~~~~~--~~p~~~~~l~-------~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~  462 (505)
                          ++..+.  .+|..++.++       +|++|++++|. +..+|.  .++.+++|+.|+|++|. +..+| .++.+++
T Consensus       524 ----~N~~lsg~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~-L~~ip~~~~l~~L~~L~~L~Ls~N~-l~~lp-~~~~L~~  596 (876)
T 4ecn_A          524 ----CNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNN-LEEFPASASLQKMVKLGLLDCVHNK-VRHLE-AFGTNVK  596 (876)
T ss_dssp             ----TCTTSCHHHHHHHHHHHHHCTTTTTTCCEEECCSSC-CCBCCCHHHHTTCTTCCEEECTTSC-CCBCC-CCCTTSE
T ss_pred             ----CCCCcccccchHHHHhhhhcccccCCccEEEeeCCc-CCccCChhhhhcCCCCCEEECCCCC-cccch-hhcCCCc
Confidence                232133  4676555554       88888888888 558887  78888888888888888 55888 7888888


Q ss_pred             CceeecCCCcccccccccccCCcc-CCcccee
Q 046115          463 LMYLHNEDTGCLRYLPAGIGELIR-LRRVREF  493 (505)
Q Consensus       463 L~~L~l~~~~~~~~~p~~i~~l~~-L~~L~~~  493 (505)
                      |++|++++|... .+|..+.++++ |+.|++-
T Consensus       597 L~~L~Ls~N~l~-~lp~~l~~l~~~L~~L~Ls  627 (876)
T 4ecn_A          597 LTDLKLDYNQIE-EIPEDFCAFTDQVEGLGFS  627 (876)
T ss_dssp             ESEEECCSSCCS-CCCTTSCEECTTCCEEECC
T ss_pred             ceEEECcCCccc-cchHHHhhccccCCEEECc
Confidence            888888888744 78877888877 8777654

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.28  E-value=3.3e-12  Score=134.04  Aligned_cols=152  Identities=15%  Similarity=0.164  Sum_probs=113.4

Q ss_pred             ceeEEEEEecCCCcc-------cc-------ccccCCC--CCCCceEEEecCCCccccccchhHHhhcCcccceEEeccc
Q 046115          330 KILHLLLTLRRGASV-------PI-------SIWGNVT--GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVR  393 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~-------~~-------~~~~~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~  393 (505)
                      .++.+.+..+.....       +.       .++..+.  .+++|++|++.+|.+.+.   +|..+.++++|++|+++  
T Consensus       207 ~L~~L~Ls~n~l~~~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~~n~l~~~---~p~~l~~l~~L~~L~Ls--  281 (636)
T 4eco_A          207 KLRQFYMGNSPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTK---LPTFLKALPEMQLINVA--  281 (636)
T ss_dssp             TCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEECCTTCSS---CCTTTTTCSSCCEEECT--
T ss_pred             CCCEEECcCCccccccccccccccccchhcccCchhhhhcccCCCCEEEecCCcCCcc---ChHHHhcCCCCCEEECc--
Confidence            567777777765541       00       0555666  788888888888877654   77778888888888888  


Q ss_pred             ccCCcccccc--ccCccccCC------CCcceeeccCCccccccch--hhhcCCCCcEEecCCCcCccccchhccccccC
Q 046115          394 ESWPRNNLIK--EIPTNIEKL------LHLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELPRGIGKLRKL  463 (505)
Q Consensus       394 ~~~~~~~~~~--~~p~~~~~l------~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L  463 (505)
                          ++..+.  .+|..++.+      ++|++|++++|. ++.+|.  .++.+++|+.|++++|.....+| .++.+++|
T Consensus       282 ----~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~-l~~ip~~~~l~~l~~L~~L~L~~N~l~g~ip-~~~~l~~L  355 (636)
T 4eco_A          282 ----CNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNN-LKTFPVETSLQKMKKLGMLECLYNQLEGKLP-AFGSEIKL  355 (636)
T ss_dssp             ----TCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSC-CSSCCCHHHHTTCTTCCEEECCSCCCEEECC-CCEEEEEE
T ss_pred             ----CCCCCccccchHHHHhhhccccCCCCCEEECCCCc-CCccCchhhhccCCCCCEEeCcCCcCccchh-hhCCCCCC
Confidence                233143  577777766      888888888888 668887  78888888888888888444888 88888888


Q ss_pred             ceeecCCCcccccccccccCCcc-CCcccee
Q 046115          464 MYLHNEDTGCLRYLPAGIGELIR-LRRVREF  493 (505)
Q Consensus       464 ~~L~l~~~~~~~~~p~~i~~l~~-L~~L~~~  493 (505)
                      ++|++++|. +..+|..+.++++ |+.|++.
T Consensus       356 ~~L~L~~N~-l~~lp~~l~~l~~~L~~L~Ls  385 (636)
T 4eco_A          356 ASLNLAYNQ-ITEIPANFCGFTEQVENLSFA  385 (636)
T ss_dssp             SEEECCSSE-EEECCTTSEEECTTCCEEECC
T ss_pred             CEEECCCCc-cccccHhhhhhcccCcEEEcc
Confidence            888888887 4488888888887 8877654

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.28  E-value=2.5e-11  Score=112.51  Aligned_cols=139  Identities=19%  Similarity=0.203  Sum_probs=91.6

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .++.+.+..+....++     .+..+++|+.|++++|.++..    +. +..+++|+.|+++       ++.+..+|...
T Consensus        42 ~L~~L~l~~n~i~~l~-----~l~~l~~L~~L~L~~N~i~~~----~~-l~~l~~L~~L~L~-------~N~l~~l~~~~  104 (263)
T 1xeu_A           42 GVQNFNGDNSNIQSLA-----GMQFFTNLKELHLSHNQISDL----SP-LKDLTKLEELSVN-------RNRLKNLNGIP  104 (263)
T ss_dssp             TCSEEECTTSCCCCCT-----TGGGCTTCCEEECCSSCCCCC----GG-GTTCSSCCEEECC-------SSCCSCCTTCC
T ss_pred             cCcEEECcCCCcccch-----HHhhCCCCCEEECCCCccCCC----hh-hccCCCCCEEECC-------CCccCCcCccc
Confidence            4555555555555443     234677788888887776653    22 6777778888877       55566665433


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                       . ++|++|++++|. ++.++. ++.+++|+.|++++|. +..+| .+..+++|++|++++|... .+ ..+..+++|+.
T Consensus       105 -~-~~L~~L~L~~N~-l~~~~~-l~~l~~L~~L~Ls~N~-i~~~~-~l~~l~~L~~L~L~~N~i~-~~-~~l~~l~~L~~  176 (263)
T 1xeu_A          105 -S-ACLSRLFLDNNE-LRDTDS-LIHLKNLEILSIRNNK-LKSIV-MLGFLSKLEVLDLHGNEIT-NT-GGLTRLKKVNW  176 (263)
T ss_dssp             -C-SSCCEEECCSSC-CSBSGG-GTTCTTCCEEECTTSC-CCBCG-GGGGCTTCCEEECTTSCCC-BC-TTSTTCCCCCE
T ss_pred             -c-CcccEEEccCCc-cCCChh-hcCcccccEEECCCCc-CCCCh-HHccCCCCCEEECCCCcCc-ch-HHhccCCCCCE
Confidence             2 777777777777 666654 7777777777777777 66665 5677777777777777643 33 45666777776


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       177 L~l~  180 (263)
T 1xeu_A          177 IDLT  180 (263)
T ss_dssp             EEEE
T ss_pred             EeCC
Confidence            6654

>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=99.28  E-value=2.2e-11  Score=113.94  Aligned_cols=147  Identities=18%  Similarity=0.155  Sum_probs=103.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-cc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~  408 (505)
                      .+..+.+..+....++.   ..+.++++|++|++++|.+...   .+..+..+++|++|+++       ++.+..++ ..
T Consensus        29 ~l~~L~ls~n~l~~~~~---~~~~~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~   95 (276)
T 2z62_A           29 STKNLDLSFNPLRHLGS---YSFFSFPELQVLDLSRCEIQTI---EDGAYQSLSHLSTLILT-------GNPIQSLALGA   95 (276)
T ss_dssp             TCCEEECTTCCCCEECT---TTTTTCTTCSEEECTTCCCCEE---CTTTTTTCTTCCEEECT-------TCCCCEECTTT
T ss_pred             CccEEECCCCcccccCH---hHhccccCCcEEECCCCcCCcc---CHHHccCCcCCCEEECC-------CCccCccChhh
Confidence            56777776666655443   2445788888888888877643   44457778888888887       55555544 55


Q ss_pred             ccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccc--cchhccccccCceeecCCCcccccccccccCCc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRE--LPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~--lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      +..+++|++|++++|. +..++. .++.+++|+.|++++|. +..  +|..+..+++|++|++++|......+..+..+.
T Consensus        96 ~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~l~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~  173 (276)
T 2z62_A           96 FSGLSSLQKLVAVETN-LASLENFPIGHLKTLKELNVAHNL-IQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLH  173 (276)
T ss_dssp             TTTCTTCCEEECTTSC-CCCSTTCCCTTCTTCCEEECCSSC-CCCCCCCGGGGGCTTCCEEECCSSCCCEECGGGGHHHH
T ss_pred             hcCCccccEEECCCCC-ccccCchhcccCCCCCEEECcCCc-cceecCchhhccCCCCCEEECCCCCCCcCCHHHhhhhh
Confidence            7788888888888887 555544 57788888888888887 443  677788888888888888875444445566666


Q ss_pred             cCCccc
Q 046115          486 RLRRVR  491 (505)
Q Consensus       486 ~L~~L~  491 (505)
                      +|+.+.
T Consensus       174 ~L~~l~  179 (276)
T 2z62_A          174 QMPLLN  179 (276)
T ss_dssp             TCTTCC
T ss_pred             hccccc
Confidence            666443

>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=99.28  E-value=2.7e-11  Score=115.23  Aligned_cols=140  Identities=23%  Similarity=0.339  Sum_probs=93.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++     .+..+++|+.|++++|.++..    +. +..+++|+.|+++       ++.+..++. +
T Consensus        86 ~L~~L~L~~n~l~~~~-----~~~~l~~L~~L~l~~n~l~~~----~~-l~~l~~L~~L~l~-------~n~l~~~~~-l  147 (308)
T 1h6u_A           86 KITELELSGNPLKNVS-----AIAGLQSIKTLDLTSTQITDV----TP-LAGLSNLQVLYLD-------LNQITNISP-L  147 (308)
T ss_dssp             SCCEEECCSCCCSCCG-----GGTTCTTCCEEECTTSCCCCC----GG-GTTCTTCCEEECC-------SSCCCCCGG-G
T ss_pred             CCCEEEccCCcCCCch-----hhcCCCCCCEEECCCCCCCCc----hh-hcCCCCCCEEECC-------CCccCcCcc-c
Confidence            4555555555544332     244666777777777766542    22 6667777777776       555555554 6


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|. +..++. +..+++|+.|++++|. +..+|+ +..+++|++|++++|. +..++ .+..+++|+.
T Consensus       148 ~~l~~L~~L~l~~n~-l~~~~~-l~~l~~L~~L~l~~n~-l~~~~~-l~~l~~L~~L~L~~N~-l~~~~-~l~~l~~L~~  221 (308)
T 1h6u_A          148 AGLTNLQYLSIGNAQ-VSDLTP-LANLSKLTTLKADDNK-ISDISP-LASLPNLIEVHLKNNQ-ISDVS-PLANTSNLFI  221 (308)
T ss_dssp             GGCTTCCEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCCCGG-GGGCTTCCEEECTTSC-CCBCG-GGTTCTTCCE
T ss_pred             cCCCCccEEEccCCc-CCCChh-hcCCCCCCEEECCCCc-cCcChh-hcCCCCCCEEEccCCc-cCccc-cccCCCCCCE
Confidence            777788888888777 666666 7778888888888877 666664 6777888888888887 34454 3777777777


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       222 L~l~  225 (308)
T 1h6u_A          222 VTLT  225 (308)
T ss_dssp             EEEE
T ss_pred             EEcc
Confidence            7654

>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=99.27  E-value=3.8e-11  Score=113.00  Aligned_cols=146  Identities=25%  Similarity=0.326  Sum_probs=120.9

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-c
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-T  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~  407 (505)
                      ..+..+.+..+....++..     ..+++|++|++++|.+..    +|..+..+.+|++|+++       ++.+..+| .
T Consensus        55 ~~L~~L~L~~n~l~~~~~~-----~~l~~L~~L~Ls~N~l~~----l~~~~~~l~~L~~L~l~-------~N~l~~l~~~  118 (290)
T 1p9a_G           55 TRLTQLNLDRAELTKLQVD-----GTLPVLGTLDLSHNQLQS----LPLLGQTLPALTVLDVS-------FNRLTSLPLG  118 (290)
T ss_dssp             TTCCEEECTTSCCCEEECC-----SCCTTCCEEECCSSCCSS----CCCCTTTCTTCCEEECC-------SSCCCCCCSS
T ss_pred             CCCCEEECCCCccCcccCC-----CCCCcCCEEECCCCcCCc----CchhhccCCCCCEEECC-------CCcCcccCHH
Confidence            3677777777776665543     478999999999999874    56667889999999999       77777776 4


Q ss_pred             cccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      .+..+++|++|++++|. ++.+|.. +..+++|+.|++++|. +..+|.. +..+++|++|++++|. +..+|..+..+.
T Consensus       119 ~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~~l~~L~~L~L~~N~-l~~ip~~~~~~~  195 (290)
T 1p9a_G          119 ALRGLGELQELYLKGNE-LKTLPPGLLTPTPKLEKLSLANNN-LTELPAGLLNGLENLDTLLLQENS-LYTIPKGFFGSH  195 (290)
T ss_dssp             TTTTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECTTSC-CSCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTC
T ss_pred             HHcCCCCCCEEECCCCC-CCccChhhcccccCCCEEECCCCc-CCccCHHHhcCcCCCCEEECCCCc-CCccChhhcccc
Confidence            58899999999999999 7777664 5789999999999999 7888876 5789999999999998 568999988888


Q ss_pred             cCCcccee
Q 046115          486 RLRRVREF  493 (505)
Q Consensus       486 ~L~~L~~~  493 (505)
                      +|+.|.+.
T Consensus       196 ~L~~l~L~  203 (290)
T 1p9a_G          196 LLPFAFLH  203 (290)
T ss_dssp             CCSEEECC
T ss_pred             cCCeEEeC
Confidence            88877654

>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=99.27  E-value=1.9e-11  Score=123.00  Aligned_cols=148  Identities=22%  Similarity=0.237  Sum_probs=67.6

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-c
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-N  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~  408 (505)
                      .+..+.+..+....++..   .+..+++|+.|++++|.+...   .+..+..+++|+.|+++      +++.++.+|. .
T Consensus       124 ~L~~L~L~~n~l~~~~~~---~~~~l~~L~~L~L~~N~l~~~---~~~~~~~l~~L~~L~l~------~~~~l~~i~~~~  191 (452)
T 3zyi_A          124 SLNTLELFDNWLTVIPSG---AFEYLSKLRELWLRNNPIESI---PSYAFNRVPSLMRLDLG------ELKKLEYISEGA  191 (452)
T ss_dssp             TCCEEECCSSCCSBCCTT---TSSSCTTCCEEECCSCCCCEE---CTTTTTTCTTCCEEECC------CCTTCCEECTTT
T ss_pred             cCCEEECCCCcCCccChh---hhcccCCCCEEECCCCCccee---CHhHHhcCCcccEEeCC------CCCCccccChhh
Confidence            344444444443333322   233555666666666655432   22234444555555554      2233333332 2


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      +..+++|++|++++|. +..+|. +..+++|+.|+|++|......|..+..+++|++|++++|......|..|.++++|+
T Consensus       192 ~~~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  269 (452)
T 3zyi_A          192 FEGLFNLKYLNLGMCN-IKDMPN-LTPLVGLEELEMSGNHFPEIRPGSFHGLSSLKKLWVMNSQVSLIERNAFDGLASLV  269 (452)
T ss_dssp             TTTCTTCCEEECTTSC-CSSCCC-CTTCTTCCEEECTTSCCSEECGGGGTTCTTCCEEECTTSCCCEECTTTTTTCTTCC
T ss_pred             ccCCCCCCEEECCCCc-cccccc-ccccccccEEECcCCcCcccCcccccCccCCCEEEeCCCcCceECHHHhcCCCCCC
Confidence            4455555555555555 444443 44555555555555552222233445555555555555543333333444444444


Q ss_pred             ccc
Q 046115          489 RVR  491 (505)
Q Consensus       489 ~L~  491 (505)
                      .|+
T Consensus       270 ~L~  272 (452)
T 3zyi_A          270 ELN  272 (452)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            443

>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=99.26  E-value=2.9e-11  Score=113.93  Aligned_cols=140  Identities=21%  Similarity=0.281  Sum_probs=113.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      +++.+.+..+....++     .+..+++|++|++++|.++..    +. +..+++|++|+++       ++.+..+|. +
T Consensus        47 ~L~~L~l~~~~i~~~~-----~~~~l~~L~~L~L~~n~l~~~----~~-l~~l~~L~~L~l~-------~n~l~~~~~-l  108 (291)
T 1h6t_A           47 SIDQIIANNSDIKSVQ-----GIQYLPNVTKLFLNGNKLTDI----KP-LANLKNLGWLFLD-------ENKVKDLSS-L  108 (291)
T ss_dssp             TCCEEECTTSCCCCCT-----TGGGCTTCCEEECCSSCCCCC----GG-GTTCTTCCEEECC-------SSCCCCGGG-G
T ss_pred             cccEEEccCCCcccCh-----hHhcCCCCCEEEccCCccCCC----cc-cccCCCCCEEECC-------CCcCCCChh-h
Confidence            5666666666655543     245789999999999998764    33 8899999999998       666777665 8


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|. +..++. +..+++|+.|++++|. +..+ +.+..+++|++|++++|.. ..++. +..+++|+.
T Consensus       109 ~~l~~L~~L~L~~n~-i~~~~~-l~~l~~L~~L~l~~n~-l~~~-~~l~~l~~L~~L~L~~N~l-~~~~~-l~~l~~L~~  182 (291)
T 1h6t_A          109 KDLKKLKSLSLEHNG-ISDING-LVHLPQLESLYLGNNK-ITDI-TVLSRLTKLDTLSLEDNQI-SDIVP-LAGLTKLQN  182 (291)
T ss_dssp             TTCTTCCEEECTTSC-CCCCGG-GGGCTTCCEEECCSSC-CCCC-GGGGGCTTCSEEECCSSCC-CCCGG-GTTCTTCCE
T ss_pred             ccCCCCCEEECCCCc-CCCChh-hcCCCCCCEEEccCCc-CCcc-hhhccCCCCCEEEccCCcc-ccchh-hcCCCccCE
Confidence            999999999999999 777765 9999999999999998 7777 5789999999999999984 45554 888888888


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++-
T Consensus       183 L~L~  186 (291)
T 1h6t_A          183 LYLS  186 (291)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            7754

>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=99.26  E-value=2.9e-11  Score=114.98  Aligned_cols=141  Identities=20%  Similarity=0.312  Sum_probs=112.2

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      ..++.+.+..+....++.     +..+++|+.|++++|.+...    + .+..+.+|+.|+++       ++.+..+|. 
T Consensus        63 ~~L~~L~L~~n~i~~~~~-----~~~l~~L~~L~L~~n~l~~~----~-~~~~l~~L~~L~l~-------~n~l~~~~~-  124 (308)
T 1h6u_A           63 NNLIGLELKDNQITDLAP-----LKNLTKITELELSGNPLKNV----S-AIAGLQSIKTLDLT-------STQITDVTP-  124 (308)
T ss_dssp             TTCCEEECCSSCCCCCGG-----GTTCCSCCEEECCSCCCSCC----G-GGTTCTTCCEEECT-------TSCCCCCGG-
T ss_pred             CCCCEEEccCCcCCCChh-----HccCCCCCEEEccCCcCCCc----h-hhcCCCCCCEEECC-------CCCCCCchh-
Confidence            367788887777665554     45889999999999987753    3 37888999999998       666777665 


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      +..+++|++|++++|. ++.++. ++.+++|+.|++++|. +..+|. +..+++|++|++++|. +..+|. +..+++|+
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~  198 (308)
T 1h6u_A          125 LAGLSNLQVLYLDLNQ-ITNISP-LAGLTNLQYLSIGNAQ-VSDLTP-LANLSKLTTLKADDNK-ISDISP-LASLPNLI  198 (308)
T ss_dssp             GTTCTTCCEEECCSSC-CCCCGG-GGGCTTCCEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCCCGG-GGGCTTCC
T ss_pred             hcCCCCCCEEECCCCc-cCcCcc-ccCCCCccEEEccCCc-CCCChh-hcCCCCCCEEECCCCc-cCcChh-hcCCCCCC
Confidence            8889999999999998 777777 8899999999999998 777776 8889999999999997 445554 77777777


Q ss_pred             cccee
Q 046115          489 RVREF  493 (505)
Q Consensus       489 ~L~~~  493 (505)
                      .|++.
T Consensus       199 ~L~L~  203 (308)
T 1h6u_A          199 EVHLK  203 (308)
T ss_dssp             EEECT
T ss_pred             EEEcc
Confidence            77653

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.26  E-value=3.5e-11  Score=112.30  Aligned_cols=145  Identities=26%  Similarity=0.345  Sum_probs=114.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .+..+.+..+....++     .+..+++|++|++.+|.+.+.    + .+..+++|++|+++       ++.+..+|+. 
T Consensus        42 ~L~~L~l~~~~i~~~~-----~l~~l~~L~~L~l~~n~l~~~----~-~l~~l~~L~~L~L~-------~n~l~~~~~~~  104 (272)
T 3rfs_A           42 SIDQIIANNSDIKSVQ-----GIQYLPNVRYLALGGNKLHDI----S-ALKELTNLTYLILT-------GNQLQSLPNGV  104 (272)
T ss_dssp             TCCEEECTTSCCCCCT-----TGGGCTTCCEEECTTSCCCCC----G-GGTTCTTCCEEECT-------TSCCCCCCTTT
T ss_pred             ceeeeeeCCCCccccc-----ccccCCCCcEEECCCCCCCCc----h-hhcCCCCCCEEECC-------CCccCccChhH
Confidence            5566666665554433     345799999999999998753    3 47889999999999       6666666654 


Q ss_pred             ccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      ++.+++|++|++++|. +..+|.. ++.+++|+.|++++|. +..+|+. ++.+++|++|++++|...+..|..+..+++
T Consensus       105 ~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~  182 (272)
T 3rfs_A          105 FDKLTNLKELVLVENQ-LQSLPDGVFDKLTNLTYLNLAHNQ-LQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQ  182 (272)
T ss_dssp             TTTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTT
T ss_pred             hcCCcCCCEEECCCCc-CCccCHHHhccCCCCCEEECCCCc-cCccCHHHhccCccCCEEECCCCCcCccCHHHhcCCcc
Confidence            6899999999999999 6666654 6899999999999998 6777765 689999999999999855443444688899


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       183 L~~L~L~  189 (272)
T 3rfs_A          183 LKDLRLY  189 (272)
T ss_dssp             CCEEECC
T ss_pred             CCEEECC
Confidence            9888765

>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=99.26  E-value=1.1e-11  Score=117.76  Aligned_cols=149  Identities=19%  Similarity=0.252  Sum_probs=108.6

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc--cCc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE--IPT  407 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~--~p~  407 (505)
                      .+..+.+..+....++.  ...+..+++|++|++.+|.+...   .+..+..+++|+.|+++       ++.+..  .|.
T Consensus       102 ~L~~L~l~~n~l~~~~~--~~~~~~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~  169 (306)
T 2z66_A          102 QLEHLDFQHSNLKQMSE--FSVFLSLRNLIYLDISHTHTRVA---FNGIFNGLSSLEVLKMA-------GNSFQENFLPD  169 (306)
T ss_dssp             TCCEEECTTSEEESSTT--TTTTTTCTTCCEEECTTSCCEEC---STTTTTTCTTCCEEECT-------TCEEGGGEECS
T ss_pred             CCCEEECCCCccccccc--chhhhhccCCCEEECCCCcCCcc---chhhcccCcCCCEEECC-------CCccccccchh
Confidence            44555544444333322  13455788888888888876543   56667788889999888       555543  677


Q ss_pred             cccCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccccccCCc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      .+..+++|++|++++|. +..+ |..+..+++|+.|++++|. +..+|. .+..+++|++|++++|...+..|..+..++
T Consensus       170 ~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~  247 (306)
T 2z66_A          170 IFTELRNLTFLDLSQCQ-LEQLSPTAFNSLSSLQVLNMSHNN-FFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFP  247 (306)
T ss_dssp             CCTTCTTCCEEECTTSC-CCEECTTTTTTCTTCCEEECTTSC-CSBCCSGGGTTCTTCCEEECTTSCCCBCSSSSCCCCC
T ss_pred             HHhhCcCCCEEECCCCC-cCCcCHHHhcCCCCCCEEECCCCc-cCccChhhccCcccCCEeECCCCCCcccCHHHHHhhh
Confidence            88889999999999998 5544 6678889999999999988 555554 678889999999999987777777787774


Q ss_pred             -cCCccce
Q 046115          486 -RLRRVRE  492 (505)
Q Consensus       486 -~L~~L~~  492 (505)
                       +|+.|++
T Consensus       248 ~~L~~L~L  255 (306)
T 2z66_A          248 SSLAFLNL  255 (306)
T ss_dssp             TTCCEEEC
T ss_pred             ccCCEEEc
Confidence             7777765

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.26  E-value=2.4e-11  Score=121.80  Aligned_cols=128  Identities=21%  Similarity=0.260  Sum_probs=72.0

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceeeccCCccccccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp~~  432 (505)
                      .+++|+.|++++|.+...   .+..+..+.+|+.|+++      +++.+..++. .+..+++|++|++++|. ++.+|. 
T Consensus       134 ~l~~L~~L~L~~N~i~~~---~~~~~~~l~~L~~L~l~------~~~~l~~i~~~~~~~l~~L~~L~L~~n~-l~~~~~-  202 (440)
T 3zyj_A          134 YLSKLKELWLRNNPIESI---PSYAFNRIPSLRRLDLG------ELKRLSYISEGAFEGLSNLRYLNLAMCN-LREIPN-  202 (440)
T ss_dssp             SCSSCCEEECCSCCCCEE---CTTTTTTCTTCCEEECC------CCTTCCEECTTTTTTCSSCCEEECTTSC-CSSCCC-
T ss_pred             ccccCceeeCCCCccccc---CHHHhhhCcccCEeCCC------CCCCcceeCcchhhcccccCeecCCCCc-Cccccc-
Confidence            444455555544444322   22234445555555554      2233444433 35566666666666666 566664 


Q ss_pred             hhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       433 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      +..+++|+.|+|++|......|..+..+++|++|++++|......|..|.++++|+.|++
T Consensus       203 ~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L  262 (440)
T 3zyj_A          203 LTPLIKLDELDLSGNHLSAIRPGSFQGLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINL  262 (440)
T ss_dssp             CTTCSSCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCEECTTSSTTCTTCCEEEC
T ss_pred             cCCCcccCEEECCCCccCccChhhhccCccCCEEECCCCceeEEChhhhcCCCCCCEEEC
Confidence            666667777777776633333555677777777777777655444555666666666654

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.25  E-value=8.9e-12  Score=132.27  Aligned_cols=121  Identities=21%  Similarity=0.258  Sum_probs=95.9

Q ss_pred             cCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCcccccc
Q 046115          350 GNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL  429 (505)
Q Consensus       350 ~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~l  429 (505)
                      ..+..+..|+.|+|++|.+..    +|..+..+.+|++|+|+       ++.+..+|..++.|++|++|+|++|. ++.+
T Consensus       218 ~~~~~l~~L~~L~Ls~n~l~~----l~~~~~~l~~L~~L~Ls-------~N~l~~lp~~~~~l~~L~~L~Ls~N~-l~~l  285 (727)
T 4b8c_D          218 DSKYDDQLWHALDLSNLQIFN----ISANIFKYDFLTRLYLN-------GNSLTELPAEIKNLSNLRVLDLSHNR-LTSL  285 (727)
T ss_dssp             ----CCCCCCEEECTTSCCSC----CCGGGGGCCSCSCCBCT-------TSCCSCCCGGGGGGTTCCEEECTTSC-CSSC
T ss_pred             hhhccCCCCcEEECCCCCCCC----CChhhcCCCCCCEEEee-------CCcCcccChhhhCCCCCCEEeCcCCc-CCcc
Confidence            345578888899998888763    45556688889999988       66677888888888999999999888 6688


Q ss_pred             chhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccC
Q 046115          430 PETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGE  483 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~  483 (505)
                      |..++.|++|+.|+|++|. +..+|..++.+++|++|++++|.+.+..|..+..
T Consensus       286 p~~~~~l~~L~~L~L~~N~-l~~lp~~~~~l~~L~~L~L~~N~l~~~~p~~~~~  338 (727)
T 4b8c_D          286 PAELGSCFQLKYFYFFDNM-VTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTE  338 (727)
T ss_dssp             CSSGGGGTTCSEEECCSSC-CCCCCSSTTSCTTCCCEECTTSCCCSHHHHHHHH
T ss_pred             ChhhcCCCCCCEEECCCCC-CCccChhhhcCCCccEEeCCCCccCCCChHHHhh
Confidence            8888888999999999887 7788888888889999999988876666665543

>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=99.25  E-value=5e-11  Score=107.33  Aligned_cols=145  Identities=17%  Similarity=0.179  Sum_probs=114.2

Q ss_pred             EEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccC
Q 046115          333 HLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEK  411 (505)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~  411 (505)
                      .+....+....+|..++      ..++.|.+++|.++...  .+..+..+++|++|+|+       ++.+..+++ .+..
T Consensus        15 ~l~~s~n~l~~iP~~~~------~~~~~L~L~~N~l~~~~--~~~~~~~l~~L~~L~L~-------~N~i~~i~~~~~~~   79 (220)
T 2v70_A           15 TVDCSNQKLNKIPEHIP------QYTAELRLNNNEFTVLE--ATGIFKKLPQLRKINFS-------NNKITDIEEGAFEG   79 (220)
T ss_dssp             EEECCSSCCSSCCSCCC------TTCSEEECCSSCCCEEC--CCCCGGGCTTCCEEECC-------SSCCCEECTTTTTT
T ss_pred             EeEeCCCCcccCccCCC------CCCCEEEcCCCcCCccC--chhhhccCCCCCEEECC-------CCcCCEECHHHhCC
Confidence            45555566666665443      45789999999987641  22347889999999998       666777655 6899


Q ss_pred             CCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCcc
Q 046115          412 LLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRV  490 (505)
Q Consensus       412 l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L  490 (505)
                      +++|++|+|++|. +..+|. .+..+++|++|+|++|......|..+..+++|++|++++|...+..|..|..+++|+.|
T Consensus        80 l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L  158 (220)
T 2v70_A           80 ASGVNEILLTSNR-LENVQHKMFKGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYDNQITTVAPGAFDTLHSLSTL  158 (220)
T ss_dssp             CTTCCEEECCSSC-CCCCCGGGGTTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTTSCCCCBCTTTTTTCTTCCEE
T ss_pred             CCCCCEEECCCCc-cCccCHhHhcCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCCCcCCEECHHHhcCCCCCCEE
Confidence            9999999999999 666654 58899999999999999444446779999999999999998666557889999999888


Q ss_pred             cee
Q 046115          491 REF  493 (505)
Q Consensus       491 ~~~  493 (505)
                      ++.
T Consensus       159 ~L~  161 (220)
T 2v70_A          159 NLL  161 (220)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            753

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.25  E-value=3e-11  Score=121.10  Aligned_cols=149  Identities=23%  Similarity=0.278  Sum_probs=106.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      ++..+.+..+....++.   ..|..+++|+.|++.+|....  ...+..+..+.+|+.|+|+       ++.+..+|. +
T Consensus       137 ~L~~L~L~~N~i~~~~~---~~~~~l~~L~~L~l~~~~~l~--~i~~~~~~~l~~L~~L~L~-------~n~l~~~~~-~  203 (440)
T 3zyj_A          137 KLKELWLRNNPIESIPS---YAFNRIPSLRRLDLGELKRLS--YISEGAFEGLSNLRYLNLA-------MCNLREIPN-L  203 (440)
T ss_dssp             SCCEEECCSCCCCEECT---TTTTTCTTCCEEECCCCTTCC--EECTTTTTTCSSCCEEECT-------TSCCSSCCC-C
T ss_pred             cCceeeCCCCcccccCH---HHhhhCcccCEeCCCCCCCcc--eeCcchhhcccccCeecCC-------CCcCccccc-c
Confidence            56666666666554443   245578889999988854322  1134457788889999998       666777774 7


Q ss_pred             cCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccc-ccccCCccC
Q 046115          410 EKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRL  487 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L  487 (505)
                      ..+++|++|+|++|. +..+ |..+..+++|+.|++++|......|..+..+++|++|++++|.+. .+| ..+..+++|
T Consensus       204 ~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~-~~~~~~~~~l~~L  281 (440)
T 3zyj_A          204 TPLIKLDELDLSGNH-LSAIRPGSFQGLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHNNLT-LLPHDLFTPLHHL  281 (440)
T ss_dssp             TTCSSCCEEECTTSC-CCEECTTTTTTCTTCCEEECTTCCCCEECTTSSTTCTTCCEEECTTSCCC-CCCTTTTSSCTTC
T ss_pred             CCCcccCEEECCCCc-cCccChhhhccCccCCEEECCCCceeEEChhhhcCCCCCCEEECCCCCCC-ccChhHhccccCC
Confidence            888889999999888 5444 667888899999999998843344556888889999999988744 444 446778888


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      +.|++.
T Consensus       282 ~~L~L~  287 (440)
T 3zyj_A          282 ERIHLH  287 (440)
T ss_dssp             CEEECC
T ss_pred             CEEEcC
Confidence            777653

>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=99.24  E-value=3e-11  Score=126.31  Aligned_cols=146  Identities=18%  Similarity=0.115  Sum_probs=116.3

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Cc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PT  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~  407 (505)
                      ..++.+.+..+....++.   ..|.++++|++|++++|.++..   .|..|..+++|++|+|+       ++.+..+ |.
T Consensus        32 ~~l~~L~Ls~n~l~~~~~---~~~~~l~~L~~L~Ls~n~l~~i---~~~~~~~l~~L~~L~Ls-------~n~l~~~~p~   98 (606)
T 3vq2_A           32 SSTKNIDLSFNPLKILKS---YSFSNFSELQWLDLSRCEIETI---EDKAWHGLHHLSNLILT-------GNPIQSFSPG   98 (606)
T ss_dssp             TTCCEEECTTSCCCEECT---TTTTTCTTCCEEECTTCCCCEE---CTTTTTTCTTCCEEECT-------TCCCCCCCTT
T ss_pred             CCcCEEECCCCCcCEeCh---hhccCCccCcEEeCCCCccccc---CHHHhhchhhcCEeECC-------CCcccccChh
Confidence            477888888777665543   3456899999999999987654   56678899999999998       5556555 77


Q ss_pred             cccCCCCcceeeccCCccccccc-hhhhcCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCcccccccccccCCc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      .++.+++|++|++++|. +..+| ..++.+++|++|++++|.... .+|..++++++|++|++++|...+..|..++.+.
T Consensus        99 ~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~  177 (606)
T 3vq2_A           99 SFSGLTSLENLVAVETK-LASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLR  177 (606)
T ss_dssp             SSTTCTTCCEEECTTSC-CCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCSSCCCEECTTTTHHHH
T ss_pred             hcCCcccCCEEEccCCc-cccccccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccCCcceecChhhhhhhh
Confidence            89999999999999999 66555 568999999999999998433 5788999999999999999986665566677666


Q ss_pred             cCC
Q 046115          486 RLR  488 (505)
Q Consensus       486 ~L~  488 (505)
                      +|+
T Consensus       178 ~L~  180 (606)
T 3vq2_A          178 ENP  180 (606)
T ss_dssp             HCT
T ss_pred             ccc
Confidence            665

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.24  E-value=7.4e-12  Score=132.86  Aligned_cols=137  Identities=20%  Similarity=0.234  Sum_probs=92.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++..+.    .+++|++|+|++|.++.    +|..+..+.+|++|+|+       ++.+..+|..+
T Consensus       225 ~L~~L~Ls~n~l~~l~~~~~----~l~~L~~L~Ls~N~l~~----lp~~~~~l~~L~~L~Ls-------~N~l~~lp~~~  289 (727)
T 4b8c_D          225 LWHALDLSNLQIFNISANIF----KYDFLTRLYLNGNSLTE----LPAEIKNLSNLRVLDLS-------HNRLTSLPAEL  289 (727)
T ss_dssp             CCCEEECTTSCCSCCCGGGG----GCCSCSCCBCTTSCCSC----CCGGGGGGTTCCEEECT-------TSCCSSCCSSG
T ss_pred             CCcEEECCCCCCCCCChhhc----CCCCCCEEEeeCCcCcc----cChhhhCCCCCCEEeCc-------CCcCCccChhh
Confidence            45666666666665555444    67788888888887662    56667778888888887       55566777777


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccc-cCceeecCCCccccccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLR-KLMYLHNEDTGCLRYLPAGIG  482 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~-~L~~L~l~~~~~~~~~p~~i~  482 (505)
                      +.|++|++|+|++|. ++.+|..|+.+++|+.|+|++|.....+|..+..+. .+..|++++|...+.+|..+.
T Consensus       290 ~~l~~L~~L~L~~N~-l~~lp~~~~~l~~L~~L~L~~N~l~~~~p~~~~~~~~~~~~l~l~~N~l~~~~p~~l~  362 (727)
T 4b8c_D          290 GSCFQLKYFYFFDNM-VTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERR  362 (727)
T ss_dssp             GGGTTCSEEECCSSC-CCCCCSSTTSCTTCCCEECTTSCCCSHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC--
T ss_pred             cCCCCCCEEECCCCC-CCccChhhhcCCCccEEeCCCCccCCCChHHHhhcchhhhHHhhccCcccCcCccccc
Confidence            788888888888777 677777777888888888888775455565554432 223456777776666666543

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.24  E-value=2.3e-11  Score=123.31  Aligned_cols=147  Identities=14%  Similarity=0.083  Sum_probs=84.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhh-cCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFE-KLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~-~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .+..+.+..+....++   +..+..+++|+.|++++|.+++.   .|..+. .+++|+.|+|+       ++.+..+|. 
T Consensus       121 ~L~~L~L~~N~l~~~~---~~~~~~l~~L~~L~Ls~N~l~~~---~~~~l~~~l~~L~~L~Ls-------~N~l~~~~~-  186 (487)
T 3oja_A          121 GKKNIYLANNKITMLR---DLDEGCRSRVQYLDLKLNEIDTV---NFAELAASSDTLEHLNLQ-------YNFIYDVKG-  186 (487)
T ss_dssp             SCEEEECCSSCCCSGG---GBCGGGGSSEEEEECTTSCCCEE---EGGGGGGGTTTCCEEECT-------TSCCCEEEC-
T ss_pred             CCCEEECCCCCCCCCC---chhhcCCCCCCEEECCCCCCCCc---ChHHHhhhCCcccEEecC-------CCccccccc-
Confidence            3455555544443332   22334566666666666666543   333333 56666666666       444444443 


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccc-ccccccccCCccC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCL-RYLPAGIGELIRL  487 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~-~~~p~~i~~l~~L  487 (505)
                      ...+++|++|+|++|. ++.+|+.+..+++|+.|++++|. +..+|..+..+++|+.|++++|... +.+|..+..++.|
T Consensus       187 ~~~l~~L~~L~Ls~N~-l~~~~~~~~~l~~L~~L~Ls~N~-l~~lp~~l~~l~~L~~L~l~~N~l~c~~~~~~~~~l~~L  264 (487)
T 3oja_A          187 QVVFAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRV  264 (487)
T ss_dssp             CCCCTTCCEEECCSSC-CCEECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTCCEEECTTCCBCHHHHHHHHTTCHHH
T ss_pred             cccCCCCCEEECCCCC-CCCCCHhHcCCCCccEEEecCCc-CcccchhhccCCCCCEEEcCCCCCcCcchHHHHHhCCCC
Confidence            3346667777777666 55566556666677777777766 5566666666667777777766644 3445555666655


Q ss_pred             Cccce
Q 046115          488 RRVRE  492 (505)
Q Consensus       488 ~~L~~  492 (505)
                      +.+..
T Consensus       265 ~~l~~  269 (487)
T 3oja_A          265 QTVAK  269 (487)
T ss_dssp             HHHHH
T ss_pred             cEEec
Confidence            55543

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.23  E-value=8.1e-11  Score=105.04  Aligned_cols=126  Identities=26%  Similarity=0.372  Sum_probs=98.6

Q ss_pred             CCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-ccCCCCcceeeccCCccccccchh-
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIEKLPET-  432 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-~~~l~~L~~L~l~~~~~~~~lp~~-  432 (505)
                      .++|+.|++++|.++..   .+..+..+++|++|+++       ++.+..+|.. +..+++|++|++++|. ++.+|.. 
T Consensus        27 ~~~l~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~   95 (208)
T 2o6s_A           27 PAQTTYLDLETNSLKSL---PNGVFDELTSLTQLYLG-------GNKLQSLPNGVFNKLTSLTYLNLSTNQ-LQSLPNGV   95 (208)
T ss_dssp             CTTCSEEECCSSCCCCC---CTTTTTTCTTCSEEECC-------SSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTT
T ss_pred             CCCCcEEEcCCCccCcC---ChhhhcccccCcEEECC-------CCccCccChhhcCCCCCcCEEECCCCc-CCccCHhH
Confidence            35899999999987654   45557788999999998       6666677654 5789999999999998 6677654 


Q ss_pred             hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccc-cccCCccCCcccee
Q 046115          433 LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVREF  493 (505)
Q Consensus       433 ~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~~  493 (505)
                      +..+++|+.|++++|. +..+|+. +..+++|++|++++|... .+|. .+..+++|+.|++.
T Consensus        96 ~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~l~-~~~~~~~~~l~~L~~L~l~  156 (208)
T 2o6s_A           96 FDKLTQLKELALNTNQ-LQSLPDGVFDKLTQLKDLRLYQNQLK-SVPDGVFDRLTSLQYIWLH  156 (208)
T ss_dssp             TTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCS-CCCTTTTTTCTTCCEEECC
T ss_pred             hcCccCCCEEEcCCCc-CcccCHhHhccCCcCCEEECCCCccc-eeCHHHhccCCCccEEEec
Confidence            5889999999999988 6667665 688999999999999754 4554 47788888877654

>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=99.23  E-value=5.2e-11  Score=119.77  Aligned_cols=148  Identities=24%  Similarity=0.308  Sum_probs=78.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .++.+.+..+....++.   ..|.++++|+.|++++|.++..   .+..+..+.+|++|+|+       ++.+..+|+. 
T Consensus        76 ~l~~L~L~~n~i~~~~~---~~~~~l~~L~~L~Ls~n~i~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~  142 (452)
T 3zyi_A           76 NTRYLNLMENNIQMIQA---DTFRHLHHLEVLQLGRNSIRQI---EVGAFNGLASLNTLELF-------DNWLTVIPSGA  142 (452)
T ss_dssp             TCSEEECCSSCCCEECT---TTTTTCTTCCEEECCSSCCCEE---CTTTTTTCTTCCEEECC-------SSCCSBCCTTT
T ss_pred             CccEEECcCCcCceECH---HHcCCCCCCCEEECCCCccCCc---ChhhccCcccCCEEECC-------CCcCCccChhh
Confidence            45555555555443322   2334566666666666655433   33445555666666665       3344444332 


Q ss_pred             ccCCCCcceeeccCCc------------------------cccccch-hhhcCCCCcEEecCCCcCccccchhccccccC
Q 046115          409 IEKLLHLKYLNLKGQK------------------------KIEKLPE-TLCELYNLERLNVDDCQNLRELPRGIGKLRKL  463 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~------------------------~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L  463 (505)
                      +..+++|++|++++|.                        .++.+|. .+..+++|+.|++++|. +..+| .+..+++|
T Consensus       143 ~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~-l~~~~-~~~~l~~L  220 (452)
T 3zyi_A          143 FEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCN-IKDMP-NLTPLVGL  220 (452)
T ss_dssp             SSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSC-CSSCC-CCTTCTTC
T ss_pred             hcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCc-ccccc-cccccccc
Confidence            4455555555555555                        3333333 24455555555555555 44444 35556666


Q ss_pred             ceeecCCCcccccccccccCCccCCccce
Q 046115          464 MYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       464 ~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      ++|++++|...+..|..|.++++|+.|++
T Consensus       221 ~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L  249 (452)
T 3zyi_A          221 EELEMSGNHFPEIRPGSFHGLSSLKKLWV  249 (452)
T ss_dssp             CEEECTTSCCSEECGGGGTTCTTCCEEEC
T ss_pred             cEEECcCCcCcccCcccccCccCCCEEEe
Confidence            66666666655444556666666666654

>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=99.23  E-value=1e-11  Score=128.31  Aligned_cols=150  Identities=21%  Similarity=0.314  Sum_probs=115.1

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      ..++.+.+..+....++   +..+.++++|++|++++|.++..   .|..+..+++|++|+|+       ++.+..+|+.
T Consensus        26 ~~L~~L~Ls~n~l~~~~---~~~~~~l~~L~~L~Ls~n~i~~~---~~~~~~~l~~L~~L~Ls-------~n~l~~~~~~   92 (549)
T 2z81_A           26 AAMKSLDLSFNKITYIG---HGDLRACANLQVLILKSSRINTI---EGDAFYSLGSLEHLDLS-------DNHLSSLSSS   92 (549)
T ss_dssp             TTCCEEECCSSCCCEEC---SSTTSSCTTCCEEECTTSCCCEE---CTTTTTTCTTCCEEECT-------TSCCCSCCHH
T ss_pred             CCccEEECcCCccCccC---hhhhhcCCcccEEECCCCCcCcc---ChhhccccccCCEEECC-------CCccCccCHH
Confidence            36777777777665443   33456889999999999987654   55668888999999998       6666666654


Q ss_pred             -ccCCCCcceeeccCCcccc--ccchhhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccccccCC
Q 046115          409 -IEKLLHLKYLNLKGQKKIE--KLPETLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPAGIGEL  484 (505)
Q Consensus       409 -~~~l~~L~~L~l~~~~~~~--~lp~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~~i~~l  484 (505)
                       ++.+++|++|++++|. +.  ..|..++.+++|++|++++|..+..+|. .+..+++|++|++++|...+..|..++.+
T Consensus        93 ~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l  171 (549)
T 2z81_A           93 WFGPLSSLKYLNLMGNP-YQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSI  171 (549)
T ss_dssp             HHTTCTTCCEEECTTCC-CSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTC
T ss_pred             HhccCCCCcEEECCCCc-ccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCeeeccCCcccccChhhhhcc
Confidence             8889999999999988 54  4566788889999999998886777764 68888899999999888777777777777


Q ss_pred             ccCCccce
Q 046115          485 IRLRRVRE  492 (505)
Q Consensus       485 ~~L~~L~~  492 (505)
                      ++|+.|++
T Consensus       172 ~~L~~L~l  179 (549)
T 2z81_A          172 RDIHHLTL  179 (549)
T ss_dssp             SEEEEEEE
T ss_pred             ccCceEec
Confidence            76666654

>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=99.22  E-value=8.4e-11  Score=105.86  Aligned_cols=140  Identities=21%  Similarity=0.281  Sum_probs=111.1

Q ss_pred             EEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCC
Q 046115          336 LTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLH  414 (505)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~  414 (505)
                      ...+....+|..++      ++|+.|.+.+|.++..   .+..+..+++|++|+|+       ++.+..+ |..+..+++
T Consensus        18 c~~~~l~~iP~~l~------~~l~~L~l~~n~i~~i---~~~~~~~l~~L~~L~Ls-------~N~i~~~~~~~~~~l~~   81 (220)
T 2v9t_B           18 CRGKGLTEIPTNLP------ETITEIRLEQNTIKVI---PPGAFSPYKKLRRIDLS-------NNQISELAPDAFQGLRS   81 (220)
T ss_dssp             CTTSCCSSCCSSCC------TTCCEEECCSSCCCEE---CTTSSTTCTTCCEEECC-------SSCCCEECTTTTTTCSS
T ss_pred             cCCCCcCcCCCccC------cCCCEEECCCCcCCCc---CHhHhhCCCCCCEEECC-------CCcCCCcCHHHhhCCcC
Confidence            33444555555432      6899999999998764   45568889999999999       5666655 778999999


Q ss_pred             cceeeccCCccccccchh-hhcCCCCcEEecCCCcCcccc-chhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          415 LKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLREL-PRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       415 L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      |++|+|++|. ++.+|.. +..+++|+.|+|++|. +..+ |..+..+++|++|++++|.+....+..|..+++|+.|++
T Consensus        82 L~~L~Ls~N~-l~~l~~~~f~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L  159 (220)
T 2v9t_B           82 LNSLVLYGNK-ITELPKSLFEGLFSLQLLLLNANK-INCLRVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQTMHL  159 (220)
T ss_dssp             CCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEEC
T ss_pred             CCEEECCCCc-CCccCHhHccCCCCCCEEECCCCC-CCEeCHHHcCCCCCCCEEECCCCcCCEECHHHHhCCCCCCEEEe
Confidence            9999999999 8888875 5889999999999999 5555 567899999999999999855444445888888888765


Q ss_pred             e
Q 046115          493 F  493 (505)
Q Consensus       493 ~  493 (505)
                      .
T Consensus       160 ~  160 (220)
T 2v9t_B          160 A  160 (220)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.22  E-value=3.7e-11  Score=114.82  Aligned_cols=148  Identities=14%  Similarity=0.079  Sum_probs=94.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHh-hcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLF-EKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~-~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .+..+.+..+....++.   ..+..+++|+.|++++|.++..   .+..+ ..+++|++|+++       ++.+..+|. 
T Consensus       121 ~L~~L~l~~N~l~~~~~---~~~~~l~~L~~L~Ls~N~l~~~---~~~~~~~~l~~L~~L~L~-------~N~l~~~~~-  186 (317)
T 3o53_A          121 GKKNIYLANNKITMLRD---LDEGCRSRVQYLDLKLNEIDTV---NFAELAASSDTLEHLNLQ-------YNFIYDVKG-  186 (317)
T ss_dssp             SCEEEECCSSCCCSGGG---BCTGGGSSEEEEECTTSCCCEE---EGGGGGGGTTTCCEEECT-------TSCCCEEEC-
T ss_pred             CCCEEECCCCCCCCccc---hhhhccCCCCEEECCCCCCCcc---cHHHHhhccCcCCEEECC-------CCcCccccc-
Confidence            45555555555444332   2334567777777777776543   22223 456777777776       555555543 


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccc-ccccccccCCccC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCL-RYLPAGIGELIRL  487 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~-~~~p~~i~~l~~L  487 (505)
                      ...+++|++|++++|. ++.+|..+..+++|+.|++++|. +..+|..+..+++|+.|++++|... +.+|..+..++.|
T Consensus       187 ~~~l~~L~~L~Ls~N~-l~~l~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~l~~L~~L~l~~N~~~~~~~~~~~~~~~~L  264 (317)
T 3o53_A          187 QVVFAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRV  264 (317)
T ss_dssp             CCCCTTCCEEECCSSC-CCEECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTCCEEECTTCCCBHHHHHHHHHTCHHH
T ss_pred             ccccccCCEEECCCCc-CCcchhhhcccCcccEEECcCCc-ccchhhHhhcCCCCCEEEccCCCccCcCHHHHHhccccc
Confidence            3347777777777777 66676667777777777777776 6677777777777777777777755 4555666667666


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      +.|++.
T Consensus       265 ~~l~l~  270 (317)
T 3o53_A          265 QTVAKQ  270 (317)
T ss_dssp             HHHHHH
T ss_pred             eEEECC
Confidence            666544

>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=99.21  E-value=4.4e-11  Score=121.21  Aligned_cols=148  Identities=26%  Similarity=0.274  Sum_probs=87.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-  408 (505)
                      .++.+.+..+....++.   ..|..+++|++|++++|.++..   .|..+..+.+|++|+|+       ++.+..+|.. 
T Consensus        33 ~l~~L~L~~n~l~~~~~---~~~~~l~~L~~L~L~~n~i~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~   99 (477)
T 2id5_A           33 ETRLLDLGKNRIKTLNQ---DEFASFPHLEELELNENIVSAV---EPGAFNNLFNLRTLGLR-------SNRLKLIPLGV   99 (477)
T ss_dssp             TCSEEECCSSCCCEECT---TTTTTCTTCCEEECTTSCCCEE---CTTTTTTCTTCCEEECC-------SSCCCSCCTTS
T ss_pred             CCcEEECCCCccceECH---hHccCCCCCCEEECCCCccCEe---ChhhhhCCccCCEEECC-------CCcCCccCccc
Confidence            56667766666554432   3445777788888877776543   45567777777777777       5555566543 


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccc-ccccCCccC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRL  487 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L  487 (505)
                      +..+++|++|++++|......|..+..+++|+.|++++|......|..+..+++|++|++++|... .+| ..+.++++|
T Consensus       100 ~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~-~~~~~~l~~l~~L  178 (477)
T 2id5_A          100 FTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCNLT-SIPTEALSHLHGL  178 (477)
T ss_dssp             STTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCEEEEESCCCS-SCCHHHHTTCTTC
T ss_pred             ccCCCCCCEEECCCCccccCChhHccccccCCEEECCCCccceeChhhccCCCCCCEEECCCCcCc-ccChhHhcccCCC
Confidence            566777777777777633333445666666666666666632333345566666666666666532 232 224444444


Q ss_pred             Cccc
Q 046115          488 RRVR  491 (505)
Q Consensus       488 ~~L~  491 (505)
                      +.|+
T Consensus       179 ~~L~  182 (477)
T 2id5_A          179 IVLR  182 (477)
T ss_dssp             CEEE
T ss_pred             cEEe
Confidence            4443

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.21  E-value=2.5e-11  Score=115.96  Aligned_cols=144  Identities=13%  Similarity=0.070  Sum_probs=116.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Ccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~  408 (505)
                      .+..+.+..+....++..      .+++|+.|++.+|.++..   .+..+..+++|++|+++       ++.+... |..
T Consensus       100 ~L~~L~l~~n~l~~~~~~------~~~~L~~L~l~~N~l~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~  163 (317)
T 3o53_A          100 SIETLHAANNNISRVSCS------RGQGKKNIYLANNKITML---RDLDEGCRSRVQYLDLK-------LNEIDTVNFAE  163 (317)
T ss_dssp             TCCEEECCSSCCSEEEEC------CCSSCEEEECCSSCCCSG---GGBCTGGGSSEEEEECT-------TSCCCEEEGGG
T ss_pred             CcCEEECCCCccCCcCcc------ccCCCCEEECCCCCCCCc---cchhhhccCCCCEEECC-------CCCCCcccHHH
Confidence            566777777666655432      467899999999998764   45567889999999999       5555554 444


Q ss_pred             c-cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccC
Q 046115          409 I-EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       409 ~-~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      + ..+++|++|++++|. ++.+|. ...+++|+.|++++|. +..+|+.+..+++|++|++++|. +..+|..+..+++|
T Consensus       164 ~~~~l~~L~~L~L~~N~-l~~~~~-~~~l~~L~~L~Ls~N~-l~~l~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~l~~L  239 (317)
T 3o53_A          164 LAASSDTLEHLNLQYNF-IYDVKG-QVVFAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNL  239 (317)
T ss_dssp             GGGGTTTCCEEECTTSC-CCEEEC-CCCCTTCCEEECCSSC-CCEECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTC
T ss_pred             HhhccCcCCEEECCCCc-Cccccc-ccccccCCEEECCCCc-CCcchhhhcccCcccEEECcCCc-ccchhhHhhcCCCC
Confidence            5 478999999999999 888876 5569999999999999 88898889999999999999998 55789889888888


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      +.|++.
T Consensus       240 ~~L~l~  245 (317)
T 3o53_A          240 EHFDLR  245 (317)
T ss_dssp             CEEECT
T ss_pred             CEEEcc
Confidence            887754

>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=99.21  E-value=6e-11  Score=121.61  Aligned_cols=149  Identities=17%  Similarity=0.287  Sum_probs=117.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~  408 (505)
                      .+..+.+..+....   ..+..+..+++|+.|++++|.++.... +|..+..+++|+.|+++       ++.+.. +|..
T Consensus       325 ~L~~L~Ls~n~l~~---~~~~~~~~l~~L~~L~L~~N~l~~l~~-~~~~~~~l~~L~~L~Ls-------~N~l~~~l~~~  393 (520)
T 2z7x_B          325 PFLHLDFSNNLLTD---TVFENCGHLTELETLILQMNQLKELSK-IAEMTTQMKSLQQLDIS-------QNSVSYDEKKG  393 (520)
T ss_dssp             CCCEEECCSSCCCT---TTTTTCCCCSSCCEEECCSSCCCBHHH-HHHHHTTCTTCCEEECC-------SSCCBCCGGGC
T ss_pred             cccEEEeECCccCh---hhhhhhccCCCCCEEEccCCccCcccc-chHHHhhCCCCCEEECC-------CCcCCcccccc
Confidence            55666666655443   234456689999999999999876422 66778999999999998       555555 7765


Q ss_pred             -ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccccc-ccCCcc
Q 046115          409 -IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG-IGELIR  486 (505)
Q Consensus       409 -~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~-i~~l~~  486 (505)
                       +..+++|++|++++|...+.+|..+.  ++|+.|++++|. +..+|..+..+++|++|++++|. +..+|.. +..+++
T Consensus       394 ~~~~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          394 DCSWTKSLLSLNMSSNILTDTIFRCLP--PRIKVLDLHSNK-IKSIPKQVVKLEALQELNVASNQ-LKSVPDGIFDRLTS  469 (520)
T ss_dssp             SCCCCTTCCEEECCSSCCCGGGGGSCC--TTCCEEECCSSC-CCCCCGGGGGCTTCCEEECCSSC-CCCCCTTTTTTCTT
T ss_pred             hhccCccCCEEECcCCCCCcchhhhhc--ccCCEEECCCCc-ccccchhhhcCCCCCEEECCCCc-CCccCHHHhccCCc
Confidence             77889999999999995566666543  789999999998 77999998899999999999998 5578876 888888


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       470 L~~L~l~  476 (520)
T 2z7x_B          470 LQKIWLH  476 (520)
T ss_dssp             CCEEECC
T ss_pred             ccEEECc
Confidence            8887754

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.21  E-value=8.1e-11  Score=126.30  Aligned_cols=125  Identities=21%  Similarity=0.224  Sum_probs=80.0

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCC--------CCcceeeccCCccccc
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKL--------LHLKYLNLKGQKKIEK  428 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l--------~~L~~L~l~~~~~~~~  428 (505)
                      +|+.|++++|.++..   .+..+..+++|+.|+|+       ++.+..+|..+...        ++|++|+|++|. +..
T Consensus       674 ~L~~L~Ls~N~L~~l---p~~~~~~l~~L~~L~Ls-------~N~L~~ip~~~~~~~~~~l~nl~~L~~L~Ls~N~-L~~  742 (876)
T 4ecn_A          674 NASTVTLSYNEIQKF---PTELFATGSPISTIILS-------NNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNK-LTS  742 (876)
T ss_dssp             CEEEEECCSSCCCSC---CHHHHHTTCCCSEEECC-------SCCCSCCCTTSSSCTTSCCTTGGGCCEEECCSSC-CCC
T ss_pred             CcCEEEccCCcCCcc---CHHHHccCCCCCEEECC-------CCcCCccChHHhccccccccccCCccEEECCCCC-Ccc
Confidence            666666666665532   23333467777777777       45555666544332        267777777776 557


Q ss_pred             cchhhh--cCCCCcEEecCCCcCccccchhccccccCceeecCC------CcccccccccccCCccCCcccee
Q 046115          429 LPETLC--ELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNED------TGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       429 lp~~~~--~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~------~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      +|..+.  .+++|+.|+|++|. +..+|..+..+++|+.|++++      |...+.+|..|.++++|+.|++-
T Consensus       743 lp~~l~~~~l~~L~~L~Ls~N~-L~~lp~~l~~L~~L~~L~Ls~N~~ls~N~l~~~ip~~l~~L~~L~~L~Ls  814 (876)
T 4ecn_A          743 LSDDFRATTLPYLSNMDVSYNC-FSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIG  814 (876)
T ss_dssp             CCGGGSTTTCTTCCEEECCSSC-CSSCCCGGGGCTTCCEEECCCCBCTTCCBCCCCCCTTGGGCSSCCEEECC
T ss_pred             chHHhhhccCCCcCEEEeCCCC-CCccchhhhcCCCCCEEECCCCCCcccccccccChHHHhcCCCCCEEECC
Confidence            777665  67777777777776 455777777777777777755      55556666667777777666553

>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=99.21  E-value=4.7e-11  Score=105.08  Aligned_cols=129  Identities=26%  Similarity=0.268  Sum_probs=101.3

Q ss_pred             EEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhH-HhhcCcccceEEecccccCCcccccccc-Ccccc
Q 046115          333 HLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQ-LFEKLTCLRALELQVRESWPRNNLIKEI-PTNIE  410 (505)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~-~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~  410 (505)
                      .+....+....+|..++      .+++.|++.+|.++..   .+. .+..+++|++|+|+       ++.+..+ |..++
T Consensus        12 ~l~~s~~~l~~ip~~~~------~~l~~L~l~~n~i~~~---~~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~~~   75 (192)
T 1w8a_A           12 TVDCTGRGLKEIPRDIP------LHTTELLLNDNELGRI---SSDGLFGRLPHLVKLELK-------RNQLTGIEPNAFE   75 (192)
T ss_dssp             EEECTTSCCSSCCSCCC------TTCSEEECCSCCCCSB---CCSCSGGGCTTCCEEECC-------SSCCCCBCTTTTT
T ss_pred             EEEcCCCCcCcCccCCC------CCCCEEECCCCcCCcc---CCccccccCCCCCEEECC-------CCCCCCcCHhHcC
Confidence            45555566666665543      3899999999998764   332 47889999999998       5666655 67899


Q ss_pred             CCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccc
Q 046115          411 KLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p  478 (505)
                      .+++|++|+|++|. ++.++. .+..+++|+.|+|++|......|..+..+++|++|++++|......+
T Consensus        76 ~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~c~c~  143 (192)
T 1w8a_A           76 GASHIQELQLGENK-IKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNCNCH  143 (192)
T ss_dssp             TCTTCCEEECCSCC-CCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBCCSGG
T ss_pred             CcccCCEEECCCCc-CCccCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCCccCcCc
Confidence            99999999999999 665554 57899999999999999555567789999999999999998665443

>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=99.20  E-value=3.9e-11  Score=126.03  Aligned_cols=135  Identities=22%  Similarity=0.222  Sum_probs=111.4

Q ss_pred             CCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceee
Q 046115          341 GASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLN  419 (505)
Q Consensus       341 ~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~  419 (505)
                      ...+|.++|      ++++.|+|++|.++..   .+..|..+++|++|+|+       ++.+..+|+ .|+.+++|++|+
T Consensus        43 l~~vP~~lp------~~~~~LdLs~N~i~~l---~~~~f~~l~~L~~L~Ls-------~N~i~~i~~~~f~~L~~L~~L~  106 (635)
T 4g8a_A           43 FYKIPDNLP------FSTKNLDLSFNPLRHL---GSYSFFSFPELQVLDLS-------RCEIQTIEDGAYQSLSHLSTLI  106 (635)
T ss_dssp             CSSCCSSSC------TTCCEEECTTSCCCEE---CTTTTTTCTTCCEEECT-------TCCCCEECTTTTTTCTTCCEEE
T ss_pred             cCccCCCCC------cCCCEEEeeCCCCCCC---CHHHHhCCCCCCEEECC-------CCcCCCcChhHhcCCCCCCEEE
Confidence            345665544      5799999999998764   55678999999999999       677777765 588999999999


Q ss_pred             ccCCccccccch-hhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccc-cccccccCCccCCcccee
Q 046115          420 LKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLR-YLPAGIGELIRLRRVREF  493 (505)
Q Consensus       420 l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~-~~p~~i~~l~~L~~L~~~  493 (505)
                      |++|+ ++.+|. .++.+++|++|++++|. +..+|+ .++++++|++|++++|.... ..|..++.+++|++|++.
T Consensus       107 Ls~N~-l~~l~~~~f~~L~~L~~L~Ls~N~-l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~  181 (635)
T 4g8a_A          107 LTGNP-IQSLALGAFSGLSSLQKLVAVETN-LASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLS  181 (635)
T ss_dssp             CTTCC-CCEECGGGGTTCTTCCEEECTTSC-CCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECC
T ss_pred             ccCCc-CCCCCHHHhcCCCCCCEEECCCCc-CCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhccc
Confidence            99999 888875 57899999999999998 777776 48999999999999998543 456778889999888754

>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=99.20  E-value=5.7e-11  Score=111.11  Aligned_cols=126  Identities=23%  Similarity=0.247  Sum_probs=105.0

Q ss_pred             CCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceeeccCCccccccc-hhh
Q 046115          356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLP-ETL  433 (505)
Q Consensus       356 ~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp-~~~  433 (505)
                      ++|++|++++|.++..   .+..+..+++|++|+++       ++.+..++. .+..+++|++|++++|. +..++ ..+
T Consensus        28 ~~l~~L~ls~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~   96 (276)
T 2z62_A           28 FSTKNLDLSFNPLRHL---GSYSFFSFPELQVLDLS-------RCEIQTIEDGAYQSLSHLSTLILTGNP-IQSLALGAF   96 (276)
T ss_dssp             TTCCEEECTTCCCCEE---CTTTTTTCTTCSEEECT-------TCCCCEECTTTTTTCTTCCEEECTTCC-CCEECTTTT
T ss_pred             CCccEEECCCCccccc---CHhHhccccCCcEEECC-------CCcCCccCHHHccCCcCCCEEECCCCc-cCccChhhh
Confidence            5799999999998764   44468899999999999       566666654 68899999999999999 65555 668


Q ss_pred             hcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccc-cccccccCCccCCcccee
Q 046115          434 CELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLR-YLPAGIGELIRLRRVREF  493 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~-~~p~~i~~l~~L~~L~~~  493 (505)
                      ..+++|+.|++++|. +..++. .++.+++|++|++++|.... .+|..+.++++|+.|++-
T Consensus        97 ~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~~~~l~~~~~~l~~L~~L~Ls  157 (276)
T 2z62_A           97 SGLSSLQKLVAVETN-LASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLS  157 (276)
T ss_dssp             TTCTTCCEEECTTSC-CCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECC
T ss_pred             cCCccccEEECCCCC-ccccCchhcccCCCCCEEECcCCccceecCchhhccCCCCCEEECC
Confidence            999999999999998 666655 68999999999999998544 368889999999988764

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.20  E-value=5.1e-11  Score=115.99  Aligned_cols=141  Identities=23%  Similarity=0.301  Sum_probs=106.3

Q ss_pred             ceeEEEEEecCCCccccccccCCC-CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVT-GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-  407 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-  407 (505)
                      .+..+.+..+....++..   .+. ++++|+.|++++|.++..   .+..|..+.+|+.|+|+       ++.+..+|+ 
T Consensus        40 ~l~~L~Ls~N~l~~l~~~---~~~~~l~~L~~L~L~~N~i~~i---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~  106 (361)
T 2xot_A           40 YTALLDLSHNNLSRLRAE---WTPTRLTNLHSLLLSHNHLNFI---SSEAFVPVPNLRYLDLS-------SNHLHTLDEF  106 (361)
T ss_dssp             TCSEEECCSSCCCEECTT---SSSSCCTTCCEEECCSSCCCEE---CTTTTTTCTTCCEEECC-------SSCCCEECTT
T ss_pred             CCCEEECCCCCCCccChh---hhhhcccccCEEECCCCcCCcc---ChhhccCCCCCCEEECC-------CCcCCcCCHH
Confidence            567777777776655543   344 788999999999988754   45568888999999998       666666654 


Q ss_pred             cccCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccchhc----cccccCceeecCCCcccccccc-cc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPRGI----GKLRKLMYLHNEDTGCLRYLPA-GI  481 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~~~----~~l~~L~~L~l~~~~~~~~~p~-~i  481 (505)
                      .+..+++|++|+|++|. +..+ |..+..+++|+.|+|++|. +..+|..+    ..+++|++|++++|. +..+|. .+
T Consensus       107 ~~~~l~~L~~L~L~~N~-i~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~  183 (361)
T 2xot_A          107 LFSDLQALEVLLLYNNH-IVVVDRNAFEDMAQLQKLYLSQNQ-ISRFPVELIKDGNKLPKLMLLDLSSNK-LKKLPLTDL  183 (361)
T ss_dssp             TTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSC-CCSCCGGGTC----CTTCCEEECCSSC-CCCCCHHHH
T ss_pred             HhCCCcCCCEEECCCCc-ccEECHHHhCCcccCCEEECCCCc-CCeeCHHHhcCcccCCcCCEEECCCCC-CCccCHHHh
Confidence            47889999999999998 5554 6678899999999999988 78888765    578899999999997 445553 45


Q ss_pred             cCCcc
Q 046115          482 GELIR  486 (505)
Q Consensus       482 ~~l~~  486 (505)
                      ..++.
T Consensus       184 ~~l~~  188 (361)
T 2xot_A          184 QKLPA  188 (361)
T ss_dssp             HHSCH
T ss_pred             hhccH
Confidence            55554

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.20  E-value=2.5e-11  Score=102.14  Aligned_cols=124  Identities=28%  Similarity=0.336  Sum_probs=100.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~  408 (505)
                      .++.+.+..+....  ..++..+..+++|+.|++.+|.++..     ..+..+++|++|+++       ++.+.. +|..
T Consensus        18 ~l~~L~l~~n~l~~--~~~~~~~~~l~~L~~L~l~~n~l~~~-----~~~~~l~~L~~L~Ls-------~n~i~~~~~~~   83 (149)
T 2je0_A           18 DVKELVLDNSRSNE--GKLEGLTDEFEELEFLSTINVGLTSI-----ANLPKLNKLKKLELS-------DNRVSGGLEVL   83 (149)
T ss_dssp             GCSEEECTTCBCBT--TBCCSCCTTCTTCCEEECTTSCCCCC-----TTCCCCTTCCEEECC-------SSCCCSCTHHH
T ss_pred             cCeEEEccCCcCCh--hHHHHHHhhcCCCcEEECcCCCCCCc-----hhhhcCCCCCEEECC-------CCcccchHHHH
Confidence            66777777766540  22334456899999999999998764     447889999999999       666666 7777


Q ss_pred             ccCCCCcceeeccCCccccccc--hhhhcCCCCcEEecCCCcCccccch----hccccccCceeecC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLP--ETLCELYNLERLNVDDCQNLRELPR----GIGKLRKLMYLHNE  469 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~lp~----~~~~l~~L~~L~l~  469 (505)
                      ++.+++|++|++++|. ++.+|  ..++.+++|+.|++++|. +..+|+    .+..+++|++|+++
T Consensus        84 ~~~l~~L~~L~ls~N~-i~~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A           84 AEKCPNLTHLNLSGNK-IKDLSTIEPLKKLENLKSLDLFNCE-VTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             HHHCTTCCEEECTTSC-CCSHHHHGGGGGCTTCCEEECTTCG-GGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             hhhCCCCCEEECCCCc-CCChHHHHHHhhCCCCCEEeCcCCc-ccchHHHHHHHHHHCCCcccccCC
Confidence            7789999999999999 77665  778999999999999998 777776    68999999999876

>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=99.20  E-value=4.8e-11  Score=120.92  Aligned_cols=141  Identities=21%  Similarity=0.254  Sum_probs=115.2

Q ss_pred             EecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCc
Q 046115          337 TLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHL  415 (505)
Q Consensus       337 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L  415 (505)
                      .......+|..++      ++++.|++++|.++..   .+..|..+++|++|+|+       ++.+..+ |..++.+++|
T Consensus        19 ~~~~l~~ip~~~~------~~l~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~i~~~~~~~~~~l~~L   82 (477)
T 2id5_A           19 HRKRFVAVPEGIP------TETRLLDLGKNRIKTL---NQDEFASFPHLEELELN-------ENIVSAVEPGAFNNLFNL   82 (477)
T ss_dssp             CSCCCSSCCSCCC------TTCSEEECCSSCCCEE---CTTTTTTCTTCCEEECT-------TSCCCEECTTTTTTCTTC
T ss_pred             CCCCcCcCCCCCC------CCCcEEECCCCccceE---CHhHccCCCCCCEEECC-------CCccCEeChhhhhCCccC
Confidence            3344555665443      5899999999998765   56678999999999999       5556555 7789999999


Q ss_pred             ceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccceeE
Q 046115          416 KYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREFV  494 (505)
Q Consensus       416 ~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~~  494 (505)
                      ++|+|++|. ++.+|.. +..+++|+.|+|++|......|..+..+++|++|++++|......|..|.++++|+.|++..
T Consensus        83 ~~L~L~~n~-l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~  161 (477)
T 2id5_A           83 RTLGLRSNR-LKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEK  161 (477)
T ss_dssp             CEEECCSSC-CCSCCTTSSTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCEEEEES
T ss_pred             CEEECCCCc-CCccCcccccCCCCCCEEECCCCccccCChhHccccccCCEEECCCCccceeChhhccCCCCCCEEECCC
Confidence            999999999 8888764 68999999999999995555567799999999999999986666677899999999888753

>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=99.20  E-value=3e-11  Score=126.35  Aligned_cols=130  Identities=17%  Similarity=0.108  Sum_probs=82.4

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc--cCccccCCCCcceeeccCCcccccc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE--IPTNIEKLLHLKYLNLKGQKKIEKL  429 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~--~p~~~~~l~~L~~L~l~~~~~~~~l  429 (505)
                      +..+++|+.|++++|.+...   .|..+..+++|+.|+++       ++.+..  .|..++.+++|++|++++|...+..
T Consensus       420 ~~~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~  489 (606)
T 3vq2_A          420 FLSLEKLLYLDISYTNTKID---FDGIFLGLTSLNTLKMA-------GNSFKDNTLSNVFANTTNLTFLDLSKCQLEQIS  489 (606)
T ss_dssp             TTTCTTCCEEECTTSCCEEC---CTTTTTTCTTCCEEECT-------TCEEGGGEECSCCTTCTTCCEEECTTSCCCEEC
T ss_pred             hhccccCCEEECcCCCCCcc---chhhhcCCCCCCEEECC-------CCcCCCcchHHhhccCCCCCEEECCCCcCCccC
Confidence            34555666666666654432   44556666666666666       333332  5666777777777777777733344


Q ss_pred             chhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCc-cCCccce
Q 046115          430 PETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELI-RLRRVRE  492 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~-~L~~L~~  492 (505)
                      |..++.+++|+.|++++|......|..+..+++|++|++++|. +..+|..+..++ +|+.|++
T Consensus       490 ~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~p~~~~~l~~~L~~l~l  552 (606)
T 3vq2_A          490 WGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNR-IETSKGILQHFPKSLAFFNL  552 (606)
T ss_dssp             TTTTTTCTTCCEEECCSSCCSCEEGGGTTTCTTCCEEECTTSC-CCCEESCGGGSCTTCCEEEC
T ss_pred             hhhhcccccCCEEECCCCcCCCcCHHHccCCCcCCEEECCCCc-CcccCHhHhhhcccCcEEEc
Confidence            5566777777777777777444446667777777777777776 446776666665 4666654

>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=99.19  E-value=5.4e-11  Score=123.17  Aligned_cols=141  Identities=23%  Similarity=0.332  Sum_probs=114.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++.     +..+++|+.|.|++|.++..    | .+..+.+|+.|+|+       ++.+..++ .+
T Consensus        66 ~L~~L~Ls~N~l~~~~~-----l~~l~~L~~L~Ls~N~l~~l----~-~l~~l~~L~~L~Ls-------~N~l~~l~-~l  127 (605)
T 1m9s_A           66 NVTKLFLNGNKLTDIKP-----LTNLKNLGWLFLDENKIKDL----S-SLKDLKKLKSLSLE-------HNGISDIN-GL  127 (605)
T ss_dssp             TCCEEECTTSCCCCCGG-----GGGCTTCCEEECCSSCCCCC----T-TSTTCTTCCEEECT-------TSCCCCCG-GG
T ss_pred             CCCEEEeeCCCCCCChh-----hccCCCCCEEECcCCCCCCC----h-hhccCCCCCEEEec-------CCCCCCCc-cc
Confidence            67788887777665554     55899999999999988753    3 37889999999998       66666664 58


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+++|+.|+|++|. +..++ .++.+++|+.|+|++|. +..+++ +..+++|++|++++|. +..+| .+..+++|+.
T Consensus       128 ~~l~~L~~L~Ls~N~-l~~l~-~l~~l~~L~~L~Ls~N~-l~~~~~-l~~l~~L~~L~Ls~N~-i~~l~-~l~~l~~L~~  201 (605)
T 1m9s_A          128 VHLPQLESLYLGNNK-ITDIT-VLSRLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNH-ISDLR-ALAGLKNLDV  201 (605)
T ss_dssp             GGCTTCSEEECCSSC-CCCCG-GGGSCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCBCG-GGTTCTTCSE
T ss_pred             cCCCccCEEECCCCc-cCCch-hhcccCCCCEEECcCCc-CCCchh-hccCCCCCEEECcCCC-CCCCh-HHccCCCCCE
Confidence            899999999999998 77774 48999999999999998 666665 8999999999999997 44554 5888888888


Q ss_pred             cceeE
Q 046115          490 VREFV  494 (505)
Q Consensus       490 L~~~~  494 (505)
                      |++..
T Consensus       202 L~L~~  206 (605)
T 1m9s_A          202 LELFS  206 (605)
T ss_dssp             EECCS
T ss_pred             EEccC
Confidence            87653

>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=99.19  E-value=7e-11  Score=123.12  Aligned_cols=82  Identities=18%  Similarity=0.246  Sum_probs=42.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Ccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~  408 (505)
                      .+..+.+..+....++.   ..|.++++|++|++++|.++..   ++..+..+++|++|+|+       ++.+..+ |..
T Consensus       100 ~L~~L~L~~n~l~~~~~---~~~~~l~~L~~L~L~~n~l~~l---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~  166 (597)
T 3oja_B          100 TIQKLYMGFNAIRYLPP---HVFQNVPLLTVLVLERNDLSSL---PRGIFHNTPKLTTLSMS-------NNNLERIEDDT  166 (597)
T ss_dssp             TCCEEECCSSCCCCCCT---TTTTTCTTCCEEECCSSCCCCC---CTTTTTTCTTCCEEECC-------SSCCCBCCTTT
T ss_pred             CCCEEECCCCcCCCCCH---HHHcCCCCCCEEEeeCCCCCCC---CHHHhccCCCCCEEEee-------CCcCCCCChhh
Confidence            34444444444333332   2234566666666666655432   33334556666666665       3333333 334


Q ss_pred             ccCCCCcceeeccCCc
Q 046115          409 IEKLLHLKYLNLKGQK  424 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~  424 (505)
                      ++.+++|++|++++|.
T Consensus       167 ~~~l~~L~~L~L~~N~  182 (597)
T 3oja_B          167 FQATTSLQNLQLSSNR  182 (597)
T ss_dssp             TTTCTTCCEEECTTSC
T ss_pred             hhcCCcCcEEECcCCC
Confidence            5666666666666665

>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=99.18  E-value=5.6e-11  Score=108.57  Aligned_cols=126  Identities=14%  Similarity=0.190  Sum_probs=59.0

Q ss_pred             CCCCceEEEecC-CCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcc---eeeccCCcccccc
Q 046115          354 GLRGLRSLLVKS-DEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLK---YLNLKGQKKIEKL  429 (505)
Q Consensus       354 ~~~~L~~L~l~~-~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~---~L~l~~~~~~~~l  429 (505)
                      ++++|++|++.+ |.++..   .+..+..+++|+.|+++       ++.+..+|. ++.+++|+   +|++++|..++.+
T Consensus        78 ~l~~L~~L~l~~~n~l~~i---~~~~f~~l~~L~~L~l~-------~n~l~~lp~-~~~l~~L~~L~~L~l~~N~~l~~i  146 (239)
T 2xwt_C           78 NLSKVTHIEIRNTRNLTYI---DPDALKELPLLKFLGIF-------NTGLKMFPD-LTKVYSTDIFFILEITDNPYMTSI  146 (239)
T ss_dssp             SCTTCCEEEEEEETTCCEE---CTTSEECCTTCCEEEEE-------EECCCSCCC-CTTCCBCCSEEEEEEESCTTCCEE
T ss_pred             CCcCCcEEECCCCCCeeEc---CHHHhCCCCCCCEEeCC-------CCCCccccc-cccccccccccEEECCCCcchhhc
Confidence            445555555554 444332   22334445555555554       333444443 44444444   5555555114444


Q ss_pred             ch-hhhcCCCCc-EEecCCCcCccccchhccccccCceeecCCCccccccc-ccccCC-ccCCccc
Q 046115          430 PE-TLCELYNLE-RLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP-AGIGEL-IRLRRVR  491 (505)
Q Consensus       430 p~-~~~~l~~L~-~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l-~~L~~L~  491 (505)
                      |. .+..+++|+ .|++++|. +..+|......++|++|++++|..+..+| ..|..+ ++|+.|+
T Consensus       147 ~~~~~~~l~~L~~~L~l~~n~-l~~i~~~~~~~~~L~~L~L~~n~~l~~i~~~~~~~l~~~L~~L~  211 (239)
T 2xwt_C          147 PVNAFQGLCNETLTLKLYNNG-FTSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLD  211 (239)
T ss_dssp             CTTTTTTTBSSEEEEECCSCC-CCEECTTTTTTCEEEEEECTTCTTCCEECTTTTTTCSBCCSEEE
T ss_pred             CcccccchhcceeEEEcCCCC-CcccCHhhcCCCCCCEEEcCCCCCcccCCHHHhhccccCCcEEE
Confidence            43 245555555 55555555 44555443333555555555553123333 234455 5555444

>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=99.18  E-value=8.7e-11  Score=121.61  Aligned_cols=123  Identities=25%  Similarity=0.351  Sum_probs=101.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++     .+..+++|+.|.+++|.++..    +. +..+++|+.|+|+       ++.+..+ +.+
T Consensus        88 ~L~~L~Ls~N~l~~l~-----~l~~l~~L~~L~Ls~N~l~~l----~~-l~~l~~L~~L~Ls-------~N~l~~l-~~l  149 (605)
T 1m9s_A           88 NLGWLFLDENKIKDLS-----SLKDLKKLKSLSLEHNGISDI----NG-LVHLPQLESLYLG-------NNKITDI-TVL  149 (605)
T ss_dssp             TCCEEECCSSCCCCCT-----TSTTCTTCCEEECTTSCCCCC----GG-GGGCTTCSEEECC-------SSCCCCC-GGG
T ss_pred             CCCEEECcCCCCCCCh-----hhccCCCCCEEEecCCCCCCC----cc-ccCCCccCEEECC-------CCccCCc-hhh
Confidence            6778888777766543     456899999999999998753    33 7889999999998       6666666 568


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~  474 (505)
                      +.+++|+.|+|++|. +..+++ +..+++|+.|+|++|. +..+| .+..+++|+.|++++|.+.
T Consensus       150 ~~l~~L~~L~Ls~N~-l~~~~~-l~~l~~L~~L~Ls~N~-i~~l~-~l~~l~~L~~L~L~~N~l~  210 (605)
T 1m9s_A          150 SRLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNH-ISDLR-ALAGLKNLDVLELFSQECL  210 (605)
T ss_dssp             GSCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCBCG-GGTTCTTCSEEECCSEEEE
T ss_pred             cccCCCCEEECcCCc-CCCchh-hccCCCCCEEECcCCC-CCCCh-HHccCCCCCEEEccCCcCc
Confidence            899999999999998 777766 9999999999999998 77775 6889999999999999854

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.18  E-value=6.4e-11  Score=115.30  Aligned_cols=140  Identities=20%  Similarity=0.231  Sum_probs=94.5

Q ss_pred             EEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhh-cCcccceEEecccccCCccccccccC-ccccC
Q 046115          334 LLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFE-KLTCLRALELQVRESWPRNNLIKEIP-TNIEK  411 (505)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~-~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~  411 (505)
                      +....+....+|..++      ..++.|++++|.++..   .+..+. .+.+|+.|+|+       ++.+..++ ..+..
T Consensus        23 l~c~~~~l~~iP~~~~------~~l~~L~Ls~N~l~~l---~~~~~~~~l~~L~~L~L~-------~N~i~~i~~~~~~~   86 (361)
T 2xot_A           23 LSCSKQQLPNVPQSLP------SYTALLDLSHNNLSRL---RAEWTPTRLTNLHSLLLS-------HNHLNFISSEAFVP   86 (361)
T ss_dssp             EECCSSCCSSCCSSCC------TTCSEEECCSSCCCEE---CTTSSSSCCTTCCEEECC-------SSCCCEECTTTTTT
T ss_pred             EEeCCCCcCccCccCC------CCCCEEECCCCCCCcc---ChhhhhhcccccCEEECC-------CCcCCccChhhccC
Confidence            3444444555554433      4577888888877654   444455 78888888887       56666665 35778


Q ss_pred             CCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCcccc-chhccccccCceeecCCCcccccccccc----cCCc
Q 046115          412 LLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLREL-PRGIGKLRKLMYLHNEDTGCLRYLPAGI----GELI  485 (505)
Q Consensus       412 l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~~p~~i----~~l~  485 (505)
                      +++|++|+|++|. +..+|. .+..+++|+.|+|++|. +..+ |..+..+++|++|++++|. +..+|..+    ..++
T Consensus        87 l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~-i~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~~~~~~~~~l~  163 (361)
T 2xot_A           87 VPNLRYLDLSSNH-LHTLDEFLFSDLQALEVLLLYNNH-IVVVDRNAFEDMAQLQKLYLSQNQ-ISRFPVELIKDGNKLP  163 (361)
T ss_dssp             CTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSC-CCSCCGGGTC----CT
T ss_pred             CCCCCEEECCCCc-CCcCCHHHhCCCcCCCEEECCCCc-ccEECHHHhCCcccCCEEECCCCc-CCeeCHHHhcCcccCC
Confidence            8888888888888 666654 46788888888888888 4444 5567888888888888887 45566553    4566


Q ss_pred             cCCccce
Q 046115          486 RLRRVRE  492 (505)
Q Consensus       486 ~L~~L~~  492 (505)
                      +|+.|++
T Consensus       164 ~L~~L~L  170 (361)
T 2xot_A          164 KLMLLDL  170 (361)
T ss_dssp             TCCEEEC
T ss_pred             cCCEEEC
Confidence            6666554

>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=99.18  E-value=7.1e-11  Score=103.90  Aligned_cols=113  Identities=26%  Similarity=0.249  Sum_probs=83.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-c
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-N  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~  408 (505)
                      .+..+.+..+....++..  ..+..+++|+.|++++|.+++.   .|..+..+.+|++|+|+       ++.+..+++ .
T Consensus        30 ~l~~L~l~~n~i~~~~~~--~~~~~l~~L~~L~Ls~N~l~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~   97 (192)
T 1w8a_A           30 HTTELLLNDNELGRISSD--GLFGRLPHLVKLELKRNQLTGI---EPNAFEGASHIQELQLG-------ENKIKEISNKM   97 (192)
T ss_dssp             TCSEEECCSCCCCSBCCS--CSGGGCTTCCEEECCSSCCCCB---CTTTTTTCTTCCEEECC-------SCCCCEECSSS
T ss_pred             CCCEEECCCCcCCccCCc--cccccCCCCCEEECCCCCCCCc---CHhHcCCcccCCEEECC-------CCcCCccCHHH
Confidence            677777777776655432  1245788999999999987764   56678888899999998       555666554 4


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELP  454 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp  454 (505)
                      +..+++|++|++++|...+..|..+..+++|+.|++++|+.....+
T Consensus        98 ~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~c~c~  143 (192)
T 1w8a_A           98 FLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNCNCH  143 (192)
T ss_dssp             STTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBCCSGG
T ss_pred             hcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCCccCcCc
Confidence            7888999999999998444557778888899999999988544443

>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=99.18  E-value=2.2e-10  Score=110.05  Aligned_cols=147  Identities=20%  Similarity=0.270  Sum_probs=75.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++..   .+.++++|+.|++.+|.+.... ..+..+..+++|++|+++       ++.+..+|..+
T Consensus       122 ~L~~L~l~~n~l~~~~~~---~~~~l~~L~~L~l~~n~l~~~~-~~~~~~~~l~~L~~L~l~-------~n~l~~l~~~~  190 (330)
T 1xku_A          122 TLQELRVHENEITKVRKS---VFNGLNQMIVVELGTNPLKSSG-IENGAFQGMKKLSYIRIA-------DTNITTIPQGL  190 (330)
T ss_dssp             TCCEEECCSSCCCBBCHH---HHTTCTTCCEEECCSSCCCGGG-BCTTGGGGCTTCCEEECC-------SSCCCSCCSSC
T ss_pred             cccEEECCCCcccccCHh---HhcCCccccEEECCCCcCCccC-cChhhccCCCCcCEEECC-------CCccccCCccc
Confidence            555666655555444332   2346677777777777664321 144456667777777776       44444444433


Q ss_pred             cCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccc-hhccccccCceeecCCCcccccccccccCCccC
Q 046115          410 EKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELP-RGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      .  ++|++|++++|. +..+ |..+..+++|+.|++++|. +..++ ..+..+++|++|++++|. +..+|..+..+++|
T Consensus       191 ~--~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~lp~~l~~l~~L  265 (330)
T 1xku_A          191 P--PSLTELHLDGNK-ITKVDAASLKGLNNLAKLGLSFNS-ISAVDNGSLANTPHLRELHLNNNK-LVKVPGGLADHKYI  265 (330)
T ss_dssp             C--TTCSEEECTTSC-CCEECTGGGTTCTTCCEEECCSSC-CCEECTTTGGGSTTCCEEECCSSC-CSSCCTTTTTCSSC
T ss_pred             c--ccCCEEECCCCc-CCccCHHHhcCCCCCCEEECCCCc-CceeChhhccCCCCCCEEECCCCc-CccCChhhccCCCc
Confidence            2  455555555555 3322 3445555555555555555 33332 245555555555555554 33455555555555


Q ss_pred             Cccce
Q 046115          488 RRVRE  492 (505)
Q Consensus       488 ~~L~~  492 (505)
                      +.|++
T Consensus       266 ~~L~l  270 (330)
T 1xku_A          266 QVVYL  270 (330)
T ss_dssp             CEEEC
T ss_pred             CEEEC
Confidence            54443

>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=99.17  E-value=4.5e-11  Score=109.21  Aligned_cols=148  Identities=18%  Similarity=0.222  Sum_probs=118.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCC-ccccccchhHHhhcCcccceEEecccccCCcc-ccccccC-
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDE-YSWSSEVLPQLFEKLTCLRALELQVRESWPRN-NLIKEIP-  406 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~-~~~~~~p-  406 (505)
                      .+..+.+..+....++..   .+.++++|++|++.+|. ++..   .+..+..+++|++|+++       + +.+..+| 
T Consensus        32 ~l~~L~l~~n~l~~i~~~---~~~~l~~L~~L~l~~n~~l~~i---~~~~f~~l~~L~~L~l~-------~~n~l~~i~~   98 (239)
T 2xwt_C           32 STQTLKLIETHLRTIPSH---AFSNLPNISRIYVSIDVTLQQL---ESHSFYNLSKVTHIEIR-------NTRNLTYIDP   98 (239)
T ss_dssp             TCCEEEEESCCCSEECTT---TTTTCTTCCEEEEECCSSCCEE---CTTTEESCTTCCEEEEE-------EETTCCEECT
T ss_pred             cccEEEEeCCcceEECHH---HccCCCCCcEEeCCCCCCccee---CHhHcCCCcCCcEEECC-------CCCCeeEcCH
Confidence            788888888887766642   45689999999999996 6653   44467889999999998       5 6777776 


Q ss_pred             ccccCCCCcceeeccCCccccccchhhhcCCCCc---EEecCCCcCccccchh-ccccccCc-eeecCCCcccccccccc
Q 046115          407 TNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLE---RLNVDDCQNLRELPRG-IGKLRKLM-YLHNEDTGCLRYLPAGI  481 (505)
Q Consensus       407 ~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~---~L~l~~~~~~~~lp~~-~~~l~~L~-~L~l~~~~~~~~~p~~i  481 (505)
                      ..+..+++|++|++++|. +..+|. ++.+++|+   .|++++|..+..+|+. +..+++|+ +|++++|.. ..+|...
T Consensus        99 ~~f~~l~~L~~L~l~~n~-l~~lp~-~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~l-~~i~~~~  175 (239)
T 2xwt_C           99 DALKELPLLKFLGIFNTG-LKMFPD-LTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGF-TSVQGYA  175 (239)
T ss_dssp             TSEECCTTCCEEEEEEEC-CCSCCC-CTTCCBCCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCCC-CEECTTT
T ss_pred             HHhCCCCCCCEEeCCCCC-Cccccc-cccccccccccEEECCCCcchhhcCcccccchhcceeEEEcCCCCC-cccCHhh
Confidence            467899999999999999 778988 88888888   9999999348888765 88999999 999999984 5777754


Q ss_pred             cCCccCCcccee
Q 046115          482 GELIRLRRVREF  493 (505)
Q Consensus       482 ~~l~~L~~L~~~  493 (505)
                      ...++|+.|++.
T Consensus       176 ~~~~~L~~L~L~  187 (239)
T 2xwt_C          176 FNGTKLDAVYLN  187 (239)
T ss_dssp             TTTCEEEEEECT
T ss_pred             cCCCCCCEEEcC
Confidence            444667666543

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.17  E-value=9.4e-11  Score=121.57  Aligned_cols=144  Identities=18%  Similarity=0.143  Sum_probs=110.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-cc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~  408 (505)
                      .++.+.+..+....++.   ..|.++++|++|++++|.++..   .|..+..+++|++|+|+       ++.+..+| ..
T Consensus        29 ~l~~L~Ls~n~l~~~~~---~~~~~l~~L~~L~Ls~n~i~~i---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~   95 (570)
T 2z63_A           29 STKNLDLSFNPLRHLGS---YSFFSFPELQVLDLSRCEIQTI---EDGAYQSLSHLSTLILT-------GNPIQSLALGA   95 (570)
T ss_dssp             SCCEEECCSCCCCEECT---TTTTTCSSCCEEECTTCCCCEE---CTTTTTTCTTCCEEECT-------TCCCCEECTTT
T ss_pred             cccEEEccCCccCccCh---hHhhCCCCceEEECCCCcCCcc---CcccccCchhCCEEeCc-------CCcCCccCHhh
Confidence            67778877777665543   3456889999999999987654   56668889999999998       55565554 56


Q ss_pred             ccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      ++.+++|++|++++|. +..+|. .++.+++|++|++++|.... .+|..++++++|++|++++|......|..++.+++
T Consensus        96 ~~~l~~L~~L~L~~n~-l~~l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~  174 (570)
T 2z63_A           96 FSGLSSLQKLVAVETN-LASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ  174 (570)
T ss_dssp             TTTCTTCCEEECTTSC-CCCSTTCSCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTTSCCCEECGGGGHHHHT
T ss_pred             hcCccccccccccccc-cccCCCccccccccccEEecCCCccceecChhhhcccCCCCEEeCcCCccceecHHHccchhc
Confidence            8889999999999988 777765 57889999999999988333 46888889999999999998755544556666666


Q ss_pred             C
Q 046115          487 L  487 (505)
Q Consensus       487 L  487 (505)
                      |
T Consensus       175 L  175 (570)
T 2z63_A          175 M  175 (570)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.17  E-value=6.6e-11  Score=114.91  Aligned_cols=140  Identities=19%  Similarity=0.197  Sum_probs=113.9

Q ss_pred             EecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCc
Q 046115          337 TLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHL  415 (505)
Q Consensus       337 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L  415 (505)
                      ..+....+|..++      ++|+.|++++|.++..   .+..+..+++|+.|+++       ++.+..+ |..++.+++|
T Consensus        39 ~~~~l~~iP~~~~------~~L~~L~l~~n~i~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~~~~l~~L  102 (353)
T 2z80_A           39 SSGSLNSIPSGLT------EAVKSLDLSNNRITYI---SNSDLQRCVNLQALVLT-------SNGINTIEEDSFSSLGSL  102 (353)
T ss_dssp             CSTTCSSCCTTCC------TTCCEEECTTSCCCEE---CTTTTTTCTTCCEEECT-------TSCCCEECTTTTTTCTTC
T ss_pred             CCCCccccccccc------ccCcEEECCCCcCccc---CHHHhccCCCCCEEECC-------CCccCccCHhhcCCCCCC
Confidence            3445566665443      5899999999998754   45468899999999998       5566665 4568999999


Q ss_pred             ceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccch--hccccccCceeecCCCcccccc-cccccCCccCCccc
Q 046115          416 KYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCLRYL-PAGIGELIRLRRVR  491 (505)
Q Consensus       416 ~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~~-p~~i~~l~~L~~L~  491 (505)
                      ++|++++|. ++.+|.. ++.+++|+.|++++|. +..+|.  .+..+++|++|++++|..+..+ |..+.++++|+.|+
T Consensus       103 ~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~n~-l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~  180 (353)
T 2z80_A          103 EHLDLSYNY-LSNLSSSWFKPLSSLTFLNLLGNP-YKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELE  180 (353)
T ss_dssp             CEEECCSSC-CSSCCHHHHTTCTTCSEEECTTCC-CSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEE
T ss_pred             CEEECCCCc-CCcCCHhHhCCCccCCEEECCCCC-CcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEE
Confidence            999999999 7788876 7899999999999998 778887  6899999999999999545555 45688999999888


Q ss_pred             eeE
Q 046115          492 EFV  494 (505)
Q Consensus       492 ~~~  494 (505)
                      +..
T Consensus       181 l~~  183 (353)
T 2z80_A          181 IDA  183 (353)
T ss_dssp             EEE
T ss_pred             CCC
Confidence            764

>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=99.16  E-value=1e-10  Score=120.73  Aligned_cols=153  Identities=14%  Similarity=0.175  Sum_probs=104.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+............+..+++|+.|++++|.++.... .+..+..+++|++|+++       ++.+..+|..+
T Consensus       335 ~L~~L~Ls~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~-~~~~~~~l~~L~~L~Ls-------~N~l~~lp~~~  406 (549)
T 2z81_A          335 SLEFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHLRSMQK-TGEILLTLKNLTSLDIS-------RNTFHPMPDSC  406 (549)
T ss_dssp             TCCEEECCSSCCCHHHHHHHTCTTSSTTCCEEECTTSCCCCHHH-HHHHGGGCTTCCEEECT-------TCCCCCCCSCC
T ss_pred             cccEEEccCCccccccccchhhhhccccCcEEEccCCccccccc-chhhhhcCCCCCEEECC-------CCCCccCChhh
Confidence            44555555554432211112234567788888888887765311 12447788888888888       66677788877


Q ss_pred             cCCCCcceeeccCCccccccchhh------------------hcCCCCcEEecCCCcCccccchhccccccCceeecCCC
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETL------------------CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDT  471 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~------------------~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~  471 (505)
                      +.+++|++|++++|. +..+|..+                  ..+++|+.|++++|. +..+|. ...+++|++|++++|
T Consensus       407 ~~~~~L~~L~Ls~N~-l~~l~~~~~~~L~~L~Ls~N~l~~~~~~l~~L~~L~Ls~N~-l~~ip~-~~~l~~L~~L~Ls~N  483 (549)
T 2z81_A          407 QWPEKMRFLNLSSTG-IRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNK-LKTLPD-ASLFPVLLVMKISRN  483 (549)
T ss_dssp             CCCTTCCEEECTTSC-CSCCCTTSCTTCSEEECCSSCCSCCCCCCTTCCEEECCSSC-CSSCCC-GGGCTTCCEEECCSS
T ss_pred             cccccccEEECCCCC-cccccchhcCCceEEECCCCChhhhcccCChhcEEECCCCc-cCcCCC-cccCccCCEEecCCC
Confidence            788888888888887 55555432                  257788888888887 678886 467888999999998


Q ss_pred             cccccccccccCCccCCcccee
Q 046115          472 GCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       472 ~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      ...+..|..+..+++|+.|++.
T Consensus       484 ~l~~~~~~~~~~l~~L~~L~l~  505 (549)
T 2z81_A          484 QLKSVPDGIFDRLTSLQKIWLH  505 (549)
T ss_dssp             CCCCCCTTGGGGCTTCCEEECC
T ss_pred             ccCCcCHHHHhcCcccCEEEec
Confidence            8655555557888888877753

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.16  E-value=3.4e-11  Score=122.03  Aligned_cols=144  Identities=13%  Similarity=0.056  Sum_probs=118.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~  408 (505)
                      .+..+.+..+....++..      .+++|+.|++.+|.+++.   .|..+..+++|+.|+|+       ++.+.. .|..
T Consensus       100 ~L~~L~L~~N~l~~~~~~------~l~~L~~L~L~~N~l~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~  163 (487)
T 3oja_A          100 SIETLHAANNNISRVSCS------RGQGKKNIYLANNKITML---RDLDEGCRSRVQYLDLK-------LNEIDTVNFAE  163 (487)
T ss_dssp             TCCEEECCSSCCCCEEEC------CCSSCEEEECCSSCCCSG---GGBCGGGGSSEEEEECT-------TSCCCEEEGGG
T ss_pred             CcCEEECcCCcCCCCCcc------ccCCCCEEECCCCCCCCC---CchhhcCCCCCCEEECC-------CCCCCCcChHH
Confidence            566777777766655543      468899999999998765   56668889999999999       555544 5666


Q ss_pred             cc-CCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccC
Q 046115          409 IE-KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       409 ~~-~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      +. .+++|++|+|++|. ++.+|. ...+++|+.|+|++|. +..+|+.+..+++|+.|++++|. +..+|..+..+++|
T Consensus       164 l~~~l~~L~~L~Ls~N~-l~~~~~-~~~l~~L~~L~Ls~N~-l~~~~~~~~~l~~L~~L~Ls~N~-l~~lp~~l~~l~~L  239 (487)
T 3oja_A          164 LAASSDTLEHLNLQYNF-IYDVKG-QVVFAKLKTLDLSSNK-LAFMGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNL  239 (487)
T ss_dssp             GGGGTTTCCEEECTTSC-CCEEEC-CCCCTTCCEEECCSSC-CCEECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTC
T ss_pred             HhhhCCcccEEecCCCc-cccccc-cccCCCCCEEECCCCC-CCCCCHhHcCCCCccEEEecCCc-CcccchhhccCCCC
Confidence            65 79999999999999 777776 5579999999999999 88898889999999999999998 55789889888888


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      +.|++.
T Consensus       240 ~~L~l~  245 (487)
T 3oja_A          240 EHFDLR  245 (487)
T ss_dssp             CEEECT
T ss_pred             CEEEcC
Confidence            887753

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.16  E-value=1.3e-10  Score=100.70  Aligned_cols=128  Identities=27%  Similarity=0.379  Sum_probs=100.8

Q ss_pred             EEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-ccC
Q 046115          333 HLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEK  411 (505)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-~~~  411 (505)
                      .+....+....+|...      .++|+.|.+.+|.+...   .+..+..+.+|++|+++       ++.+..+|+. ++.
T Consensus        11 ~l~~~~~~l~~~p~~~------~~~l~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~~~~   74 (177)
T 2o6r_A           11 EIRCNSKGLTSVPTGI------PSSATRLELESNKLQSL---PHGVFDKLTQLTKLSLS-------QNQIQSLPDGVFDK   74 (177)
T ss_dssp             EEECCSSCCSSCCTTC------CTTCSEEECCSSCCCCC---CTTTTTTCTTCSEEECC-------SSCCCCCCTTTTTT
T ss_pred             EEEecCCCCccCCCCC------CCCCcEEEeCCCcccEe---CHHHhcCcccccEEECC-------CCcceEeChhHccC
Confidence            3444445555555433      36899999999998754   55557889999999998       6667777655 689


Q ss_pred             CCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCccccccc
Q 046115          412 LLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       412 l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p  478 (505)
                      +++|++|++++|. ++.+|.. +..+++|+.|++++|. +..+|.. +..+++|++|++++|...+..|
T Consensus        75 l~~L~~L~l~~N~-l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~l~~L~~L~l~~N~~~~~~~  141 (177)
T 2o6r_A           75 LTKLTILYLHENK-LQSLPNGVFDKLTQLKELALDTNQ-LKSVPDGIFDRLTSLQKIWLHTNPWDCSCP  141 (177)
T ss_dssp             CTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCBCCCHH
T ss_pred             CCccCEEECCCCC-ccccCHHHhhCCcccCEEECcCCc-ceEeCHHHhcCCcccCEEEecCCCeeccCc
Confidence            9999999999999 7777764 5899999999999998 7788876 5889999999999998665444

>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=99.16  E-value=1.4e-10  Score=120.11  Aligned_cols=149  Identities=15%  Similarity=0.231  Sum_probs=114.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~  408 (505)
                      .+..+.+..+....   ..+..+..+++|+.|++.+|.+++... +|..+..+++|+.|+++       ++.+.. +|..
T Consensus       354 ~L~~L~l~~n~l~~---~~~~~~~~l~~L~~L~L~~N~l~~~~~-~~~~~~~l~~L~~L~l~-------~N~l~~~~~~~  422 (562)
T 3a79_B          354 SFTFLNFTQNVFTD---SVFQGCSTLKRLQTLILQRNGLKNFFK-VALMTKNMSSLETLDVS-------LNSLNSHAYDR  422 (562)
T ss_dssp             CCCEEECCSSCCCT---TTTTTCCSCSSCCEEECCSSCCCBTTH-HHHTTTTCTTCCEEECT-------TSCCBSCCSSC
T ss_pred             CceEEECCCCcccc---chhhhhcccCCCCEEECCCCCcCCccc-chhhhcCCCCCCEEECC-------CCcCCCccChh
Confidence            55666666555443   334556689999999999998876432 56668889999999998       555555 6654


Q ss_pred             -ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccccc-ccCCcc
Q 046115          409 -IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG-IGELIR  486 (505)
Q Consensus       409 -~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~-i~~l~~  486 (505)
                       +..+++|++|++++|...+.+|..+.  ++|+.|++++|. +..+|..+..+++|++|++++|. +..+|.. +..+++
T Consensus       423 ~~~~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          423 TCAWAESILVLNLSSNMLTGSVFRCLP--PKVKVLDLHNNR-IMSIPKDVTHLQALQELNVASNQ-LKSVPDGVFDRLTS  498 (562)
T ss_dssp             CCCCCTTCCEEECCSSCCCGGGGSSCC--TTCSEEECCSSC-CCCCCTTTTSSCCCSEEECCSSC-CCCCCTTSTTTCTT
T ss_pred             hhcCcccCCEEECCCCCCCcchhhhhc--CcCCEEECCCCc-CcccChhhcCCCCCCEEECCCCC-CCCCCHHHHhcCCC
Confidence             67889999999999995556665443  689999999998 88999988899999999999998 4578877 888888


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       499 L~~L~l~  505 (562)
T 3a79_B          499 LQYIWLH  505 (562)
T ss_dssp             CCCEECC
T ss_pred             CCEEEec
Confidence            8877654

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.15  E-value=1.8e-10  Score=101.36  Aligned_cols=122  Identities=19%  Similarity=0.299  Sum_probs=98.5

Q ss_pred             EEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCC
Q 046115          334 LLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKL  412 (505)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l  412 (505)
                      +....+....+|..++      ++|+.|++.+|.++.    +|..+..+.+|+.|+|+       ++.+..++ ..+..+
T Consensus        15 l~~~~~~l~~ip~~~~------~~l~~L~L~~n~i~~----ip~~~~~l~~L~~L~Ls-------~N~i~~i~~~~f~~l   77 (193)
T 2wfh_A           15 VRCSNKGLKVLPKGIP------RDVTELYLDGNQFTL----VPKELSNYKHLTLIDLS-------NNRISTLSNQSFSNM   77 (193)
T ss_dssp             EECTTSCCSSCCSCCC------TTCCEEECCSSCCCS----CCGGGGGCTTCCEEECC-------SSCCCCCCTTTTTTC
T ss_pred             EEcCCCCCCcCCCCCC------CCCCEEECCCCcCch----hHHHhhcccCCCEEECC-------CCcCCEeCHhHccCC
Confidence            4444455555665443      589999999998864    55678999999999998       66676665 458899


Q ss_pred             CCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCccc
Q 046115          413 LHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       413 ~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~  474 (505)
                      ++|++|+|++|. ++.+|+ .+..+++|+.|+|++|. +..+|.. +..+++|++|++++|...
T Consensus        78 ~~L~~L~Ls~N~-l~~i~~~~f~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~~~  139 (193)
T 2wfh_A           78 TQLLTLILSYNR-LRCIPPRTFDGLKSLRLLSLHGND-ISVVPEGAFNDLSALSHLAIGANPLY  139 (193)
T ss_dssp             TTCCEEECCSSC-CCBCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTTTCTTCCEEECCSSCEE
T ss_pred             CCCCEEECCCCc-cCEeCHHHhCCCCCCCEEECCCCC-CCeeChhhhhcCccccEEEeCCCCee
Confidence            999999999999 666654 68999999999999999 7788774 788999999999999854

>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=99.15  E-value=9.9e-11  Score=119.98  Aligned_cols=104  Identities=20%  Similarity=0.187  Sum_probs=57.9

Q ss_pred             CCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCcceeeccCCccccccchhhh
Q 046115          356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPETLC  434 (505)
Q Consensus       356 ~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp~~~~  434 (505)
                      ++|+.|++++|.+...   .|..+..+++|++|+|+       ++.+..+ |..++.+++|++|++++|. ++.+|..  
T Consensus        21 ~~L~~L~Ls~n~i~~~---~~~~~~~l~~L~~L~Ls-------~n~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~lp~~--   87 (520)
T 2z7x_B           21 QKTTILNISQNYISEL---WTSDILSLSKLRILIIS-------HNRIQYLDISVFKFNQELEYLDLSHNK-LVKISCH--   87 (520)
T ss_dssp             TTCSEEECCSSCCCCC---CHHHHTTCTTCCEEECC-------SSCCCEEEGGGGTTCTTCCEEECCSSC-CCEEECC--
T ss_pred             ccccEEECCCCccccc---ChhhccccccccEEecC-------CCccCCcChHHhhcccCCCEEecCCCc-eeecCcc--
Confidence            5566666666655433   34445566666666665       3333333 4455566666666666665 5555554  


Q ss_pred             cCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCc
Q 046115          435 ELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       435 ~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~  472 (505)
                      .+++|++|++++|.... .+|..++.+++|++|++++|.
T Consensus        88 ~l~~L~~L~L~~N~l~~~~~p~~~~~l~~L~~L~L~~n~  126 (520)
T 2z7x_B           88 PTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGLSTTH  126 (520)
T ss_dssp             CCCCCSEEECCSSCCSSCCCCGGGGGCTTCCEEEEEESS
T ss_pred             ccCCccEEeccCCccccccchhhhccCCcceEEEecCcc
Confidence            55666666666665222 245556666666666666655

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.15  E-value=9.6e-11  Score=115.41  Aligned_cols=144  Identities=13%  Similarity=0.146  Sum_probs=105.1

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-c
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-T  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~  407 (505)
                      ..++.+.+..+....+|...   +..+++|++|++.+|.+...   .+..+..+.+|++|+++       ++.+..+| .
T Consensus        45 ~~l~~l~l~~~~l~~l~~~~---~~~l~~L~~L~L~~n~i~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~  111 (390)
T 3o6n_A           45 NNQKIVTFKNSTMRKLPAAL---LDSFRQVELLNLNDLQIEEI---DTYAFAYAHTIQKLYMG-------FNAIRYLPPH  111 (390)
T ss_dssp             CCCSEEEEESCEESEECTHH---HHHCCCCSEEECTTSCCCEE---CTTTTTTCTTCCEEECC-------SSCCCCCCTT
T ss_pred             CCceEEEecCCchhhCChhH---hcccccCcEEECCCCccccc---ChhhccCCCCcCEEECC-------CCCCCcCCHH
Confidence            46777888777777666543   23678899999999887653   45567888899999998       55566654 4


Q ss_pred             cccCCCCcceeeccCCccccccchhh-hcCCCCcEEecCCCcCcccc-chhccccccCceeecCCCcccccccccccCCc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPETL-CELYNLERLNVDDCQNLREL-PRGIGKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~~-~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      .++.+++|++|++++|. +..+|..+ +.+++|++|++++|. +..+ |..+..+++|++|++++|... .++  +..++
T Consensus       112 ~~~~l~~L~~L~L~~n~-l~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~l~~n~l~-~~~--~~~l~  186 (390)
T 3o6n_A          112 VFQNVPLLTVLVLERND-LSSLPRGIFHNTPKLTTLSMSNNN-LERIEDDTFQATTSLQNLQLSSNRLT-HVD--LSLIP  186 (390)
T ss_dssp             TTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTSSCTTCCEEECCSSCCS-BCC--GGGCT
T ss_pred             HhcCCCCCCEEECCCCc-cCcCCHHHhcCCCCCcEEECCCCc-cCccChhhccCCCCCCEEECCCCcCC-ccc--ccccc
Confidence            47888999999999988 77888764 788999999999988 5555 445888899999999988743 332  33444


Q ss_pred             cCCcc
Q 046115          486 RLRRV  490 (505)
Q Consensus       486 ~L~~L  490 (505)
                      +|+.|
T Consensus       187 ~L~~L  191 (390)
T 3o6n_A          187 SLFHA  191 (390)
T ss_dssp             TCSEE
T ss_pred             cccee
Confidence            44433

>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=99.15  E-value=7.4e-11  Score=102.25  Aligned_cols=125  Identities=18%  Similarity=0.123  Sum_probs=104.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCC-CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLR-GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .+..+.+..+....++.     +..+. +|+.|++++|.+++.     ..+..+++|++|+++       ++.+..+|+.
T Consensus        20 ~L~~L~l~~n~l~~i~~-----~~~~~~~L~~L~Ls~N~l~~~-----~~l~~l~~L~~L~Ls-------~N~l~~~~~~   82 (176)
T 1a9n_A           20 RDRELDLRGYKIPVIEN-----LGATLDQFDAIDFSDNEIRKL-----DGFPLLRRLKTLLVN-------NNRICRIGEG   82 (176)
T ss_dssp             SCEEEECTTSCCCSCCC-----GGGGTTCCSEEECCSSCCCEE-----CCCCCCSSCCEEECC-------SSCCCEECSC
T ss_pred             CceEEEeeCCCCchhHH-----hhhcCCCCCEEECCCCCCCcc-----cccccCCCCCEEECC-------CCcccccCcc
Confidence            56777777776665532     22444 999999999998764     247889999999999       7778888866


Q ss_pred             c-cCCCCcceeeccCCccccccch--hhhcCCCCcEEecCCCcCccccchh----ccccccCceeecCCCcc
Q 046115          409 I-EKLLHLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELPRG----IGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       409 ~-~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~lp~~----~~~l~~L~~L~l~~~~~  473 (505)
                      + +.+++|++|++++|. ++.+|.  .+..+++|+.|++++|+ +..+|..    ++.+++|+.|++++|..
T Consensus        83 ~~~~l~~L~~L~L~~N~-i~~~~~~~~l~~l~~L~~L~l~~N~-i~~~~~~~~~~~~~l~~L~~Ld~~~n~~  152 (176)
T 1a9n_A           83 LDQALPDLTELILTNNS-LVELGDLDPLASLKSLTYLCILRNP-VTNKKHYRLYVIYKVPQVRVLDFQKVKL  152 (176)
T ss_dssp             HHHHCTTCCEEECCSCC-CCCGGGGGGGGGCTTCCEEECCSSG-GGGSTTHHHHHHHHCTTCSEETTEECCH
T ss_pred             hhhcCCCCCEEECCCCc-CCcchhhHhhhcCCCCCEEEecCCC-CCCcHhHHHHHHHHCCccceeCCCcCCH
Confidence            5 899999999999999 788887  78999999999999999 7788885    89999999999999873

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.15  E-value=1.3e-10  Score=110.79  Aligned_cols=145  Identities=19%  Similarity=0.170  Sum_probs=73.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCC-----CCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGL-----RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE  404 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~  404 (505)
                      .+..+.+..+....+|..+    ..+     ++|++|++++|.+...   .|..+..+++|+.|+++      ++...+.
T Consensus       122 ~L~~L~Ls~N~l~~~~~~~----~~l~~~~~~~L~~L~L~~N~l~~~---~~~~~~~l~~L~~L~Ls------~N~l~~~  188 (312)
T 1wwl_A          122 DLNILNLRNVSWATRDAWL----AELQQWLKPGLKVLSIAQAHSLNF---SCEQVRVFPALSTLDLS------DNPELGE  188 (312)
T ss_dssp             CCSEEEEESCBCSSSSSHH----HHHHTTCCTTCCEEEEESCSCCCC---CTTTCCCCSSCCEEECC------SCTTCHH
T ss_pred             CccEEEccCCCCcchhHHH----HHHHHhhcCCCcEEEeeCCCCccc---hHHHhccCCCCCEEECC------CCCcCcc
Confidence            4555555555554432211    122     5666666666655443   33445566666666665      1222222


Q ss_pred             --cCccc--cCCCCcceeeccCCcccccc---chhh-hcCCCCcEEecCCCcCccccc-hhccccccCceeecCCCcccc
Q 046115          405 --IPTNI--EKLLHLKYLNLKGQKKIEKL---PETL-CELYNLERLNVDDCQNLRELP-RGIGKLRKLMYLHNEDTGCLR  475 (505)
Q Consensus       405 --~p~~~--~~l~~L~~L~l~~~~~~~~l---p~~~-~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~  475 (505)
                        +|..+  +.+++|++|++++|. ++.+   +..+ ..+++|+.|++++|......| ..+..+++|++|++++|. +.
T Consensus       189 ~~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~Ls~N~-l~  266 (312)
T 1wwl_A          189 RGLISALCPLKFPTLQVLALRNAG-METPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTG-LK  266 (312)
T ss_dssp             HHHHHHSCTTSCTTCCEEECTTSC-CCCHHHHHHHHHHTTCCCSEEECTTSCCCSSCCCSCCCCCTTCCEEECTTSC-CS
T ss_pred             hHHHHHHHhccCCCCCEEECCCCc-CcchHHHHHHHHhcCCCCCEEECCCCcCCcccchhhhhhcCCCCEEECCCCc-cC
Confidence              22233  556666666666666 4422   2222 355666666666666222232 234455666666666665 33


Q ss_pred             cccccccCCccCCccc
Q 046115          476 YLPAGIGELIRLRRVR  491 (505)
Q Consensus       476 ~~p~~i~~l~~L~~L~  491 (505)
                      .+|..+.  ++|+.|+
T Consensus       267 ~ip~~~~--~~L~~L~  280 (312)
T 1wwl_A          267 QVPKGLP--AKLSVLD  280 (312)
T ss_dssp             SCCSSCC--SEEEEEE
T ss_pred             hhhhhcc--CCceEEE
Confidence            5555544  4444443

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.15  E-value=9.4e-11  Score=111.70  Aligned_cols=148  Identities=18%  Similarity=0.165  Sum_probs=113.2

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHh--hcCcccceEEecccccCCccccccccC
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLF--EKLTCLRALELQVRESWPRNNLIKEIP  406 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~--~~l~~L~~L~l~~~~~~~~~~~~~~~p  406 (505)
                      ..+..+.+..+....++.   ..+..+++|+.|++++|.+.+... .|..+  ..+++|+.|+++       ++.+..++
T Consensus       149 ~~L~~L~L~~N~l~~~~~---~~~~~l~~L~~L~Ls~N~l~~~~~-~~~~~~~~~l~~L~~L~L~-------~N~l~~~~  217 (312)
T 1wwl_A          149 PGLKVLSIAQAHSLNFSC---EQVRVFPALSTLDLSDNPELGERG-LISALCPLKFPTLQVLALR-------NAGMETPS  217 (312)
T ss_dssp             TTCCEEEEESCSCCCCCT---TTCCCCSSCCEEECCSCTTCHHHH-HHHHSCTTSCTTCCEEECT-------TSCCCCHH
T ss_pred             CCCcEEEeeCCCCccchH---HHhccCCCCCEEECCCCCcCcchH-HHHHHHhccCCCCCEEECC-------CCcCcchH
Confidence            377888888887765553   345689999999999998765322 23334  789999999998       56666433


Q ss_pred             ---cc-ccCCCCcceeeccCCccccccc--hhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccccc
Q 046115          407 ---TN-IEKLLHLKYLNLKGQKKIEKLP--ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG  480 (505)
Q Consensus       407 ---~~-~~~l~~L~~L~l~~~~~~~~lp--~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~  480 (505)
                         .. +..+++|++|++++|. +...+  ..+..+++|+.|++++|. +..+|..+.  ++|++|++++|. +..+|. 
T Consensus       218 ~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~~l~~L~~L~Ls~N~-l~~ip~~~~--~~L~~L~Ls~N~-l~~~p~-  291 (312)
T 1wwl_A          218 GVCSALAAARVQLQGLDLSHNS-LRDAAGAPSCDWPSQLNSLNLSFTG-LKQVPKGLP--AKLSVLDLSYNR-LDRNPS-  291 (312)
T ss_dssp             HHHHHHHHTTCCCSEEECTTSC-CCSSCCCSCCCCCTTCCEEECTTSC-CSSCCSSCC--SEEEEEECCSSC-CCSCCC-
T ss_pred             HHHHHHHhcCCCCCEEECCCCc-CCcccchhhhhhcCCCCEEECCCCc-cChhhhhcc--CCceEEECCCCC-CCCChh-
Confidence               22 3578999999999999 55433  345678999999999999 779998876  899999999998 455676 


Q ss_pred             ccCCccCCcccee
Q 046115          481 IGELIRLRRVREF  493 (505)
Q Consensus       481 i~~l~~L~~L~~~  493 (505)
                      +..+++|+.|++.
T Consensus       292 ~~~l~~L~~L~L~  304 (312)
T 1wwl_A          292 PDELPQVGNLSLK  304 (312)
T ss_dssp             TTTSCEEEEEECT
T ss_pred             HhhCCCCCEEecc
Confidence            8888888877653

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.14  E-value=1.2e-10  Score=114.84  Aligned_cols=128  Identities=19%  Similarity=0.188  Sum_probs=107.4

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccc-h
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLP-E  431 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp-~  431 (505)
                      .+.+++.|.+.++.+...   .+..+..+++|++|+++       ++.+..+| ..++.+++|++|++++|. +..+| .
T Consensus        43 ~l~~l~~l~l~~~~l~~l---~~~~~~~l~~L~~L~L~-------~n~i~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~  111 (390)
T 3o6n_A           43 TLNNQKIVTFKNSTMRKL---PAALLDSFRQVELLNLN-------DLQIEEIDTYAFAYAHTIQKLYMGFNA-IRYLPPH  111 (390)
T ss_dssp             GGCCCSEEEEESCEESEE---CTHHHHHCCCCSEEECT-------TSCCCEECTTTTTTCTTCCEEECCSSC-CCCCCTT
T ss_pred             ccCCceEEEecCCchhhC---ChhHhcccccCcEEECC-------CCcccccChhhccCCCCcCEEECCCCC-CCcCCHH
Confidence            468999999999987654   45557889999999998       66666665 478999999999999999 66664 5


Q ss_pred             hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          432 TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      .++.+++|+.|++++|. +..+|.. +..+++|++|++++|......|..+..+++|+.|++.
T Consensus       112 ~~~~l~~L~~L~L~~n~-l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~  173 (390)
T 3o6n_A          112 VFQNVPLLTVLVLERND-LSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLS  173 (390)
T ss_dssp             TTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECC
T ss_pred             HhcCCCCCCEEECCCCc-cCcCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECC
Confidence            57999999999999998 7889887 5899999999999998665556668999999988765

>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=99.14  E-value=1.1e-12  Score=116.35  Aligned_cols=132  Identities=20%  Similarity=0.221  Sum_probs=110.5

Q ss_pred             CCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccc
Q 046115          351 NVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP  430 (505)
Q Consensus       351 ~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp  430 (505)
                      .+..+++|++|++++|.++.    +| .+..+++|+.|+++       ++.+..+|..++.+++|++|++++|. ++.+|
T Consensus        43 ~~~~l~~L~~L~ls~n~l~~----l~-~~~~l~~L~~L~l~-------~n~l~~l~~~~~~~~~L~~L~L~~N~-l~~l~  109 (198)
T 1ds9_A           43 TLSTLKACKHLALSTNNIEK----IS-SLSGMENLRILSLG-------RNLIKKIENLDAVADTLEELWISYNQ-IASLS  109 (198)
T ss_dssp             HHHHTTTCSEEECSEEEESC----CC-CHHHHTTCCEEEEE-------EEEECSCSSHHHHHHHCSEEEEEEEE-CCCHH
T ss_pred             HHhcCCCCCEEECCCCCCcc----cc-ccccCCCCCEEECC-------CCCcccccchhhcCCcCCEEECcCCc-CCcCC
Confidence            34489999999999998876    45 58889999999999       77788889888888999999999998 77888


Q ss_pred             hhhhcCCCCcEEecCCCcCccccch--hccccccCceeecCCCccccccccc----------ccCCccCCccceeEecC
Q 046115          431 ETLCELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCLRYLPAG----------IGELIRLRRVREFVVGG  497 (505)
Q Consensus       431 ~~~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~~p~~----------i~~l~~L~~L~~~~~~~  497 (505)
                       .+..+++|+.|++++|. +..+|.  .+..+++|++|++++|...+..|..          +..+++|+.|+...+..
T Consensus       110 -~~~~l~~L~~L~l~~N~-i~~~~~~~~l~~l~~L~~L~l~~N~l~~~~~~~~~~~~~~~~~~~~l~~L~~Ld~~~i~~  186 (198)
T 1ds9_A          110 -GIEKLVNLRVLYMSNNK-ITNWGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLDGMPVDV  186 (198)
T ss_dssp             -HHHHHHHSSEEEESEEE-CCCHHHHHHHTTTTTCSEEEECSCHHHHHHHTTTTHHHHHHHHHHHCSSCSEECCGGGTT
T ss_pred             -ccccCCCCCEEECCCCc-CCchhHHHHHhcCCCCCEEEecCCccccccccccchHHHHHHHHHhCCCcEEECCcccCH
Confidence             49999999999999998 777765  6899999999999999866555542          78889999888544433

>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=99.14  E-value=1.5e-10  Score=122.86  Aligned_cols=151  Identities=22%  Similarity=0.192  Sum_probs=119.4

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-  407 (505)
                      ..++.+.+..+....++..   .|.++++|++|++.+|.++..   .|..+.++++|++|+|+       ++.+..+|+ 
T Consensus        25 ~~l~~L~Ls~n~l~~~~~~---~~~~l~~L~~L~Ls~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~l~~~   91 (680)
T 1ziw_A           25 TNITVLNLTHNQLRRLPAA---NFTRYSQLTSLDVGFNTISKL---EPELCQKLPMLKVLNLQ-------HNELSQLSDK   91 (680)
T ss_dssp             TTCSEEECCSSCCCCCCGG---GGGGGTTCSEEECCSSCCCCC---CTTHHHHCTTCCEEECC-------SSCCCCCCTT
T ss_pred             CCCcEEECCCCCCCCcCHH---HHhCCCcCcEEECCCCccCcc---CHHHHhcccCcCEEECC-------CCccCccChh
Confidence            4788888888877665543   355889999999999987764   67778999999999998       667777876 


Q ss_pred             cccCCCCcceeeccCCccccccc-hhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccccccc--CC
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIG--EL  484 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~--~l  484 (505)
                      .++.+++|++|++++|. +..+| ..++.+++|++|++++|......|..++++++|++|++++|...+..|..+.  .+
T Consensus        92 ~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~  170 (680)
T 1ziw_A           92 TFAFCTNLTELHLMSNS-IQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNNKIQALKSEELDIFAN  170 (680)
T ss_dssp             TTTTCTTCSEEECCSSC-CCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSCCCCBCHHHHGGGTT
T ss_pred             hhccCCCCCEEECCCCc-cCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEEccCCcccccCHHHhhcccc
Confidence            58899999999999998 66665 5689999999999999985555566788999999999999985444444343  45


Q ss_pred             ccCCcccee
Q 046115          485 IRLRRVREF  493 (505)
Q Consensus       485 ~~L~~L~~~  493 (505)
                      ++|+.|++.
T Consensus       171 ~~L~~L~L~  179 (680)
T 1ziw_A          171 SSLKKLELS  179 (680)
T ss_dssp             CEESEEECT
T ss_pred             ccccEEECC
Confidence            777777653

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.14  E-value=3.4e-09  Score=104.22  Aligned_cols=289  Identities=14%  Similarity=0.054  Sum_probs=169.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--CCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--AGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~~r~Ll   77 (505)
                      ++|+|||+||+.+++  ...... ..++|+++....+...+...++..++...........+..+.+...+  .+++.+|
T Consensus        52 ~~G~GKTtl~~~l~~--~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vl  129 (389)
T 1fnn_A           52 RPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFL  129 (389)
T ss_dssp             CTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCCCCHHHHHHHHHH--HHhhhcCeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEE
Confidence            479999999999998  444432 35668888888888899999999887543333334555555555544  3568999


Q ss_pred             EEeCCCCCCccChhHHHHhhcCCC----CCcEEEEEeCchHHHHHhC-------CcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           78 VLDDVWNEDYYKWEPFYKCLKNSL----HESKILITTRKETVARIMG-------STHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        78 vlDdv~~~~~~~~~~~~~~~~~~~----~~~~iLiTtr~~~~~~~~~-------~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      |+|+++..+......+...+....    .+..+|++|+.........       ....+.+++++.++..+++.......
T Consensus       130 ilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~  209 (389)
T 1fnn_A          130 VLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAG  209 (389)
T ss_dssp             EEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHH
T ss_pred             EEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhh
Confidence            999997765444555555553321    4677888887764332211       12369999999999999998765320


Q ss_pred             CCCCCCchHHHHHHHHHHHc---------CCChHHHHHHHHHhc------cC--CCHHHHHHHHhhhhhhhhhcccCchh
Q 046115          147 KTIGKRENLEKIGREIVKKC---------KGLPLAAKTIASLLR------SK--NTEKEWQNILENEIWELEAIEKGLLA  209 (505)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~---------~g~Plal~~~~~~l~------~~--~~~~~~~~~l~~~~~~l~~~~~~~~~  209 (505)
                      ..  ...-.++++..+++.+         +|.|..+..+.....      +.  -+.+.....+...          ...
T Consensus       210 ~~--~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~~~~----------~~~  277 (389)
T 1fnn_A          210 LA--EGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV----------LFG  277 (389)
T ss_dssp             BC--TTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHH----------SCC
T ss_pred             cC--CCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH----------hhh
Confidence            00  0112346678888888         788754443333211      11  1333333322211          112


Q ss_pred             hHhhccccCChhhhhhhhhhccCC---CCCCCChHHHHHHHHH----cCCCCCCCCCCHHHHHHHHHHHHHHcccccccc
Q 046115          210 PLLLSYNELPSKVKRCFSYCAVFP---KDYGIRKHKLIELWMA----QGYLSEKGAKEMEDIGEEYFNILASRSFFQDFN  282 (505)
Q Consensus       210 ~l~~s~~~L~~~~~~~ll~la~f~---~~~~i~~~~l~~~w~~----~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~  282 (505)
                      .+...+..|+...+.++..++.+.   .+..+....+...+..    .+..     ......+.++++.|...+++....
T Consensus       278 ~~~~~l~~l~~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~-----~~~~~~~~~~l~~L~~~gli~~~~  352 (389)
T 1fnn_A          278 ISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGER-----PRVHSQLWSYLNDLREKGIVETRQ  352 (389)
T ss_dssp             CCHHHHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTCC-----CCCHHHHHHHHHHHHHTTSSEEEE
T ss_pred             hHHHHHHcCCHHHHHHHHHHHHHHhhccCCCccHHHHHHHHHHHHHHcCCC-----CCCHHHHHHHHHHHHhCCCeEEee
Confidence            233446677788888887777653   2213444454443322    1111     112355778899999999998755


Q ss_pred             c----CCCCCeeEe----eehHHHHHHHHHhhcc
Q 046115          283 K----YDDGEIYKC----KMHDIVHDFAQYLCSN  308 (505)
Q Consensus       283 ~----~~~~~~~~~----~~H~lv~~~~~~~~~~  308 (505)
                      .    +..++...+    ..|++...+...+..+
T Consensus       353 ~~~~~g~~g~~~~~~l~~~~~~v~~~~~~~~~~~  386 (389)
T 1fnn_A          353 NKRGEGVRGRTTLISIGTEPLDTLEAVITKLIKE  386 (389)
T ss_dssp             C---------CEEEECCSSCHHHHHHHHHHHHHH
T ss_pred             eccCCCCCCceeEEEeCCCHHHHHHHHHHHHHHH
Confidence            4    212322222    2567777666555443

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.14  E-value=9.8e-11  Score=108.52  Aligned_cols=121  Identities=21%  Similarity=0.320  Sum_probs=102.5

Q ss_pred             CCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchh
Q 046115          353 TGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET  432 (505)
Q Consensus       353 ~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~  432 (505)
                      ..+++|+.|++++|.++.    ++ .+..+++|+.|+|+       ++.+..+|+ ++.+++|++|++++|. ++.+|. 
T Consensus        38 ~~l~~L~~L~l~~n~i~~----l~-~l~~l~~L~~L~L~-------~N~i~~~~~-l~~l~~L~~L~L~~N~-l~~l~~-  102 (263)
T 1xeu_A           38 KELSGVQNFNGDNSNIQS----LA-GMQFFTNLKELHLS-------HNQISDLSP-LKDLTKLEELSVNRNR-LKNLNG-  102 (263)
T ss_dssp             HHHTTCSEEECTTSCCCC----CT-TGGGCTTCCEEECC-------SSCCCCCGG-GTTCSSCCEEECCSSC-CSCCTT-
T ss_pred             hhcCcCcEEECcCCCccc----ch-HHhhCCCCCEEECC-------CCccCCChh-hccCCCCCEEECCCCc-cCCcCc-
Confidence            378999999999998875    34 37889999999999       777888877 9999999999999999 888887 


Q ss_pred             hhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          433 LCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       433 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      +.. ++|+.|++++|. +..+| .+..+++|++|++++|. +..+| .+..+++|+.|++.
T Consensus       103 ~~~-~~L~~L~L~~N~-l~~~~-~l~~l~~L~~L~Ls~N~-i~~~~-~l~~l~~L~~L~L~  158 (263)
T 1xeu_A          103 IPS-ACLSRLFLDNNE-LRDTD-SLIHLKNLEILSIRNNK-LKSIV-MLGFLSKLEVLDLH  158 (263)
T ss_dssp             CCC-SSCCEEECCSSC-CSBSG-GGTTCTTCCEEECTTSC-CCBCG-GGGGCTTCCEEECT
T ss_pred             ccc-CcccEEEccCCc-cCCCh-hhcCcccccEEECCCCc-CCCCh-HHccCCCCCEEECC
Confidence            444 999999999998 77776 68999999999999998 45565 68888888877653

>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=99.13  E-value=2.8e-10  Score=109.35  Aligned_cols=145  Identities=19%  Similarity=0.208  Sum_probs=107.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc---ccC
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK---EIP  406 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~---~~p  406 (505)
                      .+..+.+..+....+|..+.      ++|+.|.+.+|.+...   .+..+..+.+|+.|+++       ++.+.   ..+
T Consensus       101 ~L~~L~Ls~n~l~~l~~~~~------~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~-------~n~l~~~~~~~  164 (330)
T 1xku_A          101 KLERLYLSKNQLKELPEKMP------KTLQELRVHENEITKV---RKSVFNGLNQMIVVELG-------TNPLKSSGIEN  164 (330)
T ss_dssp             TCCEEECCSSCCSBCCSSCC------TTCCEEECCSSCCCBB---CHHHHTTCTTCCEEECC-------SSCCCGGGBCT
T ss_pred             CCCEEECCCCcCCccChhhc------ccccEEECCCCccccc---CHhHhcCCccccEEECC-------CCcCCccCcCh
Confidence            55666666666555544332      5777777777776543   56668888999999998       44443   456


Q ss_pred             ccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCcc
Q 046115          407 TNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       407 ~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      ..+..+++|++|++++|. ++.+|..+.  ++|+.|++++|......|..+..+++|++|++++|......|..+..+++
T Consensus       165 ~~~~~l~~L~~L~l~~n~-l~~l~~~~~--~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~  241 (330)
T 1xku_A          165 GAFQGMKKLSYIRIADTN-ITTIPQGLP--PSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPH  241 (330)
T ss_dssp             TGGGGCTTCCEEECCSSC-CCSCCSSCC--TTCSEEECTTSCCCEECTGGGTTCTTCCEEECCSSCCCEECTTTGGGSTT
T ss_pred             hhccCCCCcCEEECCCCc-cccCCcccc--ccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCceeChhhccCCCC
Confidence            678889999999999998 778887554  78999999999844444677899999999999999855544557888888


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       242 L~~L~L~  248 (330)
T 1xku_A          242 LRELHLN  248 (330)
T ss_dssp             CCEEECC
T ss_pred             CCEEECC
Confidence            8887764

>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=99.13  E-value=1.3e-10  Score=121.06  Aligned_cols=146  Identities=13%  Similarity=0.114  Sum_probs=109.5

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-  407 (505)
                      ..++.+.+..+....+|..+   +..+++|++|++.+|.+++.   .|..+..+++|++|+|+       ++.+..+|+ 
T Consensus        51 ~~l~~l~l~~~~l~~lp~~~---~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~  117 (597)
T 3oja_B           51 NNQKIVTFKNSTMRKLPAAL---LDSFRQVELLNLNDLQIEEI---DTYAFAYAHTIQKLYMG-------FNAIRYLPPH  117 (597)
T ss_dssp             CCCSEEEESSCEESEECTHH---HHHCCCCSEEECTTSCCCEE---CTTTTTTCTTCCEEECC-------SSCCCCCCTT
T ss_pred             CCceEEEeeCCCCCCcCHHH---HccCCCCcEEECCCCCCCCC---ChHHhcCCCCCCEEECC-------CCcCCCCCHH
Confidence            35666777766666666543   34688999999999987754   55568899999999998       555666654 


Q ss_pred             cccCCCCcceeeccCCccccccchhh-hcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCcc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPETL-CELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~~-~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      .++.+++|++|+|++|. ++.+|..+ +.+++|+.|+|++|......|..++.+++|++|++++|... .+|  ++.+++
T Consensus       118 ~~~~l~~L~~L~L~~n~-l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~-~~~--~~~l~~  193 (597)
T 3oja_B          118 VFQNVPLLTVLVLERND-LSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLT-HVD--LSLIPS  193 (597)
T ss_dssp             TTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECTTSCCS-BCC--GGGCTT
T ss_pred             HHcCCCCCCEEEeeCCC-CCCCCHHHhccCCCCCEEEeeCCcCCCCChhhhhcCCcCcEEECcCCCCC-CcC--hhhhhh
Confidence            46899999999999998 77888764 89999999999999844444556899999999999999744 343  444555


Q ss_pred             CCccc
Q 046115          487 LRRVR  491 (505)
Q Consensus       487 L~~L~  491 (505)
                      |+.|+
T Consensus       194 L~~L~  198 (597)
T 3oja_B          194 LFHAN  198 (597)
T ss_dssp             CSEEE
T ss_pred             hhhhh
Confidence            55544

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.13  E-value=2.6e-10  Score=100.29  Aligned_cols=119  Identities=18%  Similarity=0.291  Sum_probs=97.2

Q ss_pred             eEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccc-hhhhcCC
Q 046115          359 RSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLP-ETLCELY  437 (505)
Q Consensus       359 ~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~  437 (505)
                      +++.+.++.+..    +|..+  ..+|+.|+++       ++.+..+|..+..+++|++|++++|. ++.++ ..+..++
T Consensus        13 ~~l~~~~~~l~~----ip~~~--~~~l~~L~L~-------~n~i~~ip~~~~~l~~L~~L~Ls~N~-i~~i~~~~f~~l~   78 (193)
T 2wfh_A           13 TVVRCSNKGLKV----LPKGI--PRDVTELYLD-------GNQFTLVPKELSNYKHLTLIDLSNNR-ISTLSNQSFSNMT   78 (193)
T ss_dssp             TEEECTTSCCSS----CCSCC--CTTCCEEECC-------SSCCCSCCGGGGGCTTCCEEECCSSC-CCCCCTTTTTTCT
T ss_pred             CEEEcCCCCCCc----CCCCC--CCCCCEEECC-------CCcCchhHHHhhcccCCCEEECCCCc-CCEeCHhHccCCC
Confidence            578888887765    34322  3589999998       77788999999999999999999999 66665 4689999


Q ss_pred             CCcEEecCCCcCccccch-hccccccCceeecCCCcccccccc-cccCCccCCcccee
Q 046115          438 NLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVREF  493 (505)
Q Consensus       438 ~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~~  493 (505)
                      +|+.|+|++|. +..+|+ .+..+++|++|++++|. +..+|. .|..+++|+.|++.
T Consensus        79 ~L~~L~Ls~N~-l~~i~~~~f~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~  134 (193)
T 2wfh_A           79 QLLTLILSYNR-LRCIPPRTFDGLKSLRLLSLHGND-ISVVPEGAFNDLSALSHLAIG  134 (193)
T ss_dssp             TCCEEECCSSC-CCBCCTTTTTTCTTCCEEECCSSC-CCBCCTTTTTTCTTCCEEECC
T ss_pred             CCCEEECCCCc-cCEeCHHHhCCCCCCCEEECCCCC-CCeeChhhhhcCccccEEEeC
Confidence            99999999999 666665 68999999999999998 456665 47888888887653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.13  E-value=4.1e-09  Score=103.46  Aligned_cols=263  Identities=10%  Similarity=-0.009  Sum_probs=153.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccC------CCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--CC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN------FEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--AG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~------f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~   72 (505)
                      ++|+|||++|+.+++  .....      -...+|+++....+...++..++.+++...........+....+...+  .+
T Consensus        52 ~~G~GKT~l~~~~~~--~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~  129 (387)
T 2v1u_A           52 LTGTGKTAVARLVLR--RLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLR  129 (387)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHH--HHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccC
Confidence            589999999999998  44322      124568888888888999999999997544444444555566666666  34


Q ss_pred             ceEEEEEeCCCCCCcc--ChhHH---HHhhcCC--CCCcEEEEEeCchHHH----HH-hCCc--ceEeCCCCChhhHHHH
Q 046115           73 KKFLLVLDDVWNEDYY--KWEPF---YKCLKNS--LHESKILITTRKETVA----RI-MGST--HVISVNVLSEMECWSV  138 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~--~~~~~---~~~~~~~--~~~~~iLiTtr~~~~~----~~-~~~~--~~~~l~~l~~~ea~~L  138 (505)
                      ++.+||+|+++.....  ..+.+   .......  ..+..+|.||+.....    .. ....  ..+.+++++.++..++
T Consensus       130 ~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~i  209 (387)
T 2v1u_A          130 GIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDI  209 (387)
T ss_dssp             SEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHH
T ss_pred             CeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHH
Confidence            6899999999663221  11222   2222221  4456777777765211    11 1122  4788999999999999


Q ss_pred             HHHhhhC--CCCCCCCchHHHHHHHHHHHcC---CChH-HHHHHHHHh---c--c-C-CCHHHHHHHHhhhhhhhhhccc
Q 046115          139 FQSLAIS--GKTIGKRENLEKIGREIVKKCK---GLPL-AAKTIASLL---R--S-K-NTEKEWQNILENEIWELEAIEK  205 (505)
Q Consensus       139 f~~~~~~--~~~~~~~~~~~~~~~~i~~~~~---g~Pl-al~~~~~~l---~--~-~-~~~~~~~~~l~~~~~~l~~~~~  205 (505)
                      +......  ... ..+   ++++..+++.++   |.|. ++.++....   .  + . -+.+.+...++...        
T Consensus       210 l~~~~~~~~~~~-~~~---~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~~--------  277 (387)
T 2v1u_A          210 LETRAEEAFNPG-VLD---PDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIE--------  277 (387)
T ss_dssp             HHHHHHHHBCTT-TBC---SSHHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHH--------
T ss_pred             HHHHHHhhccCC-CCC---HHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh--------
Confidence            9876431  111 111   234667777777   9993 333322221   1  1 1 15555555554321        


Q ss_pred             CchhhHhhccccCChhhhhhhhhhcc-CCCCCCCChHHHHHHHHH--cCCCCCCCCCCHHHHHHHHHHHHHHcccccccc
Q 046115          206 GLLAPLLLSYNELPSKVKRCFSYCAV-FPKDYGIRKHKLIELWMA--QGYLSEKGAKEMEDIGEEYFNILASRSFFQDFN  282 (505)
Q Consensus       206 ~~~~~l~~s~~~L~~~~~~~ll~la~-f~~~~~i~~~~l~~~w~~--~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~  282 (505)
                        ...+..++..+++..+.++..++. +.....+....+......  +...   ........+.++++.|...|++....
T Consensus       278 --~~~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~L~~~gli~~~~  352 (387)
T 2v1u_A          278 --RDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLG---LEHVTLRRVSGIISELDMLGIVKSRV  352 (387)
T ss_dssp             --HHHHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHHHHHTT---CCCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             --hchHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhcC---CCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence              113455677888888888877773 322223434433222211  1110   11223456778899999999998754

>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=99.13  E-value=1.4e-10  Score=116.80  Aligned_cols=144  Identities=17%  Similarity=0.138  Sum_probs=111.0

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Cc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PT  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~  407 (505)
                      ..++.+.+..+....++   +..+.++++|++|++.+|.+.+.  ..+..+..+++|++|+|+       ++.+... |.
T Consensus        30 ~~l~~L~Ls~n~i~~~~---~~~~~~l~~L~~L~L~~n~~~~~--i~~~~~~~l~~L~~L~Ls-------~n~l~~~~~~   97 (455)
T 3v47_A           30 AHVNYVDLSLNSIAELN---ETSFSRLQDLQFLKVEQQTPGLV--IRNNTFRGLSSLIILKLD-------YNQFLQLETG   97 (455)
T ss_dssp             TTCCEEECCSSCCCEEC---TTTTSSCTTCCEEECCCCSTTCE--ECTTTTTTCTTCCEEECT-------TCTTCEECTT
T ss_pred             CccCEEEecCCccCcCC---hhHhccCccccEEECcCCcccce--ECcccccccccCCEEeCC-------CCccCccChh
Confidence            37888888887766543   34566899999999999987532  135568889999999998       5555544 77


Q ss_pred             cccCCCCcceeeccCCccccccchh--hhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCC
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPET--LCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGEL  484 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~--~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l  484 (505)
                      .++.+++|++|++++|...+.+|..  +..+++|+.|++++|......|.. +..+++|++|++++|...+..|..+..+
T Consensus        98 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l  177 (455)
T 3v47_A           98 AFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNF  177 (455)
T ss_dssp             TTTTCTTCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSCCCCGGGGGCTTCCEEECTTCCBSCCCTTTSGGG
T ss_pred             hccCcccCCEEeCCCCCCCccccCcccccCcccCCEEECCCCccCccCcccccCCCCcccEEeCCCCcccccChhhhhcc
Confidence            8999999999999999944445555  889999999999999944444665 7899999999999998666666656544

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.12  E-value=1.3e-10  Score=126.10  Aligned_cols=153  Identities=21%  Similarity=0.154  Sum_probs=120.3

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPT  407 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~  407 (505)
                      ..++.+.++.+....+.   +..|.++++|++|++++|.....  ..|..+.++++|++|+|+       ++.+.. .|.
T Consensus        24 ~~l~~LdLs~N~i~~i~---~~~~~~l~~L~~LdLs~n~~~~~--i~~~~f~~L~~L~~L~Ls-------~N~l~~~~p~   91 (844)
T 3j0a_A           24 NTTERLLLSFNYIRTVT---ASSFPFLEQLQLLELGSQYTPLT--IDKEAFRNLPNLRILDLG-------SSKIYFLHPD   91 (844)
T ss_dssp             TTCCEEEEESCCCCEEC---SSSCSSCCSCSEEEECTTCCCCE--ECTTTTSSCTTCCEEECT-------TCCCCEECTT
T ss_pred             CCcCEEECCCCcCCccC---hhHCcccccCeEEeCCCCCCccc--cCHHHhcCCCCCCEEECC-------CCcCcccCHh
Confidence            37889999888776543   34566999999999999964332  136778999999999998       555555 478


Q ss_pred             cccCCCCcceeeccCCccccccchh--hhcCCCCcEEecCCCcCccccc-hhccccccCceeecCCCcccccccccccCC
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPET--LCELYNLERLNVDDCQNLRELP-RGIGKLRKLMYLHNEDTGCLRYLPAGIGEL  484 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~--~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l  484 (505)
                      .++.+++|++|+|++|.....+|..  ++.+++|+.|++++|......| ..++++++|++|++++|...+..|..+..+
T Consensus        92 ~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~~~l~~l  171 (844)
T 3j0a_A           92 AFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEHELEPL  171 (844)
T ss_dssp             SSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCCCCCCSGGGHHH
T ss_pred             HccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcCCeeCHHHcccc
Confidence            8999999999999999954556665  8899999999999998444333 468999999999999998777777777776


Q ss_pred             --ccCCcccee
Q 046115          485 --IRLRRVREF  493 (505)
Q Consensus       485 --~~L~~L~~~  493 (505)
                        ++|+.|++.
T Consensus       172 ~~~~L~~L~L~  182 (844)
T 3j0a_A          172 QGKTLSFFSLA  182 (844)
T ss_dssp             HHCSSCCCEEC
T ss_pred             cCCccceEECC
Confidence              778777764

>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=99.12  E-value=1.8e-10  Score=115.93  Aligned_cols=135  Identities=21%  Similarity=0.211  Sum_probs=74.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Ccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~  408 (505)
                      .+..+.+..+.....   .+..+..+++|+.|++++|.+...   .|..+..+++|++|+|+       ++.+..+ |..
T Consensus       276 ~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~Ls~n~l~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~  342 (455)
T 3v47_A          276 GVKTCDLSKSKIFAL---LKSVFSHFTDLEQLTLAQNEINKI---DDNAFWGLTHLLKLNLS-------QNFLGSIDSRM  342 (455)
T ss_dssp             CCCEEECCSSCCCEE---CTTTTTTCTTCCEEECTTSCCCEE---CTTTTTTCTTCCEEECC-------SSCCCEECGGG
T ss_pred             CceEEEecCcccccc---chhhcccCCCCCEEECCCCccccc---ChhHhcCcccCCEEECC-------CCccCCcChhH
Confidence            344444444443322   223344566666666666665543   44445666666666666       3334443 444


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCccccccc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLP  478 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p  478 (505)
                      ++.+++|++|++++|......|..+..+++|+.|++++|. +..+|.. +..+++|++|++++|+..+..|
T Consensus       343 ~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~  412 (455)
T 3v47_A          343 FENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTNQ-LKSVPDGIFDRLTSLQKIWLHTNPWDCSCP  412 (455)
T ss_dssp             GTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSSCBCCCTT
T ss_pred             hcCcccCCEEECCCCcccccChhhccccccccEEECCCCc-cccCCHhHhccCCcccEEEccCCCcccCCC
Confidence            5666666666666666322335556666666666666666 4555543 4566666666666666544444

>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=99.12  E-value=3.2e-10  Score=109.71  Aligned_cols=142  Identities=20%  Similarity=0.226  Sum_probs=108.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++.     +..+++|+.|.+.+|.++..    +. +..+++|+.|+++       ++.+..++ .+
T Consensus       200 ~L~~L~l~~n~l~~~~~-----~~~~~~L~~L~l~~n~l~~~----~~-~~~l~~L~~L~l~-------~n~l~~~~-~~  261 (347)
T 4fmz_A          200 SLHYFTAYVNQITDITP-----VANMTRLNSLKIGNNKITDL----SP-LANLSQLTWLEIG-------TNQISDIN-AV  261 (347)
T ss_dssp             TCCEEECCSSCCCCCGG-----GGGCTTCCEEECCSSCCCCC----GG-GTTCTTCCEEECC-------SSCCCCCG-GG
T ss_pred             ccceeecccCCCCCCch-----hhcCCcCCEEEccCCccCCC----cc-hhcCCCCCEEECC-------CCccCCCh-hH
Confidence            45566665555544333     45788999999999987653    33 7888999999998       55566654 57


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+++|++|++++|. +..+|. +..+++|+.|++++|......|..+..+++|++|++++|... .+++ +..+++|+.
T Consensus       262 ~~l~~L~~L~l~~n~-l~~~~~-~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~L~~n~l~-~~~~-~~~l~~L~~  337 (347)
T 4fmz_A          262 KDLTKLKMLNVGSNQ-ISDISV-LNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNHIT-DIRP-LASLSKMDS  337 (347)
T ss_dssp             TTCTTCCEEECCSSC-CCCCGG-GGGCTTCSEEECCSSCCCGGGHHHHHTCTTCSEEECCSSSCC-CCGG-GGGCTTCSE
T ss_pred             hcCCCcCEEEccCCc-cCCChh-hcCCCCCCEEECcCCcCCCcChhHhhccccCCEEEccCCccc-cccC-hhhhhccce
Confidence            889999999999998 777765 889999999999999855556667889999999999999854 4444 778888888


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       338 L~l~  341 (347)
T 4fmz_A          338 ADFA  341 (347)
T ss_dssp             ESSS
T ss_pred             eehh
Confidence            7754

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.12  E-value=9.6e-11  Score=121.49  Aligned_cols=133  Identities=20%  Similarity=0.230  Sum_probs=90.5

Q ss_pred             CCCCCCceEEEecCCCccccccchh-HHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccc-ccc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLP-QLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKI-EKL  429 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~-~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~-~~l  429 (505)
                      +..+++|+.|++.+|.+...   .| ..+..+++|++|+++      ++......|..++.+++|++|++++|... ..+
T Consensus       392 ~~~l~~L~~L~l~~n~l~~~---~~~~~~~~l~~L~~L~l~------~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~  462 (570)
T 2z63_A          392 FLGLEQLEHLDFQHSNLKQM---SEFSVFLSLRNLIYLDIS------HTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFL  462 (570)
T ss_dssp             EETCTTCCEEECTTSEEESC---TTSCTTTTCTTCCEEECT------TSCCEECCTTTTTTCTTCCEEECTTCEEGGGEE
T ss_pred             ccccCCCCEEEccCCccccc---cchhhhhcCCCCCEEeCc------CCcccccchhhhhcCCcCcEEECcCCcCccccc
Confidence            34667777777777665443   22 346677777777777      23333445666777888888888888733 357


Q ss_pred             chhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          430 PETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      |..+..+++|+.|++++|......|..+..+++|++|++++|...+..|..+.++++|+.|++.
T Consensus       463 p~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~  526 (570)
T 2z63_A          463 PDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMASNQLKSVPDGIFDRLTSLQKIWLH  526 (570)
T ss_dssp             CSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECC
T ss_pred             hhhhhcccCCCEEECCCCccccCChhhhhcccCCCEEeCCCCcCCCCCHHHhhcccCCcEEEec
Confidence            7777888888888888887444446677888888888888887554444457777777776654

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.12  E-value=2.4e-10  Score=109.86  Aligned_cols=143  Identities=22%  Similarity=0.287  Sum_probs=98.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .++.+.+..+....++.   ..+.++++|++|++.+|.++..   .|..+..+++|++|+++       ++.+..+|..+
T Consensus        55 ~l~~L~l~~n~i~~~~~---~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~-------~n~l~~l~~~~  121 (332)
T 2ft3_A           55 DTTLLDLQNNDISELRK---DDFKGLQHLYALVLVNNKISKI---HEKAFSPLRKLQKLYIS-------KNHLVEIPPNL  121 (332)
T ss_dssp             TCCEEECCSSCCCEECT---TTTTTCTTCCEEECCSSCCCEE---CGGGSTTCTTCCEEECC-------SSCCCSCCSSC
T ss_pred             CCeEEECCCCcCCccCH---hHhhCCCCCcEEECCCCccCcc---CHhHhhCcCCCCEEECC-------CCcCCccCccc
Confidence            56667666666554432   3455778888888888876643   56667788888888887       66666777655


Q ss_pred             cCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCc--cccchhccccccCceeecCCCcccccccccccCCcc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNL--RELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~--~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      .  ++|++|++++|. ++.+|. .+..+++|+.|++++|...  ...|..+..+ +|++|++++|. +..+|..+.  ++
T Consensus       122 ~--~~L~~L~l~~n~-i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l-~L~~L~l~~n~-l~~l~~~~~--~~  194 (332)
T 2ft3_A          122 P--SSLVELRIHDNR-IRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGL-KLNYLRISEAK-LTGIPKDLP--ET  194 (332)
T ss_dssp             C--TTCCEEECCSSC-CCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSC-CCSCCBCCSSB-CSSCCSSSC--SS
T ss_pred             c--ccCCEEECCCCc-cCccCHhHhCCCccCCEEECCCCccccCCCCcccccCC-ccCEEECcCCC-CCccCcccc--CC
Confidence            4  788888888887 666655 4677888888888888732  1445556666 78888888887 445666543  46


Q ss_pred             CCccce
Q 046115          487 LRRVRE  492 (505)
Q Consensus       487 L~~L~~  492 (505)
                      |+.|++
T Consensus       195 L~~L~l  200 (332)
T 2ft3_A          195 LNELHL  200 (332)
T ss_dssp             CSCCBC
T ss_pred             CCEEEC
Confidence            666654

>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=99.11  E-value=2.7e-10  Score=120.74  Aligned_cols=148  Identities=20%  Similarity=0.134  Sum_probs=79.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-cc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~  408 (505)
                      .++.+.+..+....++   +..+.++++|++|++++|.++..   .+..+..+++|++|+++       ++.+..+| ..
T Consensus        50 ~L~~L~Ls~n~l~~~~---~~~~~~l~~L~~L~L~~n~l~~l---~~~~~~~l~~L~~L~L~-------~n~l~~~~~~~  116 (680)
T 1ziw_A           50 QLTSLDVGFNTISKLE---PELCQKLPMLKVLNLQHNELSQL---SDKTFAFCTNLTELHLM-------SNSIQKIKNNP  116 (680)
T ss_dssp             TCSEEECCSSCCCCCC---TTHHHHCTTCCEEECCSSCCCCC---CTTTTTTCTTCSEEECC-------SSCCCCCCSCT
T ss_pred             cCcEEECCCCccCccC---HHHHhcccCcCEEECCCCccCcc---ChhhhccCCCCCEEECC-------CCccCccChhH
Confidence            4555555544433322   22233566666666666665432   23345666666666666       44444443 34


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccch-hc--cccccCceeecCCCcccccccccccCCc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPR-GI--GKLRKLMYLHNEDTGCLRYLPAGIGELI  485 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~-~~--~~l~~L~~L~l~~~~~~~~~p~~i~~l~  485 (505)
                      ++.+++|++|++++|...+..|..++++++|+.|++++|. +..+++ .+  ..+++|++|++++|...+..|..+..+.
T Consensus       117 ~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~  195 (680)
T 1ziw_A          117 FVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNNK-IQALKSEELDIFANSSLKKLELSSNQIKEFSPGCFHAIG  195 (680)
T ss_dssp             TTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSC-CCCBCHHHHGGGTTCEESEEECTTCCCCCBCTTGGGGSS
T ss_pred             ccccCCCCEEECCCCcccccCchhhcccccCCEEEccCCc-ccccCHHHhhccccccccEEECCCCcccccChhhhhhhh
Confidence            6666666666666666333344455666666666666666 444433 22  2345666666666654444444555555


Q ss_pred             cCCccc
Q 046115          486 RLRRVR  491 (505)
Q Consensus       486 ~L~~L~  491 (505)
                      +|+.|.
T Consensus       196 ~L~~L~  201 (680)
T 1ziw_A          196 RLFGLF  201 (680)
T ss_dssp             EECEEE
T ss_pred             hhhhhh
Confidence            555543

>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=99.10  E-value=1.4e-08  Score=99.70  Aligned_cols=262  Identities=11%  Similarity=0.020  Sum_probs=153.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccC--------CCceEEEEeCCCC-CHHHHHHHHHHHc-CCCCCCChhcHHHHHHHHHHHc
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN--------FEKRTWVCVSEPF-DEFRIARAIIESL-TPGSAKDLVEFQSLMQHIEECV   70 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~--------f~~~~wv~~~~~~-~~~~~~~~l~~~l-~~~~~~~~~~~~~~~~~l~~~l   70 (505)
                      ++|+|||+||+.+++  +....        ....+|+++.... +...++..++.++ +................+...+
T Consensus        53 ~~G~GKT~la~~l~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l  130 (384)
T 2qby_B           53 LTGTGKTFVSKYIFN--EIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGT  130 (384)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH--HHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHh
Confidence            589999999999998  44222        2346688887766 8888888888887 3222222333455566777777


Q ss_pred             CCceEEEEEeCCCCCCccChhHH-HHhhcCCCCCcEEEEEeCchHH----HHHh--CCcceEeCCCCChhhHHHHHHHhh
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPF-YKCLKNSLHESKILITTRKETV----ARIM--GSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~-~~~~~~~~~~~~iLiTtr~~~~----~~~~--~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      ..++.+||+|+++.......... ...+.....+..+|+||+....    ....  .-...+.+++++.++..+++...+
T Consensus       131 ~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~  210 (384)
T 2qby_B          131 RNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYA  210 (384)
T ss_dssp             SSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHH
T ss_pred             ccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHH
Confidence            76666999999966322111122 2233322267788889887521    1111  112389999999999999998875


Q ss_pred             hC-CCCCCCCchHHHHHHHHHHHcC---CChH-HHHHHHHHh--c-c--CCCHHHHHHHHhhhhhhhhhcccCchhhHhh
Q 046115          144 IS-GKTIGKRENLEKIGREIVKKCK---GLPL-AAKTIASLL--R-S--KNTEKEWQNILENEIWELEAIEKGLLAPLLL  213 (505)
Q Consensus       144 ~~-~~~~~~~~~~~~~~~~i~~~~~---g~Pl-al~~~~~~l--~-~--~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~~  213 (505)
                      .. ......+   ++++..+++.++   |.|. ++..+....  . +  .-+.+.+...++...          ...+..
T Consensus       211 ~~~~~~~~~~---~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~~~~~i~~~~v~~~~~~~~----------~~~~~~  277 (384)
T 2qby_B          211 EYGLIKGTYD---DEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGIIRKEHVDKAIVDYE----------QERLIE  277 (384)
T ss_dssp             HHTSCTTSCC---SHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTTSSSCCCHHHHHHHHHHHH----------HHHHHH
T ss_pred             HhhcccCCcC---HHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHh----------cchHHH
Confidence            31 1111111   345667777777   8886 444333322  1 1  125666666555421          123556


Q ss_pred             ccccCChhhhhhhhhhccCCCCCCCChHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHccccccccc
Q 046115          214 SYNELPSKVKRCFSYCAVFPKDYGIRKHKLIELWMAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFNK  283 (505)
Q Consensus       214 s~~~L~~~~~~~ll~la~f~~~~~i~~~~l~~~w~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~~  283 (505)
                      ++..|++.++.++..++. ...-+-.........-..+.     .......+.++++.|...|++.....
T Consensus       278 ~~~~l~~~~~~~l~al~~-~~~~~~~~~~~~~~~~~~g~-----~~~~~~~~~~~l~~L~~~gli~~~~~  341 (384)
T 2qby_B          278 AVKALPFHYKLALRSLIE-SEDVMSAHKMYTDLCNKFKQ-----KPLSYRRFSDIISELDMFGIVKIRII  341 (384)
T ss_dssp             HHHSSCHHHHHHHHHHHT-CCBHHHHHHHHHHHHHHTTC-----CCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHcCCHHHHHHHHHHHH-hcccChHHHHHHHHHHHcCC-----CCCCHHHHHHHHHHHHhCCCEEEEec
Confidence            677888888888877776 21100001111121111121     12234567788999999999987543

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.10  E-value=3.4e-10  Score=122.84  Aligned_cols=150  Identities=19%  Similarity=0.224  Sum_probs=97.3

Q ss_pred             ceeEEEEEecCCCcccccc-ccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc-ccCc
Q 046115          330 KILHLLLTLRRGASVPISI-WGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK-EIPT  407 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-~~p~  407 (505)
                      .++.+.+..+..   ...+ +..|.++++|++|++++|.++..   .|..+..+.+|++|+|+       ++.+. ..|.
T Consensus        49 ~L~~LdLs~n~~---~~~i~~~~f~~L~~L~~L~Ls~N~l~~~---~p~~~~~l~~L~~L~Ls-------~n~l~~~~~~  115 (844)
T 3j0a_A           49 QLQLLELGSQYT---PLTIDKEAFRNLPNLRILDLGSSKIYFL---HPDAFQGLFHLFELRLY-------FCGLSDAVLK  115 (844)
T ss_dssp             SCSEEEECTTCC---CCEECTTTTSSCTTCCEEECTTCCCCEE---CTTSSCSCSSCCCEECT-------TCCCSSCCST
T ss_pred             cCeEEeCCCCCC---ccccCHHHhcCCCCCCEEECCCCcCccc---CHhHccCCcccCEeeCc-------CCCCCccccc
Confidence            455555555422   1122 34456778888888888876644   56667778888888887       33333 3444


Q ss_pred             c--ccCCCCcceeeccCCcccccc--chhhhcCCCCcEEecCCCcCccccchhcccc--ccCceeecCCCcccccccccc
Q 046115          408 N--IEKLLHLKYLNLKGQKKIEKL--PETLCELYNLERLNVDDCQNLRELPRGIGKL--RKLMYLHNEDTGCLRYLPAGI  481 (505)
Q Consensus       408 ~--~~~l~~L~~L~l~~~~~~~~l--p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l--~~L~~L~l~~~~~~~~~p~~i  481 (505)
                      .  ++.+++|++|++++|. +..+  +..++++++|+.|++++|......|..+..+  ++|+.|++++|...+..|..+
T Consensus       116 ~~~~~~L~~L~~L~Ls~N~-l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~~~l~~l~~~~L~~L~L~~n~l~~~~~~~~  194 (844)
T 3j0a_A          116 DGYFRNLKALTRLDLSKNQ-IRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFFSLAANSLYSRVSVDW  194 (844)
T ss_dssp             TCCCSSCSSCCEEEEESCC-CCCCCCCGGGGTCSSCCEEEEESSCCCCCCSGGGHHHHHCSSCCCEECCSBSCCCCCCCC
T ss_pred             CccccccCCCCEEECCCCc-ccccccchhHhhCCCCCEEECCCCcCCeeCHHHcccccCCccceEECCCCccccccccch
Confidence            3  6778888888888887 4333  2457788888888888877555566666666  778888888887666666666


Q ss_pred             cCCcc------CCcccee
Q 046115          482 GELIR------LRRVREF  493 (505)
Q Consensus       482 ~~l~~------L~~L~~~  493 (505)
                      +.+.+      |+.|++-
T Consensus       195 ~~~~~~~~~~~L~~L~Ls  212 (844)
T 3j0a_A          195 GKCMNPFRNMVLEILDVS  212 (844)
T ss_dssp             CSSSCTTTTCCBSEEBCS
T ss_pred             hhcCCccccCceeEEecC
Confidence            65554      6666553

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.10  E-value=1e-10  Score=111.30  Aligned_cols=148  Identities=16%  Similarity=0.158  Sum_probs=87.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccch-hHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVL-PQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~-~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .+..+.+..+....++   +..+..+++|++|++++|.+.+..... +..+..+++|++|+|+       ++.+..+|..
T Consensus       146 ~L~~L~Ls~n~l~~~~---~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls-------~N~l~~l~~~  215 (310)
T 4glp_A          146 GLKVLSIAQAHSPAFS---CEQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALR-------NTGMETPTGV  215 (310)
T ss_dssp             CCCEEEEECCSSCCCC---TTSCCCCTTCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCC-------SSCCCCHHHH
T ss_pred             CCCEEEeeCCCcchhh---HHHhccCCCCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECC-------CCCCCchHHH
Confidence            5556666665554333   233446677777777777654321101 1123466677777776       4555444432


Q ss_pred             ----ccCCCCcceeeccCCccccccchhhhcC---CCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccc
Q 046115          409 ----IEKLLHLKYLNLKGQKKIEKLPETLCEL---YNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGI  481 (505)
Q Consensus       409 ----~~~l~~L~~L~l~~~~~~~~lp~~~~~l---~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i  481 (505)
                          ++.+++|++|++++|......|..+..+   ++|+.|++++|. +..+|..+.  ++|++|++++|. +..+|. +
T Consensus       216 ~~~l~~~l~~L~~L~Ls~N~l~~~~p~~~~~~~~~~~L~~L~Ls~N~-l~~lp~~~~--~~L~~L~Ls~N~-l~~~~~-~  290 (310)
T 4glp_A          216 CAALAAAGVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFAG-LEQVPKGLP--AKLRVLDLSSNR-LNRAPQ-P  290 (310)
T ss_dssp             HHHHHHHTCCCSSEECTTSCCCCCCCSCCSSCCCCTTCCCEECCSSC-CCSCCSCCC--SCCSCEECCSCC-CCSCCC-T
T ss_pred             HHHHHhcCCCCCEEECCCCCCCccchhhHHhccCcCcCCEEECCCCC-CCchhhhhc--CCCCEEECCCCc-CCCCch-h
Confidence                3566777777777777333336656555   577777777777 567777654  677777777776 334443 5


Q ss_pred             cCCccCCccce
Q 046115          482 GELIRLRRVRE  492 (505)
Q Consensus       482 ~~l~~L~~L~~  492 (505)
                      ..+++|+.|++
T Consensus       291 ~~l~~L~~L~L  301 (310)
T 4glp_A          291 DELPEVDNLTL  301 (310)
T ss_dssp             TSCCCCSCEEC
T ss_pred             hhCCCccEEEC
Confidence            66666666654

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.09  E-value=2.2e-10  Score=110.15  Aligned_cols=137  Identities=23%  Similarity=0.325  Sum_probs=76.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEeccccc--CC----------
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRES--WP----------  397 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~--~~----------  397 (505)
                      .+..+.+..+....++..   .+..+++|+.|++.+|.+.... ..+..+..+ +|+.|+++++..  .+          
T Consensus       124 ~L~~L~l~~n~i~~~~~~---~~~~l~~L~~L~l~~n~l~~~~-~~~~~~~~l-~L~~L~l~~n~l~~l~~~~~~~L~~L  198 (332)
T 2ft3_A          124 SLVELRIHDNRIRKVPKG---VFSGLRNMNCIEMGGNPLENSG-FEPGAFDGL-KLNYLRISEAKLTGIPKDLPETLNEL  198 (332)
T ss_dssp             TCCEEECCSSCCCCCCSG---GGSSCSSCCEEECCSCCCBGGG-SCTTSSCSC-CCSCCBCCSSBCSSCCSSSCSSCSCC
T ss_pred             cCCEEECCCCccCccCHh---HhCCCccCCEEECCCCccccCC-CCcccccCC-ccCEEECcCCCCCccCccccCCCCEE
Confidence            556666666555544432   2346677777777777664211 123333333 444444431100  00          


Q ss_pred             --ccccccccC-ccccCCCCcceeeccCCccccccc-hhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcc
Q 046115          398 --RNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       398 --~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~  473 (505)
                        .++.+...+ ..+..+++|++|++++|. +..++ ..+..+++|+.|++++|. +..+|..+..+++|++|++++|..
T Consensus       199 ~l~~n~i~~~~~~~l~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~lp~~l~~l~~L~~L~l~~N~l  276 (332)
T 2ft3_A          199 HLDHNKIQAIELEDLLRYSKLYRLGLGHNQ-IRMIENGSLSFLPTLRELHLDNNK-LSRVPAGLPDLKLLQVVYLHTNNI  276 (332)
T ss_dssp             BCCSSCCCCCCTTSSTTCTTCSCCBCCSSC-CCCCCTTGGGGCTTCCEEECCSSC-CCBCCTTGGGCTTCCEEECCSSCC
T ss_pred             ECCCCcCCccCHHHhcCCCCCCEEECCCCc-CCcCChhHhhCCCCCCEEECCCCc-CeecChhhhcCccCCEEECCCCCC
Confidence              033333333 456667777777777776 44443 356677777777777776 667777777777777777777763

>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=99.09  E-value=3.9e-10  Score=117.89  Aligned_cols=156  Identities=17%  Similarity=0.141  Sum_probs=73.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccC---C---------
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESW---P---------  397 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~---~---------  397 (505)
                      .+..+.+..+....+|..    +..+++|++|.+.+|.+...   .|..+..+++|+.|+++++...   +         
T Consensus       279 ~L~~L~l~~n~l~~lp~~----l~~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~  351 (606)
T 3t6q_A          279 GLQELDLTATHLSELPSG----LVGLSTLKKLVLSANKFENL---CQISASNFPSLTHLSIKGNTKRLELGTGCLENLEN  351 (606)
T ss_dssp             TCSEEECTTSCCSCCCSS----CCSCTTCCEEECTTCCCSBG---GGGCGGGCTTCSEEECCSCSSCCBCCSSTTTTCTT
T ss_pred             CCCEEeccCCccCCCChh----hcccccCCEEECccCCcCcC---chhhhhccCcCCEEECCCCCcccccchhhhhccCc
Confidence            455555555555544433    34667777777777765543   3444555666666666521000   0         


Q ss_pred             ------cccccccc---CccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchh-ccccccCceee
Q 046115          398 ------RNNLIKEI---PTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLH  467 (505)
Q Consensus       398 ------~~~~~~~~---p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~  467 (505)
                            .++.+...   |..++.+++|++|++++|......|..++.+++|+.|++++|......|.. +..+++|++|+
T Consensus       352 L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~  431 (606)
T 3t6q_A          352 LRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNLHLLKVLN  431 (606)
T ss_dssp             CCEEECCSSCCCEEEESTTTTTTCTTCCEEECCSCSCEEECTTTTTTCTTCSEEECTTCCEECCTTCCTTTTCTTCCEEE
T ss_pred             CCEEECCCCccccccCcchhcccCCCCCEEECCCCcCCcCCHHHhcCCccCCeEECCCCcCCCcccchhhhCcccCCEEE
Confidence                  01111111   233444445555555544422222334445555555555555422222222 45555555555


Q ss_pred             cCCCcccccccccccCCccCCccce
Q 046115          468 NEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       468 l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      +++|......|..+..+++|+.|++
T Consensus       432 l~~n~l~~~~~~~~~~l~~L~~L~L  456 (606)
T 3t6q_A          432 LSHSLLDISSEQLFDGLPALQHLNL  456 (606)
T ss_dssp             CTTCCCBTTCTTTTTTCTTCCEEEC
T ss_pred             CCCCccCCcCHHHHhCCCCCCEEEC
Confidence            5555544444444555555555544

>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=99.09  E-value=2.6e-10  Score=118.02  Aligned_cols=122  Identities=19%  Similarity=0.196  Sum_probs=74.0

Q ss_pred             eEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Ccccc
Q 046115          332 LHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIE  410 (505)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~  410 (505)
                      +.+....+....+|..++      ++|+.|++++|.++..   .|..+..+++|++|+|+       ++.+..+ |..++
T Consensus        34 ~~l~ls~~~L~~ip~~~~------~~L~~L~Ls~N~i~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~~~~~   97 (562)
T 3a79_B           34 SMVDYSNRNLTHVPKDLP------PRTKALSLSQNSISEL---RMPDISFLSELRVLRLS-------HNRIRSLDFHVFL   97 (562)
T ss_dssp             CEEECTTSCCCSCCTTSC------TTCCEEECCSSCCCCC---CGGGTTTCTTCCEEECC-------SCCCCEECTTTTT
T ss_pred             cEEEcCCCCCccCCCCCC------CCcCEEECCCCCcccc---ChhhhccCCCccEEECC-------CCCCCcCCHHHhC
Confidence            444444444454444332      5667777777766543   44456667777777776       4444444 44566


Q ss_pred             CCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCcccc--chhccccccCceeecCCCcc
Q 046115          411 KLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLREL--PRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~l--p~~~~~l~~L~~L~l~~~~~  473 (505)
                      .+++|++|++++|. ++.+|..  .+++|++|++++|. +..+  |..++++++|++|++++|..
T Consensus        98 ~l~~L~~L~Ls~N~-l~~lp~~--~l~~L~~L~Ls~N~-l~~l~~p~~~~~l~~L~~L~L~~n~l  158 (562)
T 3a79_B           98 FNQDLEYLDVSHNR-LQNISCC--PMASLRHLDLSFND-FDVLPVCKEFGNLTKLTFLGLSAAKF  158 (562)
T ss_dssp             TCTTCCEEECTTSC-CCEECSC--CCTTCSEEECCSSC-CSBCCCCGGGGGCTTCCEEEEECSBC
T ss_pred             CCCCCCEEECCCCc-CCccCcc--ccccCCEEECCCCC-ccccCchHhhcccCcccEEecCCCcc
Confidence            67777777777776 5666664  66777777777766 4443  35666677777777776653

>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=99.08  E-value=4.5e-10  Score=108.70  Aligned_cols=143  Identities=19%  Similarity=0.243  Sum_probs=110.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++.     +..+++|+.|.+.+|.+...    +. +..+++|+.|+++       ++.+..+|. +
T Consensus       178 ~L~~L~l~~n~l~~~~~-----~~~l~~L~~L~l~~n~l~~~----~~-~~~~~~L~~L~l~-------~n~l~~~~~-~  239 (347)
T 4fmz_A          178 DLYSLSLNYNQIEDISP-----LASLTSLHYFTAYVNQITDI----TP-VANMTRLNSLKIG-------NNKITDLSP-L  239 (347)
T ss_dssp             TCSEEECTTSCCCCCGG-----GGGCTTCCEEECCSSCCCCC----GG-GGGCTTCCEEECC-------SSCCCCCGG-G
T ss_pred             CCCEEEccCCccccccc-----ccCCCccceeecccCCCCCC----ch-hhcCCcCCEEEcc-------CCccCCCcc-h
Confidence            45666666555554433     44778888888888876653    22 6788899999998       666777766 8


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+++|++|++++|. ++.++. +..+++|+.|++++|. +..+| .+..+++|++|++++|...+..|..+..+++|+.
T Consensus       240 ~~l~~L~~L~l~~n~-l~~~~~-~~~l~~L~~L~l~~n~-l~~~~-~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~  315 (347)
T 4fmz_A          240 ANLSQLTWLEIGTNQ-ISDINA-VKDLTKLKMLNVGSNQ-ISDIS-VLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTT  315 (347)
T ss_dssp             TTCTTCCEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCCCG-GGGGCTTCSEEECCSSCCCGGGHHHHHTCTTCSE
T ss_pred             hcCCCCCEEECCCCc-cCCChh-HhcCCCcCEEEccCCc-cCCCh-hhcCCCCCCEEECcCCcCCCcChhHhhccccCCE
Confidence            889999999999998 777754 8899999999999997 66664 5788999999999999876666777888888888


Q ss_pred             cceeE
Q 046115          490 VREFV  494 (505)
Q Consensus       490 L~~~~  494 (505)
                      |++..
T Consensus       316 L~L~~  320 (347)
T 4fmz_A          316 LFLSQ  320 (347)
T ss_dssp             EECCS
T ss_pred             EEccC
Confidence            87653

>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=99.08  E-value=3.3e-10  Score=118.45  Aligned_cols=147  Identities=16%  Similarity=0.086  Sum_probs=115.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~  408 (505)
                      .++.+.+..+....++   +..|.++++|++|++++|.+...   .|..|..+.+|++|+|+       ++.+.. .|..
T Consensus        34 ~l~~L~Ls~n~i~~~~---~~~~~~l~~L~~L~Ls~n~i~~~---~~~~~~~l~~L~~L~Ls-------~n~l~~~~~~~  100 (606)
T 3t6q_A           34 STECLEFSFNVLPTIQ---NTTFSRLINLTFLDLTRCQIYWI---HEDTFQSQHRLDTLVLT-------ANPLIFMAETA  100 (606)
T ss_dssp             TCCEEECTTCCCSEEC---TTTSTTCTTCSEEECTTCCCCEE---CTTTTTTCTTCCEEECT-------TCCCSEECTTT
T ss_pred             cCcEEEccCCccCcCC---hhHhccCccceEEECCCCcccee---ChhhccCccccCeeeCC-------CCcccccChhh
Confidence            6788888877776553   34566899999999999987654   67778999999999998       554544 4778


Q ss_pred             ccCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccc-hhccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELP-RGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      ++.+++|++|++++|. +..+ |..++.+++|++|++++|. +..++ +.+..+++|++|++++|......|..++.+++
T Consensus       101 ~~~l~~L~~L~L~~n~-i~~l~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~  178 (606)
T 3t6q_A          101 LSGPKALKHLFFIQTG-ISSIDFIPLHNQKTLESLYLGSNH-ISSIKLPKGFPTEKLKVLDFQNNAIHYLSKEDMSSLQQ  178 (606)
T ss_dssp             TSSCTTCCEEECTTSC-CSCGGGSCCTTCTTCCEEECCSSC-CCCCCCCTTCCCTTCCEEECCSSCCCEECHHHHHTTTT
T ss_pred             hcccccccEeeccccC-cccCCcchhccCCcccEEECCCCc-ccccCcccccCCcccCEEEcccCcccccChhhhhhhcc
Confidence            8999999999999999 6665 5678999999999999998 55542 34445899999999999866555667888888


Q ss_pred             CCccc
Q 046115          487 LRRVR  491 (505)
Q Consensus       487 L~~L~  491 (505)
                      |+.+.
T Consensus       179 L~~l~  183 (606)
T 3t6q_A          179 ATNLS  183 (606)
T ss_dssp             CCSEE
T ss_pred             cceeE
Confidence            88443

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.06  E-value=6.1e-10  Score=105.95  Aligned_cols=150  Identities=16%  Similarity=0.077  Sum_probs=102.7

Q ss_pred             cceeEEEEEecCCCccccccc-cCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccc-cc--
Q 046115          329 KKILHLLLTLRRGASVPISIW-GNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLI-KE--  404 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~-~~--  404 (505)
                      ..+..+.+..+.......... ..+..+++|++|.+++|.+...   .+..+..+++|++|+|+       ++.+ +.  
T Consensus       117 ~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~---~~~~~~~l~~L~~L~Ls-------~N~l~~~~~  186 (310)
T 4glp_A          117 LALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQAHSPAF---SCEQVRAFPALTSLDLS-------DNPGLGERG  186 (310)
T ss_dssp             BCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEECCSSCCC---CTTSCCCCTTCCEEECC-------SCTTCHHHH
T ss_pred             CCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeCCCcchh---hHHHhccCCCCCEEECC-------CCCCccchh
Confidence            356677777776553221111 2233688899999998887654   55667788889999998       4432 21  


Q ss_pred             cC--ccccCCCCcceeeccCCccccccchh----hhcCCCCcEEecCCCcCccccchhcccc---ccCceeecCCCcccc
Q 046115          405 IP--TNIEKLLHLKYLNLKGQKKIEKLPET----LCELYNLERLNVDDCQNLRELPRGIGKL---RKLMYLHNEDTGCLR  475 (505)
Q Consensus       405 ~p--~~~~~l~~L~~L~l~~~~~~~~lp~~----~~~l~~L~~L~l~~~~~~~~lp~~~~~l---~~L~~L~l~~~~~~~  475 (505)
                      ++  ..++.+++|++|++++|. ++.+|..    ++.+++|+.|++++|......|..+..+   ++|++|++++|. +.
T Consensus       187 ~~~~~~~~~l~~L~~L~Ls~N~-l~~l~~~~~~l~~~l~~L~~L~Ls~N~l~~~~p~~~~~~~~~~~L~~L~Ls~N~-l~  264 (310)
T 4glp_A          187 LMAALCPHKFPAIQNLALRNTG-METPTGVCAALAAAGVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFAG-LE  264 (310)
T ss_dssp             HHTTSCTTSSCCCCSCBCCSSC-CCCHHHHHHHHHHHTCCCSSEECTTSCCCCCCCSCCSSCCCCTTCCCEECCSSC-CC
T ss_pred             hhHHHhhhcCCCCCEEECCCCC-CCchHHHHHHHHhcCCCCCEEECCCCCCCccchhhHHhccCcCcCCEEECCCCC-CC
Confidence            32  223678889999999988 6666552    4678899999999988444457777666   689999999987 44


Q ss_pred             cccccccCCccCCccce
Q 046115          476 YLPAGIGELIRLRRVRE  492 (505)
Q Consensus       476 ~~p~~i~~l~~L~~L~~  492 (505)
                      .+|..+.  ++|+.|++
T Consensus       265 ~lp~~~~--~~L~~L~L  279 (310)
T 4glp_A          265 QVPKGLP--AKLRVLDL  279 (310)
T ss_dssp             SCCSCCC--SCCSCEEC
T ss_pred             chhhhhc--CCCCEEEC
Confidence            7787764  56666664

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.03  E-value=9.2e-10  Score=110.48  Aligned_cols=135  Identities=16%  Similarity=0.171  Sum_probs=94.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .++.+.+..+....++      +..+++|+.|++++|.+++.    +  +..+++|++|+++       ++.+..+|  +
T Consensus        65 ~L~~L~Ls~n~l~~~~------~~~l~~L~~L~Ls~N~l~~~----~--~~~l~~L~~L~L~-------~N~l~~l~--~  123 (457)
T 3bz5_A           65 GLTKLICTSNNITTLD------LSQNTNLTYLACDSNKLTNL----D--VTPLTKLTYLNCD-------TNKLTKLD--V  123 (457)
T ss_dssp             TCSEEECCSSCCSCCC------CTTCTTCSEEECCSSCCSCC----C--CTTCTTCCEEECC-------SSCCSCCC--C
T ss_pred             CCCEEEccCCcCCeEc------cccCCCCCEEECcCCCCcee----e--cCCCCcCCEEECC-------CCcCCeec--C
Confidence            5666666666655442      44677788888887776653    2  6677778888887       55555554  6


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|. ++.++  ++.+++|+.|++++|..+..+  .++.+++|++|++++|. +..+|  +..+++|+.
T Consensus       124 ~~l~~L~~L~l~~N~-l~~l~--l~~l~~L~~L~l~~n~~~~~~--~~~~l~~L~~L~ls~n~-l~~l~--l~~l~~L~~  195 (457)
T 3bz5_A          124 SQNPLLTYLNCARNT-LTEID--VSHNTQLTELDCHLNKKITKL--DVTPQTQLTTLDCSFNK-ITELD--VSQNKLLNR  195 (457)
T ss_dssp             TTCTTCCEEECTTSC-CSCCC--CTTCTTCCEEECTTCSCCCCC--CCTTCTTCCEEECCSSC-CCCCC--CTTCTTCCE
T ss_pred             CCCCcCCEEECCCCc-cceec--cccCCcCCEEECCCCCccccc--ccccCCcCCEEECCCCc-cceec--cccCCCCCE
Confidence            777888888888877 55553  777788888888888656666  36678888888888887 44455  677777776


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       196 L~l~  199 (457)
T 3bz5_A          196 LNCD  199 (457)
T ss_dssp             EECC
T ss_pred             EECc
Confidence            6543

>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=99.03  E-value=4.6e-12  Score=112.24  Aligned_cols=107  Identities=22%  Similarity=0.260  Sum_probs=92.1

Q ss_pred             hhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccc
Q 046115          375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELP  454 (505)
Q Consensus       375 ~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp  454 (505)
                      +|..+..+++|++|+++       ++.+..+| .++.+++|++|++++|. +..+|..+..+++|+.|++++|. +..+|
T Consensus        40 l~~~~~~l~~L~~L~ls-------~n~l~~l~-~~~~l~~L~~L~l~~n~-l~~l~~~~~~~~~L~~L~L~~N~-l~~l~  109 (198)
T 1ds9_A           40 MDATLSTLKACKHLALS-------TNNIEKIS-SLSGMENLRILSLGRNL-IKKIENLDAVADTLEELWISYNQ-IASLS  109 (198)
T ss_dssp             CHHHHHHTTTCSEEECS-------EEEESCCC-CHHHHTTCCEEEEEEEE-ECSCSSHHHHHHHCSEEEEEEEE-CCCHH
T ss_pred             hhHHHhcCCCCCEEECC-------CCCCcccc-ccccCCCCCEEECCCCC-cccccchhhcCCcCCEEECcCCc-CCcCC
Confidence            55579999999999999       66777788 89999999999999999 88999988888999999999998 77787


Q ss_pred             hhccccccCceeecCCCcccccccc--cccCCccCCcccee
Q 046115          455 RGIGKLRKLMYLHNEDTGCLRYLPA--GIGELIRLRRVREF  493 (505)
Q Consensus       455 ~~~~~l~~L~~L~l~~~~~~~~~p~--~i~~l~~L~~L~~~  493 (505)
                       .+..+++|++|++++|. +..+|.  .+..+++|+.|++.
T Consensus       110 -~~~~l~~L~~L~l~~N~-i~~~~~~~~l~~l~~L~~L~l~  148 (198)
T 1ds9_A          110 -GIEKLVNLRVLYMSNNK-ITNWGEIDKLAALDKLEDLLLA  148 (198)
T ss_dssp             -HHHHHHHSSEEEESEEE-CCCHHHHHHHTTTTTCSEEEEC
T ss_pred             -ccccCCCCCEEECCCCc-CCchhHHHHHhcCCCCCEEEec
Confidence             68899999999999997 455543  57888888887754

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=99.03  E-value=3.6e-10  Score=97.55  Aligned_cols=99  Identities=23%  Similarity=0.375  Sum_probs=54.4

Q ss_pred             eEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCcceeeccCCccccccchh-hhcC
Q 046115          359 RSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPET-LCEL  436 (505)
Q Consensus       359 ~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l  436 (505)
                      +.+++.++.+..    +|..+  ..+|+.|+|+       ++.+..+ |..++.+++|++|+|++|. ++.+|.. +..+
T Consensus        15 ~~l~~~~n~l~~----iP~~~--~~~L~~L~Ls-------~N~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~i~~~~~~~l   80 (174)
T 2r9u_A           15 TLVNCQNIRLAS----VPAGI--PTDKQRLWLN-------NNQITKLEPGVFDHLVNLQQLYFNSNK-LTAIPTGVFDKL   80 (174)
T ss_dssp             SEEECCSSCCSS----CCSCC--CTTCSEEECC-------SSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTC
T ss_pred             cEEEeCCCCCCc----cCCCc--CCCCcEEEeC-------CCCccccCHHHhcCCcCCCEEECCCCC-CCccChhHhCCc
Confidence            455555555433    22212  1456666665       4444444 3345566666666666665 5555543 3566


Q ss_pred             CCCcEEecCCCcCccccchh-ccccccCceeecCCCc
Q 046115          437 YNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTG  472 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~  472 (505)
                      ++|+.|+|++|. +..+|+. +..+++|++|++++|.
T Consensus        81 ~~L~~L~L~~N~-l~~l~~~~~~~l~~L~~L~L~~N~  116 (174)
T 2r9u_A           81 TQLTQLDLNDNH-LKSIPRGAFDNLKSLTHIYLYNNP  116 (174)
T ss_dssp             TTCCEEECCSSC-CCCCCTTTTTTCTTCSEEECCSSC
T ss_pred             chhhEEECCCCc-cceeCHHHhccccCCCEEEeCCCC
Confidence            666666666665 5555554 5666666666666665

>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=99.02  E-value=1.4e-10  Score=111.71  Aligned_cols=131  Identities=21%  Similarity=0.247  Sum_probs=74.3

Q ss_pred             CCCCCCceEEEecCC-CccccccchhHHhhcCcccceEEecccccCCccc-cccc--cCccccCCC-CcceeeccCCc-c
Q 046115          352 VTGLRGLRSLLVKSD-EYSWSSEVLPQLFEKLTCLRALELQVRESWPRNN-LIKE--IPTNIEKLL-HLKYLNLKGQK-K  425 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~-~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~-~~~~--~p~~~~~l~-~L~~L~l~~~~-~  425 (505)
                      +..+++|++|.+.+| .++..  .++..+..+++|+.|+++       ++ .+..  ++..+..++ +|++|++++|. .
T Consensus       138 l~~~~~L~~L~L~~~~~l~~~--~l~~~~~~~~~L~~L~l~-------~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~  208 (336)
T 2ast_B          138 LAKNSNLVRLNLSGCSGFSEF--ALQTLLSSCSRLDELNLS-------WCFDFTEKHVQVAVAHVSETITQLNLSGYRKN  208 (336)
T ss_dssp             HTTCTTCSEEECTTCBSCCHH--HHHHHHHHCTTCCEEECC-------CCTTCCHHHHHHHHHHSCTTCCEEECCSCGGG
T ss_pred             HhcCCCCCEEECCCCCCCCHH--HHHHHHhcCCCCCEEcCC-------CCCCcChHHHHHHHHhcccCCCEEEeCCCccc
Confidence            345666666666666 33321  145555666666666666       22 3332  344456666 67777777664 1


Q ss_pred             c--cccchhhhcCCCCcEEecCCCcCc-cccchhccccccCceeecCCCcccccccc---cccCCccCCcccee
Q 046115          426 I--EKLPETLCELYNLERLNVDDCQNL-RELPRGIGKLRKLMYLHNEDTGCLRYLPA---GIGELIRLRRVREF  493 (505)
Q Consensus       426 ~--~~lp~~~~~l~~L~~L~l~~~~~~-~~lp~~~~~l~~L~~L~l~~~~~~~~~p~---~i~~l~~L~~L~~~  493 (505)
                      +  ..+|..+..+++|+.|++++|..+ ...+..+..+++|++|++++|.  ...+.   .+.++++|+.|++.
T Consensus       209 ~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~l~~l~~L~~L~l~~~~--~~~~~~~~~l~~~~~L~~L~l~  280 (336)
T 2ast_B          209 LQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCY--DIIPETLLELGEIPTLKTLQVF  280 (336)
T ss_dssp             SCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCT--TCCGGGGGGGGGCTTCCEEECT
T ss_pred             CCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHHHHhCCCCCCEeeCCCCC--CCCHHHHHHHhcCCCCCEEecc
Confidence            2  445555566677777777776622 3455566666777777777764  11222   35556666665544

>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=99.01  E-value=1.9e-09  Score=108.72  Aligned_cols=139  Identities=22%  Similarity=0.355  Sum_probs=76.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++.     +..+++|+.|.+.+|.+++.    +. +..+++|+.|+++       ++.+..+++ +
T Consensus       244 ~L~~L~l~~n~l~~~~~-----~~~l~~L~~L~l~~n~l~~~----~~-~~~l~~L~~L~L~-------~n~l~~~~~-~  305 (466)
T 1o6v_A          244 NLTDLDLANNQISNLAP-----LSGLTKLTELKLGANQISNI----SP-LAGLTALTNLELN-------ENQLEDISP-I  305 (466)
T ss_dssp             TCSEEECCSSCCCCCGG-----GTTCTTCSEEECCSSCCCCC----GG-GTTCTTCSEEECC-------SSCCSCCGG-G
T ss_pred             CCCEEECCCCccccchh-----hhcCCCCCEEECCCCccCcc----cc-ccCCCccCeEEcC-------CCcccCchh-h
Confidence            34444444444433322     33556666666666655442    22 5556666666665       444444443 5


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|. +..+++ ++.+++|+.|++++|. +..+| .+..+++|+.|++++|...+..|  +..+++|+.
T Consensus       306 ~~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~l~~n~-l~~~~-~l~~l~~L~~L~l~~n~l~~~~~--~~~l~~L~~  379 (466)
T 1o6v_A          306 SNLKNLTYLTLYFNN-ISDISP-VSSLTKLQRLFFYNNK-VSDVS-SLANLTNINWLSAGHNQISDLTP--LANLTRITQ  379 (466)
T ss_dssp             GGCTTCSEEECCSSC-CSCCGG-GGGCTTCCEEECCSSC-CCCCG-GGTTCTTCCEEECCSSCCCBCGG--GTTCTTCCE
T ss_pred             cCCCCCCEEECcCCc-CCCchh-hccCccCCEeECCCCc-cCCch-hhccCCCCCEEeCCCCccCccch--hhcCCCCCE
Confidence            566666666666666 444444 5666666666666665 44443 45666666666666666443333  555555555


Q ss_pred             cce
Q 046115          490 VRE  492 (505)
Q Consensus       490 L~~  492 (505)
                      |++
T Consensus       380 L~l  382 (466)
T 1o6v_A          380 LGL  382 (466)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            544

>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=99.01  E-value=1e-10  Score=112.67  Aligned_cols=157  Identities=16%  Similarity=0.104  Sum_probs=119.6

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc--ccC
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK--EIP  406 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~--~~p  406 (505)
                      ..+..+.+..+....  ..++..+..+++|++|.+.+|.++..   .+..+..+++|++|+++      ++..+.  .+|
T Consensus        93 ~~L~~L~L~~~~l~~--~~~~~~~~~~~~L~~L~L~~~~l~~~---~~~~l~~~~~L~~L~L~------~~~~l~~~~l~  161 (336)
T 2ast_B           93 FRVQHMDLSNSVIEV--STLHGILSQCSKLQNLSLEGLRLSDP---IVNTLAKNSNLVRLNLS------GCSGFSEFALQ  161 (336)
T ss_dssp             BCCCEEECTTCEECH--HHHHHHHTTBCCCSEEECTTCBCCHH---HHHHHTTCTTCSEEECT------TCBSCCHHHHH
T ss_pred             CCCCEEEccCCCcCH--HHHHHHHhhCCCCCEEeCcCcccCHH---HHHHHhcCCCCCEEECC------CCCCCCHHHHH
Confidence            356666666554321  11334456899999999999986543   67778889999999998      232444  366


Q ss_pred             ccccCCCCcceeeccCCccccc--cchhhhcCC-CCcEEecCCCc-Cc--cccchhccccccCceeecCCCc-ccccccc
Q 046115          407 TNIEKLLHLKYLNLKGQKKIEK--LPETLCELY-NLERLNVDDCQ-NL--RELPRGIGKLRKLMYLHNEDTG-CLRYLPA  479 (505)
Q Consensus       407 ~~~~~l~~L~~L~l~~~~~~~~--lp~~~~~l~-~L~~L~l~~~~-~~--~~lp~~~~~l~~L~~L~l~~~~-~~~~~p~  479 (505)
                      ..+..+++|++|++++|..++.  ++..+..++ +|+.|++++|. .+  ..+|..+..+++|++|++++|. .....+.
T Consensus       162 ~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~  241 (336)
T 2ast_B          162 TLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQ  241 (336)
T ss_dssp             HHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGG
T ss_pred             HHHhcCCCCCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHH
Confidence            6688899999999999933653  677788999 99999999995 13  5678788899999999999998 4456777


Q ss_pred             cccCCccCCccceeEec
Q 046115          480 GIGELIRLRRVREFVVG  496 (505)
Q Consensus       480 ~i~~l~~L~~L~~~~~~  496 (505)
                      .+.++++|+.|++..+.
T Consensus       242 ~l~~l~~L~~L~l~~~~  258 (336)
T 2ast_B          242 EFFQLNYLQHLSLSRCY  258 (336)
T ss_dssp             GGGGCTTCCEEECTTCT
T ss_pred             HHhCCCCCCEeeCCCCC
Confidence            88999999999887654

>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=99.01  E-value=7.1e-10  Score=114.07  Aligned_cols=120  Identities=18%  Similarity=0.190  Sum_probs=100.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .++.+.+..+....+|.     +..+++|+.|++++|.++.    +|..++.+++|+.|+|+       ++.+..+| .+
T Consensus       442 ~L~~L~Ls~n~l~~lp~-----~~~l~~L~~L~Ls~N~l~~----lp~~~~~l~~L~~L~Ls-------~N~l~~lp-~l  504 (567)
T 1dce_A          442 DVRVLHLAHKDLTVLCH-----LEQLLLVTHLDLSHNRLRA----LPPALAALRCLEVLQAS-------DNALENVD-GV  504 (567)
T ss_dssp             TCSEEECTTSCCSSCCC-----GGGGTTCCEEECCSSCCCC----CCGGGGGCTTCCEEECC-------SSCCCCCG-GG
T ss_pred             CceEEEecCCCCCCCcC-----ccccccCcEeecCcccccc----cchhhhcCCCCCEEECC-------CCCCCCCc-cc
Confidence            46677777777776553     5589999999999999873    67789999999999999       77777888 79


Q ss_pred             cCCCCcceeeccCCcccccc--chhhhcCCCCcEEecCCCcCccccchhc----cccccCceeec
Q 046115          410 EKLLHLKYLNLKGQKKIEKL--PETLCELYNLERLNVDDCQNLRELPRGI----GKLRKLMYLHN  468 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~l--p~~~~~l~~L~~L~l~~~~~~~~lp~~~----~~l~~L~~L~l  468 (505)
                      +.+++|++|+|++|. ++.+  |..++.+++|+.|+|++|+ +..+|+.+    ..+++|+.|++
T Consensus       505 ~~l~~L~~L~Ls~N~-l~~~~~p~~l~~l~~L~~L~L~~N~-l~~~~~~~~~l~~~lp~L~~L~l  567 (567)
T 1dce_A          505 ANLPRLQELLLCNNR-LQQSAAIQPLVSCPRLVLLNLQGNS-LCQEEGIQERLAEMLPSVSSILT  567 (567)
T ss_dssp             TTCSSCCEEECCSSC-CCSSSTTGGGGGCTTCCEEECTTSG-GGGSSSCTTHHHHHCTTCSEEEC
T ss_pred             CCCCCCcEEECCCCC-CCCCCCcHHHhcCCCCCEEEecCCc-CCCCccHHHHHHHHCcccCccCC
Confidence            999999999999999 6666  8899999999999999999 77776643    44788988864

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.00  E-value=8.2e-10  Score=113.12  Aligned_cols=128  Identities=16%  Similarity=0.192  Sum_probs=89.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....+|.       .+++|+.|++++|.+++.    |.   .+++|+.|+|+       +|.+..+|. +
T Consensus       121 ~L~~L~Ls~N~l~~lp~-------~l~~L~~L~Ls~N~l~~l----p~---~l~~L~~L~Ls-------~N~L~~lp~-l  178 (571)
T 3cvr_A          121 SLKHLDVDNNQLTMLPE-------LPALLEYINADNNQLTML----PE---LPTSLEVLSVR-------NNQLTFLPE-L  178 (571)
T ss_dssp             TCCEEECCSSCCSCCCC-------CCTTCCEEECCSSCCSCC----CC---CCTTCCEEECC-------SSCCSCCCC-C
T ss_pred             CCCEEECCCCcCCCCCC-------cCccccEEeCCCCccCcC----CC---cCCCcCEEECC-------CCCCCCcch-h
Confidence            56666666666554443       356777777777776653    32   45678888887       566666776 5


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCC-------cEEecCCCcCccccchhccccccCceeecCCCccccccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNL-------ERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIG  482 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L-------~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~  482 (505)
                      +  ++|++|+|++|. ++.+|. +..  +|       +.|+|++|. +..+|..+..+++|++|++++|...+..|..+.
T Consensus       179 ~--~~L~~L~Ls~N~-L~~lp~-~~~--~L~~~~~~L~~L~Ls~N~-l~~lp~~l~~l~~L~~L~L~~N~l~~~~p~~l~  251 (571)
T 3cvr_A          179 P--ESLEALDVSTNL-LESLPA-VPV--RNHHSEETEIFFRCRENR-ITHIPENILSLDPTCTIILEDNPLSSRIRESLS  251 (571)
T ss_dssp             C--TTCCEEECCSSC-CSSCCC-CC----------CCEEEECCSSC-CCCCCGGGGGSCTTEEEECCSSSCCHHHHHHHH
T ss_pred             h--CCCCEEECcCCC-CCchhh-HHH--hhhcccccceEEecCCCc-ceecCHHHhcCCCCCEEEeeCCcCCCcCHHHHH
Confidence            4  788888888887 677777 544  66       888888887 777888887788888888888887777777776


Q ss_pred             CCcc
Q 046115          483 ELIR  486 (505)
Q Consensus       483 ~l~~  486 (505)
                      .+..
T Consensus       252 ~l~~  255 (571)
T 3cvr_A          252 QQTA  255 (571)
T ss_dssp             HHHH
T ss_pred             Hhhc
Confidence            6554

>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=98.99  E-value=2.5e-09  Score=107.88  Aligned_cols=140  Identities=21%  Similarity=0.262  Sum_probs=97.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++     .+..+++|+.|++.+|.+.+.   .+  +..+++|+.|+++       ++.+...|+ +
T Consensus       222 ~L~~L~l~~n~l~~~~-----~l~~l~~L~~L~l~~n~l~~~---~~--~~~l~~L~~L~l~-------~n~l~~~~~-~  283 (466)
T 1o6v_A          222 NLDELSLNGNQLKDIG-----TLASLTNLTDLDLANNQISNL---AP--LSGLTKLTELKLG-------ANQISNISP-L  283 (466)
T ss_dssp             TCCEEECCSSCCCCCG-----GGGGCTTCSEEECCSSCCCCC---GG--GTTCTTCSEEECC-------SSCCCCCGG-G
T ss_pred             CCCEEECCCCCcccch-----hhhcCCCCCEEECCCCccccc---hh--hhcCCCCCEEECC-------CCccCcccc-c
Confidence            4556666555544332     344677788888888776653   22  6777788888887       555666655 7


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+++|++|++++|. +..++. ++.+++|+.|++++|. +..+++ +..+++|+.|++++|... .+ +.+.++++|+.
T Consensus       284 ~~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~l~~n~l~-~~-~~l~~l~~L~~  357 (466)
T 1o6v_A          284 AGLTALTNLELNENQ-LEDISP-ISNLKNLTYLTLYFNN-ISDISP-VSSLTKLQRLFFYNNKVS-DV-SSLANLTNINW  357 (466)
T ss_dssp             TTCTTCSEEECCSSC-CSCCGG-GGGCTTCSEEECCSSC-CSCCGG-GGGCTTCCEEECCSSCCC-CC-GGGTTCTTCCE
T ss_pred             cCCCccCeEEcCCCc-ccCchh-hcCCCCCCEEECcCCc-CCCchh-hccCccCCEeECCCCccC-Cc-hhhccCCCCCE
Confidence            778888888888887 666666 7888888888888887 555544 678888888888888743 34 35777777777


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       358 L~l~  361 (466)
T 1o6v_A          358 LSAG  361 (466)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            7654

>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=98.98  E-value=2.9e-10  Score=111.78  Aligned_cols=156  Identities=15%  Similarity=0.111  Sum_probs=92.8

Q ss_pred             ceeEEEEEecCCCcccc-ccccCCCCCCCceEEEecCCCccccc-cchhHHhhcC---------cccceEEecccccCCc
Q 046115          330 KILHLLLTLRRGASVPI-SIWGNVTGLRGLRSLLVKSDEYSWSS-EVLPQLFEKL---------TCLRALELQVRESWPR  398 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~L~~L~l~~~~~~~~~-~~~~~~~~~l---------~~L~~L~l~~~~~~~~  398 (505)
                      .+..+.+..+....... .++..+..+++|++|++++|.++... ..++..+..+         ++|+.|+++       
T Consensus        95 ~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~-------  167 (386)
T 2ca6_A           95 KLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICG-------  167 (386)
T ss_dssp             TCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECC-------
T ss_pred             cccEEECCCCcCCHHHHHHHHHHHHhCCCCCEEECcCCCCCHHHHHHHHHHHHHHhhhhhcccCCCCcEEECC-------
Confidence            55666665555443110 12223346677777777777664321 1133333344         677777776       


Q ss_pred             ccccc--ccC---ccccCCCCcceeeccCCcccc------ccchhhhcCCCCcEEecCCCcCc----cccchhccccccC
Q 046115          399 NNLIK--EIP---TNIEKLLHLKYLNLKGQKKIE------KLPETLCELYNLERLNVDDCQNL----RELPRGIGKLRKL  463 (505)
Q Consensus       399 ~~~~~--~~p---~~~~~l~~L~~L~l~~~~~~~------~lp~~~~~l~~L~~L~l~~~~~~----~~lp~~~~~l~~L  463 (505)
                      ++.+.  .+|   ..+..+++|++|++++|. ++      -.|..+..+++|+.|+|++|...    ..+|..+..+++|
T Consensus       168 ~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~-l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~~~l~~~~~L  246 (386)
T 2ca6_A          168 RNRLENGSMKEWAKTFQSHRLLHTVKMVQNG-IRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNL  246 (386)
T ss_dssp             SSCCTGGGHHHHHHHHHHCTTCCEEECCSSC-CCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTC
T ss_pred             CCCCCcHHHHHHHHHHHhCCCcCEEECcCCC-CCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHHHHHccCCCc
Confidence            33332  233   345667788888888877 44      23335777788888888887732    5677777778888


Q ss_pred             ceeecCCCccccc----ccccc--cCCccCCcccee
Q 046115          464 MYLHNEDTGCLRY----LPAGI--GELIRLRRVREF  493 (505)
Q Consensus       464 ~~L~l~~~~~~~~----~p~~i--~~l~~L~~L~~~  493 (505)
                      ++|++++|.....    +|..+  +.+++|+.|++.
T Consensus       247 ~~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~  282 (386)
T 2ca6_A          247 RELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQ  282 (386)
T ss_dssp             CEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECC
T ss_pred             CEEECCCCCCchhhHHHHHHHHhhccCCCeEEEECc
Confidence            8888888875443    34555  336777777654

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=98.97  E-value=6.2e-10  Score=114.02  Aligned_cols=132  Identities=21%  Similarity=0.282  Sum_probs=106.9

Q ss_pred             cceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          329 KKILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .++..+.+..+....+|. +.    +  +|+.|++++|.+++    +|.   .+++|+.|+|+       ++.+..+|. 
T Consensus       100 ~~L~~L~Ls~N~l~~ip~-l~----~--~L~~L~Ls~N~l~~----lp~---~l~~L~~L~Ls-------~N~l~~lp~-  157 (571)
T 3cvr_A          100 ASLEYLDACDNRLSTLPE-LP----A--SLKHLDVDNNQLTM----LPE---LPALLEYINAD-------NNQLTMLPE-  157 (571)
T ss_dssp             TTCCEEECCSSCCSCCCC-CC----T--TCCEEECCSSCCSC----CCC---CCTTCCEEECC-------SSCCSCCCC-
T ss_pred             CCCCEEEccCCCCCCcch-hh----c--CCCEEECCCCcCCC----CCC---cCccccEEeCC-------CCccCcCCC-
Confidence            377888888887776665 32    3  99999999999876    343   67899999998       777777876 


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccC-------ceeecCCCcccccccccc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKL-------MYLHNEDTGCLRYLPAGI  481 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L-------~~L~l~~~~~~~~~p~~i  481 (505)
                        .+++|++|++++|. ++.+|. ++  ++|+.|+|++|. +..+|. +..  +|       +.|++++|. +..+|..+
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  226 (571)
T 3cvr_A          158 --LPTSLEVLSVRNNQ-LTFLPE-LP--ESLEALDVSTNL-LESLPA-VPV--RNHHSEETEIFFRCRENR-ITHIPENI  226 (571)
T ss_dssp             --CCTTCCEEECCSSC-CSCCCC-CC--TTCCEEECCSSC-CSSCCC-CC----------CCEEEECCSSC-CCCCCGGG
T ss_pred             --cCCCcCEEECCCCC-CCCcch-hh--CCCCEEECcCCC-CCchhh-HHH--hhhcccccceEEecCCCc-ceecCHHH
Confidence              67899999999999 777998 66  899999999998 779998 654  77       999999998 56899988


Q ss_pred             cCCccCCcccee
Q 046115          482 GELIRLRRVREF  493 (505)
Q Consensus       482 ~~l~~L~~L~~~  493 (505)
                      .++++|+.|++.
T Consensus       227 ~~l~~L~~L~L~  238 (571)
T 3cvr_A          227 LSLDPTCTIILE  238 (571)
T ss_dssp             GGSCTTEEEECC
T ss_pred             hcCCCCCEEEee
Confidence            888888887754

>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=98.96  E-value=1.8e-08  Score=98.83  Aligned_cols=263  Identities=13%  Similarity=0.072  Sum_probs=149.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC---CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC--CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF---EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA--GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f---~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~--~~r~   75 (505)
                      ++|+||||||+.+++  .....+   ..++|+++....+...++..++.+++...........+....+...+.  +++.
T Consensus        53 ~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  130 (386)
T 2qby_A           53 LTGTGKTAVVKFVLS--KLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQV  130 (386)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCE
T ss_pred             CCCCCHHHHHHHHHH--HHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeE
Confidence            589999999999998  554443   246688877767777888888887764333333334455555555553  4589


Q ss_pred             EEEEeCCCCCC----ccChhHHHHhhcC-CCCCcEEEEEeCchHHHHHhC-----C--cceEeCCCCChhhHHHHHHHhh
Q 046115           76 LLVLDDVWNED----YYKWEPFYKCLKN-SLHESKILITTRKETVARIMG-----S--THVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        76 LlvlDdv~~~~----~~~~~~~~~~~~~-~~~~~~iLiTtr~~~~~~~~~-----~--~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +||+|+++...    ...+..+...+.. ...+..+|+||+.........     .  ...+.+++++.++..+++....
T Consensus       131 vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~  210 (386)
T 2qby_A          131 VIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRA  210 (386)
T ss_dssp             EEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHH
T ss_pred             EEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHH
Confidence            99999995521    2233444443422 234566777887653221111     1  2489999999999999998754


Q ss_pred             hCCCCCCCCchHHHHHHHHHHHcC---CChHHH-HHHHHHhc-----c--CCCHHHHHHHHhhhhhhhhhcccCchhhHh
Q 046115          144 ISGKTIGKRENLEKIGREIVKKCK---GLPLAA-KTIASLLR-----S--KNTEKEWQNILENEIWELEAIEKGLLAPLL  212 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~---g~Plal-~~~~~~l~-----~--~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~  212 (505)
                      .....  ...-..+++..+++.++   |.|..+ .++.....     +  .-+.+.....++...          ...+.
T Consensus       211 ~~~~~--~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~~~----------~~~~~  278 (386)
T 2qby_A          211 QMAFK--PGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIE----------RDRVR  278 (386)
T ss_dssp             HHHBC--SSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHH----------HHHHH
T ss_pred             Hhhcc--CCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHh----------hchHH
Confidence            21110  11122455667777777   999743 33322211     1  114455554444321          12345


Q ss_pred             hccccCChhhhhhhhhhccCCC-C-CCCChHHHHHHH----HHcCCCCCCCCCCHHHHHHHHHHHHHHcccccccc
Q 046115          213 LSYNELPSKVKRCFSYCAVFPK-D-YGIRKHKLIELW----MAQGYLSEKGAKEMEDIGEEYFNILASRSFFQDFN  282 (505)
Q Consensus       213 ~s~~~L~~~~~~~ll~la~f~~-~-~~i~~~~l~~~w----~~~~~~~~~~~~~~~~~~~~~l~~L~~~~Ll~~~~  282 (505)
                      ..+..+++.++.++..++.+.. + ..+....+...+    -..+.     .......+..+++.|...|++....
T Consensus       279 ~~~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~g~-----~~~~~~~~~~~l~~L~~~gli~~~~  349 (386)
T 2qby_A          279 DIILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLGV-----EAVTQRRVSDIINELDMVGILTAKV  349 (386)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHHTC-----CCCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhcCC-----CCCCHHHHHHHHHHHHhCCCEEEEe
Confidence            5667788888888877774322 1 123333221111    11111     1112345677899999999997643

>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=98.96  E-value=2.2e-09  Score=111.32  Aligned_cols=72  Identities=26%  Similarity=0.248  Sum_probs=47.7

Q ss_pred             CCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          413 LHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       413 ~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      ++|++|++++|. ++.+|   ..+++|+.|++++|. +..+|.   .+++|++|++++|. +..+|..|.++++|+.|++
T Consensus       221 ~~L~~L~Ls~N~-L~~lp---~~l~~L~~L~Ls~N~-L~~lp~---~~~~L~~L~Ls~N~-L~~lp~~l~~l~~L~~L~L  291 (622)
T 3g06_A          221 SGLKELIVSGNR-LTSLP---VLPSELKELMVSGNR-LTSLPM---LPSGLLSLSVYRNQ-LTRLPESLIHLSSETTVNL  291 (622)
T ss_dssp             TTCCEEECCSSC-CSCCC---CCCTTCCEEECCSSC-CSCCCC---CCTTCCEEECCSSC-CCSCCGGGGGSCTTCEEEC
T ss_pred             CCCCEEEccCCc-cCcCC---CCCCcCcEEECCCCC-CCcCCc---ccccCcEEeCCCCC-CCcCCHHHhhccccCEEEe
Confidence            556677777666 55566   345667777777776 666665   45677777777776 3467777777777776665


Q ss_pred             e
Q 046115          493 F  493 (505)
Q Consensus       493 ~  493 (505)
                      .
T Consensus       292 ~  292 (622)
T 3g06_A          292 E  292 (622)
T ss_dssp             C
T ss_pred             c
Confidence            3

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=98.95  E-value=2.7e-09  Score=107.05  Aligned_cols=135  Identities=20%  Similarity=0.182  Sum_probs=104.4

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++      +..+++|++|++++|.+++.    |  +..+++|++|+++       ++.+..++  +
T Consensus        86 ~L~~L~Ls~N~l~~~~------~~~l~~L~~L~L~~N~l~~l----~--~~~l~~L~~L~l~-------~N~l~~l~--l  144 (457)
T 3bz5_A           86 NLTYLACDSNKLTNLD------VTPLTKLTYLNCDTNKLTKL----D--VSQNPLLTYLNCA-------RNTLTEID--V  144 (457)
T ss_dssp             TCSEEECCSSCCSCCC------CTTCTTCCEEECCSSCCSCC----C--CTTCTTCCEEECT-------TSCCSCCC--C
T ss_pred             CCCEEECcCCCCceee------cCCCCcCCEEECCCCcCCee----c--CCCCCcCCEEECC-------CCccceec--c
Confidence            5677777777666542      55889999999999987753    3  6788899999998       56666664  7


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|..++.+  .++.+++|+.|++++|. +..+|  +..+++|+.|++++|... .+  .++.+++|+.
T Consensus       145 ~~l~~L~~L~l~~n~~~~~~--~~~~l~~L~~L~ls~n~-l~~l~--l~~l~~L~~L~l~~N~l~-~~--~l~~l~~L~~  216 (457)
T 3bz5_A          145 SHNTQLTELDCHLNKKITKL--DVTPQTQLTTLDCSFNK-ITELD--VSQNKLLNRLNCDTNNIT-KL--DLNQNIQLTF  216 (457)
T ss_dssp             TTCTTCCEEECTTCSCCCCC--CCTTCTTCCEEECCSSC-CCCCC--CTTCTTCCEEECCSSCCS-CC--CCTTCTTCSE
T ss_pred             ccCCcCCEEECCCCCccccc--ccccCCcCCEEECCCCc-cceec--cccCCCCCEEECcCCcCC-ee--ccccCCCCCE
Confidence            78899999999999767777  37888999999999988 77777  778889999999998744 34  3777777777


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       217 L~Ls  220 (457)
T 3bz5_A          217 LDCS  220 (457)
T ss_dssp             EECC
T ss_pred             EECc
Confidence            7653

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=98.94  E-value=3.9e-09  Score=91.35  Aligned_cols=120  Identities=25%  Similarity=0.404  Sum_probs=94.7

Q ss_pred             ceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc-ccCCCCcceeeccCCccccccchh-hhc
Q 046115          358 LRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQKKIEKLPET-LCE  435 (505)
Q Consensus       358 L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~-~~~l~~L~~L~l~~~~~~~~lp~~-~~~  435 (505)
                      .+.+.+.++.+...    |.  .-..+|+.|+++       ++.+..+|+. ++.+++|++|++++|. ++.+|.. +..
T Consensus         9 ~~~l~~~~~~l~~~----p~--~~~~~l~~L~l~-------~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~   74 (177)
T 2o6r_A            9 GTEIRCNSKGLTSV----PT--GIPSSATRLELE-------SNKLQSLPHGVFDKLTQLTKLSLSQNQ-IQSLPDGVFDK   74 (177)
T ss_dssp             TTEEECCSSCCSSC----CT--TCCTTCSEEECC-------SSCCCCCCTTTTTTCTTCSEEECCSSC-CCCCCTTTTTT
T ss_pred             CCEEEecCCCCccC----CC--CCCCCCcEEEeC-------CCcccEeCHHHhcCcccccEEECCCCc-ceEeChhHccC
Confidence            46788888876653    32  234689999998       6667777654 6889999999999998 7777764 589


Q ss_pred             CCCCcEEecCCCcCccccchh-ccccccCceeecCCCccccccccc-ccCCccCCcccee
Q 046115          436 LYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAG-IGELIRLRRVREF  493 (505)
Q Consensus       436 l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~-i~~l~~L~~L~~~  493 (505)
                      +++|+.|++++|. +..+|+. +..+++|++|++++|.. ..+|.. +..+++|+.|++.
T Consensus        75 l~~L~~L~l~~N~-l~~~~~~~~~~l~~L~~L~l~~N~l-~~~~~~~~~~l~~L~~L~l~  132 (177)
T 2o6r_A           75 LTKLTILYLHENK-LQSLPNGVFDKLTQLKELALDTNQL-KSVPDGIFDRLTSLQKIWLH  132 (177)
T ss_dssp             CTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCC-SCCCTTTTTTCTTCCEEECC
T ss_pred             CCccCEEECCCCC-ccccCHHHhhCCcccCEEECcCCcc-eEeCHHHhcCCcccCEEEec
Confidence            9999999999998 6777765 68999999999999984 566665 5788888887753

>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=98.93  E-value=3.8e-09  Score=90.72  Aligned_cols=100  Identities=24%  Similarity=0.390  Sum_probs=55.5

Q ss_pred             eEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCcceeeccCCccccccchh-hhcC
Q 046115          359 RSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPET-LCEL  436 (505)
Q Consensus       359 ~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l  436 (505)
                      +.+++++|.+...    |..+  ..+|++|+|+       ++.+..+ |..+..+++|++|+|++|. +..+|.. +..+
T Consensus        12 ~~l~~s~n~l~~i----p~~~--~~~l~~L~L~-------~N~i~~~~~~~~~~l~~L~~L~Ls~N~-l~~l~~~~f~~l   77 (170)
T 3g39_A           12 TTVDCSGKSLASV----PTGI--PTTTQVLYLY-------DNQITKLEPGVFDRLTQLTRLDLDNNQ-LTVLPAGVFDKL   77 (170)
T ss_dssp             TEEECTTSCCSSC----CSCC--CTTCSEEECC-------SSCCCCCCTTTTTTCTTCSEEECCSSC-CCCCCTTTTTTC
T ss_pred             CEEEeCCCCcCcc----CccC--CCCCcEEEcC-------CCcCCccChhhhcCcccCCEEECCCCC-cCccChhhccCC
Confidence            4555666555432    2211  2456666665       4444444 3445666666666666666 5555543 3566


Q ss_pred             CCCcEEecCCCcCccccchh-ccccccCceeecCCCcc
Q 046115          437 YNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~  473 (505)
                      ++|+.|+|++|. +..+|+. +..+++|++|++++|..
T Consensus        78 ~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~~  114 (170)
T 3g39_A           78 TQLTQLSLNDNQ-LKSIPRGAFDNLKSLTHIWLLNNPW  114 (170)
T ss_dssp             TTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCB
T ss_pred             CCCCEEECCCCc-cCEeCHHHhcCCCCCCEEEeCCCCC
Confidence            666666666665 5555543 56666666666666653

>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=98.89  E-value=2.1e-09  Score=111.39  Aligned_cols=119  Identities=20%  Similarity=0.193  Sum_probs=89.0

Q ss_pred             CCCceEEEecCCCccccccchhHHhh--------------cCcccceEEecccccCCccccccccCccccCCCCcceeec
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFE--------------KLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNL  420 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~--------------~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l  420 (505)
                      +++|+.|++++|.++.....+ ..+.              .+++|+.|+++       ++.+..+|   ..+++|++|++
T Consensus       180 ~~~L~~L~Ls~N~l~~l~~~~-~~L~~L~L~~N~l~~l~~~~~~L~~L~Ls-------~N~L~~lp---~~l~~L~~L~L  248 (622)
T 3g06_A          180 PSGLQELSVSDNQLASLPTLP-SELYKLWAYNNRLTSLPALPSGLKELIVS-------GNRLTSLP---VLPSELKELMV  248 (622)
T ss_dssp             CTTCCEEECCSSCCSCCCCCC-TTCCEEECCSSCCSSCCCCCTTCCEEECC-------SSCCSCCC---CCCTTCCEEEC
T ss_pred             CCCCcEEECCCCCCCCCCCcc-chhhEEECcCCcccccCCCCCCCCEEEcc-------CCccCcCC---CCCCcCcEEEC
Confidence            366666777766665432211 1111              12667888887       56666676   45689999999


Q ss_pred             cCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          421 KGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       421 ~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ++|. ++.+|.   .+++|+.|+|++|. +..+|..+.++++|+.|++++|...+..|..+..+++...
T Consensus       249 s~N~-L~~lp~---~~~~L~~L~Ls~N~-L~~lp~~l~~l~~L~~L~L~~N~l~~~~~~~l~~L~~~~~  312 (622)
T 3g06_A          249 SGNR-LTSLPM---LPSGLLSLSVYRNQ-LTRLPESLIHLSSETTVNLEGNPLSERTLQALREITSAPG  312 (622)
T ss_dssp             CSSC-CSCCCC---CCTTCCEEECCSSC-CCSCCGGGGGSCTTCEEECCSCCCCHHHHHHHHHHHHSTT
T ss_pred             CCCC-CCcCCc---ccccCcEEeCCCCC-CCcCCHHHhhccccCEEEecCCCCCCcCHHHHHhcccccc
Confidence            9998 888988   67899999999998 7799999999999999999999988777776666554433

>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=98.85  E-value=1.8e-09  Score=106.17  Aligned_cols=141  Identities=14%  Similarity=0.105  Sum_probs=90.3

Q ss_pred             ceeEEEEEecCCCcc-ccccccCCCCCCCceEEEecCCCcc--ccccchhHHhhcCcccceEEecccccCCccccc----
Q 046115          330 KILHLLLTLRRGASV-PISIWGNVTGLRGLRSLLVKSDEYS--WSSEVLPQLFEKLTCLRALELQVRESWPRNNLI----  402 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~L~~L~l~~~~~~--~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~----  402 (505)
                      .+..+.+..+..... ...+...+..+++|++|.+.+|.++  +.....|..+..+++|+.|+|+       ++.+    
T Consensus       160 ~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls-------~n~l~~~g  232 (386)
T 2ca6_A          160 PLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQ-------DNTFTHLG  232 (386)
T ss_dssp             CCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECC-------SSCCHHHH
T ss_pred             CCcEEECCCCCCCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECc-------CCCCCcHH
Confidence            566666666655411 1111123446778888888888765  2222244356778888888887       4444    


Q ss_pred             -cccCccccCCCCcceeeccCCccccc----cchhhh--cCCCCcEEecCCCcCcc----ccchhc-cccccCceeecCC
Q 046115          403 -KEIPTNIEKLLHLKYLNLKGQKKIEK----LPETLC--ELYNLERLNVDDCQNLR----ELPRGI-GKLRKLMYLHNED  470 (505)
Q Consensus       403 -~~~p~~~~~l~~L~~L~l~~~~~~~~----lp~~~~--~l~~L~~L~l~~~~~~~----~lp~~~-~~l~~L~~L~l~~  470 (505)
                       ..+|..+..+++|++|+|++|.....    +|..+.  .+++|+.|+|++|....    .+|..+ .++++|++|++++
T Consensus       233 ~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~i~~~g~~~l~~~l~~~l~~L~~L~l~~  312 (386)
T 2ca6_A          233 SSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNG  312 (386)
T ss_dssp             HHHHHHHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCEEECTT
T ss_pred             HHHHHHHHccCCCcCEEECCCCCCchhhHHHHHHHHhhccCCCeEEEECcCCcCCHHHHHHHHHHHHhcCCCceEEEccC
Confidence             55677777888888888888873222    455553  37888888888887333    277776 5678888888888


Q ss_pred             Ccccccc
Q 046115          471 TGCLRYL  477 (505)
Q Consensus       471 ~~~~~~~  477 (505)
                      |...+..
T Consensus       313 N~l~~~~  319 (386)
T 2ca6_A          313 NRFSEED  319 (386)
T ss_dssp             SBSCTTS
T ss_pred             CcCCcch
Confidence            8755433

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.84  E-value=8.7e-09  Score=88.80  Aligned_cols=97  Identities=28%  Similarity=0.444  Sum_probs=82.1

Q ss_pred             cceEEecccccCCccccccccCccccCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccchh-cccccc
Q 046115          385 LRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPRG-IGKLRK  462 (505)
Q Consensus       385 L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~  462 (505)
                      -+.++++       ++.+..+|..+.  ++|++|+|++|. +..+ |..+..+++|+.|+|++|. +..+|.. +..+++
T Consensus        14 ~~~l~~~-------~n~l~~iP~~~~--~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~Ls~N~-l~~i~~~~~~~l~~   82 (174)
T 2r9u_A           14 QTLVNCQ-------NIRLASVPAGIP--TDKQRLWLNNNQ-ITKLEPGVFDHLVNLQQLYFNSNK-LTAIPTGVFDKLTQ   82 (174)
T ss_dssp             SSEEECC-------SSCCSSCCSCCC--TTCSEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTT
T ss_pred             CcEEEeC-------CCCCCccCCCcC--CCCcEEEeCCCC-ccccCHHHhcCCcCCCEEECCCCC-CCccChhHhCCcch
Confidence            4788888       777889998764  899999999999 6666 6678999999999999998 8888876 589999


Q ss_pred             CceeecCCCccccccccc-ccCCccCCcccee
Q 046115          463 LMYLHNEDTGCLRYLPAG-IGELIRLRRVREF  493 (505)
Q Consensus       463 L~~L~l~~~~~~~~~p~~-i~~l~~L~~L~~~  493 (505)
                      |++|++++|. +..+|.. |..+++|+.|++.
T Consensus        83 L~~L~L~~N~-l~~l~~~~~~~l~~L~~L~L~  113 (174)
T 2r9u_A           83 LTQLDLNDNH-LKSIPRGAFDNLKSLTHIYLY  113 (174)
T ss_dssp             CCEEECCSSC-CCCCCTTTTTTCTTCSEEECC
T ss_pred             hhEEECCCCc-cceeCHHHhccccCCCEEEeC
Confidence            9999999998 5567665 8889999888764

>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=98.83  E-value=1e-08  Score=88.03  Aligned_cols=98  Identities=28%  Similarity=0.409  Sum_probs=82.3

Q ss_pred             ccceEEecccccCCccccccccCccccCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccchh-ccccc
Q 046115          384 CLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPRG-IGKLR  461 (505)
Q Consensus       384 ~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~  461 (505)
                      ..+.++++       ++.+..+|..+  .++|++|+|++|. +..+ |..+..+++|+.|+|++|. +..+|+. +..++
T Consensus        10 ~~~~l~~s-------~n~l~~ip~~~--~~~l~~L~L~~N~-i~~~~~~~~~~l~~L~~L~Ls~N~-l~~l~~~~f~~l~   78 (170)
T 3g39_A           10 SGTTVDCS-------GKSLASVPTGI--PTTTQVLYLYDNQ-ITKLEPGVFDRLTQLTRLDLDNNQ-LTVLPAGVFDKLT   78 (170)
T ss_dssp             ETTEEECT-------TSCCSSCCSCC--CTTCSEEECCSSC-CCCCCTTTTTTCTTCSEEECCSSC-CCCCCTTTTTTCT
T ss_pred             CCCEEEeC-------CCCcCccCccC--CCCCcEEEcCCCc-CCccChhhhcCcccCCEEECCCCC-cCccChhhccCCC
Confidence            56889998       77788898766  4899999999999 6666 6678999999999999998 7788776 58999


Q ss_pred             cCceeecCCCcccccccc-cccCCccCCcccee
Q 046115          462 KLMYLHNEDTGCLRYLPA-GIGELIRLRRVREF  493 (505)
Q Consensus       462 ~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~~  493 (505)
                      +|++|++++|.+ ..+|. .|.++++|+.|++.
T Consensus        79 ~L~~L~L~~N~l-~~~~~~~~~~l~~L~~L~L~  110 (170)
T 3g39_A           79 QLTQLSLNDNQL-KSIPRGAFDNLKSLTHIWLL  110 (170)
T ss_dssp             TCCEEECCSSCC-CCCCTTTTTTCTTCCEEECC
T ss_pred             CCCEEECCCCcc-CEeCHHHhcCCCCCCEEEeC
Confidence            999999999984 55665 48899999888764

>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=98.82  E-value=6.7e-08  Score=88.06  Aligned_cols=105  Identities=11%  Similarity=0.143  Sum_probs=75.8

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHH-HH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETV-AR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~-~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++.+||+||++......+..+...+.....++.+++||+.... .. .......+.+++++.++..+++.......+. 
T Consensus       125 ~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~-  203 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI-  203 (250)
T ss_dssp             SSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTC-
T ss_pred             CCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCC-
Confidence            46799999999776555667777777766677888888876432 11 1233468999999999999999877643221 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                         .-.++.+..|++.|+|.|..+..+...+
T Consensus       204 ---~~~~~~~~~l~~~~~G~~~~~~~~~~~~  231 (250)
T 1njg_A          204 ---AHEPRALQLLARAAEGSLRDALSLTDQA  231 (250)
T ss_dssp             ---CBCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence               1124567889999999999888776544

>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=98.79  E-value=1.8e-08  Score=100.96  Aligned_cols=124  Identities=21%  Similarity=0.290  Sum_probs=84.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....+|     .+..+++|++|++++|.+++.    |.   .+.+|++|+++       ++.+..+| .+
T Consensus       132 ~L~~L~L~~n~l~~lp-----~~~~l~~L~~L~l~~N~l~~l----p~---~~~~L~~L~L~-------~n~l~~l~-~~  191 (454)
T 1jl5_A          132 LLEYLGVSNNQLEKLP-----ELQNSSFLKIIDVDNNSLKKL----PD---LPPSLEFIAAG-------NNQLEELP-EL  191 (454)
T ss_dssp             TCCEEECCSSCCSSCC-----CCTTCTTCCEEECCSSCCSCC----CC---CCTTCCEEECC-------SSCCSSCC-CC
T ss_pred             CCCEEECcCCCCCCCc-----ccCCCCCCCEEECCCCcCccc----CC---CcccccEEECc-------CCcCCcCc-cc
Confidence            5666666666555443     355777788888877776542    22   23477777777       55566666 57


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG  480 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~  480 (505)
                      +.+++|++|++++|. +..+|..   ..+|+.|++++|. +..+| .++.+++|++|++++|. +..+|..
T Consensus       192 ~~l~~L~~L~l~~N~-l~~l~~~---~~~L~~L~l~~n~-l~~lp-~~~~l~~L~~L~l~~N~-l~~l~~~  255 (454)
T 1jl5_A          192 QNLPFLTAIYADNNS-LKKLPDL---PLSLESIVAGNNI-LEELP-ELQNLPFLTTIYADNNL-LKTLPDL  255 (454)
T ss_dssp             TTCTTCCEEECCSSC-CSSCCCC---CTTCCEEECCSSC-CSSCC-CCTTCTTCCEEECCSSC-CSSCCSC
T ss_pred             cCCCCCCEEECCCCc-CCcCCCC---cCcccEEECcCCc-CCccc-ccCCCCCCCEEECCCCc-CCccccc
Confidence            788888888888887 6666652   2578888888887 66777 47788888888888886 3445543

>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=98.75  E-value=3.2e-08  Score=99.12  Aligned_cols=122  Identities=25%  Similarity=0.257  Sum_probs=77.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....+|.       ...+|++|++.+|.+++    +|. +..+++|+.|+++       ++.+..+|.. 
T Consensus       154 ~L~~L~l~~N~l~~lp~-------~~~~L~~L~L~~n~l~~----l~~-~~~l~~L~~L~l~-------~N~l~~l~~~-  213 (454)
T 1jl5_A          154 FLKIIDVDNNSLKKLPD-------LPPSLEFIAAGNNQLEE----LPE-LQNLPFLTAIYAD-------NNSLKKLPDL-  213 (454)
T ss_dssp             TCCEEECCSSCCSCCCC-------CCTTCCEEECCSSCCSS----CCC-CTTCTTCCEEECC-------SSCCSSCCCC-
T ss_pred             CCCEEECCCCcCcccCC-------CcccccEEECcCCcCCc----Ccc-ccCCCCCCEEECC-------CCcCCcCCCC-
Confidence            45566666655554432       22477777777777654    332 6677777777777       4555555542 


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccccc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAG  480 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~  480 (505)
                        .++|++|++++|. +..+|. ++.+++|+.|++++|. +..+|..   +++|++|++++|. +..+|..
T Consensus       214 --~~~L~~L~l~~n~-l~~lp~-~~~l~~L~~L~l~~N~-l~~l~~~---~~~L~~L~l~~N~-l~~l~~~  275 (454)
T 1jl5_A          214 --PLSLESIVAGNNI-LEELPE-LQNLPFLTTIYADNNL-LKTLPDL---PPSLEALNVRDNY-LTDLPEL  275 (454)
T ss_dssp             --CTTCCEEECCSSC-CSSCCC-CTTCTTCCEEECCSSC-CSSCCSC---CTTCCEEECCSSC-CSCCCCC
T ss_pred             --cCcccEEECcCCc-CCcccc-cCCCCCCCEEECCCCc-CCccccc---ccccCEEECCCCc-ccccCcc
Confidence              2477777777776 567774 7777777777777776 5566643   3567777777776 3345543

>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=98.62  E-value=7.2e-07  Score=79.85  Aligned_cols=156  Identities=10%  Similarity=-0.026  Sum_probs=95.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+|||++|+.+++  ..... +. ..+.++.............+..... ..               ....+++.+||
T Consensus        46 ~~G~GKT~l~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~---------------~~~~~~~~vli  107 (226)
T 2chg_A           46 PPGTGKTATAIALAR--DLFGENWRDNFIEMNASDERGIDVVRHKIKEFAR-TA---------------PIGGAPFKIIF  107 (226)
T ss_dssp             STTSSHHHHHHHHHH--HHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHHT-SC---------------CSTTCSCEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHhccccccceEEeccccccChHHHHHHHHHHhc-cc---------------CCCccCceEEE
Confidence            479999999999987  44222 22 2334444443333222221111111 00               01135689999


Q ss_pred             EeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHH-HH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHH
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETV-AR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLE  156 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~-~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~  156 (505)
                      +||++.........+...+.....++.+++||+.... .. .......+.+.+++.++..+++...+...+. .   -.+
T Consensus       108 iDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~-~---~~~  183 (226)
T 2chg_A          108 LDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGV-K---ITE  183 (226)
T ss_dssp             EETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-C---BCH
T ss_pred             EeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHHHHHcCC-C---CCH
Confidence            9999776554556677666666677888888876531 11 1233448899999999999999876532221 1   124


Q ss_pred             HHHHHHHHHcCCChHHHHHHHH
Q 046115          157 KIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       157 ~~~~~i~~~~~g~Plal~~~~~  178 (505)
                      +.+..+++.++|.|..+..+..
T Consensus       184 ~~~~~l~~~~~g~~r~l~~~l~  205 (226)
T 2chg_A          184 DGLEALIYISGGDFRKAINALQ  205 (226)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHH
Confidence            5677899999999986554443

>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=98.62  E-value=1.2e-07  Score=91.76  Aligned_cols=158  Identities=21%  Similarity=0.269  Sum_probs=97.9

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCcccc-----------------------ccchhHHhhcCcccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWS-----------------------SEVLPQLFEKLTCLR  386 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~-----------------------~~~~~~~~~~l~~L~  386 (505)
                      .+..+.+..+.+..++..   .|.++++|++|++++|.+...                       ....|..|..+++|+
T Consensus        31 ~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           31 NAIELRFVLTKLRVIQKG---AFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQ  107 (350)
T ss_dssp             TCSEEEEESCCCSEECTT---SSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCTTCC
T ss_pred             CCCEEEccCCcCCCcCHH---HHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCCcccccCchhhhhccccc
Confidence            566677777666655543   234677777777777654221                       111344466777788


Q ss_pred             eEEeccccc--CC----------------ccccccccCc-cccCC-CCcceeeccCCccccccchhhhcCCCCcEEecCC
Q 046115          387 ALELQVRES--WP----------------RNNLIKEIPT-NIEKL-LHLKYLNLKGQKKIEKLPETLCELYNLERLNVDD  446 (505)
Q Consensus       387 ~L~l~~~~~--~~----------------~~~~~~~~p~-~~~~l-~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~  446 (505)
                      +|+++++..  .+                .++.+..+|. .+..+ ..+++|++++|. ++.+|..+....+|+.|++++
T Consensus       108 ~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~-i~~i~~~~f~~~~L~~l~l~~  186 (350)
T 4ay9_X          108 YLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNG-IQEIHNSAFNGTQLDELNLSD  186 (350)
T ss_dssp             EEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSC-CCEECTTSSTTEEEEEEECTT
T ss_pred             cccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhcccccc-ccCCChhhccccchhHHhhcc
Confidence            887774211  00                1122222322 22333 357778888888 777877776677888888887


Q ss_pred             CcCccccchh-ccccccCceeecCCCccccccccc-ccCCccCCccce
Q 046115          447 CQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAG-IGELIRLRRVRE  492 (505)
Q Consensus       447 ~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~-i~~l~~L~~L~~  492 (505)
                      |..+..+|.. +..+++|++|++++|. +..+|.. +.+++.|+.++.
T Consensus       187 ~n~l~~i~~~~f~~l~~L~~LdLs~N~-l~~lp~~~~~~L~~L~~l~~  233 (350)
T 4ay9_X          187 NNNLEELPNDVFHGASGPVILDISRTR-IHSLPSYGLENLKKLRARST  233 (350)
T ss_dssp             CTTCCCCCTTTTTTEECCSEEECTTSC-CCCCCSSSCTTCCEEECTTC
T ss_pred             CCcccCCCHHHhccCcccchhhcCCCC-cCccChhhhccchHhhhccC
Confidence            6668888865 6888899999999887 5677754 566665555443

>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=98.61  E-value=7.2e-08  Score=93.20  Aligned_cols=98  Identities=26%  Similarity=0.272  Sum_probs=78.8

Q ss_pred             ccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCcCccccchhcccccc
Q 046115          384 CLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQNLRELPRGIGKLRK  462 (505)
Q Consensus       384 ~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~  462 (505)
                      .++.|+|+       ++.+..+|.......+|+.|++.++..++.+|.. +..+++|+.|++++|+ +..+|...  +.+
T Consensus       155 ~l~~L~L~-------~N~i~~i~~~~f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~-l~~lp~~~--~~~  224 (350)
T 4ay9_X          155 ESVILWLN-------KNGIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPSYG--LEN  224 (350)
T ss_dssp             SCEEEECC-------SSCCCEECTTSSTTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTSC-CCCCCSSS--CTT
T ss_pred             hhhhhccc-------cccccCCChhhccccchhHHhhccCCcccCCCHHHhccCcccchhhcCCCC-cCccChhh--hcc
Confidence            57778887       7778888888777889999999977669999874 5899999999999998 89999752  556


Q ss_pred             CceeecCCCcccccccccccCCccCCccce
Q 046115          463 LMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       463 L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      |+.|.+.++..+..+|. +.++++|+.+++
T Consensus       225 L~~L~~l~~~~l~~lP~-l~~l~~L~~l~l  253 (350)
T 4ay9_X          225 LKKLRARSTYNLKKLPT-LEKLVALMEASL  253 (350)
T ss_dssp             CCEEECTTCTTCCCCCC-TTTCCSCCEEEC
T ss_pred             chHhhhccCCCcCcCCC-chhCcChhhCcC
Confidence            77777767766788884 777777777664

>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=98.60  E-value=1e-07  Score=91.95  Aligned_cols=86  Identities=17%  Similarity=0.178  Sum_probs=50.5

Q ss_pred             CCCCCCceEEEecC-CCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCcccccc
Q 046115          352 VTGLRGLRSLLVKS-DEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKL  429 (505)
Q Consensus       352 ~~~~~~L~~L~l~~-~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~l  429 (505)
                      +..+++|+.|+|++ |.++..   .+..|..+.+|+.|+|+       ++.+..+| ..|..|++|++|+|++|. ++.+
T Consensus        27 l~~~~~L~~L~l~~~n~l~~~---~~~~~~~l~~L~~L~l~-------~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~   95 (347)
T 2ifg_A           27 LPGAENLTELYIENQQHLQHL---ELRDLRGLGELRNLTIV-------KSGLRFVAPDAFHFTPRLSRLNLSFNA-LESL   95 (347)
T ss_dssp             SCSCSCCSEEECCSCSSCCEE---CGGGSCSCCCCSEEECC-------SSCCCEECTTGGGSCSCCCEEECCSSC-CSCC
T ss_pred             CCCCCCeeEEEccCCCCCCCc---ChhHhccccCCCEEECC-------CCccceeCHHHhcCCcCCCEEeCCCCc-ccee
Confidence            33666667777764 665543   44456666666677666       44444443 345666666666666666 5556


Q ss_pred             chhhhcCCCCcEEecCCCc
Q 046115          430 PETLCELYNLERLNVDDCQ  448 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~  448 (505)
                      |..+.....|+.|+|.+|+
T Consensus        96 ~~~~~~~~~L~~l~l~~N~  114 (347)
T 2ifg_A           96 SWKTVQGLSLQELVLSGNP  114 (347)
T ss_dssp             CSTTTCSCCCCEEECCSSC
T ss_pred             CHHHcccCCceEEEeeCCC
Confidence            5544333336666666665

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=98.60  E-value=3.4e-08  Score=96.02  Aligned_cols=156  Identities=13%  Similarity=0.107  Sum_probs=93.7

Q ss_pred             ceeEEEEEecCCCcccc-ccccCCCCC-CCceEEEecCCCccccc-cchhHHhhcC-cccceEEecccccCCcccccccc
Q 046115          330 KILHLLLTLRRGASVPI-SIWGNVTGL-RGLRSLLVKSDEYSWSS-EVLPQLFEKL-TCLRALELQVRESWPRNNLIKEI  405 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~-~~~~~~~~~-~~L~~L~l~~~~~~~~~-~~~~~~~~~l-~~L~~L~l~~~~~~~~~~~~~~~  405 (505)
                      .+..+.+..+....... .+...+... ++|++|++++|.++... ..+...+..+ ++|+.|+|+       ++.+...
T Consensus        52 ~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls-------~N~l~~~  124 (362)
T 3goz_A           52 SVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLSGNFLSYKSSDELVKTLAAIPFTITVLDLG-------WNDFSSK  124 (362)
T ss_dssp             TCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECC-------SSCGGGS
T ss_pred             ceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECcCCcCChHHHHHHHHHHHhCCCCccEEECc-------CCcCCcH
Confidence            56677776665543322 122111122 78888888888876431 1122234444 788888888       5555554


Q ss_pred             Cc-c----ccC-CCCcceeeccCCcccc-----ccchhhhcCC-CCcEEecCCCcCccccchh----cccc-ccCceeec
Q 046115          406 PT-N----IEK-LLHLKYLNLKGQKKIE-----KLPETLCELY-NLERLNVDDCQNLRELPRG----IGKL-RKLMYLHN  468 (505)
Q Consensus       406 p~-~----~~~-l~~L~~L~l~~~~~~~-----~lp~~~~~l~-~L~~L~l~~~~~~~~lp~~----~~~l-~~L~~L~l  468 (505)
                      +. .    +.. .++|++|++++|. ++     .++..+..++ +|+.|++++|......+..    +... ++|++|++
T Consensus       125 ~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~L  203 (362)
T 3goz_A          125 SSSEFKQAFSNLPASITSLNLRGND-LGIKSSDELIQILAAIPANVNSLNLRGNNLASKNCAELAKFLASIPASVTSLDL  203 (362)
T ss_dssp             CHHHHHHHHTTSCTTCCEEECTTSC-GGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEEC
T ss_pred             HHHHHHHHHHhCCCceeEEEccCCc-CCHHHHHHHHHHHhcCCccccEeeecCCCCchhhHHHHHHHHHhCCCCCCEEEC
Confidence            43 2    233 3589999999888 44     4555556665 8999999998833333333    3444 58999999


Q ss_pred             CCCcccc----cccccccCC-ccCCcccee
Q 046115          469 EDTGCLR----YLPAGIGEL-IRLRRVREF  493 (505)
Q Consensus       469 ~~~~~~~----~~p~~i~~l-~~L~~L~~~  493 (505)
                      ++|....    .++..+..+ ++|+.|++-
T Consensus       204 s~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls  233 (362)
T 3goz_A          204 SANLLGLKSYAELAYIFSSIPNHVVSLNLC  233 (362)
T ss_dssp             TTSCGGGSCHHHHHHHHHHSCTTCCEEECC
T ss_pred             CCCCCChhHHHHHHHHHhcCCCCceEEECc
Confidence            9987443    155555543 477777654

>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=98.53  E-value=1.7e-07  Score=90.45  Aligned_cols=103  Identities=16%  Similarity=0.117  Sum_probs=82.5

Q ss_pred             EEEecCC-CccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccc-hhhhcC
Q 046115          360 SLLVKSD-EYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLP-ETLCEL  436 (505)
Q Consensus       360 ~L~l~~~-~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l  436 (505)
                      .++..++ .++.    +|. +..+.+|+.|+|+      +++.+..+| ..++.|++|++|+|++|. +..+| ..+..+
T Consensus        12 ~v~~~~~n~l~~----ip~-l~~~~~L~~L~l~------~~n~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~~~~~~l   79 (347)
T 2ifg_A           12 GLRCTRDGALDS----LHH-LPGAENLTELYIE------NQQHLQHLELRDLRGLGELRNLTIVKSG-LRFVAPDAFHFT   79 (347)
T ss_dssp             CEECCSSCCCTT----TTT-SCSCSCCSEEECC------SCSSCCEECGGGSCSCCCCSEEECCSSC-CCEECTTGGGSC
T ss_pred             EEEcCCCCCCCc----cCC-CCCCCCeeEEEcc------CCCCCCCcChhHhccccCCCEEECCCCc-cceeCHHHhcCC
Confidence            4577776 6654    677 8889999999998      227788777 568999999999999999 66555 467999


Q ss_pred             CCCcEEecCCCcCccccchhccccccCceeecCCCcccc
Q 046115          437 YNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLR  475 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~  475 (505)
                      ++|+.|+|++|. +..+|+.+....+|+.|++.+|....
T Consensus        80 ~~L~~L~l~~N~-l~~~~~~~~~~~~L~~l~l~~N~~~c  117 (347)
T 2ifg_A           80 PRLSRLNLSFNA-LESLSWKTVQGLSLQELVLSGNPLHC  117 (347)
T ss_dssp             SCCCEEECCSSC-CSCCCSTTTCSCCCCEEECCSSCCCC
T ss_pred             cCCCEEeCCCCc-cceeCHHHcccCCceEEEeeCCCccC
Confidence            999999999999 78888765444449999999998543

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=98.50  E-value=7.7e-08  Score=93.47  Aligned_cols=153  Identities=11%  Similarity=0.122  Sum_probs=99.8

Q ss_pred             ceeEEEEEecCCCcccc-ccccCCCCCC-CceEEEecCCCccccccchhHHhhcC-----cccceEEecccccCCccccc
Q 046115          330 KILHLLLTLRRGASVPI-SIWGNVTGLR-GLRSLLVKSDEYSWSSEVLPQLFEKL-----TCLRALELQVRESWPRNNLI  402 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~-~L~~L~l~~~~~~~~~~~~~~~~~~l-----~~L~~L~l~~~~~~~~~~~~  402 (505)
                      .+..+.+..+.....+. .+...+..++ +|+.|++++|.++..   .+..+..+     ++|+.|+|+       ++.+
T Consensus        23 ~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~---~~~~l~~~l~~~~~~L~~L~Ls-------~n~l   92 (362)
T 3goz_A           23 GVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGNSLGFK---NSDELVQILAAIPANVTSLNLS-------GNFL   92 (362)
T ss_dssp             TCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGS---CHHHHHHHHHTSCTTCCEEECC-------SSCG
T ss_pred             CceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCCCCCHH---HHHHHHHHHhccCCCccEEECc-------CCcC
Confidence            47777777776655442 1113344677 899999999987654   33334443     889999998       5555


Q ss_pred             cccCcc-----ccCC-CCcceeeccCCccccccch-hhh----c-CCCCcEEecCCCcCcc----ccchhccccc-cCce
Q 046115          403 KEIPTN-----IEKL-LHLKYLNLKGQKKIEKLPE-TLC----E-LYNLERLNVDDCQNLR----ELPRGIGKLR-KLMY  465 (505)
Q Consensus       403 ~~~p~~-----~~~l-~~L~~L~l~~~~~~~~lp~-~~~----~-l~~L~~L~l~~~~~~~----~lp~~~~~l~-~L~~  465 (505)
                      ...+..     +..+ ++|++|++++|. ++..+. .+.    . ..+|+.|++++|....    .++..+..++ +|++
T Consensus        93 ~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~  171 (362)
T 3goz_A           93 SYKSSDELVKTLAAIPFTITVLDLGWND-FSSKSSSEFKQAFSNLPASITSLNLRGNDLGIKSSDELIQILAAIPANVNS  171 (362)
T ss_dssp             GGSCHHHHHHHHHTSCTTCCEEECCSSC-GGGSCHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCE
T ss_pred             ChHHHHHHHHHHHhCCCCccEEECcCCc-CCcHHHHHHHHHHHhCCCceeEEEccCCcCCHHHHHHHHHHHhcCCccccE
Confidence            544322     4445 789999999999 554443 333    3 3689999999988332    4555566666 8999


Q ss_pred             eecCCCcccccccccc----cCC-ccCCcccee
Q 046115          466 LHNEDTGCLRYLPAGI----GEL-IRLRRVREF  493 (505)
Q Consensus       466 L~l~~~~~~~~~p~~i----~~l-~~L~~L~~~  493 (505)
                      |++++|......+..+    ..+ ++|+.|++-
T Consensus       172 L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls  204 (362)
T 3goz_A          172 LNLRGNNLASKNCAELAKFLASIPASVTSLDLS  204 (362)
T ss_dssp             EECTTSCGGGSCHHHHHHHHHTSCTTCCEEECT
T ss_pred             eeecCCCCchhhHHHHHHHHHhCCCCCCEEECC
Confidence            9999998555444333    334 477777653

>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=98.42  E-value=1.2e-07  Score=95.18  Aligned_cols=157  Identities=17%  Similarity=0.128  Sum_probs=91.8

Q ss_pred             ceeEEEEEecCCCcccc-ccccCCCCCC-CceEEEecCCCccccc-cchhHHhhcCcccceEEecccccCCcccccccc-
Q 046115          330 KILHLLLTLRRGASVPI-SIWGNVTGLR-GLRSLLVKSDEYSWSS-EVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-  405 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~-~L~~L~l~~~~~~~~~-~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-  405 (505)
                      .++.+.+..+....... .+...+.... +|++|++++|.++... ..++..+..+++|+.|+++       ++.+... 
T Consensus        57 ~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls-------~n~i~~~~  129 (461)
T 1z7x_W           57 ALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLS-------DNLLGDAG  129 (461)
T ss_dssp             TCCEEECTTCCCHHHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECC-------SSBCHHHH
T ss_pred             CcCEEeCCCCcCChHHHHHHHHHHhhCCCceeEEEccCCCCCHHHHHHHHHHHccCCceeEEECC-------CCcCchHH
Confidence            56666666554432111 1111111111 6888888888765321 2356667778888888887       3333321 


Q ss_pred             Cccc-----cCCCCcceeeccCCcccc----ccchhhhcCCCCcEEecCCCcCccccchhcc-----ccccCceeecCCC
Q 046115          406 PTNI-----EKLLHLKYLNLKGQKKIE----KLPETLCELYNLERLNVDDCQNLRELPRGIG-----KLRKLMYLHNEDT  471 (505)
Q Consensus       406 p~~~-----~~l~~L~~L~l~~~~~~~----~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~-----~l~~L~~L~l~~~  471 (505)
                      +..+     ...++|++|++++|....    .++..+..+++|+.|++++|......+..+.     ..++|++|++++|
T Consensus       130 ~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n  209 (461)
T 1z7x_W          130 LQLLCEGLLDPQCRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESC  209 (461)
T ss_dssp             HHHHHHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHHHSCCCCCEEECTTS
T ss_pred             HHHHHHHHhcCCCcceEEECCCCCCCHHHHHHHHHHHhhCCCCCEEECcCCCcchHHHHHHHHHHhcCCCCceEEEccCC
Confidence            2211     235578888888887322    2455567778888888888873222222222     2558888888888


Q ss_pred             ccccc----ccccccCCccCCcccee
Q 046115          472 GCLRY----LPAGIGELIRLRRVREF  493 (505)
Q Consensus       472 ~~~~~----~p~~i~~l~~L~~L~~~  493 (505)
                      .....    +|..+..+++|+.|++-
T Consensus       210 ~l~~~~~~~l~~~l~~~~~L~~L~Ls  235 (461)
T 1z7x_W          210 GVTSDNCRDLCGIVASKASLRELALG  235 (461)
T ss_dssp             CCBTTHHHHHHHHHHHCTTCCEEECC
T ss_pred             CCcHHHHHHHHHHHHhCCCccEEecc
Confidence            74432    46666777888877764

>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=98.39  E-value=1.6e-07  Score=94.46  Aligned_cols=157  Identities=22%  Similarity=0.157  Sum_probs=97.8

Q ss_pred             ceeEEEEEecCCCcccc-ccccCCCCCCCceEEEecCCCccccc--cchhHHhhcCcccceEEecccccCCccccccc--
Q 046115          330 KILHLLLTLRRGASVPI-SIWGNVTGLRGLRSLLVKSDEYSWSS--EVLPQLFEKLTCLRALELQVRESWPRNNLIKE--  404 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~L~~L~l~~~~~~~~~--~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~--  404 (505)
                      .+..+.+..+....... .++..+..+++|+.|++++|.++...  ...+..+..+++|+.|+++       ++.+..  
T Consensus       200 ~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~-------~n~l~~~~  272 (461)
T 1z7x_W          200 QLEALKLESCGVTSDNCRDLCGIVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIW-------ECGITAKG  272 (461)
T ss_dssp             CCCEEECTTSCCBTTHHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECT-------TSCCCHHH
T ss_pred             CceEEEccCCCCcHHHHHHHHHHHHhCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECc-------CCCCCHHH
Confidence            56666666665443211 12223346788888888888765421  1112223357888888888       444544  


Q ss_pred             ---cCccccCCCCcceeeccCCccccccchhhhc-----CCCCcEEecCCCcCccc----cchhccccccCceeecCCCc
Q 046115          405 ---IPTNIEKLLHLKYLNLKGQKKIEKLPETLCE-----LYNLERLNVDDCQNLRE----LPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       405 ---~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~-----l~~L~~L~l~~~~~~~~----lp~~~~~l~~L~~L~l~~~~  472 (505)
                         ++..+..+++|++|++++|.....-+..+..     .++|+.|++++|.....    +|..+..+++|++|++++|.
T Consensus       273 ~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~  352 (461)
T 1z7x_W          273 CGDLCRVLRAKESLKELSLAGNELGDEGARLLCETLLEPGCQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNNR  352 (461)
T ss_dssp             HHHHHHHHHHCTTCCEEECTTCCCHHHHHHHHHHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCSSCCEEECCSSB
T ss_pred             HHHHHHHHhhCCCcceEECCCCCCchHHHHHHHHHhccCCccceeeEcCCCCCchHHHHHHHHHHhhCCCccEEEccCCc
Confidence               5666777888999999988732222222322     36899999999884332    56677788899999999997


Q ss_pred             ccccccccccC-----CccCCcccee
Q 046115          473 CLRYLPAGIGE-----LIRLRRVREF  493 (505)
Q Consensus       473 ~~~~~p~~i~~-----l~~L~~L~~~  493 (505)
                      .....+..+..     .++|+.|++.
T Consensus       353 i~~~~~~~l~~~l~~~~~~L~~L~L~  378 (461)
T 1z7x_W          353 LEDAGVRELCQGLGQPGSVLRVLWLA  378 (461)
T ss_dssp             CHHHHHHHHHHHHTSTTCCCCEEECT
T ss_pred             cccccHHHHHHHHcCCCCceEEEECC
Confidence            55443443332     5577776654

>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=98.34  E-value=3.3e-06  Score=80.36  Aligned_cols=156  Identities=13%  Similarity=0.142  Sum_probs=92.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r~Ll   77 (505)
                      ++|+|||++|+.+++  ..... +. ..++++....... ...+.++..+...               ...+ .+++.++
T Consensus        50 ~~G~GKt~la~~l~~--~l~~~~~~~~~~~~~~~~~~~~-~~i~~~~~~~~~~---------------~~~~~~~~~~vi  111 (323)
T 1sxj_B           50 MPGIGKTTSVHCLAH--ELLGRSYADGVLELNASDDRGI-DVVRNQIKHFAQK---------------KLHLPPGKHKIV  111 (323)
T ss_dssp             STTSSHHHHHHHHHH--HHHGGGHHHHEEEECTTSCCSH-HHHHTHHHHHHHB---------------CCCCCTTCCEEE
T ss_pred             cCCCCHHHHHHHHHH--HhcCCcccCCEEEecCccccCh-HHHHHHHHHHHhc---------------cccCCCCCceEE
Confidence            479999999999998  44222 21 2334443332221 1112222111100               0011 3458899


Q ss_pred             EEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchH
Q 046115           78 VLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENL  155 (505)
Q Consensus        78 vlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~  155 (505)
                      |+||++.........+...+.....++.+++||+... +.. .......+.+.+++.++..+++...+...+. .   -.
T Consensus       112 iiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~-~---~~  187 (323)
T 1sxj_B          112 ILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDV-K---YT  187 (323)
T ss_dssp             EEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-C---BC
T ss_pred             EEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHcCC-C---CC
Confidence            9999977554455566666666666778888887642 111 1233458999999999999999876532221 1   12


Q ss_pred             HHHHHHHHHHcCCChH-HHHHHHH
Q 046115          156 EKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       156 ~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                      ++.+..+++.++|.|. |+..+..
T Consensus       188 ~~~~~~l~~~~~G~~r~a~~~l~~  211 (323)
T 1sxj_B          188 NDGLEAIIFTAEGDMRQAINNLQS  211 (323)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4567889999999994 4554443

>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=98.24  E-value=1.4e-06  Score=90.50  Aligned_cols=132  Identities=14%  Similarity=-0.043  Sum_probs=77.1

Q ss_pred             CCCCceEEEecCCCccccc-cchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccc---ccc
Q 046115          354 GLRGLRSLLVKSDEYSWSS-EVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKI---EKL  429 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~-~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~---~~l  429 (505)
                      .+++|++|.+.+|.+++.. ..++..+.++++|+.|+++       ++.+..+|..+..+++|++|+++.+...   ...
T Consensus       190 ~~~~L~~L~L~~n~~~~~~~~~l~~~~~~~~~L~~L~L~-------~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~  262 (592)
T 3ogk_B          190 HNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVG-------DFEILELVGFFKAAANLEEFCGGSLNEDIGMPEK  262 (592)
T ss_dssp             HCCCCCEEECTTCCCSSCCHHHHHHHHHHCTTCCEEECS-------SCBGGGGHHHHHHCTTCCEEEECBCCCCTTCTTS
T ss_pred             cCCCccEEEeeccCCCccCHHHHHHHHhhCCCCcEEecc-------CccHHHHHHHHhhhhHHHhhcccccccccchHHH
Confidence            4455666666555543111 1244445555666666665       3334445555555666666666543211   223


Q ss_pred             chhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCccccccc-ccccCCccCCcccee
Q 046115          430 PETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRLRRVREF  493 (505)
Q Consensus       430 p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L~~L~~~  493 (505)
                      +..+..+++|+.|+++++. ...+|..+..+++|++|++++|......+ ..+..+++|+.|++.
T Consensus       263 ~~~l~~~~~L~~L~l~~~~-~~~l~~~~~~~~~L~~L~Ls~~~l~~~~~~~~~~~~~~L~~L~L~  326 (592)
T 3ogk_B          263 YMNLVFPRKLCRLGLSYMG-PNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKCPNLEVLETR  326 (592)
T ss_dssp             SSCCCCCTTCCEEEETTCC-TTTGGGGGGGGGGCCEEEETTCCCCHHHHHHHHTTCTTCCEEEEE
T ss_pred             HHHhhccccccccCccccc-hhHHHHHHhhcCCCcEEecCCCcCCHHHHHHHHHhCcCCCEEecc
Confidence            3345556666666666654 56677778888899999999987333222 335788888888765

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.23  E-value=5.1e-07  Score=87.70  Aligned_cols=141  Identities=16%  Similarity=0.059  Sum_probs=91.7

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccc-cchhHHh-hcCcccceEEecccccCCccccccc---
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSS-EVLPQLF-EKLTCLRALELQVRESWPRNNLIKE---  404 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~-~~~~~~~-~~l~~L~~L~l~~~~~~~~~~~~~~---  404 (505)
                      .+..+.+..+......  ...-...+++|+.|++++|.++... ..+...+ ...++|+.|+|+       ++.++.   
T Consensus       102 ~L~~L~Ls~n~l~~~~--~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls-------~n~l~~~~~  172 (372)
T 3un9_A          102 ALDEVNLASCQLDPAG--LRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLS-------NNPLTAAGV  172 (372)
T ss_dssp             CEEEEECTTCCCCHHH--HHHTHHHHHTEEEEECCSSCCCHHHHHHHHHHHHSTTCCCCEEECC-------SSCCHHHHH
T ss_pred             CceEEEecCCCCCHHH--HHHHHHHHHhccHhhcCCCCCCHHHHHHHHHHHHhcCCccceeeCC-------CCCCChHHH
Confidence            5667777666554211  1111124568999999999875431 1122222 246789999998       444433   


Q ss_pred             --cCccccCCCCcceeeccCCcccc-----ccchhhhcCCCCcEEecCCCcCcc-----ccchhccccccCceeecCCCc
Q 046115          405 --IPTNIEKLLHLKYLNLKGQKKIE-----KLPETLCELYNLERLNVDDCQNLR-----ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       405 --~p~~~~~l~~L~~L~l~~~~~~~-----~lp~~~~~l~~L~~L~l~~~~~~~-----~lp~~~~~l~~L~~L~l~~~~  472 (505)
                        ++..+..+++|++|+|++|. ++     .++..+...++|+.|+|++|. +.     .++..+...++|++|++++|.
T Consensus       173 ~~l~~~L~~~~~L~~L~Ls~N~-l~~~g~~~L~~~L~~~~~L~~L~Ls~N~-i~~~g~~~l~~~L~~~~~L~~L~Ls~N~  250 (372)
T 3un9_A          173 AVLMEGLAGNTSVTHLSLLHTG-LGDEGLELLAAQLDRNRQLQELNVAYNG-AGDTAALALARAAREHPSLELLHLYFNE  250 (372)
T ss_dssp             HHHHHHHHTCSSCCEEECTTSS-CHHHHHHHHHHHGGGCSCCCEEECCSSC-CCHHHHHHHHHHHHHCSSCCEEECTTSS
T ss_pred             HHHHHHHhcCCCcCEEeCCCCC-CCcHHHHHHHHHHhcCCCcCeEECCCCC-CCHHHHHHHHHHHHhCCCCCEEeccCCC
Confidence              44556778899999999998 54     335556778899999999998 44     344456677899999999998


Q ss_pred             ccccccccc
Q 046115          473 CLRYLPAGI  481 (505)
Q Consensus       473 ~~~~~p~~i  481 (505)
                      +...-...+
T Consensus       251 i~~~g~~~L  259 (372)
T 3un9_A          251 LSSEGRQVL  259 (372)
T ss_dssp             CCHHHHHHH
T ss_pred             CCHHHHHHH
Confidence            544333333

>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=98.15  E-value=2.6e-06  Score=88.39  Aligned_cols=155  Identities=17%  Similarity=0.009  Sum_probs=108.6

Q ss_pred             ceeEEEEEecCCCccc-cccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVP-ISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      .+..+.+..+....+. ..+...+..+++|++|.+.+|.+.+    +|..+..+++|+.|+++....   .......+..
T Consensus       193 ~L~~L~L~~n~~~~~~~~~l~~~~~~~~~L~~L~L~~~~~~~----l~~~~~~~~~L~~L~l~~~~~---~~~~~~~~~~  265 (592)
T 3ogk_B          193 SLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILE----LVGFFKAAANLEEFCGGSLNE---DIGMPEKYMN  265 (592)
T ss_dssp             CCCEEECTTCCCSSCCHHHHHHHHHHCTTCCEEECSSCBGGG----GHHHHHHCTTCCEEEECBCCC---CTTCTTSSSC
T ss_pred             CccEEEeeccCCCccCHHHHHHHHhhCCCCcEEeccCccHHH----HHHHHhhhhHHHhhccccccc---ccchHHHHHH
Confidence            5566666555544222 2333334478999999999987654    677788999999999973110   1111344556


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccc--cchhccccccCceeecCCCcccccccccccCCcc
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRE--LPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIR  486 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~--lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~  486 (505)
                      +..+++|+.|+++.+. ...+|..+..+++|+.|++++|. +..  ++..+..+++|++|++.++.....++..+..+++
T Consensus       266 l~~~~~L~~L~l~~~~-~~~l~~~~~~~~~L~~L~Ls~~~-l~~~~~~~~~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~  343 (592)
T 3ogk_B          266 LVFPRKLCRLGLSYMG-PNEMPILFPFAAQIRKLDLLYAL-LETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQ  343 (592)
T ss_dssp             CCCCTTCCEEEETTCC-TTTGGGGGGGGGGCCEEEETTCC-CCHHHHHHHHTTCTTCCEEEEEGGGHHHHHHHHHHHCTT
T ss_pred             hhccccccccCccccc-hhHHHHHHhhcCCCcEEecCCCc-CCHHHHHHHHHhCcCCCEEeccCccCHHHHHHHHHhCCC
Confidence            7888999999999876 77888878889999999999998 432  3334688999999999855433344444467888


Q ss_pred             CCcccee
Q 046115          487 LRRVREF  493 (505)
Q Consensus       487 L~~L~~~  493 (505)
                      |+.|++.
T Consensus       344 L~~L~L~  350 (592)
T 3ogk_B          344 LKRLRIE  350 (592)
T ss_dssp             CCEEEEE
T ss_pred             CCEEEee
Confidence            8888876

>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=98.04  E-value=1.7e-06  Score=89.93  Aligned_cols=149  Identities=15%  Similarity=0.174  Sum_probs=94.0

Q ss_pred             ceeEEEEEecCCCccccccccCCC-CCCCceEEEecCCC-ccccccchhHHhhcCcccceEEecccccCCccccccc---
Q 046115          330 KILHLLLTLRRGASVPISIWGNVT-GLRGLRSLLVKSDE-YSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE---  404 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~L~~L~l~~~~-~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~---  404 (505)
                      .+..+.+........   ....+. .+++|+.|.+.+|. ++.  ..++..+..+++|++|+++       ++.+..   
T Consensus       106 ~L~~L~L~~~~~~~~---~~~~l~~~~~~L~~L~L~~~~~~~~--~~l~~~~~~~~~L~~L~L~-------~~~i~~~~~  173 (594)
T 2p1m_B          106 WLEEIRLKRMVVTDD---CLELIAKSFKNFKVLVLSSCEGFST--DGLAAIAATCRNLKELDLR-------ESDVDDVSG  173 (594)
T ss_dssp             TCCEEEEESCBCCHH---HHHHHHHHCTTCCEEEEESCEEEEH--HHHHHHHHHCTTCCEEECT-------TCEEECCCG
T ss_pred             CCCeEEeeCcEEcHH---HHHHHHHhCCCCcEEeCCCcCCCCH--HHHHHHHHhCCCCCEEeCc-------CCccCCcch
Confidence            566677666543321   112222 46788888888873 321  1255556678888888887       332222   


Q ss_pred             --cCccccCCCCcceeeccCCc-cc--cccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcc------
Q 046115          405 --IPTNIEKLLHLKYLNLKGQK-KI--EKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGC------  473 (505)
Q Consensus       405 --~p~~~~~l~~L~~L~l~~~~-~~--~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~------  473 (505)
                        ++.....+++|++|++++|. .+  ..++..+..+++|+.|++++|..+..+|..+..+++|++|++..+..      
T Consensus       174 ~~l~~~~~~~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~  253 (594)
T 2p1m_B          174 HWLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDV  253 (594)
T ss_dssp             GGGGGSCTTCCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCHHHHHHHHHHCTTCSEEECSBCCCCCCHHH
T ss_pred             HHHHHHhhcCCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcHHHHHHHHhcCCcceEcccccccCccchhh
Confidence              22323467788888888886 11  22333345678899999988866777887888888888888665531      


Q ss_pred             cccccccccCCccCCcc
Q 046115          474 LRYLPAGIGELIRLRRV  490 (505)
Q Consensus       474 ~~~~p~~i~~l~~L~~L  490 (505)
                      ...++..+.++++|+.|
T Consensus       254 ~~~l~~~l~~~~~L~~L  270 (594)
T 2p1m_B          254 YSGLSVALSGCKELRCL  270 (594)
T ss_dssp             HHHHHHHHHTCTTCCEE
T ss_pred             HHHHHHHHhcCCCcccc
Confidence            23345567777888777

>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=98.02  E-value=1.6e-05  Score=75.75  Aligned_cols=104  Identities=10%  Similarity=0.017  Sum_probs=71.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHH-HHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETV-ARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~-~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++.++|+|+++.........+...+.....++++++||....- ... ......+.+.+++.++..+++...+...+. 
T Consensus       109 ~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~-  187 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL-  187 (327)
T ss_dssp             CSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTC-
T ss_pred             CCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcCC-
Confidence            56789999999776555566677777666677888888876431 111 122347899999999999999876543222 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIASL  179 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~~~  179 (505)
                         .-.++++..+++.++|.|..+..+...
T Consensus       188 ---~~~~~~~~~l~~~~~g~~r~~~~~l~~  214 (327)
T 1iqp_A          188 ---ELTEEGLQAILYIAEGDMRRAINILQA  214 (327)
T ss_dssp             ---EECHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHHCCCCHHHHHHHHHH
Confidence               122466788999999999865544443

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.02  E-value=1.4e-06  Score=84.62  Aligned_cols=107  Identities=20%  Similarity=0.182  Sum_probs=51.8

Q ss_pred             CCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-----ccc-cCCCCcceeeccCCcccc--
Q 046115          356 RGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-----TNI-EKLLHLKYLNLKGQKKIE--  427 (505)
Q Consensus       356 ~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-----~~~-~~l~~L~~L~l~~~~~~~--  427 (505)
                      .+|+.|++++|.++..  .+......+.+|+.|+|+       ++.++...     ..+ ...++|++|+|++|. ++  
T Consensus       101 ~~L~~L~Ls~n~l~~~--~~~~l~~~L~~L~~L~Ls-------~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls~n~-l~~~  170 (372)
T 3un9_A          101 HALDEVNLASCQLDPA--GLRTLLPVFLRARKLGLQ-------LNSLGPEACKDLRDLLLHDQCQITTLRLSNNP-LTAA  170 (372)
T ss_dssp             SCEEEEECTTCCCCHH--HHHHTHHHHHTEEEEECC-------SSCCCHHHHHHHHHHHHSTTCCCCEEECCSSC-CHHH
T ss_pred             CCceEEEecCCCCCHH--HHHHHHHHHHhccHhhcC-------CCCCCHHHHHHHHHHHHhcCCccceeeCCCCC-CChH
Confidence            4566666666655321  122222334456666665       33332211     111 134556666666665 32  


Q ss_pred             ---ccchhhhcCCCCcEEecCCCcCccc-----cchhccccccCceeecCCCcc
Q 046115          428 ---KLPETLCELYNLERLNVDDCQNLRE-----LPRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       428 ---~lp~~~~~l~~L~~L~l~~~~~~~~-----lp~~~~~l~~L~~L~l~~~~~  473 (505)
                         .++..+..+++|++|+|++|. +..     ++..+...++|++|++++|..
T Consensus       171 ~~~~l~~~L~~~~~L~~L~Ls~N~-l~~~g~~~L~~~L~~~~~L~~L~Ls~N~i  223 (372)
T 3un9_A          171 GVAVLMEGLAGNTSVTHLSLLHTG-LGDEGLELLAAQLDRNRQLQELNVAYNGA  223 (372)
T ss_dssp             HHHHHHHHHHTCSSCCEEECTTSS-CHHHHHHHHHHHGGGCSCCCEEECCSSCC
T ss_pred             HHHHHHHHHhcCCCcCEEeCCCCC-CCcHHHHHHHHHHhcCCCcCeEECCCCCC
Confidence               233334555666666666665 322     233445555666666666653

>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=97.98  E-value=9.1e-05  Score=71.86  Aligned_cols=103  Identities=12%  Similarity=0.166  Sum_probs=70.6

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++.++|+|+++.........+...+.....+..+|++|.... +.. .......+.+.+++.++..+++.......+. 
T Consensus       118 ~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~-  196 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI-  196 (373)
T ss_dssp             SSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-
T ss_pred             CCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCC-
Confidence            4678999999977665566777777776666677777776532 211 1233468899999999999999866532121 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~~  178 (505)
                         .-.++++..+++.++|.|..+..+..
T Consensus       197 ---~~~~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          197 ---AHEPRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             ---CBCHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence               11245678899999999987765543

>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=97.95  E-value=1.7e-05  Score=71.80  Aligned_cols=146  Identities=12%  Similarity=0.039  Sum_probs=84.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||+.+++  ........++|+++....+.      +...                   .+.+ .++.+||+|
T Consensus        60 ~~G~GKT~la~~l~~--~~~~~~~~~~~~~~~~~~~~------~~~~-------------------~~~~-~~~~vliiD  111 (242)
T 3bos_A           60 PVKSGRTHLIHAACA--RANELERRSFYIPLGIHASI------STAL-------------------LEGL-EQFDLICID  111 (242)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEEGGGGGGS------CGGG-------------------GTTG-GGSSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCeEEEEEHHHHHHH------HHHH-------------------HHhc-cCCCEEEEe
Confidence            479999999999998  55444445667776442110      0000                   0011 345689999


Q ss_pred             CCCCCCccC--hhHHHHhhcCC-CCC-cEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCC
Q 046115           81 DVWNEDYYK--WEPFYKCLKNS-LHE-SKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGK  147 (505)
Q Consensus        81 dv~~~~~~~--~~~~~~~~~~~-~~~-~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~  147 (505)
                      |++......  ...+...+... ..+ .++++||+..         .+...+.....+.+++++.++..+++...+...+
T Consensus       112 e~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~  191 (242)
T 3bos_A          112 DVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRG  191 (242)
T ss_dssp             TGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTT
T ss_pred             ccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcC
Confidence            996643222  23333332221 122 2477777632         1222221125889999999999999987764222


Q ss_pred             CCCCCchHHHHHHHHHHHcCCChHHHHHHHH
Q 046115          148 TIGKRENLEKIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~  178 (505)
                      .    .-.++++..+++.++|.+-.+..+..
T Consensus       192 ~----~~~~~~~~~l~~~~~g~~r~l~~~l~  218 (242)
T 3bos_A          192 L----QLPEDVGRFLLNRMARDLRTLFDVLD  218 (242)
T ss_dssp             C----CCCHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             C----CCCHHHHHHHHHHccCCHHHHHHHHH
Confidence            1    11246677888999998866554433

>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=97.94  E-value=0.00014  Score=69.28  Aligned_cols=95  Identities=14%  Similarity=0.041  Sum_probs=67.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+...+.....++.+|++|.++. +... ......+.+.+++.++..+++....    . 
T Consensus       107 ~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~----~-  181 (334)
T 1a5t_A          107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV----T-  181 (334)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHC----C-
T ss_pred             CCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhc----C-
Confidence            4678899999977665556678887777666777777776642 2222 2334589999999999999987754    1 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                          -.++.+..+++.++|.|.....
T Consensus       182 ----~~~~~~~~l~~~s~G~~r~a~~  203 (334)
T 1a5t_A          182 ----MSQDALLAALRLSAGSPGAALA  203 (334)
T ss_dssp             ----CCHHHHHHHHHHTTTCHHHHHH
T ss_pred             ----CCHHHHHHHHHHcCCCHHHHHH
Confidence                1135567899999999965433

>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=97.91  E-value=4.3e-06  Score=76.40  Aligned_cols=83  Identities=19%  Similarity=0.234  Sum_probs=37.7

Q ss_pred             CCCCcceeeccCCccccc---cchhhhcCCCCcEEecCCCcCccccchhccccc--cCceeecCCCcccccccc------
Q 046115          411 KLLHLKYLNLKGQKKIEK---LPETLCELYNLERLNVDDCQNLRELPRGIGKLR--KLMYLHNEDTGCLRYLPA------  479 (505)
Q Consensus       411 ~l~~L~~L~l~~~~~~~~---lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~--~L~~L~l~~~~~~~~~p~------  479 (505)
                      .+++|+.|+|++|. +..   +|..++.+++|+.|+|++|. +..+ ..+..++  +|++|++++|+..+.+|.      
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~~  244 (267)
T 3rw6_A          168 NIPELLSLNLSNNR-LYRLDDMSSIVQKAPNLKILNLSGNE-LKSE-RELDKIKGLKLEELWLDGNSLCDTFRDQSTYIS  244 (267)
T ss_dssp             HCTTCCEEECTTSC-CCCCGGGTTHHHHSTTCCEEECTTSC-CCSG-GGGGGGTTSCCSEEECTTSTTGGGCSSHHHHHH
T ss_pred             hCCCCCEEECCCCC-CCCCccchhHHhhCCCCCEEECCCCc-cCCc-hhhhhcccCCcceEEccCCcCccccCcchhHHH
Confidence            34455555555555 222   22334455555555555555 3333 1222233  555555555554333331      


Q ss_pred             -cccCCccCCccceeEec
Q 046115          480 -GIGELIRLRRVREFVVG  496 (505)
Q Consensus       480 -~i~~l~~L~~L~~~~~~  496 (505)
                       .+..+++|+.|+...++
T Consensus       245 ~il~~~P~L~~LDg~~v~  262 (267)
T 3rw6_A          245 AIRERFPKLLRLDGHELP  262 (267)
T ss_dssp             HHHHHCTTCCEESSCBCC
T ss_pred             HHHHHCcccCeECCcCCC
Confidence             23455555555554443

>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=97.90  E-value=1e-05  Score=73.85  Aligned_cols=98  Identities=26%  Similarity=0.284  Sum_probs=70.5

Q ss_pred             EEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc---CccccCCCCcceeeccCCccccccchhhhcCC
Q 046115          361 LLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI---PTNIEKLLHLKYLNLKGQKKIEKLPETLCELY  437 (505)
Q Consensus       361 L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~---p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~  437 (505)
                      +++..|........++....++++|+.|+|+       +|.+..+   |..++.+++|++|+|++|. +..+.. +..+.
T Consensus       148 l~l~~N~~~~~~~~l~i~~~~l~~L~~L~Ls-------~N~l~~l~~l~~~~~~l~~L~~L~Ls~N~-i~~~~~-l~~l~  218 (267)
T 3rw6_A          148 IDVVLNRRSCMAATLRIIEENIPELLSLNLS-------NNRLYRLDDMSSIVQKAPNLKILNLSGNE-LKSERE-LDKIK  218 (267)
T ss_dssp             CCCCTTSHHHHHHHHHHHHHHCTTCCEEECT-------TSCCCCCGGGTTHHHHSTTCCEEECTTSC-CCSGGG-GGGGT
T ss_pred             ccccCCHHHHHHHHHHHHHhhCCCCCEEECC-------CCCCCCCccchhHHhhCCCCCEEECCCCc-cCCchh-hhhcc
Confidence            4455554333333344444678999999999       5655554   4566789999999999999 666533 55555


Q ss_pred             --CCcEEecCCCcCccccch-------hccccccCceee
Q 046115          438 --NLERLNVDDCQNLRELPR-------GIGKLRKLMYLH  467 (505)
Q Consensus       438 --~L~~L~l~~~~~~~~lp~-------~~~~l~~L~~L~  467 (505)
                        +|+.|+|++|+....+|.       .+..+|+|+.|+
T Consensus       219 ~l~L~~L~L~~Npl~~~~~~~~~y~~~il~~~P~L~~LD  257 (267)
T 3rw6_A          219 GLKLEELWLDGNSLCDTFRDQSTYISAIRERFPKLLRLD  257 (267)
T ss_dssp             TSCCSEEECTTSTTGGGCSSHHHHHHHHHHHCTTCCEES
T ss_pred             cCCcceEEccCCcCccccCcchhHHHHHHHHCcccCeEC
Confidence              999999999996666662       367889999987

>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=97.88  E-value=5.6e-06  Score=85.94  Aligned_cols=133  Identities=22%  Similarity=0.165  Sum_probs=71.1

Q ss_pred             CCCCceEEEecCCCcccc-ccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCc--------
Q 046115          354 GLRGLRSLLVKSDEYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQK--------  424 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~-~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~--------  424 (505)
                      .+++|++|.+.++. ... ...++..+..+++|+.|+++      ++..+..+|..+..+++|++|+++.+.        
T Consensus       182 ~~~~L~~L~l~~~~-~~~~~~~l~~l~~~~~~L~~L~L~------~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~  254 (594)
T 2p1m_B          182 TYTSLVSLNISCLA-SEVSFSALERLVTRCPNLKSLKLN------RAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVY  254 (594)
T ss_dssp             TCCCCCEEECTTCC-SCCCHHHHHHHHHHCTTCCEEECC------TTSCHHHHHHHHHHCTTCSEEECSBCCCCCCHHHH
T ss_pred             cCCcCcEEEecccC-CcCCHHHHHHHHHhCCCCcEEecC------CCCcHHHHHHHHhcCCcceEcccccccCccchhhH
Confidence            45566666666664 111 01133334455666666666      222333344444455555555433221        


Q ss_pred             ----------------------cccccchhhhcCCCCcEEecCCCcCccc--cchhccccccCceeecCCCccccccccc
Q 046115          425 ----------------------KIEKLPETLCELYNLERLNVDDCQNLRE--LPRGIGKLRKLMYLHNEDTGCLRYLPAG  480 (505)
Q Consensus       425 ----------------------~~~~lp~~~~~l~~L~~L~l~~~~~~~~--lp~~~~~l~~L~~L~l~~~~~~~~~p~~  480 (505)
                                            ....+|..+..+++|+.|++++|. +..  ++..+..+++|++|++.+|.....++..
T Consensus       255 ~~l~~~l~~~~~L~~Ls~~~~~~~~~l~~~~~~~~~L~~L~L~~~~-l~~~~l~~~~~~~~~L~~L~l~~~~~~~~l~~l  333 (594)
T 2p1m_B          255 SGLSVALSGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYAT-VQSYDLVKLLCQCPKLQRLWVLDYIEDAGLEVL  333 (594)
T ss_dssp             HHHHHHHHTCTTCCEEECCBTCCGGGGGGGHHHHTTCCEEECTTCC-CCHHHHHHHHTTCTTCCEEEEEGGGHHHHHHHH
T ss_pred             HHHHHHHhcCCCcccccCCcccchhhHHHHHHhhCCCCEEEccCCC-CCHHHHHHHHhcCCCcCEEeCcCccCHHHHHHH
Confidence                                  023345444567788888888877 432  2223567788888888877322222322


Q ss_pred             ccCCccCCccceeE
Q 046115          481 IGELIRLRRVREFV  494 (505)
Q Consensus       481 i~~l~~L~~L~~~~  494 (505)
                      ...+++|+.|++..
T Consensus       334 ~~~~~~L~~L~L~~  347 (594)
T 2p1m_B          334 ASTCKDLRELRVFP  347 (594)
T ss_dssp             HHHCTTCCEEEEEC
T ss_pred             HHhCCCCCEEEEec
Confidence            34577788887654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.87  E-value=0.00033  Score=65.53  Aligned_cols=137  Identities=10%  Similarity=-0.009  Sum_probs=79.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-----C-C-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc---
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-----F-E-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV---   70 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-----f-~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l---   70 (505)
                      ++|+|||++|+.+++  +....     . . ..+.+++....+....+..|++++........... +....+...+   
T Consensus        53 pPGTGKT~~v~~v~~--~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~-~~L~~~f~~~~~~  129 (318)
T 3te6_A           53 ADDSTKFQLVNDVMD--ELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISL-EALNFYITNVPKA  129 (318)
T ss_dssp             CCSHHHHHHHHHHHH--HHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCH-HHHHHHHHHSCGG
T ss_pred             CCCCCHHHHHHHHHH--HHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHH-HHHHHHHHHhhhc
Confidence            489999999999998  44321     1 1 34578888888889999999999963322111222 2233333332   


Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhc--CCC-CCcEEEEEeCchH-----HHH----HhCCcceEeCCCCChhhHHHH
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLK--NSL-HESKILITTRKET-----VAR----IMGSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~--~~~-~~~~iLiTtr~~~-----~~~----~~~~~~~~~l~~l~~~ea~~L  138 (505)
                      .+++++++||.++.-.  .-+.+...+.  ... ....||.++...+     +..    .+. ...+...+.+.+|-.++
T Consensus       130 ~~~~~ii~lDE~d~l~--~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~-~~~i~F~pYt~~el~~I  206 (318)
T 3te6_A          130 KKRKTLILIQNPENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAH-FTEIKLNKVDKNELQQM  206 (318)
T ss_dssp             GSCEEEEEEECCSSSC--CTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHHHTCHHHHTT-EEEEECCCCCHHHHHHH
T ss_pred             cCCceEEEEecHHHhh--cchHHHHHHhcccccCCcEEEEEEecCcccchhhcchhhhccCC-ceEEEeCCCCHHHHHHH
Confidence            4568999999996643  2222332222  121 2223344443321     111    111 24789999999999999


Q ss_pred             HHHhh
Q 046115          139 FQSLA  143 (505)
Q Consensus       139 f~~~~  143 (505)
                      +....
T Consensus       207 l~~Rl  211 (318)
T 3te6_A          207 IITRL  211 (318)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            97765

>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=97.87  E-value=0.00011  Score=69.48  Aligned_cols=102  Identities=7%  Similarity=-0.016  Sum_probs=68.9

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++.++|+|+++.........+...+.....++.+++||.... +.. .......+.+.+++.++..+++...+...+. 
T Consensus       101 ~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~-  179 (319)
T 2chq_A          101 APFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGV-  179 (319)
T ss_dssp             CCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCC-
T ss_pred             CCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            5678999999976554445556666666566778888876643 211 1233458999999999999999876643222 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIA  177 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~  177 (505)
                         .-.++.+..+++.++|.+..+....
T Consensus       180 ---~i~~~~l~~l~~~~~G~~r~~~~~l  204 (319)
T 2chq_A          180 ---KITEDGLEALIYISGGDFRKAINAL  204 (319)
T ss_dssp             ---CBCHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence               1124567889999999997654433

>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=97.85  E-value=3.3e-05  Score=76.61  Aligned_cols=154  Identities=16%  Similarity=0.122  Sum_probs=89.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC--ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE--KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~--~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+|||+||+.+++  .....+.  .+++++..      .+...+...+...      .    ...+...+..+..+|+
T Consensus       138 p~G~GKTtLa~aia~--~l~~~~~~~~v~~v~~~------~~~~~~~~~~~~~------~----~~~~~~~~~~~~~vL~  199 (440)
T 2z4s_A          138 GVGLGKTHLLQSIGN--YVVQNEPDLRVMYITSE------KFLNDLVDSMKEG------K----LNEFREKYRKKVDILL  199 (440)
T ss_dssp             SSSSSHHHHHHHHHH--HHHHHCCSSCEEEEEHH------HHHHHHHHHHHTT------C----HHHHHHHHTTTCSEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeHH------HHHHHHHHHHHcc------c----HHHHHHHhcCCCCEEE
Confidence            479999999999998  5555442  24456543      2334444444311      1    1123333443567999


Q ss_pred             EeCCCCCCc--cChhHHHHhhcC-CCCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCC
Q 046115           79 LDDVWNEDY--YKWEPFYKCLKN-SLHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISG  146 (505)
Q Consensus        79 lDdv~~~~~--~~~~~~~~~~~~-~~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~  146 (505)
                      +||++....  ...+.+...+.. ...+..|++||...         .+...+.....+.+++++.++-.+++...+...
T Consensus       200 IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~  279 (440)
T 2z4s_A          200 IDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIE  279 (440)
T ss_dssp             EECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHH
T ss_pred             EeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHc
Confidence            999965432  122334433322 23567899988762         222223333578899999999999998776322


Q ss_pred             CCCCCCchHHHHHHHHHHHcCCChHHHHHH
Q 046115          147 KTIGKRENLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                      +. .-+   ++++..|++.+.|.+-.+..+
T Consensus       280 ~~-~i~---~e~l~~la~~~~gn~R~l~~~  305 (440)
T 2z4s_A          280 HG-ELP---EEVLNFVAENVDDNLRRLRGA  305 (440)
T ss_dssp             TC-CCC---TTHHHHHHHHCCSCHHHHHHH
T ss_pred             CC-CCC---HHHHHHHHHhcCCCHHHHHHH
Confidence            21 111   244677888888888655443

>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=97.85  E-value=2.8e-05  Score=74.11  Aligned_cols=76  Identities=14%  Similarity=0.213  Sum_probs=41.6

Q ss_pred             CCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccchh-ccccccCc-eeecCCCccccccc-ccccCCccC
Q 046115          412 LLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLM-YLHNEDTGCLRYLP-AGIGELIRL  487 (505)
Q Consensus       412 l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~-~L~l~~~~~~~~~p-~~i~~l~~L  487 (505)
                      +++|+.+++++|. +..+|. .+..+.+|+.+++.+|  +..++.. +.++++|+ .+.+..+  +..++ ..|.+|++|
T Consensus       225 ~~~L~~l~L~~n~-i~~I~~~aF~~~~~L~~l~l~~n--i~~I~~~aF~~~~~L~~~l~l~~~--l~~I~~~aF~~c~~L  299 (329)
T 3sb4_A          225 MPNLVSLDISKTN-ATTIPDFTFAQKKYLLKIKLPHN--LKTIGQRVFSNCGRLAGTLELPAS--VTAIEFGAFMGCDNL  299 (329)
T ss_dssp             CTTCCEEECTTBC-CCEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCEEEEECTT--CCEECTTTTTTCTTE
T ss_pred             cCCCeEEECCCCC-cceecHhhhhCCCCCCEEECCcc--cceehHHHhhCChhccEEEEEccc--ceEEchhhhhCCccC
Confidence            4566666666655 555554 3455666666666653  4555443 55566666 6666552  23332 345666666


Q ss_pred             Cccce
Q 046115          488 RRVRE  492 (505)
Q Consensus       488 ~~L~~  492 (505)
                      +.+.+
T Consensus       300 ~~l~l  304 (329)
T 3sb4_A          300 RYVLA  304 (329)
T ss_dssp             EEEEE
T ss_pred             CEEEe
Confidence            55543

>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=97.80  E-value=4.2e-05  Score=72.93  Aligned_cols=122  Identities=11%  Similarity=0.138  Sum_probs=88.3

Q ss_pred             CCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCc-cccCCCCcceeeccCCccccccch-h
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPT-NIEKLLHLKYLNLKGQKKIEKLPE-T  432 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~-~~~~l~~L~~L~l~~~~~~~~lp~-~  432 (505)
                      ..++..+.+.++-...   ........+.+|+.++|.       ++.+..+|. .|..+.+|+.+++..|  +..++. .
T Consensus       201 ~~~~~~l~~~~~l~~~---~~~~l~~~~~~L~~l~L~-------~n~i~~I~~~aF~~~~~L~~l~l~~n--i~~I~~~a  268 (329)
T 3sb4_A          201 PRDINFLTIEGKLDNA---DFKLIRDYMPNLVSLDIS-------KTNATTIPDFTFAQKKYLLKIKLPHN--LKTIGQRV  268 (329)
T ss_dssp             GGGCSEEEEEECCCHH---HHHHHHHHCTTCCEEECT-------TBCCCEECTTTTTTCTTCCEEECCTT--CCEECTTT
T ss_pred             ccccceEEEeeeecHH---HHHHHHHhcCCCeEEECC-------CCCcceecHhhhhCCCCCCEEECCcc--cceehHHH
Confidence            3455555555542211   122222347899999998       666777765 4788999999999986  677765 5


Q ss_pred             hhcCCCCc-EEecCCCcCccccch-hccccccCceeecCCCccccccc-ccccCCccCCccc
Q 046115          433 LCELYNLE-RLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRLRRVR  491 (505)
Q Consensus       433 ~~~l~~L~-~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L~~L~  491 (505)
                      +..+.+|+ .+++.+ . +..+++ .+.++++|+.+++.+|. +..++ ..|.++++|+.+.
T Consensus       269 F~~~~~L~~~l~l~~-~-l~~I~~~aF~~c~~L~~l~l~~n~-i~~I~~~aF~~~~~L~~ly  327 (329)
T 3sb4_A          269 FSNCGRLAGTLELPA-S-VTAIEFGAFMGCDNLRYVLATGDK-ITTLGDELFGNGVPSKLIY  327 (329)
T ss_dssp             TTTCTTCCEEEEECT-T-CCEECTTTTTTCTTEEEEEECSSC-CCEECTTTTCTTCCCCEEE
T ss_pred             hhCChhccEEEEEcc-c-ceEEchhhhhCCccCCEEEeCCCc-cCccchhhhcCCcchhhhc
Confidence            78999999 999998 4 777764 58999999999998887 44554 4689999998764

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.77  E-value=2.8e-05  Score=67.27  Aligned_cols=115  Identities=13%  Similarity=0.068  Sum_probs=81.1

Q ss_pred             CCCCCCCceEEEecCC-Ccccc-ccchhHHhhcCcccceEEecccccCCccccccc-----cCccccCCCCcceeeccCC
Q 046115          351 NVTGLRGLRSLLVKSD-EYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-----IPTNIEKLLHLKYLNLKGQ  423 (505)
Q Consensus       351 ~~~~~~~L~~L~l~~~-~~~~~-~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-----~p~~~~~l~~L~~L~l~~~  423 (505)
                      .+...+.|+.|++++| .+... ...+...+...++|++|+|+       ++.++.     +...+...++|++|+|++|
T Consensus        31 ~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls-------~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N  103 (185)
T 1io0_A           31 IQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIV-------GTRSNDPVAFALAEMLKVNNTLKSLNVESN  103 (185)
T ss_dssp             HHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECT-------TSCCCHHHHHHHHHHHHHCSSCCEEECCSS
T ss_pred             HHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECc-------CCCCChHHHHHHHHHHHhCCCcCEEECcCC
Confidence            3446789999999998 76432 11245556777889999998       444432     3444566688999999999


Q ss_pred             ccccc-----cchhhhcCCCCcEEec--CCCcCccc----cchhccccccCceeecCCCcc
Q 046115          424 KKIEK-----LPETLCELYNLERLNV--DDCQNLRE----LPRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       424 ~~~~~-----lp~~~~~l~~L~~L~l--~~~~~~~~----lp~~~~~l~~L~~L~l~~~~~  473 (505)
                      . ++.     +...+...++|+.|+|  ++|.....    +-..+...++|++|++++|..
T Consensus       104 ~-i~~~g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~g~~~l~~~L~~n~~L~~L~L~~n~i  163 (185)
T 1io0_A          104 F-ISGSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQQ  163 (185)
T ss_dssp             C-CCHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSSH
T ss_pred             c-CCHHHHHHHHHHHHhCCCceEEEecCCCCCCCHHHHHHHHHHHHhCCCcCEEeccCCCC
Confidence            8 543     4566777888999999  77773222    344566668899999999863

>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=97.76  E-value=0.00015  Score=68.80  Aligned_cols=148  Identities=15%  Similarity=0.090  Sum_probs=86.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  ....   ..+++++.......++    ...+                  ...+ .+..+|++|
T Consensus        46 ~~GtGKT~la~~i~~--~~~~---~~~~~~~~~~~~~~~l----~~~l------------------~~~~-~~~~~l~lD   97 (324)
T 1hqc_A           46 PPGLGKTTLAHVIAH--ELGV---NLRVTSGPAIEKPGDL----AAIL------------------ANSL-EEGDILFID   97 (324)
T ss_dssp             CTTCCCHHHHHHHHH--HHTC---CEEEECTTTCCSHHHH----HHHH------------------TTTC-CTTCEEEET
T ss_pred             CCCCCHHHHHHHHHH--HhCC---CEEEEeccccCChHHH----HHHH------------------HHhc-cCCCEEEEE
Confidence            479999999999988  3322   2234544332222111    1111                  1111 245689999


Q ss_pred             CCCCCCccChhHHHHhhcCCC------------------CCcEEEEEeCchH-HHHHh-CCc-ceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDYYKWEPFYKCLKNSL------------------HESKILITTRKET-VARIM-GST-HVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~------------------~~~~iLiTtr~~~-~~~~~-~~~-~~~~l~~l~~~ea~~Lf  139 (505)
                      ++..........+...+....                  .+..++.||.... +...+ ... ..+.+.+++.+|...++
T Consensus        98 Ei~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l  177 (324)
T 1hqc_A           98 EIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGV  177 (324)
T ss_dssp             TTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHH
T ss_pred             CCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHH
Confidence            997755434444444443321                  2345666665432 11111 122 47899999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLL  180 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l  180 (505)
                      ...+...+.    .-.++++..+++.+.|.|..+..+...+
T Consensus       178 ~~~~~~~~~----~~~~~~~~~l~~~~~G~~r~l~~~l~~~  214 (324)
T 1hqc_A          178 MRDARLLGV----RITEEAALEIGRRSRGTMRVAKRLFRRV  214 (324)
T ss_dssp             HHHHHTTTC----CCCHHHHHHHHHHSCSCHHHHHHHHHHH
T ss_pred             HHHHHhcCC----CCCHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            877643222    1224668889999999998877766554

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.75  E-value=0.00036  Score=69.05  Aligned_cols=150  Identities=17%  Similarity=0.156  Sum_probs=82.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHH-HcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEE-CVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~-~l~~~r~Llvl   79 (505)
                      .+|+||||||+.+++  .....|     +.++.........+.+                  ...... ...+++.+|++
T Consensus        58 ppGtGKTtlAr~ia~--~~~~~f-----~~l~a~~~~~~~ir~~------------------~~~a~~~~~~~~~~iLfI  112 (447)
T 3pvs_A           58 PPGTGKTTLAEVIAR--YANADV-----ERISAVTSGVKEIREA------------------IERARQNRNAGRRTILFV  112 (447)
T ss_dssp             STTSSHHHHHHHHHH--HTTCEE-----EEEETTTCCHHHHHHH------------------HHHHHHHHHTTCCEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HhCCCe-----EEEEeccCCHHHHHHH------------------HHHHHHhhhcCCCcEEEE
Confidence            479999999999998  443332     2222211111111111                  111111 12457889999


Q ss_pred             eCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH--H-HHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCC---CCCc
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET--V-ARIMGSTHVISVNVLSEMECWSVFQSLAISGKTI---GKRE  153 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~--~-~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~---~~~~  153 (505)
                      |++........+.+...+.. +.-.-|..||.++.  + ........++.+.+++.++...++..........   ....
T Consensus       113 DEI~~l~~~~q~~LL~~le~-~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~  191 (447)
T 3pvs_A          113 DEVHRFNKSQQDAFLPHIED-GTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIV  191 (447)
T ss_dssp             ETTTCC------CCHHHHHT-TSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEE
T ss_pred             eChhhhCHHHHHHHHHHHhc-CceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCc
Confidence            99977655455566666654 22223334555542  1 1222345588899999999999998776431110   1112


Q ss_pred             hHHHHHHHHHHHcCCChHHHHHH
Q 046115          154 NLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       154 ~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                      -.+++...+++.++|.+-.+..+
T Consensus       192 i~~~al~~L~~~~~Gd~R~lln~  214 (447)
T 3pvs_A          192 LPDETRRAIAELVNGDARRALNT  214 (447)
T ss_dssp             CCHHHHHHHHHHHCSCHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCHHHHHHH
Confidence            23567788888899988654433

>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=97.64  E-value=2.6e-05  Score=66.02  Aligned_cols=87  Identities=20%  Similarity=0.237  Sum_probs=62.0

Q ss_pred             CcccceEEecccccCCccccccc-cCccccCCCCcceeeccCCcccccc-chhhhcC----CCCcEEecCCCcCcccc-c
Q 046115          382 LTCLRALELQVRESWPRNNLIKE-IPTNIEKLLHLKYLNLKGQKKIEKL-PETLCEL----YNLERLNVDDCQNLREL-P  454 (505)
Q Consensus       382 l~~L~~L~l~~~~~~~~~~~~~~-~p~~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l----~~L~~L~l~~~~~~~~l-p  454 (505)
                      -.+|+.|+++       ++.+.. --..+..+++|+.|+|++|..++.- -..++.+    ++|+.|+|++|..+..- -
T Consensus        60 ~~~L~~LDLs-------~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl  132 (176)
T 3e4g_A           60 KYKIQAIDAT-------DSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGI  132 (176)
T ss_dssp             CCCEEEEEEE-------SCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHH
T ss_pred             CceEeEEeCc-------CCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHH
Confidence            3579999999       333332 2344678999999999999866632 2335554    47999999999866542 1


Q ss_pred             hhccccccCceeecCCCcccc
Q 046115          455 RGIGKLRKLMYLHNEDTGCLR  475 (505)
Q Consensus       455 ~~~~~l~~L~~L~l~~~~~~~  475 (505)
                      ..+..+++|++|++++|..+.
T Consensus       133 ~~L~~~~~L~~L~L~~c~~It  153 (176)
T 3e4g_A          133 IALHHFRNLKYLFLSDLPGVK  153 (176)
T ss_dssp             HHGGGCTTCCEEEEESCTTCC
T ss_pred             HHHhcCCCCCEEECCCCCCCC
Confidence            246788999999999997443

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.58  E-value=0.0027  Score=60.43  Aligned_cols=145  Identities=17%  Similarity=0.151  Sum_probs=82.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  .....   .+.+++......                      ......+. . ..+..+|++|
T Consensus        63 ~~GtGKT~la~~ia~--~~~~~---~~~~~~~~~~~~----------------------~~~~~~~~-~-~~~~~vl~lD  113 (338)
T 3pfi_A           63 PAGLGKTTLANIISY--EMSAN---IKTTAAPMIEKS----------------------GDLAAILT-N-LSEGDILFID  113 (338)
T ss_dssp             STTSSHHHHHHHHHH--HTTCC---EEEEEGGGCCSH----------------------HHHHHHHH-T-CCTTCEEEEE
T ss_pred             cCCCCHHHHHHHHHH--HhCCC---eEEecchhccch----------------------hHHHHHHH-h-ccCCCEEEEe
Confidence            479999999999987  43322   223333222111                      11111111 1 2355789999


Q ss_pred             CCCCCCccChhHHHHhhcCCC------------------CCcEEEEEeCchH-HHHH-hCCc-ceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDYYKWEPFYKCLKNSL------------------HESKILITTRKET-VARI-MGST-HVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~------------------~~~~iLiTtr~~~-~~~~-~~~~-~~~~l~~l~~~ea~~Lf  139 (505)
                      ++..........+...+....                  ++..++.+|.... +... .... ..+.+.+++.++...++
T Consensus       114 Ei~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il  193 (338)
T 3pfi_A          114 EIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALIL  193 (338)
T ss_dssp             TGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHH
T ss_pred             chhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHH
Confidence            997655444445555444322                  1245555555422 1111 1222 57899999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIAS  178 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~  178 (505)
                      ...+.....    .-.++++..+++.+.|.|-.+..+..
T Consensus       194 ~~~~~~~~~----~~~~~~~~~l~~~~~G~~r~l~~~l~  228 (338)
T 3pfi_A          194 QKAALKLNK----TCEEKAALEIAKRSRSTPRIALRLLK  228 (338)
T ss_dssp             HHHHHHTTC----EECHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             HHHHHhcCC----CCCHHHHHHHHHHHCcCHHHHHHHHH
Confidence            876643221    12356678888999999965554433

>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=97.55  E-value=0.00092  Score=63.35  Aligned_cols=147  Identities=15%  Similarity=0.159  Sum_probs=80.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  .....-..++++++.      .....+...+..      .....    +..... +..+|++|
T Consensus        45 ~~GtGKT~la~~i~~--~~~~~~~~~~~i~~~------~~~~~~~~~~~~------~~~~~----~~~~~~-~~~vL~iD  105 (324)
T 1l8q_A           45 SVGTGKTHLLQAAGN--EAKKRGYRVIYSSAD------DFAQAMVEHLKK------GTINE----FRNMYK-SVDLLLLD  105 (324)
T ss_dssp             SSSSSHHHHHHHHHH--HHHHTTCCEEEEEHH------HHHHHHHHHHHH------TCHHH----HHHHHH-TCSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HHHHCCCEEEEEEHH------HHHHHHHHHHHc------CcHHH----HHHHhc-CCCEEEEc
Confidence            479999999999998  443322234566543      233333333320      01111    122221 35699999


Q ss_pred             CCCCCCc--cChhHHHHhhcC-CCCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           81 DVWNEDY--YKWEPFYKCLKN-SLHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        81 dv~~~~~--~~~~~~~~~~~~-~~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      +++....  ...+.+...+.. ...+..|++||...         .+...+.....+.+++ +.++..+++...+...+.
T Consensus       106 Ei~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~  184 (324)
T 1l8q_A          106 DVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNL  184 (324)
T ss_dssp             CGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTC
T ss_pred             CcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhcCC
Confidence            9965432  122333333321 12455788887642         2222333335789999 999999999877643222


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHH
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                       .   -.++++..+++.+ |..-.
T Consensus       185 -~---l~~~~l~~l~~~~-g~~r~  203 (324)
T 1l8q_A          185 -E---LRKEVIDYLLENT-KNVRE  203 (324)
T ss_dssp             -C---CCHHHHHHHHHHC-SSHHH
T ss_pred             -C---CCHHHHHHHHHhC-CCHHH
Confidence             1   1245677888888 76643

>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=97.53  E-value=0.00038  Score=66.97  Aligned_cols=103  Identities=7%  Similarity=0.089  Sum_probs=67.0

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HH-HHhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VA-RIMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~-~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|++..-+......+...+.....++.+|++|.+.. +. ........+.+.+++.++..+.+...+...+..
T Consensus       133 ~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~  212 (354)
T 1sxj_E          133 HRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQ  212 (354)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCE
T ss_pred             CCCeEEEEeCccccCHHHHHHHHHHHHhhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCC
Confidence            3667999999977655455667766666556677888876632 21 112334688999999999999998765322211


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKTIA  177 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~~~  177 (505)
                      -.   .++.+..|++.++|.+-.+..+.
T Consensus       213 ~~---~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          213 LE---TKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             EC---CSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CC---cHHHHHHHHHHcCCCHHHHHHHH
Confidence            11   03557788899999886544443

>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=97.52  E-value=0.0015  Score=59.76  Aligned_cols=154  Identities=12%  Similarity=0.097  Sum_probs=79.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  +....   .+.+++..-.+.          .      ...........+.......+.+|++|
T Consensus        47 ~~GtGKT~la~~la~--~~~~~---~~~~~~~~~~~~----------~------~~~~~~~~~~~~~~a~~~~~~vl~iD  105 (262)
T 2qz4_A           47 PPGCGKTLLAKAVAT--EAQVP---FLAMAGAEFVEV----------I------GGLGAARVRSLFKEARARAPCIVYID  105 (262)
T ss_dssp             CTTSSHHHHHHHHHH--HHTCC---EEEEETTTTSSS----------S------TTHHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HhCCC---EEEechHHHHhh----------c------cChhHHHHHHHHHHHHhcCCeEEEEe
Confidence            479999999999998  44322   234444332110          0      01111112222233333457899999


Q ss_pred             CCCCCC------------c---cChhHHHHhhcCC--CCCcEEEEEeCchHHHH-Hh-C--C-cceEeCCCCChhhHHHH
Q 046115           81 DVWNED------------Y---YKWEPFYKCLKNS--LHESKILITTRKETVAR-IM-G--S-THVISVNVLSEMECWSV  138 (505)
Q Consensus        81 dv~~~~------------~---~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~-~~-~--~-~~~~~l~~l~~~ea~~L  138 (505)
                      +++...            .   ..+..+...+...  ..+..|+.||....... .. .  . ...+.++..+.++-.++
T Consensus       106 eid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~i  185 (262)
T 2qz4_A          106 EIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREI  185 (262)
T ss_dssp             CC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHH
T ss_pred             CcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHH
Confidence            996531            1   1122333333322  23556777776543211 11 1  2 25777889999999999


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                      +.........   ..........+++.+.|++- .|..+..
T Consensus       186 l~~~~~~~~~---~~~~~~~~~~l~~~~~g~~~~~l~~l~~  223 (262)
T 2qz4_A          186 FEQHLKSLKL---TQSSTFYSQRLAELTPGFSGADIANICN  223 (262)
T ss_dssp             HHHHHHHTTC---CBTHHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             HHHHHHhCCC---CcchhhHHHHHHHHCCCCCHHHHHHHHH
Confidence            9876532222   12222235678888887653 4544443

>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=97.52  E-value=0.0011  Score=63.71  Aligned_cols=100  Identities=7%  Similarity=0.014  Sum_probs=65.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      .++-+|++|++..........+...+.......+++++|.... +... ......+.+.+++.++....+...+...+. 
T Consensus       132 ~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~-  210 (353)
T 1sxj_D          132 PPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENV-  210 (353)
T ss_dssp             CSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTC-
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHHHHHHHHHHhCC-
Confidence            3567999999966554445566666665555667777775532 2111 112347889999999999999876543222 


Q ss_pred             CCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                         .-.++++..|++.++|.|..+..
T Consensus       211 ---~i~~~~l~~l~~~~~G~~r~~~~  233 (353)
T 1sxj_D          211 ---KCDDGVLERILDISAGDLRRGIT  233 (353)
T ss_dssp             ---CCCHHHHHHHHHHTSSCHHHHHH
T ss_pred             ---CCCHHHHHHHHHHcCCCHHHHHH
Confidence               11246788999999999876443

>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=97.51  E-value=5.5e-05  Score=64.06  Aligned_cols=89  Identities=12%  Similarity=0.120  Sum_probs=64.1

Q ss_pred             CCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCC----CCcceeeccCCcccccc
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKL----LHLKYLNLKGQKKIEKL  429 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l----~~L~~L~l~~~~~~~~l  429 (505)
                      -..|+.|+++++.++...  +. .+..+++|+.|+|++      +..++.- -..++.+    ++|++|+|++|..++.-
T Consensus        60 ~~~L~~LDLs~~~Itd~G--L~-~L~~~~~L~~L~L~~------C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~  130 (176)
T 3e4g_A           60 KYKIQAIDATDSCIMSIG--FD-HMEGLQYVEKIRLCK------CHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDK  130 (176)
T ss_dssp             CCCEEEEEEESCCCCGGG--GG-GGTTCSCCCEEEEES------CTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHH
T ss_pred             CceEeEEeCcCCCccHHH--HH-HhcCCCCCCEEEeCC------CCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHH
Confidence            457999999999875431  33 367899999999993      3334331 1224443    47999999999877632


Q ss_pred             -chhhhcCCCCcEEecCCCcCccc
Q 046115          430 -PETLCELYNLERLNVDDCQNLRE  452 (505)
Q Consensus       430 -p~~~~~l~~L~~L~l~~~~~~~~  452 (505)
                       -..+..+++|+.|+|++|+.+..
T Consensus       131 Gl~~L~~~~~L~~L~L~~c~~Itd  154 (176)
T 3e4g_A          131 GIIALHHFRNLKYLFLSDLPGVKE  154 (176)
T ss_dssp             HHHHGGGCTTCCEEEEESCTTCCC
T ss_pred             HHHHHhcCCCCCEEECCCCCCCCc
Confidence             23478899999999999986665

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.51  E-value=0.00026  Score=68.07  Aligned_cols=135  Identities=17%  Similarity=0.140  Sum_probs=80.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhh--cCcccceEEecccccCC-ccccccccC
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFE--KLTCLRALELQVRESWP-RNNLIKEIP  406 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~--~l~~L~~L~l~~~~~~~-~~~~~~~~p  406 (505)
                      .++.+.+..+....++.     + .+++|+.|.+..+.+...   ....+.  .+++|+.|+|+...... .+..+..+.
T Consensus       173 ~L~~L~L~g~~~l~l~~-----~-~~~~L~~L~L~~~~l~~~---~l~~l~~~~lp~L~~L~L~~~~~~~~~~~~~~~l~  243 (362)
T 2ra8_A          173 LLNNLKIKGTNNLSIGK-----K-PRPNLKSLEIISGGLPDS---VVEDILGSDLPNLEKLVLYVGVEDYGFDGDMNVFR  243 (362)
T ss_dssp             TCCEEEEECCBTCBCCS-----C-BCTTCSEEEEECSBCCHH---HHHHHHHSBCTTCCEEEEECBCGGGTCCSCGGGTG
T ss_pred             CCcEEEEeCCCCceecc-----c-cCCCCcEEEEecCCCChH---HHHHHHHccCCCCcEEEEeccccccccchhHHHHH
Confidence            56666665542211211     2 378899999988775432   112233  68889999885210000 011122222


Q ss_pred             ccc--cCCCCcceeeccCCccccccchhhh---cCCCCcEEecCCCcCccc-----cchhccccccCceeecCCCccc
Q 046115          407 TNI--EKLLHLKYLNLKGQKKIEKLPETLC---ELYNLERLNVDDCQNLRE-----LPRGIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       407 ~~~--~~l~~L~~L~l~~~~~~~~lp~~~~---~l~~L~~L~l~~~~~~~~-----lp~~~~~l~~L~~L~l~~~~~~  474 (505)
                      ..+  ..+++|++|+|++|......+..+.   .+++|+.|+|+.|. +..     ++..+.++++|+.|++++|...
T Consensus       244 ~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~-L~d~G~~~L~~~L~~l~~L~~L~L~~n~i~  320 (362)
T 2ra8_A          244 PLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGV-LTDEGARLLLDHVDKIKHLKFINMKYNYLS  320 (362)
T ss_dssp             GGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSC-CBHHHHHHHHTTHHHHTTCSEEECCSBBCC
T ss_pred             HHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCC-CChHHHHHHHhhcccCCcceEEECCCCcCC
Confidence            222  3578999999998884333333333   47789999998887 443     4555677889999999988644

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.47  E-value=7.4e-05  Score=64.61  Aligned_cols=110  Identities=16%  Similarity=0.131  Sum_probs=80.0

Q ss_pred             hhHHhhcCcccceEEecccccCCccc-cccc-----cCccccCCCCcceeeccCCcccc-----ccchhhhcCCCCcEEe
Q 046115          375 LPQLFEKLTCLRALELQVRESWPRNN-LIKE-----IPTNIEKLLHLKYLNLKGQKKIE-----KLPETLCELYNLERLN  443 (505)
Q Consensus       375 ~~~~~~~l~~L~~L~l~~~~~~~~~~-~~~~-----~p~~~~~l~~L~~L~l~~~~~~~-----~lp~~~~~l~~L~~L~  443 (505)
                      +...+...++|+.|+|+       ++ .++.     +...+...++|++|+|++|. ++     .+...+...++|++|+
T Consensus        28 l~~~l~~~~~L~~L~L~-------~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~-i~~~g~~~l~~~L~~n~~L~~L~   99 (185)
T 1io0_A           28 LKRIQNNDPDLEEVNLN-------NIMNIPVPTLKACAEALKTNTYVKKFSIVGTR-SNDPVAFALAEMLKVNNTLKSLN   99 (185)
T ss_dssp             HHHHHTTCTTCCEEECT-------TCTTCCHHHHHHHHHHHTTCCSCCEEECTTSC-CCHHHHHHHHHHHHHCSSCCEEE
T ss_pred             HHHHHhcCCCCCEEEec-------CCCCCCHHHHHHHHHHHHhCCCcCEEECcCCC-CChHHHHHHHHHHHhCCCcCEEE
Confidence            55667788999999998       33 4432     44556678899999999999 54     3445566778999999


Q ss_pred             cCCCcCccc-----cchhccccccCceeec--CCCccccc----ccccccCCccCCcccee
Q 046115          444 VDDCQNLRE-----LPRGIGKLRKLMYLHN--EDTGCLRY----LPAGIGELIRLRRVREF  493 (505)
Q Consensus       444 l~~~~~~~~-----lp~~~~~l~~L~~L~l--~~~~~~~~----~p~~i~~l~~L~~L~~~  493 (505)
                      |++|. +..     +...+...++|++|++  ++|.....    +...+...++|+.|++.
T Consensus       100 L~~N~-i~~~g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~g~~~l~~~L~~n~~L~~L~L~  159 (185)
T 1io0_A          100 VESNF-ISGSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYH  159 (185)
T ss_dssp             CCSSC-CCHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECC
T ss_pred             CcCCc-CCHHHHHHHHHHHHhCCCceEEEecCCCCCCCHHHHHHHHHHHHhCCCcCEEecc
Confidence            99998 543     4556788889999999  88875433    23345555778877763

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.47  E-value=0.00018  Score=69.12  Aligned_cols=129  Identities=15%  Similarity=0.117  Sum_probs=82.2

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCcccc--CCCCcceeeccCCcc---
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTNIE--KLLHLKYLNLKGQKK---  425 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~~~--~l~~L~~L~l~~~~~---  425 (505)
                      +..+++|+.|.+.++....    ++. + .+.+|+.|+|.       .+.+.. ....++  .+++|++|+|+.+..   
T Consensus       168 l~~~P~L~~L~L~g~~~l~----l~~-~-~~~~L~~L~L~-------~~~l~~~~l~~l~~~~lp~L~~L~L~~~~~~~~  234 (362)
T 2ra8_A          168 LDAMPLLNNLKIKGTNNLS----IGK-K-PRPNLKSLEII-------SGGLPDSVVEDILGSDLPNLEKLVLYVGVEDYG  234 (362)
T ss_dssp             HHTCTTCCEEEEECCBTCB----CCS-C-BCTTCSEEEEE-------CSBCCHHHHHHHHHSBCTTCCEEEEECBCGGGT
T ss_pred             HhcCCCCcEEEEeCCCCce----ecc-c-cCCCCcEEEEe-------cCCCChHHHHHHHHccCCCCcEEEEeccccccc
Confidence            3467899999999873111    333 3 37899999997       333221 112233  689999999863211   


Q ss_pred             ----ccccchhh--hcCCCCcEEecCCCcCccccchhc---cccccCceeecCCCccccc----ccccccCCccCCccce
Q 046115          426 ----IEKLPETL--CELYNLERLNVDDCQNLRELPRGI---GKLRKLMYLHNEDTGCLRY----LPAGIGELIRLRRVRE  492 (505)
Q Consensus       426 ----~~~lp~~~--~~l~~L~~L~l~~~~~~~~lp~~~---~~l~~L~~L~l~~~~~~~~----~p~~i~~l~~L~~L~~  492 (505)
                          +..+...+  ..+++|+.|+|++|......+..+   ..+++|++|+++.|.....    ++..+.++++|+.|++
T Consensus       235 ~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~L~d~G~~~L~~~L~~l~~L~~L~L  314 (362)
T 2ra8_A          235 FDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGVLTDEGARLLLDHVDKIKHLKFINM  314 (362)
T ss_dssp             CCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSCCBHHHHHHHHTTHHHHTTCSEEEC
T ss_pred             cchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCCCChHHHHHHHhhcccCCcceEEEC
Confidence                22222223  357899999999988443333333   3688999999999975442    4445566778888776


Q ss_pred             e
Q 046115          493 F  493 (505)
Q Consensus       493 ~  493 (505)
                      .
T Consensus       315 ~  315 (362)
T 2ra8_A          315 K  315 (362)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.45  E-value=0.0004  Score=59.94  Aligned_cols=68  Identities=10%  Similarity=0.009  Sum_probs=38.3

Q ss_pred             CCceEEEEEeCCCCCC-------ccChhHHHHhhcCCCCCcEEEEEeCchHHHH-------HhCCcceEeCCCCChhhHH
Q 046115           71 AGKKFLLVLDDVWNED-------YYKWEPFYKCLKNSLHESKILITTRKETVAR-------IMGSTHVISVNVLSEMECW  136 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~-------~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-------~~~~~~~~~l~~l~~~ea~  136 (505)
                      .+++.+||+||++...       ...+......+...+ +..++.||.......       .......+.+..++.++..
T Consensus       113 ~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~l~~r~~~i~~~~p~~~~~~  191 (195)
T 1jbk_A          113 QEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARG-ELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTI  191 (195)
T ss_dssp             STTTEEEEEETGGGGTT------CCCCHHHHHHHHHTT-SCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHH
T ss_pred             cCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhhccC-CeEEEEeCCHHHHHHHHhcCHHHHHHhceeecCCCCHHHHH
Confidence            3567899999996542       123333333333333 345666666554221       1123336788888888866


Q ss_pred             HHH
Q 046115          137 SVF  139 (505)
Q Consensus       137 ~Lf  139 (505)
                      +++
T Consensus       192 ~il  194 (195)
T 1jbk_A          192 AIL  194 (195)
T ss_dssp             TTC
T ss_pred             HHh
Confidence            543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.38  E-value=0.002  Score=62.12  Aligned_cols=97  Identities=12%  Similarity=0.112  Sum_probs=58.9

Q ss_pred             eEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeC-----------c-h-HH-HHHhCCcceEeCCCCChhhHHHHH
Q 046115           74 KFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTR-----------K-E-TV-ARIMGSTHVISVNVLSEMECWSVF  139 (505)
Q Consensus        74 r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr-----------~-~-~~-~~~~~~~~~~~l~~l~~~ea~~Lf  139 (505)
                      +.+|++|+++.........+...+...... .++++|.           + . .+ .........+.+++++.++..+++
T Consensus       190 ~~vl~IDEi~~l~~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il  268 (368)
T 3uk6_A          190 PGVLFIDEVHMLDIESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQIL  268 (368)
T ss_dssp             BCEEEEESGGGSBHHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHH
T ss_pred             CceEEEhhccccChHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHH
Confidence            459999999776554555566655554444 3444443           1 1 11 111233446899999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcC-CChHHHHH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCK-GLPLAAKT  175 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~-g~Plal~~  175 (505)
                      ...+...+.    .-.++++..+++.+. |.|-.+..
T Consensus       269 ~~~~~~~~~----~~~~~~l~~l~~~~~~G~~r~~~~  301 (368)
T 3uk6_A          269 RIRCEEEDV----EMSEDAYTVLTRIGLETSLRYAIQ  301 (368)
T ss_dssp             HHHHHHTTC----CBCHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHcCC----CCCHHHHHHHHHHhcCCCHHHHHH
Confidence            876543222    122456778888887 77754443

>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=97.35  E-value=0.0012  Score=66.95  Aligned_cols=161  Identities=12%  Similarity=0.132  Sum_probs=83.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC-CC-hhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA-KD-LVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~-~~-~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      ++|+|||++|+.+++  +.  .+ .++.++++...... .....+........ .. ......     .....+++.+|+
T Consensus        85 ppGtGKTtla~~la~--~l--~~-~~i~in~s~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~~-----~~~~~~~~~vli  153 (516)
T 1sxj_A           85 PPGIGKTTAAHLVAQ--EL--GY-DILEQNASDVRSKT-LLNAGVKNALDNMSVVGYFKHNEE-----AQNLNGKHFVII  153 (516)
T ss_dssp             STTSSHHHHHHHHHH--HT--TC-EEEEECTTSCCCHH-HHHHTGGGGTTBCCSTTTTTC---------CCSSTTSEEEE
T ss_pred             CCCCCHHHHHHHHHH--Hc--CC-CEEEEeCCCcchHH-HHHHHHHHHhccccHHHHHhhhhh-----hhhccCCCeEEE
Confidence            479999999999998  44  12 23345555444432 22222222211110 00 000000     001235678999


Q ss_pred             EeCCCCCCcc---ChhHHHHhhcCCCCCcEEEEEeCchH---HHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCC
Q 046115           79 LDDVWNEDYY---KWEPFYKCLKNSLHESKILITTRKET---VARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKR  152 (505)
Q Consensus        79 lDdv~~~~~~---~~~~~~~~~~~~~~~~~iLiTtr~~~---~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~  152 (505)
                      +|+++.....   .+..+...+...  +..|++++.+..   +.........+.+++++.++..+.+...+...+.... 
T Consensus       154 IDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~-  230 (516)
T 1sxj_A          154 MDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD-  230 (516)
T ss_dssp             ECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC-
T ss_pred             EECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCC-
Confidence            9999654321   124444444432  233555554422   2221122457899999999999988776543222111 


Q ss_pred             chHHHHHHHHHHHcCCC-hHHHHHHHH
Q 046115          153 ENLEKIGREIVKKCKGL-PLAAKTIAS  178 (505)
Q Consensus       153 ~~~~~~~~~i~~~~~g~-Plal~~~~~  178 (505)
                         ++++..|++.++|. +-++..+..
T Consensus       231 ---~~~l~~la~~s~GdiR~~i~~L~~  254 (516)
T 1sxj_A          231 ---PNVIDRLIQTTRGDIRQVINLLST  254 (516)
T ss_dssp             ---TTHHHHHHHHTTTCHHHHHHHHTH
T ss_pred             ---HHHHHHHHHHcCCcHHHHHHHHHH
Confidence               24477888999984 455555433

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.34  E-value=0.0029  Score=58.62  Aligned_cols=150  Identities=17%  Similarity=0.113  Sum_probs=77.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  .....   .+.++...              +....  ...........+.......+.+|++|
T Consensus        59 ~~GtGKT~la~~la~--~~~~~---~~~v~~~~--------------~~~~~--~~~~~~~~~~~~~~~~~~~~~vl~iD  117 (285)
T 3h4m_A           59 PPGTGKTLLAKAVAT--ETNAT---FIRVVGSE--------------LVKKF--IGEGASLVKDIFKLAKEKAPSIIFID  117 (285)
T ss_dssp             SSSSSHHHHHHHHHH--HTTCE---EEEEEGGG--------------GCCCS--TTHHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HhCCC---EEEEehHH--------------HHHhc--cchHHHHHHHHHHHHHHcCCeEEEEE
Confidence            479999999999998  43222   22333221              11000  01111111222222333456899999


Q ss_pred             CCCCC-----------Cc---cChhHHHHhhc--CCCCCcEEEEEeCchHHHH-H-hC--C-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNE-----------DY---YKWEPFYKCLK--NSLHESKILITTRKETVAR-I-MG--S-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~-----------~~---~~~~~~~~~~~--~~~~~~~iLiTtr~~~~~~-~-~~--~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++..           ..   ..+..+...+.  ....+..||.||....... . ..  . ...+.++..+.++..+++
T Consensus       118 Eid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il  197 (285)
T 3h4m_A          118 EIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEIL  197 (285)
T ss_dssp             TTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHH
T ss_pred             CHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHH
Confidence            99441           10   11222222222  2234567788887643211 1 11  2 247889999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCC-ChHHHHHH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKG-LPLAAKTI  176 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g-~Plal~~~  176 (505)
                      ......... ....+    ...+++.+.| .|-.+..+
T Consensus       198 ~~~~~~~~~-~~~~~----~~~l~~~~~g~~~~~i~~l  230 (285)
T 3h4m_A          198 KIHTRKMNL-AEDVN----LEEIAKMTEGCVGAELKAI  230 (285)
T ss_dssp             HHHHTTSCB-CTTCC----HHHHHHHCTTCCHHHHHHH
T ss_pred             HHHHhcCCC-CCcCC----HHHHHHHcCCCCHHHHHHH
Confidence            877632221 12222    4567777776 45444443

>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=97.25  E-value=0.0038  Score=57.38  Aligned_cols=139  Identities=17%  Similarity=0.179  Sum_probs=71.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||++|+.+++  ....  . .+.++...             .+. +. ............+......+..+|++|
T Consensus        72 ~~GtGKT~la~~ia~--~~~~--~-~~~i~~~~-------------~~~-g~-~~~~~~~~~~~~~~~~~~~~~~vl~iD  131 (272)
T 1d2n_A           72 PPHSGKTALAAKIAE--ESNF--P-FIKICSPD-------------KMI-GF-SETAKCQAMKKIFDDAYKSQLSCVVVD  131 (272)
T ss_dssp             STTSSHHHHHHHHHH--HHTC--S-EEEEECGG-------------GCT-TC-CHHHHHHHHHHHHHHHHTSSEEEEEEC
T ss_pred             CCCCcHHHHHHHHHH--HhCC--C-EEEEeCHH-------------Hhc-CC-chHHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            479999999999998  3322  2 12233221             111 00 001111222233333445678999999


Q ss_pred             CCCCC---------CccCh-hHHHHhhcC---CCCCcEEEEEeCchHHHHH---hCC-cceEeCCCCCh-hhHHHHHHHh
Q 046115           81 DVWNE---------DYYKW-EPFYKCLKN---SLHESKILITTRKETVARI---MGS-THVISVNVLSE-MECWSVFQSL  142 (505)
Q Consensus        81 dv~~~---------~~~~~-~~~~~~~~~---~~~~~~iLiTtr~~~~~~~---~~~-~~~~~l~~l~~-~ea~~Lf~~~  142 (505)
                      +++..         ....+ ..+...+..   .+....||.||........   ... ...+.+++++. ++...++...
T Consensus       132 Eid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~~  211 (272)
T 1d2n_A          132 DIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELL  211 (272)
T ss_dssp             CHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHHH
T ss_pred             ChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHHHHhc
Confidence            98432         11111 223332222   2334456777877654443   122 34678888888 5555555442


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCC
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKG  168 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g  168 (505)
                      .    .  .   .++.+..+++.+.|
T Consensus       212 ~----~--~---~~~~~~~l~~~~~g  228 (272)
T 1d2n_A          212 G----N--F---KDKERTTIAQQVKG  228 (272)
T ss_dssp             T----C--S---CHHHHHHHHHHHTT
T ss_pred             C----C--C---CHHHHHHHHHHhcC
Confidence            1    1  1   13457778888877

>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=97.20  E-value=0.0037  Score=59.94  Aligned_cols=153  Identities=11%  Similarity=-0.017  Sum_probs=79.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  +....   .+.++..          .+.....    .  .........+......++.+|+||
T Consensus        92 ppGtGKT~la~ala~--~~~~~---~~~v~~~----------~l~~~~~----g--~~~~~~~~~f~~a~~~~~~vl~iD  150 (355)
T 2qp9_X           92 PPGTGKSYLAKAVAT--EANST---FFSVSSS----------DLVSKWM----G--ESEKLVKQLFAMARENKPSIIFID  150 (355)
T ss_dssp             STTSCHHHHHHHHHH--HHTCE---EEEEEHH----------HHHSCC---------CHHHHHHHHHHHHHTSSEEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HhCCC---EEEeeHH----------HHhhhhc----c--hHHHHHHHHHHHHHHcCCeEEEEe
Confidence            479999999999998  44322   2223321          1111111    0  011111112222223567899999


Q ss_pred             CCCCCCcc-----------ChhHHHHhhcC---CCCCcEEEEEeCchHHH-HH-h-CCcceEeCCCCChhhHHHHHHHhh
Q 046115           81 DVWNEDYY-----------KWEPFYKCLKN---SLHESKILITTRKETVA-RI-M-GSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        81 dv~~~~~~-----------~~~~~~~~~~~---~~~~~~iLiTtr~~~~~-~~-~-~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +++.....           ....+...+..   ...+..||.||..+... .. . .-...+.++..+.++-.+++....
T Consensus       151 Eid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l  230 (355)
T 2qp9_X          151 QVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINV  230 (355)
T ss_dssp             CGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHH
T ss_pred             chHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHH
Confidence            99653210           02333333332   23455666677654211 11 1 223567888889999999998766


Q ss_pred             hCCCCCCCCchHHHHHHHHHHHcCC-ChHHHHHHHH
Q 046115          144 ISGKTIGKRENLEKIGREIVKKCKG-LPLAAKTIAS  178 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~g-~Plal~~~~~  178 (505)
                      .......    .......|++.+.| .+-.|..+..
T Consensus       231 ~~~~~~~----~~~~l~~la~~t~G~sg~dl~~l~~  262 (355)
T 2qp9_X          231 GDTPSVL----TKEDYRTLGAMTEGYSGSDIAVVVK  262 (355)
T ss_dssp             TTSCBCC----CHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             hhCCCCC----CHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3222111    13456788888887 4555655554

>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=97.17  E-value=0.0015  Score=61.88  Aligned_cols=141  Identities=16%  Similarity=0.163  Sum_probs=77.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHH--cCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEEC--VAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~--l~~~r~Llv   78 (505)
                      .+|+|||++|+.+++  ...   ..++.++.+...  ....+..+...                  ...  ..+++.+++
T Consensus        56 ~~G~GKT~la~~la~--~l~---~~~~~i~~~~~~--~~~i~~~~~~~------------------~~~~~~~~~~~vli  110 (324)
T 3u61_B           56 SPGTGKTTVAKALCH--DVN---ADMMFVNGSDCK--IDFVRGPLTNF------------------ASAASFDGRQKVIV  110 (324)
T ss_dssp             STTSSHHHHHHHHHH--HTT---EEEEEEETTTCC--HHHHHTHHHHH------------------HHBCCCSSCEEEEE
T ss_pred             cCCCCHHHHHHHHHH--HhC---CCEEEEcccccC--HHHHHHHHHHH------------------HhhcccCCCCeEEE
Confidence            379999999999998  442   223455543321  22222222111                  111  123678999


Q ss_pred             EeCCCCCC-ccChhHHHHhhcCCCCCcEEEEEeCchH-----HHHHhCCcceEeCCCCChhhHHHH-------HHHhhhC
Q 046115           79 LDDVWNED-YYKWEPFYKCLKNSLHESKILITTRKET-----VARIMGSTHVISVNVLSEMECWSV-------FQSLAIS  145 (505)
Q Consensus        79 lDdv~~~~-~~~~~~~~~~~~~~~~~~~iLiTtr~~~-----~~~~~~~~~~~~l~~l~~~ea~~L-------f~~~~~~  145 (505)
                      +|+++... ......+...+.....++.+++||....     +...   ...+.+++++.++-.++       +...+..
T Consensus       111 iDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR---~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~  187 (324)
T 3u61_B          111 IDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSR---CRVITFGQPTDEDKIEMMKQMIRRLTEICKH  187 (324)
T ss_dssp             EESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHH---SEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhh---CcEEEeCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99996654 3344555555554445677888887643     2222   34789999998874333       2222211


Q ss_pred             CCCCCCCchHHHHHHHHHHHcCCChHH
Q 046115          146 GKTIGKRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       146 ~~~~~~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                      .+. .-++  .+++..+++.++|.+..
T Consensus       188 ~~~-~~~~--~~~~~~l~~~~~gd~R~  211 (324)
T 3u61_B          188 EGI-AIAD--MKVVAALVKKNFPDFRK  211 (324)
T ss_dssp             HTC-CBSC--HHHHHHHHHHTCSCTTH
T ss_pred             cCC-CCCc--HHHHHHHHHhCCCCHHH
Confidence            111 1111  25677788888777653

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.16  E-value=0.0061  Score=57.52  Aligned_cols=155  Identities=13%  Similarity=0.017  Sum_probs=79.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  +..+  ...+.++...-..              ....  .........+......++.+|++|
T Consensus        53 ppGtGKT~la~ala~--~~~~--~~~~~i~~~~l~~--------------~~~g--~~~~~~~~lf~~a~~~~~~vl~iD  112 (322)
T 1xwi_A           53 PPGTGKSYLAKAVAT--EANN--STFFSISSSDLVS--------------KWLG--ESEKLVKNLFQLARENKPSIIFID  112 (322)
T ss_dssp             SSSSCHHHHHHHHHH--HTTS--CEEEEEECCSSCC--------------SSCC--SCHHHHHHHHHHHHHTSSEEEEEE
T ss_pred             CCCccHHHHHHHHHH--HcCC--CcEEEEEhHHHHh--------------hhhh--HHHHHHHHHHHHHHhcCCcEEEee
Confidence            479999999999998  4311  1122333332110              0000  111111122222223567899999


Q ss_pred             CCCCCCc------cC-----hhHHHHhhcC---CCCCcEEEEEeCchHHH-HHh--CCcceEeCCCCChhhHHHHHHHhh
Q 046115           81 DVWNEDY------YK-----WEPFYKCLKN---SLHESKILITTRKETVA-RIM--GSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        81 dv~~~~~------~~-----~~~~~~~~~~---~~~~~~iLiTtr~~~~~-~~~--~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +++....      ..     ...+...+..   ...+..||.||..+... ...  .-...+.++..+.++-.+++....
T Consensus       113 Eid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l  192 (322)
T 1xwi_A          113 EIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHL  192 (322)
T ss_dssp             TTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHH
T ss_pred             cHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHH
Confidence            9955310      01     1223333332   23455566667554211 111  223577888889999889998765


Q ss_pred             hCCCCCCCCchHHHHHHHHHHHcCCC-hHHHHHHHHH
Q 046115          144 ISGKTIGKRENLEKIGREIVKKCKGL-PLAAKTIASL  179 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~g~-Plal~~~~~~  179 (505)
                      ..... .   -.......|++.+.|+ +-.|..+...
T Consensus       193 ~~~~~-~---l~~~~l~~la~~t~G~sgadl~~l~~~  225 (322)
T 1xwi_A          193 GTTQN-S---LTEADFRELGRKTDGYSGADISIIVRD  225 (322)
T ss_dssp             TTCCB-C---CCHHHHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             hcCCC-C---CCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            32221 1   1234577889999887 5556665543

>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=97.13  E-value=0.0035  Score=59.29  Aligned_cols=153  Identities=13%  Similarity=0.041  Sum_probs=81.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHH-HHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIE-ECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~-~~l~~~r~Llvl   79 (505)
                      .+|+|||+||+.+++  +....|   +.++..          .+....       ....+.....+. .....++.+|++
T Consensus        59 ppGtGKT~la~aia~--~~~~~~---~~v~~~----------~l~~~~-------~g~~~~~~~~~f~~a~~~~~~vl~i  116 (322)
T 3eie_A           59 PPGTGKSYLAKAVAT--EANSTF---FSVSSS----------DLVSKW-------MGESEKLVKQLFAMARENKPSIIFI  116 (322)
T ss_dssp             SSSSCHHHHHHHHHH--HHTCEE---EEEEHH----------HHHTTT-------GGGHHHHHHHHHHHHHHTSSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HHCCCE---EEEchH----------HHhhcc-------cchHHHHHHHHHHHHHhcCCeEEEe
Confidence            479999999999998  443222   233321          111111       111222222222 222346689999


Q ss_pred             eCCCCCCcc-----------ChhHHHHhhc---CCCCCcEEEEEeCchHHH-HHh--CCcceEeCCCCChhhHHHHHHHh
Q 046115           80 DDVWNEDYY-----------KWEPFYKCLK---NSLHESKILITTRKETVA-RIM--GSTHVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        80 Ddv~~~~~~-----------~~~~~~~~~~---~~~~~~~iLiTtr~~~~~-~~~--~~~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      |+++.....           ....+...+.   ....+..||.||..+... ..+  .-...+.++..+.++-.+++...
T Consensus       117 DEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~  196 (322)
T 3eie_A          117 DQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEIN  196 (322)
T ss_dssp             ECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHH
T ss_pred             chhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHH
Confidence            999542110           0233333333   234456666677664321 111  11346778888999999999887


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCC-ChHHHHHHHHH
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKG-LPLAAKTIASL  179 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g-~Plal~~~~~~  179 (505)
                      ........    .......+++.+.| .+-.|..+...
T Consensus       197 ~~~~~~~~----~~~~l~~la~~t~g~sg~di~~l~~~  230 (322)
T 3eie_A          197 VGDTPCVL----TKEDYRTLGAMTEGYSGSDIAVVVKD  230 (322)
T ss_dssp             HTTCCCCC----CHHHHHHHHHTTTTCCHHHHHHHHHH
T ss_pred             hccCCCCC----CHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            64322111    13456788888887 45555555443

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=97.11  E-value=0.0013  Score=64.16  Aligned_cols=75  Identities=9%  Similarity=0.131  Sum_probs=44.9

Q ss_pred             CCcceeeccCCccccccc-hhhhcCCCCcEEecCCCcCcc-----ccch-hccccccCceeecCCCccccccc-ccccCC
Q 046115          413 LHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLR-----ELPR-GIGKLRKLMYLHNEDTGCLRYLP-AGIGEL  484 (505)
Q Consensus       413 ~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~-----~lp~-~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l  484 (505)
                      .+|+.+.+. +. +..++ ..+..+.+|+.+.+.++. +.     .++. .+..+++|+.+.+..+  +..++ ..|.+|
T Consensus       248 ~~L~~i~lp-~~-i~~I~~~aF~~c~~L~~l~l~~~~-~~~~~~~~I~~~aF~~c~~L~~l~l~~~--i~~I~~~aF~~c  322 (401)
T 4fdw_A          248 SGITTVKLP-NG-VTNIASRAFYYCPELAEVTTYGST-FNDDPEAMIHPYCLEGCPKLARFEIPES--IRILGQGLLGGN  322 (401)
T ss_dssp             CCCSEEEEE-TT-CCEECTTTTTTCTTCCEEEEESSC-CCCCTTCEECTTTTTTCTTCCEECCCTT--CCEECTTTTTTC
T ss_pred             CCccEEEeC-CC-ccEEChhHhhCCCCCCEEEeCCcc-ccCCcccEECHHHhhCCccCCeEEeCCc--eEEEhhhhhcCC
Confidence            445555553 22 34443 345677788888877655 32     3443 4677778888887743  34444 347777


Q ss_pred             ccCCccce
Q 046115          485 IRLRRVRE  492 (505)
Q Consensus       485 ~~L~~L~~  492 (505)
                      .+|+.+.+
T Consensus       323 ~~L~~l~l  330 (401)
T 4fdw_A          323 RKVTQLTI  330 (401)
T ss_dssp             CSCCEEEE
T ss_pred             CCccEEEE
Confidence            77777654

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.10  E-value=0.0036  Score=58.68  Aligned_cols=71  Identities=11%  Similarity=0.157  Sum_probs=47.0

Q ss_pred             eEEEEEeCCCCC---------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH--h-C----C-cceEeCCCCChhhHH
Q 046115           74 KFLLVLDDVWNE---------DYYKWEPFYKCLKNSLHESKILITTRKETVARI--M-G----S-THVISVNVLSEMECW  136 (505)
Q Consensus        74 r~LlvlDdv~~~---------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~--~-~----~-~~~~~l~~l~~~ea~  136 (505)
                      ..+|++|+++.-         .......+...+.....+..+|.||........  . +    . ...+.+++++.++-.
T Consensus       131 ~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~  210 (309)
T 3syl_A          131 GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELF  210 (309)
T ss_dssp             TSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHH
T ss_pred             CCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHH
Confidence            359999999632         333345666666666667788888865432111  0 1    1 257899999999999


Q ss_pred             HHHHHhhh
Q 046115          137 SVFQSLAI  144 (505)
Q Consensus       137 ~Lf~~~~~  144 (505)
                      +++.....
T Consensus       211 ~il~~~l~  218 (309)
T 3syl_A          211 EIAGHMLD  218 (309)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99977654

>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=97.08  E-value=0.005  Score=58.64  Aligned_cols=96  Identities=6%  Similarity=0.059  Sum_probs=61.5

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      .+-++|+|+++.........+...+......+.++++|.... +.. .......+.+.+++.++..+.+...+..... .
T Consensus       110 ~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~-~  188 (340)
T 1sxj_C          110 GFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKL-K  188 (340)
T ss_dssp             SCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTC-C
T ss_pred             CceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcCC-C
Confidence            467899999966554445556666665556667777776532 211 1123447889999999988888766532221 1


Q ss_pred             CCchHHHHHHHHHHHcCCChHH
Q 046115          151 KRENLEKIGREIVKKCKGLPLA  172 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Pla  172 (505)
                         -.++.+..+++.++|.+--
T Consensus       189 ---i~~~~~~~i~~~s~G~~r~  207 (340)
T 1sxj_C          189 ---LSPNAEKALIELSNGDMRR  207 (340)
T ss_dssp             ---BCHHHHHHHHHHHTTCHHH
T ss_pred             ---CCHHHHHHHHHHcCCCHHH
Confidence               1245677888888988764

>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=96.97  E-value=0.0014  Score=61.25  Aligned_cols=124  Identities=12%  Similarity=-0.021  Sum_probs=76.5

Q ss_pred             CCCCcHHHHHHHHhcCc-ccccCCCceEEEEeCC-CCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNG-DVERNFEKRTWVCVSE-PFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~-~~~~~f~~~~wv~~~~-~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      ++|+|||++|+.+++.- ..........+++... .... +..+++...+....                 ..+++-++|
T Consensus        26 p~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~i-d~ir~li~~~~~~p-----------------~~~~~kvvi   87 (305)
T 2gno_A           26 EDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGI-DDIRTIKDFLNYSP-----------------ELYTRKYVI   87 (305)
T ss_dssp             SSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCH-HHHHHHHHHHTSCC-----------------SSSSSEEEE
T ss_pred             CCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCH-HHHHHHHHHHhhcc-----------------ccCCceEEE
Confidence            47999999999998720 0111223344554332 1121 22233333332100                 124567899


Q ss_pred             EeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHHhCCcceEeCCCCChhhHHHHHHHhh
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARIMGSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +|+++.........+...+......+.+|++|.++ .+.+.+... .+++.+++.++..+.+....
T Consensus        88 Idead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           88 VHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             ETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEECCCCHHHHHHHHHHH
T ss_pred             eccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCCCCCHHHHHHHHHHHh
Confidence            99998776666777888888776677777766553 343334444 89999999999999997765

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.90  E-value=0.056  Score=51.96  Aligned_cols=143  Identities=17%  Similarity=0.145  Sum_probs=76.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHH-HHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQ-HIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~-~l~~~l~~~r~Llvl   79 (505)
                      ++|.|||.||+++++  +....|   +.++.+.              +.   .....+.+..+. .....-...+++|++
T Consensus       190 PPGTGKTllAkAiA~--e~~~~f---~~v~~s~--------------l~---sk~vGese~~vr~lF~~Ar~~aP~IIFi  247 (405)
T 4b4t_J          190 PPGTGKTLLARAVAH--HTDCKF---IRVSGAE--------------LV---QKYIGEGSRMVRELFVMAREHAPSIIFM  247 (405)
T ss_dssp             CSSSSHHHHHHHHHH--HHTCEE---EEEEGGG--------------GS---CSSTTHHHHHHHHHHHHHHHTCSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--hhCCCc---eEEEhHH--------------hh---ccccchHHHHHHHHHHHHHHhCCceEee
Confidence            589999999999998  443333   2333322              11   000111112222 222222456899999


Q ss_pred             eCCCCCCc--------------cChhHHHHhhcCC--CCCcEEEEEeCchHHH-HHh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNEDY--------------YKWEPFYKCLKNS--LHESKILITTRKETVA-RIM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~~--------------~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~-~~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |+++....              ..+..++..+...  ..+..||.||..++.. ..+   +. ...+.++..+.++-.++
T Consensus       248 DEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~I  327 (405)
T 4b4t_J          248 DEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEI  327 (405)
T ss_dssp             ESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHH
T ss_pred             ecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHH
Confidence            99854210              0123344444432  3455667777764331 111   22 46888998898888889


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |+.+.-.-.. ....+    ...+++.+.|+.
T Consensus       328 l~~~~~~~~l-~~dvd----l~~lA~~t~G~S  354 (405)
T 4b4t_J          328 LRIHSRKMNL-TRGIN----LRKVAEKMNGCS  354 (405)
T ss_dssp             HHHHHTTSBC-CSSCC----HHHHHHHCCSCC
T ss_pred             HHHHhcCCCC-CccCC----HHHHHHHCCCCC
Confidence            8776532221 22223    456777887754

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.89  E-value=0.00087  Score=58.64  Aligned_cols=93  Identities=22%  Similarity=0.293  Sum_probs=47.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||+.+++  ....+...++|+++.      .+...+...+...      ........+..     .-+||||
T Consensus        62 ~~GtGKT~la~~i~~--~~~~~~~~~~~~~~~------~~~~~~~~~~~~~------~~~~~~~~~~~-----~~~lilD  122 (202)
T 2w58_A           62 SFGVGKTYLLAAIAN--ELAKRNVSSLIVYVP------ELFRELKHSLQDQ------TMNEKLDYIKK-----VPVLMLD  122 (202)
T ss_dssp             STTSSHHHHHHHHHH--HHHTTTCCEEEEEHH------HHHHHHHHC---C------CCHHHHHHHHH-----SSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCeEEEEEhH------HHHHHHHHHhccc------hHHHHHHHhcC-----CCEEEEc
Confidence            479999999999998  554444456677653      3444444333211      11222222221     1399999


Q ss_pred             CCCCCCccCh--hHHHH-hhcCC-CCCcEEEEEeCc
Q 046115           81 DVWNEDYYKW--EPFYK-CLKNS-LHESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~--~~~~~-~~~~~-~~~~~iLiTtr~  112 (505)
                      |++......|  ..+.. .+... ..+.++|+||..
T Consensus       123 ei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~  158 (202)
T 2w58_A          123 DLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNF  158 (202)
T ss_dssp             EECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Confidence            9965432222  21222 22211 234578888874

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.86  E-value=0.0013  Score=56.26  Aligned_cols=93  Identities=20%  Similarity=0.242  Sum_probs=47.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .+|+||||||+.+++  ...... ..+++++.      .++...+..........      .....    +. +.-+|||
T Consensus        46 ~~G~GKTtL~~~i~~--~~~~~~g~~~~~~~~------~~~~~~~~~~~~~~~~~------~~~~~----~~-~~~llil  106 (180)
T 3ec2_A           46 SPGVGKTHLAVATLK--AIYEKKGIRGYFFDT------KDLIFRLKHLMDEGKDT------KFLKT----VL-NSPVLVL  106 (180)
T ss_dssp             SSSSSHHHHHHHHHH--HHHHHSCCCCCEEEH------HHHHHHHHHHHHHTCCS------HHHHH----HH-TCSEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHHcCCeEEEEEH------HHHHHHHHHHhcCchHH------HHHHH----hc-CCCEEEE
Confidence            479999999999998  443111 12334442      33444443333211111      11111    21 3458999


Q ss_pred             eCCCCCCccCh--hHHHHhhcCC-CCCcEEEEEeCc
Q 046115           80 DDVWNEDYYKW--EPFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~--~~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      |++.......+  ..+...+... ..+..+|+||..
T Consensus       107 DE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A          107 DDLGSERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             ETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             eCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence            99974322222  2233333222 256788888874

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.74  E-value=0.027  Score=52.25  Aligned_cols=150  Identities=14%  Similarity=0.047  Sum_probs=76.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHH-HHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQ-HIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~-~l~~~l~~~r~Llvl   79 (505)
                      ++|+|||++|+.++.  .....   .+.+++..-..              ....   +.+.... .+.......+.+|++
T Consensus        62 p~GtGKT~la~~la~--~~~~~---~~~i~~~~l~~--------------~~~~---~~~~~~~~~~~~~~~~~~~vl~i  119 (297)
T 3b9p_A           62 PPGNGKTLLARAVAT--ECSAT---FLNISAASLTS--------------KYVG---DGEKLVRALFAVARHMQPSIIFI  119 (297)
T ss_dssp             SSSSCHHHHHHHHHH--HTTCE---EEEEESTTTSS--------------SSCS---CHHHHHHHHHHHHHHTCSEEEEE
T ss_pred             cCCCCHHHHHHHHHH--HhCCC---eEEeeHHHHhh--------------cccc---hHHHHHHHHHHHHHHcCCcEEEe
Confidence            479999999999998  43222   23344432110              0011   1122221 222222346789999


Q ss_pred             eCCCCCCcc-----------ChhHHHHhhcCC-----CCCcEEEEEeCchH-----HHHHhCCcceEeCCCCChhhHHHH
Q 046115           80 DDVWNEDYY-----------KWEPFYKCLKNS-----LHESKILITTRKET-----VARIMGSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~~~-----------~~~~~~~~~~~~-----~~~~~iLiTtr~~~-----~~~~~~~~~~~~l~~l~~~ea~~L  138 (505)
                      |++......           ....+...+...     +.+..|+.||..+.     +...+  ...+.++..+.++...+
T Consensus       120 DEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~R~--~~~i~~~~p~~~~r~~i  197 (297)
T 3b9p_A          120 DEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALRRF--TKRVYVSLPDEQTRELL  197 (297)
T ss_dssp             ETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHHHC--CEEEECCCCCHHHHHHH
T ss_pred             ccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHhhC--CeEEEeCCcCHHHHHHH
Confidence            999542110           011222222211     13456677777642     22222  24677777788888888


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                      +.........    .-..+.+..+++.+.|++- +|..+..
T Consensus       198 l~~~~~~~~~----~~~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          198 LNRLLQKQGS----PLDTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             HHHHHGGGSC----CSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHhcCC----CCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            8766532111    1113457788888888775 5544443

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.72  E-value=0.00099  Score=55.07  Aligned_cols=79  Identities=11%  Similarity=0.027  Sum_probs=43.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ..|+|||+|++.++.  .....=..+++++.......                              ..+ .+.-+||+|
T Consensus        44 ~~G~GKTtL~~~i~~--~~~~~g~~~~~~~~~~~~~~------------------------------~~~-~~~~lLilD   90 (149)
T 2kjq_A           44 EEGAGKSHLLQAWVA--QALEAGKNAAYIDAASMPLT------------------------------DAA-FEAEYLAVD   90 (149)
T ss_dssp             SSTTTTCHHHHHHHH--HHHTTTCCEEEEETTTSCCC------------------------------GGG-GGCSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCcEEEEcHHHhhHH------------------------------HHH-hCCCEEEEe
Confidence            379999999999998  33322112567765442211                              011 234588999


Q ss_pred             CCCCCCccChhHHHHhhcCC-CCCc-EEEEEeCc
Q 046115           81 DVWNEDYYKWEPFYKCLKNS-LHES-KILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~-~~~~-~iLiTtr~  112 (505)
                      ++........+.+...+... ..|. .+|+||+.
T Consensus        91 E~~~~~~~~~~~l~~li~~~~~~g~~~iiits~~  124 (149)
T 2kjq_A           91 QVEKLGNEEQALLFSIFNRFRNSGKGFLLLGSEY  124 (149)
T ss_dssp             STTCCCSHHHHHHHHHHHHHHHHTCCEEEEEESS
T ss_pred             CccccChHHHHHHHHHHHHHHHcCCcEEEEECCC
Confidence            99664432233333333321 1233 48888874

>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=96.71  E-value=0.012  Score=56.53  Aligned_cols=153  Identities=10%  Similarity=0.018  Sum_probs=79.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHH-HHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHI-EECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l-~~~l~~~r~Llvl   79 (505)
                      .+|+|||+||+.+++  +...   ..+.+++..-..              ..   ..........+ ......++.+|+|
T Consensus       125 ppGtGKT~la~aia~--~~~~---~~~~i~~~~l~~--------------~~---~g~~~~~~~~~~~~a~~~~~~vl~i  182 (357)
T 3d8b_A          125 PPGTGKTLIGKCIAS--QSGA---TFFSISASSLTS--------------KW---VGEGEKMVRALFAVARCQQPAVIFI  182 (357)
T ss_dssp             STTSSHHHHHHHHHH--HTTC---EEEEEEGGGGCC--------------SS---TTHHHHHHHHHHHHHHHTCSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HcCC---eEEEEehHHhhc--------------cc---cchHHHHHHHHHHHHHhcCCeEEEE
Confidence            479999999999998  4322   223444432110              00   00111112222 2222346789999


Q ss_pred             eCCCCCCc-----------cChhHHHHhhcC----CCCCcEEEEEeCchH-HHHH-hCC-cceEeCCCCChhhHHHHHHH
Q 046115           80 DDVWNEDY-----------YKWEPFYKCLKN----SLHESKILITTRKET-VARI-MGS-THVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        80 Ddv~~~~~-----------~~~~~~~~~~~~----~~~~~~iLiTtr~~~-~~~~-~~~-~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      |+++....           .....+...+..    ...+..||.||.... +... ... ...+.+...+.++..+++..
T Consensus       183 DEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~  262 (357)
T 3d8b_A          183 DEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVIN  262 (357)
T ss_dssp             ETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHH
T ss_pred             eCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHH
Confidence            99843210           012233433332    123455665676532 2111 122 24678888899998888877


Q ss_pred             hhhCCCCCCCCchHHHHHHHHHHHcCC-ChHHHHHHHHH
Q 046115          142 LAISGKTIGKRENLEKIGREIVKKCKG-LPLAAKTIASL  179 (505)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~i~~~~~g-~Plal~~~~~~  179 (505)
                      .+..... .   -..+.+..+++.+.| .+-.|..+...
T Consensus       263 ~~~~~~~-~---l~~~~l~~la~~t~G~s~~dl~~l~~~  297 (357)
T 3d8b_A          263 LMSKEQC-C---LSEEEIEQIVQQSDAFSGADMTQLCRE  297 (357)
T ss_dssp             HHHTSCB-C---CCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHhhcCC-C---ccHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            6532221 1   113557788888888 55566655443

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=96.71  E-value=0.0051  Score=60.01  Aligned_cols=60  Identities=13%  Similarity=0.130  Sum_probs=32.0

Q ss_pred             cccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCc
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~  472 (505)
                      .|..+++|+.+.+.+ . +..++. .+..+.+|+.+.|..+  +..++. .+.++ +|+.+.+.+|.
T Consensus       295 aF~~c~~L~~l~l~~-~-i~~I~~~aF~~c~~L~~l~lp~~--l~~I~~~aF~~~-~L~~l~l~~n~  356 (401)
T 4fdw_A          295 CLEGCPKLARFEIPE-S-IRILGQGLLGGNRKVTQLTIPAN--VTQINFSAFNNT-GIKEVKVEGTT  356 (401)
T ss_dssp             TTTTCTTCCEECCCT-T-CCEECTTTTTTCCSCCEEEECTT--CCEECTTSSSSS-CCCEEEECCSS
T ss_pred             HhhCCccCCeEEeCC-c-eEEEhhhhhcCCCCccEEEECcc--ccEEcHHhCCCC-CCCEEEEcCCC
Confidence            345566666666652 2 444433 3455666666666442  444443 35555 66666666664

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.69  E-value=0.0031  Score=51.75  Aligned_cols=84  Identities=11%  Similarity=-0.017  Sum_probs=48.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||++|+.+++.  ....-...+ +++....+.                   ....   ..+...   ....|++|
T Consensus        32 ~~GtGKt~lA~~i~~~--~~~~~~~~v-~~~~~~~~~-------------------~~~~---~~~~~a---~~g~l~ld   83 (145)
T 3n70_A           32 APGTGRMTGARYLHQF--GRNAQGEFV-YRELTPDNA-------------------PQLN---DFIALA---QGGTLVLS   83 (145)
T ss_dssp             STTSSHHHHHHHHHHS--STTTTSCCE-EEECCTTTS-------------------SCHH---HHHHHH---TTSCEEEE
T ss_pred             CCCCCHHHHHHHHHHh--CCccCCCEE-EECCCCCcc-------------------hhhh---cHHHHc---CCcEEEEc
Confidence            3799999999999883  222112233 666653322                   0111   111111   22478999


Q ss_pred             CCCCCCccChhHHHHhhcCCCCCcEEEEEeCc
Q 046115           81 DVWNEDYYKWEPFYKCLKNSLHESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~  112 (505)
                      +++.-.......+...+.......++|.||..
T Consensus        84 ei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           84 HPEHLTREQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             CGGGSCHHHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             ChHHCCHHHHHHHHHHHhhcCCCEEEEEECCc
Confidence            99776655556667666555556778777764

>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=96.64  E-value=0.015  Score=54.22  Aligned_cols=145  Identities=12%  Similarity=0.132  Sum_probs=75.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  .....     ++.+.    ..++....   .+ ..   ...   ....+.......+.+|++|
T Consensus        57 p~GtGKT~la~ala~--~~~~~-----~i~v~----~~~l~~~~---~g-~~---~~~---~~~~f~~a~~~~p~il~iD  115 (301)
T 3cf0_A           57 PPGCGKTLLAKAIAN--ECQAN-----FISIK----GPELLTMW---FG-ES---EAN---VREIFDKARQAAPCVLFFD  115 (301)
T ss_dssp             SSSSSHHHHHHHHHH--HTTCE-----EEEEC----HHHHHHHH---HT-TC---TTH---HHHHHHHHHHTCSEEEEEC
T ss_pred             CCCcCHHHHHHHHHH--HhCCC-----EEEEE----hHHHHhhh---cC-ch---HHH---HHHHHHHHHhcCCeEEEEE
Confidence            479999999999998  44322     22222    11222221   11 11   111   1222222333467899999


Q ss_pred             CCCCCC--------------ccChhHHHHhhcC--CCCCcEEEEEeCchHHH-HH-hC--C-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNED--------------YYKWEPFYKCLKN--SLHESKILITTRKETVA-RI-MG--S-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~--------------~~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~-~~-~~--~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++...              ......+...+..  ...+..||.||..+... .. ..  . ...+.++..+.++-.+++
T Consensus       116 Eid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il  195 (301)
T 3cf0_A          116 ELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAIL  195 (301)
T ss_dssp             STTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHH
T ss_pred             ChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHH
Confidence            995310              0012344444432  23456677777765322 11 11  2 347889999999988888


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCChH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                      ......... ....+    ...+++.+.|+|=
T Consensus       196 ~~~l~~~~~-~~~~~----~~~la~~~~g~sg  222 (301)
T 3cf0_A          196 KANLRKSPV-AKDVD----LEFLAKMTNGFSG  222 (301)
T ss_dssp             HHHHTTSCB-CSSCC----HHHHHHTCSSCCH
T ss_pred             HHHHccCCC-Cccch----HHHHHHHcCCCCH
Confidence            776532221 22222    3356667777764

>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=96.62  E-value=0.013  Score=57.89  Aligned_cols=154  Identities=16%  Similarity=0.093  Sum_probs=78.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.+++  +..    +.-++.+....        +..... +..  .........   ......+.+|+||
T Consensus       175 ppGtGKT~lA~aia~--~~~----~~~~~~v~~~~--------l~~~~~-g~~--~~~~~~~f~---~a~~~~~~vl~iD  234 (444)
T 2zan_A          175 PPGTGKSYLAKAVAT--EAN----NSTFFSISSSD--------LVSKWL-GES--EKLVKNLFQ---LARENKPSIIFID  234 (444)
T ss_dssp             STTSSHHHHHHHHHH--HCC----SSEEEEECCC------------------C--CCTHHHHHH---HHHHSCSEEEEES
T ss_pred             CCCCCHHHHHHHHHH--HcC----CCCEEEEeHHH--------HHhhhc-chH--HHHHHHHHH---HHHHcCCeEEEEe
Confidence            479999999999998  431    12233333221        111111 001  111222221   1223467899999


Q ss_pred             CCCCCCc-------cCh----hHHHHhhcC---CCCCcEEEEEeCchHHH-HH-hCC-cceEeCCCCChhhHHHHHHHhh
Q 046115           81 DVWNEDY-------YKW----EPFYKCLKN---SLHESKILITTRKETVA-RI-MGS-THVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        81 dv~~~~~-------~~~----~~~~~~~~~---~~~~~~iLiTtr~~~~~-~~-~~~-~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      +++....       ...    ..+...+..   ...+..||.||..+... .. ... ...+.++..+.++-..++....
T Consensus       235 Eid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l  314 (444)
T 2zan_A          235 EIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHL  314 (444)
T ss_dssp             CTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHH
T ss_pred             chHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHH
Confidence            9965310       011    223332322   23456677677654321 11 122 2467788888888888887765


Q ss_pred             hCCCCCCCCchHHHHHHHHHHHcCCC-hHHHHHHHH
Q 046115          144 ISGKTIGKRENLEKIGREIVKKCKGL-PLAAKTIAS  178 (505)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~g~-Plal~~~~~  178 (505)
                      .....    .-.......|++.+.|+ +-.|..+..
T Consensus       315 ~~~~~----~l~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          315 GSTQN----SLTEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             TTSCE----ECCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             hcCCC----CCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            32211    11234567888889884 555555544

>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=96.51  E-value=0.0077  Score=53.15  Aligned_cols=78  Identities=22%  Similarity=0.169  Sum_probs=45.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCC-----------CCCCChhcHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTP-----------GSAKDLVEFQSLMQHIEEC   69 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~-----------~~~~~~~~~~~~~~~l~~~   69 (505)
                      .+|+||||||..++.     ..-..++|++.....+...+. .+...++.           .......+..+....++..
T Consensus        28 ~~GsGKTtl~~~l~~-----~~~~~v~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  101 (220)
T 2cvh_A           28 PYASGKTTLALQTGL-----LSGKKVAYVDTEGGFSPERLV-QMAETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKT  101 (220)
T ss_dssp             STTSSHHHHHHHHHH-----HHCSEEEEEESSCCCCHHHHH-HHHHTTTCCHHHHHHHEEEECCTTTSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH-----HcCCcEEEEECCCCCCHHHHH-HHHHhcCCChHHHhhcEEEEecCCHHHHHHHHHHHHHH
Confidence            479999999999987     122467788877655554433 23333221           1111222223344555555


Q ss_pred             cCCceEEEEEeCCCC
Q 046115           70 VAGKKFLLVLDDVWN   84 (505)
Q Consensus        70 l~~~r~LlvlDdv~~   84 (505)
                      ...+.-++|+|.+..
T Consensus       102 ~~~~~~lliiD~~~~  116 (220)
T 2cvh_A          102 VDSNFALVVVDSITA  116 (220)
T ss_dssp             CCTTEEEEEEECCCC
T ss_pred             hhcCCCEEEEcCcHH
Confidence            544577999999854

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.51  E-value=0.015  Score=56.73  Aligned_cols=144  Identities=15%  Similarity=0.145  Sum_probs=70.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||.||+++++  +....|   +.++.+.-.+                ...........+.....-...+++|++|
T Consensus       214 PPGtGKT~lakAiA~--~~~~~~---~~v~~~~l~~----------------~~~Ge~e~~ir~lF~~A~~~aP~IifiD  272 (428)
T 4b4t_K          214 PPGTGKTMLVKAVAN--STKAAF---IRVNGSEFVH----------------KYLGEGPRMVRDVFRLARENAPSIIFID  272 (428)
T ss_dssp             CTTTTHHHHHHHHHH--HHTCEE---EEEEGGGTCC----------------SSCSHHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HhCCCe---EEEecchhhc----------------cccchhHHHHHHHHHHHHHcCCCeeech
Confidence            589999999999998  443332   2344332110                0001111112222222224568999999


Q ss_pred             CCCC--------C--Cc----cChhHHHHhhcC--CCCCcEEEEEeCchHH-HHHh---CC-cceEeCCCCCh-hhHHHH
Q 046115           81 DVWN--------E--DY----YKWEPFYKCLKN--SLHESKILITTRKETV-ARIM---GS-THVISVNVLSE-MECWSV  138 (505)
Q Consensus        81 dv~~--------~--~~----~~~~~~~~~~~~--~~~~~~iLiTtr~~~~-~~~~---~~-~~~~~l~~l~~-~ea~~L  138 (505)
                      +++.        .  ..    ..+..++..+..  ...+..||.||..++. ...+   +. ...+.++.+.. ++-..+
T Consensus       273 EiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~I  352 (428)
T 4b4t_K          273 EVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLI  352 (428)
T ss_dssp             CTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHH
T ss_pred             hhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHH
Confidence            9832        0  00    012334444442  2345567778876432 1111   22 34677766644 444556


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |..+.-. .......+    ...+++.+.|+-
T Consensus       353 l~~~~~~-~~l~~~~d----l~~lA~~t~G~s  379 (428)
T 4b4t_K          353 FGTIASK-MSLAPEAD----LDSLIIRNDSLS  379 (428)
T ss_dssp             HHHHHHS-SCBCTTCC----HHHHHHHTTTCC
T ss_pred             HHHHhcC-CCCCcccC----HHHHHHHCCCCC
Confidence            6555422 22122223    456777777654

>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=96.47  E-value=0.25  Score=46.56  Aligned_cols=48  Identities=17%  Similarity=0.197  Sum_probs=34.9

Q ss_pred             eEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHH
Q 046115          124 VISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKT  175 (505)
Q Consensus       124 ~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~  175 (505)
                      .+.+++.+.++-.+++.+.+.....    ....+.+..|++.+.|.|-.+..
T Consensus       174 ~~~Ld~~~~~~l~~iL~~~~~~~~~----~~~~~~~~~ia~~~~G~~R~a~~  221 (334)
T 1in4_A          174 ILELDFYTVKELKEIIKRAASLMDV----EIEDAAAEMIAKRSRGTPRIAIR  221 (334)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHTTC----CBCHHHHHHHHHTSTTCHHHHHH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHcCC----CcCHHHHHHHHHhcCCChHHHHH
Confidence            5789999999999999877532221    22356788999999999965433

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.36  E-value=0.013  Score=54.90  Aligned_cols=103  Identities=14%  Similarity=0.133  Sum_probs=52.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhc-HHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVE-FQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~-~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .+|+|||++|+.++.  .....-...+.++++...... ....+   ++......... .......+.   .....+++|
T Consensus        55 ~~GtGKt~la~~la~--~~~~~~~~~~~~~~~~~~~~~-~~~~l---~g~~~~~~~~~~~~~~~~~~~---~~~~~vl~l  125 (311)
T 4fcw_A           55 PTGVGKTELAKTLAA--TLFDTEEAMIRIDMTEYMEKH-AVSRL---IGAPPGYVGYEEGGQLTEAVR---RRPYSVILF  125 (311)
T ss_dssp             CSSSSHHHHHHHHHH--HHHSCGGGEEEEEGGGCCSTT-HHHHH---HCCCTTSTTTTTCCHHHHHHH---HCSSEEEEE
T ss_pred             CCCcCHHHHHHHHHH--HHcCCCcceEEeecccccccc-cHHHh---cCCCCccccccccchHHHHHH---hCCCeEEEE
Confidence            479999999999998  443332345566665543321 11222   22111100000 011112222   123469999


Q ss_pred             eCCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |++..........+...+....           ..+.+|.||..
T Consensus       126 DEi~~l~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~  169 (311)
T 4fcw_A          126 DAIEKAHPDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNL  169 (311)
T ss_dssp             ETGGGSCHHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEEST
T ss_pred             eChhhcCHHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEeccc
Confidence            9997665544555555554321           23447777765

>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=96.13  E-value=0.033  Score=55.56  Aligned_cols=150  Identities=11%  Similarity=0.106  Sum_probs=78.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||++|+.+++  +....   .+.+++.          .+...+.      ..........+.....+++.+|+||
T Consensus       246 ppGtGKT~lAraia~--~~~~~---fv~vn~~----------~l~~~~~------g~~~~~~~~~f~~A~~~~p~iLfLD  304 (489)
T 3hu3_A          246 PPGTGKTLIARAVAN--ETGAF---FFLINGP----------EIMSKLA------GESESNLRKAFEEAEKNAPAIIFID  304 (489)
T ss_dssp             STTSSHHHHHHHHHH--HCSSE---EEEEEHH----------HHHTSCT------THHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             cCCCCHHHHHHHHHH--HhCCC---EEEEEch----------Hhhhhhc------chhHHHHHHHHHHHHhcCCcEEEec
Confidence            479999999999988  43222   2334421          1111111      1112222333334445567899999


Q ss_pred             CCCCCCc-----------cChhHHHHhhcC--CCCCcEEEEEeCchHH-HHHh---CC-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNEDY-----------YKWEPFYKCLKN--SLHESKILITTRKETV-ARIM---GS-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~~~-----------~~~~~~~~~~~~--~~~~~~iLiTtr~~~~-~~~~---~~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      +++....           .....+...+..  ...+..||.||..... ....   +. ...+.+...+.++-.+++...
T Consensus       305 EId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~  384 (489)
T 3hu3_A          305 ELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIH  384 (489)
T ss_dssp             SHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHH
T ss_pred             chhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHH
Confidence            9832110           112334444442  2334556667765432 2111   12 346889999999999999877


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCC-hHHHHHH
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGL-PLAAKTI  176 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~-Plal~~~  176 (505)
                      ...... .....    ...+++.+.|+ +-.|..+
T Consensus       385 ~~~~~l-~~~~~----l~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          385 TKNMKL-ADDVD----LEQVANETHGHVGADLAAL  414 (489)
T ss_dssp             TTTSCB-CTTCC----HHHHHHTCTTCCHHHHHHH
T ss_pred             HhcCCC-cchhh----HHHHHHHccCCcHHHHHHH
Confidence            532221 12222    34566777664 4444444

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.10  E-value=0.043  Score=53.57  Aligned_cols=144  Identities=15%  Similarity=0.114  Sum_probs=74.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||.||+++++  +....|   +.++.+.              +.....  ..............-...+++|++|
T Consensus       251 PPGTGKTlLAkAiA~--e~~~~f---i~vs~s~--------------L~sk~v--Gesek~ir~lF~~Ar~~aP~IIfiD  309 (467)
T 4b4t_H          251 PPGTGKTLCARAVAN--RTDATF---IRVIGSE--------------LVQKYV--GEGARMVRELFEMARTKKACIIFFD  309 (467)
T ss_dssp             CTTSSHHHHHHHHHH--HHTCEE---EEEEGGG--------------GCCCSS--SHHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CCCCcHHHHHHHHHh--ccCCCe---EEEEhHH--------------hhcccC--CHHHHHHHHHHHHHHhcCCceEeec
Confidence            589999999999998  443332   2333322              110000  1111111222222234568999999


Q ss_pred             CCCCCCc--------------cChhHHHHhhcCC--CCCcEEEEEeCchHH-HHHh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDY--------------YKWEPFYKCLKNS--LHESKILITTRKETV-ARIM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~--------------~~~~~~~~~~~~~--~~~~~iLiTtr~~~~-~~~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++....              .....++..+...  ..+..||.||..+.. ...+   +. ...+.++..+.++-.++|
T Consensus       310 EiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Il  389 (467)
T 4b4t_H          310 EIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIF  389 (467)
T ss_dssp             CCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHH
T ss_pred             ccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHH
Confidence            9854210              0112233333332  334556677765432 1111   22 457888888888888888


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ..+...-. .....+    ...|++.+.|+-
T Consensus       390 k~~l~~~~-l~~dvd----l~~LA~~T~GfS  415 (467)
T 4b4t_H          390 RIHSKSMS-VERGIR----WELISRLCPNST  415 (467)
T ss_dssp             HHHHTTSC-BCSSCC----HHHHHHHCCSCC
T ss_pred             HHHhcCCC-CCCCCC----HHHHHHHCCCCC
Confidence            77653221 122223    356777887754

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=96.07  E-value=0.097  Score=47.30  Aligned_cols=150  Identities=10%  Similarity=0.059  Sum_probs=73.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||+||+.+++  .....   .+.++...-.+          ...      ..........+.......+.++++|
T Consensus        53 ~~GtGKT~la~~la~--~~~~~---~~~i~~~~~~~----------~~~------~~~~~~~~~~~~~a~~~~~~il~iD  111 (257)
T 1lv7_A           53 PPGTGKTLLAKAIAG--EAKVP---FFTISGSDFVE----------MFV------GVGASRVRDMFEQAKKAAPCIIFID  111 (257)
T ss_dssp             CTTSCHHHHHHHHHH--HHTCC---EEEECSCSSTT----------SCC------CCCHHHHHHHHHHHHTTCSEEEEET
T ss_pred             cCCCCHHHHHHHHHH--HcCCC---EEEEeHHHHHH----------Hhh------hhhHHHHHHHHHHHHHcCCeeehhh
Confidence            479999999999998  43222   23343322110          000      0111222223333334567899999


Q ss_pred             CCCCCCc--------------cChhHHHHhhcC--CCCCcEEEEEeCchHH-HHHh-C--C-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDY--------------YKWEPFYKCLKN--SLHESKILITTRKETV-ARIM-G--S-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~--------------~~~~~~~~~~~~--~~~~~~iLiTtr~~~~-~~~~-~--~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++....              .....+...+..  ...+..||.||..+.. .... .  . ...+.++..+.++-.+++
T Consensus       112 eid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il  191 (257)
T 1lv7_A          112 EIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL  191 (257)
T ss_dssp             THHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHH
T ss_pred             hhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHH
Confidence            9832110              011223333322  2334567777766532 1111 1  1 346777777888877787


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCC-ChHHHHHH
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKG-LPLAAKTI  176 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g-~Plal~~~  176 (505)
                      ....... .......    ...++..+.| .+--|..+
T Consensus       192 ~~~~~~~-~l~~~~~----~~~la~~~~G~~~~dl~~l  224 (257)
T 1lv7_A          192 KVHMRRV-PLAPDID----AAIIARGTPGFSGADLANL  224 (257)
T ss_dssp             HHHHTTS-CBCTTCC----HHHHHHTCTTCCHHHHHHH
T ss_pred             HHHHhcC-CCCcccc----HHHHHHHcCCCCHHHHHHH
Confidence            6654221 1111111    3456677777 56544433

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.07  E-value=0.044  Score=53.46  Aligned_cols=143  Identities=17%  Similarity=0.188  Sum_probs=76.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHH-HHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQ-HIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~-~l~~~l~~~r~Llvl   79 (505)
                      ++|.|||.||+++++  +....|   +.++.+.-              .   .......+.... .....-...+++|++
T Consensus       223 PPGtGKTllAkAiA~--e~~~~~---~~v~~s~l--------------~---sk~~Gese~~ir~~F~~A~~~~P~Iifi  280 (437)
T 4b4t_L          223 PPGTGKTLLAKAVAA--TIGANF---IFSPASGI--------------V---DKYIGESARIIREMFAYAKEHEPCIIFM  280 (437)
T ss_dssp             CTTSSHHHHHHHHHH--HHTCEE---EEEEGGGT--------------C---CSSSSHHHHHHHHHHHHHHHSCSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HhCCCE---EEEehhhh--------------c---cccchHHHHHHHHHHHHHHhcCCceeee
Confidence            589999999999998  443332   23443321              1   000111111222 222222456899999


Q ss_pred             eCCCCCC-------c-------cChhHHHHhhcCC--CCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNED-------Y-------YKWEPFYKCLKNS--LHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~-------~-------~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |+++..-       .       ..+..++..+...  ..+..||.||..++... .+   +. ...+.++..+.++-.++
T Consensus       281 DEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~I  360 (437)
T 4b4t_L          281 DEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEI  360 (437)
T ss_dssp             ECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHH
T ss_pred             ecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHH
Confidence            9985310       0       0122344444432  34567788887654322 11   11 34678888888888888


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |..+...-.. ....+    ...+++.+.|+.
T Consensus       361 l~~~~~~~~~-~~d~d----l~~lA~~t~G~s  387 (437)
T 4b4t_L          361 FKIHTAKVKK-TGEFD----FEAAVKMSDGFN  387 (437)
T ss_dssp             HHHHHHTSCB-CSCCC----HHHHHHTCCSCC
T ss_pred             HHHHhcCCCC-CcccC----HHHHHHhCCCCC
Confidence            8776533222 22223    456777887754

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.04  E-value=0.081  Score=51.25  Aligned_cols=103  Identities=10%  Similarity=0.026  Sum_probs=54.2

Q ss_pred             CceEEEEEeCCCCCC-----------ccChhHHHHhhc---C-CCCCcEEEEEeCchHH-HHH-hCCc-ceEeCCCCChh
Q 046115           72 GKKFLLVLDDVWNED-----------YYKWEPFYKCLK---N-SLHESKILITTRKETV-ARI-MGST-HVISVNVLSEM  133 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~-----------~~~~~~~~~~~~---~-~~~~~~iLiTtr~~~~-~~~-~~~~-~~~~l~~l~~~  133 (505)
                      ..+.+|+||+++...           ......+...+.   . ......||.||..... ... .... ..+.+...+.+
T Consensus       206 ~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~  285 (389)
T 3vfd_A          206 LQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEE  285 (389)
T ss_dssp             SSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHH
T ss_pred             cCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHH
Confidence            356799999995420           000112222222   1 1234455656655321 111 1222 46788889999


Q ss_pred             hHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChH-HHHHHHH
Q 046115          134 ECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPL-AAKTIAS  178 (505)
Q Consensus       134 ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-al~~~~~  178 (505)
                      +-.+++...+.....    .-..+.+..+++.+.|+.- +|..+..
T Consensus       286 ~r~~il~~~~~~~~~----~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          286 TRLLLLKNLLCKQGS----PLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             HHHHHHHHHHTTSCC----CSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCC----CCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999876633221    1123456788888887553 5544433

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.98  E-value=0.051  Score=50.35  Aligned_cols=15  Identities=20%  Similarity=0.386  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||+||+.+++
T Consensus        44 ppGtGKT~la~aiA~   58 (293)
T 3t15_A           44 GKGQGKSFQCELVFR   58 (293)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999998

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=95.98  E-value=0.0058  Score=52.41  Aligned_cols=110  Identities=21%  Similarity=0.158  Sum_probs=60.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCC---CCCHHHHHHHHH---HHcCCCCCCC-------hhcHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE---PFDEFRIARAII---ESLTPGSAKD-------LVEFQSLMQHIEE   68 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~---~~~~~~~~~~l~---~~l~~~~~~~-------~~~~~~~~~~l~~   68 (505)
                      .|.||||.|...+-  +..++=-.+.++-+..   ......++..+.   ..++.+..-.       ............+
T Consensus        37 ~GkGKTTaA~Glal--RA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~l~~a~~  114 (196)
T 1g5t_A           37 NGKGKTTAAFGTAA--RAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKR  114 (196)
T ss_dssp             SSSCHHHHHHHHHH--HHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH--HHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHHHHHHHH
Confidence            58999999977766  3333322344443322   233334444431   0001111101       1122334455555


Q ss_pred             HcCCc-eEEEEEeCCCC---CCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           69 CVAGK-KFLLVLDDVWN---EDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        69 ~l~~~-r~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      .+.+. -=|||||.+..   -.....+.+...+........|++|+|..
T Consensus       115 ~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          115 MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            66554 45999999832   23446677788787777788999999984

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.96  E-value=0.007  Score=51.63  Aligned_cols=15  Identities=27%  Similarity=0.251  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+|||++|+.+++
T Consensus        51 ~~G~GKT~la~~~~~   65 (187)
T 2p65_A           51 DPGVGKTAIVEGLAI   65 (187)
T ss_dssp             CGGGCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>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=95.87  E-value=0.11  Score=48.40  Aligned_cols=19  Identities=11%  Similarity=0.172  Sum_probs=16.1

Q ss_pred             ceEeCCCCChhhHHHHHHH
Q 046115          123 HVISVNVLSEMECWSVFQS  141 (505)
Q Consensus       123 ~~~~l~~l~~~ea~~Lf~~  141 (505)
                      ..+.+++++.++..+++..
T Consensus       195 ~~i~~~~~~~~~~~~il~~  213 (310)
T 1ofh_A          195 IRVELTALSAADFERILTE  213 (310)
T ss_dssp             EEEECCCCCHHHHHHHHHS
T ss_pred             ceEEcCCcCHHHHHHHHHh
Confidence            4689999999998888874

>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=95.86  E-value=0.027  Score=51.37  Aligned_cols=103  Identities=13%  Similarity=0.043  Sum_probs=48.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||++|+.+++  .....-...+.++++... ...+...+..... +.....  .......+..   ...-+|+||
T Consensus        37 ~~GtGKt~la~~i~~--~~~~~~~~~~~v~~~~~~-~~~~~~~l~g~~~-~~~~g~--~~~~~~~l~~---a~~~~l~lD  107 (265)
T 2bjv_A           37 ERGTGKELIASRLHY--LSSRWQGPFISLNCAALN-ENLLDSELFGHEA-GAFTGA--QKRHPGRFER---ADGGTLFLD  107 (265)
T ss_dssp             CTTSCHHHHHHHHHH--TSTTTTSCEEEEEGGGSC-HHHHHHHHHCCC------------CCCCHHHH---TTTSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--hcCccCCCeEEEecCCCC-hhHHHHHhcCCcc-cccccc--cccccchhhh---cCCcEEEEe
Confidence            379999999999998  332221234456666532 1111112211100 000000  0000001111   123489999


Q ss_pred             CCCCCCccChhHHHHhhcCC-----------CCCcEEEEEeCc
Q 046115           81 DVWNEDYYKWEPFYKCLKNS-----------LHESKILITTRK  112 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~-----------~~~~~iLiTtr~  112 (505)
                      ++..........+...+...           ....+||.||..
T Consensus       108 Ei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~  150 (265)
T 2bjv_A          108 ELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNA  150 (265)
T ss_dssp             SGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESS
T ss_pred             chHhcCHHHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCc
Confidence            99776544444555544432           134678888775

>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=95.65  E-value=0.012  Score=63.36  Aligned_cols=124  Identities=14%  Similarity=0.136  Sum_probs=57.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-----C-C-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-C-
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-----F-E-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-A-   71 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-----f-~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~-   71 (505)
                      .+|+|||++|+.+++  .+...     . . .+++++++.-..              +. ....+.......+...+ . 
T Consensus       199 ~pG~GKT~la~~la~--~l~~~~~p~~l~~~~~~~l~~~~l~~--------------g~-~~~g~~~~~l~~~~~~~~~~  261 (854)
T 1qvr_A          199 EPGVGKTAIVEGLAQ--RIVKGDVPEGLKGKRIVSLQMGSLLA--------------GA-KYRGEFEERLKAVIQEVVQS  261 (854)
T ss_dssp             CTTSCHHHHHHHHHH--HHHHTCSCTTSTTCEEEEECC--------------------------CHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHH--HHhcCCCchhhcCCeEEEeehHHhhc--------------cC-ccchHHHHHHHHHHHHHHhc
Confidence            479999999999998  44221     1 1 233444322100              00 00112222222222222 2 


Q ss_pred             CceEEEEEeCCCCCCc-------cChhHHHHhhcCCCCCcEEEEEeCchHHH-----HHh-CCcceEeCCCCChhhHHHH
Q 046115           72 GKKFLLVLDDVWNEDY-------YKWEPFYKCLKNSLHESKILITTRKETVA-----RIM-GSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~-------~~~~~~~~~~~~~~~~~~iLiTtr~~~~~-----~~~-~~~~~~~l~~l~~~ea~~L  138 (505)
                      +++.+|++|++..-..       ......+..+...+. ..+|.+|......     ... .....+.+++++.++..++
T Consensus       262 ~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~~~~-i~~I~at~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~i  340 (854)
T 1qvr_A          262 QGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGE-LRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISI  340 (854)
T ss_dssp             CSSEEEEECCC-------------------HHHHHTTC-CCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHH
T ss_pred             CCCeEEEEecHHHHhccCCccchHHHHHHHHHHHhCCC-eEEEEecCchHHhhhccCHHHHhCCceEEeCCCCHHHHHHH
Confidence            3678999999965320       111222333333333 3455555433221     111 2244688999999999999


Q ss_pred             HHHh
Q 046115          139 FQSL  142 (505)
Q Consensus       139 f~~~  142 (505)
                      +...
T Consensus       341 L~~~  344 (854)
T 1qvr_A          341 LRGL  344 (854)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            9644

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.55  E-value=0.036  Score=53.60  Aligned_cols=143  Identities=17%  Similarity=0.132  Sum_probs=74.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHH-HHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHI-EECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l-~~~l~~~r~Llvl   79 (505)
                      ++|.|||.||+++++  +....|   +.++.+.              +...   ...+.+.....+ ...-...+++|++
T Consensus       224 PPGTGKTlLAkAiA~--e~~~~f---i~v~~s~--------------l~sk---~vGesek~ir~lF~~Ar~~aP~IIfi  281 (437)
T 4b4t_I          224 APGTGKTLLAKAVAN--QTSATF---LRIVGSE--------------LIQK---YLGDGPRLCRQIFKVAGENAPSIVFI  281 (437)
T ss_dssp             STTTTHHHHHHHHHH--HHTCEE---EEEESGG--------------GCCS---SSSHHHHHHHHHHHHHHHTCSEEEEE
T ss_pred             CCCchHHHHHHHHHH--HhCCCE---EEEEHHH--------------hhhc---cCchHHHHHHHHHHHHHhcCCcEEEE
Confidence            589999999999998  443333   2233221              1100   111112222222 2222356899999


Q ss_pred             eCCCCCC------c--------cChhHHHHhhcC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNED------Y--------YKWEPFYKCLKN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~------~--------~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |+++...      .        ..+..++..+..  ...+..||.||..++... .+   +. ...+.++..+.++-.++
T Consensus       282 DEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~I  361 (437)
T 4b4t_I          282 DEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKI  361 (437)
T ss_dssp             EEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHH
T ss_pred             ehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHH
Confidence            9985310      0        012233333332  234556777887654432 11   12 34677888888888888


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |..+.-.-. .....+    ...+++.+.|+-
T Consensus       362 l~~~l~~~~-l~~dvd----l~~LA~~T~GfS  388 (437)
T 4b4t_I          362 LGIHTSKMN-LSEDVN----LETLVTTKDDLS  388 (437)
T ss_dssp             HHHHHTTSC-BCSCCC----HHHHHHHCCSCC
T ss_pred             HHHHhcCCC-CCCcCC----HHHHHHhCCCCC
Confidence            877653222 122223    446777777654

>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=95.55  E-value=0.15  Score=50.46  Aligned_cols=144  Identities=13%  Similarity=0.109  Sum_probs=76.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.++.  +....   .+.++.+.-...          +      ...........+.......+.+|++|
T Consensus        57 ppGtGKT~Laraia~--~~~~~---f~~is~~~~~~~----------~------~g~~~~~~r~lf~~A~~~~p~ILfID  115 (476)
T 2ce7_A           57 PPGTGKTLLARAVAG--EANVP---FFHISGSDFVEL----------F------VGVGAARVRDLFAQAKAHAPCIVFID  115 (476)
T ss_dssp             CTTSSHHHHHHHHHH--HHTCC---EEEEEGGGTTTC----------C------TTHHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HcCCC---eeeCCHHHHHHH----------H------hcccHHHHHHHHHHHHhcCCCEEEEe
Confidence            479999999999998  43222   223443321110          0      01111222333444445678999999


Q ss_pred             CCCCCCc--------------cChhHHHHhhcC--CCCCcEEEEEeCchHHHH-H-h--CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDY--------------YKWEPFYKCLKN--SLHESKILITTRKETVAR-I-M--GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~--------------~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~-~--~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++.-..              .....+...+..  ...+..||.||..++... . .  +. ...+.++..+.++-.+++
T Consensus       116 Eid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il  195 (476)
T 2ce7_A          116 EIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKIL  195 (476)
T ss_dssp             TGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHH
T ss_pred             chhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHH
Confidence            9954211              112334433332  124566777777654322 1 1  12 237788888888877888


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ..+.... ......+    ...+++.+.|+.
T Consensus       196 ~~~~~~~-~l~~~v~----l~~la~~t~G~s  221 (476)
T 2ce7_A          196 EIHTRNK-PLAEDVN----LEIIAKRTPGFV  221 (476)
T ss_dssp             HHHHTTS-CBCTTCC----HHHHHHTCTTCC
T ss_pred             HHHHHhC-CCcchhh----HHHHHHhcCCCc
Confidence            7665321 1111222    345778888877

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.54  E-value=0.063  Score=50.00  Aligned_cols=129  Identities=10%  Similarity=0.053  Sum_probs=60.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHH-HHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQ-SLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~-~~~~~l~~~l~~~r~Llvl   79 (505)
                      .+|+|||++|+.+++.  ....-...+.++++....  .++..   .+............ .....+...   ....|+|
T Consensus        33 e~GtGKt~lAr~i~~~--~~~~~~~~v~v~~~~~~~--~l~~~---~lfg~~~g~~tg~~~~~~g~~~~a---~~g~L~L  102 (304)
T 1ojl_A           33 DSGTGKELVARALHAC--SARSDRPLVTLNCAALNE--SLLES---ELFGHEKGAFTGADKRREGRFVEA---DGGTLFL  102 (304)
T ss_dssp             CTTSCHHHHHHHHHHH--SSCSSSCCCEEECSSCCH--HHHHH---HHTCCCSSCCC---CCCCCHHHHH---TTSEEEE
T ss_pred             CCCchHHHHHHHHHHh--CcccCCCeEEEeCCCCCh--HHHHH---HhcCccccccCchhhhhcCHHHhc---CCCEEEE
Confidence            3799999999999872  221111234466654322  22221   12111110000000 000011111   1246899


Q ss_pred             eCCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCch--H----------HHHHhCCcceEeCCCCC--hhh
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRKE--T----------VARIMGSTHVISVNVLS--EME  134 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~~--~----------~~~~~~~~~~~~l~~l~--~~e  134 (505)
                      |++..........+...+....           ...+||.||...  .          +...+. ...+.++++.  .+|
T Consensus       103 DEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~Rl~-~~~i~lPpL~eR~ed  181 (304)
T 1ojl_A          103 DEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLN-VVAIEMPSLRQRRED  181 (304)
T ss_dssp             ESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHHHHS-SEEEECCCSGGGGGG
T ss_pred             eccccCCHHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHhhcC-eeEEeccCHHHhHhh
Confidence            9997765444455555554331           346777777653  1          111111 2246788887  455


Q ss_pred             HHHHHH
Q 046115          135 CWSVFQ  140 (505)
Q Consensus       135 a~~Lf~  140 (505)
                      ...++.
T Consensus       182 i~~l~~  187 (304)
T 1ojl_A          182 IPLLAD  187 (304)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            554444

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=95.50  E-value=0.035  Score=53.92  Aligned_cols=98  Identities=15%  Similarity=0.191  Sum_probs=53.4

Q ss_pred             hhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch-
Q 046115          379 FEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-  455 (505)
Q Consensus       379 ~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-  455 (505)
                      +..+.+|+.+.+.       ++ +..++ ..+..+.+|+.+++..+  +..++. .+..+.+|+.+.+..+  +..++. 
T Consensus       293 F~~~~~L~~i~l~-------~~-i~~I~~~aF~~c~~L~~i~lp~~--v~~I~~~aF~~c~~L~~i~lp~~--l~~I~~~  360 (394)
T 4fs7_A          293 FYGCSSLTEVKLL-------DS-VKFIGEEAFESCTSLVSIDLPYL--VEEIGKRSFRGCTSLSNINFPLS--LRKIGAN  360 (394)
T ss_dssp             TTTCTTCCEEEEC-------TT-CCEECTTTTTTCTTCCEECCCTT--CCEECTTTTTTCTTCCEECCCTT--CCEECTT
T ss_pred             ccccccccccccc-------cc-cceechhhhcCCCCCCEEEeCCc--ccEEhHHhccCCCCCCEEEECcc--ccEehHH
Confidence            4445556666654       22 22332 33556666777766532  444432 4566677777776543  455544 


Q ss_pred             hccccccCceeecCCCcccccccccccCCccCCcc
Q 046115          456 GIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRV  490 (505)
Q Consensus       456 ~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L  490 (505)
                      .+.++++|+.+.+..+  +..+...|.++++|+.+
T Consensus       361 aF~~C~~L~~i~lp~~--~~~~~~~F~~c~~L~~I  393 (394)
T 4fs7_A          361 AFQGCINLKKVELPKR--LEQYRYDFEDTTKFKWI  393 (394)
T ss_dssp             TBTTCTTCCEEEEEGG--GGGGGGGBCTTCEEEEE
T ss_pred             HhhCCCCCCEEEECCC--CEEhhheecCCCCCcEE
Confidence            3666667777766544  23344456666666543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.46  E-value=0.033  Score=54.31  Aligned_cols=143  Identities=17%  Similarity=0.133  Sum_probs=74.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHH-HcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEE-CVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~-~l~~~r~Llvl   79 (505)
                      ++|.|||.||+++++  +....|   +.++.+.              +....   ....+.....+.. .-...+++|++
T Consensus       223 PPGTGKTllAkAiA~--e~~~~f---~~v~~s~--------------l~~~~---vGese~~ir~lF~~A~~~aP~Iifi  280 (434)
T 4b4t_M          223 PPGTGKTLLARACAA--QTNATF---LKLAAPQ--------------LVQMY---IGEGAKLVRDAFALAKEKAPTIIFI  280 (434)
T ss_dssp             CTTSSHHHHHHHHHH--HHTCEE---EEEEGGG--------------GCSSC---SSHHHHHHHHHHHHHHHHCSEEEEE
T ss_pred             cCCCCHHHHHHHHHH--HhCCCE---EEEehhh--------------hhhcc---cchHHHHHHHHHHHHHhcCCeEEee
Confidence            589999999999998  443332   2333222              11000   1111122222222 22345799999


Q ss_pred             eCCCCC-----C-c--------cChhHHHHhhcCC--CCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNE-----D-Y--------YKWEPFYKCLKNS--LHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~-----~-~--------~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      |+++..     . .        ..+..++..+...  ..+..||.||..++... .+   +. ...+.++..+.++-.++
T Consensus       281 DEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~I  360 (434)
T 4b4t_M          281 DELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQI  360 (434)
T ss_dssp             ECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHH
T ss_pred             cchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHH
Confidence            998320     0 0        0122344444433  23455666887654322 21   12 34778888888888888


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |+.+...-.. ....+    ...+++.+.|+-
T Consensus       361 l~~~~~~~~~-~~dvd----l~~lA~~t~G~s  387 (434)
T 4b4t_M          361 LQIHSRKMTT-DDDIN----WQELARSTDEFN  387 (434)
T ss_dssp             HHHHHHHSCB-CSCCC----HHHHHHHCSSCC
T ss_pred             HHHHhcCCCC-CCcCC----HHHHHHhCCCCC
Confidence            8766532221 22223    356777887754

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.45  E-value=0.26  Score=45.01  Aligned_cols=121  Identities=13%  Similarity=0.118  Sum_probs=63.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r~Llvl   79 (505)
                      ++|+||||||+.++.  ....   ..+.++...-.+                 .........+..+.+.. ...+.++++
T Consensus        52 p~GtGKTtLakala~--~~~~---~~i~i~g~~l~~-----------------~~~~~~~~~i~~vf~~a~~~~p~i~~~  109 (274)
T 2x8a_A           52 PPGCGKTLLAKAVAN--ESGL---NFISVKGPELLN-----------------MYVGESERAVRQVFQRAKNSAPCVIFF  109 (274)
T ss_dssp             STTSCHHHHHHHHHH--HTTC---EEEEEETTTTCS-----------------STTHHHHHHHHHHHHHHHHTCSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HcCC---CEEEEEcHHHHh-----------------hhhhHHHHHHHHHHHHHHhcCCCeEee
Confidence            479999999999998  3322   234454332110                 00111112222222222 345789999


Q ss_pred             eCCCCCCc-----------cChhHHHHhhcCC--CCCcEEEEEeCchHHHHH-h---CC-cceEeCCCCChhhHHHHHHH
Q 046115           80 DDVWNEDY-----------YKWEPFYKCLKNS--LHESKILITTRKETVARI-M---GS-THVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        80 Ddv~~~~~-----------~~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~~-~---~~-~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      |++.....           .....+...+...  ....-++.+|..+.+... .   +. ...+.++..+.++-.+++..
T Consensus       110 Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~  189 (274)
T 2x8a_A          110 DEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKT  189 (274)
T ss_dssp             ETCTTTCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHH
T ss_pred             ehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHH
Confidence            99854210           0112233333221  234456667776654221 1   12 45678888899888888877


Q ss_pred             hh
Q 046115          142 LA  143 (505)
Q Consensus       142 ~~  143 (505)
                      ..
T Consensus       190 ~~  191 (274)
T 2x8a_A          190 IT  191 (274)
T ss_dssp             HT
T ss_pred             HH
Confidence            65

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.43  E-value=0.036  Score=58.89  Aligned_cols=120  Identities=15%  Similarity=0.231  Sum_probs=64.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||++|+.+++  ...+.-...+.++++...+.              ....   .......++.   ....+|+||
T Consensus       529 p~GtGKT~lA~ala~--~l~~~~~~~i~i~~s~~~~~--------------~~~~---~~~l~~~~~~---~~~~vl~lD  586 (758)
T 3pxi_A          529 PTGVGKTELARALAE--SIFGDEESMIRIDMSEYMEK--------------HSTS---GGQLTEKVRR---KPYSVVLLD  586 (758)
T ss_dssp             CTTSSHHHHHHHHHH--HHHSCTTCEEEEEGGGGCSS--------------CCCC------CHHHHHH---CSSSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HhcCCCcceEEEechhcccc--------------cccc---cchhhHHHHh---CCCeEEEEe
Confidence            479999999999998  44333334556665542211              0000   1111111211   233489999


Q ss_pred             CCCCCCccChhHHHHhhcCC-----------CCCcEEEEEeCc-----hHH----HHH-----hCC-cceEeCCCCChhh
Q 046115           81 DVWNEDYYKWEPFYKCLKNS-----------LHESKILITTRK-----ETV----ARI-----MGS-THVISVNVLSEME  134 (505)
Q Consensus        81 dv~~~~~~~~~~~~~~~~~~-----------~~~~~iLiTtr~-----~~~----~~~-----~~~-~~~~~l~~l~~~e  134 (505)
                      ++..........+...+...           ...+.||.||..     ..+    ...     ... ...+.+.+++.++
T Consensus       587 Ei~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~  666 (758)
T 3pxi_A          587 AIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKH  666 (758)
T ss_dssp             CGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHH
T ss_pred             CccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHH
Confidence            99776655556666655542           135678888873     111    111     122 2478888898888


Q ss_pred             HHHHHHHh
Q 046115          135 CWSVFQSL  142 (505)
Q Consensus       135 a~~Lf~~~  142 (505)
                      ..+++...
T Consensus       667 ~~~i~~~~  674 (758)
T 3pxi_A          667 LTEIVSLM  674 (758)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77776554

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.36  E-value=0.0063  Score=56.99  Aligned_cols=29  Identities=21%  Similarity=0.180  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHhcCcccc-cCCCceEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-RNFEKRTWVCV   31 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-~~f~~~~wv~~   31 (505)
                      .+|+|||+||..+++  ... ..-..++++++
T Consensus       160 ~~GtGKT~La~aia~--~~~~~~g~~v~~~~~  189 (308)
T 2qgz_A          160 DMGIGKSYLLAAMAH--ELSEKKGVSTTLLHF  189 (308)
T ss_dssp             STTSSHHHHHHHHHH--HHHHHSCCCEEEEEH
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCCcEEEEEH
Confidence            479999999999998  444 33334556654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=95.23  E-value=0.019  Score=57.25  Aligned_cols=67  Identities=16%  Similarity=0.095  Sum_probs=35.2

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHH-------HhCCcceEeCCCCChhhHHHHHHHhh
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVAR-------IMGSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-------~~~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      ..++.+|++|.  ..   .....+......+ ..++|.+|.......       .......+.++..+.++..+++....
T Consensus       265 ~~~~~iLfiD~--~~---~a~~~L~~~L~~g-~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~  338 (468)
T 3pxg_A          265 QAGNIILFIDA--AI---DASNILKPSLARG-ELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLR  338 (468)
T ss_dssp             TCCCCEEEECC-------------CCCTTSS-SCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             hcCCeEEEEeC--ch---hHHHHHHHhhcCC-CEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHH
Confidence            35678899992  11   1111222222222 345555554433111       11234578999999999999998654

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.13  E-value=0.012  Score=48.14  Aligned_cols=38  Identities=5%  Similarity=-0.040  Sum_probs=24.0

Q ss_pred             EEEEEeCCCCCCccChhHHHHhhcCC-CCCcEEEEEeCc
Q 046115           75 FLLVLDDVWNEDYYKWEPFYKCLKNS-LHESKILITTRK  112 (505)
Q Consensus        75 ~LlvlDdv~~~~~~~~~~~~~~~~~~-~~~~~iLiTtr~  112 (505)
                      -.|++|++..........+...+... ..+.++|.||..
T Consensus        77 ~~l~lDei~~l~~~~q~~Ll~~l~~~~~~~~~iI~~tn~  115 (143)
T 3co5_A           77 GVLYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCSY  115 (143)
T ss_dssp             SEEEEEECTTCCHHHHHHHHHHHHHHTTTTCEEEEEEEE
T ss_pred             CeEEEeChHHCCHHHHHHHHHHHHhCCCCCEEEEEecCC
Confidence            47889999776544445555555443 345678877763

>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=95.11  E-value=0.038  Score=49.41  Aligned_cols=83  Identities=16%  Similarity=0.113  Sum_probs=46.0

Q ss_pred             CCCCcHHHHHHHHhcCccccc----CCCceEEEEeCCCCCHHHHHHHHHHHcCCCC-----------CCChhcHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVER----NFEKRTWVCVSEPFDEFRIARAIIESLTPGS-----------AKDLVEFQSLMQH   65 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~----~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~-----------~~~~~~~~~~~~~   65 (505)
                      .+|+||||||+.++.......    .-..++|++....+....+ ..++..++...           .....+..+....
T Consensus        32 ~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (243)
T 1n0w_A           32 EFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL-LAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQ  110 (243)
T ss_dssp             CTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH-HHHHHHcCCCHHHHhhCeEEEecCCHHHHHHHHHH
Confidence            479999999999987211111    2357889987775554433 33444443221           1111222222333


Q ss_pred             HHHHcC-CceEEEEEeCCCC
Q 046115           66 IEECVA-GKKFLLVLDDVWN   84 (505)
Q Consensus        66 l~~~l~-~~r~LlvlDdv~~   84 (505)
                      +...+. .+.-++|+|.+..
T Consensus       111 ~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          111 ASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHhcCCceEEEEeCchH
Confidence            444443 4677999999854

>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=95.04  E-value=0.0077  Score=55.91  Aligned_cols=61  Identities=23%  Similarity=0.350  Sum_probs=38.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEe--CCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCV--SEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~--~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      ++|+|||+||.+++.  .   .-..++|++.  .+..+.               .  ..+.++..+.+.+.+.+.+ ++|
T Consensus       131 pPGsGKTtLAlqlA~--~---~G~~VlyIs~~~eE~v~~---------------~--~~~le~~l~~i~~~l~~~~-LLV  187 (331)
T 2vhj_A          131 KGNSGKTPLVHALGE--A---LGGKDKYATVRFGEPLSG---------------Y--NTDFNVFVDDIARAMLQHR-VIV  187 (331)
T ss_dssp             SCSSSHHHHHHHHHH--H---HHTTSCCEEEEBSCSSTT---------------C--BCCHHHHHHHHHHHHHHCS-EEE
T ss_pred             CCCCCHHHHHHHHHH--h---CCCCEEEEEecchhhhhh---------------h--hcCHHHHHHHHHHHHhhCC-EEE
Confidence            589999999999987  3   1123557777  332110               0  0344555555566665555 999


Q ss_pred             EeCCCC
Q 046115           79 LDDVWN   84 (505)
Q Consensus        79 lDdv~~   84 (505)
                      +|++..
T Consensus       188 IDsI~a  193 (331)
T 2vhj_A          188 IDSLKN  193 (331)
T ss_dssp             EECCTT
T ss_pred             Eecccc
Confidence            999954

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=94.82  E-value=0.064  Score=49.62  Aligned_cols=77  Identities=10%  Similarity=0.156  Sum_probs=48.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC--CceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHH-HHHHHHH--c-
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF--EKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSL-MQHIEEC--V-   70 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f--~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~-~~~l~~~--l-   70 (505)
                      .+|+||||||.+++.  ...+.+  ..++||+....++..     .+++++.....    ...+.++. ...+...  + 
T Consensus        36 ~pGsGKTtL~Lq~~~--~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~i~  108 (333)
T 3io5_A           36 PSKSFKSNFGLTMVS--SYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDAIE  108 (333)
T ss_dssp             SSSSSHHHHHHHHHH--HHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHHhh
Confidence            479999999998887  444443  357799988888764     25666643221    12344444 3333332  3 


Q ss_pred             CCceEEEEEeCCCC
Q 046115           71 AGKKFLLVLDDVWN   84 (505)
Q Consensus        71 ~~~r~LlvlDdv~~   84 (505)
                      ..+.-++|+|.+..
T Consensus       109 ~~~~~lvVIDSI~a  122 (333)
T 3io5_A          109 RGEKVVVFIDSLGN  122 (333)
T ss_dssp             TTCCEEEEEECSTT
T ss_pred             ccCceEEEEecccc
Confidence            44678999999955

>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=94.76  E-value=0.0096  Score=54.46  Aligned_cols=72  Identities=7%  Similarity=0.020  Sum_probs=39.7

Q ss_pred             CceEEEEEeCCCCCCc---------------cChhHHHHhhcCC---CCCcEEEEEeCchHHHH-H-hC--C-cceEeCC
Q 046115           72 GKKFLLVLDDVWNEDY---------------YKWEPFYKCLKNS---LHESKILITTRKETVAR-I-MG--S-THVISVN  128 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~---------------~~~~~~~~~~~~~---~~~~~iLiTtr~~~~~~-~-~~--~-~~~~~l~  128 (505)
                      ..+.+|++|+++....               ..+..+...+...   .....|+.||....... . ..  . ...+.++
T Consensus       102 ~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~  181 (268)
T 2r62_A          102 QAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVD  181 (268)
T ss_dssp             SCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCC
T ss_pred             cCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEec
Confidence            3567999999954211               1123333333322   12355677776553211 1 11  1 2467788


Q ss_pred             CCChhhHHHHHHHhh
Q 046115          129 VLSEMECWSVFQSLA  143 (505)
Q Consensus       129 ~l~~~ea~~Lf~~~~  143 (505)
                      ..+.++-.+++....
T Consensus       182 ~p~~~~r~~il~~~~  196 (268)
T 2r62_A          182 KPDFNGRVEILKVHI  196 (268)
T ss_dssp             CCCTTTHHHHHHHHT
T ss_pred             CcCHHHHHHHHHHHH
Confidence            888888888887654

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=94.66  E-value=0.05  Score=43.42  Aligned_cols=47  Identities=21%  Similarity=0.288  Sum_probs=33.6

Q ss_pred             ccccc--ccCccccCCCCcceeeccCCccccccchh-hhcCCCCcEEecCCCc
Q 046115          399 NNLIK--EIPTNIEKLLHLKYLNLKGQKKIEKLPET-LCELYNLERLNVDDCQ  448 (505)
Q Consensus       399 ~~~~~--~~p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~  448 (505)
                      ++.+.  .+|..+  ..+|++|+|++|. ++.+|.. +..+++|+.|+|++|+
T Consensus        17 ~~~L~~~~vP~~l--p~~l~~L~Ls~N~-l~~l~~~~f~~l~~L~~L~L~~NP   66 (130)
T 3rfe_A           17 RRGLTWASLPTAF--PVDTTELVLTGNN-LTALPPGLLDALPALRTAHLGANP   66 (130)
T ss_dssp             SSCCCTTTSCSCC--CTTCSEEECTTSC-CSSCCTTTGGGCTTCCEEECCSSC
T ss_pred             CCCCccccCCCCC--CcCCCEEECCCCc-CCccChhhhhhccccCEEEecCCC
Confidence            45555  666543  4468888888888 7777664 4678888888888876

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=94.58  E-value=0.071  Score=50.91  Aligned_cols=77  Identities=17%  Similarity=0.110  Sum_probs=48.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcCC-ceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVAG-KKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~~-~r~   75 (505)
                      .+|+|||+||.+++.  .....-..++|++....++..     .+..++....    ....+.++..+.+....+. ..-
T Consensus        82 ~pGsGKTtlal~la~--~~~~~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~~~~~  154 (366)
T 1xp8_A           82 PESGGKTTLALAIVA--QAQKAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  154 (366)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             CCCCChHHHHHHHHH--HHHHCCCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHHHHhcCCCC
Confidence            379999999999987  443333468899988877654     2344442211    1123455555555555443 456


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      +||+|.+..
T Consensus       155 lVVIDsl~~  163 (366)
T 1xp8_A          155 VVVVDSVAA  163 (366)
T ss_dssp             EEEEECTTT
T ss_pred             EEEEeChHH
Confidence            899999854

>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=94.53  E-value=0.13  Score=54.36  Aligned_cols=144  Identities=12%  Similarity=0.109  Sum_probs=76.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+++++  +....|   +.++..          ++....      ...................+++|++|
T Consensus       246 PPGTGKT~LAraiA~--elg~~~---~~v~~~----------~l~sk~------~gese~~lr~lF~~A~~~~PsIIfID  304 (806)
T 3cf2_A          246 PPGTGKTLIARAVAN--ETGAFF---FLINGP----------EIMSKL------AGESESNLRKAFEEAEKNAPAIIFID  304 (806)
T ss_dssp             CTTSCHHHHHHHHHT--TTTCEE---EEEEHH----------HHHSSC------TTHHHHHHHHHHHHHTTSCSEEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HhCCeE---EEEEhH----------Hhhccc------chHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            589999999999998  443332   344422          111111      11122223333344445678999999


Q ss_pred             CCCCCCc------cC-----hhHHHHhhcCC--CCCcEEEEEeCchHHH-HHhC---C-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNEDY------YK-----WEPFYKCLKNS--LHESKILITTRKETVA-RIMG---S-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~~~------~~-----~~~~~~~~~~~--~~~~~iLiTtr~~~~~-~~~~---~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      +++.-..      ..     ..++...+...  ..+..||.||..++.. ..+.   . ...+.++..+.++-.++|+.+
T Consensus       305 EiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~  384 (806)
T 3cf2_A          305 ELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIH  384 (806)
T ss_dssp             SGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHT
T ss_pred             hhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHH
Confidence            9854210      01     12233323222  2345567777765432 2211   2 347888888888888888766


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ...... ....+    ...+++.+.|+.
T Consensus       385 l~~~~~-~~dvd----l~~lA~~T~Gfs  407 (806)
T 3cf2_A          385 TKNMKL-ADDVD----LEQVANETHGHV  407 (806)
T ss_dssp             CSSSEE-CTTCC----HHHHHHHCCSCC
T ss_pred             hcCCCC-CcccC----HHHHHHhcCCCC
Confidence            422111 22223    456777887764

>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=94.38  E-value=0.069  Score=54.17  Aligned_cols=41  Identities=10%  Similarity=0.171  Sum_probs=24.6

Q ss_pred             CcEEEEEeCchHH-H-HHhCCcceEeCCCCChhhHHHHHHHhh
Q 046115          103 ESKILITTRKETV-A-RIMGSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus       103 ~~~iLiTtr~~~~-~-~~~~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      ...+|.||..... . .......++.+..++.++-.+++..+.
T Consensus       224 ~v~iI~ttN~~~~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          224 KVLFIATANNLATIPGPLRDRMEIINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             SCEEEEECSSTTTSCHHHHHHEEEEECCCCCHHHHHHHHHHTH
T ss_pred             ceEEEeccCccccCCHHHHhhcceeeeCCCCHHHHHHHHHHHH
Confidence            3456666665321 1 111123478899999999888887654

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=94.32  E-value=0.13  Score=49.75  Aligned_cols=124  Identities=15%  Similarity=0.237  Sum_probs=82.1

Q ss_pred             cCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccc
Q 046115          350 GNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEK  428 (505)
Q Consensus       350 ~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~  428 (505)
                      ..|.++..|+.+.+..+...    .-...|..+..|+.+.+.       .. +..++ ..|..+.+|+.+.|..+  ++.
T Consensus       259 ~aF~~c~~L~~i~lp~~~~~----I~~~aF~~c~~L~~i~l~-------~~-i~~I~~~aF~~c~~L~~i~lp~~--v~~  324 (394)
T 4gt6_A          259 HAFDSCAYLASVKMPDSVVS----IGTGAFMNCPALQDIEFS-------SR-ITELPESVFAGCISLKSIDIPEG--ITQ  324 (394)
T ss_dssp             TTTTTCSSCCEEECCTTCCE----ECTTTTTTCTTCCEEECC-------TT-CCEECTTTTTTCTTCCEEECCTT--CCE
T ss_pred             ceeeecccccEEecccccce----ecCcccccccccccccCC-------Cc-ccccCceeecCCCCcCEEEeCCc--ccE
Confidence            34667888888887655432    123346778889988885       33 34443 34678899999999753  555


Q ss_pred             cch-hhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          429 LPE-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       429 lp~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      ++. .+..+.+|+.+.|.. . +..++. .+.++++|+.+.+.++..  .. ..+..+.+|+.+.+
T Consensus       325 I~~~aF~~C~~L~~i~ip~-s-v~~I~~~aF~~C~~L~~i~~~~~~~--~~-~~~~~~~~L~~i~i  385 (394)
T 4gt6_A          325 ILDDAFAGCEQLERIAIPS-S-VTKIPESAFSNCTALNNIEYSGSRS--QW-NAISTDSGLQNLPV  385 (394)
T ss_dssp             ECTTTTTTCTTCCEEEECT-T-CCBCCGGGGTTCTTCCEEEESSCHH--HH-HTCBCCCCC-----
T ss_pred             ehHhHhhCCCCCCEEEECc-c-cCEEhHhHhhCCCCCCEEEECCcee--eh-hhhhccCCCCEEEe
Confidence            644 577889999999965 2 667765 488899999999988752  22 34666677776654

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=94.30  E-value=0.21  Score=47.97  Aligned_cols=119  Identities=13%  Similarity=0.215  Sum_probs=62.9

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLP  430 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp  430 (505)
                      +.++..|+.+.+..+- ...   -...+..+.+|+.+.+.       .+ +..++ ..+..+.+|+.+.+.++. +..++
T Consensus       236 f~~~~~L~~i~lp~~v-~~I---~~~aF~~~~~l~~i~l~-------~~-i~~i~~~aF~~c~~L~~i~l~~~~-i~~I~  302 (379)
T 4h09_A          236 FYGMKALDEIAIPKNV-TSI---GSFLLQNCTALKTLNFY-------AK-VKTVPYLLCSGCSNLTKVVMDNSA-IETLE  302 (379)
T ss_dssp             TTTCSSCCEEEECTTC-CEE---CTTTTTTCTTCCEEEEC-------CC-CSEECTTTTTTCTTCCEEEECCTT-CCEEC
T ss_pred             ccCCccceEEEcCCCc-cEe---Cccccceeehhcccccc-------cc-ceeccccccccccccccccccccc-cceeh
Confidence            3355566665554431 111   12234555566666664       22 22332 235566777777776665 55554


Q ss_pred             h-hhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccc-cccccCCccC
Q 046115          431 E-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYL-PAGIGELIRL  487 (505)
Q Consensus       431 ~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~-p~~i~~l~~L  487 (505)
                      . .+..+.+|+.+.|..  .++.++. .+.++++|+.+.+..+  +..+ ...|.++..+
T Consensus       303 ~~aF~~c~~L~~i~lp~--~l~~I~~~aF~~C~~L~~i~ip~~--v~~I~~~aF~~c~~~  358 (379)
T 4h09_A          303 PRVFMDCVKLSSVTLPT--ALKTIQVYAFKNCKALSTISYPKS--ITLIESGAFEGSSIT  358 (379)
T ss_dssp             TTTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCCCCCCCTT--CCEECTTTTTTSSCC
T ss_pred             hhhhcCCCCCCEEEcCc--cccEEHHHHhhCCCCCCEEEECCc--cCEEchhHhhCCCCC
Confidence            3 456677777777754  2555554 3666677777776543  2233 2345555433

>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=94.28  E-value=0.2  Score=49.60  Aligned_cols=94  Identities=14%  Similarity=0.087  Sum_probs=58.8

Q ss_pred             EEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEE---------eC----chHH-HHHhCCcceEeCCCCChhhHHHHHH
Q 046115           75 FLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILIT---------TR----KETV-ARIMGSTHVISVNVLSEMECWSVFQ  140 (505)
Q Consensus        75 ~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiT---------tr----~~~~-~~~~~~~~~~~l~~l~~~ea~~Lf~  140 (505)
                      -++++|++..........+...+.......-|+.|         |.    ...+ .........+.+.+++.++..+++.
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~~~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL~  376 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIK  376 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTTCCEEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccCCCEEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHHH
Confidence            48999999777666677777777766555434455         33    1111 1122334467999999999999997


Q ss_pred             HhhhCCCCCCCCchHHHHHHHHHHHc-CCChHH
Q 046115          141 SLAISGKTIGKRENLEKIGREIVKKC-KGLPLA  172 (505)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~i~~~~-~g~Pla  172 (505)
                      ..+...+.    .-.++++..|++.+ +|.|..
T Consensus       377 ~~~~~~~~----~~~~~~~~~i~~~a~~g~~r~  405 (456)
T 2c9o_A          377 IRAQTEGI----NISEEALNHLGEIGTKTTLRY  405 (456)
T ss_dssp             HHHHHHTC----CBCHHHHHHHHHHHHHSCHHH
T ss_pred             HHHHHhCC----CCCHHHHHHHHHHccCCCHHH
Confidence            76521111    11245567777777 777753

>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=94.27  E-value=0.14  Score=48.20  Aligned_cols=48  Identities=23%  Similarity=0.187  Sum_probs=31.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccC----CCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN----FEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~----f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||.+++........    -..++|++....++...+. .++..++
T Consensus       115 ~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g  166 (324)
T 2z43_A          115 EFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALG  166 (324)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTT
T ss_pred             CCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhC
Confidence            3799999999998863211111    2467899988877665544 3455554

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=94.26  E-value=0.98  Score=42.57  Aligned_cols=102  Identities=10%  Similarity=-0.058  Sum_probs=69.4

Q ss_pred             CCceEEEEEeCCCC-CCccChhHHHHhhcCCCCCcEEEEEeCc-------hHHHHHhC-CcceEeCCCCChhhHHHHHHH
Q 046115           71 AGKKFLLVLDDVWN-EDYYKWEPFYKCLKNSLHESKILITTRK-------ETVARIMG-STHVISVNVLSEMECWSVFQS  141 (505)
Q Consensus        71 ~~~r~LlvlDdv~~-~~~~~~~~~~~~~~~~~~~~~iLiTtr~-------~~~~~~~~-~~~~~~l~~l~~~ea~~Lf~~  141 (505)
                      -+++-++|+|++.. ........+...+....+++.+|+++.+       ..+.+.+. ....++..+++..+....+..
T Consensus        74 f~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~  153 (343)
T 1jr3_D           74 FASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAA  153 (343)
T ss_dssp             CCSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHH
Confidence            35567888999866 4444567788877766667777776643       23444433 346889999999999888877


Q ss_pred             hhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHH
Q 046115          142 LAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTI  176 (505)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~  176 (505)
                      .+...+.    .-.++++..+++.++|....+...
T Consensus       154 ~~~~~g~----~i~~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          154 RAKQLNL----ELDDAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             HHHHTTC----EECHHHHHHHHHSSTTCHHHHHHH
T ss_pred             HHHHcCC----CCCHHHHHHHHHHhchHHHHHHHH
Confidence            6533221    123567888999999988766553

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=94.15  E-value=0.22  Score=47.83  Aligned_cols=124  Identities=15%  Similarity=0.186  Sum_probs=86.1

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCcceeeccCCccccccc
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLP  430 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp  430 (505)
                      +..+.+|..+.+..+-.    ......+..+..|+.+.+.       .+ +..+ ...+..+.+|+.+.+..+  +..++
T Consensus       213 f~~~~~l~~i~~~~~~~----~i~~~~f~~~~~L~~i~lp-------~~-v~~I~~~aF~~~~~l~~i~l~~~--i~~i~  278 (379)
T 4h09_A          213 FSYGKNLKKITITSGVT----TLGDGAFYGMKALDEIAIP-------KN-VTSIGSFLLQNCTALKTLNFYAK--VKTVP  278 (379)
T ss_dssp             TTTCSSCSEEECCTTCC----EECTTTTTTCSSCCEEEEC-------TT-CCEECTTTTTTCTTCCEEEECCC--CSEEC
T ss_pred             cccccccceeeecccee----EEccccccCCccceEEEcC-------CC-ccEeCccccceeehhcccccccc--ceecc
Confidence            44667788877755422    1123346678889999886       33 3333 344667888999888643  55555


Q ss_pred             h-hhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCccccccc-ccccCCccCCccce
Q 046115          431 E-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRLRRVRE  492 (505)
Q Consensus       431 ~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L~~L~~  492 (505)
                      . .+..+.+|+.+.+.++. +..++. .+.++.+|+.+.+..+  +..++ ..|.+|++|+.+.+
T Consensus       279 ~~aF~~c~~L~~i~l~~~~-i~~I~~~aF~~c~~L~~i~lp~~--l~~I~~~aF~~C~~L~~i~i  340 (379)
T 4h09_A          279 YLLCSGCSNLTKVVMDNSA-IETLEPRVFMDCVKLSSVTLPTA--LKTIQVYAFKNCKALSTISY  340 (379)
T ss_dssp             TTTTTTCTTCCEEEECCTT-CCEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCCCCC
T ss_pred             ccccccccccccccccccc-cceehhhhhcCCCCCCEEEcCcc--ccEEHHHHhhCCCCCCEEEE
Confidence            4 46788999999998866 777765 4788899999999755  34444 45889999988865

>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=94.13  E-value=0.11  Score=49.29  Aligned_cols=48  Identities=17%  Similarity=0.144  Sum_probs=31.1

Q ss_pred             CCCCcHHHHHHHHhcCccccc----CCCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER----NFEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~----~f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||.+++.......    .-..++|++....++...+. .++..++
T Consensus       130 ~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g  181 (343)
T 1v5w_A          130 EFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFN  181 (343)
T ss_dssp             CTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcC
Confidence            379999999999887321211    22467799988877765544 3344444

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.11  E-value=0.2  Score=44.20  Aligned_cols=108  Identities=19%  Similarity=0.076  Sum_probs=54.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----------------------Chhc
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----------------------DLVE   58 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----------------------~~~~   58 (505)
                      .+|+|||||++.++.  .....=..++|++...  ....+...+ ..++.....                      ...+
T Consensus        31 ~~GsGKTtl~~~l~~--~~~~~~~~v~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (235)
T 2w0m_A           31 EPGTGKTIFSLHFIA--KGLRDGDPCIYVTTEE--SRDSIIRQA-KQFNWDFEEYIEKKLIIIDALMKEKEDQWSLVNLT  105 (235)
T ss_dssp             STTSSHHHHHHHHHH--HHHHHTCCEEEEESSS--CHHHHHHHH-HHTTCCCGGGBTTTEEEEECCC----CTTBCSSCC
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCeEEEEEccc--CHHHHHHHH-HHhcchHHHHhhCCEEEEeccccccCceeeecCCC
Confidence            379999999999986  3332223466776544  233333322 233211100                      0113


Q ss_pred             HHHHHHHHHHHc---CCceEEEEEeCCCCC---CccChhHHHHhhcCC--CCCcEEEEEeCch
Q 046115           59 FQSLMQHIEECV---AGKKFLLVLDDVWNE---DYYKWEPFYKCLKNS--LHESKILITTRKE  113 (505)
Q Consensus        59 ~~~~~~~l~~~l---~~~r~LlvlDdv~~~---~~~~~~~~~~~~~~~--~~~~~iLiTtr~~  113 (505)
                      .++....+...+   .-++.+||+|.....   +......+...+...  ..++.|+++|...
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~  168 (235)
T 2w0m_A          106 PEELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYA  168 (235)
T ss_dssp             HHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC--
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccC
Confidence            444444444433   223359999998532   222334444443321  3467888888765

>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=93.86  E-value=0.086  Score=56.06  Aligned_cols=100  Identities=17%  Similarity=0.237  Sum_probs=49.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r~Llvl   79 (505)
                      .+|+|||++|+.+++  ...   ...+.++++...+...     ...+. +........++. ..+...+ .....+|+|
T Consensus       496 ~~GtGKT~la~~la~--~l~---~~~~~i~~s~~~~~~~-----~~~l~-g~~~g~~g~~~~-~~l~~~~~~~~~~vl~l  563 (758)
T 1r6b_X          496 PTGVGKTEVTVQLSK--ALG---IELLRFDMSEYMERHT-----VSRLI-GAPPGYVGFDQG-GLLTDAVIKHPHAVLLL  563 (758)
T ss_dssp             STTSSHHHHHHHHHH--HHT---CEEEEEEGGGCSSSSC-----CSSSC-CCCSCSHHHHHT-THHHHHHHHCSSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--Hhc---CCEEEEechhhcchhh-----Hhhhc-CCCCCCcCcccc-chHHHHHHhCCCcEEEE
Confidence            479999999999998  442   2344556554322100     00111 111111111111 1111111 234679999


Q ss_pred             eCCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |++..........+...+....           ..+.||.||..
T Consensus       564 DEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~  607 (758)
T 1r6b_X          564 DEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNA  607 (758)
T ss_dssp             ETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECS
T ss_pred             eCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCc
Confidence            9997765545555655554321           23557777764

>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=93.79  E-value=0.098  Score=49.62  Aligned_cols=77  Identities=21%  Similarity=0.198  Sum_probs=46.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  .....=..++|++....++..     .+.+++....    ....+.++....+...++ .+.-
T Consensus        69 ppGsGKSTLal~la~--~~~~~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~~~~d  141 (356)
T 3hr8_A           69 QESSGKTTLALHAIA--EAQKMGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDELVRSGVVD  141 (356)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTSCCS
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHHHHhhhcCCC
Confidence            479999999999987  443332357799887777654     3444443211    122344555555554442 3455


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      ++|+|.+..
T Consensus       142 lvVIDSi~~  150 (356)
T 3hr8_A          142 LIVVDSVAA  150 (356)
T ss_dssp             EEEEECTTT
T ss_pred             eEEehHhhh
Confidence            888999844

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=93.63  E-value=0.11  Score=41.52  Aligned_cols=34  Identities=21%  Similarity=0.302  Sum_probs=23.2

Q ss_pred             ccceEEecccccCCccccccccCcc-ccCCCCcceeeccCCc
Q 046115          384 CLRALELQVRESWPRNNLIKEIPTN-IEKLLHLKYLNLKGQK  424 (505)
Q Consensus       384 ~L~~L~l~~~~~~~~~~~~~~~p~~-~~~l~~L~~L~l~~~~  424 (505)
                      +|+.|+|+       +|.+..+|.. +..+++|++|+|++|+
T Consensus        32 ~l~~L~Ls-------~N~l~~l~~~~f~~l~~L~~L~L~~NP   66 (130)
T 3rfe_A           32 DTTELVLT-------GNNLTALPPGLLDALPALRTAHLGANP   66 (130)
T ss_dssp             TCSEEECT-------TSCCSSCCTTTGGGCTTCCEEECCSSC
T ss_pred             CCCEEECC-------CCcCCccChhhhhhccccCEEEecCCC
Confidence            57777776       6666666544 4567777777777776

>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=93.50  E-value=0.21  Score=53.02  Aligned_cols=125  Identities=16%  Similarity=0.192  Sum_probs=63.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccC------CCceEE-EEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN------FEKRTW-VCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~------f~~~~w-v~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~   72 (505)
                      .+|+|||++|+.++.  .+...      ....+| ++.+.-             +. +. ......++....+...+ ..
T Consensus       215 ~~GtGKT~la~~la~--~l~~~~v~~~~~~~~~~~~~~~~l-------------~~-~~-~~~g~~e~~l~~~~~~~~~~  277 (758)
T 1r6b_X          215 ESGVGKTAIAEGLAW--RIVQGDVPEVMADCTIYSLDIGSL-------------LA-GT-KYRGDFEKRFKALLKQLEQD  277 (758)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHTCSCGGGTTCEEEECCCC----------------C-CC-CCSSCHHHHHHHHHHHHSSS
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCChhhcCCEEEEEcHHHH-------------hc-cc-cccchHHHHHHHHHHHHHhc
Confidence            479999999999987  33221      122222 222110             00 01 11122333333333333 34


Q ss_pred             ceEEEEEeCCCCC--------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH-------hCCcceEeCCCCChhhHHH
Q 046115           73 KKFLLVLDDVWNE--------DYYKWEPFYKCLKNSLHESKILITTRKETVARI-------MGSTHVISVNVLSEMECWS  137 (505)
Q Consensus        73 ~r~LlvlDdv~~~--------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~-------~~~~~~~~l~~l~~~ea~~  137 (505)
                      ++.+|++|++...        .......++..+... ....+|.+|........       ......+.++..+.++..+
T Consensus       278 ~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~-~~~~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~  356 (758)
T 1r6b_X          278 TNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS-GKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQ  356 (758)
T ss_dssp             SCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS-CCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHH
T ss_pred             CCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhC-CCeEEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHH
Confidence            5789999999653        111122233333333 34566666655432211       1123468899999999888


Q ss_pred             HHHHhh
Q 046115          138 VFQSLA  143 (505)
Q Consensus       138 Lf~~~~  143 (505)
                      ++....
T Consensus       357 il~~l~  362 (758)
T 1r6b_X          357 IINGLK  362 (758)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=93.47  E-value=0.07  Score=56.72  Aligned_cols=67  Identities=16%  Similarity=0.112  Sum_probs=36.2

Q ss_pred             CCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHH-------HhCCcceEeCCCCChhhHHHHHHHhh
Q 046115           71 AGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVAR-------IMGSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        71 ~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~-------~~~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      ..++.+|++|.-  .   .....+...... ...++|.||.......       .......+.++..+.++..+++....
T Consensus       265 ~~~~~iLfiD~~--~---~~~~~L~~~l~~-~~v~~I~at~~~~~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~  338 (758)
T 3pxi_A          265 QAGNIILFIDAA--I---DASNILKPSLAR-GELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLR  338 (758)
T ss_dssp             TCCCCEEEECC-------------CCCTTS-SSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             hcCCEEEEEcCc--h---hHHHHHHHHHhc-CCEEEEeCCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence            456789999921  1   111222222222 3355666665443111       01134578999999999999998654

>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=93.39  E-value=0.038  Score=48.71  Aligned_cols=104  Identities=13%  Similarity=-0.039  Sum_probs=54.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC-ChhcHHHHHHHHHHHcCCc-eEEEEE
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK-DLVEFQSLMQHIEECVAGK-KFLLVL   79 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~l~~~l~~~-r~Llvl   79 (505)
                      .|+||||+|..++.  +...+-..++.+......  . ....++.+++..... ......+..+.+.+.+.+. .-+||+
T Consensus        21 mGsGKTT~ll~~~~--r~~~~g~kVli~~~~~d~--r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvViI   95 (223)
T 2b8t_A           21 MFAGKTAELIRRLH--RLEYADVKYLVFKPKIDT--R-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGI   95 (223)
T ss_dssp             TTSCHHHHHHHHHH--HHHHTTCCEEEEEECCCG--G-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEEE
T ss_pred             CCCcHHHHHHHHHH--HHHhcCCEEEEEEeccCc--h-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEEEE
Confidence            59999999988887  444433334444333211  1 112334444322111 1223344555555554444 459999


Q ss_pred             eCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE  113 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~  113 (505)
                      |.++.-....++.+ ..+.+  .+..|++|-++.
T Consensus        96 DEaQ~l~~~~ve~l-~~L~~--~gi~Vil~Gl~~  126 (223)
T 2b8t_A           96 DEVQFFDDRICEVA-NILAE--NGFVVIISGLDK  126 (223)
T ss_dssp             CSGGGSCTHHHHHH-HHHHH--TTCEEEEECCSB
T ss_pred             ecCccCcHHHHHHH-HHHHh--CCCeEEEEeccc
Confidence            99976443333333 33333  267899999843

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=93.33  E-value=2.5  Score=38.33  Aligned_cols=143  Identities=11%  Similarity=0.090  Sum_probs=69.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHH-HHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQH-IEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~-l~~~l~~~r~Llvl   79 (505)
                      .+|+||||||+.++.  ...   .+.+.++..          .+.....       ......... .+..-.....++++
T Consensus        81 p~GtGKTtl~~~i~~--~~~---~~~i~~~~~----------~~~~~~~-------~~~~~~i~~~~~~~~~~~~~i~~i  138 (278)
T 1iy2_A           81 PPGVGKTHLARAVAG--EAR---VPFITASGS----------DFVEMFV-------GVGAARVRDLFETAKRHAPCIVFI  138 (278)
T ss_dssp             CTTSSHHHHHHHHHH--HTT---CCEEEEEHH----------HHHHSTT-------THHHHHHHHHHHHHHTSCSEEEEE
T ss_pred             CCcChHHHHHHHHHH--HcC---CCEEEecHH----------HHHHHHh-------hHHHHHHHHHHHHHHhcCCcEEeh
Confidence            479999999999998  443   233444421          1111110       001111222 22222345689999


Q ss_pred             eCCCCC--C--------ccC----hhHHHHhhcCC--CCCcEEEEEeCchHHHH-H-h---CCcceEeCCCCChhhHHHH
Q 046115           80 DDVWNE--D--------YYK----WEPFYKCLKNS--LHESKILITTRKETVAR-I-M---GSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~--~--------~~~----~~~~~~~~~~~--~~~~~iLiTtr~~~~~~-~-~---~~~~~~~l~~l~~~ea~~L  138 (505)
                      |++...  .        ...    ...+...+...  .....++.||..+.... . .   .-...+.++..+.++-.++
T Consensus       139 Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~i  218 (278)
T 1iy2_A          139 DEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI  218 (278)
T ss_dssp             ETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHH
T ss_pred             hhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHH
Confidence            998321  0        001    12222222222  12234555666654321 1 1   1245788888888888888


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      +...... ........    ...+++.+.|+.
T Consensus       219 l~~~~~~-~~~~~~~~----~~~la~~~~G~~  245 (278)
T 1iy2_A          219 LRIHARG-KPLAEDVD----LALLAKRTPGFV  245 (278)
T ss_dssp             HHHHHTT-SCBCTTCC----HHHHHHTCTTCC
T ss_pred             HHHHHcc-CCCCcccC----HHHHHHHcCCCC
Confidence            8765521 11111112    345677777755

>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=93.24  E-value=0.16  Score=47.76  Aligned_cols=48  Identities=21%  Similarity=0.199  Sum_probs=31.0

Q ss_pred             CCCCcHHHHHHHHhcCccccc---------CC-----CceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER---------NF-----EKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~---------~f-----~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||+||.+++.......         ..     ..++|++....++...+.. ++..++
T Consensus       106 ~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g  167 (322)
T 2i1q_A          106 VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAG  167 (322)
T ss_dssp             STTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcC
Confidence            379999999999886321211         11     3677999888776665553 345554

>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=93.23  E-value=0.12  Score=55.62  Aligned_cols=103  Identities=14%  Similarity=0.161  Sum_probs=49.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCC-CCChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGS-AKDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      .+|+|||++|+.+++  ...+.-...+.++++...... ....+   ++.+. .............+..   ....+|+|
T Consensus       596 p~GtGKT~lA~~la~--~~~~~~~~~i~i~~~~~~~~~-~~s~l---~g~~~~~~G~~~~g~l~~~~~~---~~~~vl~l  666 (854)
T 1qvr_A          596 PTGVGKTELAKTLAA--TLFDTEEAMIRIDMTEYMEKH-AVSRL---IGAPPGYVGYEEGGQLTEAVRR---RPYSVILF  666 (854)
T ss_dssp             CSSSSHHHHHHHHHH--HHHSSGGGEEEECTTTCCSSG-GGGGC-----------------CHHHHHHH---CSSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HhcCCCCcEEEEechhccchh-HHHHH---cCCCCCCcCccccchHHHHHHh---CCCeEEEE
Confidence            479999999999988  442222234456655433211 00111   01000 0000000111222222   23468999


Q ss_pred             eCCCCCCccChhHHHHhhcCCC-----------CCcEEEEEeCc
Q 046115           80 DDVWNEDYYKWEPFYKCLKNSL-----------HESKILITTRK  112 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~~~~-----------~~~~iLiTtr~  112 (505)
                      |++..........+...+....           .++.||.||..
T Consensus       667 DEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~  710 (854)
T 1qvr_A          667 DEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNL  710 (854)
T ss_dssp             SSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             ecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCc
Confidence            9997766555566666655431           24447777764

>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=92.89  E-value=2.5  Score=37.63  Aligned_cols=143  Identities=11%  Similarity=0.082  Sum_probs=70.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r~Llvl   79 (505)
                      .+|+||||||+.++.  ...   .+.+.++..          .+.....       .........+.+.. .....++++
T Consensus        57 ~~G~GKTtl~~~i~~--~~~---~~~i~~~~~----------~~~~~~~-------~~~~~~i~~~~~~~~~~~~~i~~~  114 (254)
T 1ixz_A           57 PPGVGKTHLARAVAG--EAR---VPFITASGS----------DFVEMFV-------GVGAARVRDLFETAKRHAPCIVFI  114 (254)
T ss_dssp             CTTSSHHHHHHHHHH--HTT---CCEEEEEHH----------HHHHSCT-------THHHHHHHHHHHHHTTSSSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HhC---CCEEEeeHH----------HHHHHHh-------hHHHHHHHHHHHHHHhcCCeEEEe
Confidence            479999999999998  433   233344321          1111110       01112222223332 345689999


Q ss_pred             eCCCCCC----------ccC----hhHHHHhhcCC--CCCcEEEEEeCchHHHHH-h----CCcceEeCCCCChhhHHHH
Q 046115           80 DDVWNED----------YYK----WEPFYKCLKNS--LHESKILITTRKETVARI-M----GSTHVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~~----------~~~----~~~~~~~~~~~--~~~~~iLiTtr~~~~~~~-~----~~~~~~~l~~l~~~ea~~L  138 (505)
                      |+++...          ...    ...+...+...  ....-++.||..+..... .    .-...+.++..+.++-.++
T Consensus       115 Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~i  194 (254)
T 1ixz_A          115 DEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI  194 (254)
T ss_dssp             ETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHH
T ss_pred             hhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHH
Confidence            9983210          001    12333333322  223345556666544221 1    1134678888888888888


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      +...... .......+    ...+++.+.|+.
T Consensus       195 l~~~~~~-~~~~~~~~----~~~la~~~~G~~  221 (254)
T 1ixz_A          195 LRIHARG-KPLAEDVD----LALLAKRTPGFV  221 (254)
T ss_dssp             HHHHHTT-SCBCTTCC----HHHHHHTCTTCC
T ss_pred             HHHHHcC-CCCCcccC----HHHHHHHcCCCC
Confidence            8765421 11111112    345677777654

>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=92.64  E-value=0.23  Score=47.06  Aligned_cols=77  Identities=17%  Similarity=0.125  Sum_probs=46.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  .....=..++|++.....+..     ....++....    ....+.++....+..... .+.-
T Consensus        69 ~pGsGKTtLal~la~--~~~~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~~~~~  141 (349)
T 2zr9_A           69 PESSGKTTVALHAVA--NAQAAGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADMLVRSGALD  141 (349)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            379999999999987  343333467899988776653     2344442211    112234555554444443 3456


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      +||+|.+..
T Consensus       142 lIVIDsl~~  150 (349)
T 2zr9_A          142 IIVIDSVAA  150 (349)
T ss_dssp             EEEEECGGG
T ss_pred             EEEEcChHh
Confidence            899999844

>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=92.42  E-value=0.2  Score=47.63  Aligned_cols=77  Identities=16%  Similarity=0.132  Sum_probs=44.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHc-CCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECV-AGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l-~~~r~   75 (505)
                      .+|+||||||.+++.  .....=..++|++....++...     +..++.....    ...+.++..+.+.... ..+.-
T Consensus        71 ~pGsGKTtLal~la~--~~~~~g~~vlyid~E~s~~~~~-----a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~~~~~  143 (356)
T 1u94_A           71 PESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  143 (356)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCeEEEEeCCCCccHHH-----HHHcCCChhheeeeCCCCHHHHHHHHHHHHhccCCC
Confidence            379999999999987  4433334688999888776542     3444422110    1123344444433332 23445


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      +||+|.+..
T Consensus       144 lVVIDsl~~  152 (356)
T 1u94_A          144 VIVVDSVAA  152 (356)
T ss_dssp             EEEEECGGG
T ss_pred             EEEEcCHHH
Confidence            899999843

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=92.25  E-value=1.2  Score=44.40  Aligned_cols=140  Identities=10%  Similarity=0.072  Sum_probs=71.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcC----CceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVA----GKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~----~~r~L   76 (505)
                      .+|+|||+||+.++.  ...   ...+.++...-.+               ..  .   ......+...+.    ..+.+
T Consensus        72 ppGtGKTtLaraIa~--~~~---~~~i~i~g~~~~~---------------~~--~---g~~~~~v~~lfq~a~~~~p~i  126 (499)
T 2dhr_A           72 PPGVGKTHLARAVAG--EAR---VPFITASGSDFVE---------------MF--V---GVGAARVRDLFETAKRHAPCI  126 (499)
T ss_dssp             SSSSSHHHHHHHHHH--HTT---CCEEEEEGGGGTS---------------SC--T---THHHHHHHHHTTTSSSSSSCE
T ss_pred             CCCCCHHHHHHHHHH--HhC---CCEEEEehhHHHH---------------hh--h---hhHHHHHHHHHHHHHhcCCCE
Confidence            479999999999998  433   2334444332100               00  0   011112222222    23579


Q ss_pred             EEEeCCCCCCc----------c----ChhHHHHhhcCC--CCCcEEEEEeCchHHHHH-h----CCcceEeCCCCChhhH
Q 046115           77 LVLDDVWNEDY----------Y----KWEPFYKCLKNS--LHESKILITTRKETVARI-M----GSTHVISVNVLSEMEC  135 (505)
Q Consensus        77 lvlDdv~~~~~----------~----~~~~~~~~~~~~--~~~~~iLiTtr~~~~~~~-~----~~~~~~~l~~l~~~ea  135 (505)
                      +++|+++....          .    .+..+...+...  .....++.||..+..... .    .-...+.++..+.++-
T Consensus       127 l~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R  206 (499)
T 2dhr_A          127 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR  206 (499)
T ss_dssp             EEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHH
T ss_pred             EEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHH
Confidence            99999943210          0    112333333322  234456667766654221 1    1134778888888888


Q ss_pred             HHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          136 WSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       136 ~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      .+++..+.-. ........    ...++..+.|+.
T Consensus       207 ~~IL~~~~~~-~~l~~dv~----l~~lA~~t~G~~  236 (499)
T 2dhr_A          207 EQILRIHARG-KPLAEDVD----LALLAKRTPGFV  236 (499)
T ss_dssp             HHHHHHTTSS-SCCCCSST----THHHHTTSCSCC
T ss_pred             HHHHHHHHhc-CCCChHHH----HHHHHHhcCCCC
Confidence            8888765421 11111212    345777787766

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=92.11  E-value=0.27  Score=46.28  Aligned_cols=69  Identities=12%  Similarity=0.134  Sum_probs=40.2

Q ss_pred             EEEEEeCCCCCCccChhHHHHhhcC-----------CCCCcEEEEEeCchH------H-HHHhCCcc-eEeCCCCChhhH
Q 046115           75 FLLVLDDVWNEDYYKWEPFYKCLKN-----------SLHESKILITTRKET------V-ARIMGSTH-VISVNVLSEMEC  135 (505)
Q Consensus        75 ~LlvlDdv~~~~~~~~~~~~~~~~~-----------~~~~~~iLiTtr~~~------~-~~~~~~~~-~~~l~~l~~~ea  135 (505)
                      .++++|++..........+...+..           ......|+.|+....      + ........ .+.++..+.++-
T Consensus       111 ~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~Rf~~~i~i~~p~~~~~  190 (331)
T 2r44_A          111 NFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVDRFMMKIHLTYLDKESE  190 (331)
T ss_dssp             SEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHTTSSEEEECCCCCHHHH
T ss_pred             cEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHhheeEEEEcCCCCHHHH
Confidence            5899999976554444444444332           123445555665221      1 11123333 488999999998


Q ss_pred             HHHHHHhh
Q 046115          136 WSVFQSLA  143 (505)
Q Consensus       136 ~~Lf~~~~  143 (505)
                      .+++....
T Consensus       191 ~~il~~~~  198 (331)
T 2r44_A          191 LEVMRRVS  198 (331)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhcc
Confidence            88887765

>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=91.89  E-value=0.29  Score=47.02  Aligned_cols=15  Identities=40%  Similarity=0.344  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||++|+.+++
T Consensus        80 p~GtGKT~la~~la~   94 (376)
T 1um8_A           80 PTGSGKTLMAQTLAK   94 (376)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

>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=91.80  E-value=0.25  Score=46.92  Aligned_cols=83  Identities=20%  Similarity=0.150  Sum_probs=43.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC---Cc-eEEEEeCCCCCHHHHHHHHHHHcCCCC-----------CCChhcHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF---EK-RTWVCVSEPFDEFRIARAIIESLTPGS-----------AKDLVEFQSLMQH   65 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f---~~-~~wv~~~~~~~~~~~~~~l~~~l~~~~-----------~~~~~~~~~~~~~   65 (505)
                      .+|+|||||+..++.........   .+ ++|++....+... .+..+........           ........+....
T Consensus       139 ~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~-~i~~i~q~~~~~~~~v~~ni~~~~~~~~~~~~~~l~~  217 (349)
T 1pzn_A          139 EFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPE-RIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQ  217 (349)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHH-HHHHHHHTTTCCHHHHGGGEEEEECCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHH-HHHHHHHHcCCCHHHHhhCEEEEecCChHHHHHHHHH
Confidence            37999999999998731111111   23 4799876654332 2333444433210           0111122233334


Q ss_pred             HHHHcC------CceEEEEEeCCCC
Q 046115           66 IEECVA------GKKFLLVLDDVWN   84 (505)
Q Consensus        66 l~~~l~------~~r~LlvlDdv~~   84 (505)
                      +...+.      .+.-+||+|.+..
T Consensus       218 ~~~~~~~lS~G~~~~~llIlDs~ta  242 (349)
T 1pzn_A          218 AEDKIKELLNTDRPVKLLIVDSLTS  242 (349)
T ss_dssp             HHHHHHHSSSSSSCEEEEEEETSST
T ss_pred             HHHHHHHhccccCCCCEEEEeCchH
Confidence            444443      4677999999854

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=91.09  E-value=0.67  Score=43.18  Aligned_cols=43  Identities=16%  Similarity=0.120  Sum_probs=28.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIES   47 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~   47 (505)
                      .+|+||||||..++..  ...+-..++|++...  +...+...++..
T Consensus        76 ~pG~GKTtl~l~ia~~--~a~~g~~vl~~slE~--s~~~l~~R~~~~  118 (315)
T 3bh0_A           76 RPSMGKTAFALKQAKN--MSDNDDVVNLHSLEM--GKKENIKRLIVT  118 (315)
T ss_dssp             CTTSSHHHHHHHHHHH--HHTTTCEEEEEESSS--CHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH--HHHcCCeEEEEECCC--CHHHHHHHHHHH
Confidence            3799999999998863  322225677888763  455555555543

>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=90.43  E-value=0.44  Score=46.69  Aligned_cols=42  Identities=19%  Similarity=0.251  Sum_probs=26.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCC-CceEEEEeCCCCC-HHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF-EKRTWVCVSEPFD-EFRIARAII   45 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f-~~~~wv~~~~~~~-~~~~~~~l~   45 (505)
                      +|+||||||..++.  ....++ +..+++-+++..+ ..++..++.
T Consensus       160 sGvGKTtL~~~l~~--~~~~~~~~i~V~~~iGerttev~el~~~l~  203 (473)
T 1sky_E          160 AGVGKTVLIQELIH--NIAQEHGGISVFAGVGERTREGNDLYHEMK  203 (473)
T ss_dssp             SSSCHHHHHHHHHH--HHHHHTCCCEEEEEESSCHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHh--hhhhccCcEEEEeeeccCchHHHHHHHHhh
Confidence            79999999999987  444444 3445666666543 334444443

>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=90.00  E-value=0.76  Score=40.25  Aligned_cols=36  Identities=25%  Similarity=0.207  Sum_probs=22.7

Q ss_pred             CCCCcHHHHHHHHhcCccc---cc-CCCceEEEEeCCCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDV---ER-NFEKRTWVCVSEPFD   36 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~---~~-~f~~~~wv~~~~~~~   36 (505)
                      .+|+|||||++.++.....   .. .-..++|++......
T Consensus        33 ~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~   72 (231)
T 4a74_A           33 EFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFR   72 (231)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCC
T ss_pred             CCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCC
Confidence            4799999999999762111   11 124577887655443

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=89.95  E-value=0.94  Score=43.63  Aligned_cols=102  Identities=11%  Similarity=0.265  Sum_probs=73.4

Q ss_pred             HhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch-
Q 046115          378 LFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-  455 (505)
Q Consensus       378 ~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-  455 (505)
                      .|..+.+|+.+.+.       ++....-...+..+..|+.+.+.. . +..++. .+..+.+|+.+.|..+  +..+.. 
T Consensus       260 aF~~c~~L~~i~lp-------~~~~~I~~~aF~~c~~L~~i~l~~-~-i~~I~~~aF~~c~~L~~i~lp~~--v~~I~~~  328 (394)
T 4gt6_A          260 AFDSCAYLASVKMP-------DSVVSIGTGAFMNCPALQDIEFSS-R-ITELPESVFAGCISLKSIDIPEG--ITQILDD  328 (394)
T ss_dssp             TTTTCSSCCEEECC-------TTCCEECTTTTTTCTTCCEEECCT-T-CCEECTTTTTTCTTCCEEECCTT--CCEECTT
T ss_pred             eeeecccccEEecc-------cccceecCcccccccccccccCCC-c-ccccCceeecCCCCcCEEEeCCc--ccEehHh
Confidence            46677888888886       333332334567888999999863 3 566665 5678999999999763  666765 


Q ss_pred             hccccccCceeecCCCccccccc-ccccCCccCCccce
Q 046115          456 GIGKLRKLMYLHNEDTGCLRYLP-AGIGELIRLRRVRE  492 (505)
Q Consensus       456 ~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~L~~L~~  492 (505)
                      .+.++.+|+.+.+..+  +..+. ..|.+|++|+.+.+
T Consensus       329 aF~~C~~L~~i~ip~s--v~~I~~~aF~~C~~L~~i~~  364 (394)
T 4gt6_A          329 AFAGCEQLERIAIPSS--VTKIPESAFSNCTALNNIEY  364 (394)
T ss_dssp             TTTTCTTCCEEEECTT--CCBCCGGGGTTCTTCCEEEE
T ss_pred             HhhCCCCCCEEEECcc--cCEEhHhHhhCCCCCCEEEE
Confidence            4888999999999755  34444 46899999988764

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=89.89  E-value=1.1  Score=43.13  Aligned_cols=126  Identities=17%  Similarity=0.174  Sum_probs=70.2

Q ss_pred             CCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCC------
Q 046115          351 NVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQ------  423 (505)
Q Consensus       351 ~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~------  423 (505)
                      .|.++.+|+.+.+..+ +...   -...|..+.+|+.+++.       ++ +..++ ..+..+..|+.+.+..+      
T Consensus        66 AF~~c~~L~~i~lp~~-i~~I---~~~aF~~c~~L~~i~lp-------~~-l~~I~~~aF~~c~~L~~i~~p~~l~~i~~  133 (394)
T 4fs7_A           66 AFQGCRKVTEIKIPST-VREI---GEFAFENCSKLEIINIP-------DS-VKMIGRCTFSGCYALKSILLPLMLKSIGV  133 (394)
T ss_dssp             TTTTCTTEEEEECCTT-CCEE---CTTTTTTCTTCCEECCC-------TT-CCEECTTTTTTCTTCCCCCCCTTCCEECT
T ss_pred             HhhCCCCceEEEeCCC-ccCc---chhHhhCCCCCcEEEeC-------CC-ceEccchhhcccccchhhcccCceeeecc
Confidence            4557778888777533 2221   23346677778887775       22 22222 22344444444443321      


Q ss_pred             ------c--------ccccc-chhhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCccccccc-ccccCCcc
Q 046115          424 ------K--------KIEKL-PETLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLP-AGIGELIR  486 (505)
Q Consensus       424 ------~--------~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p-~~i~~l~~  486 (505)
                            .        ....+ ...+..+.+|+.+.+.++  +..++. .+..+++|+.+.+..+  +..++ ..|.++..
T Consensus       134 ~aF~~~~~~~~~~~~~~~~i~~~aF~~c~~L~~i~l~~~--~~~I~~~~F~~c~~L~~i~l~~~--~~~I~~~~F~~~~~  209 (394)
T 4fs7_A          134 EAFKGCDFKEITIPEGVTVIGDEAFATCESLEYVSLPDS--METLHNGLFSGCGKLKSIKLPRN--LKIIRDYCFAECIL  209 (394)
T ss_dssp             TTTTTCCCSEEECCTTCCEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCBCCCCTT--CCEECTTTTTTCTT
T ss_pred             eeeecccccccccCccccccchhhhcccCCCcEEecCCc--cceeccccccCCCCceEEEcCCC--ceEeCchhhccccc
Confidence                  1        01111 124667788888888763  445554 4677888888888766  23333 34677777


Q ss_pred             CCccce
Q 046115          487 LRRVRE  492 (505)
Q Consensus       487 L~~L~~  492 (505)
                      |+.+.+
T Consensus       210 L~~i~~  215 (394)
T 4fs7_A          210 LENMEF  215 (394)
T ss_dssp             CCBCCC
T ss_pred             cceeec
Confidence            776653

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=89.70  E-value=0.34  Score=41.50  Aligned_cols=111  Identities=14%  Similarity=0.139  Sum_probs=65.8

Q ss_pred             CCCCceEEEecCC-Ccccc-ccchhHHhhcCcccceEEecccccCCccccccc-----cCccccCCCCcceeeccCCccc
Q 046115          354 GLRGLRSLLVKSD-EYSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-----IPTNIEKLLHLKYLNLKGQKKI  426 (505)
Q Consensus       354 ~~~~L~~L~l~~~-~~~~~-~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-----~p~~~~~l~~L~~L~l~~~~~~  426 (505)
                      .-+.|+.|+|.++ .+... ...+-..+..-++|+.|+|+       ++.++.     +...+..-+.|++|+|++|. +
T Consensus        39 ~n~~L~~L~L~~nn~igd~ga~~la~aL~~N~~L~~L~L~-------~n~igd~ga~alA~aL~~N~tL~~L~L~~N~-I  110 (197)
T 1pgv_A           39 DDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLA-------NTAISDSEARGLIELIETSPSLRVLNVESNF-L  110 (197)
T ss_dssp             TCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECT-------TSCCBHHHHTTHHHHHHHCSSCCEEECCSSB-C
T ss_pred             cCCCccEEECCCCCCCCHHHHHHHHHHHhhCCCcCEEEcc-------CCCCChHHHHHHHHHHhcCCccCeEecCCCc-C
Confidence            4567888888875 54321 01244445666778888887       444432     22334455678888888888 4


Q ss_pred             c-----ccchhhhcCCCCcEEecCCCcC--cc-----ccchhccccccCceeecCCCc
Q 046115          427 E-----KLPETLCELYNLERLNVDDCQN--LR-----ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       427 ~-----~lp~~~~~l~~L~~L~l~~~~~--~~-----~lp~~~~~l~~L~~L~l~~~~  472 (505)
                      +     .+-..+..-..|+.|+|++|..  +.     .+-..+..-++|+.|+++.|.
T Consensus       111 g~~Ga~ala~aL~~N~tL~~L~L~n~~~~~ig~~g~~~ia~aL~~N~tL~~L~l~~~~  168 (197)
T 1pgv_A          111 TPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFAS  168 (197)
T ss_dssp             CHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECCCCC
T ss_pred             CHHHHHHHHHHHhhCCceeEEECCCCcCcCcCHHHHHHHHHHHHhCCCcCeEeccCCC
Confidence            4     2223344456688888886542  22     122334555678888887664

>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=89.47  E-value=0.92  Score=47.86  Aligned_cols=144  Identities=13%  Similarity=0.151  Sum_probs=59.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|.|||.+|+++++  +....     ++.+..        .+++....      ..............-+..+++|+||
T Consensus       519 PPGtGKT~lAkaiA~--e~~~~-----f~~v~~--------~~l~s~~v------Gese~~vr~lF~~Ar~~~P~IifiD  577 (806)
T 3cf2_A          519 PPGCGKTLLAKAIAN--ECQAN-----FISIKG--------PELLTMWF------GESEANVREIFDKARQAAPCVLFFD  577 (806)
T ss_dssp             STTSSHHHHHHHHHH--TTTCE-----EEECCH--------HHHHTTTC------SSCHHHHHHHHHHHHTTCSEEEECS
T ss_pred             CCCCCchHHHHHHHH--HhCCc-----eEEecc--------chhhcccc------chHHHHHHHHHHHHHHcCCceeech
Confidence            589999999999998  44322     344331        22333222      1111222233333335578999999


Q ss_pred             CCCCCC--------------ccChhHHHHhhcCCC--CCcEEEEEeCchHH-HHHh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNED--------------YYKWEPFYKCLKNSL--HESKILITTRKETV-ARIM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~--------------~~~~~~~~~~~~~~~--~~~~iLiTtr~~~~-~~~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      +++.-.              .....+++..+....  .+.-||-||..++. ...+   +. ...+.++..+.++-.++|
T Consensus       578 EiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il  657 (806)
T 3cf2_A          578 ELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAIL  657 (806)
T ss_dssp             CGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTT
T ss_pred             hhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHH
Confidence            985411              001234444444332  23334446654332 1111   12 456777776776666777


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ..+... .......+    ...+++.+.|+.
T Consensus       658 ~~~l~~-~~~~~~~d----l~~la~~t~g~S  683 (806)
T 3cf2_A          658 KANLRK-SPVAKDVD----LEFLAKMTNGFS  683 (806)
T ss_dssp             TTTSSC-C--CCC------------------
T ss_pred             HHHhcC-CCCCCCCC----HHHHHHhCCCCC
Confidence            655422 11122222    345666666543

>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=89.34  E-value=0.12  Score=43.45  Aligned_cols=15  Identities=13%  Similarity=0.186  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ~~GsGKST~a~~La~   25 (178)
T 1qhx_A           11 GSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999997

>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=89.07  E-value=0.8  Score=44.16  Aligned_cols=48  Identities=15%  Similarity=0.124  Sum_probs=29.2

Q ss_pred             CCCCcHHHHHHHHhcCccccc----CCCceEEEEeCCCCCHHHHHHHHHHHcC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER----NFEKRTWVCVSEPFDEFRIARAIIESLT   49 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~----~f~~~~wv~~~~~~~~~~~~~~l~~~l~   49 (505)
                      .+|+|||||+..++-......    .-..++|++....+....+ ..+...++
T Consensus       186 ~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~g  237 (400)
T 3lda_A          186 EFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFG  237 (400)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTT
T ss_pred             CCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcC
Confidence            379999999997753111111    2345789987776655433 33555554

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=87.00  E-value=0.099  Score=44.57  Aligned_cols=40  Identities=10%  Similarity=-0.016  Sum_probs=25.2

Q ss_pred             cCCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCc
Q 046115           70 VAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRK  112 (505)
Q Consensus        70 l~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~  112 (505)
                      +.++.-+|++|.++.-+. .|...+..+.+.  +..|++|.++
T Consensus        73 ~~~~~dvviIDE~Q~~~~-~~~~~l~~l~~~--~~~Vi~~Gl~  112 (184)
T 2orw_A           73 IEEDTRGVFIDEVQFFNP-SLFEVVKDLLDR--GIDVFCAGLD  112 (184)
T ss_dssp             CCTTEEEEEECCGGGSCT-THHHHHHHHHHT--TCEEEEEEES
T ss_pred             hcCCCCEEEEECcccCCH-HHHHHHHHHHHC--CCCEEEEeec
Confidence            334567999999977543 344444433333  6789998874

>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=86.73  E-value=2.2  Score=41.79  Aligned_cols=44  Identities=27%  Similarity=0.319  Sum_probs=29.6

Q ss_pred             CCCcHHHHHHHHhcCccccc-CCCceEEEEeCCCC-CHHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEPF-DEFRIARAIIES   47 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~~-~~~~~~~~l~~~   47 (505)
                      +|+|||+|+.++++  .+.+ +-+.++++-+++.. +..++..++...
T Consensus       162 ~G~GKT~L~~~i~~--~~~~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          162 AGVGKTVLIMELIN--NVAKAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             TTSSHHHHHHHHHH--HTTTTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHH--hhHhhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            69999999999987  4433 23556677777654 445566666553

>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=86.54  E-value=0.25  Score=41.14  Aligned_cols=15  Identities=20%  Similarity=-0.108  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         9 ~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            9 PDCCFKSTVAAKLSK   23 (173)
T ss_dssp             SSSSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=86.45  E-value=0.26  Score=41.41  Aligned_cols=15  Identities=33%  Similarity=0.270  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        10 ~~GsGKST~a~~L~~   24 (181)
T 1ly1_A           10 CPGSGKSTWAREFIA   24 (181)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHh
Confidence            589999999999987

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=86.36  E-value=0.56  Score=40.72  Aligned_cols=33  Identities=21%  Similarity=0.118  Sum_probs=24.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      ||+||||+|..++.  .....- .++-++.....+.
T Consensus        10 GGvGKTT~a~~LA~--~la~~g-~VlliD~D~q~~~   42 (209)
T 3cwq_A           10 GGVGKTTTAVHLSA--YLALQG-ETLLIDGDPNRSA   42 (209)
T ss_dssp             TTSSHHHHHHHHHH--HHHTTS-CEEEEEECTTCHH
T ss_pred             CCCcHHHHHHHHHH--HHHhcC-CEEEEECCCCCCH
Confidence            89999999999987  554443 6667887765443

>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=86.01  E-value=0.24  Score=47.13  Aligned_cols=75  Identities=16%  Similarity=0.170  Sum_probs=39.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-Cc-eEEEEeCCCCCHHHHHHHHHHHcCC----CCCCChhcHHHH--------HHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-EK-RTWVCVSEPFDEFRIARAIIESLTP----GSAKDLVEFQSL--------MQHI   66 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-~~-~~wv~~~~~~~~~~~~~~l~~~l~~----~~~~~~~~~~~~--------~~~l   66 (505)
                      .+|+|||||++.+++  .+..+. +. ++++-+++....   ..++.+.+..    ....++....-.        .+.+
T Consensus       182 ~sG~GKTtLl~~Iar--~i~~~~~~v~~I~~lIGER~~E---v~~~~~~~~~~vV~atadep~~~r~~~a~~alt~AEyf  256 (422)
T 3ice_A          182 PPKAGKTMLLQNIAQ--SIAYNHPDCVLMVLLIDERPEE---VTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRL  256 (422)
T ss_dssp             CSSSSHHHHHHHHHH--HHHHHCTTSEEEEEEESSCHHH---HHHHHTTCSSEEEEECTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCChhHHHHHHHH--HHhhcCCCeeEEEEEecCChHH---HHHHHHHhCeEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Confidence            379999999999987  554333 22 335656654322   3333444421    111122111111        1122


Q ss_pred             HHHcCCceEEEEEeCC
Q 046115           67 EECVAGKKFLLVLDDV   82 (505)
Q Consensus        67 ~~~l~~~r~LlvlDdv   82 (505)
                      ++  .++.+||++||+
T Consensus       257 rd--~G~dVLil~Dsl  270 (422)
T 3ice_A          257 VE--HKKDVIILLDSI  270 (422)
T ss_dssp             HH--TSCEEEEEEECH
T ss_pred             Hh--cCCCEEEEEeCc
Confidence            22  578999999998

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=85.65  E-value=1.1  Score=38.50  Aligned_cols=43  Identities=21%  Similarity=0.103  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~   46 (505)
                      -|+||||.++.++.  ....+-..+++...-......+..+.++.
T Consensus         9 DGsGKsTq~~~L~~--~L~~~g~~v~~treP~~t~~~~~ir~~l~   51 (197)
T 3hjn_A            9 DGSGKSTQIQLLAQ--YLEKRGKKVILKREPGGTETGEKIRKILL   51 (197)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH--HHHHCCCcEEEEECCCCCcHHHHHHHHhh
Confidence            59999999999987  55444333444432222333444444443

>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=85.45  E-value=0.34  Score=41.23  Aligned_cols=15  Identities=40%  Similarity=0.461  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||++.++.
T Consensus        17 ~~GsGKSTl~~~La~   31 (191)
T 1zp6_A           17 HPGSGKSTIAEALAN   31 (191)
T ss_dssp             CTTSCHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHh
Confidence            589999999999998

>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=85.35  E-value=0.33  Score=40.47  Aligned_cols=13  Identities=38%  Similarity=0.652  Sum_probs=12.2

Q ss_pred             CCCCcHHHHHHHH
Q 046115            1 MGGIGKTTLAQFA   13 (505)
Q Consensus         1 ~~G~GKT~LA~~~   13 (505)
                      ++|+||||+|+.+
T Consensus         9 ~~GsGKsT~a~~L   21 (179)
T 3lw7_A            9 MPGSGKSEFAKLL   21 (179)
T ss_dssp             CTTSCHHHHHHHH
T ss_pred             CCCCCHHHHHHHH
Confidence            5899999999999

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=85.32  E-value=0.48  Score=40.24  Aligned_cols=15  Identities=27%  Similarity=0.454  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         9 ~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            9 IPGVGKSTVLAKVKE   23 (194)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999988

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=85.31  E-value=0.82  Score=44.98  Aligned_cols=75  Identities=20%  Similarity=0.205  Sum_probs=40.2

Q ss_pred             CCCcHHHHH-HHHhcCcccccCCCc-eEEEEeCCCC-CHHHHHHHHHHHcCC-------CCCCChhcHHH--------HH
Q 046115            2 GGIGKTTLA-QFAYNNGDVERNFEK-RTWVCVSEPF-DEFRIARAIIESLTP-------GSAKDLVEFQS--------LM   63 (505)
Q Consensus         2 ~G~GKT~LA-~~~~~~~~~~~~f~~-~~wv~~~~~~-~~~~~~~~l~~~l~~-------~~~~~~~~~~~--------~~   63 (505)
                      +|+|||+|| ..+++  ..  +-+. ++++-+++.. +..++...+...-..       ...+++.....        ..
T Consensus       171 ~g~GKT~Lal~~I~~--~~--~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a~~~a~tiA  246 (502)
T 2qe7_A          171 RQTGKTTIAIDTIIN--QK--GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYLAPYAGCAMG  246 (502)
T ss_dssp             SSSCHHHHHHHHHHG--GG--SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHH--hh--cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            699999996 57776  33  2343 3566677654 344555555442110       11112111111        11


Q ss_pred             HHHHHHcCCceEEEEEeCC
Q 046115           64 QHIEECVAGKKFLLVLDDV   82 (505)
Q Consensus        64 ~~l~~~l~~~r~LlvlDdv   82 (505)
                      +.++.  .++.+||++||+
T Consensus       247 Eyfrd--~G~dVLl~~Dsl  263 (502)
T 2qe7_A          247 EYFMY--KGKHALVVYDDL  263 (502)
T ss_dssp             HHHHT--TTCEEEEEEECH
T ss_pred             HHHHH--cCCcEEEEEecH
Confidence            22322  578999999998

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=85.26  E-value=0.32  Score=41.18  Aligned_cols=15  Identities=27%  Similarity=0.361  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        13 ~~GsGKst~a~~La~   27 (185)
T 3trf_A           13 LMGAGKTSVGSQLAK   27 (185)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=85.14  E-value=0.55  Score=40.38  Aligned_cols=34  Identities=24%  Similarity=0.127  Sum_probs=23.7

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      ||+||||+|..++.  ....+=..++-++.....+.
T Consensus        11 gG~GKTt~a~~la~--~la~~g~~vlliD~D~~~~~   44 (206)
T 4dzz_A           11 GGSGKTTAVINIAT--ALSRSGYNIAVVDTDPQMSL   44 (206)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTCCEEEEECCTTCHH
T ss_pred             CCccHHHHHHHHHH--HHHHCCCeEEEEECCCCCCH
Confidence            89999999999987  45443335667777654433

>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=85.13  E-value=3.1  Score=40.93  Aligned_cols=43  Identities=21%  Similarity=0.219  Sum_probs=30.4

Q ss_pred             CCCcHHHHHHHHhcCccccc-CCCceEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|+.++++  .+.+ +-+.++++-+++.. +..++..++..
T Consensus       174 ~GvGKT~L~~~l~~--~~a~~~~~v~V~~~iGER~rEv~e~~~~~~~  218 (498)
T 1fx0_B          174 AGVGKTVLIMELIN--NIAKAHGGVSVFGGVGERTREGNDLYMEMKE  218 (498)
T ss_dssp             SSSSHHHHHHHHHH--HTTTTCSSCEEEEEESCCSHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHH--HHHhhCCCEEEEEEcccCcHHHHHHHHhhhc
Confidence            69999999999988  4433 33567788777765 45566666654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=85.05  E-value=0.33  Score=41.73  Aligned_cols=15  Identities=40%  Similarity=0.366  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        33 ~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           33 YMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999997

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=84.75  E-value=0.36  Score=40.30  Aligned_cols=15  Identities=27%  Similarity=0.295  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+++.++.
T Consensus        12 ~~GsGKSTl~~~La~   26 (173)
T 1kag_A           12 PMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=84.70  E-value=0.67  Score=40.57  Aligned_cols=31  Identities=23%  Similarity=0.040  Sum_probs=19.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE   33 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~   33 (505)
                      .||+||||+|..++.  ....+=..++.+++..
T Consensus        14 kgGvGKTt~a~~la~--~l~~~G~~V~v~d~D~   44 (228)
T 2r8r_A           14 APGVGKTYAMLQAAH--AQLRQGVRVMAGVVET   44 (228)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEECCC
T ss_pred             CCCCcHHHHHHHHHH--HHHHCCCCEEEEEeCC
Confidence            389999999988887  4433322344455544

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=84.61  E-value=0.37  Score=40.43  Aligned_cols=15  Identities=40%  Similarity=0.439  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~~GsGKsTla~~La~   26 (175)
T 1via_A           12 FMGSGKSTLARALAK   26 (175)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=84.28  E-value=0.52  Score=39.92  Aligned_cols=15  Identities=40%  Similarity=0.481  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        21 ~~GsGKsT~~~~L~~   35 (186)
T 2yvu_A           21 LPGSGKTTIATRLAD   35 (186)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>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=84.08  E-value=0.39  Score=40.74  Aligned_cols=15  Identities=40%  Similarity=0.656  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ~~GsGKsT~~~~L~~   25 (192)
T 1kht_A           11 VPGVGSTTSSQLAMD   25 (192)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>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=83.88  E-value=0.4  Score=40.81  Aligned_cols=15  Identities=40%  Similarity=0.321  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        13 ~~GsGKST~~~~L~~   27 (193)
T 2rhm_A           13 HPATGKTTLSQALAT   27 (193)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=83.79  E-value=1.2  Score=44.01  Aligned_cols=75  Identities=23%  Similarity=0.224  Sum_probs=40.1

Q ss_pred             CCCcHHHHH-HHHhcCcccccCCCc-eEEEEeCCCC-CHHHHHHHHHHHc--C-----CCCCCChhcHHH--------HH
Q 046115            2 GGIGKTTLA-QFAYNNGDVERNFEK-RTWVCVSEPF-DEFRIARAIIESL--T-----PGSAKDLVEFQS--------LM   63 (505)
Q Consensus         2 ~G~GKT~LA-~~~~~~~~~~~~f~~-~~wv~~~~~~-~~~~~~~~l~~~l--~-----~~~~~~~~~~~~--------~~   63 (505)
                      +|+|||+|| ..+++  ..  +-+. ++++-+++.. +..++...+...=  .     ....+++.....        ..
T Consensus       184 ~g~GKT~Lal~~I~~--~~--~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~~~a~tiA  259 (515)
T 2r9v_A          184 RQTGKTAIAIDTIIN--QK--GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIAPYAGCAMG  259 (515)
T ss_dssp             TTSSHHHHHHHHHHT--TT--TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHH--hh--cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            699999996 57777  33  2443 3566677654 3445555554411  0     011122211111        11


Q ss_pred             HHHHHHcCCceEEEEEeCC
Q 046115           64 QHIEECVAGKKFLLVLDDV   82 (505)
Q Consensus        64 ~~l~~~l~~~r~LlvlDdv   82 (505)
                      +.++.  .++.+||++||+
T Consensus       260 Eyfrd--~G~dVLli~Dsl  276 (515)
T 2r9v_A          260 EYFAY--SGRDALVVYDDL  276 (515)
T ss_dssp             HHHHT--TTCEEEEEEETH
T ss_pred             HHHHH--cCCcEEEEeccH
Confidence            22222  578999999998

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=83.61  E-value=0.41  Score=41.20  Aligned_cols=15  Identities=20%  Similarity=0.428  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        26 ~~GsGKSTla~~L~~   40 (202)
T 3t61_A           26 VSGSGKSSVGEAIAE   40 (202)
T ss_dssp             STTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=83.51  E-value=0.73  Score=41.04  Aligned_cols=35  Identities=26%  Similarity=0.134  Sum_probs=24.4

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEF   38 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~   38 (505)
                      ||+||||+|..++.  ..++.=..++-|+.....+..
T Consensus         9 GGvGKTt~a~~LA~--~la~~g~~VlliD~D~~~~l~   43 (254)
T 3kjh_A            9 GGVGKTTVAAGLIK--IMASDYDKIYAVDGDPDSCLG   43 (254)
T ss_dssp             SSHHHHHHHHHHHH--HHTTTCSCEEEEEECTTSCHH
T ss_pred             CCCCHHHHHHHHHH--HHHHCCCeEEEEeCCCCcChH
Confidence            89999999999987  454433456667766555443

>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=83.19  E-value=1.5  Score=42.58  Aligned_cols=43  Identities=9%  Similarity=0.059  Sum_probs=27.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCC----ceEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFE----KRTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~----~~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|+.++++  ....+.+    .++++-+++.. +..++..++..
T Consensus       160 ~G~GKt~L~~~Ia~--~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~  207 (465)
T 3vr4_D          160 SGLPHKELAAQIAR--QATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQ  207 (465)
T ss_dssp             TTSCHHHHHHHHHH--HCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             CCcChHHHHHHHHH--HHHhccCCCceEEEEEEecCCcHHHHHHHHHHhh
Confidence            69999999999988  3333222    45566666543 44455555444

>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=83.08  E-value=11  Score=36.53  Aligned_cols=15  Identities=33%  Similarity=0.297  Sum_probs=13.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||++..++.
T Consensus       108 ~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A          108 IQGSGKTTTVAKLAR  122 (443)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHH
Confidence            379999999988876

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=82.96  E-value=3.6  Score=38.52  Aligned_cols=43  Identities=12%  Similarity=0.020  Sum_probs=27.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIES   47 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~   47 (505)
                      .+|+||||||..++.  ....+=..++|++...  +...+...++..
T Consensus        54 ~pG~GKTt~al~ia~--~~a~~g~~Vl~fSlEm--s~~ql~~Rlls~   96 (338)
T 4a1f_A           54 RPSMGKTSLMMNMVL--SALNDDRGVAVFSLEM--SAEQLALRALSD   96 (338)
T ss_dssp             CTTSCHHHHHHHHHH--HHHHTTCEEEEEESSS--CHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCeEEEEeCCC--CHHHHHHHHHHH
Confidence            379999999999987  3333223566777643  345555555443

>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=82.88  E-value=0.47  Score=39.96  Aligned_cols=15  Identities=40%  Similarity=0.488  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        19 ~~GsGKst~~~~l~~   33 (180)
T 3iij_A           19 TPGVGKTTLGKELAS   33 (180)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=82.67  E-value=0.49  Score=39.27  Aligned_cols=15  Identities=40%  Similarity=0.284  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      +.|+||||+|+.++.
T Consensus        15 ~~GsGKSTva~~La~   29 (168)
T 1zuh_A           15 FMGSGKSSLAQELGL   29 (168)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=82.57  E-value=0.49  Score=40.64  Aligned_cols=15  Identities=27%  Similarity=0.304  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      +.|+||||+|+.++.
T Consensus         8 ~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            8 TVGAGKSTISAEISK   22 (205)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCccCHHHHHHHHHH
Confidence            579999999999987

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=82.46  E-value=0.49  Score=42.55  Aligned_cols=15  Identities=27%  Similarity=0.078  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||||+.++.
T Consensus         9 ~~GSGKSTla~~La~   23 (253)
T 2ze6_A            9 PTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHh
Confidence            579999999999987

>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=82.46  E-value=0.49  Score=40.71  Aligned_cols=15  Identities=40%  Similarity=0.481  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        33 ~sGsGKSTl~~~La~   47 (200)
T 3uie_A           33 LSGSGKSTLACALNQ   47 (200)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=82.29  E-value=1.8  Score=50.20  Aligned_cols=77  Identities=16%  Similarity=0.132  Sum_probs=49.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHc-CCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECV-AGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l-~~~r~   75 (505)
                      .+|+||||||.+++.  .....=..++|++.....+...     +..++.....    ...+.++..+.++... ....-
T Consensus       391 ~pGsGKTtLaLqia~--~~a~~G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~~lv~~~~~~  463 (2050)
T 3cmu_A          391 PESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  463 (2050)
T ss_dssp             CTTSSHHHHHHHHHH--HHHTTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHHHHHHhcCCc
Confidence            479999999999987  4444334678999888777642     4555532211    2344555555555433 23456


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      +||+|.+..
T Consensus       464 lIVIDSL~a  472 (2050)
T 3cmu_A          464 VIVVDSVAA  472 (2050)
T ss_dssp             EEEESCGGG
T ss_pred             EEEECCHHH
Confidence            999999854

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=82.27  E-value=0.8  Score=53.09  Aligned_cols=76  Identities=16%  Similarity=0.132  Sum_probs=46.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHc-CCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECV-AGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l-~~~r~   75 (505)
                      ++|+|||+||.+++.  +...+=..++|+++....+...     ++.++....    ......++....+.+.. ..+.-
T Consensus      1435 ppGtGKT~LA~ala~--ea~~~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~~~~ 1507 (2050)
T 3cmu_A         1435 PESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD 1507 (2050)
T ss_dssp             CTTSSHHHHHHHHHH--HHHTTTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHHHHHhcCCCC
Confidence            589999999999987  4433334577898888877655     344442111    01122334444444433 24567


Q ss_pred             EEEEeCCC
Q 046115           76 LLVLDDVW   83 (505)
Q Consensus        76 LlvlDdv~   83 (505)
                      +||+|.+.
T Consensus      1508 lVVIDsi~ 1515 (2050)
T 3cmu_A         1508 VIVVDSVA 1515 (2050)
T ss_dssp             EEEESCGG
T ss_pred             EEEEcChh
Confidence            99999983

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=82.23  E-value=0.21  Score=47.40  Aligned_cols=31  Identities=26%  Similarity=0.327  Sum_probs=20.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCC-Cc-eEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNF-EK-RTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f-~~-~~wv~~~~~   34 (505)
                      +|+|||+|+.++++  .+..+. +. ++++-+++.
T Consensus       184 ~g~GKT~Ll~~Ia~--~i~~~~~dv~~V~~lIGER  216 (427)
T 3l0o_A          184 PKAGKTTILKEIAN--GIAENHPDTIRIILLIDER  216 (427)
T ss_dssp             TTCCHHHHHHHHHH--HHHHHCTTSEEEEEECSCC
T ss_pred             CCCChhHHHHHHHH--HHhhcCCCeEEEEEEeccC
Confidence            69999999999988  544332 32 245556553

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=82.13  E-value=0.52  Score=39.80  Aligned_cols=15  Identities=33%  Similarity=0.182  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~~GsGKST~~~~La~   26 (186)
T 3cm0_A           12 PPGAGKGTQASRLAQ   26 (186)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999986

>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=82.00  E-value=0.53  Score=39.37  Aligned_cols=15  Identities=27%  Similarity=0.408  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        16 ~~GsGKSTl~~~l~~   30 (175)
T 1knq_A           16 VSGSGKSAVASEVAH   30 (175)
T ss_dssp             STTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>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=81.95  E-value=0.53  Score=39.75  Aligned_cols=15  Identities=27%  Similarity=0.419  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        10 ~~GsGKsT~a~~La~   24 (184)
T 2iyv_A           10 LPGSGKSTIGRRLAK   24 (184)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>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=81.82  E-value=0.55  Score=39.08  Aligned_cols=15  Identities=27%  Similarity=0.242  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        10 ~~GsGKsT~a~~La~   24 (173)
T 1e6c_A           10 ARGCGMTTVGRELAR   24 (173)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>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=81.73  E-value=1.3  Score=40.96  Aligned_cols=82  Identities=11%  Similarity=0.050  Sum_probs=40.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCCC--CCChhcHHHH-HHHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPGS--AKDLVEFQSL-MQHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~~--~~~~~~~~~~-~~~l~~~l~~~r~L   76 (505)
                      .+|+||||++..++.  ..+..-..+.+++..... ...+.+..+....+.+.  .....+.... .+.+...+....-+
T Consensus       112 ~~GsGKTTl~~~LA~--~l~~~g~kV~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al~~a~~~~~dv  189 (306)
T 1vma_A          112 VNGTGKTTSCGKLAK--MFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAHALARNKDV  189 (306)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCChHHHHHHHHHH--HHHhcCCEEEEEccccccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHHHHhcCCCE
Confidence            379999999999987  444332234455543221 11223344455443221  1111222222 23344444444457


Q ss_pred             EEEeCCCC
Q 046115           77 LVLDDVWN   84 (505)
Q Consensus        77 lvlDdv~~   84 (505)
                      +|+|-...
T Consensus       190 vIiDtpg~  197 (306)
T 1vma_A          190 VIIDTAGR  197 (306)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            88887643

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=81.72  E-value=2  Score=36.68  Aligned_cols=112  Identities=19%  Similarity=0.136  Sum_probs=70.5

Q ss_pred             hhHHhhcCcccceEEecccccCCccccccc-----cCccccCCCCcceeeccCCcccc-----ccchhhhcCCCCcEEec
Q 046115          375 LPQLFEKLTCLRALELQVRESWPRNNLIKE-----IPTNIEKLLHLKYLNLKGQKKIE-----KLPETLCELYNLERLNV  444 (505)
Q Consensus       375 ~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-----~p~~~~~l~~L~~L~l~~~~~~~-----~lp~~~~~l~~L~~L~l  444 (505)
                      +...+.+-++|+.|+|+      +++.++.     +-..+..-+.|+.|+|++|. ++     .+...+..-..|+.|+|
T Consensus        33 l~~ll~~n~~L~~L~L~------~nn~igd~ga~~la~aL~~N~~L~~L~L~~n~-igd~ga~alA~aL~~N~tL~~L~L  105 (197)
T 1pgv_A           33 INRLREDDTDLKEVNIN------NMKRVSKERIRSLIEAACNSKHIEKFSLANTA-ISDSEARGLIELIETSPSLRVLNV  105 (197)
T ss_dssp             HHHHHTTCSSCCEEECT------TCCSSCHHHHHHHHHHHTTCSCCCEEECTTSC-CBHHHHTTHHHHHHHCSSCCEEEC
T ss_pred             HHHHHhcCCCccEEECC------CCCCCCHHHHHHHHHHHhhCCCcCEEEccCCC-CChHHHHHHHHHHhcCCccCeEec
Confidence            44445667789999998      2224432     33445666789999999999 54     33344556688999999


Q ss_pred             CCCcCcc----ccchhccccccCceeecCCCcc--cc-----cccccccCCccCCcccee
Q 046115          445 DDCQNLR----ELPRGIGKLRKLMYLHNEDTGC--LR-----YLPAGIGELIRLRRVREF  493 (505)
Q Consensus       445 ~~~~~~~----~lp~~~~~l~~L~~L~l~~~~~--~~-----~~p~~i~~l~~L~~L~~~  493 (505)
                      ++|....    .+=..+..-+.|++|++++|..  ++     .+...+..-+.|+.|++.
T Consensus       106 ~~N~Ig~~Ga~ala~aL~~N~tL~~L~L~n~~~~~ig~~g~~~ia~aL~~N~tL~~L~l~  165 (197)
T 1pgv_A          106 ESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGIS  165 (197)
T ss_dssp             CSSBCCHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECC
T ss_pred             CCCcCCHHHHHHHHHHHhhCCceeEEECCCCcCcCcCHHHHHHHHHHHHhCCCcCeEecc
Confidence            9998321    1223455567899999986531  22     122233344566666653

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=81.37  E-value=0.59  Score=38.71  Aligned_cols=15  Identities=20%  Similarity=0.220  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         8 ~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            8 FMCSGKSTVGSLLSR   22 (168)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>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=81.30  E-value=0.44  Score=40.53  Aligned_cols=15  Identities=33%  Similarity=0.499  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||++++..
T Consensus         9 PSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            9 PSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=81.25  E-value=0.58  Score=40.35  Aligned_cols=15  Identities=33%  Similarity=0.474  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||++.++.
T Consensus        20 ~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           20 PSGVGKGTLIKKVLS   34 (204)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=81.22  E-value=12  Score=36.36  Aligned_cols=15  Identities=40%  Similarity=0.273  Sum_probs=13.3

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+||||++..++.
T Consensus       105 ~~GsGKTTt~~kLA~  119 (433)
T 3kl4_A          105 VQGSGKTTTAGKLAY  119 (433)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999886

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=81.18  E-value=0.63  Score=40.00  Aligned_cols=25  Identities=24%  Similarity=0.315  Sum_probs=18.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVS   32 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~   32 (505)
                      ++|+||||||+.++.  ..     +.++++..
T Consensus        37 ~~GsGKSTl~~~L~~--~~-----g~~~i~~d   61 (200)
T 4eun_A           37 VSGSGKTTIAHGVAD--ET-----GLEFAEAD   61 (200)
T ss_dssp             CTTSCHHHHHHHHHH--HH-----CCEEEEGG
T ss_pred             CCCCCHHHHHHHHHH--hh-----CCeEEccc
Confidence            479999999999987  33     44566543

>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=81.16  E-value=0.62  Score=39.53  Aligned_cols=15  Identities=27%  Similarity=0.344  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||++.++.
T Consensus        10 ~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A           10 PAGVGKSTTCKRLAA   24 (189)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHhc
Confidence            479999999999975

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=80.92  E-value=0.89  Score=40.29  Aligned_cols=32  Identities=25%  Similarity=0.160  Sum_probs=22.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      .+|+||||||.+++.  .....=..++|++....
T Consensus        31 ~~GsGKTtl~~~~~~--~~~~~~~~v~~~~~e~~   62 (247)
T 2dr3_A           31 GPGTGKTIFSQQFLW--NGLKMGEPGIYVALEEH   62 (247)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHTTCCEEEEESSSC
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCeEEEEEccCC
Confidence            479999999988876  33333346778876543

>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=80.91  E-value=0.61  Score=39.49  Aligned_cols=15  Identities=33%  Similarity=0.508  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        18 ~~GsGKSTv~~~La~   32 (184)
T 1y63_A           18 TPGTGKTSMAEMIAA   32 (184)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=80.87  E-value=1.7  Score=42.92  Aligned_cols=43  Identities=14%  Similarity=0.189  Sum_probs=25.9

Q ss_pred             CCCcHHHHH-HHHhcCccccc------CCCc-eEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLA-QFAYNNGDVER------NFEK-RTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA-~~~~~~~~~~~------~f~~-~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|| ..+++  +...      +-+. ++++-+++.. +..++...+..
T Consensus       171 ~g~GKT~Lal~~I~~--q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~  222 (510)
T 2ck3_A          171 RQTGKTSIAIDTIIN--QKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTD  222 (510)
T ss_dssp             TTSSHHHHHHHHHHH--THHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHH--HHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHh
Confidence            699999996 56666  3331      2343 5577777654 34455555544

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=80.87  E-value=0.61  Score=39.61  Aligned_cols=15  Identities=27%  Similarity=0.144  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ~~GsGKsT~a~~L~~   25 (196)
T 1tev_A           11 GPGAGKGTQCARIVE   25 (196)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=80.85  E-value=0.62  Score=39.26  Aligned_cols=15  Identities=13%  Similarity=0.355  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||++.+..
T Consensus        13 psGsGKSTL~~~L~~   27 (180)
T 1kgd_A           13 AHGVGRRHIKNTLIT   27 (180)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHh
Confidence            479999999999987

>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=80.66  E-value=3.2  Score=38.13  Aligned_cols=77  Identities=14%  Similarity=0.025  Sum_probs=37.3

Q ss_pred             CCCCcHHHHHHHHhcCccccc-CCCceEEEEeCCC-CCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVER-NFEKRTWVCVSEP-FDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~~~~~-~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      .+|+||||++..++.  .... .=..+..++.... ....+.+.......+.+.... .+.......+. .+ ...=++|
T Consensus       113 ~~GsGKTTl~~~LA~--~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~-~~~~~l~~al~-~~-~~~dlvI  187 (296)
T 2px0_A          113 STGAGKTTTLAKLAA--ISMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQAPLEVC-YTKEEFQQAKE-LF-SEYDHVF  187 (296)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCCEEEEECCCSSTTHHHHHHHHHTTTTCCCCBC-SSHHHHHHHHH-HG-GGSSEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCCEEEEEecCcccchHHHHHHHHHHhcCCCeEec-CCHHHHHHHHH-Hh-cCCCEEE
Confidence            379999999999987  3432 1123445554322 223333444444443222111 12233333333 23 3445788


Q ss_pred             EeCC
Q 046115           79 LDDV   82 (505)
Q Consensus        79 lDdv   82 (505)
                      +|-.
T Consensus       188 iDT~  191 (296)
T 2px0_A          188 VDTA  191 (296)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            8854

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=80.47  E-value=0.64  Score=40.16  Aligned_cols=15  Identities=27%  Similarity=0.488  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~~GsGKsT~~~~L~~   26 (213)
T 2plr_A           12 IDGSGKSSQATLLKD   26 (213)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999987

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=80.38  E-value=1.1  Score=40.33  Aligned_cols=31  Identities=26%  Similarity=0.201  Sum_probs=21.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      ||+||||+|..++.  ..+.+=..++-|+....
T Consensus        10 GGvGKTT~a~nLA~--~la~~G~~VlliD~D~q   40 (269)
T 1cp2_A           10 GGIGKSTTTQNLTS--GLHAMGKTIMVVGCDPK   40 (269)
T ss_dssp             TTSSHHHHHHHHHH--HHHTTTCCEEEEEECTT
T ss_pred             CCCcHHHHHHHHHH--HHHHCCCcEEEEcCCCC
Confidence            89999999998887  44443234566776543

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=80.34  E-value=0.47  Score=39.96  Aligned_cols=15  Identities=33%  Similarity=0.261  Sum_probs=9.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        13 ~~GsGKST~a~~La~   27 (183)
T 2vli_A           13 PFGVGKTHTAHTLHE   27 (183)
T ss_dssp             CC----CHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999986

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=80.31  E-value=4.4  Score=39.64  Aligned_cols=42  Identities=14%  Similarity=0.079  Sum_probs=26.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIE   46 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~   46 (505)
                      .+|+||||||..++.  ....+=..++|++...+..  .+...++.
T Consensus       205 ~pG~GKTtlal~ia~--~~a~~g~~vl~fSlEms~~--ql~~R~~~  246 (444)
T 3bgw_A          205 RPSMGKTAFALKQAK--NMSDNDDVVNLHSLEMGKK--ENIKRLIV  246 (444)
T ss_dssp             CSSSSHHHHHHHHHH--HHHHTTCEEEEECSSSCTT--HHHHHHHH
T ss_pred             CCCCChHHHHHHHHH--HHHHcCCEEEEEECCCCHH--HHHHHHHH
Confidence            379999999999987  3433323566777665433  34444443

>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=80.21  E-value=0.65  Score=41.90  Aligned_cols=15  Identities=27%  Similarity=0.525  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~pGSGKSTla~~La~   26 (260)
T 3a4m_A           12 LPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=80.11  E-value=1.9  Score=49.36  Aligned_cols=78  Identities=15%  Similarity=0.115  Sum_probs=48.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC----CChhcHHHHHHHHHHHc-CCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA----KDLVEFQSLMQHIEECV-AGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~~~~~l~~~l-~~~r~   75 (505)
                      .+|+||||||.+++.  .....=..++|++...+.+...     +..++....    ....+.++..+.+.... ..+.-
T Consensus       391 ~pGsGKTtLaLq~a~--~~~~~G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~i~~~~~~e~~l~~l~~lv~~~~~~  463 (1706)
T 3cmw_A          391 PESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  463 (1706)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHH--HHHHhCCCeEEEEccCchHHHH-----HHHcCCCHHHeEEcCCCCHHHHHHHHHHHHHhcCCC
Confidence            379999999999987  4444435788999888877642     445543211    11234455555554433 23456


Q ss_pred             EEEEeCCCCC
Q 046115           76 LLVLDDVWNE   85 (505)
Q Consensus        76 LlvlDdv~~~   85 (505)
                      ++|+|.+...
T Consensus       464 lVVIDSL~al  473 (1706)
T 3cmw_A          464 VIVVDSVAAL  473 (1706)
T ss_dssp             EEEESCSTTC
T ss_pred             EEEECCHHHh
Confidence            9999998553

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=80.04  E-value=0.68  Score=39.42  Aligned_cols=15  Identities=27%  Similarity=0.158  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        17 ~~GsGKsT~~~~La~   31 (196)
T 2c95_A           17 GPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            579999999999987

---

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	505
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-41
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	6e-05
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	4e-04
d1ogqa_	313	c.10.2.8 (A:) Polygalacturonase inhibiting protein	0.001

>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 =  148 bits (373), Expect = 1e-41
 Identities = 43/242 (17%), Positives = 75/242 (30%), Gaps = 31/242 (12%)

Query: 1   MGGIGKTTLAQFAYNNGD--VERNFEKRTWVCVSEPFDEFRIARAIIESLT--------- 49
             G GK+ +A  A +  D  +  N++   W+  S    +          L          
Sbjct: 52  RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLN 111

Query: 50  PGSAKDLVEFQSLMQHIEECVAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILIT 109
             S + +             +     L V DDV  E+  +W    +         + L+T
Sbjct: 112 FPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRL--------RCLVT 163

Query: 110 TRKETVARIMGST-HVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKG 168
           TR   ++     T   I V  L   EC+   ++  +      K E+   +  + ++   G
Sbjct: 164 TRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEED---VLNKTIELSSG 220

Query: 169 LPLAAKTIASLLRSKNTE--KEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCF 226
            P            K  E   +  N LE+          G+      SY  L   ++RC 
Sbjct: 221 NPATLMMFFKSCEPKTFEKMAQLNNKLESRGLV------GVECITPYSYKSLAMALQRCV 274

Query: 227 SY 228
             
Sbjct: 275 EV 276

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]} Length = 353

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]

 Score = 42.9 bits (99), Expect = 6e-05
 Identities = 22/101 (21%), Positives = 41/101 (40%), Gaps = 16/101 (15%)

Query: 368 YSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIE 427
            + SS  +  L +    L  L +        NN + E+P    +   L+ L       + 
Sbjct: 269 LNASSNEIRSLCDLPPSLEELNV-------SNNKLIELPALPPR---LERLIASF-NHLA 317

Query: 428 KLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHN 468
           ++PE      NL++L+V+    LRE P     +  L  +++
Sbjct: 318 EVPELPQ---NLKQLHVEYNP-LREFPDIPESVEDL-RMNS 353

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]} Length = 305

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]

 Score = 40.0 bits (92), Expect = 4e-04
 Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 7/94 (7%)

Query: 383 TCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERL 442
                L+LQ       N + +    + + L +L  L L   K  +  P     L  LERL
Sbjct: 31  PDTALLDLQ------NNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERL 84

Query: 443 NVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRY 476
            +   Q L+ELP  + K  + + +H  +   +R 
Sbjct: 85  YLSKNQ-LKELPEKMPKTLQELRVHENEITKVRK 117

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]} Length = 313

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]

 Score = 39.0 bits (89), Expect = 0.001
 Identities = 10/57 (17%), Positives = 21/57 (36%), Gaps = 1/57 (1%)

Query: 398 RNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELP 454
            N +   +P  + +L  L  LN+       ++P+    L   +     + + L   P
Sbjct: 253 NNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQ-GGNLQRFDVSAYANNKCLCGSP 308

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	505
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.97
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.4
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.35
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.22
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.18
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.15
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.15
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.15
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.12
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.11
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.11
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.1
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.08
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.05
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.04
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.01
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.95
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.92
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	98.91
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	98.9
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	98.89
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.8
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.78
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	98.77
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.74
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	98.7
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.58
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.56
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.55
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.35
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.33
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.17
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	98.13
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	98.11
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.02
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.98
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.96
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.89
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	97.86
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.85
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.82
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.8
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.61
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.6
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.59
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.41
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.27
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	97.26
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.25
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.2
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.03
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.02
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	97.01
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.97
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.96
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	96.85
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.84
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.84
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.33
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.04
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.04
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	95.93
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	95.43
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.35
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.94
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.92
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	94.1
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	94.1
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	93.63
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.07
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.03
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	92.8
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	92.54
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	91.97
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	91.92
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	91.67
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.49
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	91.28
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	91.13
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	90.67
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	90.64
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	90.45
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	89.93
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	89.87
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	89.8
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	89.72
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	89.61
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	89.35
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	89.25
d1ls1a2	207	GTPase domain of the signal sequence recognition p	89.22
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	88.88
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	88.85
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	88.36
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	88.19
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	88.03
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	87.8
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	87.73
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	87.57
d2qy9a2	211	GTPase domain of the signal recognition particle r	87.43
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	87.42
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	87.11
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	86.75
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	86.7
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	86.47
d1okkd2	207	GTPase domain of the signal recognition particle r	86.37
d1xpua3	289	Transcription termination factor Rho, ATPase domai	85.37
d2awna2	232	Maltose transport protein MalK, N-terminal domain	85.36
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	85.09
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.93
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	84.9
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	84.89
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	84.89
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	84.76
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	84.75
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	84.62
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	84.46
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	83.61
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	83.61
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	83.49
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	83.16
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	82.88
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	82.32
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	82.16
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	82.02
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	81.8
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	81.53
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	81.48
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	81.36
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	80.36

>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=99.97  E-value=8.6e-32  Score=249.71  Aligned_cols=214  Identities=17%  Similarity=0.173  Sum_probs=162.8

Q ss_pred             CCCCcHHHHHHHHhcCcc--cccCCCceEEEEeCCCCCHHHHHHHHHH---HcCCCC------CCChhcHHHHHHHHHHH
Q 046115            1 MGGIGKTTLAQFAYNNGD--VERNFEKRTWVCVSEPFDEFRIARAIIE---SLTPGS------AKDLVEFQSLMQHIEEC   69 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~--~~~~f~~~~wv~~~~~~~~~~~~~~l~~---~l~~~~------~~~~~~~~~~~~~l~~~   69 (505)
                      |||+||||||++++++..  ...+|++++|+++++.++...+...+..   .+....      .....+.......+...
T Consensus        52 mgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (277)
T d2a5yb3          52 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNAL  131 (277)
T ss_dssp             STTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHH
Confidence            899999999999987432  5667899999999998887666555533   333211      11223334445567788


Q ss_pred             cCCceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhCCc-ceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           70 VAGKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKETVARIMGST-HVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        70 l~~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~~~-~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      +.++|+|+||||||+...  +..+.      ..+|+||||||++.++..+... +.|++++|+.+||++||..+++... 
T Consensus       132 L~~kr~LlVLDDv~~~~~--~~~~~------~~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~-  202 (277)
T d2a5yb3         132 IDRPNTLFVFDDVVQEET--IRWAQ------ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMP-  202 (277)
T ss_dssp             TTSTTEEEEEEEECCHHH--HHHHH------HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC-
T ss_pred             hccCCeeEecchhhHHhh--hhhhc------ccCceEEEEeehHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCcc-
Confidence            899999999999998653  32222      2579999999999988776543 6899999999999999999886443 


Q ss_pred             CCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCHHHHHHHHhhhhhhhhhcccCchhhHhhccccCChhhhhhhhh
Q 046115          149 IGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTEKEWQNILENEIWELEAIEKGLLAPLLLSYNELPSKVKRCFSY  228 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~~s~~~L~~~~~~~ll~  228 (505)
                        ..+..++++++|+++|+|+||||+++|+.++.+ +.+.|.........   .....+..++..||+.|+++.|.||.+
T Consensus       203 --~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k-~~~~~~~~~~~L~~---~~~~~v~~il~~sY~~L~~~lk~c~~~  276 (277)
T d2a5yb3         203 --VGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK-TFEKMAQLNNKLES---RGLVGVECITPYSYKSLAMALQRCVEV  276 (277)
T ss_dssp             ----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS-SHHHHHHHHHHHHH---HCSSTTCCCSSSSSSSHHHHHHHHHHT
T ss_pred             --CchhhHHHHHHHHHHhCCCHHHHHHHHHHhccC-CHHHHHHHHHHHhc---CcHHHHHHHHHHHHhcccHHHHHHHHh
Confidence              344567889999999999999999999999766 67788765554321   234678899999999999999999976


Q ss_pred             h
Q 046115          229 C  229 (505)
Q Consensus       229 l  229 (505)
                      +
T Consensus       277 l  277 (277)
T d2a5yb3         277 L  277 (277)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.40  E-value=3.2e-13  Score=113.05  Aligned_cols=131  Identities=21%  Similarity=0.182  Sum_probs=109.7

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccch
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE  431 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~  431 (505)
                      +.++..++.|++++|.++..    +..+..+.+|+.|+|+       ++.+..++ .++.+++|++|++++|. +..+|.
T Consensus        14 ~~n~~~lr~L~L~~n~I~~i----~~~~~~l~~L~~L~Ls-------~N~i~~l~-~~~~l~~L~~L~ls~N~-i~~l~~   80 (162)
T d1a9na_          14 YTNAVRDRELDLRGYKIPVI----ENLGATLDQFDAIDFS-------DNEIRKLD-GFPLLRRLKTLLVNNNR-ICRIGE   80 (162)
T ss_dssp             EECTTSCEEEECTTSCCCSC----CCGGGGTTCCSEEECC-------SSCCCEEC-CCCCCSSCCEEECCSSC-CCEECS
T ss_pred             ccCcCcCcEEECCCCCCCcc----CccccccccCCEEECC-------CCCCCccC-CcccCcchhhhhccccc-ccCCCc
Confidence            34778899999999998764    4445778999999999       77788875 48899999999999999 888876


Q ss_pred             hh-hcCCCCcEEecCCCcCccccch--hccccccCceeecCCCcccccccc----cccCCccCCccceeEecC
Q 046115          432 TL-CELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCLRYLPA----GIGELIRLRRVREFVVGG  497 (505)
Q Consensus       432 ~~-~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~~p~----~i~~l~~L~~L~~~~~~~  497 (505)
                      .+ ..+++|+.|++++|. +..++.  .+..+++|++|++++|+ +...|.    .+..+++|+.|+...|+.
T Consensus        81 ~~~~~l~~L~~L~L~~N~-i~~~~~l~~l~~l~~L~~L~l~~N~-i~~~~~~r~~~i~~lp~L~~LD~~~i~~  151 (162)
T d1a9na_          81 GLDQALPDLTELILTNNS-LVELGDLDPLASLKSLTYLCILRNP-VTNKKHYRLYVIYKVPQVRVLDFQKVKL  151 (162)
T ss_dssp             CHHHHCTTCCEEECCSCC-CCCGGGGGGGGGCTTCCEEECCSSG-GGGSTTHHHHHHHHCTTCSEETTEECCH
T ss_pred             cccccccccccceecccc-ccccccccccccccccchhhcCCCc-cccccchHHHHHHHCCCcCeeCCCCCCH
Confidence            55 679999999999998 777764  57889999999999998 455653    478899999999887765

>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=99.35  E-value=2e-12  Score=102.76  Aligned_cols=101  Identities=18%  Similarity=0.281  Sum_probs=88.7

Q ss_pred             eEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCC
Q 046115          359 RSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYN  438 (505)
Q Consensus       359 ~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~  438 (505)
                      |+|++++|.++..    +. +..+.+|++|+++       ++.+..+|+.++.+++|++|++++|. ++.+|. +..+++
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~~   66 (124)
T d1dcea3           1 RVLHLAHKDLTVL----CH-LEQLLLVTHLDLS-------HNRLRALPPALAALRCLEVLQASDNA-LENVDG-VANLPR   66 (124)
T ss_dssp             SEEECTTSCCSSC----CC-GGGGTTCCEEECC-------SSCCCCCCGGGGGCTTCCEEECCSSC-CCCCGG-GTTCSS
T ss_pred             CEEEcCCCCCCCC----cc-cccCCCCCEEECC-------CCccCcchhhhhhhhccccccccccc-ccccCc-cccccc
Confidence            6799999998753    33 7889999999999       78889999889999999999999999 888886 999999


Q ss_pred             CcEEecCCCcCccccch--hccccccCceeecCCCccc
Q 046115          439 LERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       439 L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~  474 (505)
                      |+.|++++|+ +..+|.  .+..+++|++|++++|+..
T Consensus        67 L~~L~l~~N~-i~~~~~~~~l~~~~~L~~L~l~~N~i~  103 (124)
T d1dcea3          67 LQELLLCNNR-LQQSAAIQPLVSCPRLVLLNLQGNSLC  103 (124)
T ss_dssp             CCEEECCSSC-CCSSSTTGGGGGCTTCCEEECTTSGGG
T ss_pred             cCeEECCCCc-cCCCCCchhhcCCCCCCEEECCCCcCC
Confidence            9999999998 777764  5889999999999999843

>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=99.22  E-value=5.6e-11  Score=104.00  Aligned_cols=140  Identities=24%  Similarity=0.347  Sum_probs=112.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++.     +..+++|+.|.+++|.++.    +|. +..+++|+.|++.       ++....++ .+
T Consensus        69 ~L~~L~L~~n~i~~l~~-----~~~l~~L~~L~l~~n~i~~----l~~-l~~l~~L~~L~l~-------~~~~~~~~-~l  130 (210)
T d1h6ta2          69 NVTKLFLNGNKLTDIKP-----LANLKNLGWLFLDENKVKD----LSS-LKDLKKLKSLSLE-------HNGISDIN-GL  130 (210)
T ss_dssp             TCCEEECCSSCCCCCGG-----GTTCTTCCEEECCSSCCCC----GGG-GTTCTTCCEEECT-------TSCCCCCG-GG
T ss_pred             CCCEEeCCCccccCccc-----cccCccccccccccccccc----ccc-ccccccccccccc-------cccccccc-cc
Confidence            67788887777665543     3478999999999998765    443 7788999999998       55455544 47


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+++++.+++++|. +...+. ++.+++|+.+++++|. +..+++ +.++++|++|++++|. +..+| .+.++++|++
T Consensus       131 ~~l~~l~~l~~~~n~-l~~~~~-~~~l~~L~~l~l~~n~-l~~i~~-l~~l~~L~~L~Ls~N~-i~~l~-~l~~l~~L~~  204 (210)
T d1h6ta2         131 VHLPQLESLYLGNNK-ITDITV-LSRLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNH-ISDLR-ALAGLKNLDV  204 (210)
T ss_dssp             GGCTTCCEEECCSSC-CCCCGG-GGGCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCBCG-GGTTCTTCSE
T ss_pred             ccccccccccccccc-cccccc-cccccccccccccccc-cccccc-ccCCCCCCEEECCCCC-CCCCh-hhcCCCCCCE
Confidence            889999999999988 666654 8889999999999998 677764 8899999999999997 55676 5899999999


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       205 L~Ls  208 (210)
T d1h6ta2         205 LELF  208 (210)
T ss_dssp             EEEE
T ss_pred             EEcc
Confidence            9875

>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=99.18  E-value=3.3e-11  Score=95.51  Aligned_cols=95  Identities=26%  Similarity=0.331  Sum_probs=81.6

Q ss_pred             ceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCce
Q 046115          386 RALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMY  465 (505)
Q Consensus       386 ~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~  465 (505)
                      |+|+|+       ++.+..++. ++.+++|++|++++|. ++.+|+.++.+++|+.|++++|. +..+| ++..+++|++
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~~   69 (124)
T d1dcea3           1 RVLHLA-------HKDLTVLCH-LEQLLLVTHLDLSHNR-LRALPPALAALRCLEVLQASDNA-LENVD-GVANLPRLQE   69 (124)
T ss_dssp             SEEECT-------TSCCSSCCC-GGGGTTCCEEECCSSC-CCCCCGGGGGCTTCCEEECCSSC-CCCCG-GGTTCSSCCE
T ss_pred             CEEEcC-------CCCCCCCcc-cccCCCCCEEECCCCc-cCcchhhhhhhhccccccccccc-ccccC-ccccccccCe
Confidence            578998       777888874 8999999999999999 89999889999999999999998 88887 5899999999


Q ss_pred             eecCCCcccccccc--cccCCccCCccce
Q 046115          466 LHNEDTGCLRYLPA--GIGELIRLRRVRE  492 (505)
Q Consensus       466 L~l~~~~~~~~~p~--~i~~l~~L~~L~~  492 (505)
                      |++++|. +..+|.  .+..+++|+.|++
T Consensus        70 L~l~~N~-i~~~~~~~~l~~~~~L~~L~l   97 (124)
T d1dcea3          70 LLLCNNR-LQQSAAIQPLVSCPRLVLLNL   97 (124)
T ss_dssp             EECCSSC-CCSSSTTGGGGGCTTCCEEEC
T ss_pred             EECCCCc-cCCCCCchhhcCCCCCCEEEC
Confidence            9999998 555653  4677777777765

>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=99.15  E-value=1.7e-10  Score=100.00  Aligned_cols=137  Identities=21%  Similarity=0.334  Sum_probs=92.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++.     +.++++|+.|++.+|....    ++. +..+.+|+.|+++       ++.....+ .+
T Consensus        63 nL~~L~Ls~N~l~~~~~-----l~~l~~L~~L~l~~n~~~~----~~~-l~~l~~L~~L~l~-------~~~~~~~~-~~  124 (199)
T d2omxa2          63 NLTQINFSNNQLTDITP-----LKNLTKLVDILMNNNQIAD----ITP-LANLTNLTGLTLF-------NNQITDID-PL  124 (199)
T ss_dssp             TCCEEECCSSCCCCCGG-----GTTCTTCCEEECCSSCCCC----CGG-GTTCTTCSEEECC-------SSCCCCCG-GG
T ss_pred             CcCcCccccccccCccc-----ccCCccccccccccccccc----ccc-ccccccccccccc-------cccccccc-cc
Confidence            56666666665544332     4477777788777776543    232 6677777777776       44343333 36


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+++|++|++++|. +..++. +..+++|+.|++++|. +..+| .++++++|++|++++|+ +..+| .+.++++|+.
T Consensus       125 ~~l~~L~~L~l~~n~-l~~~~~-l~~~~~L~~L~l~~n~-l~~l~-~l~~l~~L~~L~ls~N~-i~~i~-~l~~L~~L~~  198 (199)
T d2omxa2         125 KNLTNLNRLELSSNT-ISDISA-LSGLTSLQQLNFSSNQ-VTDLK-PLANLTTLERLDISSNK-VSDIS-VLAKLTNLES  198 (199)
T ss_dssp             TTCTTCSEEECCSSC-CCCCGG-GTTCTTCSEEECCSSC-CCCCG-GGTTCTTCCEEECCSSC-CCCCG-GGGGCTTCSE
T ss_pred             chhhhhHHhhhhhhh-hccccc-cccccccccccccccc-ccCCc-cccCCCCCCEEECCCCC-CCCCc-cccCCCCCCc
Confidence            677888888888887 666664 7788888888888877 66665 37778888888888886 44554 4667777765


Q ss_pred             c
Q 046115          490 V  490 (505)
Q Consensus       490 L  490 (505)
                      |
T Consensus       199 L  199 (199)
T d2omxa2         199 L  199 (199)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.15  E-value=4.6e-11  Score=111.68  Aligned_cols=148  Identities=20%  Similarity=0.240  Sum_probs=115.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecC-CCccccccchhHHhhcCcccceEEecccccCCccccccccCcc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKS-DEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~-~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~  408 (505)
                      ++..+.+....... ...++..++++++|++|++++ |.+++.   +|..+.++++|++|+|+      ++...+..|..
T Consensus        51 ~v~~L~L~~~~l~g-~~~lp~~l~~L~~L~~L~Ls~~N~l~g~---iP~~i~~L~~L~~L~Ls------~N~l~~~~~~~  120 (313)
T d1ogqa_          51 RVNNLDLSGLNLPK-PYPIPSSLANLPYLNFLYIGGINNLVGP---IPPAIAKLTQLHYLYIT------HTNVSGAIPDF  120 (313)
T ss_dssp             CEEEEEEECCCCSS-CEECCGGGGGCTTCSEEEEEEETTEESC---CCGGGGGCTTCSEEEEE------EECCEEECCGG
T ss_pred             EEEEEECCCCCCCC-CCCCChHHhcCccccccccccccccccc---cccccccccccchhhhc------ccccccccccc
Confidence            57777777765542 123455667999999999987 666654   78889999999999998      23334445566


Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccC-ceeecCCCcccccccccccCCccC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKL-MYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L-~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      +..+.+|++++++.|.....+|..++.+++|+.+++++|.....+|..+..+.++ +.+.+++|...+..|..+..+..+
T Consensus       121 ~~~~~~L~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~~~  200 (313)
T d1ogqa_         121 LSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLA  200 (313)
T ss_dssp             GGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCCS
T ss_pred             ccchhhhcccccccccccccCchhhccCcccceeeccccccccccccccccccccccccccccccccccccccccccccc
Confidence            7889999999999998778889999999999999999999777899988888876 888899998777777777665433

>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=99.15  E-value=7.5e-11  Score=107.34  Aligned_cols=126  Identities=26%  Similarity=0.300  Sum_probs=76.5

Q ss_pred             CCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCcceeeccCCccccccchh
Q 046115          354 GLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPET  432 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp~~  432 (505)
                      .+++|++|++++|.+..    .+..+..+.+|+.|+++       ++.+..+ +..+..+.++++|++++|. +..+|..
T Consensus        75 ~l~~L~~L~Ls~N~l~~----~~~~~~~l~~L~~L~l~-------~~~~~~~~~~~~~~l~~l~~L~l~~n~-l~~l~~~  142 (266)
T d1p9ag_          75 TLPVLGTLDLSHNQLQS----LPLLGQTLPALTVLDVS-------FNRLTSLPLGALRGLGELQELYLKGNE-LKTLPPG  142 (266)
T ss_dssp             CCTTCCEEECCSSCCSS----CCCCTTTCTTCCEEECC-------SSCCCCCCSSTTTTCTTCCEEECTTSC-CCCCCTT
T ss_pred             ccccccccccccccccc----ccccccccccccccccc-------ccccceeeccccccccccccccccccc-cceeccc
Confidence            44555555555554433    22234445555555555       2223232 2334455666666666665 5555543


Q ss_pred             -hhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          433 -LCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       433 -~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                       +..+++|+.+++++|. +..+|. .+..+++|++|++++|. +..+|..+..+++|+.|.+.
T Consensus       143 ~~~~l~~l~~l~l~~N~-l~~~~~~~~~~l~~L~~L~Ls~N~-L~~lp~~~~~~~~L~~L~L~  203 (266)
T d1p9ag_         143 LLTPTPKLEKLSLANNN-LTELPAGLLNGLENLDTLLLQENS-LYTIPKGFFGSHLLPFAFLH  203 (266)
T ss_dssp             TTTTCTTCCEEECTTSC-CSCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCCCSEEECC
T ss_pred             cccccccchhccccccc-ccccCccccccccccceeecccCC-CcccChhHCCCCCCCEEEec
Confidence             3567788888888887 555654 46778888888888887 55788888777777777653

>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=99.12  E-value=2.6e-10  Score=98.72  Aligned_cols=140  Identities=21%  Similarity=0.269  Sum_probs=111.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .++.+.+.......++     .+..+++|++|++++|.++..    +. +..+++|+.|+++       ++.+..++. +
T Consensus        41 ~l~~L~l~~~~i~~l~-----~l~~l~nL~~L~Ls~N~l~~~----~~-l~~l~~L~~L~l~-------~n~~~~~~~-l  102 (199)
T d2omxa2          41 QVTTLQADRLGIKSID-----GVEYLNNLTQINFSNNQLTDI----TP-LKNLTKLVDILMN-------NNQIADITP-L  102 (199)
T ss_dssp             TCCEEECTTSCCCCCT-----TGGGCTTCCEEECCSSCCCCC----GG-GTTCTTCCEEECC-------SSCCCCCGG-G
T ss_pred             CCCEEECCCCCCCCcc-----ccccCCCcCcCccccccccCc----cc-ccCCccccccccc-------ccccccccc-c
Confidence            5566666666665543     234789999999999998764    33 7899999999998       666666664 8


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|++|++++|. ...++. +..+++|+.|++++|. +..+| .+..+++|+.|++.+|. +..++ .++++++|+.
T Consensus       103 ~~l~~L~~L~l~~~~-~~~~~~-~~~l~~L~~L~l~~n~-l~~~~-~l~~~~~L~~L~l~~n~-l~~l~-~l~~l~~L~~  176 (199)
T d2omxa2         103 ANLTNLTGLTLFNNQ-ITDIDP-LKNLTNLNRLELSSNT-ISDIS-ALSGLTSLQQLNFSSNQ-VTDLK-PLANLTTLER  176 (199)
T ss_dssp             TTCTTCSEEECCSSC-CCCCGG-GTTCTTCSEEECCSSC-CCCCG-GGTTCTTCSEEECCSSC-CCCCG-GGTTCTTCCE
T ss_pred             ccccccccccccccc-cccccc-cchhhhhHHhhhhhhh-hcccc-ccccccccccccccccc-ccCCc-cccCCCCCCE
Confidence            899999999999998 555655 8899999999999998 66665 57889999999999997 44555 4888888888


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       177 L~ls  180 (199)
T d2omxa2         177 LDIS  180 (199)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8764

>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=99.11  E-value=3.1e-10  Score=103.12  Aligned_cols=147  Identities=19%  Similarity=0.177  Sum_probs=116.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++..   .|.++++|+.|++.+|.++..    |. +..+++|+.|+|+       ++.+...|..+
T Consensus        32 ~l~~L~Ls~N~i~~l~~~---~f~~l~~L~~L~L~~N~l~~l----~~-~~~l~~L~~L~Ls-------~N~l~~~~~~~   96 (266)
T d1p9ag_          32 DTTILHLSENLLYTFSLA---TLMPYTRLTQLNLDRAELTKL----QV-DGTLPVLGTLDLS-------HNQLQSLPLLG   96 (266)
T ss_dssp             TCCEEECTTSCCSEEEGG---GGTTCTTCCEEECTTSCCCEE----EC-CSCCTTCCEEECC-------SSCCSSCCCCT
T ss_pred             CCCEEECcCCcCCCcCHH---Hhhcccccccccccccccccc----cc-ccccccccccccc-------ccccccccccc
Confidence            677787777777766543   345889999999999988753    33 5678999999998       67777888888


Q ss_pred             cCCCCcceeeccCCcccccc-chhhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccccccCCccC
Q 046115          410 EKLLHLKYLNLKGQKKIEKL-PETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      ..+++|++|+++++. ...+ +..+..+.+++.|++++|. +..+|+. +..+++|+.+++++|......+..|..+++|
T Consensus        97 ~~l~~L~~L~l~~~~-~~~~~~~~~~~l~~l~~L~l~~n~-l~~l~~~~~~~l~~l~~l~l~~N~l~~~~~~~~~~l~~L  174 (266)
T d1p9ag_          97 QTLPALTVLDVSFNR-LTSLPLGALRGLGELQELYLKGNE-LKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENL  174 (266)
T ss_dssp             TTCTTCCEEECCSSC-CCCCCSSTTTTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTC
T ss_pred             ccccccccccccccc-cceeeccccccccccccccccccc-cceeccccccccccchhcccccccccccCcccccccccc
Confidence            999999999999998 5544 4456789999999999998 7777765 6778999999999998554444558889999


Q ss_pred             Ccccee
Q 046115          488 RRVREF  493 (505)
Q Consensus       488 ~~L~~~  493 (505)
                      ++|++.
T Consensus       175 ~~L~Ls  180 (266)
T d1p9ag_         175 DTLLLQ  180 (266)
T ss_dssp             CEEECC
T ss_pred             ceeecc
Confidence            888764

>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=99.11  E-value=9e-13  Score=114.25  Aligned_cols=132  Identities=20%  Similarity=0.214  Sum_probs=107.8

Q ss_pred             CCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccch
Q 046115          352 VTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE  431 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~  431 (505)
                      +..+++|+.|++++|.++..    +. +..+++|+.|+|+       ++.+..+|.....+++|++|++++|. ++.++.
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~~  110 (198)
T d1m9la_          44 LSTLKACKHLALSTNNIEKI----SS-LSGMENLRILSLG-------RNLIKKIENLDAVADTLEELWISYNQ-IASLSG  110 (198)
T ss_dssp             HHHTTTCCEEECSEEEESCC----CC-HHHHTTCCEEECC-------EEEECSCSSHHHHHHHCCEEECSEEE-CCCHHH
T ss_pred             HhcccccceeECcccCCCCc----cc-ccCCccccChhhc-------cccccccccccccccccccccccccc-cccccc
Confidence            44789999999999988753    32 7789999999998       77788888766667889999999998 888876


Q ss_pred             hhhcCCCCcEEecCCCcCccccch--hccccccCceeecCCCccccccccc----------ccCCccCCccceeEecCc
Q 046115          432 TLCELYNLERLNVDDCQNLRELPR--GIGKLRKLMYLHNEDTGCLRYLPAG----------IGELIRLRRVREFVVGGG  498 (505)
Q Consensus       432 ~~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~~p~~----------i~~l~~L~~L~~~~~~~~  498 (505)
                       +..+++|+.|++++|. +..++.  .+..+++|++|++++|+.....+..          +..+++|+.|+...|+..
T Consensus       111 -~~~l~~L~~L~L~~N~-i~~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~~~~r~~vi~~lp~L~~LD~~~I~~~  187 (198)
T d1m9la_         111 -IEKLVNLRVLYMSNNK-ITNWGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLDGMPVDVD  187 (198)
T ss_dssp             -HHHHHHSSEEEESEEE-CCCHHHHHHHTTTTTCSEEEECSSHHHHHHCTTTTHHHHHHHHHHHCSSCCEESSGGGTTT
T ss_pred             -ccccccccccccccch-hccccccccccCCCccceeecCCCccccCcccccchhhHHHHHHHHCCCcCEeCCccCCHH
Confidence             8899999999999998 777763  6899999999999999854433322          567889999987776653

>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=99.10  E-value=2e-10  Score=107.13  Aligned_cols=125  Identities=22%  Similarity=0.306  Sum_probs=69.1

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcC
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCEL  436 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l  436 (505)
                      .++.|++.++.+++... +|..++++++|++|+|+++     ++..+.+|..++.+++|++|+|++|...+..|..+..+
T Consensus        51 ~v~~L~L~~~~l~g~~~-lp~~l~~L~~L~~L~Ls~~-----N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~  124 (313)
T d1ogqa_          51 RVNNLDLSGLNLPKPYP-IPSSLANLPYLNFLYIGGI-----NNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQI  124 (313)
T ss_dssp             CEEEEEEECCCCSSCEE-CCGGGGGCTTCSEEEEEEE-----TTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGC
T ss_pred             EEEEEECCCCCCCCCCC-CChHHhcCccccccccccc-----cccccccccccccccccchhhhccccccccccccccch
Confidence            45566666665554322 4555666666666666510     22334556666666666666666666333344445556


Q ss_pred             CCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccC
Q 046115          437 YNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       437 ~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      .+|+.+++++|.....+|..+.++++|+++++++|...+.+|..+..+..+
T Consensus       125 ~~L~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l  175 (313)
T d1ogqa_         125 KTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKL  175 (313)
T ss_dssp             TTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTT
T ss_pred             hhhcccccccccccccCchhhccCcccceeecccccccccccccccccccc
Confidence            666666666665555556666666666666666665555555555544443

>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=99.08  E-value=2.1e-10  Score=98.74  Aligned_cols=119  Identities=27%  Similarity=0.314  Sum_probs=86.0

Q ss_pred             cCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-cCccccCCCCcce
Q 046115          339 RRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-IPTNIEKLLHLKY  417 (505)
Q Consensus       339 ~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~p~~~~~l~~L~~  417 (505)
                      +....+|.+++      +++++|++++|.++...  .+..|..+.+|+.|+|+       ++.+.. .+..+..+++|++
T Consensus        18 ~~L~~iP~~lp------~~l~~L~Ls~N~i~~~~--~~~~f~~l~~L~~L~L~-------~N~i~~~~~~~~~~~~~L~~   82 (192)
T d1w8aa_          18 RGLKEIPRDIP------LHTTELLLNDNELGRIS--SDGLFGRLPHLVKLELK-------RNQLTGIEPNAFEGASHIQE   82 (192)
T ss_dssp             SCCSSCCSCCC------TTCSEEECCSCCCCSBC--CSCSGGGCTTCCEEECC-------SSCCCCBCTTTTTTCTTCCE
T ss_pred             CCcCccCCCCC------CCCCEEEeCCCCCcccc--cccccCCCceEeeeecc-------ccccccccccccccccccce
Confidence            34445554443      57888888888876431  34446778888888887       444444 4556777888888


Q ss_pred             eeccCCccccccch-hhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCccc
Q 046115          418 LNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       418 L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~  474 (505)
                      |+|++|+ +..+|+ .+..+++|+.|+|++|. +..+|+. +..+++|++|++++|...
T Consensus        83 L~Ls~N~-l~~l~~~~F~~l~~L~~L~L~~N~-l~~i~~~~f~~l~~L~~l~L~~N~~~  139 (192)
T d1w8aa_          83 LQLGENK-IKEISNKMFLGLHQLKTLNLYDNQ-ISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             EECCSCC-CCEECSSSSTTCTTCCEEECCSSC-CCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             eeecccc-ccccCHHHHhCCCcccccccCCcc-ccccCHHHhcCCcccccccccccccc
Confidence            8888888 777755 46788888888888888 7777654 678888888888888743

>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=99.05  E-value=1.2e-10  Score=96.90  Aligned_cols=104  Identities=20%  Similarity=0.191  Sum_probs=87.4

Q ss_pred             hhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchh-c
Q 046115          379 FEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRG-I  457 (505)
Q Consensus       379 ~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~-~  457 (505)
                      +.++.+++.|+|+       ++.+..+|..+..+++|++|++++|. +..++. +..+++|++|++++|. +..+|+. +
T Consensus        14 ~~n~~~lr~L~L~-------~n~I~~i~~~~~~l~~L~~L~Ls~N~-i~~l~~-~~~l~~L~~L~ls~N~-i~~l~~~~~   83 (162)
T d1a9na_          14 YTNAVRDRELDLR-------GYKIPVIENLGATLDQFDAIDFSDNE-IRKLDG-FPLLRRLKTLLVNNNR-ICRIGEGLD   83 (162)
T ss_dssp             EECTTSCEEEECT-------TSCCCSCCCGGGGTTCCSEEECCSSC-CCEECC-CCCCSSCCEEECCSSC-CCEECSCHH
T ss_pred             ccCcCcCcEEECC-------CCCCCccCccccccccCCEEECCCCC-CCccCC-cccCcchhhhhccccc-ccCCCcccc
Confidence            4567789999999       88888888767889999999999999 888875 8999999999999999 8888776 4


Q ss_pred             cccccCceeecCCCcccccccc--cccCCccCCcccee
Q 046115          458 GKLRKLMYLHNEDTGCLRYLPA--GIGELIRLRRVREF  493 (505)
Q Consensus       458 ~~l~~L~~L~l~~~~~~~~~p~--~i~~l~~L~~L~~~  493 (505)
                      ..+++|++|++++|. +..++.  .+..+++|++|++.
T Consensus        84 ~~l~~L~~L~L~~N~-i~~~~~l~~l~~l~~L~~L~l~  120 (162)
T d1a9na_          84 QALPDLTELILTNNS-LVELGDLDPLASLKSLTYLCIL  120 (162)
T ss_dssp             HHCTTCCEEECCSCC-CCCGGGGGGGGGCTTCCEEECC
T ss_pred             ccccccccceecccc-ccccccccccccccccchhhcC
Confidence            679999999999997 455553  46777777777655

>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=99.04  E-value=7.7e-10  Score=96.56  Aligned_cols=140  Identities=21%  Similarity=0.264  Sum_probs=110.2

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....+++     +..+++|++|++++|.++..    +. +..+++|++|+++       ++.+..+| .+
T Consensus        47 ~L~~L~l~~~~i~~l~~-----l~~l~~L~~L~L~~n~i~~l----~~-~~~l~~L~~L~l~-------~n~i~~l~-~l  108 (210)
T d1h6ta2          47 SIDQIIANNSDIKSVQG-----IQYLPNVTKLFLNGNKLTDI----KP-LANLKNLGWLFLD-------ENKVKDLS-SL  108 (210)
T ss_dssp             TCCEEECTTSCCCCCTT-----GGGCTTCCEEECCSSCCCCC----GG-GTTCTTCCEEECC-------SSCCCCGG-GG
T ss_pred             CccEEECcCCCCCCchh-----HhhCCCCCEEeCCCccccCc----cc-cccCccccccccc-------cccccccc-cc
Confidence            45555555555554432     34789999999999998764    33 6789999999998       66777777 48


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      +.+++|+.|++++|. ...++. +..+++|+.+++++|. +...+ .+..+++|+++++++|.. ..++ .+.++++|+.
T Consensus       109 ~~l~~L~~L~l~~~~-~~~~~~-l~~l~~l~~l~~~~n~-l~~~~-~~~~l~~L~~l~l~~n~l-~~i~-~l~~l~~L~~  182 (210)
T d1h6ta2         109 KDLKKLKSLSLEHNG-ISDING-LVHLPQLESLYLGNNK-ITDIT-VLSRLTKLDTLSLEDNQI-SDIV-PLAGLTKLQN  182 (210)
T ss_dssp             TTCTTCCEEECTTSC-CCCCGG-GGGCTTCCEEECCSSC-CCCCG-GGGGCTTCSEEECCSSCC-CCCG-GGTTCTTCCE
T ss_pred             ccccccccccccccc-cccccc-cccccccccccccccc-ccccc-cccccccccccccccccc-cccc-cccCCCCCCE
Confidence            899999999999998 667765 8899999999999988 55544 577899999999999984 4555 4888888988


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++.
T Consensus       183 L~Ls  186 (210)
T d1h6ta2         183 LYLS  186 (210)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8764

>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=99.01  E-value=8.1e-10  Score=101.41  Aligned_cols=131  Identities=25%  Similarity=0.320  Sum_probs=80.1

Q ss_pred             CCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCcccccc
Q 046115          351 NVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKL  429 (505)
Q Consensus       351 ~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~l  429 (505)
                      .+.++++|++|.+.+|.....   .+..+..+.+|+.++++       ++.+..+| ..+..+++|+.|++++|. +..+
T Consensus       100 ~~~~l~~L~~L~l~~n~~~~~---~~~~~~~~~~L~~l~l~-------~N~l~~i~~~~f~~~~~L~~L~l~~N~-l~~l  168 (284)
T d1ozna_         100 TFHGLGRLHTLHLDRCGLQEL---GPGLFRGLAALQYLYLQ-------DNALQALPDDTFRDLGNLTHLFLHGNR-ISSV  168 (284)
T ss_dssp             TTTTCTTCCEEECTTSCCCCC---CTTTTTTCTTCCEEECC-------SSCCCCCCTTTTTTCTTCCEEECCSSC-CCEE
T ss_pred             hhcccccCCEEecCCcccccc---cccccchhcccchhhhc-------cccccccChhHhccccchhhcccccCc-cccc
Confidence            345667777777777765433   23335556667777776       55555554 335566677777777776 5555


Q ss_pred             c-hhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCccce
Q 046115          430 P-ETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       430 p-~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      | ..+..+++|+.+++++|......|..+..+++|++|++++|......|..|.++++|+.|++
T Consensus       169 ~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~i~~~~~~~~~~~~~L~~L~l  232 (284)
T d1ozna_         169 PERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQYLRL  232 (284)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCCCHHHHTTCTTCCEEEC
T ss_pred             chhhhccccccchhhhhhccccccChhHhhhhhhcccccccccccccccccccccccccCEEEe
Confidence            3 34466777777777777644444566677777777777777644444445666666666554

>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=98.95  E-value=1.4e-09  Score=93.49  Aligned_cols=122  Identities=16%  Similarity=0.150  Sum_probs=94.2

Q ss_pred             ceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccc-c-CccccCCCCcceeeccCCccccccchhhhc
Q 046115          358 LRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKE-I-PTNIEKLLHLKYLNLKGQKKIEKLPETLCE  435 (505)
Q Consensus       358 L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-~-p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~  435 (505)
                      .++++.+++.++.    +|..+  ..+++.|+|+       ++.+.. . +..+..+++|+.|++++|......+..+..
T Consensus        10 ~~~v~Cs~~~L~~----iP~~l--p~~l~~L~Ls-------~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~   76 (192)
T d1w8aa_          10 GTTVDCTGRGLKE----IPRDI--PLHTTELLLN-------DNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEG   76 (192)
T ss_dssp             TTEEECTTSCCSS----CCSCC--CTTCSEEECC-------SCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTT
T ss_pred             CCEEEEeCCCcCc----cCCCC--CCCCCEEEeC-------CCCCcccccccccCCCceEeeeecccccccccccccccc
Confidence            4567788887765    34322  2589999999       666653 4 455789999999999999955555667789


Q ss_pred             CCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          436 LYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       436 l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      +++|+.|++++|+ +..+|+ .+.++++|++|++++|.+...-|..|..+++|++|++.
T Consensus        77 ~~~L~~L~Ls~N~-l~~l~~~~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~  134 (192)
T d1w8aa_          77 ASHIQELQLGENK-IKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLA  134 (192)
T ss_dssp             CTTCCEEECCSCC-CCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECT
T ss_pred             ccccceeeecccc-ccccCHHHHhCCCcccccccCCccccccCHHHhcCCccccccccc
Confidence            9999999999998 777766 48999999999999998544334458889988888753

>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=98.92  E-value=5.6e-09  Score=92.16  Aligned_cols=78  Identities=21%  Similarity=0.384  Sum_probs=66.1

Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      +..+++|++|++++|. +...+. ++++++|+.|++++|. +..+|+ +.++++|++|++++|+ +..+|+ ++++++|+
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~  220 (227)
T d1h6ua2         147 LAGLTNLQYLSIGNAQ-VSDLTP-LANLSKLTTLKADDNK-ISDISP-LASLPNLIEVHLKNNQ-ISDVSP-LANTSNLF  220 (227)
T ss_dssp             GGGCTTCCEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCCCGG-GGGCTTCCEEECTTSC-CCBCGG-GTTCTTCC
T ss_pred             hccccccccccccccc-cccchh-hcccccceecccCCCc-cCCChh-hcCCCCCCEEECcCCc-CCCCcc-cccCCCCC
Confidence            6778899999999998 666665 8899999999999997 788864 7899999999999997 556763 88888888


Q ss_pred             ccce
Q 046115          489 RVRE  492 (505)
Q Consensus       489 ~L~~  492 (505)
                      .|++
T Consensus       221 ~L~l  224 (227)
T d1h6ua2         221 IVTL  224 (227)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            8875

>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=98.91  E-value=4e-09  Score=97.73  Aligned_cols=156  Identities=21%  Similarity=0.253  Sum_probs=85.5

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEeccccc--CC----------
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRES--WP----------  397 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~--~~----------  397 (505)
                      .++.+.+..+....++..   .|.++++|++|++.+|.+...   .|..|..+++|+.|+++++..  .+          
T Consensus        32 ~l~~L~Ls~N~i~~l~~~---~f~~l~~L~~L~l~~n~~~~i---~~~~f~~l~~L~~L~l~~n~l~~l~~~~~~~l~~L  105 (305)
T d1xkua_          32 DTALLDLQNNKITEIKDG---DFKNLKNLHTLILINNKISKI---SPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQEL  105 (305)
T ss_dssp             TCCEEECCSSCCCCBCTT---TTTTCTTCCEEECCSSCCCCB---CTTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEE
T ss_pred             CCCEEECcCCcCCCcChh---Hhhcccccccccccccccccc---chhhhhCCCccCEecccCCccCcCccchhhhhhhh
Confidence            677777777776666542   234677788888877776543   455566777777777653210  00          


Q ss_pred             --cccccccc---------------------------CccccCCC---------------------CcceeeccCCcccc
Q 046115          398 --RNNLIKEI---------------------------PTNIEKLL---------------------HLKYLNLKGQKKIE  427 (505)
Q Consensus       398 --~~~~~~~~---------------------------p~~~~~l~---------------------~L~~L~l~~~~~~~  427 (505)
                        ..+.+..+                           +..+..++                     +|+.|++++|....
T Consensus       106 ~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~~~~L~~L~l~~n~~~~  185 (305)
T d1xkua_         106 RVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITK  185 (305)
T ss_dssp             ECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSCCTTCSEEECTTSCCCE
T ss_pred             hccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCcccCCccCEEECCCCcCCC
Confidence              00000000                           00112222                     34444444444333


Q ss_pred             ccchhhhcCCCCcEEecCCCcCcccc-chhccccccCceeecCCCcccccccccccCCccCCcccee
Q 046115          428 KLPETLCELYNLERLNVDDCQNLREL-PRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       428 ~lp~~~~~l~~L~~L~l~~~~~~~~l-p~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      ..+..+..++.++.|++++|. +..+ |..+.++++|++|++++|. +..+|..|.++++|++|++.
T Consensus       186 ~~~~~~~~~~~l~~L~~s~n~-l~~~~~~~~~~l~~L~~L~L~~N~-L~~lp~~l~~l~~L~~L~Ls  250 (305)
T d1xkua_         186 VDAASLKGLNNLAKLGLSFNS-ISAVDNGSLANTPHLRELHLNNNK-LVKVPGGLADHKYIQVVYLH  250 (305)
T ss_dssp             ECTGGGTTCTTCCEEECCSSC-CCEECTTTGGGSTTCCEEECCSSC-CSSCCTTTTTCSSCCEEECC
T ss_pred             CChhHhhcccccccccccccc-ccccccccccccccceeeeccccc-ccccccccccccCCCEEECC
Confidence            334445566666777777666 4444 3346666777777777775 45666666667666666654

>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=98.90  E-value=3.7e-09  Score=96.88  Aligned_cols=152  Identities=25%  Similarity=0.337  Sum_probs=111.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCcccc----------------------ccchhHHhhcCcccce
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWS----------------------SEVLPQLFEKLTCLRA  387 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~----------------------~~~~~~~~~~l~~L~~  387 (505)
                      .+..+.+..+....++..   .|.++++|+.|++++|.+...                      ....+..+..+++|++
T Consensus        33 ~~~~L~Ls~N~i~~i~~~---~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~  109 (284)
T d1ozna_          33 ASQRIFLHGNRISHVPAA---SFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHT  109 (284)
T ss_dssp             TCSEEECTTSCCCEECTT---TTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCE
T ss_pred             CCCEEECcCCcCCCCCHH---HhhccccccccccccccccccccccccccccccccccccccccccccchhhcccccCCE
Confidence            567777777776666543   355788899999988875322                      1112445777888888


Q ss_pred             EEecccccCCcccccccc-CccccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch-hccccccCc
Q 046115          388 LELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-GIGKLRKLM  464 (505)
Q Consensus       388 L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~  464 (505)
                      |+++       ++.+..+ +..+..+.+|+.+++++|. ++.+|. .+..+.+|+.|++++|. +..+|+ .+..+++|+
T Consensus       110 L~l~-------~n~~~~~~~~~~~~~~~L~~l~l~~N~-l~~i~~~~f~~~~~L~~L~l~~N~-l~~l~~~~f~~l~~L~  180 (284)
T d1ozna_         110 LHLD-------RCGLQELGPGLFRGLAALQYLYLQDNA-LQALPDDTFRDLGNLTHLFLHGNR-ISSVPERAFRGLHSLD  180 (284)
T ss_dssp             EECT-------TSCCCCCCTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC-CCEECTTTTTTCTTCC
T ss_pred             EecC-------Ccccccccccccchhcccchhhhcccc-ccccChhHhccccchhhcccccCc-ccccchhhhccccccc
Confidence            8887       4444444 3456678889999999888 677754 56788889999999988 666654 578889999


Q ss_pred             eeecCCCcccccccccccCCccCCcccee
Q 046115          465 YLHNEDTGCLRYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       465 ~L~l~~~~~~~~~p~~i~~l~~L~~L~~~  493 (505)
                      ++++.+|......|..|.++++|+.|++.
T Consensus       181 ~l~l~~N~l~~i~~~~f~~l~~L~~L~l~  209 (284)
T d1ozna_         181 RLLLHQNRVAHVHPHAFRDLGRLMTLYLF  209 (284)
T ss_dssp             EEECCSSCCCEECTTTTTTCTTCCEEECC
T ss_pred             hhhhhhccccccChhHhhhhhhccccccc
Confidence            99999998776667888888888877654

>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=98.89  E-value=5.6e-09  Score=99.95  Aligned_cols=79  Identities=20%  Similarity=0.359  Sum_probs=66.7

Q ss_pred             cccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccC
Q 046115          408 NIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRL  487 (505)
Q Consensus       408 ~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L  487 (505)
                      .+..++++++|++++|. +..++. +..+++|+.|++++|+ +..+| .+.++++|++|++++|+. ..+++ +.++++|
T Consensus       302 ~~~~~~~l~~L~ls~n~-l~~l~~-l~~l~~L~~L~L~~n~-l~~l~-~l~~l~~L~~L~l~~N~l-~~l~~-l~~l~~L  375 (384)
T d2omza2         302 PISNLKNLTYLTLYFNN-ISDISP-VSSLTKLQRLFFANNK-VSDVS-SLANLTNINWLSAGHNQI-SDLTP-LANLTRI  375 (384)
T ss_dssp             GGGGCTTCSEEECCSSC-CSCCGG-GGGCTTCCEEECCSSC-CCCCG-GGGGCTTCCEEECCSSCC-CBCGG-GTTCTTC
T ss_pred             ccchhcccCeEECCCCC-CCCCcc-cccCCCCCEEECCCCC-CCCCh-hHcCCCCCCEEECCCCcC-CCChh-hccCCCC
Confidence            46788899999999998 777776 8899999999999997 77776 689999999999999984 45553 8888888


Q ss_pred             Cccce
Q 046115          488 RRVRE  492 (505)
Q Consensus       488 ~~L~~  492 (505)
                      +.|++
T Consensus       376 ~~L~L  380 (384)
T d2omza2         376 TQLGL  380 (384)
T ss_dssp             SEEEC
T ss_pred             CEeeC
Confidence            88775

>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=98.80  E-value=1.6e-08  Score=89.17  Aligned_cols=79  Identities=25%  Similarity=0.370  Sum_probs=56.1

Q ss_pred             ccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLR  488 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~  488 (505)
                      +...+.+..+.++++. +...+. +..+++|+.|++++|. +...+ .++++++|+.|++++|. +..+|. +.++++|+
T Consensus       125 ~~~~~~~~~l~~~~~~-~~~~~~-~~~~~~L~~L~l~~n~-~~~~~-~l~~l~~L~~L~Ls~n~-l~~l~~-l~~l~~L~  198 (227)
T d1h6ua2         125 LAGLSNLQVLYLDLNQ-ITNISP-LAGLTNLQYLSIGNAQ-VSDLT-PLANLSKLTTLKADDNK-ISDISP-LASLPNLI  198 (227)
T ss_dssp             GTTCTTCCEEECCSSC-CCCCGG-GGGCTTCCEEECCSSC-CCCCG-GGTTCTTCCEEECCSSC-CCCCGG-GGGCTTCC
T ss_pred             hccccchhhhhchhhh-hchhhh-hccccccccccccccc-cccch-hhcccccceecccCCCc-cCCChh-hcCCCCCC
Confidence            3444555555555555 333333 6778899999999988 55554 47889999999999997 455653 78888888


Q ss_pred             cccee
Q 046115          489 RVREF  493 (505)
Q Consensus       489 ~L~~~  493 (505)
                      +|++-
T Consensus       199 ~L~Ls  203 (227)
T d1h6ua2         199 EVHLK  203 (227)
T ss_dssp             EEECT
T ss_pred             EEECc
Confidence            87754

>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=98.78  E-value=2e-10  Score=99.09  Aligned_cols=107  Identities=22%  Similarity=0.259  Sum_probs=89.8

Q ss_pred             hhHHhhcCcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccc
Q 046115          375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELP  454 (505)
Q Consensus       375 ~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp  454 (505)
                      ++..+..+++|+.|+|+       ++.+..++ .++.+++|++|++++|. ++.+|.....+++|+.|++++|. +..++
T Consensus        40 l~~sl~~L~~L~~L~Ls-------~n~I~~i~-~l~~l~~L~~L~Ls~N~-i~~i~~~~~~~~~L~~L~l~~N~-i~~l~  109 (198)
T d1m9la_          40 MDATLSTLKACKHLALS-------TNNIEKIS-SLSGMENLRILSLGRNL-IKKIENLDAVADTLEELWISYNQ-IASLS  109 (198)
T ss_dssp             CHHHHHHTTTCCEEECS-------EEEESCCC-CHHHHTTCCEEECCEEE-ECSCSSHHHHHHHCCEEECSEEE-CCCHH
T ss_pred             hhhHHhcccccceeECc-------ccCCCCcc-cccCCccccChhhcccc-ccccccccccccccccccccccc-ccccc
Confidence            66778999999999999       77788886 58999999999999998 88898766677889999999998 77775


Q ss_pred             hhccccccCceeecCCCccccccc--ccccCCccCCcccee
Q 046115          455 RGIGKLRKLMYLHNEDTGCLRYLP--AGIGELIRLRRVREF  493 (505)
Q Consensus       455 ~~~~~l~~L~~L~l~~~~~~~~~p--~~i~~l~~L~~L~~~  493 (505)
                       .+..+++|++|++++|. +..++  ..+..+++|+.|++.
T Consensus       110 -~~~~l~~L~~L~L~~N~-i~~~~~~~~l~~l~~L~~L~L~  148 (198)
T d1m9la_         110 -GIEKLVNLRVLYMSNNK-ITNWGEIDKLAALDKLEDLLLA  148 (198)
T ss_dssp             -HHHHHHHSSEEEESEEE-CCCHHHHHHHTTTTTCSEEEEC
T ss_pred             -cccccccccccccccch-hccccccccccCCCccceeecC
Confidence             57889999999999997 45554  357888888888754

>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=98.77  E-value=2.2e-08  Score=92.50  Aligned_cols=106  Identities=16%  Similarity=0.168  Sum_probs=70.9

Q ss_pred             CCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-CccccCCCCcceeeccCCccccccchhh
Q 046115          355 LRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTNIEKLLHLKYLNLKGQKKIEKLPETL  433 (505)
Q Consensus       355 ~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~~~~l~~L~~L~l~~~~~~~~lp~~~  433 (505)
                      +++|+.|.+.+|.....   .+..+..+..+++|+++       ++.+..+ +..+..+++|++|+|++|+ ++.+|..+
T Consensus       170 ~~~L~~L~l~~n~~~~~---~~~~~~~~~~l~~L~~s-------~n~l~~~~~~~~~~l~~L~~L~L~~N~-L~~lp~~l  238 (305)
T d1xkua_         170 PPSLTELHLDGNKITKV---DAASLKGLNNLAKLGLS-------FNSISAVDNGSLANTPHLRELHLNNNK-LVKVPGGL  238 (305)
T ss_dssp             CTTCSEEECTTSCCCEE---CTGGGTTCTTCCEEECC-------SSCCCEECTTTGGGSTTCCEEECCSSC-CSSCCTTT
T ss_pred             CCccCEEECCCCcCCCC---ChhHhhccccccccccc-------cccccccccccccccccceeeeccccc-cccccccc
Confidence            45677777777765443   45556677777777776       4444444 4456677777777777776 67777777


Q ss_pred             hcCCCCcEEecCCCcCccccchh-------ccccccCceeecCCCc
Q 046115          434 CELYNLERLNVDDCQNLRELPRG-------IGKLRKLMYLHNEDTG  472 (505)
Q Consensus       434 ~~l~~L~~L~l~~~~~~~~lp~~-------~~~l~~L~~L~l~~~~  472 (505)
                      ..+++|+.|++++|+ ++.++..       ...+++|+.|++++|+
T Consensus       239 ~~l~~L~~L~Ls~N~-i~~i~~~~f~~~~~~~~~~~L~~L~L~~N~  283 (305)
T d1xkua_         239 ADHKYIQVVYLHNNN-ISAIGSNDFCPPGYNTKKASYSGVSLFSNP  283 (305)
T ss_dssp             TTCSSCCEEECCSSC-CCCCCTTSSSCSSCCTTSCCCSEEECCSSS
T ss_pred             ccccCCCEEECCCCc-cCccChhhccCcchhcccCCCCEEECCCCc
Confidence            777777777777776 6666542       2345677777777776

>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=98.74  E-value=1.7e-08  Score=83.00  Aligned_cols=90  Identities=14%  Similarity=0.108  Sum_probs=53.1

Q ss_pred             hHHhhcCcccceEEecccccCCccccccccC-ccccCCCCcceeeccCCccccccc-hhhhcCCCCcEEecCCCcCcccc
Q 046115          376 PQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKLLHLKYLNLKGQKKIEKLP-ETLCELYNLERLNVDDCQNLREL  453 (505)
Q Consensus       376 ~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l~~L~~L~l~~~~~~~~lp-~~~~~l~~L~~L~l~~~~~~~~l  453 (505)
                      |..+..+++|+.|++.      +++.+..++ ..|..+++|+.|++++|+ ++.++ ..+..+++|++|+|++|+ +..+
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   95 (156)
T d2ifga3          24 LHHLPGAENLTELYIE------NQQHLQHLELRDLRGLGELRNLTIVKSG-LRFVAPDAFHFTPRLSRLNLSFNA-LESL   95 (156)
T ss_dssp             TTTSCSCSCCSEEECC------SCSSCCEECGGGSCSCCCCSEEECCSSC-CCEECTTGGGSCSCCCEEECCSSC-CSCC
T ss_pred             cccccCccccCeeecC------CCccccccCchhhccccccCcceeeccc-cCCcccccccccccccceeccCCC-Cccc
Confidence            3334555666666665      233455554 335666666666666666 55553 345666667777776666 6666


Q ss_pred             chhccccccCceeecCCCcc
Q 046115          454 PRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       454 p~~~~~l~~L~~L~l~~~~~  473 (505)
                      |.++....+|++|++++|+.
T Consensus        96 ~~~~~~~~~l~~L~L~~Np~  115 (156)
T d2ifga3          96 SWKTVQGLSLQELVLSGNPL  115 (156)
T ss_dssp             CSTTTCSCCCCEEECCSSCC
T ss_pred             ChhhhccccccccccCCCcc
Confidence            66544444566666666653

>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=98.70  E-value=8e-08  Score=91.62  Aligned_cols=140  Identities=20%  Similarity=0.260  Sum_probs=101.8

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      .+..+.+..+....++     .+..+++|+.|.+.+|.+++.    +. +..+++|+.|+++       ++.+..+++ +
T Consensus       220 ~L~~L~l~~n~l~~~~-----~l~~l~~L~~L~l~~n~l~~~----~~-~~~~~~L~~L~l~-------~~~l~~~~~-~  281 (384)
T d2omza2         220 NLDELSLNGNQLKDIG-----TLASLTNLTDLDLANNQISNL----AP-LSGLTKLTELKLG-------ANQISNISP-L  281 (384)
T ss_dssp             TCCEEECCSSCCCCCG-----GGGGCTTCSEEECCSSCCCCC----GG-GTTCTTCSEEECC-------SSCCCCCGG-G
T ss_pred             CCCEEECCCCCCCCcc-----hhhcccccchhccccCccCCC----Cc-ccccccCCEeecc-------CcccCCCCc-c
Confidence            4555555555544332     234677888888888876653    22 6677788888887       555555543 6


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                      ..+..++.+.+..|. +..++. +..+++++.|++++|. +..+++ +..+++|++|++++|. +..+| .+.++++|++
T Consensus       282 ~~~~~l~~l~~~~n~-l~~~~~-~~~~~~l~~L~ls~n~-l~~l~~-l~~l~~L~~L~L~~n~-l~~l~-~l~~l~~L~~  355 (384)
T d2omza2         282 AGLTALTNLELNENQ-LEDISP-ISNLKNLTYLTLYFNN-ISDISP-VSSLTKLQRLFFANNK-VSDVS-SLANLTNINW  355 (384)
T ss_dssp             TTCTTCSEEECCSSC-CSCCGG-GGGCTTCSEEECCSSC-CSCCGG-GGGCTTCCEEECCSSC-CCCCG-GGGGCTTCCE
T ss_pred             ccccccccccccccc-cccccc-cchhcccCeEECCCCC-CCCCcc-cccCCCCCEEECCCCC-CCCCh-hHcCCCCCCE
Confidence            677888888888887 666554 8889999999999998 777763 7889999999999997 45565 5888888888


Q ss_pred             ccee
Q 046115          490 VREF  493 (505)
Q Consensus       490 L~~~  493 (505)
                      |++-
T Consensus       356 L~l~  359 (384)
T d2omza2         356 LSAG  359 (384)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8764

>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=98.58  E-value=9.2e-08  Score=78.49  Aligned_cols=102  Identities=16%  Similarity=0.079  Sum_probs=80.6

Q ss_pred             CcccceEEecccccCCccccccccCccccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCccccch-hccc
Q 046115          382 LTCLRALELQVRESWPRNNLIKEIPTNIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNLRELPR-GIGK  459 (505)
Q Consensus       382 l~~L~~L~l~~~~~~~~~~~~~~~p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~lp~-~~~~  459 (505)
                      ......++..       ++.....|..+..+++|+.|++.+++.++.++. .+..+++|+.|++++|. +..+++ .+..
T Consensus         7 c~~~~~l~c~-------~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~-l~~i~~~~f~~   78 (156)
T d2ifga3           7 PHGSSGLRCT-------RDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSG-LRFVAPDAFHF   78 (156)
T ss_dssp             CSSSSCEECC-------SSCCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSC-CCEECTTGGGS
T ss_pred             cCCCCeEEec-------CCCCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeeccc-cCCcccccccc
Confidence            3345567776       566667788888999999999988876888865 57899999999999999 777754 5899


Q ss_pred             cccCceeecCCCcccccccccccCCccCCccce
Q 046115          460 LRKLMYLHNEDTGCLRYLPAGIGELIRLRRVRE  492 (505)
Q Consensus       460 l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~L~~  492 (505)
                      +++|++|++++|. +..+|..+-...+|+.|++
T Consensus        79 l~~L~~L~Ls~N~-l~~l~~~~~~~~~l~~L~L  110 (156)
T d2ifga3          79 TPRLSRLNLSFNA-LESLSWKTVQGLSLQELVL  110 (156)
T ss_dssp             CSCCCEEECCSSC-CSCCCSTTTCSCCCCEEEC
T ss_pred             cccccceeccCCC-CcccChhhhcccccccccc
Confidence            9999999999998 5688876544445666543

>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=98.56  E-value=4.7e-07  Score=82.01  Aligned_cols=111  Identities=10%  Similarity=0.070  Sum_probs=66.9

Q ss_pred             cCCceEEEEEeCCCCC---CccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhC------------CcceEeCCCCChhh
Q 046115           70 VAGKKFLLVLDDVWNE---DYYKWEPFYKCLKNSLHESKILITTRKETVARIMG------------STHVISVNVLSEME  134 (505)
Q Consensus        70 l~~~r~LlvlDdv~~~---~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~------------~~~~~~l~~l~~~e  134 (505)
                      ...+++++|+|++..-   ....+................+++.+.........            ....+.+++|+.+|
T Consensus       133 ~~~~~~~i~id~~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e  212 (283)
T d2fnaa2         133 ASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREE  212 (283)
T ss_dssp             TCSSCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHH
T ss_pred             hcccccccccchhhhhcccchHHHHHHHHHHHHhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHH
Confidence            4567899999997432   11222223333323334445555555433222111            13468899999999


Q ss_pred             HHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHHHHHHHHhccCCCH
Q 046115          135 CWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAAKTIASLLRSKNTE  186 (505)
Q Consensus       135 a~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~  186 (505)
                      +.+++.+.......  ..++    +.++++.++|+|..|..++..+......
T Consensus       213 ~~~~l~~~~~~~~~--~~~~----~~~i~~~~~G~P~~L~~~~~~~~~~~~~  258 (283)
T d2fnaa2         213 AIEFLRRGFQEADI--DFKD----YEVVYEKIGGIPGWLTYFGFIYLDNKNL  258 (283)
T ss_dssp             HHHHHHHHHHHHTC--CCCC----HHHHHHHHCSCHHHHHHHHHHHHHHCCH
T ss_pred             HHHHHHhhhhhcCC--CHHH----HHHHHHHhCCCHHHHHHHHHHHHhcccH
Confidence            99999775432221  1112    5689999999999999998877554433

>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=98.55  E-value=2.2e-08  Score=91.44  Aligned_cols=134  Identities=19%  Similarity=0.190  Sum_probs=72.8

Q ss_pred             CCCCCCceEEEecCCC-ccccccchhHHhhcCcccceEEecccccCCcccccc--ccCccccC-CCCcceeeccCCcc-c
Q 046115          352 VTGLRGLRSLLVKSDE-YSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK--EIPTNIEK-LLHLKYLNLKGQKK-I  426 (505)
Q Consensus       352 ~~~~~~L~~L~l~~~~-~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~--~~p~~~~~-l~~L~~L~l~~~~~-~  426 (505)
                      +..+++|+.|+++++. ++..  .+......+++|++|++++      +..+.  .++..+.. .++|+.|+++++.. +
T Consensus        91 l~~~~~L~~L~Ls~c~~itd~--~l~~l~~~~~~L~~L~ls~------c~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~i  162 (284)
T d2astb2          91 LAKNSNLVRLNLSGCSGFSEF--ALQTLLSSCSRLDELNLSW------CFDFTEKHVQVAVAHVSETITQLNLSGYRKNL  162 (284)
T ss_dssp             HTTCTTCSEEECTTCBSCCHH--HHHHHHHHCTTCCEEECCC------CTTCCHHHHHHHHHHSCTTCCEEECCSCGGGS
T ss_pred             HhcCCCCcCcccccccccccc--ccchhhHHHHhcccccccc------ccccccccchhhhcccccccchhhhccccccc
Confidence            3355666666666532 2211  1233334556666666652      12221  11112222 35677777776531 2


Q ss_pred             c--ccchhhhcCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCccc-ccccccccCCccCCcccee
Q 046115          427 E--KLPETLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTGCL-RYLPAGIGELIRLRRVREF  493 (505)
Q Consensus       427 ~--~lp~~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~~~-~~~p~~i~~l~~L~~L~~~  493 (505)
                      +  .+..-...+++|+.|++++|..+. ..+..+.++++|++|++++|..+ +.....++++++|+.|++.
T Consensus       163 ~~~~l~~l~~~~~~L~~L~L~~~~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~  233 (284)
T d2astb2         163 QKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVF  233 (284)
T ss_dssp             CHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECT
T ss_pred             ccccccccccccccccccccccccCCCchhhhhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeee
Confidence            2  233333567888888888876554 34556777888888888887432 2333446667777777654

>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=98.35  E-value=1.2e-06  Score=77.49  Aligned_cols=132  Identities=22%  Similarity=0.247  Sum_probs=88.9

Q ss_pred             CCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccC-ccccCC-CCcceeeccCCccccc
Q 046115          351 NVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIP-TNIEKL-LHLKYLNLKGQKKIEK  428 (505)
Q Consensus       351 ~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p-~~~~~l-~~L~~L~l~~~~~~~~  428 (505)
                      .+.++++|+.|.+.++.+....  ....+..+..+..+...       +..+..++ ..+..+ ..+..|++++|. ++.
T Consensus        98 ~~~~l~~L~~l~l~~~~l~~~~--~~~~~~~l~~l~~~~~~-------n~~l~~i~~~~~~~~~~~l~~L~l~~n~-l~~  167 (242)
T d1xwdc1          98 AFQNLPNLQYLLISNTGIKHLP--DVHKIHSLQKVLLDIQD-------NINIHTIERNSFVGLSFESVILWLNKNG-IQE  167 (242)
T ss_dssp             SEECCTTCCEEEEESCCCCSCC--CCTTTCBSSCEEEEEES-------CTTCCEECTTSSTTSBSSCEEEECCSSC-CCE
T ss_pred             cccccccccccccchhhhcccc--ccccccccccccccccc-------ccccccccccccccccccceeeeccccc-ccc
Confidence            3456777888888777664321  11123344444444444       44455543 334444 478899999988 788


Q ss_pred             cchhhhcCCCCcEEecCCCcCccccchh-ccccccCceeecCCCcccccccc-cccCCccCCcccee
Q 046115          429 LPETLCELYNLERLNVDDCQNLRELPRG-IGKLRKLMYLHNEDTGCLRYLPA-GIGELIRLRRVREF  493 (505)
Q Consensus       429 lp~~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~~L~~L~l~~~~~~~~~p~-~i~~l~~L~~L~~~  493 (505)
                      ++.......+++.+....+..++.+|.. +.++++|++|++++|. +..+|. .|.+++.|+.++.+
T Consensus       168 i~~~~~~~~~l~~~~~l~~n~l~~l~~~~f~~l~~L~~L~Ls~N~-l~~l~~~~~~~l~~L~~l~~~  233 (242)
T d1xwdc1         168 IHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPSYGLENLKKLRARSTY  233 (242)
T ss_dssp             ECTTTTTTCCEEEEECTTCTTCCCCCTTTTTTSCCCSEEECTTSC-CCCCCSSSCTTCCEEESSSEE
T ss_pred             cccccccchhhhccccccccccccccHHHhcCCCCCCEEECCCCc-CCccCHHHHcCCcccccCcCC
Confidence            8877777777766655444448899875 6889999999999998 557765 47888888888765

>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=98.33  E-value=3.9e-07  Score=82.87  Aligned_cols=112  Identities=14%  Similarity=0.159  Sum_probs=67.5

Q ss_pred             CCCCceEEEecCCC-ccccccchhHHhhc-CcccceEEecccccCCccccc--cccCccccCCCCcceeeccCCcccc-c
Q 046115          354 GLRGLRSLLVKSDE-YSWSSEVLPQLFEK-LTCLRALELQVRESWPRNNLI--KEIPTNIEKLLHLKYLNLKGQKKIE-K  428 (505)
Q Consensus       354 ~~~~L~~L~l~~~~-~~~~~~~~~~~~~~-l~~L~~L~l~~~~~~~~~~~~--~~~p~~~~~l~~L~~L~l~~~~~~~-~  428 (505)
                      .+++|+.|+++++. ++.  ..++..+.. ..+|+.|+++++.     ..+  ..+..-...+++|++|++++|..++ .
T Consensus       119 ~~~~L~~L~ls~c~~~~~--~~~~~~~~~~~~~L~~L~l~~~~-----~~i~~~~l~~l~~~~~~L~~L~L~~~~~itd~  191 (284)
T d2astb2         119 SCSRLDELNLSWCFDFTE--KHVQVAVAHVSETITQLNLSGYR-----KNLQKSDLSTLVRRCPNLVHLDLSDSVMLKND  191 (284)
T ss_dssp             HCTTCCEEECCCCTTCCH--HHHHHHHHHSCTTCCEEECCSCG-----GGSCHHHHHHHHHHCTTCSEEECTTCTTCCGG
T ss_pred             HHHhcccccccccccccc--ccchhhhcccccccchhhhcccc-----cccccccccccccccccccccccccccCCCch
Confidence            56788888887753 221  112332333 3568888876321     111  1122223567788888888776554 4


Q ss_pred             cchhhhcCCCCcEEecCCCcCcc-ccchhccccccCceeecCCCc
Q 046115          429 LPETLCELYNLERLNVDDCQNLR-ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       429 lp~~~~~l~~L~~L~l~~~~~~~-~lp~~~~~l~~L~~L~l~~~~  472 (505)
                      .+..+.++++|+.|++++|..+. .-...++++++|++|++.+|.
T Consensus       192 ~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~~  236 (284)
T d2astb2         192 CFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGIV  236 (284)
T ss_dssp             GGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTSS
T ss_pred             hhhhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeeeCCC
Confidence            45567778888888888876543 233356777888888887773

>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=98.17  E-value=3.6e-06  Score=74.26  Aligned_cols=142  Identities=16%  Similarity=0.255  Sum_probs=83.0

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccccc-Ccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEI-PTN  408 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~-p~~  408 (505)
                      .+..+.+..+....++..   .|.++++|++|++++|......  .+..|..+..+..+.+.      .++.+... +..
T Consensus        30 ~l~~L~Ls~n~i~~l~~~---~f~~l~~L~~L~ls~n~~~~~i--~~~~f~~l~~l~~l~~~------~~n~l~~~~~~~   98 (242)
T d1xwdc1          30 NAIELRFVLTKLRVIQKG---AFSGFGDLEKIEISQNDVLEVI--EADVFSNLPKLHEIRIE------KANNLLYINPEA   98 (242)
T ss_dssp             CCSEEEEESCCCCEECTT---TTTTCTTCCEEEEESCTTCCEE--CSSSEESCTTCCEEEEE------CCTTCCEECTTS
T ss_pred             CCCEEECcCCcCCccChh---Hhhccchhhhhhhcccccccee--ecccccccccccccccc------cccccccccccc
Confidence            566777777766655543   2447788888888887654321  23335667777777765      23334333 445


Q ss_pred             ccCCCCcceeeccCCccccccch--hhhcCCCCcEEecCCCcCccccchh-ccccc-cCceeecCCCcccccccccccCC
Q 046115          409 IEKLLHLKYLNLKGQKKIEKLPE--TLCELYNLERLNVDDCQNLRELPRG-IGKLR-KLMYLHNEDTGCLRYLPAGIGEL  484 (505)
Q Consensus       409 ~~~l~~L~~L~l~~~~~~~~lp~--~~~~l~~L~~L~l~~~~~~~~lp~~-~~~l~-~L~~L~l~~~~~~~~~p~~i~~l  484 (505)
                      +..+++|+++++++|. +...+.  .+..+..+..+...++. +..++.. +..++ .+..|++.+|. +..++....+.
T Consensus        99 ~~~l~~L~~l~l~~~~-l~~~~~~~~~~~l~~l~~~~~~n~~-l~~i~~~~~~~~~~~l~~L~l~~n~-l~~i~~~~~~~  175 (242)
T d1xwdc1          99 FQNLPNLQYLLISNTG-IKHLPDVHKIHSLQKVLLDIQDNIN-IHTIERNSFVGLSFESVILWLNKNG-IQEIHNCAFNG  175 (242)
T ss_dssp             EECCTTCCEEEEESCC-CCSCCCCTTTCBSSCEEEEEESCTT-CCEECTTSSTTSBSSCEEEECCSSC-CCEECTTTTTT
T ss_pred             ccccccccccccchhh-hcccccccccccccccccccccccc-cccccccccccccccceeeeccccc-ccccccccccc
Confidence            6778888888888877 554443  22344455555445544 5555543 44443 67778888776 34555443333


Q ss_pred             c
Q 046115          485 I  485 (505)
Q Consensus       485 ~  485 (505)
                      .
T Consensus       176 ~  176 (242)
T d1xwdc1         176 T  176 (242)
T ss_dssp             C
T ss_pred             h
Confidence            3

>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=98.13  E-value=2.1e-07  Score=76.85  Aligned_cols=85  Identities=20%  Similarity=0.144  Sum_probs=50.9

Q ss_pred             cCCCCcceeeccCCcccccc---chhhhcCCCCcEEecCCCcCccccch-hccccccCceeecCCCcccccccc------
Q 046115          410 EKLLHLKYLNLKGQKKIEKL---PETLCELYNLERLNVDDCQNLRELPR-GIGKLRKLMYLHNEDTGCLRYLPA------  479 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~l---p~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~~~~p~------  479 (505)
                      ..+++|++|+|++|+ ++.+   +..+..+++|+.|++++|. +..+++ ......+|+.|++++|+.......      
T Consensus        62 ~~~~~L~~L~Ls~N~-i~~l~~~~~~~~~l~~L~~L~Ls~N~-i~~l~~l~~l~~~~L~~L~L~~Npl~~~~~~~~~y~~  139 (162)
T d1koha1          62 ENIPELLSLNLSNNR-LYRLDDMSSIVQKAPNLKILNLSGNE-LKSERELDKIKGLKLEELWLDGNSLSDTFRDQSTYIS  139 (162)
T ss_dssp             HHCTTCCCCCCCSSC-CCCCSGGGTHHHHSTTCCCCCCTTSC-CCCGGGHHHHTTCCCSSCCCTTSTTSSSSSSHHHHHH
T ss_pred             HhCCCCCEeeCCCcc-ccCCchhHHHHhhCCcccccccccCc-cccchhhhhhhccccceeecCCCCcCcCcccchhHHH
Confidence            456677777777776 4443   3345567777777777776 666654 222334577777777764432221      


Q ss_pred             -cccCCccCCccceeEec
Q 046115          480 -GIGELIRLRRVREFVVG  496 (505)
Q Consensus       480 -~i~~l~~L~~L~~~~~~  496 (505)
                       .+..+++|+.|+...+.
T Consensus       140 ~i~~~~P~L~~LDg~~v~  157 (162)
T d1koha1         140 AIRERFPKLLRLDGHELP  157 (162)
T ss_dssp             HHHTTSTTCCEETTEECC
T ss_pred             HHHHHCCCCCEECcCCCc
Confidence             14566777777766654

>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=98.11  E-value=4.4e-06  Score=77.94  Aligned_cols=130  Identities=25%  Similarity=0.278  Sum_probs=88.1

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      ....+.++......+|.       .+++|++|++++|.++.    +|.   .+.+|+.|++.       ++.+..++.- 
T Consensus        39 ~l~~LdLs~~~L~~lp~-------~~~~L~~L~Ls~N~l~~----lp~---~~~~L~~L~l~-------~n~l~~l~~l-   96 (353)
T d1jl5a_          39 QAHELELNNLGLSSLPE-------LPPHLESLVASCNSLTE----LPE---LPQSLKSLLVD-------NNNLKALSDL-   96 (353)
T ss_dssp             TCSEEECTTSCCSCCCS-------CCTTCSEEECCSSCCSS----CCC---CCTTCCEEECC-------SSCCSCCCSC-
T ss_pred             CCCEEEeCCCCCCCCCC-------CCCCCCEEECCCCCCcc----ccc---chhhhhhhhhh-------hcccchhhhh-
Confidence            45677777777666653       24689999999998764    443   34678888888       5555555431 


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcccccccccccCCccCCc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGCLRYLPAGIGELIRLRR  489 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~~p~~i~~l~~L~~  489 (505)
                        .+.|++|++++|. +..+|. ++.+.+|+.|++++|. +...|...   ..+..+.+..+...  .+..+..++.++.
T Consensus        97 --p~~L~~L~L~~n~-l~~lp~-~~~l~~L~~L~l~~~~-~~~~~~~~---~~l~~l~~~~~~~~--~~~~l~~l~~l~~  166 (353)
T d1jl5a_          97 --PPLLEYLGVSNNQ-LEKLPE-LQNSSFLKIIDVDNNS-LKKLPDLP---PSLEFIAAGNNQLE--ELPELQNLPFLTA  166 (353)
T ss_dssp             --CTTCCEEECCSSC-CSSCCC-CTTCTTCCEEECCSSC-CSCCCCCC---TTCCEEECCSSCCS--SCCCCTTCTTCCE
T ss_pred             --ccccccccccccc-cccccc-hhhhccceeecccccc-cccccccc---ccccchhhcccccc--cccccccccccee
Confidence              2469999999998 888886 7889999999999988 66666543   44556666655422  2334555555555


Q ss_pred             cc
Q 046115          490 VR  491 (505)
Q Consensus       490 L~  491 (505)
                      +.
T Consensus       167 L~  168 (353)
T d1jl5a_         167 IY  168 (353)
T ss_dssp             EE
T ss_pred             cc
Confidence            44

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.02  E-value=4.4e-05  Score=65.18  Aligned_cols=91  Identities=11%  Similarity=0.022  Sum_probs=67.5

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      +++-++|+|+++.........+...+.....++.++.||++.. +... ......+.+.+++.++....+.....     
T Consensus       107 ~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~~~~~-----  181 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT-----  181 (207)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC-----
T ss_pred             CccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEEecCCCCHHHHHHHHHHcCC-----
Confidence            4567999999988776677888888888878888887777743 3322 24456899999999999998875431     


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                       .   .++.+..+++.++|.|-
T Consensus       182 -~---~~~~~~~i~~~s~Gs~r  199 (207)
T d1a5ta2         182 -M---SQDALLAALRLSAGSPG  199 (207)
T ss_dssp             -C---CHHHHHHHHHHTTTCHH
T ss_pred             -C---CHHHHHHHHHHcCCCHH
Confidence             1   13557788889999884

>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=97.98  E-value=0.00016  Score=63.22  Aligned_cols=101  Identities=11%  Similarity=0.133  Sum_probs=68.4

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHHH-hCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVARI-MGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~~-~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      ++.-++|+|+++.........+...+......+.++.+|.+. .+... ......+.+.+++.++-.+.+...+...+..
T Consensus       114 ~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~  193 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA  193 (239)
T ss_dssp             SSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccC
Confidence            345688999997765545566777777766777777777663 22222 2345688999999999988887765433321


Q ss_pred             CCCchHHHHHHHHHHHcCCChH-HHHHH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL-AAKTI  176 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl-al~~~  176 (505)
                          -.++++..|++.++|.+- |+..+
T Consensus       194 ----~~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         194 ----HEPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             ----BCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             ----CCHHHHHHHHHHcCCCHHHHHHHH
Confidence                124567889999999884 45443

>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=97.96  E-value=2e-05  Score=68.45  Aligned_cols=150  Identities=11%  Similarity=0.056  Sum_probs=90.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC-C-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF-E-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f-~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      ++|+||||+|+.+++  ++...+ . .++-++.+...........+.........               ....+.-++|
T Consensus        44 p~G~GKTt~a~~la~--~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~---------------~~~~~~kvii  106 (224)
T d1sxjb2          44 MPGIGKTTSVHCLAH--ELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLH---------------LPPGKHKIVI  106 (224)
T ss_dssp             STTSSHHHHHHHHHH--HHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCC---------------CCTTCCEEEE
T ss_pred             CCCCCchhhHHHHHH--HHhccccccccccccccccCCceehhhHHHHHHHhhcc---------------CCCcceEEEE
Confidence            479999999999998  444332 1 23344444444433332222221110000               0123556888


Q ss_pred             EeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHH
Q 046115           79 LDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENLE  156 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~  156 (505)
                      +|++..........+...+......+.+++|+.+. .+.. .......+.+++++.++-...+...+...+..    -.+
T Consensus       107 iDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~----i~~  182 (224)
T d1sxjb2         107 LDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVK----YTN  182 (224)
T ss_dssp             EESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC----BCH
T ss_pred             EecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhcccC----CCH
Confidence            99997766555566666666666677777777663 2222 22445689999999999999988766433321    124


Q ss_pred             HHHHHHHHHcCCChH
Q 046115          157 KIGREIVKKCKGLPL  171 (505)
Q Consensus       157 ~~~~~i~~~~~g~Pl  171 (505)
                      +.+..|++.|+|.+.
T Consensus       183 ~~l~~I~~~s~Gd~R  197 (224)
T d1sxjb2         183 DGLEAIIFTAEGDMR  197 (224)
T ss_dssp             HHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHcCCcHH
Confidence            567889999998774

>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=97.89  E-value=0.00063  Score=60.28  Aligned_cols=141  Identities=15%  Similarity=0.122  Sum_probs=89.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC-ceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--CCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE-KRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--AGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~-~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~~r~Ll   77 (505)
                      ++|+|||++|+.+++  ....... ..+|++.............+....+................+.+..  ......+
T Consensus        51 ppGtGKT~l~~~l~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (276)
T d1fnna2          51 RPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFL  128 (276)
T ss_dssp             CTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCCCCHHHHHHHHHH--HHhcccCCcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhccccccc
Confidence            589999999999998  6655543 3458888888888899999999887665555555555555555544  3356777


Q ss_pred             EEeCCCCCCccChhHHHHh---hcC-CCCCcEEEEEeCchHHHHHh-------CCcceEeCCCCChhhHHHHHHHhh
Q 046115           78 VLDDVWNEDYYKWEPFYKC---LKN-SLHESKILITTRKETVARIM-------GSTHVISVNVLSEMECWSVFQSLA  143 (505)
Q Consensus        78 vlDdv~~~~~~~~~~~~~~---~~~-~~~~~~iLiTtr~~~~~~~~-------~~~~~~~l~~l~~~ea~~Lf~~~~  143 (505)
                      ++|++++............   ... ......++.++.........       .....+.+.+.+.++..+++....
T Consensus       129 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         129 VLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             EEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             chhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence            7888765443222222211   111 12334455555553332211       113467899999999999987654

>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=97.86  E-value=3.1e-05  Score=71.97  Aligned_cols=116  Identities=22%  Similarity=0.301  Sum_probs=86.3

Q ss_pred             ceeEEEEEecCCCccccccccCCCCCCCceEEEecCCCccccccchhHHhhcCcccceEEecccccCCccccccccCccc
Q 046115          330 KILHLLLTLRRGASVPISIWGNVTGLRGLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIKEIPTNI  409 (505)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p~~~  409 (505)
                      ++..+.+..+....+|.       .+.+|+.|.+.+|.++.... +|      ..|++|+++       ++.+..+|. +
T Consensus        59 ~L~~L~Ls~N~l~~lp~-------~~~~L~~L~l~~n~l~~l~~-lp------~~L~~L~L~-------~n~l~~lp~-~  116 (353)
T d1jl5a_          59 HLESLVASCNSLTELPE-------LPQSLKSLLVDNNNLKALSD-LP------PLLEYLGVS-------NNQLEKLPE-L  116 (353)
T ss_dssp             TCSEEECCSSCCSSCCC-------CCTTCCEEECCSSCCSCCCS-CC------TTCCEEECC-------SSCCSSCCC-C
T ss_pred             CCCEEECCCCCCccccc-------chhhhhhhhhhhcccchhhh-hc------ccccccccc-------ccccccccc-h
Confidence            78888888887776664       34689999999998765432 22      469999998       777888885 6


Q ss_pred             cCCCCcceeeccCCccccccchhhhcCCCCcEEecCCCcCccccchhccccccCceeecCCCcc
Q 046115          410 EKLLHLKYLNLKGQKKIEKLPETLCELYNLERLNVDDCQNLRELPRGIGKLRKLMYLHNEDTGC  473 (505)
Q Consensus       410 ~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~~~~lp~~~~~l~~L~~L~l~~~~~  473 (505)
                      +.+++|++|+++++. +...|..   ...+..+.+..+...  .+..+..++.++.+.+.+|..
T Consensus       117 ~~l~~L~~L~l~~~~-~~~~~~~---~~~l~~l~~~~~~~~--~~~~l~~l~~l~~L~l~~n~~  174 (353)
T d1jl5a_         117 QNSSFLKIIDVDNNS-LKKLPDL---PPSLEFIAAGNNQLE--ELPELQNLPFLTAIYADNNSL  174 (353)
T ss_dssp             TTCTTCCEEECCSSC-CSCCCCC---CTTCCEEECCSSCCS--SCCCCTTCTTCCEEECCSSCC
T ss_pred             hhhccceeecccccc-ccccccc---cccccchhhcccccc--ccccccccccceecccccccc
Confidence            889999999999988 6666653   455677777775522  234567788999999988863

>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=97.85  E-value=1.9e-05  Score=68.75  Aligned_cols=94  Identities=6%  Similarity=0.061  Sum_probs=65.9

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-H-HHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-V-ARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~-~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      ++..+|+|++..........+...+......+.++++|.... + .........+.+.+++.++-..++.+.+...+..-
T Consensus        99 ~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i  178 (227)
T d1sxjc2          99 GFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKL  178 (227)
T ss_dssp             SCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCB
T ss_pred             CeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccccccccccC
Confidence            456889999977665556677777777777888888887632 2 22234456889999999999999987765433311


Q ss_pred             CCchHHHHHHHHHHHcCCCh
Q 046115          151 KRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~P  170 (505)
                          .++++..|++.++|..
T Consensus       179 ----~~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         179 ----SPNAEKALIELSNGDM  194 (227)
T ss_dssp             ----CHHHHHHHHHHHTTCH
T ss_pred             ----CHHHHHHHHHHcCCcH
Confidence                2456778888888864

>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=97.82  E-value=6.3e-05  Score=65.69  Aligned_cols=158  Identities=8%  Similarity=0.008  Sum_probs=91.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccC---CCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN---FEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLL   77 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~---f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~Ll   77 (505)
                      ++|+||||+|+.+++  ++...   ....+.++.+...........+-............      ..+......+.-++
T Consensus        41 p~G~GKTtl~~~i~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~vi  112 (237)
T d1sxjd2          41 PPGTGKTSTILALTK--ELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSK------HDLENYPCPPYKII  112 (237)
T ss_dssp             STTSSHHHHHHHHHH--HHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCT------THHHHSCCCSCEEE
T ss_pred             CCCCChHHHHHHHHH--HHcCCcccccchhheeccccccchHHHHHHHHHhhhhhhhhhH------HHHhhccccCceEE
Confidence            479999999999998  43221   23344455555544433332222211111111110      11122233445579


Q ss_pred             EEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-H-HHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCchH
Q 046115           78 VLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-V-ARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRENL  155 (505)
Q Consensus        78 vlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~-~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~  155 (505)
                      |+|++..........+...+......+.+++|+.+.. + .........+.+.+++.++..+++...+...+..    -.
T Consensus       113 iiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~----i~  188 (237)
T d1sxjd2         113 ILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVK----CD  188 (237)
T ss_dssp             EETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCC----CC
T ss_pred             EEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhccccccccccchhhhhhhhhhcCc----CC
Confidence            9999977655455566666666667777777766521 1 1111224588999999999999998876543331    12


Q ss_pred             HHHHHHHHHHcCCCh
Q 046115          156 EKIGREIVKKCKGLP  170 (505)
Q Consensus       156 ~~~~~~i~~~~~g~P  170 (505)
                      ++++..|++.++|..
T Consensus       189 ~~~l~~ia~~s~gd~  203 (237)
T d1sxjd2         189 DGVLERILDISAGDL  203 (237)
T ss_dssp             HHHHHHHHHHTSSCH
T ss_pred             HHHHHHHHHHcCCCH
Confidence            466788899988765

>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=97.80  E-value=5.1e-05  Score=67.00  Aligned_cols=96  Identities=8%  Similarity=0.131  Sum_probs=62.3

Q ss_pred             ceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-H-HHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCC
Q 046115           73 KKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-V-ARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIG  150 (505)
Q Consensus        73 ~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~-~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~  150 (505)
                      +.-++|+|+++.........+...+......+++++||.+.. + .+.......+.+.+++.++..+++....-..+.  
T Consensus       131 ~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~--  208 (252)
T d1sxje2         131 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERI--  208 (252)
T ss_dssp             CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC--
T ss_pred             CceEEEeccccccccccchhhhcccccccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCC--
Confidence            445889999977655455666666666667788777776632 1 111233457889999999999988765422221  


Q ss_pred             CCchHHHHHHHHHHHcCCChH
Q 046115          151 KRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       151 ~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                       .-..++++..|++.+.|.+.
T Consensus       209 -~~~~~~~l~~i~~~s~Gd~R  228 (252)
T d1sxje2         209 -QLETKDILKRIAQASNGNLR  228 (252)
T ss_dssp             -EECCSHHHHHHHHHHTTCHH
T ss_pred             -CCCcHHHHHHHHHHcCCcHH
Confidence             11123567788888888764

>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=97.61  E-value=0.00039  Score=59.20  Aligned_cols=143  Identities=17%  Similarity=0.222  Sum_probs=81.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      .+|+|||.|+.++++  +..+....+++++..      +....+...+..      ....+..+    .+. .--+|++|
T Consensus        44 ~~G~GKTHLl~A~~~--~~~~~~~~~~~~~~~------~~~~~~~~~~~~------~~~~~~~~----~~~-~~dll~iD  104 (213)
T d1l8qa2          44 SVGTGKTHLLQAAGN--EAKKRGYRVIYSSAD------DFAQAMVEHLKK------GTINEFRN----MYK-SVDLLLLD  104 (213)
T ss_dssp             SSSSSHHHHHHHHHH--HHHHTTCCEEEEEHH------HHHHHHHHHHHH------TCHHHHHH----HHH-TCSEEEEE
T ss_pred             CCCCcHHHHHHHHHH--HhccCccceEEechH------HHHHHHHHHHHc------cchhhHHH----HHh-hccchhhh
Confidence            379999999999999  666666667777644      333444444330      01111111    121 23489999


Q ss_pred             CCCCCC-ccChhH-HHHhhcCC-CCCcEEEEEeCch---------HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCC
Q 046115           81 DVWNED-YYKWEP-FYKCLKNS-LHESKILITTRKE---------TVARIMGSTHVISVNVLSEMECWSVFQSLAISGKT  148 (505)
Q Consensus        81 dv~~~~-~~~~~~-~~~~~~~~-~~~~~iLiTtr~~---------~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~  148 (505)
                      |++... ...|+. +...+... ..|.+||+||+..         ++...+....++.++ .+.++-.++++..+-..+.
T Consensus       105 Di~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl  183 (213)
T d1l8qa2         105 DVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNL  183 (213)
T ss_dssp             CGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTC
T ss_pred             hhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCC
Confidence            996532 123333 33333322 3577899999862         344444555677885 5777777777777643332


Q ss_pred             CCCCchHHHHHHHHHHHcC
Q 046115          149 IGKRENLEKIGREIVKKCK  167 (505)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~  167 (505)
                       .-+   ++++.-|++.+.
T Consensus       184 -~l~---~~v~~yl~~~~~  198 (213)
T d1l8qa2         184 -ELR---KEVIDYLLENTK  198 (213)
T ss_dssp             -CCC---HHHHHHHHHHCS
T ss_pred             -CCC---HHHHHHHHHhcC
Confidence             222   355666666653

>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=97.60  E-value=2e-05  Score=64.54  Aligned_cols=85  Identities=26%  Similarity=0.284  Sum_probs=63.2

Q ss_pred             hhHHhhcCcccceEEecccccCCccccccccC---ccccCCCCcceeeccCCccccccch-hhhcCCCCcEEecCCCcCc
Q 046115          375 LPQLFEKLTCLRALELQVRESWPRNNLIKEIP---TNIEKLLHLKYLNLKGQKKIEKLPE-TLCELYNLERLNVDDCQNL  450 (505)
Q Consensus       375 ~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~p---~~~~~l~~L~~L~l~~~~~~~~lp~-~~~~l~~L~~L~l~~~~~~  450 (505)
                      ++..+..+.+|++|+|+       ++.+..++   ..+..+++|++|++++|. ++.++. ...+..+|+.|++++|+..
T Consensus        57 l~~~~~~~~~L~~L~Ls-------~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~-i~~l~~l~~l~~~~L~~L~L~~Npl~  128 (162)
T d1koha1          57 LRIIEENIPELLSLNLS-------NNRLYRLDDMSSIVQKAPNLKILNLSGNE-LKSERELDKIKGLKLEELWLDGNSLS  128 (162)
T ss_dssp             HHHHHHHCTTCCCCCCC-------SSCCCCCSGGGTHHHHSTTCCCCCCTTSC-CCCGGGHHHHTTCCCSSCCCTTSTTS
T ss_pred             hHHHHHhCCCCCEeeCC-------CccccCCchhHHHHhhCCcccccccccCc-cccchhhhhhhccccceeecCCCCcC
Confidence            45555678999999999       66666653   446689999999999999 887776 2234567999999999844


Q ss_pred             cccch-------hccccccCceee
Q 046115          451 RELPR-------GIGKLRKLMYLH  467 (505)
Q Consensus       451 ~~lp~-------~~~~l~~L~~L~  467 (505)
                      .....       -+..+|+|+.||
T Consensus       129 ~~~~~~~~y~~~i~~~~P~L~~LD  152 (162)
T d1koha1         129 DTFRDQSTYISAIRERFPKLLRLD  152 (162)
T ss_dssp             SSSSSHHHHHHHHHTTSTTCCEET
T ss_pred             cCcccchhHHHHHHHHCCCCCEEC
Confidence            43332       257789999886

>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=97.59  E-value=0.00023  Score=61.67  Aligned_cols=96  Identities=9%  Similarity=0.046  Sum_probs=64.2

Q ss_pred             CceEEEEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCch-HHHH-HhCCcceEeCCCCChhhHHHHHHHhhhCCCCC
Q 046115           72 GKKFLLVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKE-TVAR-IMGSTHVISVNVLSEMECWSVFQSLAISGKTI  149 (505)
Q Consensus        72 ~~r~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~-~~~~-~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~  149 (505)
                      .++.++++|++..........+...+......+.++.||... .+.. .......+.+.+.+..+....+.+.+...+. 
T Consensus       108 ~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i-  186 (231)
T d1iqpa2         108 ASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL-  186 (231)
T ss_dssp             CSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTC-
T ss_pred             CCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHHHHHhCC-
Confidence            467889999997766555666777666665556666666553 2222 1233568899999999999999887654332 


Q ss_pred             CCCchHHHHHHHHHHHcCCChH
Q 046115          150 GKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                         .-.++++..|++.++|..-
T Consensus       187 ---~i~~~~l~~I~~~~~gdiR  205 (231)
T d1iqpa2         187 ---ELTEEGLQAILYIAEGDMR  205 (231)
T ss_dssp             ---EECHHHHHHHHHHHTTCHH
T ss_pred             ---CCCHHHHHHHHHHcCCCHH
Confidence               1124567889999988653

>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=97.41  E-value=5.2e-05  Score=73.05  Aligned_cols=105  Identities=21%  Similarity=0.309  Sum_probs=51.7

Q ss_pred             CceEEEecCCCccccccchhHHhhcCcccceEEecccccCCcccccc-----ccCccccCCCCcceeeccCCccccc---
Q 046115          357 GLRSLLVKSDEYSWSSEVLPQLFEKLTCLRALELQVRESWPRNNLIK-----EIPTNIEKLLHLKYLNLKGQKKIEK---  428 (505)
Q Consensus       357 ~L~~L~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-----~~p~~~~~l~~L~~L~l~~~~~~~~---  428 (505)
                      +|+.|++++++++...  +...+..++++++|+|.       ++.+.     .++..+..+++|++|+|++|. ++.   
T Consensus         3 ~l~~ld~~~~~i~~~~--~~~l~~~l~~l~~L~L~-------~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~-i~~~~~   72 (460)
T d1z7xw1           3 DIQSLDIQCEELSDAR--WAELLPLLQQCQVVRLD-------DCGLTEARCKDISSALRVNPALAELNLRSNE-LGDVGV   72 (460)
T ss_dssp             EEEEEEEESCCCCHHH--HHHHHHHHTTCSEEEEE-------SSCCCHHHHHHHHHHHHTCTTCCEEECTTCC-CHHHHH
T ss_pred             CCCEEEeeCCcCChHH--HHHHHHhCCCCCEEEeC-------CCCCCHHHHHHHHHHHhcCCCCCEEECcCCc-CChHHH
Confidence            4556666666655421  33334555666666665       22222     223334555666666666665 321   


Q ss_pred             --cchhhh-cCCCCcEEecCCCcCccc-----cchhccccccCceeecCCCc
Q 046115          429 --LPETLC-ELYNLERLNVDDCQNLRE-----LPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       429 --lp~~~~-~l~~L~~L~l~~~~~~~~-----lp~~~~~l~~L~~L~l~~~~  472 (505)
                        +...+. ...+|+.|++++|. +..     ++..+..+++|++|++++|.
T Consensus        73 ~~l~~~l~~~~~~L~~L~L~~n~-it~~~~~~l~~~l~~~~~L~~L~L~~N~  123 (460)
T d1z7xw1          73 HCVLQGLQTPSCKIQKLSLQNCC-LTGAGCGVLSSTLRTLPTLQELHLSDNL  123 (460)
T ss_dssp             HHHHHTTCSTTCCCCEEECTTSC-CBGGGHHHHHHHTTSCTTCCEEECCSSB
T ss_pred             HHHHHHHhcCCCCCCEEECCCCC-ccccccccccchhhcccccccccccccc
Confidence              111111 12346666666665 321     33445555666666666664

>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=97.27  E-value=0.0008  Score=58.98  Aligned_cols=127  Identities=17%  Similarity=0.159  Sum_probs=75.7

Q ss_pred             CCCCcHHHHHHHHhcCc---ccccCC-CceE-EEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-CCce
Q 046115            1 MGGIGKTTLAQFAYNNG---DVERNF-EKRT-WVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-AGKK   74 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~---~~~~~f-~~~~-wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~~~r   74 (505)
                      .+|+|||+++..+++..   .+.... ...+ +++.+.              +- .......++++....+...+ +.++
T Consensus        47 ~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~--------------li-ag~~~~g~~e~r~~~i~~~~~~~~~  111 (268)
T d1r6bx2          47 ESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS--------------LL-AGTKYRGDFEKRFKALLKQLEQDTN  111 (268)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC------------------CCCCCSSCHHHHHHHHHHHHSSSSC
T ss_pred             CCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeech--------------Hh-ccCccchhHHHHHHHHHHHhhccCC
Confidence            48999999999998731   111111 2233 344332              11 11223445555555555554 4567


Q ss_pred             EEEEEeCCCCC--------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhC-------CcceEeCCCCChhhHHHHH
Q 046115           75 FLLVLDDVWNE--------DYYKWEPFYKCLKNSLHESKILITTRKETVARIMG-------STHVISVNVLSEMECWSVF  139 (505)
Q Consensus        75 ~LlvlDdv~~~--------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~-------~~~~~~l~~l~~~ea~~Lf  139 (505)
                      .++++|++..-        .......++.++...+ .-++|.||..........       .+..+.+.+.+.+++.+++
T Consensus       112 iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg-~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL  190 (268)
T d1r6bx2         112 SILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSG-KIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQII  190 (268)
T ss_dssp             EEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSC-CCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHH
T ss_pred             ceEEecchHHHhcCCCCCCccccHHHHhhHHHhCC-CCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHH
Confidence            99999997442        1123455555555543 467888888766654322       2568899999999999999


Q ss_pred             HHhh
Q 046115          140 QSLA  143 (505)
Q Consensus       140 ~~~~  143 (505)
                      ....
T Consensus       191 ~~~~  194 (268)
T d1r6bx2         191 NGLK  194 (268)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            7643

>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=97.26  E-value=0.00013  Score=67.72  Aligned_cols=67  Identities=18%  Similarity=0.106  Sum_probs=45.4

Q ss_pred             ccccCCCCcceeeccCCccccc------cchhhhcCCCCcEEecCCCcCcc----ccchhccccccCceeecCCCccc
Q 046115          407 TNIEKLLHLKYLNLKGQKKIEK------LPETLCELYNLERLNVDDCQNLR----ELPRGIGKLRKLMYLHNEDTGCL  474 (505)
Q Consensus       407 ~~~~~l~~L~~L~l~~~~~~~~------lp~~~~~l~~L~~L~l~~~~~~~----~lp~~~~~l~~L~~L~l~~~~~~  474 (505)
                      ..+...++|+.|++++|. ++.      +...+..+++|+.|++++|....    .+...+...++|++|++++|...
T Consensus       180 ~~l~~~~~L~~L~L~~n~-i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~~g~~~L~~~l~~~~~L~~L~Ls~n~i~  256 (344)
T d2ca6a1         180 KTFQSHRLLHTVKMVQNG-IRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLS  256 (344)
T ss_dssp             HHHHHCTTCCEEECCSSC-CCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTTCCCC
T ss_pred             chhhhhhhhccccccccc-ccccccccchhhhhcchhhhcccccccccccccccccccccccccccchhhhhhcCccC
Confidence            335567788888888887 432      22345677888888888887322    24445677788888888888743

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.25  E-value=0.0047  Score=54.63  Aligned_cols=141  Identities=14%  Similarity=0.165  Sum_probs=83.3

Q ss_pred             CCCCcHHHHHHHHhcCccccc-----CC-CceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--CC
Q 046115            1 MGGIGKTTLAQFAYNNGDVER-----NF-EKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--AG   72 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~-----~f-~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~   72 (505)
                      ++|+|||++|+.+++  ....     .. ....++++............+...+.................+....  .+
T Consensus        54 ppGtGKT~l~~~l~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  131 (287)
T d1w5sa2          54 RVGIGKTTLAKFTVK--RVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVEN  131 (287)
T ss_dssp             CCSSSHHHHHHHHHH--HHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHH--HHHhhcccccCCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhcc
Confidence            589999999999998  3322     11 34557888888888888888888887555555555555555555544  34


Q ss_pred             ceEEEEEeCCCCC---CccC---h---hHHHHhhcC---CCCCcEEEEEeCchHHHH------H-h-CCcceEeCCCCCh
Q 046115           73 KKFLLVLDDVWNE---DYYK---W---EPFYKCLKN---SLHESKILITTRKETVAR------I-M-GSTHVISVNVLSE  132 (505)
Q Consensus        73 ~r~LlvlDdv~~~---~~~~---~---~~~~~~~~~---~~~~~~iLiTtr~~~~~~------~-~-~~~~~~~l~~l~~  132 (505)
                      ...++++|.+...   ....   .   ..+...+..   ......|++++.......      . . .....+..++.+.
T Consensus       132 ~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~  211 (287)
T d1w5sa2         132 HYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKS  211 (287)
T ss_dssp             CEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCH
T ss_pred             CccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcH
Confidence            5677788876321   1101   1   111221222   122233444444332211      1 1 1245788999999


Q ss_pred             hhHHHHHHHhh
Q 046115          133 MECWSVFQSLA  143 (505)
Q Consensus       133 ~ea~~Lf~~~~  143 (505)
                      ++..+++...+
T Consensus       212 ~el~~Il~~r~  222 (287)
T d1w5sa2         212 RELYTILEQRA  222 (287)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhhH
Confidence            99999998765

>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=97.20  E-value=0.0011  Score=57.98  Aligned_cols=154  Identities=12%  Similarity=0.096  Sum_probs=79.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC-CChhcHHHHHHHHHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA-KDLVEFQSLMQHIEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~~~l~~~l~~~r~Llvl   79 (505)
                      ++|+||||+|+.+++  +..   ..+++++.+...+...+-.. ......... ......    .........+..++++
T Consensus        60 PpG~GKTt~a~~la~--~~~---~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~----~~~~~~~~~~~~vi~i  129 (253)
T d1sxja2          60 PPGIGKTTAAHLVAQ--ELG---YDILEQNASDVRSKTLLNAG-VKNALDNMSVVGYFKH----NEEAQNLNGKHFVIIM  129 (253)
T ss_dssp             STTSSHHHHHHHHHH--HTT---CEEEEECTTSCCCHHHHHHT-GGGGTTBCCSTTTTTC--------CCSSTTSEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHH---hhhhccccccchhhHHHHHH-HHHHhhcchhhhhhhh----hhhcccccccceEEEe
Confidence            589999999999998  332   23456666655544333222 222211111 000000    0011123456788999


Q ss_pred             eCCCCCCccC---hhHHHHhhcCCCCCcEEEEEeCc--h-HHHHHhCCcceEeCCCCChhhHHHHHHHhhhCCCCCCCCc
Q 046115           80 DDVWNEDYYK---WEPFYKCLKNSLHESKILITTRK--E-TVARIMGSTHVISVNVLSEMECWSVFQSLAISGKTIGKRE  153 (505)
Q Consensus        80 Ddv~~~~~~~---~~~~~~~~~~~~~~~~iLiTtr~--~-~~~~~~~~~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~  153 (505)
                      |++.......   +..+.........  .+++|+.+  . .+.........+.+.+.+.++-...+.......+..-+. 
T Consensus       130 de~~~~~~~~~~~~~~~~~~~~~~~~--~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~-  206 (253)
T d1sxja2         130 DEVDGMSGGDRGGVGQLAQFCRKTST--PLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP-  206 (253)
T ss_dssp             CSGGGCCTTSTTHHHHHHHHHHHCSS--CEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT-
T ss_pred             eeccccccchhhhhHHHhhhhccccc--ccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH-
Confidence            9985533212   3333433333322  34444332  2 222222335688999999999888887765332221111 


Q ss_pred             hHHHHHHHHHHHcCCCh
Q 046115          154 NLEKIGREIVKKCKGLP  170 (505)
Q Consensus       154 ~~~~~~~~i~~~~~g~P  170 (505)
                         +++..|++.++|..
T Consensus       207 ---~~l~~i~~~s~GDi  220 (253)
T d1sxja2         207 ---NVIDRLIQTTRGDI  220 (253)
T ss_dssp             ---THHHHHHHHTTTCH
T ss_pred             ---HHHHHHHHhCCCcH
Confidence               34678888898866

>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=97.03  E-value=0.0023  Score=55.53  Aligned_cols=143  Identities=11%  Similarity=0.080  Sum_probs=75.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHH-HHHHcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQH-IEECVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~-l~~~l~~~r~Llvl   79 (505)
                      ++|+|||++|+.+++  +....   .+-++.+          .+....       ..+.++.... ....-...+++|++
T Consensus        50 ppGtGKT~la~aia~--~~~~~---~~~i~~~----------~l~~~~-------~g~~~~~l~~~f~~a~~~~p~Ii~i  107 (247)
T d1ixza_          50 PPGVGKTHLARAVAG--EARVP---FITASGS----------DFVEMF-------VGVGAARVRDLFETAKRHAPCIVFI  107 (247)
T ss_dssp             CTTSSHHHHHHHHHH--HTTCC---EEEEEHH----------HHHHSC-------TTHHHHHHHHHHHHHTTSSSEEEEE
T ss_pred             CCCCChhHHHHHHHH--HcCCC---EEEEEhH----------Hhhhcc-------ccHHHHHHHHHHHHHHHcCCEEEEE
Confidence            589999999999998  44322   2333322          111111       1111222222 23333457899999


Q ss_pred             eCCCCC-------Cc---c----ChhHHHHhhcCC--CCCcEEEEEeCchHH-HHHh---CC-cceEeCCCCChhhHHHH
Q 046115           80 DDVWNE-------DY---Y----KWEPFYKCLKNS--LHESKILITTRKETV-ARIM---GS-THVISVNVLSEMECWSV  138 (505)
Q Consensus        80 Ddv~~~-------~~---~----~~~~~~~~~~~~--~~~~~iLiTtr~~~~-~~~~---~~-~~~~~l~~l~~~ea~~L  138 (505)
                      ||++.-       ..   .    ....+...+...  ..+.-|+-||..+.. ...+   +. ...+.++..+.++-.++
T Consensus       108 Deid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~i  187 (247)
T d1ixza_         108 DEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI  187 (247)
T ss_dssp             ETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHH
T ss_pred             EChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHH
Confidence            998320       00   0    122233333322  233334447766433 2222   22 35889999999999999


Q ss_pred             HHHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          139 FQSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       139 f~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      |..+...... ....+    ...+++.+.|+.
T Consensus       188 l~~~l~~~~~-~~~~~----~~~la~~t~g~s  214 (247)
T d1ixza_         188 LRIHARGKPL-AEDVD----LALLAKRTPGFV  214 (247)
T ss_dssp             HHHHHTTSCB-CTTCC----HHHHHHTCTTCC
T ss_pred             HHHHhcccCC-ccccC----HHHHHHHCCCCC
Confidence            9877643332 22223    446777887764

>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=97.02  E-value=0.0014  Score=54.10  Aligned_cols=121  Identities=12%  Similarity=0.094  Sum_probs=69.6

Q ss_pred             CCCCcHHHHHHHHhcCcccc-----cCC-Cc-eEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc--C
Q 046115            1 MGGIGKTTLAQFAYNNGDVE-----RNF-EK-RTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV--A   71 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~-----~~f-~~-~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~   71 (505)
                      .+|+|||+++..++..  +.     ... +. ++.++.+              .+- .......++++....+...+  .
T Consensus        51 ~pGVGKTalv~~LA~r--i~~~~vp~~L~~~~i~~ld~~--------------~Li-Ag~~~rG~~E~rl~~il~e~~~~  113 (195)
T d1jbka_          51 EPGVGKTAIVEGLAQR--IINGEVPEGLKGRRVLALDMG--------------ALV-AGAKYRGEFEERLKGVLNDLAKQ  113 (195)
T ss_dssp             CTTSCHHHHHHHHHHH--HHHTCSCGGGTTCEEEEECHH--------------HHH-TTTCSHHHHHHHHHHHHHHHHHS
T ss_pred             cCCcccHHHHHHHHHH--HHhCCCCHHHcCceEEEeeHH--------------HHh-ccCCccHHHHHHHHHHHHHHhcC
Confidence            3799999999999873  32     111 23 3344422              121 11223334555444444333  3


Q ss_pred             CceEEEEEeCCCCC-------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHHh-------CCcceEeCCCCChhhHHH
Q 046115           72 GKKFLLVLDDVWNE-------DYYKWEPFYKCLKNSLHESKILITTRKETVARIM-------GSTHVISVNVLSEMECWS  137 (505)
Q Consensus        72 ~~r~LlvlDdv~~~-------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~-------~~~~~~~l~~l~~~ea~~  137 (505)
                      ..+++|++|++..-       ...+...++.+....+. -++|.||-........       ..++.+.+.+.+.+++.+
T Consensus       114 ~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~rg~-l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~  192 (195)
T d1jbka_         114 EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGE-LHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIA  192 (195)
T ss_dssp             TTTEEEEEETGGGGTT------CCCCHHHHHHHHHTTS-CCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHT
T ss_pred             CCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhCCC-ceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCCHHHHHH
Confidence            45899999998441       11245566666665544 5677777665544332       346789999999998876


Q ss_pred             HH
Q 046115          138 VF  139 (505)
Q Consensus       138 Lf  139 (505)
                      ++
T Consensus       193 IL  194 (195)
T d1jbka_         193 IL  194 (195)
T ss_dssp             TC
T ss_pred             Hh
Confidence            53

>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=97.01  E-value=0.00034  Score=64.66  Aligned_cols=111  Identities=16%  Similarity=0.227  Sum_probs=73.5

Q ss_pred             CCCCceEEEecCCCcccc--ccchhHHhhcCcccceEEecccccCCcccccc-----ccCccccCCCCcceeeccCCccc
Q 046115          354 GLRGLRSLLVKSDEYSWS--SEVLPQLFEKLTCLRALELQVRESWPRNNLIK-----EIPTNIEKLLHLKYLNLKGQKKI  426 (505)
Q Consensus       354 ~~~~L~~L~l~~~~~~~~--~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-----~~p~~~~~l~~L~~L~l~~~~~~  426 (505)
                      .++.|+.|.+..|.++..  ...+...+..+++|+.|+|+       ++.++     .+...+..+++|++|++++|. +
T Consensus       184 ~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls-------~N~i~~~g~~~L~~~l~~~~~L~~L~Ls~n~-i  255 (344)
T d2ca6a1         184 SHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQ-------DNTFTHLGSSALAIALKSWPNLRELGLNDCL-L  255 (344)
T ss_dssp             HCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECC-------SSCCHHHHHHHHHHHGGGCTTCCEEECTTCC-C
T ss_pred             hhhhhcccccccccccccccccchhhhhcchhhhcccccc-------cccccccccccccccccccccchhhhhhcCc-c
Confidence            567888999988876532  11233446678889999988       33332     244556778889999999988 4


Q ss_pred             cc-----cchhhhc--CCCCcEEecCCCcCccc-----cchhcc-ccccCceeecCCCcc
Q 046115          427 EK-----LPETLCE--LYNLERLNVDDCQNLRE-----LPRGIG-KLRKLMYLHNEDTGC  473 (505)
Q Consensus       427 ~~-----lp~~~~~--l~~L~~L~l~~~~~~~~-----lp~~~~-~l~~L~~L~l~~~~~  473 (505)
                      +.     +-..+.+  ...|+.|++++|. +..     +...+. ++++|++|++++|.+
T Consensus       256 ~~~g~~~l~~~l~~~~~~~L~~L~ls~N~-i~~~~~~~l~~~l~~~~~~L~~L~l~~N~~  314 (344)
T d2ca6a1         256 SARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGNRF  314 (344)
T ss_dssp             CHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTSBS
T ss_pred             CchhhHHHHHHhhhccCCCCCEEECCCCc-CChHHHHHHHHHHHccCCCCCEEECCCCcC
Confidence            32     2223333  3568999999987 432     333443 567899999998874

>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=96.97  E-value=0.0046  Score=53.32  Aligned_cols=48  Identities=17%  Similarity=0.190  Sum_probs=34.2

Q ss_pred             cceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHH
Q 046115          122 THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       122 ~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                      ...+.++..+.++...++.........    ...++.+..+++.++|.+-.+
T Consensus       156 ~~~~~~~~~~~~~~~~~l~~~~~~~~~----~~~~~~l~~i~~~s~gd~R~a  203 (238)
T d1in4a2         156 GIILELDFYTVKELKEIIKRAASLMDV----EIEDAAAEMIAKRSRGTPRIA  203 (238)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHHHTTC----CBCHHHHHHHHHTSTTCHHHH
T ss_pred             eEEEEecCCCHHHHHHHHHHhhhhccc----hhhHHHHHHHHHhCCCCHHHH
Confidence            346789999999999999876643332    223456888899988876544

>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=96.96  E-value=0.0062  Score=52.99  Aligned_cols=144  Identities=11%  Similarity=0.056  Sum_probs=77.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+.+++  +....   .+-++.+.-.+              ..  ...........+...-...+++|++|
T Consensus        53 ppGtGKT~la~~iA~--~~~~~---~~~i~~~~l~~--------------~~--~g~~~~~l~~~f~~A~~~~P~il~iD  111 (256)
T d1lv7a_          53 PPGTGKTLLAKAIAG--EAKVP---FFTISGSDFVE--------------MF--VGVGASRVRDMFEQAKKAAPCIIFID  111 (256)
T ss_dssp             CTTSCHHHHHHHHHH--HHTCC---EEEECSCSSTT--------------SC--CCCCHHHHHHHHHHHHTTCSEEEEET
T ss_pred             CCCCCccHHHHHHHH--HcCCC---EEEEEhHHhhh--------------cc--hhHHHHHHHHHHHHHHHcCCEEEEEE
Confidence            589999999999998  44322   22233322110              00  01112222233333335678899999


Q ss_pred             CCCCC------C----ccC----hhHHHHhhcC--CCCCcEEEEEeCchHHH-HHh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNE------D----YYK----WEPFYKCLKN--SLHESKILITTRKETVA-RIM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~------~----~~~----~~~~~~~~~~--~~~~~~iLiTtr~~~~~-~~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      |++.-      .    ...    +..+...+..  ...+.-||.||..+... ..+   +. ...+.++..+.++-.++|
T Consensus       112 eiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il  191 (256)
T d1lv7a_         112 EIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL  191 (256)
T ss_dssp             THHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHH
T ss_pred             ChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHH
Confidence            98320      0    001    1234444432  23444566688875432 222   22 468899999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ..+...... ....+    ...+++.+.|+.
T Consensus       192 ~~~l~~~~~-~~~~~----~~~la~~t~G~s  217 (256)
T d1lv7a_         192 KVHMRRVPL-APDID----AAIIARGTPGFS  217 (256)
T ss_dssp             HHHHTTSCB-CTTCC----HHHHHHTCTTCC
T ss_pred             HHhccCCCc-CcccC----HHHHHHhCCCCC
Confidence            877633222 22233    356777888765

>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=96.85  E-value=0.00021  Score=68.56  Aligned_cols=102  Identities=15%  Similarity=0.172  Sum_probs=71.9

Q ss_pred             cccceEEecccccCCcccccccc--CccccCCCCcceeeccCCcccc-----ccchhhhcCCCCcEEecCCCcCccc---
Q 046115          383 TCLRALELQVRESWPRNNLIKEI--PTNIEKLLHLKYLNLKGQKKIE-----KLPETLCELYNLERLNVDDCQNLRE---  452 (505)
Q Consensus       383 ~~L~~L~l~~~~~~~~~~~~~~~--p~~~~~l~~L~~L~l~~~~~~~-----~lp~~~~~l~~L~~L~l~~~~~~~~---  452 (505)
                      .+|++|+++       ++.+...  ..-+..+++++.|+|++|. ++     .++..+..+++|+.|+|++|. +..   
T Consensus         2 ~~l~~ld~~-------~~~i~~~~~~~l~~~l~~l~~L~L~~~~-i~~~~~~~l~~~L~~~~~L~~LdLs~N~-i~~~~~   72 (460)
T d1z7xw1           2 LDIQSLDIQ-------CEELSDARWAELLPLLQQCQVVRLDDCG-LTEARCKDISSALRVNPALAELNLRSNE-LGDVGV   72 (460)
T ss_dssp             EEEEEEEEE-------SCCCCHHHHHHHHHHHTTCSEEEEESSC-CCHHHHHHHHHHHHTCTTCCEEECTTCC-CHHHHH
T ss_pred             CCCCEEEee-------CCcCChHHHHHHHHhCCCCCEEEeCCCC-CCHHHHHHHHHHHhcCCCCCEEECcCCc-CChHHH
Confidence            368999998       5555432  2235668999999999998 44     445667889999999999997 432   


Q ss_pred             --cchhccc-cccCceeecCCCccccc----ccccccCCccCCcccee
Q 046115          453 --LPRGIGK-LRKLMYLHNEDTGCLRY----LPAGIGELIRLRRVREF  493 (505)
Q Consensus       453 --lp~~~~~-l~~L~~L~l~~~~~~~~----~p~~i~~l~~L~~L~~~  493 (505)
                        +...+.. .++|++|++++|.....    ++..+..+++|+.|++.
T Consensus        73 ~~l~~~l~~~~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~  120 (460)
T d1z7xw1          73 HCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLS  120 (460)
T ss_dssp             HHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECC
T ss_pred             HHHHHHHhcCCCCCCEEECCCCCccccccccccchhhccccccccccc
Confidence              2223322 34799999999985432    45567778888887753

>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=96.84  E-value=0.0031  Score=55.25  Aligned_cols=145  Identities=10%  Similarity=0.070  Sum_probs=78.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||++|+++++  +....   .+.++.+              .+...  ............+...-...+++|++|
T Consensus        46 ppGtGKT~l~~ala~--~~~~~---~~~i~~~--------------~l~~~--~~g~~~~~l~~~f~~A~~~~p~il~iD  104 (258)
T d1e32a2          46 PPGTGKTLIARAVAN--ETGAF---FFLINGP--------------EIMSK--LAGESESNLRKAFEEAEKNAPAIIFID  104 (258)
T ss_dssp             CTTSSHHHHHHHHHH--HTTCE---EEEECHH--------------HHTTS--CTTHHHHHHHHHHHHHHHTCSEEEEES
T ss_pred             CCCCCchHHHHHHHH--HhCCe---EEEEEch--------------hhccc--ccccHHHHHHHHHHHHHhcCCeEEEeh
Confidence            589999999999998  33322   2222211              11101  011112222222333335678999999


Q ss_pred             CCCCCC-------ccC----hhHHHHhhcC--CCCCcEEEEEeCchHHHH-Hh---CC-cceEeCCCCChhhHHHHHHHh
Q 046115           81 DVWNED-------YYK----WEPFYKCLKN--SLHESKILITTRKETVAR-IM---GS-THVISVNVLSEMECWSVFQSL  142 (505)
Q Consensus        81 dv~~~~-------~~~----~~~~~~~~~~--~~~~~~iLiTtr~~~~~~-~~---~~-~~~~~l~~l~~~ea~~Lf~~~  142 (505)
                      |++.-.       ...    ...+...+..  ...+.-|+.||..+.... ..   +. ...+.++..+.++-.++|..+
T Consensus       105 eid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~  184 (258)
T d1e32a2         105 ELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIH  184 (258)
T ss_dssp             SGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHT
T ss_pred             hhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhh
Confidence            995421       001    1222222222  234455666888754322 22   12 468899999999999999876


Q ss_pred             hhCCCCCCCCchHHHHHHHHHHHcCCChH
Q 046115          143 AISGKTIGKRENLEKIGREIVKKCKGLPL  171 (505)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl  171 (505)
                      .... ......+    ...|++.+.|+--
T Consensus       185 l~~~-~~~~~~~----~~~la~~t~G~s~  208 (258)
T d1e32a2         185 TKNM-KLADDVD----LEQVANETHGHVG  208 (258)
T ss_dssp             TTTS-CBCTTCC----HHHHHHHCTTCCH
T ss_pred             ccCc-ccccccc----hhhhhhcccCCCH
Confidence            5322 2122222    4578889988653

>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=96.84  E-value=0.0069  Score=52.20  Aligned_cols=48  Identities=17%  Similarity=-0.033  Sum_probs=33.6

Q ss_pred             cceEeCCCCChhhHHHHHHHhhhCCCCCCCCchHHHHHHHHHHHcCCChHHH
Q 046115          122 THVISVNVLSEMECWSVFQSLAISGKTIGKRENLEKIGREIVKKCKGLPLAA  173 (505)
Q Consensus       122 ~~~~~l~~l~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal  173 (505)
                      ...+.+...+.++...++.......+.    ....+.+..|++.+.|.+-..
T Consensus       157 ~~~~~~~~~~~~~~~~i~~~~~~~~~i----~~~~~~l~~ia~~s~gd~R~a  204 (239)
T d1ixsb2         157 GIVEHLEYYTPEELAQGVMRDARLLGV----RITEEAALEIGRRSRGTMRVA  204 (239)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHGGGCC----CBCHHHHHHHHHHTTSSHHHH
T ss_pred             ceeeEeeccChhhhhHHHHHHHHHhCC----ccchHHHHHHHHHcCCCHHHH
Confidence            557788999999988887766533222    123567889999999977443

>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=96.33  E-value=0.0053  Score=53.91  Aligned_cols=144  Identities=13%  Similarity=0.155  Sum_probs=74.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEEEEEe
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFLLVLD   80 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~LlvlD   80 (505)
                      ++|+|||+||+.++.  +....|     +.++.        ..+..    ...  ..........+...-...+++|++|
T Consensus        49 p~GtGKT~l~~ala~--~~~~~~-----~~~~~--------~~l~~----~~~--~~~~~~l~~~f~~A~~~~p~il~id  107 (265)
T d1r7ra3          49 PPGCGKTLLAKAIAN--ECQANF-----ISIKG--------PELLT----MWF--GESEANVREIFDKARQAAPCVLFFD  107 (265)
T ss_dssp             CTTSSHHHHHHHHHH--HTTCEE-----EEECH--------HHHHT----SCT--TTHHHHHHHHHHHHHHTCSEEEEES
T ss_pred             CCCCcchhHHHHHHH--HhCCcE-----EEEEH--------HHhhh----ccc--cchHHHHHHHHHHHHhcCCcceeHH
Confidence            479999999999998  443332     22221        11111    111  1111222222333334578999999


Q ss_pred             CCCCCCc------cC--------hhHHHHhhcC--CCCCcEEEEEeCchHHH-HHh---CC-cceEeCCCCChhhHHHHH
Q 046115           81 DVWNEDY------YK--------WEPFYKCLKN--SLHESKILITTRKETVA-RIM---GS-THVISVNVLSEMECWSVF  139 (505)
Q Consensus        81 dv~~~~~------~~--------~~~~~~~~~~--~~~~~~iLiTtr~~~~~-~~~---~~-~~~~~l~~l~~~ea~~Lf  139 (505)
                      |++.--.      .+        ...+...+..  ...+.-||.||..+... ..+   +. ...+.++..+.++-.++|
T Consensus       108 eid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il  187 (265)
T d1r7ra3         108 ELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAIL  187 (265)
T ss_dssp             SGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHH
T ss_pred             hhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHH
Confidence            9953210      01        1223333322  22345677788765432 222   12 458899999999999999


Q ss_pred             HHhhhCCCCCCCCchHHHHHHHHHHHcCCCh
Q 046115          140 QSLAISGKTIGKRENLEKIGREIVKKCKGLP  170 (505)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  170 (505)
                      ...... .......+    ...+++.+.|+.
T Consensus       188 ~~~l~~-~~~~~~~~----l~~la~~t~g~s  213 (265)
T d1r7ra3         188 KANLRK-SPVAKDVD----LEFLAKMTNGFS  213 (265)
T ss_dssp             HHHTTC-C----CCC----CHHHHHHHCSSC
T ss_pred             HHHhcc-CCchhhhh----HHHHHhcCCCCC
Confidence            866532 11112222    346777777765

>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=96.24  E-value=0.0059  Score=52.87  Aligned_cols=15  Identities=33%  Similarity=0.146  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||++|+.+++
T Consensus        48 ppGtGKT~la~alA~   62 (246)
T d1d2na_          48 PPHSGKTALAAKIAE   62 (246)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHhh
Confidence            589999999999998

>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=96.04  E-value=0.061  Score=49.42  Aligned_cols=127  Identities=19%  Similarity=0.179  Sum_probs=64.0

Q ss_pred             CCCCcHHHHHHHHhcC---cccccC-CCceE-EEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHc-C-Cc
Q 046115            1 MGGIGKTTLAQFAYNN---GDVERN-FEKRT-WVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECV-A-GK   73 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~---~~~~~~-f~~~~-wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l-~-~~   73 (505)
                      .+|+|||+|+..++..   ..+-.. .+..+ +++++.              +. .......++++....+...+ . ..
T Consensus        51 ~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~--------------l~-ag~~~~g~~e~r~~~i~~~~~~~~~  115 (387)
T d1qvra2          51 EPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS--------------LL-AGAKYRGEFEERLKAVIQEVVQSQG  115 (387)
T ss_dssp             CTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--------------------------CHHHHHHHHHHHHHTTCS
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh--------------hh-cccCcchhHHHHHHHHHHHhccCCC
Confidence            4799999999877762   111111 23334 455443              11 11111233444444443333 3 34


Q ss_pred             eEEEEEeCCCCC-------CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH------hCCcceEeCCCCChhhHHHHHH
Q 046115           74 KFLLVLDDVWNE-------DYYKWEPFYKCLKNSLHESKILITTRKETVARI------MGSTHVISVNVLSEMECWSVFQ  140 (505)
Q Consensus        74 r~LlvlDdv~~~-------~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~------~~~~~~~~l~~l~~~ea~~Lf~  140 (505)
                      +++|++|++..-       ...+...++.+....+. -++|-+|-.......      ...++.+.+.+.+.+++..++.
T Consensus       116 ~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~-~~~I~~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~  194 (387)
T d1qvra2         116 EVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGE-LRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILR  194 (387)
T ss_dssp             SEEEEECCC-------------------HHHHHTTC-CCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHH
T ss_pred             ceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCC-cceeeecCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHHHH
Confidence            799999998442       11244556666665555 345555555443321      1236799999999999999997


Q ss_pred             Hhh
Q 046115          141 SLA  143 (505)
Q Consensus       141 ~~~  143 (505)
                      ...
T Consensus       195 ~~~  197 (387)
T d1qvra2         195 GLK  197 (387)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=96.04  E-value=0.0087  Score=49.82  Aligned_cols=109  Identities=14%  Similarity=0.016  Sum_probs=63.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC---CceEEEEeCC-CCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHHHcCCceEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF---EKRTWVCVSE-PFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEECVAGKKFL   76 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f---~~~~wv~~~~-~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~r~L   76 (505)
                      .+|+|||++|..+++  .+...+   ..+.++.... ...+ +..+++.+.+....                 ..+++-+
T Consensus        23 ~~g~gk~~~a~~l~~--~i~~~~~~h~D~~~i~~~~~~I~I-d~IR~i~~~~~~~~-----------------~~~~~Kv   82 (198)
T d2gnoa2          23 EDLSYPREVSLELPE--YVEKFPPKASDVLEIDPEGENIGI-DDIRTIKDFLNYSP-----------------ELYTRKY   82 (198)
T ss_dssp             SSSSHHHHHHHHHHH--HHHTSCCCTTTEEEECCSSSCBCH-HHHHHHHHHHTSCC-----------------SSSSSEE
T ss_pred             CCCCCHHHHHHHHHH--HHhccccCCCCEEEEeCCcCCCCH-HHHHHHHHHHhhCc-----------------ccCCCEE
Confidence            379999999999987  443221   2344554221 1112 22233333332111                 1235558


Q ss_pred             EEEeCCCCCCccChhHHHHhhcCCCCCcEEEEEeCchH-HHHHh-CCcceEeCCC
Q 046115           77 LVLDDVWNEDYYKWEPFYKCLKNSLHESKILITTRKET-VARIM-GSTHVISVNV  129 (505)
Q Consensus        77 lvlDdv~~~~~~~~~~~~~~~~~~~~~~~iLiTtr~~~-~~~~~-~~~~~~~l~~  129 (505)
                      +|+|+++.........++..+.....++.++++|.+.. +.... .....+.+..
T Consensus        83 iIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~  137 (198)
T d2gnoa2          83 VIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNV  137 (198)
T ss_dssp             EEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCC
T ss_pred             EEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCC
Confidence            99999988887788889999988777777777776643 32222 2334566654

>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=95.93  E-value=0.0051  Score=49.77  Aligned_cols=110  Identities=14%  Similarity=0.102  Sum_probs=65.0

Q ss_pred             CCCCceEEEecCCC-cccc-ccchhHHhhcCcccceEEecccccCCcccccc-----ccCccccCCCCcceeeccCCccc
Q 046115          354 GLRGLRSLLVKSDE-YSWS-SEVLPQLFEKLTCLRALELQVRESWPRNNLIK-----EIPTNIEKLLHLKYLNLKGQKKI  426 (505)
Q Consensus       354 ~~~~L~~L~l~~~~-~~~~-~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-----~~p~~~~~l~~L~~L~l~~~~~~  426 (505)
                      +.++|+.|+++++. ++.. ...+-..+...++|+.|+|+       ++.++     .+...+...+.|+.|+|++|. +
T Consensus        13 n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls-------~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~-i   84 (167)
T d1pgva_          13 DDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLA-------NTAISDSEARGLIELIETSPSLRVLNVESNF-L   84 (167)
T ss_dssp             TCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECT-------TSCCBHHHHTTHHHHHHHCSSCCEEECCSSB-C
T ss_pred             CCCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeecc-------ccccchhHHHHHhhhhhhcccccceeeehhh-c
Confidence            45778888887643 3221 01133345666778888887       33332     222334556778888888887 4


Q ss_pred             c-----ccchhhhcCCCCcEEecCCCcCccc--------cchhccccccCceeecCCCc
Q 046115          427 E-----KLPETLCELYNLERLNVDDCQNLRE--------LPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       427 ~-----~lp~~~~~l~~L~~L~l~~~~~~~~--------lp~~~~~l~~L~~L~l~~~~  472 (505)
                      +     .+-..+..-+.|+.|++++|. ...        +-..+..-++|+.|+++.+.
T Consensus        85 ~~~g~~~l~~aL~~n~sL~~L~l~~n~-~~~~g~~~~~~l~~~L~~n~sL~~l~l~~~~  142 (167)
T d1pgva_          85 TPELLARLLRSTLVTQSIVEFKADNQR-QSVLGNQVEMDMMMAIEENESLLRVGISFAS  142 (167)
T ss_dssp             CHHHHHHHHHHTTTTCCCSEEECCCCS-SCCCCHHHHHHHHHHHHHCSSCCEEECCCCC
T ss_pred             chHHHHHHHHHHHhCCcCCEEECCCCc-CCCccHHHHHHHHHHHHhCCCccEeeCcCCC
Confidence            3     233345566778888888765 222        23334555777788776653

>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=95.43  E-value=0.0059  Score=49.39  Aligned_cols=108  Identities=18%  Similarity=0.083  Sum_probs=70.7

Q ss_pred             hhcCcccceEEecccccCCcccccc-----ccCccccCCCCcceeeccCCccc----cccchhhhcCCCCcEEecCCCcC
Q 046115          379 FEKLTCLRALELQVRESWPRNNLIK-----EIPTNIEKLLHLKYLNLKGQKKI----EKLPETLCELYNLERLNVDDCQN  449 (505)
Q Consensus       379 ~~~l~~L~~L~l~~~~~~~~~~~~~-----~~p~~~~~l~~L~~L~l~~~~~~----~~lp~~~~~l~~L~~L~l~~~~~  449 (505)
                      ..+.++|+.|+|++      .+.++     .+-..+...++|++|+|++|..-    ..+...+...+.|+.|+|++|..
T Consensus        11 ~~n~~~L~~L~L~~------~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i   84 (167)
T d1pgva_          11 REDDTDLKEVNINN------MKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFL   84 (167)
T ss_dssp             HTTCSSCCEEECTT------CCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBC
T ss_pred             HhCCCCCcEEEeCC------CCCCCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhc
Confidence            34568899999982      22232     23344667788999999999832    13334456778999999999983


Q ss_pred             ccc----cchhccccccCceeecCCCccc--c-----cccccccCCccCCccce
Q 046115          450 LRE----LPRGIGKLRKLMYLHNEDTGCL--R-----YLPAGIGELIRLRRVRE  492 (505)
Q Consensus       450 ~~~----lp~~~~~l~~L~~L~l~~~~~~--~-----~~p~~i~~l~~L~~L~~  492 (505)
                      ...    +=..+..-++|++|++++|...  +     .+...+...++|+.|.+
T Consensus        85 ~~~g~~~l~~aL~~n~sL~~L~l~~n~~~~~g~~~~~~l~~~L~~n~sL~~l~l  138 (167)
T d1pgva_          85 TPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGI  138 (167)
T ss_dssp             CHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEEC
T ss_pred             chHHHHHHHHHHHhCCcCCEEECCCCcCCCccHHHHHHHHHHHHhCCCccEeeC
Confidence            322    2224677789999999987421  1     12334455577777654

>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=95.35  E-value=0.023  Score=49.38  Aligned_cols=77  Identities=16%  Similarity=0.114  Sum_probs=50.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+|||+||.+++.  ...+.=..++||+....++.+.     +++++...+.    .....++..+.+....+ ++.-
T Consensus        68 ~~~~GKT~l~l~~~~--~~q~~g~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~~~~  140 (269)
T d1mo6a1          68 PESSGKTTVALHAVA--NAQAAGGVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALD  140 (269)
T ss_dssp             SSSSSHHHHHHHHHH--HHHHTTCEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTTCEE
T ss_pred             CCCcHHHHHHHHHHH--HHhcCCCEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            369999999988887  3434434678999999888754     4555543321    23445666665555443 4577


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      |||+|.+..
T Consensus       141 liIiDSi~a  149 (269)
T d1mo6a1         141 IVVIDSVAA  149 (269)
T ss_dssp             EEEEECSTT
T ss_pred             EEEEecccc
Confidence            999999843

>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=94.94  E-value=0.027  Score=48.99  Aligned_cols=77  Identities=17%  Similarity=0.114  Sum_probs=51.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHcCC-ceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECVAG-KKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l~~-~r~   75 (505)
                      .+|+|||+||.+++..  ..+.=..++|++....++.+     ++++++...+.    ...+.++..+.+....+. ..-
T Consensus        65 ~~~sGKT~l~l~~~~~--aqk~g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~~~  137 (268)
T d1xp8a1          65 PESGGKTTLALAIVAQ--AQKAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  137 (268)
T ss_dssp             STTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             CCccchHHHHHHHHHH--HHhCCCEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCCCc
Confidence            3689999999888873  33322457899999888874     56667654332    334556666666555543 456


Q ss_pred             EEEEeCCCC
Q 046115           76 LLVLDDVWN   84 (505)
Q Consensus        76 LlvlDdv~~   84 (505)
                      |||+|.+..
T Consensus       138 liIiDSi~a  146 (268)
T d1xp8a1         138 VVVVDSVAA  146 (268)
T ss_dssp             EEEEECTTT
T ss_pred             EEEEecccc
Confidence            888998833

>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=94.92  E-value=0.017  Score=50.19  Aligned_cols=75  Identities=16%  Similarity=0.150  Sum_probs=46.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCC----ChhcHHHHHHHHHHHcC-CceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAK----DLVEFQSLMQHIEECVA-GKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~----~~~~~~~~~~~l~~~l~-~~r~   75 (505)
                      .+|+||||||.+++.  ...+.=..++|++....++..     .++.++...+.    .....++..+.+....+ +..-
T Consensus        62 ~~gsGKTtl~l~~~~--~~q~~g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~~~~~  134 (263)
T d1u94a1          62 PESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  134 (263)
T ss_dssp             STTSSHHHHHHHHHH--HHHHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCcHHHHHHHHHHH--HHHcCCCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            379999999999987  444444567899998888764     34555543221    22334445544444432 2334


Q ss_pred             EEEEeCC
Q 046115           76 LLVLDDV   82 (505)
Q Consensus        76 LlvlDdv   82 (505)
                      |||+|.+
T Consensus       135 liViDSi  141 (263)
T d1u94a1         135 VIVVDSV  141 (263)
T ss_dssp             EEEEECG
T ss_pred             EEEEECc
Confidence            7788887

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

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: Chicken (Gallus gallus) [TaxId: 9031]

Probab=94.10  E-value=0.037  Score=44.29  Aligned_cols=112  Identities=15%  Similarity=0.126  Sum_probs=64.9

Q ss_pred             CCCCceEEEecCC-Cccccc-cchhHHhhcCcccceEEecccccCCccccccc-----cCccccCCCCcceeeccCCccc
Q 046115          354 GLRGLRSLLVKSD-EYSWSS-EVLPQLFEKLTCLRALELQVRESWPRNNLIKE-----IPTNIEKLLHLKYLNLKGQKKI  426 (505)
Q Consensus       354 ~~~~L~~L~l~~~-~~~~~~-~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~-----~p~~~~~l~~L~~L~l~~~~~~  426 (505)
                      +.+.|+.|.+.++ .++... ..+-..+...++|+.|+++       ++.++.     +-..+...++++.+++++|...
T Consensus        15 ~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls-------~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~   87 (166)
T d1io0a_          15 NDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIV-------GTRSNDPVAFALAEMLKVNNTLKSLNVESNFIS   87 (166)
T ss_dssp             TCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECT-------TSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCC
T ss_pred             cCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeecc-------CCcccHHHHHHHHHHHhhcccchhhhhcccccc
Confidence            5577888888763 332211 1133335567778888887       333222     2233456677888888887732


Q ss_pred             ----cccchhhhcCCCCcEEecCCCcC-cc-----ccchhccccccCceeecCCCc
Q 046115          427 ----EKLPETLCELYNLERLNVDDCQN-LR-----ELPRGIGKLRKLMYLHNEDTG  472 (505)
Q Consensus       427 ----~~lp~~~~~l~~L~~L~l~~~~~-~~-----~lp~~~~~l~~L~~L~l~~~~  472 (505)
                          ..+...+.+.++|+.++|+.+.. +.     .+-..+...++|++|+++.+.
T Consensus        88 ~~g~~~l~~~l~~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~~~~  143 (166)
T d1io0a_          88 GSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQ  143 (166)
T ss_dssp             HHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             chhHHHHHHHHHhCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCcCCC
Confidence                23334566777788766654321 21     233345667788888877664

>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=94.10  E-value=0.0094  Score=48.45  Aligned_cols=28  Identities=11%  Similarity=0.049  Sum_probs=21.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~~~~wv~   30 (505)
                      ++|+||||+|++++.  ..... ++...+++
T Consensus        14 ~~GsGKTTia~~La~--~L~~~~~~~~~~~~   42 (183)
T d1m8pa3          14 YMNSGKDAIARALQV--TLNQQGGRSVSLLL   42 (183)
T ss_dssp             STTSSHHHHHHHHHH--HHHHHCSSCEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHhhcCCCchhhhh
Confidence            689999999999998  65444 45555654

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

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: Chicken (Gallus gallus) [TaxId: 9031]

Probab=93.63  E-value=0.019  Score=46.16  Aligned_cols=113  Identities=15%  Similarity=0.088  Sum_probs=73.1

Q ss_pred             hhHHhhcCcccceEEecccccCCcccccc-----ccCccccCCCCcceeeccCCcccc----ccchhhhcCCCCcEEecC
Q 046115          375 LPQLFEKLTCLRALELQVRESWPRNNLIK-----EIPTNIEKLLHLKYLNLKGQKKIE----KLPETLCELYNLERLNVD  445 (505)
Q Consensus       375 ~~~~~~~l~~L~~L~l~~~~~~~~~~~~~-----~~p~~~~~l~~L~~L~l~~~~~~~----~lp~~~~~l~~L~~L~l~  445 (505)
                      +.....+.++|+.|+|++      .+.++     .+-..+...++|+.|++++|..-.    .+-..+...+.++.++++
T Consensus         9 l~~~~~~~~~L~~L~L~~------~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~   82 (166)
T d1io0a_           9 LKRIQNNDPDLEEVNLNN------IMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVE   82 (166)
T ss_dssp             HHHHHTTCTTCCEEECTT------CTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECC
T ss_pred             HHHHHhcCCCCcEEEcCC------CCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhc
Confidence            455456778999999982      23222     233345678899999999998322    333455678999999999


Q ss_pred             CCcCcc----ccchhccccccCceeecC--CCcccc----cccccccCCccCCcccee
Q 046115          446 DCQNLR----ELPRGIGKLRKLMYLHNE--DTGCLR----YLPAGIGELIRLRRVREF  493 (505)
Q Consensus       446 ~~~~~~----~lp~~~~~l~~L~~L~l~--~~~~~~----~~p~~i~~l~~L~~L~~~  493 (505)
                      +|....    .+-..+...++|+.++++  +|....    .+...+...+.|+.|++.
T Consensus        83 ~~~~~~~g~~~l~~~l~~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~  140 (166)
T d1io0a_          83 SNFISGSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYH  140 (166)
T ss_dssp             SSCCCHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECC
T ss_pred             cccccchhHHHHHHHHHhCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCc
Confidence            987332    233456777889876665  444322    233345567788887753

>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=93.07  E-value=0.04  Score=49.32  Aligned_cols=88  Identities=15%  Similarity=0.154  Sum_probs=42.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCC--CChhcHHHHHHHHHHHcCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSA--KDLVEFQSLMQHIEECVAGKKFLLV   78 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~l~~~l~~~r~Llv   78 (505)
                      +.|+|||.+|+.+++  .+-+.-...+-++.+...+....     ..+.....  ..........+.++   +....+++
T Consensus        61 p~G~GKt~lak~la~--~l~~~~~~~~~~~~~~~~~~~~~-----~~L~g~~~gyvG~~~~~~l~~~~~---~~p~~Vvl  130 (315)
T d1qvra3          61 PTGVGKTELAKTLAA--TLFDTEEAMIRIDMTEYMEKHAV-----SRLIGAPPGYVGYEEGGQLTEAVR---RRPYSVIL  130 (315)
T ss_dssp             CSSSSHHHHHHHHHH--HHHSSGGGEEEECTTTCCSSGGG-----GGC--------------CHHHHHH---HCSSEEEE
T ss_pred             CCcchHHHHHHHHHH--HhcCCCcceEEEeccccccchhh-----hhhcCCCCCCcCcccCChHHHHHH---hCCCcEEE
Confidence            479999999999998  44222233444554443322111     11110000  00011111222222   34578999


Q ss_pred             EeCCCCCCccChhHHHHhhc
Q 046115           79 LDDVWNEDYYKWEPFYKCLK   98 (505)
Q Consensus        79 lDdv~~~~~~~~~~~~~~~~   98 (505)
                      ||+++......+..+...+.
T Consensus       131 ~DEieK~~~~v~~~ll~~l~  150 (315)
T d1qvra3         131 FDEIEKAHPDVFNILLQILD  150 (315)
T ss_dssp             ESSGGGSCHHHHHHHHHHHT
T ss_pred             EehHhhcCHHHHHHHHHHhc
Confidence            99997766545555555443

>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=93.03  E-value=0.016  Score=46.10  Aligned_cols=15  Identities=27%  Similarity=0.295  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.++.
T Consensus        10 ~~GsGKSTvak~La~   24 (169)
T d1kaga_          10 PMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999998

>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=92.80  E-value=0.014  Score=48.13  Aligned_cols=27  Identities=19%  Similarity=0.030  Sum_probs=20.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWV   29 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv   29 (505)
                      ++|+||||+|++++.  .....+....++
T Consensus        27 ~pGSGKTTiAk~La~--~l~~~~~~~~~~   53 (195)
T d1x6va3          27 LSGAGKTTVSMALEE--YLVCHGIPCYTL   53 (195)
T ss_dssp             SCHHHHHHHHHHHHH--HHHHTTCCEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHhcCCCccch
Confidence            589999999999998  555555544444

>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=92.54  E-value=0.034  Score=49.86  Aligned_cols=86  Identities=15%  Similarity=0.202  Sum_probs=44.7

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCHHHHHHHHHHHcCCCCCCChhcHHHHHHHHHH-HcCCceEEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDEFRIARAIIESLTPGSAKDLVEFQSLMQHIEE-CVAGKKFLLVL   79 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~-~l~~~r~Llvl   79 (505)
                      ++|+|||.||+.++.  ..   +...+-++++.-.+...     ...+. +....-...... ..+.. ..+....+++|
T Consensus        60 p~GvGKT~lak~la~--~l---~~~~i~~d~s~~~~~~~-----~~~l~-g~~~gy~g~~~~-~~l~~~~~~~~~~vvl~  127 (315)
T d1r6bx3          60 PTGVGKTEVTVQLSK--AL---GIELLRFDMSEYMERHT-----VSRLI-GAPPGYVGFDQG-GLLTDAVIKHPHAVLLL  127 (315)
T ss_dssp             STTSSHHHHHHHHHH--HH---TCEEEEEEGGGCSSSSC-----CSSSC-CCCSCSHHHHHT-THHHHHHHHCSSEEEEE
T ss_pred             CCcchhHHHHHHHHh--hc---cCCeeEeccccccchhh-----hhhhc-ccCCCccccccC-ChhhHHHHhCccchhhh
Confidence            579999999999998  33   23344555544221110     11122 111111111111 11111 22356779999


Q ss_pred             eCCCCCCccChhHHHHhhc
Q 046115           80 DDVWNEDYYKWEPFYKCLK   98 (505)
Q Consensus        80 Ddv~~~~~~~~~~~~~~~~   98 (505)
                      |++.......+..+.+.+.
T Consensus       128 DeieKa~~~V~~~lLqild  146 (315)
T d1r6bx3         128 DEIEKAHPDVFNILLQVMD  146 (315)
T ss_dssp             ETGGGSCHHHHHHHHHHHH
T ss_pred             cccccccchHhhhhHHhhc
Confidence            9997776666666666554

>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=91.97  E-value=0.027  Score=44.19  Aligned_cols=15  Identities=33%  Similarity=0.270  Sum_probs=13.4

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|++++.
T Consensus        10 ~pGsGKTTla~~L~~   24 (152)
T d1ly1a_          10 CPGSGKSTWAREFIA   24 (152)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999876

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=91.92  E-value=0.027  Score=45.21  Aligned_cols=15  Identities=40%  Similarity=0.488  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~pGsGKTTia~~La~   26 (173)
T d1rkba_          12 TPGVGKTTLGKELAS   26 (173)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999987

>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=91.67  E-value=0.025  Score=45.28  Aligned_cols=15  Identities=27%  Similarity=0.419  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.++.
T Consensus         9 ~~G~GKSTig~~La~   23 (165)
T d2iyva1           9 LPGSGKSTIGRRLAK   23 (165)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999998

>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=91.49  E-value=0.032  Score=44.74  Aligned_cols=15  Identities=27%  Similarity=0.344  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|++++.
T Consensus        10 ~~GsGKTTva~~L~~   24 (176)
T d2bdta1          10 PAGVGKSTTCKRLAA   24 (176)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=91.28  E-value=0.032  Score=45.32  Aligned_cols=15  Identities=20%  Similarity=0.078  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||||+.++.
T Consensus        15 ~~GsGKTTla~~La~   29 (192)
T d1lw7a2          15 GESSGKSVLVNKLAA   29 (192)
T ss_dssp             CTTSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999997

>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=91.13  E-value=0.27  Score=42.37  Aligned_cols=43  Identities=26%  Similarity=0.284  Sum_probs=29.6

Q ss_pred             CCCcHHHHHHHHhcCcccc-cCCCceEEEEeCCCC-CHHHHHHHHHH
Q 046115            2 GGIGKTTLAQFAYNNGDVE-RNFEKRTWVCVSEPF-DEFRIARAIIE   46 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~-~~f~~~~wv~~~~~~-~~~~~~~~l~~   46 (505)
                      +|+|||+|+..+++  ... .+=+.++++-+++.. +..++.+++.+
T Consensus        77 ~g~GKt~l~~~i~~--~~~~~~~~v~V~~~iGer~~ev~~~~~~~~~  121 (276)
T d2jdid3          77 AGVGKTVLIMELIN--NVAKAHGGYSVFAGVGERTREGNDLYHEMIE  121 (276)
T ss_dssp             TTSSHHHHHHHHHH--HHTTTCSSEEEEEEESCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH--HHHhhCCCeEEEEEeccChHHHHHHHHHHHh
Confidence            69999999999987  322 333456788788754 45566666665

>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=90.67  E-value=0.033  Score=44.34  Aligned_cols=15  Identities=40%  Similarity=0.439  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.++.
T Consensus         8 ~~GsGKsTi~k~La~   22 (161)
T d1viaa_           8 FMGSGKSTLARALAK   22 (161)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            789999999999998

>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=90.64  E-value=0.058  Score=43.56  Aligned_cols=15  Identities=47%  Similarity=0.512  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||||+++++.
T Consensus         9 ~~GtGKTtl~~~i~~   23 (189)
T d2i3ba1           9 PPGVGKTTLIHKASE   23 (189)
T ss_dssp             CCSSCHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHH
Confidence            589999999999987

>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=90.45  E-value=0.047  Score=43.86  Aligned_cols=15  Identities=27%  Similarity=0.242  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      |+|+||||+|+.++.
T Consensus        10 ~~GsGKSTia~~LA~   24 (170)
T d1e6ca_          10 ARGCGMTTVGRELAR   24 (170)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999997

>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=89.93  E-value=0.054  Score=43.12  Aligned_cols=15  Identities=40%  Similarity=0.410  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+|||||++++++
T Consensus        10 ~~GSGKTTL~~~L~~   24 (170)
T d1np6a_          10 WSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999997

>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=89.87  E-value=0.054  Score=43.36  Aligned_cols=15  Identities=33%  Similarity=0.508  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        13 ~~GsGKTT~~~~La~   27 (174)
T d1y63a_          13 TPGTGKTSMAEMIAA   27 (174)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=89.80  E-value=0.051  Score=43.56  Aligned_cols=15  Identities=13%  Similarity=0.186  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.+++
T Consensus        11 ~~GsGKsTva~~L~~   25 (178)
T d1qhxa_          11 GSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999998

>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=89.72  E-value=0.2  Score=44.32  Aligned_cols=21  Identities=24%  Similarity=0.175  Sum_probs=17.2

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF   23 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f   23 (505)
                      ++|+|||.||+.++.  +...++
T Consensus       131 ~pG~GKT~la~ala~--~~~~~~  151 (321)
T d1w44a_         131 KGNSGKTPLVHALGE--ALGGKD  151 (321)
T ss_dssp             SSSSCHHHHHHHHHH--HHHTTS
T ss_pred             CCCccHHHHHHHHHH--HhcCCC
Confidence            489999999999998  665443

>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=89.61  E-value=0.064  Score=42.95  Aligned_cols=15  Identities=40%  Similarity=0.461  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        12 ~~GsGKSTia~~La~   26 (176)
T d1zp6a1          12 HPGSGKSTIAEALAN   26 (176)
T ss_dssp             CTTSCHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=89.35  E-value=0.062  Score=44.62  Aligned_cols=15  Identities=20%  Similarity=0.202  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+++++
T Consensus        10 lpgsGKSTla~~L~~   24 (213)
T d1bifa1          10 LPARGKTYISKKLTR   24 (213)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999997

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.25  E-value=0.065  Score=42.76  Aligned_cols=15  Identities=27%  Similarity=0.408  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        14 ~~GsGKsT~a~~La~   28 (171)
T d1knqa_          14 VSGSGKSAVASEVAH   28 (171)
T ss_dssp             STTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=89.22  E-value=1.4  Score=36.02  Aligned_cols=49  Identities=18%  Similarity=0.018  Sum_probs=29.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC-CHHHHHHHHHHHcCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF-DEFRIARAIIESLTPG   51 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~-~~~~~~~~l~~~l~~~   51 (505)
                      +.|+||||.+.+++.  ..+.+-..+..++..... ...+.++...+.++.+
T Consensus        18 p~GvGKTTTiaKLA~--~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2          18 LQGSGKTTTAAKLAL--YYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             CTTTTHHHHHHHHHH--HHHHTTCCEEEEECCSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCcEEEEecccccchHHHHHHHHHHhcCCc
Confidence            479999999988877  344333345556554322 3345556666666543

>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=88.88  E-value=0.089  Score=44.43  Aligned_cols=30  Identities=27%  Similarity=0.142  Sum_probs=23.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSE   33 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~   33 (505)
                      ||+||||+|..++.  ..+++-..++.|++..
T Consensus        11 GGvGKTtia~nlA~--~la~~g~~VlliD~D~   40 (232)
T d1hyqa_          11 GGTGKTTITANLGV--ALAQLGHDVTIVDADI   40 (232)
T ss_dssp             SCSCHHHHHHHHHH--HHHHTTCCEEEEECCC
T ss_pred             CCChHHHHHHHHHH--HHHhCCCCEEEEeCCC
Confidence            89999999999987  5555545677888653

>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=88.85  E-value=0.068  Score=46.40  Aligned_cols=20  Identities=30%  Similarity=0.496  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN   22 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~   22 (505)
                      ++|+|||+||+.++.  +....
T Consensus        40 pPGtGKT~la~~la~--~~~~~   59 (273)
T d1gvnb_          40 QPGSGKTSLRSAIFE--ETQGN   59 (273)
T ss_dssp             CTTSCTHHHHHHHHH--HTTTC
T ss_pred             CCCCCHHHHHHHHHH--Hhhcc
Confidence            589999999999998  55433

>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=88.36  E-value=0.087  Score=42.30  Aligned_cols=15  Identities=33%  Similarity=0.370  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|++++.
T Consensus        22 ~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          22 FPGAGKSTFIQEHLV   36 (172)
T ss_dssp             CTTSSHHHHHHHHTG
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999876

>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=88.19  E-value=0.14  Score=44.91  Aligned_cols=34  Identities=18%  Similarity=0.232  Sum_probs=23.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCCCH
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPFDE   37 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~~~   37 (505)
                      ||+||||+|..++.  ..+++=..+.-|+.....+.
T Consensus        17 GGVGKTTvaa~lA~--~lA~~G~rVLlvD~Dp~~~l   50 (296)
T d1ihua1          17 GGVGKTSISCATAI--RLAEQGKRVLLVSTDPASNV   50 (296)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTCCEEEEECCTTCCH
T ss_pred             CcChHHHHHHHHHH--HHHHCCCCEEEEeCCCCCCH
Confidence            89999999988887  55444234566776544443

>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=88.03  E-value=0.9  Score=38.41  Aligned_cols=14  Identities=29%  Similarity=0.603  Sum_probs=12.7

Q ss_pred             CCCcHHHHHHHHhc
Q 046115            2 GGIGKTTLAQFAYN   15 (505)
Q Consensus         2 ~G~GKT~LA~~~~~   15 (505)
                      .|+|||++|+.+..
T Consensus        32 ~GtGK~~~A~~ih~   45 (247)
T d1ny5a2          32 SGVGKEVVARLIHK   45 (247)
T ss_dssp             TTSSHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHH
Confidence            59999999999976

>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=87.80  E-value=0.14  Score=41.46  Aligned_cols=28  Identities=14%  Similarity=0.179  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~   30 (505)
                      ++|+||||+|+.++.  ....+...+..+.
T Consensus         9 ~~GsGKTT~~~~La~--~L~~~~~~~~~~~   36 (194)
T d1nksa_           9 IPGVGKSTVLAKVKE--ILDNQGINNKIIN   36 (194)
T ss_dssp             CTTSCHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHHcCCCEEEEE
Confidence            579999999999987  5544433334444

>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=87.73  E-value=0.52  Score=40.57  Aligned_cols=32  Identities=16%  Similarity=0.106  Sum_probs=22.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEPF   35 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~~   35 (505)
                      +|+|||+|+.....  ....+-..++++-+++..
T Consensus        76 ~g~GKt~l~~~~~~--~~~~~~~v~V~~~iGer~  107 (276)
T d1fx0a3          76 RQTGKTAVATDTIL--NQQGQNVICVYVAIGQKA  107 (276)
T ss_dssp             SSSSHHHHHHHHHH--TCCTTTCEEEEEEESCCH
T ss_pred             CCCChHHHHHHHHh--hhcccCceeeeeeecchh
Confidence            59999999987665  334444566777777654

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=87.57  E-value=0.13  Score=41.88  Aligned_cols=28  Identities=21%  Similarity=0.080  Sum_probs=19.1

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~   30 (505)
                      .+|+||||||+++..  ........+..++
T Consensus        30 ~~GSGKSTla~~L~~--~l~~~~~~~~~~~   57 (198)
T d1rz3a_          30 LSRSGKTTLANQLSQ--TLREQGISVCVFH   57 (198)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CCCCCHHHHHHHHHH--Hhccccccceecc
Confidence            379999999999987  4444443444333

>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=87.43  E-value=0.8  Score=37.57  Aligned_cols=80  Identities=14%  Similarity=0.010  Sum_probs=40.3

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceE-EEEeCCCC-CHHHHHHHHHHHcCCCC--CCChhcHHHHHHHHHHHc-CCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRT-WVCVSEPF-DEFRIARAIIESLTPGS--AKDLVEFQSLMQHIEECV-AGKKF   75 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~-wv~~~~~~-~~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~l~~~l-~~~r~   75 (505)
                      +.|+||||-+.+++.  ..+. ....+ -+...... .-.+.++...+.++.+.  .....+............ .+..=
T Consensus        17 ptGvGKTTTiAKLA~--~~~~-~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a~~~~~d   93 (211)
T d2qy9a2          17 VNGVGKTTTIGKLAR--QFEQ-QGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAKARNID   93 (211)
T ss_dssp             CTTSCHHHHHHHHHH--HHHT-TTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCCCHHHHHHHHHH--HHHH-CCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHHHHcCCC
Confidence            479999999988887  4432 22334 34333221 23466666777776442  223334444333322221 12223


Q ss_pred             EEEEeCCC
Q 046115           76 LLVLDDVW   83 (505)
Q Consensus        76 LlvlDdv~   83 (505)
                      ++++|=..
T Consensus        94 ~ilIDTaG  101 (211)
T d2qy9a2          94 VLIADTAG  101 (211)
T ss_dssp             EEEECCCC
T ss_pred             EEEeccCC
Confidence            56666654

>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=87.42  E-value=0.16  Score=43.03  Aligned_cols=32  Identities=25%  Similarity=0.222  Sum_probs=26.0

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      .+|+|||+||.+++.  ...++...++|++...+
T Consensus        34 ~pGsGKT~l~~qia~--~~~~~~~~~~~is~e~~   65 (242)
T d1tf7a2          34 ATGTGKTLLVSRFVE--NACANKERAILFAYEES   65 (242)
T ss_dssp             CTTSSHHHHHHHHHH--HHHTTTCCEEEEESSSC
T ss_pred             CCCCCHHHHHHHHHH--HHHHhccccceeeccCC
Confidence            379999999999998  56677778889987653

>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=87.11  E-value=0.11  Score=43.28  Aligned_cols=28  Identities=21%  Similarity=0.119  Sum_probs=19.8

Q ss_pred             CCCCcHHHHHHHHhcCccccc-CCCceEEEE
Q 046115            1 MGGIGKTTLAQFAYNNGDVER-NFEKRTWVC   30 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~-~f~~~~wv~   30 (505)
                      ++|+||||||+++..  .... ....+++++
T Consensus        32 lsGsGKTTia~~L~~--~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          32 LSASGKSTLAVELEH--QLVRDRRVHAYRLD   60 (208)
T ss_dssp             STTSSHHHHHHHHHH--HHHHHHCCCEEEEC
T ss_pred             CCCCCHHHHHHHHHH--HHHHhcCceEEEEc
Confidence            589999999999987  4432 233555665

>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=86.75  E-value=0.2  Score=42.17  Aligned_cols=29  Identities=28%  Similarity=0.126  Sum_probs=22.1

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVS   32 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~   32 (505)
                      ||+||||+|..++.  ..+..-..++-|+..
T Consensus        12 GGvGKTtia~nLA~--~la~~g~~VlliD~D   40 (237)
T d1g3qa_          12 GGTGKTTVTANLSV--ALGDRGRKVLAVDGD   40 (237)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTCCEEEEECC
T ss_pred             CCCcHHHHHHHHHH--HHHhCCCCEEEEeCC
Confidence            89999999999987  555544457777764

>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=86.70  E-value=0.12  Score=41.47  Aligned_cols=15  Identities=40%  Similarity=0.494  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      .+|+|||||++.++.
T Consensus         8 ~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           8 EPGVGKTTLVKKIVE   22 (178)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHh
Confidence            479999999999987

>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=86.47  E-value=0.17  Score=40.65  Aligned_cols=21  Identities=29%  Similarity=0.513  Sum_probs=16.5

Q ss_pred             CCCCcHHHHHHHHhcCcccccCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNF   23 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f   23 (505)
                      ++|+||||+++.++.  ......
T Consensus         9 ~~GsGKsT~~~~L~~--~l~~~~   29 (190)
T d1khta_           9 VPGVGSTTSSQLAMD--NLRKEG   29 (190)
T ss_dssp             CTTSCHHHHHHHHHH--HHHTTT
T ss_pred             CCCCCHHHHHHHHHH--HHHHcC
Confidence            589999999999987  554443

>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=86.37  E-value=2.9  Score=33.97  Aligned_cols=48  Identities=15%  Similarity=-0.063  Sum_probs=29.6

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCCceEEEEeCCC-CCHHHHHHHHHHHcCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP-FDEFRIARAIIESLTP   50 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~-~~~~~~~~~l~~~l~~   50 (505)
                      +.|+||||-+.+++.  ....+=..+..|+.... ..-.+.++...+.++.
T Consensus        14 ptGvGKTTTiaKLA~--~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~i   62 (207)
T d1okkd2          14 VNGVGKTTTIAKLGR--YYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSI   62 (207)
T ss_dssp             STTSSHHHHHHHHHH--HHHTTTCCEEEECCCCSSTTHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHH--HHHHCCCcEEEEEeccccccchhhHhhcccccCc
Confidence            479999999988877  33322234557765542 3444666666666654

>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=85.37  E-value=0.17  Score=43.98  Aligned_cols=14  Identities=36%  Similarity=0.200  Sum_probs=13.0

Q ss_pred             CCCcHHHHHHHHhc
Q 046115            2 GGIGKTTLAQFAYN   15 (505)
Q Consensus         2 ~G~GKT~LA~~~~~   15 (505)
                      +|+|||+|+.++++
T Consensus        52 ~g~GKT~l~~~i~~   65 (289)
T d1xpua3          52 PKAGKTMLLQNIAQ   65 (289)
T ss_dssp             SSSSHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH
Confidence            69999999999987

>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=85.36  E-value=0.83  Score=38.10  Aligned_cols=53  Identities=11%  Similarity=0.098  Sum_probs=30.5

Q ss_pred             HHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcC--CCCCcEEEEEeCchHHHHH
Q 046115           66 IEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKN--SLHESKILITTRKETVARI  118 (505)
Q Consensus        66 l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~--~~~~~~iLiTtr~~~~~~~  118 (505)
                      +.+.+...+-+|++|.-... +...-..+...+..  ...|..||++|-+.+.+..
T Consensus       141 iAraL~~~P~illlDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~~~a~~  196 (232)
T d2awna2         141 IGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQVEAMT  196 (232)
T ss_dssp             HHHHHHTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCHHHHHH
T ss_pred             HHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            55566667779999996442 22222233333333  1246678888888665554

>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=85.09  E-value=0.13  Score=45.70  Aligned_cols=15  Identities=33%  Similarity=0.430  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+|||.||+.+++
T Consensus        57 PpG~GKT~lAkalA~   71 (309)
T d1ofha_          57 PTGVGKTEIARRLAK   71 (309)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHhh
Confidence            689999999999998

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=84.93  E-value=0.16  Score=41.33  Aligned_cols=15  Identities=27%  Similarity=0.262  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        14 ~PGSGKtT~a~~La~   28 (189)
T d2ak3a1          14 APGSGKGTVSSRITK   28 (189)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            689999999999997

>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=84.90  E-value=0.22  Score=43.21  Aligned_cols=31  Identities=23%  Similarity=0.161  Sum_probs=20.5

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      ||+||||+|..++.  ..+..=..++-|+....
T Consensus        29 GGVGKTT~a~nLA~--~lA~~G~rVllvD~Dp~   59 (279)
T d1ihua2          29 GGVGKTTMAAAIAV--RLADMGFDVHLTTSDPA   59 (279)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTCCEEEEESCCC
T ss_pred             CCCCHHHHHHHHHH--HHHHCCCcEEEEeCCCC
Confidence            89999999877766  44333234556765543

>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=84.89  E-value=0.16  Score=40.84  Aligned_cols=15  Identities=33%  Similarity=0.339  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         8 ~pGSGKsT~a~~La~   22 (182)
T d1zina1           8 LPGAGKGTQAEKIVA   22 (182)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=84.89  E-value=0.28  Score=42.28  Aligned_cols=29  Identities=28%  Similarity=0.227  Sum_probs=20.6

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVS   32 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~   32 (505)
                      ||+||||+|..++.  .....=..++-|++.
T Consensus        10 GGvGKTT~a~nLA~--~LA~~G~rVllID~D   38 (269)
T d1cp2a_          10 GGIGKSTTTQNLTS--GLHAMGKTIMVVGCD   38 (269)
T ss_dssp             TTSSHHHHHHHHHH--HHHTTTCCEEEEEEC
T ss_pred             CcCCHHHHHHHHHH--HHHhCCCcEEEEecC
Confidence            89999999998887  554443345556654

>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=84.76  E-value=0.16  Score=41.39  Aligned_cols=15  Identities=27%  Similarity=0.111  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        14 ~pGSGKsT~a~~La~   28 (194)
T d1qf9a_          14 GPGSGKGTQCANIVR   28 (194)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=84.75  E-value=0.17  Score=40.79  Aligned_cols=15  Identities=33%  Similarity=0.146  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         8 ~pGsGKsT~a~~La~   22 (181)
T d2cdna1           8 PPGAGKGTQAVKLAE   22 (181)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999997

>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=84.62  E-value=0.14  Score=40.57  Aligned_cols=25  Identities=28%  Similarity=0.193  Sum_probs=17.9

Q ss_pred             CCCCcHHHHHHHHhcCcccccC-CCceE
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN-FEKRT   27 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~-f~~~~   27 (505)
                      ..|+|||||+.+++.  +.+.+ +...+
T Consensus         9 ~~gSGKTTli~~l~~--~L~~~g~~v~v   34 (165)
T d1xjca_           9 YKHSGKTTLMEKWVA--AAVREGWRVGT   34 (165)
T ss_dssp             CTTSSHHHHHHHHHH--HHHHTTCCEEE
T ss_pred             CCCCCHHHHHHHHHH--HHHhCCCeEEE
Confidence            369999999999988  55444 44333

>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=84.46  E-value=0.17  Score=41.08  Aligned_cols=15  Identities=20%  Similarity=0.175  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ppGsGKsT~a~~La~   25 (189)
T d1zaka1          11 APASGKGTQCELIKT   25 (189)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=83.61  E-value=0.2  Score=40.30  Aligned_cols=15  Identities=33%  Similarity=0.191  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        10 ~pGSGKtT~a~~La~   24 (180)
T d1akya1          10 PPGAGKGTQAPNLQE   24 (180)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=83.61  E-value=0.2  Score=40.41  Aligned_cols=15  Identities=33%  Similarity=0.350  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         8 ~pGSGKsT~a~~La~   22 (182)
T d1s3ga1           8 LPGAGKGTQADRIVE   22 (182)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999998

>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=83.49  E-value=0.53  Score=39.54  Aligned_cols=38  Identities=13%  Similarity=0.065  Sum_probs=25.4

Q ss_pred             CCCCcHHHHHHHHhcCcccccC----CCceEEEEeCCCCCHH
Q 046115            1 MGGIGKTTLAQFAYNNGDVERN----FEKRTWVCVSEPFDEF   38 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~----f~~~~wv~~~~~~~~~   38 (505)
                      .+|+|||+||.+++........    -..++|++.....+..
T Consensus        42 ~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   83 (251)
T d1szpa2          42 EFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV   83 (251)
T ss_dssp             STTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGG
T ss_pred             CCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHH
Confidence            3799999999999864322222    2456788877766543

>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=83.16  E-value=1.3  Score=37.09  Aligned_cols=59  Identities=12%  Similarity=0.204  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHH
Q 046115           60 QSLMQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARI  118 (505)
Q Consensus        60 ~~~~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~  118 (505)
                      +...-.+.+.+-.++=+||||+.... +...-..+...+.....+..+|+.|-+......
T Consensus       144 q~QRvalARal~~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~~~~~  203 (241)
T d2pmka1         144 QRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKN  203 (241)
T ss_dssp             HHHHHHHHHHHTTCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSGGGGTT
T ss_pred             HHHHHhhhhhhhcccchhhhhCCccccCHHHHHHHHHHHHHHhCCCEEEEEECCHHHHHh
Confidence            33444466666677779999998552 222223334444332335566666666555443

>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=82.88  E-value=0.22  Score=40.68  Aligned_cols=15  Identities=27%  Similarity=0.173  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        16 ppGSGKsT~a~~La~   30 (196)
T d1ukza_          16 GPGAGKGTQCEKLVK   30 (196)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=82.32  E-value=0.37  Score=42.03  Aligned_cols=31  Identities=29%  Similarity=0.245  Sum_probs=21.0

Q ss_pred             CCCcHHHHHHHHhcCcccccCCCceEEEEeCCC
Q 046115            2 GGIGKTTLAQFAYNNGDVERNFEKRTWVCVSEP   34 (505)
Q Consensus         2 ~G~GKT~LA~~~~~~~~~~~~f~~~~wv~~~~~   34 (505)
                      ||+||||+|..++.  ..+..=..++-|++..+
T Consensus        11 GGVGKTT~a~NLA~--~LA~~G~rVLlID~DpQ   41 (289)
T d2afhe1          11 GGIGKSTTTQNLVA--ALAEMGKKVMIVGCDPK   41 (289)
T ss_dssp             TTSSHHHHHHHHHH--HHHHTTCCEEEEEECSS
T ss_pred             CCCCHHHHHHHHHH--HHHHCCCCEEEEecCCC
Confidence            89999999988876  44443224556776543

>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=82.16  E-value=3.1  Score=34.73  Aligned_cols=59  Identities=14%  Similarity=0.077  Sum_probs=30.8

Q ss_pred             HHHHHHHHcCCceEEEEEeCCCCC-CccChhHHHHhhcCCCCCcEEEEEeCchHHHHHhC
Q 046115           62 LMQHIEECVAGKKFLLVLDDVWNE-DYYKWEPFYKCLKNSLHESKILITTRKETVARIMG  120 (505)
Q Consensus        62 ~~~~l~~~l~~~r~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iLiTtr~~~~~~~~~  120 (505)
                      ..-.+.+.+-.++=+|+||..... +...-..+...+.....+..||++|-+......++
T Consensus       146 QRv~iARal~~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~~~~~~D  205 (242)
T d1mv5a_         146 QRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDAD  205 (242)
T ss_dssp             HHHHHHHHHHHCCSEEEEECCSCSSCSSSCCHHHHHHHHHHTTSEEEEECCSHHHHHHCS
T ss_pred             HHHHHHHHHhcCCCEEEecCCccccCHHHHHHHHHHHHHHcCCCEEEEEECCHHHHHhCC
Confidence            333455555556668999997431 11122223333332223567777777766665443

>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=82.02  E-value=0.25  Score=40.17  Aligned_cols=15  Identities=27%  Similarity=0.144  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         9 ppGSGKsT~a~~La~   23 (194)
T d1teva_           9 GPGAGKGTQCARIVE   23 (194)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=81.80  E-value=0.26  Score=39.96  Aligned_cols=15  Identities=33%  Similarity=0.173  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 ~pGSGKsT~a~~La~   25 (190)
T d1ak2a1          11 PPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=81.53  E-value=0.26  Score=39.44  Aligned_cols=15  Identities=40%  Similarity=0.339  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus         8 ~pGSGKsT~~~~La~   22 (179)
T d1e4va1           8 APVAGKGTQAQFIME   22 (179)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999987

>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=81.48  E-value=0.26  Score=41.08  Aligned_cols=15  Identities=27%  Similarity=0.335  Sum_probs=13.9

Q ss_pred             CCCCcHHHHHHHHhc
Q 046115            1 MGGIGKTTLAQFAYN   15 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~   15 (505)
                      ++|+||||+|+.++.
T Consensus        11 p~GsGKgT~ak~La~   25 (223)
T d1q3ta_          11 PASSGKSTVAKIIAK   25 (223)
T ss_dssp             SSCSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            589999999999998

>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=81.36  E-value=0.26  Score=38.50  Aligned_cols=14  Identities=43%  Similarity=0.522  Sum_probs=12.6

Q ss_pred             CCcHHHHHHHHhcC
Q 046115            3 GIGKTTLAQFAYNN   16 (505)
Q Consensus         3 G~GKT~LA~~~~~~   16 (505)
                      |+||||+++.+++.
T Consensus        43 GaGKTtfvr~~~~~   56 (158)
T d1htwa_          43 GAGKTTLTRGMLQG   56 (158)
T ss_dssp             TSSHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHhh
Confidence            89999999999864

>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=80.36  E-value=0.23  Score=40.22  Aligned_cols=22  Identities=27%  Similarity=0.460  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHhcCcccccCCC
Q 046115            1 MGGIGKTTLAQFAYNNGDVERNFE   24 (505)
Q Consensus         1 ~~G~GKT~LA~~~~~~~~~~~~f~   24 (505)
                      ++|+|||||+++++.  +....|.
T Consensus         9 psG~GK~tl~~~L~~--~~~~~~~   30 (186)
T d1gkya_           9 PSGTGKSTLLKKLFA--EYPDSFG   30 (186)
T ss_dssp             CTTSSHHHHHHHHHH--HCTTTEE
T ss_pred             CCCCCHHHHHHHHHH--hCCccee
Confidence            579999999999987  4444443