Citrus Sinensis ID: 041097

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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-
Protein Sequence
MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQLYPYGI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccEEccccccccHHHHHHHHHHccccccEEEcccccEEcEEEEcHHHHHHHHHHHHHcccEEEEcccccccccccEEEEEEEcccccccccccccccEEEEEEEcccccccccHHHHHccccccEEEEEEEcccccccccccccccccccEEcccccccccccHHHHHHHccccccccccccEEEEcccccccccccccccccEEEEccccccccccccccccccccccccEEEEEEEEcccccHHHHcccccccEEEEEEEcccccEEEccccccccccEEEccccccccHHHcccccccccEEEEEcccHHHHHHHHHcccccEEEEEEccccc
Secondary Structure Prediction (SSPRO)
cccEccccccHHHHHHHHHHHccHHEHEHHEEEEEcccccccHHHHHHHHHHHcccHccccccccHHHHHHHHHHHHHccEEEEEEEcccccEEEEEHHHHHHHHHHHHHHHcccEEEEcccccEEcccccEEEEEEccccccccHHcccccccEEEEEEcccccccHHHHHHHHHHccEEEEEEccccccccccHHHHHHHHHHHHHcccccccccccHHHHHcccccccccEcHHHEEEcccccccHHHHHHHHHcccEHHccccccccccHHHHHcccccccEEEEEEccccccccHHHHHHcHccEEEEEEccccccHHEcccccccccEEEEEccHHHHHHcHHHHHHHHHHcEEEccccHHHHHHHHHccccHHHcEEEEEcccc
Coil and Loop (DISEMBL)
mavldsigldkTAFAAEAYSSNYVKHYFDCHawvqeslpydadqILYDIIkfvmpspegfipdnneATVEKYLEQLINggfvgagkrsdigrintcsipgrcspalLTVVFegeflispimdQEVRLRENVKRFtahrklndfaflddFDSFLHSLLYltsgsqyldptyCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLnipslkslpssrkilrlsgnsqFHFSLASLLLYYQSLLSKSLCRLSCLESLKLaneskmprrsniilaeyqfppslthlsfsnielmddpipaleKLSVLQVLKLKQNLYSEERtmgirampklecliinpyAHLKRIHEQLWCLKSLnklelwwpepeLRQQLREFEDkeqygiqlypygi
Flexible Loop (DISEMBL)
MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLispimdqevRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKlaneskmprrSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLRefedkeqygiqlypygi
Low Complexity Region (SEG)
MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNdfaflddfdsflhsllYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFslaslllyyqsllskslcrlscleslklANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPAleklsvlqvlklkqnlYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQLYPYGI
Disordered region (IsUnstruct)
*****SIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLAN******RSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFE**EQYGIQLY****
Disordered Region (DISOPRED)
*AVLDS*GLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQE*R*RENVKRFTAHRKLND*A**DDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELR*****FEDKEQYGIQLYPYG*
Disordered Region (DISEMBL)
MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQLYPYGI
Disordered Region (DISPRO)
*AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQLYPYGI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQLYPYGI
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

No hits with e-value below 0.001 by BLAST

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	391
115476476	907	Os08g0424700 [Oryza sativa Japonica Grou	0.411	0.177	0.301	9e-09
222640579	854	hypothetical protein OsJ_27368 [Oryza sa	0.411	0.188	0.301	9e-09
297734140	965	unnamed protein product [Vitis vinifera]	0.831	0.336	0.257	3e-08
359474448	931	PREDICTED: disease resistance protein RP	0.404	0.169	0.297	4e-08
147766268	931	hypothetical protein VITISV_032893 [Viti	0.406	0.170	0.299	5e-08
147783531	751	hypothetical protein VITISV_034095 [Viti	0.685	0.356	0.272	4e-07
359474883	874	PREDICTED: probable disease resistance R	0.432	0.193	0.283	4e-06
297744668	1560	unnamed protein product [Vitis vinifera]	0.432	0.108	0.283	5e-06
359485772	914	PREDICTED: disease resistance protein RP	0.404	0.172	0.272	5e-06
147774669	816	hypothetical protein VITISV_022431 [Viti	0.404	0.193	0.272	5e-06

>gi|115476476|ref|NP_001061834.1| Os08g0424700 [Oryza sativa Japonica Group] gi|27817976|dbj|BAC55740.1| putative disease resistance gene homolog [Oryza sativa Japonica Group] gi|37806292|dbj|BAC99807.1| putative disease resistance gene homolog [Oryza sativa Japonica Group] gi|113623803|dbj|BAF23748.1| Os08g0424700 [Oryza sativa Japonica Group] gi|161376418|gb|ABX71479.1| putative disease resistance-like protein [Oryza sativa Japonica Group]

 Score = 67.8 bits (164), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 80/169 (47%), Gaps = 8/169 (4%)

Query: 58  EGFIPDNNEATVE----KYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEG 113
           EGFI ++ E+T+E    +YL +LI+ G V      D GR+ +CS+       ++    E 
Sbjct: 445 EGFIKNDQESTLEDTAGRYLTELIDRGMVQVADFYDYGRVKSCSVHDMLREIIILKSTED 504

Query: 114 EFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEK 173
            F I P+     ++R NV+R +     +DF   D+  + L +L     G+  +  T    
Sbjct: 505 NFGI-PVTRGVNKVRGNVRRLSIINTNDDF-LEDNSCTNLRTLFVF--GASSISTTSLHA 560

Query: 174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK 222
               F+ LR+LDL    +   P  + +LF LRYL L    +  LP S K
Sbjct: 561 FLVGFRLLRILDLEGAPVESLPDELPDLFYLRYLSLRNTRIDKLPKSLK 609

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222640579|gb|EEE68711.1| hypothetical protein OsJ_27368 [Oryza sativa Japonica Group]

 Score = 67.8 bits (164), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 80/169 (47%), Gaps = 8/169 (4%)

Query: 58  EGFIPDNNEATVE----KYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEG 113
           EGFI ++ E+T+E    +YL +LI+ G V      D GR+ +CS+       ++    E 
Sbjct: 392 EGFIKNDQESTLEDTAGRYLTELIDRGMVQVADFYDYGRVKSCSVHDMLREIIILKSTED 451

Query: 114 EFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEK 173
            F I P+     ++R NV+R +     +DF   D+  + L +L     G+  +  T    
Sbjct: 452 NFGI-PVTRGVNKVRGNVRRLSIINTNDDF-LEDNSCTNLRTLFVF--GASSISTTSLHA 507

Query: 174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK 222
               F+ LR+LDL    +   P  + +LF LRYL L    +  LP S K
Sbjct: 508 FLVGFRLLRILDLEGAPVESLPDELPDLFYLRYLSLRNTRIDKLPKSLK 556

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734140|emb|CBI15387.3| unnamed protein product [Vitis vinifera]

 Score = 65.9 bits (159), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 105/408 (25%), Positives = 154/408 (37%), Gaps = 83/408 (20%)

Query: 1   MAVLDSIGLDKTAFAAEAYSSNYVKHYFD-----CHAWVQESLPYDADQIL---YDIIKF 52
           ++++   GL KT  A + Y SN VK  FD      H W     P    +IL   Y  + +
Sbjct: 189 LSIVGMAGLGKTTLAKKLYHSNDVKKNFDFFLQSVH-WQLAQDPTQCAEILALSYSDLPY 247

Query: 53  VMPSPE---GFIPDNNEATVEKYLEQLINGGFV---GAGKRSDIGRINTCSIPGRCSPAL 106
            + S     G  P++ E +  + +   +  GFV   G     D+       + GR     
Sbjct: 248 YLKSCFLYFGLFPEDYEISARRLILLWVAEGFVQPRGQEPLEDVAEDYLEELVGRS---- 303

Query: 107 LTVVFEGEFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYL 166
                         M Q    + N +  T  R L  F                       
Sbjct: 304 --------------MIQVATRKSNGRIKTCFRSLLCF--------------------DIC 329

Query: 167 DPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRL 226
           +P++ E   + FK LR+LDL  + + R  S I NL  LRYL L    LK LP S      
Sbjct: 330 EPSFQE--LRKFKLLRILDLEGVYISRLHSSIGNLIHLRYLGLRGTWLKKLPPS------ 381

Query: 227 SGNSQFHFSLASLLLYYQSL--LSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPS 284
               QF  +L +L L    L  +   + ++  L  L      +M   +  +     FP +
Sbjct: 382 ---IQFLLNLQTLDLRSTLLNPIPIVIWKMQKLRHLYFNELEEMALHTRDLFDAEYFPQN 438

Query: 285 LTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLY-SEERTMGIRAMPKLECLIINPYAH 343
           LT LS     LM+DP+  LE L  L+VLKLK + Y  +E        P+L  L       
Sbjct: 439 LTELSLKGSFLMEDPMVKLEMLQSLRVLKLKHSAYLGKEMICSCGGFPQLHFL------- 491

Query: 344 LKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQLYPYGI 391
                     L  LN +E W  E     +LR+ E  E   +++ P G+
Sbjct: 492 ---------KLSFLNTVERWRIEDGAMGRLRQLEIIECKRLKIVPRGL 530

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359474448|ref|XP_003631469.1| PREDICTED: disease resistance protein RPM1-like [Vitis vinifera]

 Score = 65.5 bits (158), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 79/168 (47%), Gaps = 10/168 (5%)

Query: 58  EGFIPDNNEATVEK----YLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEG 113
           EGF+      T E+    YL +L+N   V    R+  GR++TC +       +++    G
Sbjct: 463 EGFVEAKGRKTQEEVGEGYLNELVNRSLVQVATRTRNGRVSTCRVHDLLREIIVSKSRGG 522

Query: 114 EFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCE 172
           + L++   ++ VR  E ++R   H+ L +     D +   L SLL  +  S    PT   
Sbjct: 523 QNLVAIANEENVRWPEKIRRLAVHKTLENVP--QDMELGQLRSLLMFSLPSGDCIPTLSS 580

Query: 173 KICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS 220
                 + L+VLDL    L   P+ + NLF LRYL L+   +K +PSS
Sbjct: 581 ---GGLRLLKVLDLQGAPLEIIPNEVWNLFNLRYLSLSRTKVKVIPSS 625

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147766268|emb|CAN74463.1| hypothetical protein VITISV_032893 [Vitis vinifera]

 Score = 65.5 bits (158), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/167 (29%), Positives = 77/167 (46%), Gaps = 8/167 (4%)

Query: 58  EGFIPDNNEATVEK----YLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEG 113
           EGF+      T E+    YL +L+N   V    R+  GR++TC +        ++    G
Sbjct: 463 EGFVEAKGRKTQEEVGEGYLNELVNRSLVQVATRTRNGRVSTCRVHDLLREIXVSXSRGG 522

Query: 114 EFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEK 173
           + L++   ++ VR  E ++R   H+ L +    D     L SLL  +  S    PT    
Sbjct: 523 QNLVAIANEENVRWPEKIRRLAVHKTLENVP-QDMVLGQLRSLLMFSLPSGDCIPTLSSG 581

Query: 174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS 220
                + L+VLDL    L   P+ + NLF LRYL L+   +K +PSS
Sbjct: 582 ---GLRLLKVLDLQGAPLEIIPNEVWNLFNLRYLSLSRTKVKVIPSS 625

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783531|emb|CAN68449.1| hypothetical protein VITISV_034095 [Vitis vinifera]

 Score = 62.4 bits (150), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 89/327 (27%), Positives = 132/327 (40%), Gaps = 59/327 (18%)

Query: 56  SPEGFIPDNNEA----TVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVF 111
           + EGF+P+ ++       E YL +LIN   +   + S   R+  C +        +    
Sbjct: 416 TAEGFVPEQDDRRMKDVAEVYLNELINRNLILVVRMSVNARVTKCRVHDLVRELAIEKAK 475

Query: 112 EGEFLISPIMDQEVRLRENVKRFTAHRKL---NDF---AFLDDFDSFLHSLLYLTSGSQY 165
           E  F+ + I D       +    +  R+    +DF   A ++    +L SLL+   G   
Sbjct: 476 EQNFIGTNIADPPPSSTSSSLFSSKSRRRXIYSDFERCASIEHLTPYLRSLLFFNLGKN- 534

Query: 166 LDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLR---------YLKLNIPSLKS 216
              +  + I K FK LRVLDL  L +   PS I  L  LR              +PSLKS
Sbjct: 535 CRASQLDFIXKCFKVLRVLDLEGLXIECJPSMIGELIHLRCEVEGAXFSNSIXKLPSLKS 594

Query: 217 LPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL 276
           L      L+ S +S    S+    + Y            CL   KL  +  M +   II 
Sbjct: 595 L-----YLKASDDS----SIPPFAINY------------CLHLSKLDIKGHMQKLPEII- 632

Query: 277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSE-ERTMGIRAMPKLEC 335
              +F P+LT L+     L  DP+  LEKL  L  L+L+   Y E E  +     P+L+ 
Sbjct: 633 ---EFSPNLTQLTLEASRLNHDPMVVLEKLPKLLTLRLRAKSYLEKEMHVSANGFPQLKV 689

Query: 336 LIINPYAHLKRIHEQLWCLKSLNKLEL 362
           L             QL+ L+ LNKL +
Sbjct: 690 L-------------QLFGLRELNKLNI 703

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359474883|ref|XP_003631548.1| PREDICTED: probable disease resistance RPP8-like protein 2-like [Vitis vinifera]

 Score = 58.9 bits (141), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 76/180 (42%), Gaps = 11/180 (6%)

Query: 56  SPEGFIPDNNEATV----EKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVF 111
           + EGF+P+ ++  +    E YL +L N   +   +RS   R+  C +        +    
Sbjct: 436 TAEGFVPEQDDGRMKDMAEVYLNELSNRNLIQVVRRSVNARVTKCQVHDLVRELAIEKAK 495

Query: 112 EGEFLISPIMD------QEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQY 165
           E  F+ + I D               +R + +     +A ++    +L SLL+   G   
Sbjct: 496 EQNFIGTNIADPLSPSTSLSLFSPKSRRRSIYSDFESYASIEHLTPYLRSLLFFNLGKN- 554

Query: 166 LDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILR 225
              +  + I K FK LRVLDL  L +   PS I  L  LRYL L    LK LP S   LR
Sbjct: 555 CRASQLDFIAKCFKVLRVLDLEGLEIECLPSIIGELIHLRYLGLRHTGLKMLPPSIGNLR 614

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744668|emb|CBI37930.3| unnamed protein product [Vitis vinifera]

 Score = 58.5 bits (140), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 76/180 (42%), Gaps = 11/180 (6%)

Query: 56  SPEGFIPDNNEATV----EKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVF 111
           + EGF+P+ ++  +    E YL +L N   +   +RS   R+  C +        +    
Sbjct: 392 TAEGFVPEQDDGRMKDMAEVYLNELSNRNLIQVVRRSVNARVTKCQVHDLVRELAIEKAK 451

Query: 112 EGEFLISPIMD------QEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQY 165
           E  F+ + I D               +R + +     +A ++    +L SLL+   G   
Sbjct: 452 EQNFIGTNIADPLSPSTSLSLFSPKSRRRSIYSDFESYASIEHLTPYLRSLLFFNLGKN- 510

Query: 166 LDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILR 225
              +  + I K FK LRVLDL  L +   PS I  L  LRYL L    LK LP S   LR
Sbjct: 511 CRASQLDFIAKCFKVLRVLDLEGLEIECLPSIIGELIHLRYLGLRHTGLKMLPPSIGNLR 570

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485772|ref|XP_003633333.1| PREDICTED: disease resistance protein RPM1-like [Vitis vinifera]

 Score = 58.5 bits (140), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 68/165 (41%), Gaps = 7/165 (4%)

Query: 58  EGFIPDNN----EATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEG 113
           EGFI +      E   E+YL +LI    V   + +D GR+ TC +        +T   E 
Sbjct: 448 EGFITERKGMTMEEIAEEYLTELIFRSMVQVTETNDEGRVKTCRVHDLMRELAMTTS-EK 506

Query: 114 EFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEK 173
           E   +    +E RL   + R + + +  +          L S     +      P    +
Sbjct: 507 EDFCTASDGRETRLERKIHRLSVYNRGENIRLSGRMSRGLRSFFVFETDVS--SPFSLNE 564

Query: 174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLP 218
           +   FK LRVLDL  + +   PS +  LF LRYL L    ++ LP
Sbjct: 565 VLAKFKLLRVLDLQGVSIETVPSSLLGLFNLRYLNLRETKVRELP 609

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147774669|emb|CAN67705.1| hypothetical protein VITISV_022431 [Vitis vinifera]

 Score = 58.5 bits (140), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 68/165 (41%), Gaps = 7/165 (4%)

Query: 58  EGFIPDNN----EATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEG 113
           EGFI +      E   E+YL +LI    V   + +D GR+ TC +        +T   E 
Sbjct: 395 EGFITERKGMTMEEIAEEYLTELIFRSMVQVTETNDEGRVKTCRVHDLMRELAMTTS-EK 453

Query: 114 EFLISPIMDQEVRLRENVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEK 173
           E   +    +E RL   + R + + +  +          L S     +      P    +
Sbjct: 454 EDFCTASDGRETRLERKIHRLSVYNRGENIRLSGRMSRGLRSFFVFETDVS--SPFSLNE 511

Query: 174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLP 218
           +   FK LRVLDL  + +   PS +  LF LRYL L    ++ LP
Sbjct: 512 VLAKFKLLRVLDLQGVSIETVPSSLLGLFNLRYLNLRETKVRELP 556

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	391
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.112	0.051	0.477	0.00027
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.184	0.079	0.273	0.00032

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

 Score = 95 (38.5 bits), Expect = 0.00027, Sum P(2) = 0.00027
 Identities = 21/44 (47%), Positives = 24/44 (54%)

Query:     8 GLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIK 51
             GL KTA A + Y+S  VK  FDC AW   S  Y    IL  II+
Sbjct:   195 GLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTRDILIRIIR 238

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 81 (33.6 bits), Expect = 0.00032, Sum P(3) = 0.00032
 Identities = 20/73 (27%), Positives = 37/73 (50%)

Query:     8 GLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEA 67
             G+ KT  A + +  + V+ +FD  AWV  S  +    +   I++ + P  +G I   +E+
Sbjct:   195 GIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTLKHVWQRILQELQPH-DGNILQMDES 253

Query:    68 TVEKYLEQLINGG 80
              ++  L QL+  G
Sbjct:   254 ALQPKLFQLLETG 266

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

---

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	391
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	0.001

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

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 20/75 (26%), Positives = 34/75 (45%)

Query: 8   GLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEA 67
           G+ KT  A + Y+ + V  +FD  AWV  S  Y   ++  DI++ +      ++  N   
Sbjct: 29  GVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLDDSDWVEKNESE 88

Query: 68  TVEKYLEQLINGGFV 82
              K  E L+   F+
Sbjct: 89  LAVKIKEALLRKRFL 103

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	391
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.9
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.62
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.6
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.57
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.44
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.44
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.38
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.31
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.28
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.22
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.22
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.18
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.15
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.14
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.09
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.07
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.03
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.99
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.86
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.77
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.74
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.73
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.59
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.56
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.47
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.47
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.46
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.37
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.27
cd01128	249	rho_factor Transcription termination factor rho is	98.23
PRK09376	416	rho transcription termination factor Rho; Provisio	98.23
PRK08118	167	topology modulation protein; Reviewed	98.21
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.07
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.02
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	97.99
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	97.98
PLN03150	623	hypothetical protein; Provisional	97.93
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	97.91
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.85
PRK15386	426	type III secretion protein GogB; Provisional	97.83
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	97.82
PRK15386	426	type III secretion protein GogB; Provisional	97.76
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	97.67
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.62
PLN03150	623	hypothetical protein; Provisional	97.58
TIGR00767	415	rho transcription termination factor Rho. Members	97.56
PRK07261	171	topology modulation protein; Provisional	97.52
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	97.31
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.27
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.23
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.23
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.14
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.13
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.08
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.99
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	96.98
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.97
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.84
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.83
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.72
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	96.63
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.56
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	96.54
PTZ00301	210	uridine kinase; Provisional	96.48
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.44
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	96.37
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.36
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.36
PRK08233	182	hypothetical protein; Provisional	96.36
PRK05480	209	uridine/cytidine kinase; Provisional	96.34
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.34
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	96.27
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.26
KOG2028	554	consensus ATPase related to the helicase subunit o	96.24
PRK06762	166	hypothetical protein; Provisional	96.24
PRK03839	180	putative kinase; Provisional	96.23
PRK05541	176	adenylylsulfate kinase; Provisional	96.16
PRK00411	394	cdc6 cell division control protein 6; Reviewed	96.14
KOG2982	418	consensus Uncharacterized conserved protein [Funct	96.13
PRK06696	223	uridine kinase; Validated	96.1
PRK04040	188	adenylate kinase; Provisional	96.1
smart00382	148	AAA ATPases associated with a variety of cellular	96.1
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.03
PRK00625	173	shikimate kinase; Provisional	96.01
PRK06217	183	hypothetical protein; Validated	95.97
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.97
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.96
PRK06547	172	hypothetical protein; Provisional	95.96
KOG2982	418	consensus Uncharacterized conserved protein [Funct	95.95
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.95
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.94
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	95.94
PF05729	166	NACHT: NACHT domain	95.94
PRK07667	193	uridine kinase; Provisional	95.9
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.89
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.87
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	95.86
COG1100	219	GTPase SAR1 and related small G proteins [General	95.83
PF00004	132	AAA: ATPase family associated with various cellula	95.82
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.81
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	95.81
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	95.79
PRK13949	169	shikimate kinase; Provisional	95.76
PRK13947	171	shikimate kinase; Provisional	95.75
PHA00729	226	NTP-binding motif containing protein	95.7
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.69
KOG3864	221	consensus Uncharacterized conserved protein [Funct	95.69
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	95.68
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.68
PRK00131	175	aroK shikimate kinase; Reviewed	95.66
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.65
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.65
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.64
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.62
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.61
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.52
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.49
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	95.46
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	95.43
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	95.42
PRK13946	184	shikimate kinase; Provisional	95.4
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.4
PRK00889	175	adenylylsulfate kinase; Provisional	95.39
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.37
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	95.36
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.35
PRK06893	229	DNA replication initiation factor; Validated	95.33
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.32
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.31
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	95.3
PF07726	131	AAA_3: ATPase family associated with various cellu	95.3
PRK03846	198	adenylylsulfate kinase; Provisional	95.29
PRK13695	174	putative NTPase; Provisional	95.27
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	95.26
PF13173	128	AAA_14: AAA domain	95.22
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.22
PRK05057	172	aroK shikimate kinase I; Reviewed	95.22
PRK14530	215	adenylate kinase; Provisional	95.21
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.21
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.18
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.16
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.15
PRK00300	205	gmk guanylate kinase; Provisional	95.14
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	95.14
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.13
PRK13975	196	thymidylate kinase; Provisional	95.12
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.12
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.09
PRK06620	214	hypothetical protein; Validated	95.08
cd01876	170	YihA_EngB The YihA (EngB) subfamily. This subfamil	95.07
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	95.05
PRK13948	182	shikimate kinase; Provisional	95.03
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	95.03
PRK06761	282	hypothetical protein; Provisional	95.02
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.0
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	94.99
PRK12377	248	putative replication protein; Provisional	94.97
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	94.96
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	94.95
KOG2123	388	consensus Uncharacterized conserved protein [Funct	94.94
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	94.93
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	94.92
PRK05439	311	pantothenate kinase; Provisional	94.91
PRK08084	235	DNA replication initiation factor; Provisional	94.9
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	94.9
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	94.89
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	94.88
cd03114	148	ArgK-like The function of this protein family is u	94.86
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	94.85
KOG3308	225	consensus Uncharacterized protein of the uridine k	94.85
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	94.82
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	94.81
PRK03731	171	aroL shikimate kinase II; Reviewed	94.81
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	94.8
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	94.78
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	94.76
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	94.76
PRK13768	253	GTPase; Provisional	94.75
PLN02796	347	D-glycerate 3-kinase	94.73
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	94.73
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	94.73
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	94.71
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.71
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	94.7
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	94.68
PRK09087	226	hypothetical protein; Validated	94.67
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	94.67
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	94.67
cd02034	116	CooC The accessory protein CooC, which contains a	94.66
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.66
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	94.64
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	94.63
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	94.62
TIGR00101	199	ureG urease accessory protein UreG. This model rep	94.62
PRK08356	195	hypothetical protein; Provisional	94.62
PRK04182	180	cytidylate kinase; Provisional	94.59
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.57
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	94.57
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	94.53
PRK01184	184	hypothetical protein; Provisional	94.53
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	94.53
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	94.53
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	94.51
PRK08727	233	hypothetical protein; Validated	94.51
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	94.49
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	94.47
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	94.44
PRK13230	279	nitrogenase reductase-like protein; Reviewed	94.43
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	94.41
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	94.41
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	94.38
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	94.37
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	94.37
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	94.37
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	94.36
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	94.35
cd04162	164	Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily. Arl9	94.33
PTZ00088	229	adenylate kinase 1; Provisional	94.31
PRK12339	197	2-phosphoglycerate kinase; Provisional	94.3
PRK13342	413	recombination factor protein RarA; Reviewed	94.28
PRK09825	176	idnK D-gluconate kinase; Provisional	94.27
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	94.27
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	94.25
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	94.24
PRK08903	227	DnaA regulatory inactivator Hda; Validated	94.24
PRK07952	244	DNA replication protein DnaC; Validated	94.24
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	94.21
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	94.17
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	94.17
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	94.16
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	94.14
PHA02575	227	1 deoxynucleoside monophosphate kinase; Provisiona	94.14
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	94.13
cd04123	162	Rab21 Rab21 subfamily. The localization and functi	94.12
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	94.12
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	94.11
PRK13232	273	nifH nitrogenase reductase; Reviewed	94.11
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.1
cd02117	212	NifH_like This family contains the NifH (iron prot	94.08
PRK08099	399	bifunctional DNA-binding transcriptional repressor	94.08
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	94.08
TIGR01281	268	DPOR_bchL light-independent protochlorophyllide re	94.06
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	94.05
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	94.05
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	94.05
PLN02348	395	phosphoribulokinase	94.05
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	94.04
cd04140	165	ARHI_like ARHI subfamily. ARHI (A Ras homolog memb	94.04
cd04150	159	Arf1_5_like Arf1-Arf5-like subfamily. This subfami	94.03
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	94.02
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	94.0
PRK10536	262	hypothetical protein; Provisional	93.98
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	93.98
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	93.98
PRK14730	195	coaE dephospho-CoA kinase; Provisional	93.97
cd04161	167	Arl2l1_Arl13_like Arl2l1/Arl13 subfamily. Arl2l1 (	93.97
PRK14527	191	adenylate kinase; Provisional	93.96
PRK02496	184	adk adenylate kinase; Provisional	93.96
cd03115	173	SRP The signal recognition particle (SRP) mediates	93.95
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	93.95
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	93.95
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	93.94
PRK14490	369	putative bifunctional molybdopterin-guanine dinucl	93.93
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	93.93
cd04146	165	RERG_RasL11_like RERG/RasL11-like subfamily. RERG	93.92
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	93.92
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	93.92
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	93.92
cd04103	158	Centaurin_gamma Centaurin gamma. The centaurins (a	93.91
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	93.9
cd01673	193	dNK Deoxyribonucleoside kinase (dNK) catalyzes the	93.9
cd04175	164	Rap1 Rap1 subgroup. The Rap1 subgroup is part of t	93.88
PRK14738	206	gmk guanylate kinase; Provisional	93.88
PRK15453	290	phosphoribulokinase; Provisional	93.88
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	93.87
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	93.86
PLN02200	234	adenylate kinase family protein	93.84
PRK00454	196	engB GTP-binding protein YsxC; Reviewed	93.84
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.84
PRK14532	188	adenylate kinase; Provisional	93.84
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	93.84
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	93.84
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	93.83
cd03269	210	ABC_putative_ATPase This subfamily is involved in	93.82
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	93.82
PRK13341	725	recombination factor protein RarA/unknown domain f	93.82
CHL00072	290	chlL photochlorophyllide reductase subunit L	93.82
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	93.81
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	93.79
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	93.79
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	93.79
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	93.78
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	93.78
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	93.77
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	93.76
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	93.76
PRK05416	288	glmZ(sRNA)-inactivating NTPase; Provisional	93.76
PTZ00202	550	tuzin; Provisional	93.75
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	93.75
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	93.74
cd04120	202	Rab12 Rab12 subfamily. Rab12 was first identified	93.74
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	93.73
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	93.73
PRK08181	269	transposase; Validated	93.73
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	93.72
PRK03992	389	proteasome-activating nucleotidase; Provisional	93.71
cd02040	270	NifH NifH gene encodes component II (iron protein)	93.7
cd00877	166	Ran Ran (Ras-related nuclear proteins) /TC4 subfam	93.7
PLN03046	460	D-glycerate 3-kinase; Provisional	93.69
cd01888	203	eIF2_gamma eIF2-gamma (gamma subunit of initiation	93.69
cd04107	201	Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38	93.68
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	93.68
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	93.67
PRK09183	259	transposase/IS protein; Provisional	93.67
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	93.66
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	93.64
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	93.63
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	93.63
PRK04301	317	radA DNA repair and recombination protein RadA; Va	93.61
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	93.61
PRK14531	183	adenylate kinase; Provisional	93.6
cd04122	166	Rab14 Rab14 subfamily. Rab14 GTPases are localized	93.6
PRK00279	215	adk adenylate kinase; Reviewed	93.58
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	93.57
cd01394	218	radB RadB. The archaeal protein radB shares simila	93.57
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	93.57
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	93.56
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	93.56
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	93.56
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	93.55
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	93.55
cd03116	159	MobB Molybdenum is an essential trace element in t	93.54
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	93.54
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	93.54
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	93.54
cd04135	174	Tc10 TC10 subfamily. TC10 is a Rho family protein	93.53
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	93.52
TIGR02770	230	nickel_nikD nickel import ATP-binding protein NikD	93.52
cd04117	161	Rab15 Rab15 subfamily. Rab15 colocalizes with the	93.51
PF00142	273	Fer4_NifH: 4Fe-4S iron sulfur cluster binding prot	93.51
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	93.51
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	93.51
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	93.5
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	93.5
PRK14732	196	coaE dephospho-CoA kinase; Provisional	93.5
PTZ00369	189	Ras-like protein; Provisional	93.48
PRK14733	204	coaE dephospho-CoA kinase; Provisional	93.47
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	93.46
TIGR03598	179	GTPase_YsxC ribosome biogenesis GTP-binding protei	93.45
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	93.44
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	93.43
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	93.42
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	93.4
PRK14737	186	gmk guanylate kinase; Provisional	93.4
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.39
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	93.39
cd03246	173	ABCC_Protease_Secretion This family represents the	93.38
cd04108	170	Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found pr	93.35
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	93.35
smart00174	174	RHO Rho (Ras homology) subfamily of Ras-like small	93.34
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	93.34
cd04144	190	Ras2 Ras2 subfamily. The Ras2 subfamily, found exc	93.33
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	93.33
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	93.33
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	93.32
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	93.32
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	93.32
PRK08116	268	hypothetical protein; Validated	93.32
PRK05642	234	DNA replication initiation factor; Validated	93.32
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	93.32
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	93.31
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	93.31
cd02032	267	Bchl_like This family of proteins contains bchL an	93.31
cd04118	193	Rab24 Rab24 subfamily. Rab24 is distinct from othe	93.3
cd04141	172	Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like p	93.3
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	93.28
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	93.28
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	93.27
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	93.26
PRK00698	205	tmk thymidylate kinase; Validated	93.26
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	93.26
cd01865	165	Rab3 Rab3 subfamily. The Rab3 subfamily contains R	93.25
TIGR01978	243	sufC FeS assembly ATPase SufC. SufC is part of the	93.25
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	93.24
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	93.24
cd04125	188	RabA_like RabA-like subfamily. RabA was first iden	93.23
PRK14526	211	adenylate kinase; Provisional	93.22
PRK13235	274	nifH nitrogenase reductase; Reviewed	93.22
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	93.21
PLN02318	656	phosphoribulokinase/uridine kinase	93.2
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	93.19
PTZ00133	182	ADP-ribosylation factor; Provisional	93.19
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	93.19
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	93.19
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	93.19
cd04129	187	Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that	93.18
PRK10416	318	signal recognition particle-docking protein FtsY;	93.17
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	93.17
PRK06526	254	transposase; Provisional	93.17
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	93.16
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	93.16
PRK04213	201	GTP-binding protein; Provisional	93.16
PRK13233	275	nifH nitrogenase reductase; Reviewed	93.15
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	93.13
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	93.13
smart00178	184	SAR Sar1p-like members of the Ras-family of small	93.12
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	93.12
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	93.11
PF13479	213	AAA_24: AAA domain	93.11
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	93.11
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	93.1
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	93.1
TIGR02324	224	CP_lyasePhnL phosphonate C-P lyase system protein	93.1
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	93.09
PRK07429	327	phosphoribulokinase; Provisional	93.09
cd03216	163	ABC_Carb_Monos_I This family represents the domain	93.09
PRK14245	250	phosphate ABC transporter ATP-binding protein; Pro	93.08
CHL00181	287	cbbX CbbX; Provisional	93.08
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	93.07
cd04132	187	Rho4_like Rho4-like subfamily. Rho4 is a GTPase th	93.07
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	93.07
cd03215	182	ABC_Carb_Monos_II This family represents domain II	93.06
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	93.06
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	93.06
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	93.06
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	93.06
PRK09435	332	membrane ATPase/protein kinase; Provisional	93.04
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	93.04
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	93.03
PRK14247	250	phosphate ABC transporter ATP-binding protein; Pro	93.03
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	93.02
PRK10908	222	cell division protein FtsE; Provisional	93.01
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	93.01
cd02042	104	ParA ParA and ParB of Caulobacter crescentus belon	93.01
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.01
TIGR00064	272	ftsY signal recognition particle-docking protein F	92.99
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	92.99
cd01874	175	Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPas	92.99
PRK14528	186	adenylate kinase; Provisional	92.99
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	92.98
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	92.96
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	92.96
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	92.94
PTZ00132	215	GTP-binding nuclear protein Ran; Provisional	92.94
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	92.94
cd01870	175	RhoA_like RhoA-like subfamily. The RhoA subfamily	92.92
PRK11264	250	putative amino-acid ABC transporter ATP-binding pr	92.92
TIGR00972	247	3a0107s01c2 phosphate ABC transporter, ATP-binding	92.91
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	92.91
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	92.9
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	92.9
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	92.89
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	92.89
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	92.86
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	92.85
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	92.85
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	92.85
COG3638	258	ABC-type phosphate/phosphonate transport system, A	92.83
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	92.83
cd04149	168	Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor	92.83
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	92.83
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	92.81
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	92.79
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	92.79
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	92.78
PRK14256	252	phosphate ABC transporter ATP-binding protein; Pro	92.78
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	92.78
cd04171	164	SelB SelB subfamily. SelB is an elongation factor	92.78
PRK13231	264	nitrogenase reductase-like protein; Reviewed	92.77
PLN02165	334	adenylate isopentenyltransferase	92.75
TIGR03873	256	F420-0_ABC_ATP proposed F420-0 ABC transporter, AT	92.75
cd04121	189	Rab40 Rab40 subfamily. This subfamily contains Rab	92.75
PRK14239	252	phosphate transporter ATP-binding protein; Provisi	92.75
PRK14241	258	phosphate transporter ATP-binding protein; Provisi	92.74
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	92.73
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	92.71
PRK06921	266	hypothetical protein; Provisional	92.7
PRK11831	269	putative ABC transporter ATP-binding protein YrbF;	92.7
cd04148	221	RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Ki	92.7
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	92.7
PRK13638	271	cbiO cobalt transporter ATP-binding subunit; Provi	92.69
cd01873	195	RhoBTB RhoBTB subfamily. Members of the RhoBTB sub	92.69
cd04104	197	p47_IIGP_like p47 (47-kDa) family. The p47 GTPase	92.66
PRK14274	259	phosphate ABC transporter ATP-binding protein; Pro	92.65
COG4240	300	Predicted kinase [General function prediction only	92.63
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	92.63
cd04134	189	Rho3 Rho3 subfamily. Rho3 is a member of the Rho f	92.62
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	92.61
PRK14731	208	coaE dephospho-CoA kinase; Provisional	92.6
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	92.59
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	92.59
PRK14238	271	phosphate transporter ATP-binding protein; Provisi	92.59
COG4619	223	ABC-type uncharacterized transport system, ATPase	92.59
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	92.59
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	92.58
cd04116	170	Rab9 Rab9 subfamily. Rab9 is found in late endosom	92.57
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	92.57
PRK11701	258	phnK phosphonate C-P lyase system protein PhnK; Pr	92.57
TIGR03005	252	ectoine_ehuA ectoine/hydroxyectoine ABC transporte	92.57

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.7e-35  Score=300.27  Aligned_cols=279  Identities=27%  Similarity=0.323  Sum_probs=189.7

Q ss_pred             cCCCCCCCCCC-----hHHHHHHHHHHHHcCccEEeeeccCCCceeeEEcCcchHHHHHhhcc-----ccCceeeccc--
Q 041097           54 MPSPEGFIPDN-----NEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVF-----EGEFLISPIM--  121 (391)
Q Consensus        54 ~~~~eg~~~~~-----~~~~~~~~~~~L~~k~~l~~~~~~~~~~~~~~~~hdl~~~~~~~~~~-----~~~~~~~~~~--  121 (391)
                      .|+||||+...     +++.|..|+.+|+.++++...+..  ++..+|+|||++|++|+++++     ++++.. ..+  
T Consensus       436 yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~--~~~~~~kmHDvvRe~al~ias~~~~~~e~~iv-~~~~~  512 (889)
T KOG4658|consen  436 YWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDE--GRKETVKMHDVVREMALWIASDFGKQEENQIV-SDGVG  512 (889)
T ss_pred             HHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcccc--cceeEEEeeHHHHHHHHHHhccccccccceEE-ECCcC
Confidence            49999988652     789999999999999999876654  677899999999999999998     555332 111  


Q ss_pred             ---CCcccccCceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCc-cccCCc
Q 041097          122 ---DQEVRLRENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLV-LIRYPS  196 (391)
Q Consensus       122 ---~~~~~~~~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-l~~~p~  196 (391)
                         ..+......+|++++.++.... ...... +++++|.+..+...  .......+|..++.|+|||+++|. +.++|+
T Consensus       513 ~~~~~~~~~~~~~rr~s~~~~~~~~-~~~~~~~~~L~tLll~~n~~~--l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~  589 (889)
T KOG4658|consen  513 LSEIPQVKSWNSVRRMSLMNNKIEH-IAGSSENPKLRTLLLQRNSDW--LLEISGEFFRSLPLLRVLDLSGNSSLSKLPS  589 (889)
T ss_pred             ccccccccchhheeEEEEeccchhh-ccCCCCCCccceEEEeecchh--hhhcCHHHHhhCcceEEEECCCCCccCcCCh
Confidence               1122245678999998443333 556666 88999999887531  112344668999999999999876 779999


Q ss_pred             ccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCcc-Cc-------c-eeeEEecc-------------------
Q 041097          197 GIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQ-FH-------F-SLASLLLY-------------------  242 (391)
Q Consensus       197 ~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l-~~-------L-~L~~L~l~-------------------  242 (391)
                      .|++|.+||||+++++.+++||.+++      +||+..+.- ..       + +||.|.+.                   
T Consensus       590 ~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~~~~~~~~l~el~~Le~  669 (889)
T KOG4658|consen  590 SIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLPRSALSNDKLLLKELENLEH  669 (889)
T ss_pred             HHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccccchhhhcccccEEEeeccccccchhhHHhhhcccc
Confidence            99999999999999999999999998      888886531 10       1 33333332                   


Q ss_pred             -----------------------------------cccchhHHhcCCCCCCEEEecCCC-----C-----------CCch
Q 041097          243 -----------------------------------YQSLLSKSLCRLSCLESLKLANES-----K-----------MPRR  271 (391)
Q Consensus       243 -----------------------------------~~~~lp~~i~~l~~L~~L~l~~~~-----~-----------lp~L  271 (391)
                                                         .....+++++.|.+|+.|.+....     .           +|++
T Consensus       670 L~~ls~~~~s~~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~~~~~~l~~L~~L~i~~~~~~e~~~~~~~~~~~~~~f~~l  749 (889)
T KOG4658|consen  670 LENLSITISSVLLLEDLLGMTRLRSLLQSLSIEGCSKRTLISSLGSLGNLEELSILDCGISEIVIEWEESLIVLLCFPNL  749 (889)
T ss_pred             hhhheeecchhHhHhhhhhhHHHHHHhHhhhhcccccceeecccccccCcceEEEEcCCCchhhcccccccchhhhHHHH
Confidence                                               112234456667777777776610     0           2222


Q ss_pred             hhh------cc---ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc-ccCCCcccccceeee
Q 041097          272 SNI------IL---AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER-TMGIRAMPKLECLII  338 (391)
Q Consensus       272 ~~L------lp---~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~-~~~~~~~~~L~~L~l  338 (391)
                      .++      .|   ....+|++|+.|.+..|...+++++...++..+..+-+.++.+.+.. ..+.+.|+++..+.+
T Consensus       750 ~~~~~~~~~~~r~l~~~~f~~~L~~l~l~~~~~~e~~i~~~k~~~~l~~~i~~f~~~~~l~~~~~l~~l~~i~~~~l  826 (889)
T KOG4658|consen  750 SKVSILNCHMLRDLTWLLFAPHLTSLSLVSCRLLEDIIPKLKALLELKELILPFNKLEGLRMLCSLGGLPQLYWLPL  826 (889)
T ss_pred             HHHHhhccccccccchhhccCcccEEEEecccccccCCCHHHHhhhcccEEecccccccceeeecCCCCceeEeccc
Confidence            222      22   22234588888888888877777777777777776666655665552 333344444333333

>PLN03210 Resistant to P

Probab=99.90  E-value=8.3e-23  Score=219.87  Aligned_cols=268  Identities=19%  Similarity=0.108  Sum_probs=152.9

Q ss_pred             eEEcCcchHHHHHhhccccCcee----ecccCCc-------ccccCceEEEEEeccCCCcc-cc-cCC-C-CCccEEEEE
Q 041097           95 TCSIPGRCSPALLTVVFEGEFLI----SPIMDQE-------VRLRENVKRFTAHRKLNDFA-FL-DDF-D-SFLHSLLYL  159 (391)
Q Consensus        95 ~~~~hdl~~~~~~~~~~~~~~~~----~~~~~~~-------~~~~~~~r~l~~~~~~~~~~-~~-~~~-~-~~lrsl~~~  159 (391)
                      .++|||++++||..+++++.-..    ..+...+       .....+++.+++........ +. ... + ..++.|.+.
T Consensus       487 ~~~MHdLl~~~~r~i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~m~~L~~L~~~  566 (1153)
T PLN03210        487 IVEMHSLLQEMGKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMRNLLFLKFY  566 (1153)
T ss_pred             eEEhhhHHHHHHHHHHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhcCccccEEEEe
Confidence            57899999999999987653100    0111100       01234566666652222211 11 112 2 677777665


Q ss_pred             ecCCcC--CCchhhHHhhccC-CcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCc
Q 041097          160 TSGSQY--LDPTYCEKICKMF-KFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNS  230 (391)
Q Consensus       160 ~~~~~~--~~~~~~~~~~~~~-~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~  230 (391)
                      ......  .....++..+..+ ..||.|++.++.+..+|..+ ...+|+.|++.++.+..+|.++.      .|+++++.
T Consensus       567 ~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f-~~~~L~~L~L~~s~l~~L~~~~~~l~~Lk~L~Ls~~~  645 (1153)
T PLN03210        567 TKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKYPLRCMPSNF-RPENLVKLQMQGSKLEKLWDGVHSLTGLRNIDLRGSK  645 (1153)
T ss_pred             cccccccccceeecCcchhhcCcccEEEEecCCCCCCCCCcC-CccCCcEEECcCccccccccccccCCCCCEEECCCCC
Confidence            432110  0111233344443 46999999999988899887 46789999999998888887765      88888752


Q ss_pred             -cCcc-------eeeEEecc---cccchhHHhcCCCCCCEEEecC-CC--CCC------chhhh-------ccccccCCC
Q 041097          231 -QFHF-------SLASLLLY---YQSLLSKSLCRLSCLESLKLAN-ES--KMP------RRSNI-------ILAEYQFPP  283 (391)
Q Consensus       231 -l~~L-------~L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~-~~--~lp------~L~~L-------lp~~~~l~~  283 (391)
                       +..+       +|+.|++.   ....+|.+++++++|+.|++.+ ..  .+|      +|+.|       ++.+...++
T Consensus       646 ~l~~ip~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i~l~sL~~L~Lsgc~~L~~~p~~~~  725 (1153)
T PLN03210        646 NLKEIPDLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGINLKSLYRLNLSGCSRLKSFPDIST  725 (1153)
T ss_pred             CcCcCCccccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcCCCCCCCEEeCCCCCCccccccccC
Confidence             3332       78899888   4667889999999999999987 22  222      11111       000111114


Q ss_pred             CccEEEeecccCCCCChhhhcCCC-------------------------------CCCEEEcCCCCCcCccccCCCcccc
Q 041097          284 SLTHLSFSNIELMDDPIPALEKLS-------------------------------VLQVLKLKQNLYSEERTMGIRAMPK  332 (391)
Q Consensus       284 ~L~~L~l~~~~~~~~~~~~l~~l~-------------------------------~L~~L~l~~~~~~~~~~~~~~~~~~  332 (391)
                      +|+.|++.++.+...|. . ..++                               +|+.|+++.|......+...+.+++
T Consensus       726 nL~~L~L~~n~i~~lP~-~-~~l~~L~~L~l~~~~~~~l~~~~~~l~~~~~~~~~sL~~L~Ls~n~~l~~lP~si~~L~~  803 (1153)
T PLN03210        726 NISWLDLDETAIEEFPS-N-LRLENLDELILCEMKSEKLWERVQPLTPLMTMLSPSLTRLFLSDIPSLVELPSSIQNLHK  803 (1153)
T ss_pred             CcCeeecCCCccccccc-c-ccccccccccccccchhhccccccccchhhhhccccchheeCCCCCCccccChhhhCCCC
Confidence            55555555554433221 1 1223                               3444444422222222222356667


Q ss_pred             cceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          333 LECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       333 L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      |+.|+|++|..++.+|..+ .+++|++|++++|.
T Consensus       804 L~~L~Ls~C~~L~~LP~~~-~L~sL~~L~Ls~c~  836 (1153)
T PLN03210        804 LEHLEIENCINLETLPTGI-NLESLESLDLSGCS  836 (1153)
T ss_pred             CCEEECCCCCCcCeeCCCC-CccccCEEECCCCC
Confidence            7777777777677777655 56777777777665

syringae 6; Provisional

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

Probab=99.62  E-value=3.6e-15  Score=159.95  Aligned_cols=204  Identities=25%  Similarity=0.261  Sum_probs=101.6

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccCCCCC-ccCCCCc------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNIPSLK-SLPSSRK------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~~~i~-~lp~~~~------  222 (391)
                      +.+++|.+.++...    ...+..+..+++|++|++++|.+. .+|..++++.+|++|++++|.+. .+|..++      
T Consensus       140 ~~L~~L~Ls~n~~~----~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~  215 (968)
T PLN00113        140 PNLETLDLSNNMLS----GEIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLK  215 (968)
T ss_pred             CCCCEEECcCCccc----ccCChHHhcCCCCCEEECccCcccccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCcc
Confidence            45555554443321    123345566677777777777654 56666777777777777766654 3555444      


Q ss_pred             EEEeeCCccCcc---------eeeEEecc---cccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEE
Q 041097          223 ILRLSGNSQFHF---------SLASLLLY---YQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLS  289 (391)
Q Consensus       223 ~L~l~~~~l~~L---------~L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~  289 (391)
                      +|++++|.+...         +|+.|+++   ....+|..++++++|++|++.+..    +...+| .+..+ ++|+.|+
T Consensus       216 ~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~----l~~~~p~~l~~l-~~L~~L~  290 (968)
T PLN00113        216 WIYLGYNNLSGEIPYEIGGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNK----LSGPIPPSIFSL-QKLISLD  290 (968)
T ss_pred             EEECcCCccCCcCChhHhcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCe----eeccCchhHhhc-cCcCEEE
Confidence            666666654321         56666666   123456666666666666665511    000033 34444 4555555


Q ss_pred             eecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEee
Q 041097          290 FSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELW  363 (391)
Q Consensus       290 l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~  363 (391)
                      +++|.+....+..++++++|+.|+++.|...+..+...+.+++|+.|++++|.-...+|.+++.+++|+.|+++
T Consensus       291 Ls~n~l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~p~~l~~~~~L~~L~Ls  364 (968)
T PLN00113        291 LSDNSLSGEIPELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVLQLWSNKFSGEIPKNLGKHNNLTVLDLS  364 (968)
T ss_pred             CcCCeeccCCChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEEECcCCCCcCcCChHHhCCCCCcEEECC
Confidence            55444443333444444555555554333332222222344444444444443222344444444444444443

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

Probab=99.60  E-value=3.2e-17  Score=156.21  Aligned_cols=211  Identities=22%  Similarity=0.213  Sum_probs=144.9

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-------E
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-------I  223 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-------~  223 (391)
                      +.+|++++..+...   ...+++-+-.++.|.+|||+.|++.+.|..+.+-+++-.|+|++|+|..+|.++.       .
T Consensus        78 p~LRsv~~R~N~LK---nsGiP~diF~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N~IetIPn~lfinLtDLLf  154 (1255)
T KOG0444|consen   78 PRLRSVIVRDNNLK---NSGIPTDIFRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYNNIETIPNSLFINLTDLLF  154 (1255)
T ss_pred             hhhHHHhhhccccc---cCCCCchhcccccceeeecchhhhhhcchhhhhhcCcEEEEcccCccccCCchHHHhhHhHhh
Confidence            67777776655432   2234456667788888888888888888888887888888888888888888777       7


Q ss_pred             EEeeCCccCcc---------------------------------------------------------eeeEEecc--cc
Q 041097          224 LRLSGNSQFHF---------------------------------------------------------SLASLLLY--YQ  244 (391)
Q Consensus       224 L~l~~~~l~~L---------------------------------------------------------~L~~L~l~--~~  244 (391)
                      |||++|+++.|                                                         +|+.++++  +.
T Consensus       155 LDLS~NrLe~LPPQ~RRL~~LqtL~Ls~NPL~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~N~L  234 (1255)
T KOG0444|consen  155 LDLSNNRLEMLPPQIRRLSMLQTLKLSNNPLNHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDLHNLRDVDLSENNL  234 (1255)
T ss_pred             hccccchhhhcCHHHHHHhhhhhhhcCCChhhHHHHhcCccchhhhhhhcccccchhhcCCCchhhhhhhhhccccccCC
Confidence            77777776655                                                         44444444  44


Q ss_pred             cchhHHhcCCCCCCEEEecCC---C-CC-----Cchhhh---------cc-ccccCCCCccEEEeecccCCCCC-hhhhc
Q 041097          245 SLLSKSLCRLSCLESLKLANE---S-KM-----PRRSNI---------IL-AEYQFPPSLTHLSFSNIELMDDP-IPALE  304 (391)
Q Consensus       245 ~~lp~~i~~l~~L~~L~l~~~---~-~l-----p~L~~L---------lp-~~~~l~~~L~~L~l~~~~~~~~~-~~~l~  304 (391)
                      ..+|+.+-++.+|+.|++++.   . .+     .+++.|         +| .++++ +.|+.|++.+|++.-+. +.-+|
T Consensus       235 p~vPecly~l~~LrrLNLS~N~iteL~~~~~~W~~lEtLNlSrNQLt~LP~avcKL-~kL~kLy~n~NkL~FeGiPSGIG  313 (1255)
T KOG0444|consen  235 PIVPECLYKLRNLRRLNLSGNKITELNMTEGEWENLETLNLSRNQLTVLPDAVCKL-TKLTKLYANNNKLTFEGIPSGIG  313 (1255)
T ss_pred             CcchHHHhhhhhhheeccCcCceeeeeccHHHHhhhhhhccccchhccchHHHhhh-HHHHHHHhccCcccccCCccchh
Confidence            455566666666666666651   1 11     122222         67 77777 77888877777665433 35677


Q ss_pred             CCCCCCEEEcCCCCCcCccccCC--CcccccceeeeccccccccchHhhcCCCCCCEEEeeCCcHHHH
Q 041097          305 KLSVLQVLKLKQNLYSEERTMGI--RAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELR  370 (391)
Q Consensus       305 ~l~~L~~L~l~~~~~~~~~~~~~--~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~~~l~  370 (391)
                      +|.+|+.+....|...   .+++  ..+++|+.|.++ |+.+-.+|+.|--|+.|+.|++.++| ++.
T Consensus       314 KL~~Levf~aanN~LE---lVPEglcRC~kL~kL~L~-~NrLiTLPeaIHlL~~l~vLDlreNp-nLV  376 (1255)
T KOG0444|consen  314 KLIQLEVFHAANNKLE---LVPEGLCRCVKLQKLKLD-HNRLITLPEAIHLLPDLKVLDLRENP-NLV  376 (1255)
T ss_pred             hhhhhHHHHhhccccc---cCchhhhhhHHHHHhccc-ccceeechhhhhhcCCcceeeccCCc-Ccc
Confidence            7888877777633322   3333  477899999999 55788999999999999999999988 553

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

Probab=99.57  E-value=1.4e-14  Score=155.43  Aligned_cols=211  Identities=23%  Similarity=0.197  Sum_probs=135.8

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccCCCCC-ccCCCCc------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNIPSLK-SLPSSRK------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~~~i~-~lp~~~~------  222 (391)
                      ++++.|.+.++...    ...+..+.+++.|++|++++|.+. .+|..++++.+|++|++++|.+. .+|..++      
T Consensus       164 ~~L~~L~L~~n~l~----~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~  239 (968)
T PLN00113        164 SSLKVLDLGGNVLV----GKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNNLSGEIPYEIGGLTSLN  239 (968)
T ss_pred             CCCCEEECccCccc----ccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCccCCcCChhHhcCCCCC
Confidence            67777776555431    124456777888888888888866 67788888888888888888766 5666555      


Q ss_pred             EEEeeCCccCcc---------eeeEEecc---cccchhHHhcCCCCCCEEEecCCC---CC-------Cchhhh------
Q 041097          223 ILRLSGNSQFHF---------SLASLLLY---YQSLLSKSLCRLSCLESLKLANES---KM-------PRRSNI------  274 (391)
Q Consensus       223 ~L~l~~~~l~~L---------~L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~~~---~l-------p~L~~L------  274 (391)
                      +|++++|.+...         +|+.|+++   -...+|.+++++++|++|++++..   .+       ++|+.|      
T Consensus       240 ~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~l~~n~  319 (968)
T PLN00113        240 HLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLSDNSLSGEIPELVIQLQNLEILHLFSNN  319 (968)
T ss_pred             EEECcCceeccccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEECcCCeeccCCChhHcCCCCCcEEECCCCc
Confidence            788887765432         67777777   223567777788888888776611   11       122211      


Q ss_pred             ----cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchH
Q 041097          275 ----IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHE  349 (391)
Q Consensus       275 ----lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~  349 (391)
                          +| .+..+ ++|+.|++++|.+....+..++.+++|+.|+++.|...+..+.....+++|+.|++++|.-...+|.
T Consensus       320 ~~~~~~~~~~~l-~~L~~L~L~~n~l~~~~p~~l~~~~~L~~L~Ls~n~l~~~~p~~~~~~~~L~~L~l~~n~l~~~~p~  398 (968)
T PLN00113        320 FTGKIPVALTSL-PRLQVLQLWSNKFSGEIPKNLGKHNNLTVLDLSTNNLTGEIPEGLCSSGNLFKLILFSNSLEGEIPK  398 (968)
T ss_pred             cCCcCChhHhcC-CCCCEEECcCCCCcCcCChHHhCCCCCcEEECCCCeeEeeCChhHhCcCCCCEEECcCCEecccCCH
Confidence                34 45556 6666666666666555555666666666666665544443222234556777777776654446777


Q ss_pred             hhcCCCCCCEEEeeCCc
Q 041097          350 QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       350 ~~~~l~~L~~L~l~~~~  366 (391)
                      ++..+++|+.|++.+|.
T Consensus       399 ~~~~~~~L~~L~L~~n~  415 (968)
T PLN00113        399 SLGACRSLRRVRLQDNS  415 (968)
T ss_pred             HHhCCCCCCEEECcCCE
Confidence            77778888888887764

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

Probab=99.44  E-value=4.2e-14  Score=128.75  Aligned_cols=189  Identities=26%  Similarity=0.264  Sum_probs=134.2

Q ss_pred             hccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-----EEEeeCCccCcc---------------
Q 041097          175 CKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-----ILRLSGNSQFHF---------------  234 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~l~~~~l~~L---------------  234 (391)
                      .+.+..+.+||+..|++.++|..++.+..|.+|+++++.|+.+|.+++     .|-+.+|.++.+               
T Consensus       248 ~~~L~~l~vLDLRdNklke~Pde~clLrsL~rLDlSNN~is~Lp~sLgnlhL~~L~leGNPlrTiRr~ii~~gT~~vLKy  327 (565)
T KOG0472|consen  248 LKHLNSLLVLDLRDNKLKEVPDEICLLRSLERLDLSNNDISSLPYSLGNLHLKFLALEGNPLRTIRREIISKGTQEVLKY  327 (565)
T ss_pred             hcccccceeeeccccccccCchHHHHhhhhhhhcccCCccccCCcccccceeeehhhcCCchHHHHHHHHcccHHHHHHH
Confidence            347889999999999999999999999999999999999999999999     455566766554               


Q ss_pred             -----------------------------------eeeEEecc--cccchhHHhcCCCC---CCEEEecCCC--CCC---
Q 041097          235 -----------------------------------SLASLLLY--YQSLLSKSLCRLSC---LESLKLANES--KMP---  269 (391)
Q Consensus       235 -----------------------------------~L~~L~l~--~~~~lp~~i~~l~~---L~~L~l~~~~--~lp---  269 (391)
                                                         ..|.|+++  ....+|+..-.-..   ....+++...  .+|   
T Consensus       328 Lrs~~~~dglS~se~~~e~~~t~~~~~~~~~~~~i~tkiL~~s~~qlt~VPdEVfea~~~~~Vt~VnfskNqL~elPk~L  407 (565)
T KOG0472|consen  328 LRSKIKDDGLSQSEGGTETAMTLPSESFPDIYAIITTKILDVSDKQLTLVPDEVFEAAKSEIVTSVNFSKNQLCELPKRL  407 (565)
T ss_pred             HHHhhccCCCCCCcccccccCCCCCCcccchhhhhhhhhhcccccccccCCHHHHHHhhhcceEEEecccchHhhhhhhh
Confidence                                               33344433  22233332111111   2222222211  112   


Q ss_pred             -chhhh-------------cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc-----------
Q 041097          270 -RRSNI-------------IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER-----------  323 (391)
Q Consensus       270 -~L~~L-------------lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~-----------  323 (391)
                       .+..+             .| .++.+ ++|+.|+|++|-+...| ..++.+..|+.|+++.|.|..-.           
T Consensus       408 ~~lkelvT~l~lsnn~isfv~~~l~~l-~kLt~L~L~NN~Ln~LP-~e~~~lv~Lq~LnlS~NrFr~lP~~~y~lq~lEt  485 (565)
T KOG0472|consen  408 VELKELVTDLVLSNNKISFVPLELSQL-QKLTFLDLSNNLLNDLP-EEMGSLVRLQTLNLSFNRFRMLPECLYELQTLET  485 (565)
T ss_pred             HHHHHHHHHHHhhcCccccchHHHHhh-hcceeeecccchhhhcc-hhhhhhhhhheecccccccccchHHHhhHHHHHH
Confidence             11111             55 78889 99999999999877766 67788888999999987653211           


Q ss_pred             ----------ccC--CCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          324 ----------TMG--IRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       324 ----------~~~--~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                                +.+  .+.|.+|..|++.++ .+..+|..++++++|++|+++|.|
T Consensus       486 llas~nqi~~vd~~~l~nm~nL~tLDL~nN-dlq~IPp~LgnmtnL~hLeL~gNp  539 (565)
T KOG0472|consen  486 LLASNNQIGSVDPSGLKNMRNLTTLDLQNN-DLQQIPPILGNMTNLRHLELDGNP  539 (565)
T ss_pred             HHhccccccccChHHhhhhhhcceeccCCC-chhhCChhhccccceeEEEecCCc
Confidence                      111  246779999999977 589999999999999999999988

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

Probab=99.44  E-value=4.8e-15  Score=141.55  Aligned_cols=190  Identities=26%  Similarity=0.255  Sum_probs=149.3

Q ss_pred             hHHhhccCCcccEEEcCCCccc--cCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcc--------
Q 041097          171 CEKICKMFKFLRVLDLGSLVLI--RYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHF--------  234 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~--~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L--------  234 (391)
                      +...++.++.||.+++..|++.  -+|..|-+|..|..|+|+.|++++.|..+.      .|+|++|+|+.+        
T Consensus        70 vhGELs~Lp~LRsv~~R~N~LKnsGiP~diF~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N~IetIPn~lfinL  149 (1255)
T KOG0444|consen   70 VHGELSDLPRLRSVIVRDNNLKNSGIPTDIFRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYNNIETIPNSLFINL  149 (1255)
T ss_pred             hhhhhccchhhHHHhhhccccccCCCCchhcccccceeeecchhhhhhcchhhhhhcCcEEEEcccCccccCCchHHHhh
Confidence            3355677888999999999987  789999999999999999999999999887      999999999876        


Q ss_pred             -eeeEEecc--cccchhHHhcCCCCCCEEEecCCC-------CCCchhhh--------------cc-ccccCCCCccEEE
Q 041097          235 -SLASLLLY--YQSLLSKSLCRLSCLESLKLANES-------KMPRRSNI--------------IL-AEYQFPPSLTHLS  289 (391)
Q Consensus       235 -~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~-------~lp~L~~L--------------lp-~~~~l~~~L~~L~  289 (391)
                       .|-.|+++  ..+.+|+-+.+|.+|++|.+++..       .+|.+..|              +| .+..+ .||+.++
T Consensus       150 tDLLfLDLS~NrLe~LPPQ~RRL~~LqtL~Ls~NPL~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l-~NL~dvD  228 (1255)
T KOG0444|consen  150 TDLLFLDLSNNRLEMLPPQIRRLSMLQTLKLSNNPLNHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDL-HNLRDVD  228 (1255)
T ss_pred             HhHhhhccccchhhhcCHHHHHHhhhhhhhcCCChhhHHHHhcCccchhhhhhhcccccchhhcCCCchhhh-hhhhhcc
Confidence             67778888  678899999999999999999821       34544444              77 77888 8999999


Q ss_pred             eecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeC
Q 041097          290 FSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWW  364 (391)
Q Consensus       290 l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~  364 (391)
                      ++.|.+...| ..+-++++|+.|++++|.... .....+...+|+.|+++.+ ++..+|..+..|++|++|+..+
T Consensus       229 lS~N~Lp~vP-ecly~l~~LrrLNLS~N~ite-L~~~~~~W~~lEtLNlSrN-QLt~LP~avcKL~kL~kLy~n~  300 (1255)
T KOG0444|consen  229 LSENNLPIVP-ECLYKLRNLRRLNLSGNKITE-LNMTEGEWENLETLNLSRN-QLTVLPDAVCKLTKLTKLYANN  300 (1255)
T ss_pred             ccccCCCcch-HHHhhhhhhheeccCcCceee-eeccHHHHhhhhhhccccc-hhccchHHHhhhHHHHHHHhcc
Confidence            9988876655 777899999999999666532 2223345567777777765 4677777777777776665543

>PLN03210 Resistant to P

Probab=99.38  E-value=7.2e-12  Score=135.71  Aligned_cols=228  Identities=24%  Similarity=0.233  Sum_probs=123.4

Q ss_pred             CceEEEEEeccCCCcccccC-CC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCc-cccCCcccCCCCccc
Q 041097          129 ENVKRFTAHRKLNDFAFLDD-FD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLV-LIRYPSGIENLFLLR  205 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~-~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-l~~~p~~i~~l~~L~  205 (391)
                      .+.+.|.+....... .... .. ++++.+.+......    ..+ +.+..+++|+.|++++|. +..+|..++++.+|+
T Consensus       611 ~~L~~L~L~~s~l~~-L~~~~~~l~~Lk~L~Ls~~~~l----~~i-p~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~  684 (1153)
T PLN03210        611 ENLVKLQMQGSKLEK-LWDGVHSLTGLRNIDLRGSKNL----KEI-PDLSMATNLETLKLSDCSSLVELPSSIQYLNKLE  684 (1153)
T ss_pred             cCCcEEECcCccccc-cccccccCCCCCEEECCCCCCc----CcC-CccccCCcccEEEecCCCCccccchhhhccCCCC
Confidence            455666665222222 2222 23 67777766543321    012 235566777777777765 557777777777777


Q ss_pred             EEEccCC-CCCccCCCCc-----EEEeeCCc-cCcc-----eeeEEecc--cccchhHHhcCCCCCCEEEecC-CC----
Q 041097          206 YLKLNIP-SLKSLPSSRK-----ILRLSGNS-QFHF-----SLASLLLY--YQSLLSKSLCRLSCLESLKLAN-ES----  266 (391)
Q Consensus       206 ~L~l~~~-~i~~lp~~~~-----~L~l~~~~-l~~L-----~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~-~~----  266 (391)
                      +|++++| .++.+|..+.     .|++++|. +..+     +|+.|+++  ....+|..+ .+++|++|.+.+ ..    
T Consensus       685 ~L~L~~c~~L~~Lp~~i~l~sL~~L~Lsgc~~L~~~p~~~~nL~~L~L~~n~i~~lP~~~-~l~~L~~L~l~~~~~~~l~  763 (1153)
T PLN03210        685 DLDMSRCENLEILPTGINLKSLYRLNLSGCSRLKSFPDISTNISWLDLDETAIEEFPSNL-RLENLDELILCEMKSEKLW  763 (1153)
T ss_pred             EEeCCCCCCcCccCCcCCCCCCCEEeCCCCCCccccccccCCcCeeecCCCccccccccc-cccccccccccccchhhcc
Confidence            7777765 4666666543     66666652 2221     45555555  333444332 233343333322 00    


Q ss_pred             ----C--------CCchhhh----------cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCC--------------
Q 041097          267 ----K--------MPRRSNI----------IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVL--------------  309 (391)
Q Consensus       267 ----~--------lp~L~~L----------lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L--------------  309 (391)
                          .        .++|+.|          +| .++.+ ++|+.|++.+|...... +....+++|              
T Consensus       764 ~~~~~l~~~~~~~~~sL~~L~Ls~n~~l~~lP~si~~L-~~L~~L~Ls~C~~L~~L-P~~~~L~sL~~L~Ls~c~~L~~~  841 (1153)
T PLN03210        764 ERVQPLTPLMTMLSPSLTRLFLSDIPSLVELPSSIQNL-HKLEHLEIENCINLETL-PTGINLESLESLDLSGCSRLRTF  841 (1153)
T ss_pred             ccccccchhhhhccccchheeCCCCCCccccChhhhCC-CCCCEEECCCCCCcCee-CCCCCccccCEEECCCCCccccc
Confidence                0        0111211          44 45555 55555555554321111 111134444              


Q ss_pred             -------CEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          310 -------QVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       310 -------~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                             +.|+++.|... ..+...+.+++|+.|++++|++++.+|..+..+++|+.+++++|+
T Consensus       842 p~~~~nL~~L~Ls~n~i~-~iP~si~~l~~L~~L~L~~C~~L~~l~~~~~~L~~L~~L~l~~C~  904 (1153)
T PLN03210        842 PDISTNISDLNLSRTGIE-EVPWWIEKFSNLSFLDMNGCNNLQRVSLNISKLKHLETVDFSDCG  904 (1153)
T ss_pred             cccccccCEeECCCCCCc-cChHHHhcCCCCCEEECCCCCCcCccCcccccccCCCeeecCCCc
Confidence                   44444433222 112223578899999999999999999888899999999999987

syringae 6; Provisional

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

Probab=99.31  E-value=2.2e-12  Score=122.67  Aligned_cols=37  Identities=27%  Similarity=0.316  Sum_probs=30.9

Q ss_pred             cccccceeeeccccccccch-HhhcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~~~  366 (391)
                      .++.|+.|++.++ +++.+| ..+..+++|++|++.+++
T Consensus       390 gl~~LrkL~l~gN-qlk~I~krAfsgl~~LE~LdL~~Na  427 (873)
T KOG4194|consen  390 GLPSLRKLRLTGN-QLKSIPKRAFSGLEALEHLDLGDNA  427 (873)
T ss_pred             cchhhhheeecCc-eeeecchhhhccCcccceecCCCCc
Confidence            4889999999987 588888 467889999999998765

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

Probab=99.28  E-value=8.9e-14  Score=126.62  Aligned_cols=191  Identities=24%  Similarity=0.193  Sum_probs=125.0

Q ss_pred             hHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc----------------------------
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK----------------------------  222 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~----------------------------  222 (391)
                      +++.+.++..+..++.+.+++..+|+.++.+..++.++.+.+.+.++|++++                            
T Consensus        83 lp~aig~l~~l~~l~vs~n~ls~lp~~i~s~~~l~~l~~s~n~~~el~~~i~~~~~l~dl~~~~N~i~slp~~~~~~~~l  162 (565)
T KOG0472|consen   83 LPAAIGELEALKSLNVSHNKLSELPEQIGSLISLVKLDCSSNELKELPDSIGRLLDLEDLDATNNQISSLPEDMVNLSKL  162 (565)
T ss_pred             CCHHHHHHHHHHHhhcccchHhhccHHHhhhhhhhhhhccccceeecCchHHHHhhhhhhhccccccccCchHHHHHHHH
Confidence            4455555555555555555555555555555555555555555555555555                            


Q ss_pred             -EEEeeCCccCcc--------eeeEEecc--cccchhHHhcCCCCCCEEEecCCC-CCCchhhhccccccCCCCccEEEe
Q 041097          223 -ILRLSGNSQFHF--------SLASLLLY--YQSLLSKSLCRLSCLESLKLANES-KMPRRSNIILAEYQFPPSLTHLSF  290 (391)
Q Consensus       223 -~L~l~~~~l~~L--------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~-~lp~L~~Llp~~~~l~~~L~~L~l  290 (391)
                       .+++.+|.+..+        .|++|+..  ..+++|+.++.|.+|..|++.... .+      +|.+... +.|..|.+
T Consensus       163 ~~l~~~~n~l~~l~~~~i~m~~L~~ld~~~N~L~tlP~~lg~l~~L~~LyL~~Nki~~------lPef~gc-s~L~Elh~  235 (565)
T KOG0472|consen  163 SKLDLEGNKLKALPENHIAMKRLKHLDCNSNLLETLPPELGGLESLELLYLRRNKIRF------LPEFPGC-SLLKELHV  235 (565)
T ss_pred             HHhhccccchhhCCHHHHHHHHHHhcccchhhhhcCChhhcchhhhHHHHhhhccccc------CCCCCcc-HHHHHHHh
Confidence             344444444433        45555555  455666666666666666665422 11      6666667 78888888


Q ss_pred             ecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCcHHHH
Q 041097          291 SNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPELR  370 (391)
Q Consensus       291 ~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~~~l~  370 (391)
                      ..|.++..+...+.+++++..|++.+|... +.+.+..-+.+|++|+++++ .++.+|.+++++ .|+.|.+.|.|-.-.
T Consensus       236 g~N~i~~lpae~~~~L~~l~vLDLRdNklk-e~Pde~clLrsL~rLDlSNN-~is~Lp~sLgnl-hL~~L~leGNPlrTi  312 (565)
T KOG0472|consen  236 GENQIEMLPAEHLKHLNSLLVLDLRDNKLK-EVPDEICLLRSLERLDLSNN-DISSLPYSLGNL-HLKFLALEGNPLRTI  312 (565)
T ss_pred             cccHHHhhHHHHhcccccceeeeccccccc-cCchHHHHhhhhhhhcccCC-ccccCCcccccc-eeeehhhcCCchHHH
Confidence            888877777777789999999999955543 22333356778999999977 589999999999 999999999996544


Q ss_pred             H
Q 041097          371 Q  371 (391)
Q Consensus       371 ~  371 (391)
                      +
T Consensus       313 R  313 (565)
T KOG0472|consen  313 R  313 (565)
T ss_pred             H
Confidence            3

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

Probab=99.22  E-value=1.4e-13  Score=111.61  Aligned_cols=161  Identities=24%  Similarity=0.278  Sum_probs=104.9

Q ss_pred             cCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecc--cccchhHHhcCC
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLY--YQSLLSKSLCRL  254 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~--~~~~lp~~i~~l  254 (391)
                      .+.+...|-++++++..+|..|..+.+|+.|++++++++++|.+++.|.         +||.|.++  ....+|.++|.+
T Consensus        31 ~~s~ITrLtLSHNKl~~vppnia~l~nlevln~~nnqie~lp~~issl~---------klr~lnvgmnrl~~lprgfgs~  101 (264)
T KOG0617|consen   31 NMSNITRLTLSHNKLTVVPPNIAELKNLEVLNLSNNQIEELPTSISSLP---------KLRILNVGMNRLNILPRGFGSF  101 (264)
T ss_pred             chhhhhhhhcccCceeecCCcHHHhhhhhhhhcccchhhhcChhhhhch---------hhhheecchhhhhcCccccCCC
Confidence            4455666778888888888888888888888888888888877665221         33333333  233667777777


Q ss_pred             CCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccc
Q 041097          255 SCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPK  332 (391)
Q Consensus       255 ~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~  332 (391)
                      +-|+.|++...+ .    ++.+| .+..+ +.|+.|+|..|..+..| +..+++.+|+.|.+.+|.... .+-+.|.+..
T Consensus       102 p~levldltynnl~----e~~lpgnff~m-~tlralyl~dndfe~lp-~dvg~lt~lqil~lrdndll~-lpkeig~lt~  174 (264)
T KOG0617|consen  102 PALEVLDLTYNNLN----ENSLPGNFFYM-TTLRALYLGDNDFEILP-PDVGKLTNLQILSLRDNDLLS-LPKEIGDLTR  174 (264)
T ss_pred             chhhhhhccccccc----cccCCcchhHH-HHHHHHHhcCCCcccCC-hhhhhhcceeEEeeccCchhh-CcHHHHHHHH
Confidence            777777776511 0    00055 44456 77777777777655544 677888888888887554322 1223477778


Q ss_pred             cceeeeccccccccchHhhcCC
Q 041097          333 LECLIINPYAHLKRIHEQLWCL  354 (391)
Q Consensus       333 L~~L~l~~c~~l~~lp~~~~~l  354 (391)
                      |++|.|.++ .+..+|..++++
T Consensus       175 lrelhiqgn-rl~vlppel~~l  195 (264)
T KOG0617|consen  175 LRELHIQGN-RLTVLPPELANL  195 (264)
T ss_pred             HHHHhcccc-eeeecChhhhhh
Confidence            888888876 477777766554

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=99.22  E-value=2.9e-11  Score=111.50  Aligned_cols=88  Identities=20%  Similarity=0.226  Sum_probs=71.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhhcCCCCCC-CCCChHHHHHHHHHHHHcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGF-IPDNNEATVEKYLEQLING   79 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~-~~~~~~~~~~~~~~~L~~k   79 (391)
                      |+|+||||+||||||+.+|++..++++|+.++|+.++...+...+.+++...+.-..... .....++....+.+.|.++
T Consensus        22 v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~~  101 (287)
T PF00931_consen   22 VAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLKDK  101 (287)
T ss_dssp             EEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHCCT
T ss_pred             EEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhccc
Confidence            689999999999999999997779999999999999999999999999887765543433 3334677788888888888


Q ss_pred             ccEEeeecc
Q 041097           80 GFVGAGKRS   88 (391)
Q Consensus        80 ~~l~~~~~~   88 (391)
                      +.+.+.++.
T Consensus       102 ~~LlVlDdv  110 (287)
T PF00931_consen  102 RCLLVLDDV  110 (287)
T ss_dssp             SEEEEEEEE
T ss_pred             cceeeeeee
Confidence            888887763

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.

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

Probab=99.18  E-value=1.1e-11  Score=123.61  Aligned_cols=89  Identities=25%  Similarity=0.248  Sum_probs=62.7

Q ss_pred             ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc---------------------ccCCCccccc
Q 041097          275 ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER---------------------TMGIRAMPKL  333 (391)
Q Consensus       275 lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~---------------------~~~~~~~~~L  333 (391)
                      +|-+..+ .+|+.|.|++|.+...|...+.+++.|+.|++++|......                     +++...++.|
T Consensus       376 ~p~l~~~-~hLKVLhLsyNrL~~fpas~~~kle~LeeL~LSGNkL~~Lp~tva~~~~L~tL~ahsN~l~~fPe~~~l~qL  454 (1081)
T KOG0618|consen  376 FPVLVNF-KHLKVLHLSYNRLNSFPASKLRKLEELEELNLSGNKLTTLPDTVANLGRLHTLRAHSNQLLSFPELAQLPQL  454 (1081)
T ss_pred             hhhhccc-cceeeeeecccccccCCHHHHhchHHhHHHhcccchhhhhhHHHHhhhhhHHHhhcCCceeechhhhhcCcc
Confidence            5544455 78888888888877777777788888888888766543211                     4445678899


Q ss_pred             ceeeecccccccc--chHhhcCCCCCCEEEeeCCc
Q 041097          334 ECLIINPYAHLKR--IHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       334 ~~L~l~~c~~l~~--lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +.++++ |++++.  +|..... ++|++|+++|++
T Consensus       455 ~~lDlS-~N~L~~~~l~~~~p~-p~LkyLdlSGN~  487 (1081)
T KOG0618|consen  455 KVLDLS-CNNLSEVTLPEALPS-PNLKYLDLSGNT  487 (1081)
T ss_pred             eEEecc-cchhhhhhhhhhCCC-cccceeeccCCc
Confidence            999998 556664  3433322 789999999988

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.15  E-value=3.2e-10  Score=115.65  Aligned_cols=75  Identities=24%  Similarity=0.159  Sum_probs=53.4

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEe
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLEL  362 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l  362 (391)
                      .+|+.|++++|.+...|.    ..++|+.|+++.|....  ++  ..+.+|+.|+++++ +++.+|.++..+++|+.|++
T Consensus       382 ~~L~~LdLs~N~Lt~LP~----l~s~L~~LdLS~N~Lss--IP--~l~~~L~~L~Ls~N-qLt~LP~sl~~L~~L~~LdL  452 (788)
T PRK15387        382 SGLKELIVSGNRLTSLPV----LPSELKELMVSGNRLTS--LP--MLPSGLLSLSVYRN-QLTRLPESLIHLSSETTVNL  452 (788)
T ss_pred             cccceEEecCCcccCCCC----cccCCCEEEccCCcCCC--CC--cchhhhhhhhhccC-cccccChHHhhccCCCeEEC
Confidence            567777777776654331    13567777887555432  11  12447889999876 58899999999999999999


Q ss_pred             eCCc
Q 041097          363 WWPE  366 (391)
Q Consensus       363 ~~~~  366 (391)
                      +++|
T Consensus       453 s~N~  456 (788)
T PRK15387        453 EGNP  456 (788)
T ss_pred             CCCC
Confidence            9876

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

Probab=99.14  E-value=9.8e-13  Score=106.80  Aligned_cols=151  Identities=22%  Similarity=0.267  Sum_probs=125.4

Q ss_pred             ccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCc
Q 041097          197 GIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPR  270 (391)
Q Consensus       197 ~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~  270 (391)
                      ++-++.++.-|.++.+++...|+.|.      .|++.+|+++             ++|.+|+.|++|+.|++.-      
T Consensus        28 gLf~~s~ITrLtLSHNKl~~vppnia~l~nlevln~~nnqie-------------~lp~~issl~klr~lnvgm------   88 (264)
T KOG0617|consen   28 GLFNMSNITRLTLSHNKLTVVPPNIAELKNLEVLNLSNNQIE-------------ELPTSISSLPKLRILNVGM------   88 (264)
T ss_pred             cccchhhhhhhhcccCceeecCCcHHHhhhhhhhhcccchhh-------------hcChhhhhchhhhheecch------
Confidence            34456677788999999999999887      7888888888             9999999999999999864      


Q ss_pred             hhhh--cc-ccccCCCCccEEEeecccCCCCC-hhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecccccccc
Q 041097          271 RSNI--IL-AEYQFPPSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKR  346 (391)
Q Consensus       271 L~~L--lp-~~~~l~~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~  346 (391)
                       ++|  +| .++.+ +.|+.|+|++|++.+.. +.-+-.|+.|+.|++.+|.+.. .+.+.|.+.+||-|.+..+. +-+
T Consensus        89 -nrl~~lprgfgs~-p~levldltynnl~e~~lpgnff~m~tlralyl~dndfe~-lp~dvg~lt~lqil~lrdnd-ll~  164 (264)
T KOG0617|consen   89 -NRLNILPRGFGSF-PALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGDNDFEI-LPPDVGKLTNLQILSLRDND-LLS  164 (264)
T ss_pred             -hhhhcCccccCCC-chhhhhhccccccccccCCcchhHHHHHHHHHhcCCCccc-CChhhhhhcceeEEeeccCc-hhh
Confidence             333  88 99999 99999999999887654 3456677899999999887764 24456999999999999874 679


Q ss_pred             chHhhcCCCCCCEEEeeC-----CcHHHH
Q 041097          347 IHEQLWCLKSLNKLELWW-----PEPELR  370 (391)
Q Consensus       347 lp~~~~~l~~L~~L~l~~-----~~~~l~  370 (391)
                      +|..++.++.|++|+|.|     .|+|+.
T Consensus       165 lpkeig~lt~lrelhiqgnrl~vlppel~  193 (264)
T KOG0617|consen  165 LPKEIGDLTRLRELHIQGNRLTVLPPELA  193 (264)
T ss_pred             CcHHHHHHHHHHHHhcccceeeecChhhh
Confidence            999999999999999987     466654

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.09  E-value=3.2e-10  Score=116.07  Aligned_cols=79  Identities=18%  Similarity=0.198  Sum_probs=53.9

Q ss_pred             CCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhh----cCCCCC
Q 041097          282 PPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQL----WCLKSL  357 (391)
Q Consensus       282 ~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~----~~l~~L  357 (391)
                      |++|+.|++++|.+...| ..+  .++|+.|+++.|....   ++......|+.|++++| ++..+|.++    ..++.+
T Consensus       345 ~~sL~~L~Ls~N~L~~LP-~~l--p~~L~~LdLs~N~Lt~---LP~~l~~sL~~LdLs~N-~L~~LP~sl~~~~~~~~~l  417 (754)
T PRK15370        345 PPELQVLDVSKNQITVLP-ETL--PPTITTLDVSRNALTN---LPENLPAALQIMQASRN-NLVRLPESLPHFRGEGPQP  417 (754)
T ss_pred             cCcccEEECCCCCCCcCC-hhh--cCCcCEEECCCCcCCC---CCHhHHHHHHHHhhccC-CcccCchhHHHHhhcCCCc
Confidence            368888888888776544 222  2688888888665432   12222347888999876 577777655    345888


Q ss_pred             CEEEeeCCcH
Q 041097          358 NKLELWWPEP  367 (391)
Q Consensus       358 ~~L~l~~~~~  367 (391)
                      ..|++.++|-
T Consensus       418 ~~L~L~~Npl  427 (754)
T PRK15370        418 TRIIVEYNPF  427 (754)
T ss_pred             cEEEeeCCCc
Confidence            9999999884

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.07  E-value=4e-10  Score=115.35  Aligned_cols=171  Identities=24%  Similarity=0.276  Sum_probs=89.5

Q ss_pred             cccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc----EEEeeCCccCcc------eeeEEecc--cccch
Q 041097          180 FLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK----ILRLSGNSQFHF------SLASLLLY--YQSLL  247 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~----~L~l~~~~l~~L------~L~~L~l~--~~~~l  247 (391)
                      .|+.|++++|.+..+|..+.  .+|++|++++|.++++|..+.    .|++++|.+..+      +|+.|+++  ....+
T Consensus       200 ~L~~L~Ls~N~LtsLP~~l~--~nL~~L~Ls~N~LtsLP~~l~~~L~~L~Ls~N~L~~LP~~l~s~L~~L~Ls~N~L~~L  277 (754)
T PRK15370        200 QITTLILDNNELKSLPENLQ--GNIKTLYANSNQLTSIPATLPDTIQEMELSINRITELPERLPSALQSLDLFHNKISCL  277 (754)
T ss_pred             CCcEEEecCCCCCcCChhhc--cCCCEEECCCCccccCChhhhccccEEECcCCccCcCChhHhCCCCEEECcCCccCcc
Confidence            46666666666666665544  366666666666665554433    666666665544      46666665  34456


Q ss_pred             hHHhcCCCCCCEEEecCCC--CCC-----chhhh---------ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCE
Q 041097          248 SKSLCRLSCLESLKLANES--KMP-----RRSNI---------ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQV  311 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~--~lp-----~L~~L---------lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~  311 (391)
                      |..+.  ++|++|++++..  .+|     .|+.|         +|.  .+|++|+.|.+.+|.+...+ ..+  .++|+.
T Consensus       278 P~~l~--~sL~~L~Ls~N~Lt~LP~~lp~sL~~L~Ls~N~Lt~LP~--~l~~sL~~L~Ls~N~Lt~LP-~~l--~~sL~~  350 (754)
T PRK15370        278 PENLP--EELRYLSVYDNSIRTLPAHLPSGITHLNVQSNSLTALPE--TLPPGLKTLEAGENALTSLP-ASL--PPELQV  350 (754)
T ss_pred             ccccC--CCCcEEECCCCccccCcccchhhHHHHHhcCCccccCCc--cccccceeccccCCccccCC-hhh--cCcccE
Confidence            66553  467777776622  111     12211         220  11256666666666555433 122  146666


Q ss_pred             EEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCC
Q 041097          312 LKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       312 L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~  365 (391)
                      |+++.|....   ++....++|+.|++++| .+..+|..+.  ++|+.|+++++
T Consensus       351 L~Ls~N~L~~---LP~~lp~~L~~LdLs~N-~Lt~LP~~l~--~sL~~LdLs~N  398 (754)
T PRK15370        351 LDVSKNQITV---LPETLPPTITTLDVSRN-ALTNLPENLP--AALQIMQASRN  398 (754)
T ss_pred             EECCCCCCCc---CChhhcCCcCEEECCCC-cCCCCCHhHH--HHHHHHhhccC
Confidence            6666444321   11222346666666665 3566665543  24555555543

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

Probab=99.03  E-value=2.5e-10  Score=109.04  Aligned_cols=176  Identities=22%  Similarity=0.203  Sum_probs=98.3

Q ss_pred             HhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcceeeEEeccccc
Q 041097          173 KICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHFSLASLLLYYQS  245 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L~L~~L~l~~~~  245 (391)
                      ..|.++++|+.+.+..|.+..+|...+..-||..|+|..|.|.++-.+ +.      +|||+.|.+.             
T Consensus        96 ~~f~nl~nLq~v~l~~N~Lt~IP~f~~~sghl~~L~L~~N~I~sv~se~L~~l~alrslDLSrN~is-------------  162 (873)
T KOG4194|consen   96 EFFYNLPNLQEVNLNKNELTRIPRFGHESGHLEKLDLRHNLISSVTSEELSALPALRSLDLSRNLIS-------------  162 (873)
T ss_pred             HHHhcCCcceeeeeccchhhhcccccccccceeEEeeeccccccccHHHHHhHhhhhhhhhhhchhh-------------
Confidence            455666666666666666666666666666666666666655543211 11      5566665555             


Q ss_pred             chhH-HhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc-
Q 041097          246 LLSK-SLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER-  323 (391)
Q Consensus       246 ~lp~-~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~-  323 (391)
                      ++|. ++..-.++++|++++.+ +..++  .-.+..+ .+|..|.|+.|+++..|..++.+|++|+.|++..|...... 
T Consensus       163 ~i~~~sfp~~~ni~~L~La~N~-It~l~--~~~F~~l-nsL~tlkLsrNrittLp~r~Fk~L~~L~~LdLnrN~irive~  238 (873)
T KOG4194|consen  163 EIPKPSFPAKVNIKKLNLASNR-ITTLE--TGHFDSL-NSLLTLKLSRNRITTLPQRSFKRLPKLESLDLNRNRIRIVEG  238 (873)
T ss_pred             cccCCCCCCCCCceEEeecccc-ccccc--ccccccc-chheeeecccCcccccCHHHhhhcchhhhhhccccceeeehh
Confidence            4442 34444566677666511 00000  0023345 55566666666666555555555666666666544432111 


Q ss_pred             --------------------ccCCC---cccccceeeeccccccccch-HhhcCCCCCCEEEeeCCc
Q 041097          324 --------------------TMGIR---AMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       324 --------------------~~~~~---~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~~~  366 (391)
                                          ....|   .+.++++|++..+ ++..+- .|+-.|++|+.|+++.+.
T Consensus       239 ltFqgL~Sl~nlklqrN~I~kL~DG~Fy~l~kme~l~L~~N-~l~~vn~g~lfgLt~L~~L~lS~Na  304 (873)
T KOG4194|consen  239 LTFQGLPSLQNLKLQRNDISKLDDGAFYGLEKMEHLNLETN-RLQAVNEGWLFGLTSLEQLDLSYNA  304 (873)
T ss_pred             hhhcCchhhhhhhhhhcCcccccCcceeeecccceeecccc-hhhhhhcccccccchhhhhccchhh
Confidence                                22334   3447778888755 455554 467789999999988744

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

Probab=98.99  E-value=9.3e-11  Score=117.24  Aligned_cols=162  Identities=23%  Similarity=0.238  Sum_probs=101.6

Q ss_pred             hHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcc----------
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHF----------  234 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L----------  234 (391)
                      ++..+..+.+|..++...|.+..+|..+.....|++|....|.++.+|....      +|||..|++..+          
T Consensus       256 lp~wi~~~~nle~l~~n~N~l~~lp~ri~~~~~L~~l~~~~nel~yip~~le~~~sL~tLdL~~N~L~~lp~~~l~v~~~  335 (1081)
T KOG0618|consen  256 LPEWIGACANLEALNANHNRLVALPLRISRITSLVSLSAAYNELEYIPPFLEGLKSLRTLDLQSNNLPSLPDNFLAVLNA  335 (1081)
T ss_pred             chHHHHhcccceEecccchhHHhhHHHHhhhhhHHHHHhhhhhhhhCCCcccccceeeeeeehhccccccchHHHhhhhH
Confidence            4456667777777777776666666666666666666666665555555444      556655555443          


Q ss_pred             ------------------------------------------------eeeEEecc--cccchhH-HhcCCCCCCEEEec
Q 041097          235 ------------------------------------------------SLASLLLY--YQSLLSK-SLCRLSCLESLKLA  263 (391)
Q Consensus       235 ------------------------------------------------~L~~L~l~--~~~~lp~-~i~~l~~L~~L~l~  263 (391)
                                                                      +||.|+++  ...++|. .+.++..|+.|+++
T Consensus       336 ~l~~ln~s~n~l~~lp~~~e~~~~~Lq~LylanN~Ltd~c~p~l~~~~hLKVLhLsyNrL~~fpas~~~kle~LeeL~LS  415 (1081)
T KOG0618|consen  336 SLNTLNVSSNKLSTLPSYEENNHAALQELYLANNHLTDSCFPVLVNFKHLKVLHLSYNRLNSFPASKLRKLEELEELNLS  415 (1081)
T ss_pred             HHHHHhhhhccccccccccchhhHHHHHHHHhcCcccccchhhhccccceeeeeecccccccCCHHHHhchHHhHHHhcc
Confidence                                                            56666665  2344553 35556666666666


Q ss_pred             CCCCCCchhhh--cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcc-cccceeeec
Q 041097          264 NESKMPRRSNI--IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAM-PKLECLIIN  339 (391)
Q Consensus       264 ~~~~lp~L~~L--lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~-~~L~~L~l~  339 (391)
                      |       ++|  +| .+..+ ..|++|....|.+...  |.+.+++.|+.++++.|..... ..+.... |+|++|+++
T Consensus       416 G-------NkL~~Lp~tva~~-~~L~tL~ahsN~l~~f--Pe~~~l~qL~~lDlS~N~L~~~-~l~~~~p~p~LkyLdlS  484 (1081)
T KOG0618|consen  416 G-------NKLTTLPDTVANL-GRLHTLRAHSNQLLSF--PELAQLPQLKVLDLSCNNLSEV-TLPEALPSPNLKYLDLS  484 (1081)
T ss_pred             c-------chhhhhhHHHHhh-hhhHHHhhcCCceeec--hhhhhcCcceEEecccchhhhh-hhhhhCCCcccceeecc
Confidence            5       222  66 66667 7777777777766553  3788889999999986554432 2333333 899999999


Q ss_pred             cccc
Q 041097          340 PYAH  343 (391)
Q Consensus       340 ~c~~  343 (391)
                      ++.+
T Consensus       485 GN~~  488 (1081)
T KOG0618|consen  485 GNTR  488 (1081)
T ss_pred             CCcc
Confidence            8864

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.86  E-value=2.2e-08  Score=102.45  Aligned_cols=79  Identities=23%  Similarity=0.235  Sum_probs=53.6

Q ss_pred             cccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc---EEEeeCCccCcc-----eeeEEecc--cccchhH
Q 041097          180 FLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK---ILRLSGNSQFHF-----SLASLLLY--YQSLLSK  249 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~---~L~l~~~~l~~L-----~L~~L~l~--~~~~lp~  249 (391)
                      +|+.|++.+|.+..+|..   +++|++|++++|.++.+|....   .|++++|.+..+     +|+.|++.  ....+|.
T Consensus       223 ~L~~L~L~~N~Lt~LP~l---p~~Lk~LdLs~N~LtsLP~lp~sL~~L~Ls~N~L~~Lp~lp~~L~~L~Ls~N~Lt~LP~  299 (788)
T PRK15387        223 HITTLVIPDNNLTSLPAL---PPELRTLEVSGNQLTSLPVLPPGLLELSIFSNPLTHLPALPSGLCKLWIFGNQLTSLPV  299 (788)
T ss_pred             CCCEEEccCCcCCCCCCC---CCCCcEEEecCCccCcccCcccccceeeccCCchhhhhhchhhcCEEECcCCccccccc
Confidence            677788888887777753   4577888888887777664433   777777766654     56667766  4445554


Q ss_pred             HhcCCCCCCEEEecC
Q 041097          250 SLCRLSCLESLKLAN  264 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~  264 (391)
                         .+++|+.|++++
T Consensus       300 ---~p~~L~~LdLS~  311 (788)
T PRK15387        300 ---LPPGLQELSVSD  311 (788)
T ss_pred             ---cccccceeECCC
Confidence               246788888876

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

Probab=98.77  E-value=2.5e-10  Score=108.74  Aligned_cols=172  Identities=23%  Similarity=0.185  Sum_probs=118.5

Q ss_pred             hHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-----EEEeeCCccCcceeeEEeccccc
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-----ILRLSGNSQFHFSLASLLLYYQS  245 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~l~~~~l~~L~L~~L~l~~~~  245 (391)
                      ++..+..+-.|..+.++.|.+..+|+.++++..|.||+++.|+++.+|..++     .|-+++|++.             
T Consensus        90 lp~~~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~lpLkvli~sNNkl~-------------  156 (722)
T KOG0532|consen   90 LPEEACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSNQLSHLPDGLCDLPLKVLIVSNNKLT-------------  156 (722)
T ss_pred             CchHHHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccchhhcCChhhhcCcceeEEEecCccc-------------
Confidence            4455556666777788888888888888888888999988888888888887     6666777777             


Q ss_pred             chhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc
Q 041097          246 LLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT  324 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~  324 (391)
                      .+|+.|+.+..|..|+.+..+    ++. +| .++.+ .+|+.|.+..|++...| .++..| .|..|++++|.. ...+
T Consensus       157 ~lp~~ig~~~tl~~ld~s~ne----i~s-lpsql~~l-~slr~l~vrRn~l~~lp-~El~~L-pLi~lDfScNki-s~iP  227 (722)
T KOG0532|consen  157 SLPEEIGLLPTLAHLDVSKNE----IQS-LPSQLGYL-TSLRDLNVRRNHLEDLP-EELCSL-PLIRLDFSCNKI-SYLP  227 (722)
T ss_pred             cCCcccccchhHHHhhhhhhh----hhh-chHHhhhH-HHHHHHHHhhhhhhhCC-HHHhCC-ceeeeecccCce-eecc
Confidence            788888877777777776622    111 45 66777 78888888777766555 555543 466777773332 2234


Q ss_pred             cCCCcccccceeeeccccccccchHhh---cCCCCCCEEEeeCC
Q 041097          325 MGIRAMPKLECLIINPYAHLKRIHEQL---WCLKSLNKLELWWP  365 (391)
Q Consensus       325 ~~~~~~~~L~~L~l~~c~~l~~lp~~~---~~l~~L~~L~l~~~  365 (391)
                      +....|..|++|-|.+++ |.+-|-.+   +...-.++|++..|
T Consensus       228 v~fr~m~~Lq~l~LenNP-LqSPPAqIC~kGkVHIFKyL~~qA~  270 (722)
T KOG0532|consen  228 VDFRKMRHLQVLQLENNP-LQSPPAQICEKGKVHIFKYLSTQAC  270 (722)
T ss_pred             hhhhhhhhheeeeeccCC-CCCChHHHHhccceeeeeeecchhc
Confidence            455677777777777665 66666554   44555667776655

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

Probab=98.74  E-value=7e-10  Score=101.36  Aligned_cols=203  Identities=24%  Similarity=0.225  Sum_probs=135.1

Q ss_pred             hhHHhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccC-CCCCccCCCCc-------EEEeeCCccCcc------
Q 041097          170 YCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNI-PSLKSLPSSRK-------ILRLSGNSQFHF------  234 (391)
Q Consensus       170 ~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~-~~i~~lp~~~~-------~L~l~~~~l~~L------  234 (391)
                      ..+..|+.++.||.|||+.|.|+ ..|..|..+..|..|-+.+ ++|+.+|+...       .|.+.-+.+..+      
T Consensus        82 iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~slqrLllNan~i~Cir~~al~  161 (498)
T KOG4237|consen   82 IPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSSLQRLLLNANHINCIRQDALR  161 (498)
T ss_pred             CChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHHHHHHhcChhhhcchhHHHHH
Confidence            45578899999999999999988 6678888888887776655 88999998876       344444443322      


Q ss_pred             ---eeeEEecc--cccchhH-HhcCCCCCCEEEecC-C---C-CCC----------------------------------
Q 041097          235 ---SLASLLLY--YQSLLSK-SLCRLSCLESLKLAN-E---S-KMP----------------------------------  269 (391)
Q Consensus       235 ---~L~~L~l~--~~~~lp~-~i~~l~~L~~L~l~~-~---~-~lp----------------------------------  269 (391)
                         +|+.|.+.  ....++. ++..+..++++++.. .   + .+|                                  
T Consensus       162 dL~~l~lLslyDn~~q~i~~~tf~~l~~i~tlhlA~np~icdCnL~wla~~~a~~~ietsgarc~~p~rl~~~Ri~q~~a  241 (498)
T KOG4237|consen  162 DLPSLSLLSLYDNKIQSICKGTFQGLAAIKTLHLAQNPFICDCNLPWLADDLAMNPIETSGARCVSPYRLYYKRINQEDA  241 (498)
T ss_pred             HhhhcchhcccchhhhhhccccccchhccchHhhhcCccccccccchhhhHHhhchhhcccceecchHHHHHHHhcccch
Confidence               55555555  4445554 566666666665543 1   0 111                                  


Q ss_pred             -----chhhh-------------cc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC-
Q 041097          270 -----RRSNI-------------IL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR-  328 (391)
Q Consensus       270 -----~L~~L-------------lp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~-  328 (391)
                           +++.+             .|  -+..+ ++|++|+|++|+++......+..+..++.|.+..|...   .++.+ 
T Consensus       242 ~kf~c~~esl~s~~~~~d~~d~~cP~~cf~~L-~~L~~lnlsnN~i~~i~~~aFe~~a~l~eL~L~~N~l~---~v~~~~  317 (498)
T KOG4237|consen  242 RKFLCSLESLPSRLSSEDFPDSICPAKCFKKL-PNLRKLNLSNNKITRIEDGAFEGAAELQELYLTRNKLE---FVSSGM  317 (498)
T ss_pred             hhhhhhHHhHHHhhccccCcCCcChHHHHhhc-ccceEeccCCCccchhhhhhhcchhhhhhhhcCcchHH---HHHHHh
Confidence                 11111             23  24567 88888888888877766677788888888888755543   23333 


Q ss_pred             --cccccceeeeccccccccc-hHhhcCCCCCCEEEeeC------CcHHH-HHHhhhcc
Q 041097          329 --AMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWW------PEPEL-RQQLREFE  377 (391)
Q Consensus       329 --~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~------~~~~l-~~~~~~~~  377 (391)
                        .+.+|+.|++.++. ++.+ |..+..+.+|.+|++-+      |.-+| .+|++..+
T Consensus       318 f~~ls~L~tL~L~~N~-it~~~~~aF~~~~~l~~l~l~~Np~~CnC~l~wl~~Wlr~~~  375 (498)
T KOG4237|consen  318 FQGLSGLKTLSLYDNQ-ITTVAPGAFQTLFSLSTLNLLSNPFNCNCRLAWLGEWLRKKS  375 (498)
T ss_pred             hhccccceeeeecCCe-eEEEecccccccceeeeeehccCcccCccchHHHHHHHhhCC
Confidence              56688999999884 5554 67788899999999875      44443 36666643

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

Probab=98.73  E-value=1.8e-08  Score=94.28  Aligned_cols=205  Identities=24%  Similarity=0.132  Sum_probs=120.6

Q ss_pred             CCccEEEEEecCCcC-CCch-hhHHhhccCCcccEEEcCCCccc-cCCcccCCCCc---ccEEEccCCCCCc--------
Q 041097          151 SFLHSLLYLTSGSQY-LDPT-YCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFL---LRYLKLNIPSLKS--------  216 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~-~~~~-~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~---L~~L~l~~~~i~~--------  216 (391)
                      +.++.+.+....... ...+ .....+..+..|+.|+++++.+. ..+..+..+.+   |++|+++++.+..        
T Consensus        51 ~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~  130 (319)
T cd00116          51 PSLKELCLSLNETGRIPRGLQSLLQGLTKGCGLQELDLSDNALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAK  130 (319)
T ss_pred             CCceEEeccccccCCcchHHHHHHHHHHhcCceeEEEccCCCCChhHHHHHHHHhccCcccEEEeeCCccchHHHHHHHH
Confidence            446666554433220 0111 23455666778888888888765 34444444444   8888888776651        


Q ss_pred             -c---CCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEe
Q 041097          217 -L---PSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSF  290 (391)
Q Consensus       217 -l---p~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l  290 (391)
                       +   |..+..|++++|.+..        .....++..+..+++|++|++.+.. .-..+.. ++ .+..+ ++|+.|++
T Consensus       131 ~l~~~~~~L~~L~L~~n~l~~--------~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~-l~~~l~~~-~~L~~L~L  200 (319)
T cd00116         131 GLKDLPPALEKLVLGRNRLEG--------ASCEALAKALRANRDLKELNLANNGIGDAGIRA-LAEGLKAN-CNLEVLDL  200 (319)
T ss_pred             HHHhCCCCceEEEcCCCcCCc--------hHHHHHHHHHHhCCCcCEEECcCCCCchHHHHH-HHHHHHhC-CCCCEEec
Confidence             1   1222355555544330        0111345667778889999987722 0000000 22 34456 79999999


Q ss_pred             ecccCCCCC----hhhhcCCCCCCEEEcCCCCCcCccccCC-C----cccccceeeecccccc-----ccchHhhcCCCC
Q 041097          291 SNIELMDDP----IPALEKLSVLQVLKLKQNLYSEERTMGI-R----AMPKLECLIINPYAHL-----KRIHEQLWCLKS  356 (391)
Q Consensus       291 ~~~~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~~~~~-~----~~~~L~~L~l~~c~~l-----~~lp~~~~~l~~  356 (391)
                      ++|.+....    ...+..+++|++|+++.|.......... .    ..+.|++|++++|. +     ..++..+..+++
T Consensus       201 ~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~l~~~~~~~l~~~~~~~~~~L~~L~l~~n~-i~~~~~~~l~~~~~~~~~  279 (319)
T cd00116         201 NNNGLTDEGASALAETLASLKSLEVLNLGDNNLTDAGAAALASALLSPNISLLTLSLSCND-ITDDGAKDLAEVLAEKES  279 (319)
T ss_pred             cCCccChHHHHHHHHHhcccCCCCEEecCCCcCchHHHHHHHHHHhccCCCceEEEccCCC-CCcHHHHHHHHHHhcCCC
Confidence            998876433    2345677889999999766554222111 1    24789999999884 4     245566677789


Q ss_pred             CCEEEeeCCc
Q 041097          357 LNKLELWWPE  366 (391)
Q Consensus       357 L~~L~l~~~~  366 (391)
                      |+++++++++
T Consensus       280 L~~l~l~~N~  289 (319)
T cd00116         280 LLELDLRGNK  289 (319)
T ss_pred             ccEEECCCCC
Confidence            9999998865

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=98.59  E-value=7.3e-08  Score=90.09  Aligned_cols=201  Identities=21%  Similarity=0.108  Sum_probs=123.0

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccC---CcccEEEcCCCccc-----cCCcccCCC-CcccEEEccCCCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMF---KFLRVLDLGSLVLI-----RYPSGIENL-FLLRYLKLNIPSLKS-----  216 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~---~~L~~L~l~~~~l~-----~~p~~i~~l-~~L~~L~l~~~~i~~-----  216 (391)
                      ++++.+.+.++....    .....+..+   +.|+.|++++|.+.     .+...+..+ .+|+.|++++|.+..     
T Consensus        81 ~~L~~L~l~~~~~~~----~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~  156 (319)
T cd00116          81 CGLQELDLSDNALGP----DGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCEA  156 (319)
T ss_pred             CceeEEEccCCCCCh----hHHHHHHHHhccCcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHHH
Confidence            577777776555421    122333333   55999999999876     233456667 899999999998772     


Q ss_pred             cCC------CCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEE
Q 041097          217 LPS------SRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHL  288 (391)
Q Consensus       217 lp~------~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L  288 (391)
                      ++.      .+.+|++++|.+..        .....++..+..+++|++|++++.. .=..... ++ .+..+ ++|+.|
T Consensus       157 ~~~~~~~~~~L~~L~l~~n~l~~--------~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~-l~~~~~~~-~~L~~L  226 (319)
T cd00116         157 LAKALRANRDLKELNLANNGIGD--------AGIRALAEGLKANCNLEVLDLNNNGLTDEGASA-LAETLASL-KSLEVL  226 (319)
T ss_pred             HHHHHHhCCCcCEEECcCCCCch--------HHHHHHHHHHHhCCCCCEEeccCCccChHHHHH-HHHHhccc-CCCCEE
Confidence            211      12266666665440        0111355667777899999998721 0000010 23 45667 899999


Q ss_pred             EeecccCCCCChhhhc-C----CCCCCEEEcCCCCCcCccc---cC-CCcccccceeeecccccccc-----chHhhcCC
Q 041097          289 SFSNIELMDDPIPALE-K----LSVLQVLKLKQNLYSEERT---MG-IRAMPKLECLIINPYAHLKR-----IHEQLWCL  354 (391)
Q Consensus       289 ~l~~~~~~~~~~~~l~-~----l~~L~~L~l~~~~~~~~~~---~~-~~~~~~L~~L~l~~c~~l~~-----lp~~~~~l  354 (391)
                      ++++|.+....+..+. .    .++|+.|++.+|.......   .. ...+++|++++++++. +..     +...+...
T Consensus       227 ~ls~n~l~~~~~~~l~~~~~~~~~~L~~L~l~~n~i~~~~~~~l~~~~~~~~~L~~l~l~~N~-l~~~~~~~~~~~~~~~  305 (319)
T cd00116         227 NLGDNNLTDAGAAALASALLSPNISLLTLSLSCNDITDDGAKDLAEVLAEKESLLELDLRGNK-FGEEGAQLLAESLLEP  305 (319)
T ss_pred             ecCCCcCchHHHHHHHHHHhccCCCceEEEccCCCCCcHHHHHHHHHHhcCCCccEEECCCCC-CcHHHHHHHHHHHhhc
Confidence            9999987653322222 2    4799999999666542211   11 1355899999999874 432     33344444


Q ss_pred             -CCCCEEEeeCCc
Q 041097          355 -KSLNKLELWWPE  366 (391)
Q Consensus       355 -~~L~~L~l~~~~  366 (391)
                       +.|+++++.+.|
T Consensus       306 ~~~~~~~~~~~~~  318 (319)
T cd00116         306 GNELESLWVKDDS  318 (319)
T ss_pred             CCchhhcccCCCC
Confidence             688888886654

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).

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.56  E-value=5.9e-08  Score=101.17  Aligned_cols=169  Identities=26%  Similarity=0.210  Sum_probs=112.0

Q ss_pred             CCcccEEEcCCCc--cccCCcc-cCCCCcccEEEccCC-CCCccCCCCc------EEEeeCCccCcceeeEEecccccch
Q 041097          178 FKFLRVLDLGSLV--LIRYPSG-IENLFLLRYLKLNIP-SLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLL  247 (391)
Q Consensus       178 ~~~L~~L~l~~~~--l~~~p~~-i~~l~~L~~L~l~~~-~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~l  247 (391)
                      .+.|++|-+.++.  +...+.. |..++.||+|+|++| ++.+||.+|+      +|+++++.+.             .+
T Consensus       544 ~~~L~tLll~~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~-------------~L  610 (889)
T KOG4658|consen  544 NPKLRTLLLQRNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGIS-------------HL  610 (889)
T ss_pred             CCccceEEEeecchhhhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCcc-------------cc
Confidence            3468888877775  5555544 677999999999966 6789999998      6666666666             99


Q ss_pred             hHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCC--CCChhhhcCCCCCCEEEcCCCCCcCccc
Q 041097          248 SKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELM--DDPIPALEKLSVLQVLKLKQNLYSEERT  324 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~  324 (391)
                      |.++++|++|.+|++...+.   +.. +| ....+ ++|++|.+......  ......+.+|.+|+.+.++..+.  ...
T Consensus       611 P~~l~~Lk~L~~Lnl~~~~~---l~~-~~~i~~~L-~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s~--~~~  683 (889)
T KOG4658|consen  611 PSGLGNLKKLIYLNLEVTGR---LES-IPGILLEL-QSLRVLRLPRSALSNDKLLLKELENLEHLENLSITISSV--LLL  683 (889)
T ss_pred             chHHHHHHhhheeccccccc---ccc-ccchhhhc-ccccEEEeeccccccchhhHHhhhcccchhhheeecchh--HhH
Confidence            99999999999999987220   000 34 34458 99999999886522  22356677778888777762222  111


Q ss_pred             cCCCcccccc----eeeeccccccccchHhhcCCCCCCEEEeeCCcH
Q 041097          325 MGIRAMPKLE----CLIINPYAHLKRIHEQLWCLKSLNKLELWWPEP  367 (391)
Q Consensus       325 ~~~~~~~~L~----~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~~  367 (391)
                      .....++.|.    .+.+.+| .....+..+..+.+|+.|.|.+|..
T Consensus       684 e~l~~~~~L~~~~~~l~~~~~-~~~~~~~~~~~l~~L~~L~i~~~~~  729 (889)
T KOG4658|consen  684 EDLLGMTRLRSLLQSLSIEGC-SKRTLISSLGSLGNLEELSILDCGI  729 (889)
T ss_pred             hhhhhhHHHHHHhHhhhhccc-ccceeecccccccCcceEEEEcCCC
Confidence            1113333333    3333333 3455666677778888888877763

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

Probab=98.47  E-value=1.9e-07  Score=78.53  Aligned_cols=42  Identities=21%  Similarity=0.145  Sum_probs=8.7

Q ss_pred             ccCCcccEEEcCCCccccCCcccC-CCCcccEEEccCCCCCccC
Q 041097          176 KMFKFLRVLDLGSLVLIRYPSGIE-NLFLLRYLKLNIPSLKSLP  218 (391)
Q Consensus       176 ~~~~~L~~L~l~~~~l~~~p~~i~-~l~~L~~L~l~~~~i~~lp  218 (391)
                      .+...++.|+|+++.|+.+ +.++ .+.+|+.|++++|.|+.++
T Consensus        16 ~n~~~~~~L~L~~n~I~~I-e~L~~~l~~L~~L~Ls~N~I~~l~   58 (175)
T PF14580_consen   16 NNPVKLRELNLRGNQISTI-ENLGATLDKLEVLDLSNNQITKLE   58 (175)
T ss_dssp             ---------------------S--TT-TT--EEE-TTS--S--T
T ss_pred             ccccccccccccccccccc-cchhhhhcCCCEEECCCCCCcccc
Confidence            3444577888888887754 3455 5677888888888777654

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

Probab=98.47  E-value=6.2e-09  Score=99.39  Aligned_cols=171  Identities=23%  Similarity=0.216  Sum_probs=122.3

Q ss_pred             hhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEeccc
Q 041097          170 YCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYY  243 (391)
Q Consensus       170 ~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~  243 (391)
                      .++..+..+..|.+++++.|++..+|..++.| -|+.|-+++|+++.+|..++      .||.+.|.+.           
T Consensus       112 ~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~l-pLkvli~sNNkl~~lp~~ig~~~tl~~ld~s~nei~-----------  179 (722)
T KOG0532|consen  112 TIPEAICNLEALTFLDLSSNQLSHLPDGLCDL-PLKVLIVSNNKLTSLPEEIGLLPTLAHLDVSKNEIQ-----------  179 (722)
T ss_pred             ecchhhhhhhHHHHhhhccchhhcCChhhhcC-cceeEEEecCccccCCcccccchhHHHhhhhhhhhh-----------
Confidence            35577788889999999999999999988877 58889999999999999998      6677777777           


Q ss_pred             ccchhHHhcCCCCCCEEEecCCCCCCchhhh--cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCc
Q 041097          244 QSLLSKSLCRLSCLESLKLANESKMPRRSNI--IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYS  320 (391)
Q Consensus       244 ~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~L--lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~  320 (391)
                        ++|+-++.+.+|+.|.+..       +++  +| .+..|  .|..|++++|++...| -.+.+|..|++|.|..|...
T Consensus       180 --slpsql~~l~slr~l~vrR-------n~l~~lp~El~~L--pLi~lDfScNkis~iP-v~fr~m~~Lq~l~LenNPLq  247 (722)
T KOG0532|consen  180 --SLPSQLGYLTSLRDLNVRR-------NHLEDLPEELCSL--PLIRLDFSCNKISYLP-VDFRKMRHLQVLQLENNPLQ  247 (722)
T ss_pred             --hchHHhhhHHHHHHHHHhh-------hhhhhCCHHHhCC--ceeeeecccCceeecc-hhhhhhhhheeeeeccCCCC
Confidence              8999999999999988876       222  66 66766  7899999999888777 56789999999999844433


Q ss_pred             Ccc--ccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCcHH
Q 041097          321 EER--TMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEPE  368 (391)
Q Consensus       321 ~~~--~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~~~  368 (391)
                      ...  +-..|...=-++|++.-|..  .  ..+.-.+.++-...+.|+.+
T Consensus       248 SPPAqIC~kGkVHIFKyL~~qA~q~--~--~a~~~~t~~RP~~~~~c~~e  293 (722)
T KOG0532|consen  248 SPPAQICEKGKVHIFKYLSTQACQS--G--GALDLYTTLRPRHFSSCHVE  293 (722)
T ss_pred             CChHHHHhccceeeeeeecchhccc--c--CCcccccccCCcccCCcchh
Confidence            210  11123333457788887731  1  11222344444445556643

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

Probab=98.46  E-value=9.9e-08  Score=84.62  Aligned_cols=188  Identities=19%  Similarity=0.177  Sum_probs=103.6

Q ss_pred             CCccEEEEEecCCcCCCc----hhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCcc----CCCCc
Q 041097          151 SFLHSLLYLTSGSQYLDP----TYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSL----PSSRK  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~----~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~l----p~~~~  222 (391)
                      ..+..|.+..........    ..++.-+..+++|+.+.++.|.-+++-.-...-+.|+.+..+.+.+...    |....
T Consensus       182 ~~l~~l~vs~~~~p~~~sni~~~~l~f~l~~f~~l~~~~~s~~~~~~i~~~~~~kptl~t~~v~~s~~~~~~~l~pe~~~  261 (490)
T KOG1259|consen  182 TQLVALVVTPVKDPIDRSNIIPNRLSFNLNAFRNLKTLKFSALSTENIVDIELLKPTLQTICVHNTTIQDVPSLLPETIL  261 (490)
T ss_pred             hheeEEEecCCCCCCccccccccccccchHHhhhhheeeeeccchhheeceeecCchhheeeeecccccccccccchhhh
Confidence            567777776554432111    1222333456677777777766443322222334566666665544322    21111


Q ss_pred             --------------------------EEEeeCCccCcc--------eeeEEecc-cccchhHHhcCCCCCCEEEecCCCC
Q 041097          223 --------------------------ILRLSGNSQFHF--------SLASLLLY-YQSLLSKSLCRLSCLESLKLANESK  267 (391)
Q Consensus       223 --------------------------~L~l~~~~l~~L--------~L~~L~l~-~~~~lp~~i~~l~~L~~L~l~~~~~  267 (391)
                                                ++|+++|.+..+        .+|.|+++ +......++..|++|+.|++++   
T Consensus       262 ~D~~~~E~~t~~G~~~~~~dTWq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i~~v~nLa~L~~L~~LDLS~---  338 (490)
T KOG1259|consen  262 ADPSGSEPSTSNGSALVSADTWQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRIRTVQNLAELPQLQLLDLSG---  338 (490)
T ss_pred             cCccCCCCCccCCceEEecchHhhhhhccccccchhhhhhhhhhccceeEEeccccceeeehhhhhcccceEeeccc---
Confidence                                      677777766643        56666666 2222334466677777777766   


Q ss_pred             CCchhhh--cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc-ccCCCcccccceeeeccccc
Q 041097          268 MPRRSNI--IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER-TMGIRAMPKLECLIINPYAH  343 (391)
Q Consensus       268 lp~L~~L--lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~-~~~~~~~~~L~~L~l~~c~~  343 (391)
                          +.|  +- |-.++ -|+++|.|..|.++.  +.-+++|=+|.+|++++|...... +-..|.+|.|+.+.+.+++ 
T Consensus       339 ----N~Ls~~~Gwh~KL-GNIKtL~La~N~iE~--LSGL~KLYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~~NP-  410 (490)
T KOG1259|consen  339 ----NLLAECVGWHLKL-GNIKTLKLAQNKIET--LSGLRKLYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLTGNP-  410 (490)
T ss_pred             ----chhHhhhhhHhhh-cCEeeeehhhhhHhh--hhhhHhhhhheeccccccchhhHHHhcccccccHHHHHhhcCCC-
Confidence                111  22 44456 677777777766544  456667777777777766554322 3334777777777777665 


Q ss_pred             cccchH
Q 041097          344 LKRIHE  349 (391)
Q Consensus       344 l~~lp~  349 (391)
                      +..+|+
T Consensus       411 l~~~vd  416 (490)
T KOG1259|consen  411 LAGSVD  416 (490)
T ss_pred             ccccch
Confidence            444443

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

Probab=98.37  E-value=3.4e-07  Score=88.44  Aligned_cols=168  Identities=27%  Similarity=0.276  Sum_probs=106.9

Q ss_pred             HhhccCCcccEEEcCCCccccCCcccCCCC-cccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEeccccc
Q 041097          173 KICKMFKFLRVLDLGSLVLIRYPSGIENLF-LLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQS  245 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~-~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~  245 (391)
                      ..+..+..++.|++.++.+..+|..++.+. +|++|+++++.+..+|..++      .|+++.|.+.             
T Consensus       110 ~~~~~~~~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~l~-------------  176 (394)
T COG4886         110 SELLELTNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLS-------------  176 (394)
T ss_pred             hhhhcccceeEEecCCcccccCccccccchhhcccccccccchhhhhhhhhccccccccccCCchhh-------------
Confidence            334455677778888888777777777774 88888888887777765544      6666666666             


Q ss_pred             chhHHhcCCCCCCEEEecCCC--CCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCc
Q 041097          246 LLSKSLCRLSCLESLKLANES--KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEE  322 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~--~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~  322 (391)
                      ++|...+.+++|+.|++++..  .       +| .+... .+|++|.+.++..... +..+.++.++..|.+..|.... 
T Consensus       177 ~l~~~~~~~~~L~~L~ls~N~i~~-------l~~~~~~~-~~L~~l~~~~N~~~~~-~~~~~~~~~l~~l~l~~n~~~~-  246 (394)
T COG4886         177 DLPKLLSNLSNLNNLDLSGNKISD-------LPPEIELL-SALEELDLSNNSIIEL-LSSLSNLKNLSGLELSNNKLED-  246 (394)
T ss_pred             hhhhhhhhhhhhhheeccCCcccc-------Cchhhhhh-hhhhhhhhcCCcceec-chhhhhcccccccccCCceeee-
Confidence            777766677777777777622  1       34 22333 5677777777643332 3556667777777655222211 


Q ss_pred             cccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCC
Q 041097          323 RTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       323 ~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~  365 (391)
                      .+-..+.+++|+.|+++++ .++.++. ++.+.+|+.|++++.
T Consensus       247 ~~~~~~~l~~l~~L~~s~n-~i~~i~~-~~~~~~l~~L~~s~n  287 (394)
T COG4886         247 LPESIGNLSNLETLDLSNN-QISSISS-LGSLTNLRELDLSGN  287 (394)
T ss_pred             ccchhccccccceeccccc-ccccccc-ccccCccCEEeccCc
Confidence            1122356667777777765 4666665 777777777777764

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

Probab=98.27  E-value=1e-06  Score=74.22  Aligned_cols=110  Identities=25%  Similarity=0.219  Sum_probs=44.8

Q ss_pred             CCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc-CCCccc
Q 041097          253 RLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM-GIRAMP  331 (391)
Q Consensus       253 ~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~-~~~~~~  331 (391)
                      .+.+|+.|++++..    +.+ ++.+..+ ++|+.|.+++|.+..........+|+|+.|+++.|.......+ ....+|
T Consensus        40 ~l~~L~~L~Ls~N~----I~~-l~~l~~L-~~L~~L~L~~N~I~~i~~~l~~~lp~L~~L~L~~N~I~~l~~l~~L~~l~  113 (175)
T PF14580_consen   40 TLDKLEVLDLSNNQ----ITK-LEGLPGL-PRLKTLDLSNNRISSISEGLDKNLPNLQELYLSNNKISDLNELEPLSSLP  113 (175)
T ss_dssp             T-TT--EEE-TTS------S---TT-----TT--EEE--SS---S-CHHHHHH-TT--EEE-TTS---SCCCCGGGGG-T
T ss_pred             hhcCCCEEECCCCC----Ccc-ccCccCh-hhhhhcccCCCCCCccccchHHhCCcCCEEECcCCcCCChHHhHHHHcCC
Confidence            45666777776522    000 2234456 7888888888877664422224578888888886665432222 235778


Q ss_pred             ccceeeeccccccccch----HhhcCCCCCCEEEeeCCcHHH
Q 041097          332 KLECLIINPYAHLKRIH----EQLWCLKSLNKLELWWPEPEL  369 (391)
Q Consensus       332 ~L~~L~l~~c~~l~~lp----~~~~~l~~L~~L~l~~~~~~l  369 (391)
                      +|+.|++.+++ +..-+    .-+..+|+|+.||-..+.++=
T Consensus       114 ~L~~L~L~~NP-v~~~~~YR~~vi~~lP~Lk~LD~~~V~~~E  154 (175)
T PF14580_consen  114 KLRVLSLEGNP-VCEKKNYRLFVIYKLPSLKVLDGQDVTEEE  154 (175)
T ss_dssp             T--EEE-TT-G-GGGSTTHHHHHHHH-TT-SEETTEETTS-B
T ss_pred             CcceeeccCCc-ccchhhHHHHHHHHcChhheeCCEEccHHH
Confidence            88888888776 23222    245788999999877666443

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

Probab=98.23  E-value=1.5e-06  Score=77.73  Aligned_cols=48  Identities=6%  Similarity=-0.109  Sum_probs=42.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCC--cChHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLP--YDADQILYDI   49 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~--~~~~~i~~~~   49 (391)
                      ++|+|.+|+|||||++.+|++...+ +|+.++|+.++.+  +++.++++.+
T Consensus        19 ~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I   68 (249)
T cd01128          19 GLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSV   68 (249)
T ss_pred             EEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHh
Confidence            4799999999999999999975444 8999999998887  8999988877

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.23  E-value=7.7e-07  Score=83.22  Aligned_cols=49  Identities=10%  Similarity=-0.039  Sum_probs=40.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCc--ChHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPY--DADQILYDII   50 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~--~~~~i~~~~~   50 (391)
                      ++|+|.+|+||||||+.||++...+ +|+.++|+.++.++  ++.++++++.
T Consensus       172 ~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIl  222 (416)
T PRK09376        172 GLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVK  222 (416)
T ss_pred             EEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhc
Confidence            4799999999999999999964444 89999999999998  5666666553

>PRK08118 topology modulation protein; Reviewed

Probab=98.21  E-value=3.1e-07  Score=77.28  Aligned_cols=61  Identities=15%  Similarity=0.128  Sum_probs=41.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccc-ccccEEE----EEEcCCCcChHHHHHHHHHhhcCCCCCCCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVK-HYFDCHA----WVQESLPYDADQILYDIIKFVMPSPEGFIP   62 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk-~~F~~~~----~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~   62 (391)
                      |.|+|++|+||||||+.+++...+. .+||...    |..++++ ....+++.++..-.|+-+|...
T Consensus         4 I~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~-~~~~~~~~~~~~~~wVidG~~~   69 (167)
T PRK08118          4 IILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVPKE-EQITVQNELVKEDEWIIDGNYG   69 (167)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcCCCHH-HHHHHHHHHhcCCCEEEeCCcc
Confidence            5799999999999999999865555 5677777    4445443 4444555555445677777543

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

Probab=98.07  E-value=2.6e-07  Score=84.91  Aligned_cols=52  Identities=17%  Similarity=0.239  Sum_probs=40.0

Q ss_pred             EEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCC-Cc-------EEEeeCCccCcc
Q 041097          183 VLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSS-RK-------ILRLSGNSQFHF  234 (391)
Q Consensus       183 ~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~-~~-------~L~l~~~~l~~L  234 (391)
                      .++|+.|+|..+| ..|+.+.+||-|+|++|.|+.+-+. +.       .++..+|+|+.|
T Consensus        71 eirLdqN~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l  131 (498)
T KOG4237|consen   71 EIRLDQNQISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDL  131 (498)
T ss_pred             EEEeccCCcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhh
Confidence            3789999999888 4678999999999999999986443 33       445555888843

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

Probab=98.02  E-value=8.6e-07  Score=82.53  Aligned_cols=40  Identities=15%  Similarity=0.185  Sum_probs=27.2

Q ss_pred             CCcccccceeeeccccccccc--hHh-----hcCCCCCCEEEeeCCcH
Q 041097          327 IRAMPKLECLIINPYAHLKRI--HEQ-----LWCLKSLNKLELWWPEP  367 (391)
Q Consensus       327 ~~~~~~L~~L~l~~c~~l~~l--p~~-----~~~l~~L~~L~l~~~~~  367 (391)
                      .+.||.|.-|.++.| ++.++  |+.     ...+++|++|++..++.
T Consensus       267 ~~~l~~L~~Lnls~t-gi~si~~~d~~s~~kt~~f~kL~~L~i~~N~I  313 (505)
T KOG3207|consen  267 VGTLPGLNQLNLSST-GIASIAEPDVESLDKTHTFPKLEYLNISENNI  313 (505)
T ss_pred             cccccchhhhhcccc-CcchhcCCCccchhhhcccccceeeecccCcc
Confidence            367888888888877 34433  433     24678899998887764

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

Probab=97.99  E-value=2e-06  Score=80.16  Aligned_cols=40  Identities=18%  Similarity=0.284  Sum_probs=18.2

Q ss_pred             cccCCCCccEEEeecccCCCCC------hhhhcCCCCCCEEEcCCCC
Q 041097          278 EYQFPPSLTHLSFSNIELMDDP------IPALEKLSVLQVLKLKQNL  318 (391)
Q Consensus       278 ~~~l~~~L~~L~l~~~~~~~~~------~~~l~~l~~L~~L~l~~~~  318 (391)
                      ++.| +.|+.|+++.|.+....      ......+++|++|++..|.
T Consensus       267 ~~~l-~~L~~Lnls~tgi~si~~~d~~s~~kt~~f~kL~~L~i~~N~  312 (505)
T KOG3207|consen  267 VGTL-PGLNQLNLSSTGIASIAEPDVESLDKTHTFPKLEYLNISENN  312 (505)
T ss_pred             cccc-cchhhhhccccCcchhcCCCccchhhhcccccceeeecccCc
Confidence            3445 55555555555443211      1112344555555555443

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

Probab=97.98  E-value=5e-06  Score=80.31  Aligned_cols=155  Identities=28%  Similarity=0.287  Sum_probs=89.2

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCC-cccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------E
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFK-FLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------I  223 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~-~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~  223 (391)
                      +.+..+.+......     .+++....+. +|+.|+++++.+..+|..++.+++|+.|+++.+++.++|...+      .
T Consensus       116 ~~l~~L~l~~n~i~-----~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~~  190 (394)
T COG4886         116 TNLTSLDLDNNNIT-----DIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNN  190 (394)
T ss_pred             cceeEEecCCcccc-----cCccccccchhhcccccccccchhhhhhhhhccccccccccCCchhhhhhhhhhhhhhhhh
Confidence            34555555444432     2334444553 8889999999998888888899999999999999988888652      7


Q ss_pred             EEeeCCccCcc--------eeeEEecc-c-ccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeec
Q 041097          224 LRLSGNSQFHF--------SLASLLLY-Y-QSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSN  292 (391)
Q Consensus       224 L~l~~~~l~~L--------~L~~L~l~-~-~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~  292 (391)
                      |++++|++..+        .|++|.+. + ....+..+.+++++..+.+.+..    +.. +| .++.+ ++++.|++.+
T Consensus       191 L~ls~N~i~~l~~~~~~~~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l~~n~----~~~-~~~~~~~l-~~l~~L~~s~  264 (394)
T COG4886         191 LDLSGNKISDLPPEIELLSALEELDLSNNSIIELLSSLSNLKNLSGLELSNNK----LED-LPESIGNL-SNLETLDLSN  264 (394)
T ss_pred             eeccCCccccCchhhhhhhhhhhhhhcCCcceecchhhhhcccccccccCCce----eee-ccchhccc-cccceecccc
Confidence            88888887732        23333333 1 23444444444444444433200    000 13 34444 5555555555


Q ss_pred             ccCCCCChhhhcCCCCCCEEEcCCCC
Q 041097          293 IELMDDPIPALEKLSVLQVLKLKQNL  318 (391)
Q Consensus       293 ~~~~~~~~~~l~~l~~L~~L~l~~~~  318 (391)
                      |.+...+  .++.+.+|+.|+++.+.
T Consensus       265 n~i~~i~--~~~~~~~l~~L~~s~n~  288 (394)
T COG4886         265 NQISSIS--SLGSLTNLRELDLSGNS  288 (394)
T ss_pred             ccccccc--cccccCccCEEeccCcc
Confidence            5554433  25555555555555333

>PLN03150 hypothetical protein; Provisional

Probab=97.93  E-value=2.4e-05  Score=79.82  Aligned_cols=99  Identities=20%  Similarity=0.217  Sum_probs=71.4

Q ss_pred             cchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc
Q 041097          245 SLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER  323 (391)
Q Consensus       245 ~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~  323 (391)
                      ..+|..+++|++|+.|++++..    +...+| .++.+ ++|+.|+|++|.+....+..+++|++|+.|+++.|...+..
T Consensus       432 g~ip~~i~~L~~L~~L~Ls~N~----l~g~iP~~~~~l-~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls~N~l~g~i  506 (623)
T PLN03150        432 GFIPNDISKLRHLQSINLSGNS----IRGNIPPSLGSI-TSLEVLDLSYNSFNGSIPESLGQLTSLRILNLNGNSLSGRV  506 (623)
T ss_pred             ccCCHHHhCCCCCCEEECCCCc----ccCcCChHHhCC-CCCCEEECCCCCCCCCCchHHhcCCCCCEEECcCCcccccC
Confidence            4788889999999999998722    100166 77888 99999999999888777788899999999999977776654


Q ss_pred             ccCCCc-ccccceeeeccccccccch
Q 041097          324 TMGIRA-MPKLECLIINPYAHLKRIH  348 (391)
Q Consensus       324 ~~~~~~-~~~L~~L~l~~c~~l~~lp  348 (391)
                      +...+. +.++..+++.++..+-..|
T Consensus       507 P~~l~~~~~~~~~l~~~~N~~lc~~p  532 (623)
T PLN03150        507 PAALGGRLLHRASFNFTDNAGLCGIP  532 (623)
T ss_pred             ChHHhhccccCceEEecCCccccCCC
Confidence            333332 3466677777665544333

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

Probab=97.91  E-value=1.5e-06  Score=77.26  Aligned_cols=127  Identities=20%  Similarity=0.225  Sum_probs=81.6

Q ss_pred             CCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcc-eeeEEecc--cccchhHHhcCC
Q 041097          178 FKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHF-SLASLLLY--YQSLLSKSLCRL  254 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L-~L~~L~l~--~~~~lp~~i~~l  254 (391)
                      .+.|..+|+++|.|..+-+++.-++.+|.|+++.|++..+-. +.          .| +|++|+++  ...++...-.+|
T Consensus       283 Wq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i~~v~n-La----------~L~~L~~LDLS~N~Ls~~~Gwh~KL  351 (490)
T KOG1259|consen  283 WQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRIRTVQN-LA----------ELPQLQLLDLSGNLLAECVGWHLKL  351 (490)
T ss_pred             HhhhhhccccccchhhhhhhhhhccceeEEeccccceeeehh-hh----------hcccceEeecccchhHhhhhhHhhh
Confidence            345566666666666666666666666666666666543221 11          01 44444444  122555556678


Q ss_pred             CCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCC-hhhhcCCCCCCEEEcCCCCCcC
Q 041097          255 SCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLKQNLYSE  321 (391)
Q Consensus       255 ~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~~~~~~~  321 (391)
                      .|.++|.+.+..    ++. +..++++ -+|..|++.+|++++.. ...+|+||.|+.|.+.+|...+
T Consensus       352 GNIKtL~La~N~----iE~-LSGL~KL-YSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~~NPl~~  413 (490)
T KOG1259|consen  352 GNIKTLKLAQNK----IET-LSGLRKL-YSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLTGNPLAG  413 (490)
T ss_pred             cCEeeeehhhhh----Hhh-hhhhHhh-hhheeccccccchhhHHHhcccccccHHHHHhhcCCCccc
Confidence            888999998711    000 2266788 89999999999887633 6789999999999999666544

>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=97.85  E-value=1.3e-05  Score=50.89  Aligned_cols=41  Identities=27%  Similarity=0.336  Sum_probs=35.5

Q ss_pred             CcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCC
Q 041097          179 KFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPS  219 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~  219 (391)
                      ++|++|++++|++..+|..+++|++|++|++++|.++.+|.
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i~~   41 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDISP   41 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBEGG
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCCcC
Confidence            47899999999999999889999999999999999987763

...

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.83  E-value=5.4e-05  Score=71.76  Aligned_cols=134  Identities=15%  Similarity=0.106  Sum_probs=81.8

Q ss_pred             HhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCC-CCCccCC----CCcEEEeeCC-ccCcceeeEEecccccc
Q 041097          173 KICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIP-SLKSLPS----SRKILRLSGN-SQFHFSLASLLLYYQSL  246 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~-~i~~lp~----~~~~L~l~~~-~l~~L~L~~L~l~~~~~  246 (391)
                      ..+..+..++.|++++|.+..+| .+.  .+|+.|.++++ .+..+|.    .+..|++++| .+.             .
T Consensus        46 ~r~~~~~~l~~L~Is~c~L~sLP-~LP--~sLtsL~Lsnc~nLtsLP~~LP~nLe~L~Ls~Cs~L~-------------s  109 (426)
T PRK15386         46 PQIEEARASGRLYIKDCDIESLP-VLP--NELTEITIENCNNLTTLPGSIPEGLEKLTVCHCPEIS-------------G  109 (426)
T ss_pred             HHHHHhcCCCEEEeCCCCCcccC-CCC--CCCcEEEccCCCCcccCCchhhhhhhheEccCccccc-------------c
Confidence            44566789999999999988888 222  26889999875 4555554    3337777666 444             5


Q ss_pred             hhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeeccc-CCCCChhhhcCC-CCCCEEEcCCCCCcCccc
Q 041097          247 LSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIE-LMDDPIPALEKL-SVLQVLKLKQNLYSEERT  324 (391)
Q Consensus       247 lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~-~~~~~~~~l~~l-~~L~~L~l~~~~~~~~~~  324 (391)
                      +|+      +|++|.+.+..        .+.+..+|++|+.|.+.++. ......+  ..+ ++|++|++..|...   .
T Consensus       110 LP~------sLe~L~L~~n~--------~~~L~~LPssLk~L~I~~~n~~~~~~lp--~~LPsSLk~L~Is~c~~i---~  170 (426)
T PRK15386        110 LPE------SVRSLEIKGSA--------TDSIKNVPNGLTSLSINSYNPENQARID--NLISPSLKTLSLTGCSNI---I  170 (426)
T ss_pred             ccc------ccceEEeCCCC--------CcccccCcchHhheeccccccccccccc--cccCCcccEEEecCCCcc---c
Confidence            665      35666665411        11345677889988885432 1111111  134 58999999843322   1


Q ss_pred             cCCCcccccceeeeccc
Q 041097          325 MGIRAMPKLECLIINPY  341 (391)
Q Consensus       325 ~~~~~~~~L~~L~l~~c  341 (391)
                      .+.+-..+|+.|.++.+
T Consensus       171 LP~~LP~SLk~L~ls~n  187 (426)
T PRK15386        171 LPEKLPESLQSITLHIE  187 (426)
T ss_pred             CcccccccCcEEEeccc
Confidence            22333458999998765

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

Probab=97.82  E-value=1.6e-05  Score=54.63  Aligned_cols=36  Identities=28%  Similarity=0.338  Sum_probs=17.1

Q ss_pred             cccccceeeeccccccccch-HhhcCCCCCCEEEeeCC
Q 041097          329 AMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWWP  365 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~~  365 (391)
                      .+++|++|++++| .++.+| ..+..+++|++|+++++
T Consensus        23 ~l~~L~~L~l~~N-~l~~i~~~~f~~l~~L~~L~l~~N   59 (61)
T PF13855_consen   23 NLPNLETLDLSNN-NLTSIPPDAFSNLPNLRYLDLSNN   59 (61)
T ss_dssp             TGTTESEEEETSS-SESEEETTTTTTSTTESEEEETSS
T ss_pred             CCCCCCEeEccCC-ccCccCHHHHcCCCCCCEEeCcCC
Confidence            3444444444433 344443 23455555555555544

...

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.76  E-value=0.00016  Score=68.58  Aligned_cols=158  Identities=17%  Similarity=0.133  Sum_probs=94.6

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCc-cccCCcccCCCCcccEEEccCC-CCCccCCCCcEEEeeC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLV-LIRYPSGIENLFLLRYLKLNIP-SLKSLPSSRKILRLSG  228 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-l~~~p~~i~~l~~L~~L~l~~~-~i~~lp~~~~~L~l~~  228 (391)
                      ..++.|.+..+...     .++   .-...|+.|.+++|. +..+|+.+.  .+|++|.+++| .+..+|..+..|+++.
T Consensus        52 ~~l~~L~Is~c~L~-----sLP---~LP~sLtsL~Lsnc~nLtsLP~~LP--~nLe~L~Ls~Cs~L~sLP~sLe~L~L~~  121 (426)
T PRK15386         52 RASGRLYIKDCDIE-----SLP---VLPNELTEITIENCNNLTTLPGSIP--EGLEKLTVCHCPEISGLPESVRSLEIKG  121 (426)
T ss_pred             cCCCEEEeCCCCCc-----ccC---CCCCCCcEEEccCCCCcccCCchhh--hhhhheEccCcccccccccccceEEeCC
Confidence            66778877766332     222   112469999998865 667787664  48999999998 8889999999888876


Q ss_pred             CccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCC
Q 041097          229 NSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSV  308 (391)
Q Consensus       229 ~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~  308 (391)
                      +...          ....+|+++      +.|.+.+........  +|  ..+|++|+.|++.+|.....| +.+.  .+
T Consensus       122 n~~~----------~L~~LPssL------k~L~I~~~n~~~~~~--lp--~~LPsSLk~L~Is~c~~i~LP-~~LP--~S  178 (426)
T PRK15386        122 SATD----------SIKNVPNGL------TSLSINSYNPENQAR--ID--NLISPSLKTLSLTGCSNIILP-EKLP--ES  178 (426)
T ss_pred             CCCc----------ccccCcchH------hheeccccccccccc--cc--cccCCcccEEEecCCCcccCc-cccc--cc
Confidence            6543          122566654      455543200000000  11  136789999999988754433 1111  48


Q ss_pred             CCEEEcCCCCCcCccccCCCcc-cccceeeeccccc
Q 041097          309 LQVLKLKQNLYSEERTMGIRAM-PKLECLIINPYAH  343 (391)
Q Consensus       309 L~~L~l~~~~~~~~~~~~~~~~-~~L~~L~l~~c~~  343 (391)
                      |+.|.++.+...... +....+ +++ .|.+.+|..
T Consensus       179 Lk~L~ls~n~~~sLe-I~~~sLP~nl-~L~f~n~lk  212 (426)
T PRK15386        179 LQSITLHIEQKTTWN-ISFEGFPDGL-DIDLQNSVL  212 (426)
T ss_pred             CcEEEeccccccccc-Cccccccccc-Eechhhhcc
Confidence            889998744322111 112233 366 788887743

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

Probab=97.67  E-value=5.8e-05  Score=51.84  Aligned_cols=40  Identities=35%  Similarity=0.406  Sum_probs=29.1

Q ss_pred             CcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccC
Q 041097          179 KFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLP  218 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp  218 (391)
                      +.|++|++++|++..+| ..+..+.+|++|++++|.+..+|
T Consensus         1 p~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~   41 (61)
T PF13855_consen    1 PNLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNLTSIP   41 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTTTGTTESEEEETSSSESEEE
T ss_pred             CcCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCccCccC
Confidence            35777888888777666 45677888888888777776655

...

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=97.62  E-value=1.5e-05  Score=72.37  Aligned_cols=88  Identities=20%  Similarity=0.192  Sum_probs=46.6

Q ss_pred             cccCCCCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCCCcCccccC-----CCcccccceeeeccccccc---
Q 041097          278 EYQFPPSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNLYSEERTMG-----IRAMPKLECLIINPYAHLK---  345 (391)
Q Consensus       278 ~~~l~~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~~~~-----~~~~~~L~~L~l~~c~~l~---  345 (391)
                      +... ++|+.|+|..|.++...    ...+..+++|+.|++.+|....+....     ....|+|+.|.+.+|. ++   
T Consensus       209 l~~~-~~LevLdl~DNtft~egs~~LakaL~s~~~L~El~l~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNe-It~da  286 (382)
T KOG1909|consen  209 LEHC-PHLEVLDLRDNTFTLEGSVALAKALSSWPHLRELNLGDCLLENEGAIAFVDALKESAPSLEVLELAGNE-ITRDA  286 (382)
T ss_pred             HHhC-CcceeeecccchhhhHHHHHHHHHhcccchheeecccccccccccHHHHHHHHhccCCCCceeccCcch-hHHHH
Confidence            3455 66666666666554432    234455566666666644443222110     1236677777766663 21   


Q ss_pred             --cchHhhcCCCCCCEEEeeCCcH
Q 041097          346 --RIHEQLWCLKSLNKLELWWPEP  367 (391)
Q Consensus       346 --~lp~~~~~l~~L~~L~l~~~~~  367 (391)
                        .+-..+...+.|++|++++|.-
T Consensus       287 ~~~la~~~~ek~dL~kLnLngN~l  310 (382)
T KOG1909|consen  287 ALALAACMAEKPDLEKLNLNGNRL  310 (382)
T ss_pred             HHHHHHHHhcchhhHHhcCCcccc
Confidence              1223345566777777776653

>PLN03150 hypothetical protein; Provisional

Probab=97.58  E-value=0.00012  Score=74.75  Aligned_cols=89  Identities=16%  Similarity=0.157  Sum_probs=47.5

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCC-C
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCL-K  355 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l-~  355 (391)
                      .++.+ ++|+.|+|++|.+....+..++.+++|+.|+++.|...+..+...+.+++|+.|++++|.--..+|..++.+ .
T Consensus       437 ~i~~L-~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls~N~l~g~iP~~l~~~~~  515 (623)
T PLN03150        437 DISKL-RHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNLNGNSLSGRVPAALGGRLL  515 (623)
T ss_pred             HHhCC-CCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEECcCCcccccCChHHhhccc
Confidence            45555 666666666665554444555666666666666555544433333556666666666554223555555432 3


Q ss_pred             CCCEEEeeCCc
Q 041097          356 SLNKLELWWPE  366 (391)
Q Consensus       356 ~L~~L~l~~~~  366 (391)
                      ++..+++.+++
T Consensus       516 ~~~~l~~~~N~  526 (623)
T PLN03150        516 HRASFNFTDNA  526 (623)
T ss_pred             cCceEEecCCc
Confidence            44455555443

>TIGR00767 rho transcription termination factor Rho

Probab=97.56  E-value=9.5e-05  Score=69.77  Aligned_cols=49  Identities=6%  Similarity=-0.072  Sum_probs=40.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCC--cChHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLP--YDADQILYDII   50 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~--~~~~~i~~~~~   50 (391)
                      ++|+|.+|+|||||++.+++... +++|+.++|+.++.+  .++.++++.+.
T Consensus       171 ~~IvG~~g~GKTtL~~~i~~~I~-~nhfdv~v~VlLIgER~~EVtDLqrsIl  221 (415)
T TIGR00767       171 GLIVAPPKAGKTVLLQKIAQAIT-RNHPEVELIVLLIDERPEEVTDMQRSVK  221 (415)
T ss_pred             EEEECCCCCChhHHHHHHHHhhc-ccCCceEEEEEEcCCCCccHHHHHHHhh
Confidence            47999999999999999999533 337998889999877  78888888764

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

>PRK07261 topology modulation protein; Provisional

Probab=97.52  E-value=0.0001  Score=62.34  Aligned_cols=35  Identities=14%  Similarity=0.163  Sum_probs=24.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccc-ccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVK-HYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk-~~F~~~~~~~   35 (391)
                      |.|+|++|+||||||+.+.....++ -+.|...|-+
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~   38 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQP   38 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEecc
Confidence            6899999999999999987632232 2345555543

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=97.31  E-value=3e-05  Score=69.18  Aligned_cols=164  Identities=21%  Similarity=0.172  Sum_probs=94.8

Q ss_pred             hHHhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccCCC-CCccCCCCcEEEeeCCccCcceeeEEecccccchh
Q 041097          171 CEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNIPS-LKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLS  248 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~~~-i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp  248 (391)
                      +...++.+..|+-|.+.|.++. .+-..|.+-.+|+.|+++.++ +++                            ..+.
T Consensus       202 l~~iLs~C~kLk~lSlEg~~LdD~I~~~iAkN~~L~~lnlsm~sG~t~----------------------------n~~~  253 (419)
T KOG2120|consen  202 LHGILSQCSKLKNLSLEGLRLDDPIVNTIAKNSNLVRLNLSMCSGFTE----------------------------NALQ  253 (419)
T ss_pred             HHHHHHHHHhhhhccccccccCcHHHHHHhccccceeeccccccccch----------------------------hHHH
Confidence            3344555566666666666655 333445555556666655542 221                            0222


Q ss_pred             HHhcCCCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeeccc--CCCCChhhh-cCCCCCCEEEcCCCCCcCcc
Q 041097          249 KSLCRLSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIE--LMDDPIPAL-EKLSVLQVLKLKQNLYSEER  323 (391)
Q Consensus       249 ~~i~~l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~--~~~~~~~~l-~~l~~L~~L~l~~~~~~~~~  323 (391)
                      --+..++.|+.|+++... .-+.    +. .+.+.+++|+.|+|+++.  +....+..+ ..+|+|..|++++|......
T Consensus       254 ll~~scs~L~~LNlsWc~l~~~~----Vtv~V~hise~l~~LNlsG~rrnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~  329 (419)
T KOG2120|consen  254 LLLSSCSRLDELNLSWCFLFTEK----VTVAVAHISETLTQLNLSGYRRNLQKSHLSTLVRRCPNLVHLDLSDSVMLKND  329 (419)
T ss_pred             HHHHhhhhHhhcCchHhhccchh----hhHHHhhhchhhhhhhhhhhHhhhhhhHHHHHHHhCCceeeeccccccccCch
Confidence            345667777777776611 0000    11 233445788888888863  223334444 46789999999855433222


Q ss_pred             c-cCCCcccccceeeeccccccccchHh---hcCCCCCCEEEeeCCcHH
Q 041097          324 T-MGIRAMPKLECLIINPYAHLKRIHEQ---LWCLKSLNKLELWWPEPE  368 (391)
Q Consensus       324 ~-~~~~~~~~L~~L~l~~c~~l~~lp~~---~~~l~~L~~L~l~~~~~~  368 (391)
                      . .+.-.|+.|++|.++.|..+  +|..   +.+.|+|.+|++.||-++
T Consensus       330 ~~~~~~kf~~L~~lSlsRCY~i--~p~~~~~l~s~psl~yLdv~g~vsd  376 (419)
T KOG2120|consen  330 CFQEFFKFNYLQHLSLSRCYDI--IPETLLELNSKPSLVYLDVFGCVSD  376 (419)
T ss_pred             HHHHHHhcchheeeehhhhcCC--ChHHeeeeccCcceEEEEeccccCc
Confidence            2 22357888999999999643  3443   367788999998887554

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.27  E-value=0.00016  Score=58.78  Aligned_cols=33  Identities=9%  Similarity=0.259  Sum_probs=26.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc-ccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY-FDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~-F~~~~~~~   35 (391)
                      |+|.||+|+||||+++.+.+  .++.. |....|++
T Consensus         8 i~ITG~PGvGKtTl~~ki~e--~L~~~g~kvgGf~t   41 (179)
T COG1618           8 IFITGRPGVGKTTLVLKIAE--KLREKGYKVGGFIT   41 (179)
T ss_pred             EEEeCCCCccHHHHHHHHHH--HHHhcCceeeeEEe
Confidence            68999999999999999998  45544 77666654

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

Probab=97.23  E-value=0.00019  Score=73.47  Aligned_cols=110  Identities=24%  Similarity=0.303  Sum_probs=61.4

Q ss_pred             hHHhcC-CCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCC-CcC-c
Q 041097          248 SKSLCR-LSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNL-YSE-E  322 (391)
Q Consensus       248 p~~i~~-l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~-~~~-~  322 (391)
                      |..+|. +|+|++|.+.+.. .-..    +- -..+| ++|..|+++++.+..  +.-++.|+||+.|.+. |. +.. .
T Consensus       140 ~~kig~~LPsL~sL~i~~~~~~~~d----F~~lc~sF-pNL~sLDIS~TnI~n--l~GIS~LknLq~L~mr-nLe~e~~~  211 (699)
T KOG3665|consen  140 PKKIGTMLPSLRSLVISGRQFDNDD----FSQLCASF-PNLRSLDISGTNISN--LSGISRLKNLQVLSMR-NLEFESYQ  211 (699)
T ss_pred             HHHHhhhCcccceEEecCceecchh----HHHHhhcc-CccceeecCCCCccC--cHHHhccccHHHHhcc-CCCCCchh
Confidence            344444 6788888887711 0000    00 22457 788888887777655  3566777777777776 22 111 1


Q ss_pred             cccCCCcccccceeeecccccccc--ch----HhhcCCCCCCEEEeeCC
Q 041097          323 RTMGIRAMPKLECLIINPYAHLKR--IH----EQLWCLKSLNKLELWWP  365 (391)
Q Consensus       323 ~~~~~~~~~~L~~L~l~~c~~l~~--lp----~~~~~l~~L~~L~l~~~  365 (391)
                      ...+.-.+.+|+.||||.-.....  +.    +.-..||+|+.||.++.
T Consensus       212 ~l~~LF~L~~L~vLDIS~~~~~~~~~ii~qYlec~~~LpeLrfLDcSgT  260 (699)
T KOG3665|consen  212 DLIDLFNLKKLRVLDISRDKNNDDTKIIEQYLECGMVLPELRFLDCSGT  260 (699)
T ss_pred             hHHHHhcccCCCeeeccccccccchHHHHHHHHhcccCccccEEecCCc
Confidence            122234677788888875543221  11    12245788888888763

>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=97.23  E-value=0.0004  Score=44.09  Aligned_cols=35  Identities=23%  Similarity=0.210  Sum_probs=27.1

Q ss_pred             cccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          331 PKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       331 ~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ++|++|+++++ +++.+|..++++++|++|++++++
T Consensus         1 ~~L~~L~l~~N-~i~~l~~~l~~l~~L~~L~l~~N~   35 (44)
T PF12799_consen    1 KNLEELDLSNN-QITDLPPELSNLPNLETLNLSNNP   35 (44)
T ss_dssp             TT-SEEEETSS-S-SSHGGHGTTCTTSSEEEETSSC
T ss_pred             CcceEEEccCC-CCcccCchHhCCCCCCEEEecCCC
Confidence            46888888877 578888778888888888888876

...

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.14  E-value=0.00022  Score=56.44  Aligned_cols=20  Identities=20%  Similarity=0.250  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|++|+||||+|+.+.+
T Consensus         2 I~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

...

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=97.13  E-value=0.00016  Score=65.85  Aligned_cols=95  Identities=25%  Similarity=0.345  Sum_probs=62.9

Q ss_pred             chhHHhcCCCCCCEEEecCCCCCCchhhh-cc-ccccCCCCccEEEeecccCCCCCh----hhh-cCCCCCCEEEcCCCC
Q 041097          246 LLSKSLCRLSCLESLKLANESKMPRRSNI-IL-AEYQFPPSLTHLSFSNIELMDDPI----PAL-EKLSVLQVLKLKQNL  318 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~~lp~L~~L-lp-~~~~l~~~L~~L~l~~~~~~~~~~----~~l-~~l~~L~~L~l~~~~  318 (391)
                      .+..++..+++|+.|++...- |..-... +. .+..+ ++|+.|++.+|.+.....    ..+ +..|+|+.|.+.+|.
T Consensus       204 al~eal~~~~~LevLdl~DNt-ft~egs~~LakaL~s~-~~L~El~l~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNe  281 (382)
T KOG1909|consen  204 ALAEALEHCPHLEVLDLRDNT-FTLEGSVALAKALSSW-PHLRELNLGDCLLENEGAIAFVDALKESAPSLEVLELAGNE  281 (382)
T ss_pred             HHHHHHHhCCcceeeecccch-hhhHHHHHHHHHhccc-chheeecccccccccccHHHHHHHHhccCCCCceeccCcch
Confidence            455678899999999998610 0000000 22 34456 799999999998876542    233 346999999999666


Q ss_pred             CcCcc----ccCCCcccccceeeecccc
Q 041097          319 YSEER----TMGIRAMPKLECLIINPYA  342 (391)
Q Consensus       319 ~~~~~----~~~~~~~~~L~~L~l~~c~  342 (391)
                      ...+.    .......|.|+.|.+++|.
T Consensus       282 It~da~~~la~~~~ek~dL~kLnLngN~  309 (382)
T KOG1909|consen  282 ITRDAALALAACMAEKPDLEKLNLNGNR  309 (382)
T ss_pred             hHHHHHHHHHHHHhcchhhHHhcCCccc
Confidence            54332    1122458999999999995

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

Probab=97.08  E-value=0.0018  Score=51.85  Aligned_cols=82  Identities=7%  Similarity=0.020  Sum_probs=53.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc-----ccEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY-----FDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQ   75 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~-----F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~   75 (391)
                      +-|+|..|+||||+++.+.++  ....     -..++|+.....-+.+.+.+.+...+.-...+  .....+....+...
T Consensus         7 ~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~l~~~~~~~   82 (131)
T PF13401_consen    7 LVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKS--RQTSDELRSLLIDA   82 (131)
T ss_dssp             EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS--TS-HHHHHHHHHHH
T ss_pred             cEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccc--cCCHHHHHHHHHHH
Confidence            358999999999999998873  2211     23556887776668889988888877543333  23356677777777


Q ss_pred             HHcCcc-EEeee
Q 041097           76 LINGGF-VGAGK   86 (391)
Q Consensus        76 L~~k~~-l~~~~   86 (391)
                      +...+. +.+.+
T Consensus        83 l~~~~~~~lviD   94 (131)
T PF13401_consen   83 LDRRRVVLLVID   94 (131)
T ss_dssp             HHHCTEEEEEEE
T ss_pred             HHhcCCeEEEEe
Confidence            766655 34443

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

Probab=96.99  E-value=0.00067  Score=65.18  Aligned_cols=47  Identities=15%  Similarity=0.018  Sum_probs=37.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILY   47 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~   47 (391)
                      |-++|++|+||||+|+.+.+.......|+.+.|+++++.+...+.+.
T Consensus       197 iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~  243 (459)
T PRK11331        197 IILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQ  243 (459)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhc
Confidence            45899999999999999987433345778899999998888777654

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=96.98  E-value=0.00023  Score=69.14  Aligned_cols=43  Identities=23%  Similarity=0.255  Sum_probs=29.4

Q ss_pred             hccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCcc
Q 041097          175 CKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSL  217 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~l  217 (391)
                      +..++.|..|++.++.+..+...+..+.+|++|++++|.|..+
T Consensus        91 l~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N~I~~i  133 (414)
T KOG0531|consen   91 LSKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFNKITKL  133 (414)
T ss_pred             cccccceeeeeccccchhhcccchhhhhcchheeccccccccc
Confidence            4566677777777777776555566777777777777766654

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

Probab=96.97  E-value=0.00065  Score=69.63  Aligned_cols=15  Identities=27%  Similarity=0.388  Sum_probs=8.8

Q ss_pred             HhcCCCCCCEEEecC
Q 041097          250 SLCRLSCLESLKLAN  264 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~  264 (391)
                      .+.+|++|+.|+++.
T Consensus       215 ~LF~L~~L~vLDIS~  229 (699)
T KOG3665|consen  215 DLFNLKKLRVLDISR  229 (699)
T ss_pred             HHhcccCCCeeeccc
Confidence            345566666666655

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.84  E-value=0.00059  Score=54.36  Aligned_cols=20  Identities=25%  Similarity=0.235  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|+||||+|+.+..
T Consensus         1 I~i~G~~GsGKtTia~~L~~   20 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAE   20 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            78999999999999999876

...

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

Probab=96.83  E-value=0.0036  Score=56.93  Aligned_cols=50  Identities=14%  Similarity=0.110  Sum_probs=32.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhh
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFV   53 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~   53 (391)
                      +.|+|..|+||||+++.+++.... ... ..+++. ....+..++++.+...+
T Consensus        46 ~~l~G~~G~GKTtl~~~l~~~l~~-~~~-~~~~~~-~~~~~~~~~l~~i~~~l   95 (269)
T TIGR03015        46 ILITGEVGAGKTTLIRNLLKRLDQ-ERV-VAAKLV-NTRVDAEDLLRMVAADF   95 (269)
T ss_pred             EEEEcCCCCCHHHHHHHHHHhcCC-CCe-EEeeee-CCCCCHHHHHHHHHHHc
Confidence            368999999999999999984221 111 122332 22356677777766554

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.

>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=96.72  E-value=0.00092  Score=58.05  Aligned_cols=26  Identities=23%  Similarity=0.194  Sum_probs=20.4

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccE
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDC   30 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~   30 (391)
                      .||++|+||||||+.+.+  +....|..
T Consensus        55 f~GPPG~GKTTLA~IIA~--e~~~~~~~   80 (233)
T PF05496_consen   55 FYGPPGLGKTTLARIIAN--ELGVNFKI   80 (233)
T ss_dssp             EESSTTSSHHHHHHHHHH--HCT--EEE
T ss_pred             EECCCccchhHHHHHHHh--ccCCCeEe
Confidence            699999999999999998  56655643

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.

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

Probab=96.63  E-value=0.00013  Score=57.82  Aligned_cols=100  Identities=21%  Similarity=0.173  Sum_probs=62.9

Q ss_pred             CcccEEEcCCCccc---cCCcccCCCCcccEEEccCCCCCccCCCCc-------EEEeeCCccCcceeeEEecccccchh
Q 041097          179 KFLRVLDLGSLVLI---RYPSGIENLFLLRYLKLNIPSLKSLPSSRK-------ILRLSGNSQFHFSLASLLLYYQSLLS  248 (391)
Q Consensus       179 ~~L~~L~l~~~~l~---~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-------~L~l~~~~l~~L~L~~L~l~~~~~lp  248 (391)
                      +.+..++|+.|++.   ..+..+....+|...++++|.++.+|+.+.       +|++++|.+.             .+|
T Consensus        27 kE~h~ldLssc~lm~i~davy~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neis-------------dvP   93 (177)
T KOG4579|consen   27 KELHFLDLSSCQLMYIADAVYMLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEIS-------------DVP   93 (177)
T ss_pred             HHhhhcccccchhhHHHHHHHHHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhh-------------hch
Confidence            34556677777655   333444555667777788877777776655       6777777777             777


Q ss_pred             HHhcCCCCCCEEEecCCCCCCchhhh--cc-ccccCCCCccEEEeecccCCCCC
Q 041097          249 KSLCRLSCLESLKLANESKMPRRSNI--IL-AEYQFPPSLTHLSFSNIELMDDP  299 (391)
Q Consensus       249 ~~i~~l~~L~~L~l~~~~~lp~L~~L--lp-~~~~l~~~L~~L~l~~~~~~~~~  299 (391)
                      ..+..|+.|+.|+++...       +  .| -+..| .++-.|+..++...+.+
T Consensus        94 eE~Aam~aLr~lNl~~N~-------l~~~p~vi~~L-~~l~~Lds~~na~~eid  139 (177)
T KOG4579|consen   94 EELAAMPALRSLNLRFNP-------LNAEPRVIAPL-IKLDMLDSPENARAEID  139 (177)
T ss_pred             HHHhhhHHhhhcccccCc-------cccchHHHHHH-HhHHHhcCCCCccccCc
Confidence            777777777777776511       1  33 33345 66666666665554444

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

Probab=96.56  E-value=0.0012  Score=57.06  Aligned_cols=20  Identities=20%  Similarity=0.263  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|.+|+||||+|+.+..
T Consensus         2 IgI~G~sgSGKTTla~~L~~   21 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLAKRLAQ   21 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999876

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 ....

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=96.54  E-value=8.3e-05  Score=73.82  Aligned_cols=125  Identities=22%  Similarity=0.215  Sum_probs=71.7

Q ss_pred             cccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCE
Q 041097          180 FLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLES  259 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~  259 (391)
                      .|.+.++++|.+..+-+++.-+.+|+.|+|+.|++..                               ...+..+++|++
T Consensus       165 ~L~~a~fsyN~L~~mD~SLqll~ale~LnLshNk~~~-------------------------------v~~Lr~l~~Lkh  213 (1096)
T KOG1859|consen  165 KLATASFSYNRLVLMDESLQLLPALESLNLSHNKFTK-------------------------------VDNLRRLPKLKH  213 (1096)
T ss_pred             hHhhhhcchhhHHhHHHHHHHHHHhhhhccchhhhhh-------------------------------hHHHHhcccccc
Confidence            3445566666666555666666666666666665432                               235666777777


Q ss_pred             EEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc-CCCcccccceeee
Q 041097          260 LKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM-GIRAMPKLECLII  338 (391)
Q Consensus       260 L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~-~~~~~~~L~~L~l  338 (391)
                      |+++.+.    |.. +|.++.---.|..|.++||.+..  +..+.+|.+|+.|++++|+..+-... ..+++..|+.|.+
T Consensus       214 LDlsyN~----L~~-vp~l~~~gc~L~~L~lrnN~l~t--L~gie~LksL~~LDlsyNll~~hseL~pLwsLs~L~~L~L  286 (1096)
T KOG1859|consen  214 LDLSYNC----LRH-VPQLSMVGCKLQLLNLRNNALTT--LRGIENLKSLYGLDLSYNLLSEHSELEPLWSLSSLIVLWL  286 (1096)
T ss_pred             cccccch----hcc-ccccchhhhhheeeeecccHHHh--hhhHHhhhhhhccchhHhhhhcchhhhHHHHHHHHHHHhh
Confidence            7776511    100 34221110247777777777655  45667777777777776665442222 2356666666666


Q ss_pred             cccc
Q 041097          339 NPYA  342 (391)
Q Consensus       339 ~~c~  342 (391)
                      .+++
T Consensus       287 eGNP  290 (1096)
T KOG1859|consen  287 EGNP  290 (1096)
T ss_pred             cCCc
Confidence            6654

>PTZ00301 uridine kinase; Provisional

Probab=96.48  E-value=0.0015  Score=56.90  Aligned_cols=20  Identities=15%  Similarity=0.313  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|.||||||+.+.+
T Consensus         6 IgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          6 IGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             EEEECCCcCCHHHHHHHHHH
Confidence            79999999999999998876

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

Probab=96.44  E-value=0.0021  Score=60.07  Aligned_cols=31  Identities=19%  Similarity=0.155  Sum_probs=25.0

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      .||++|+||||||+.+-.  ..+..|.....+.
T Consensus        53 l~GPPG~GKTTlA~liA~--~~~~~f~~~sAv~   83 (436)
T COG2256          53 LWGPPGTGKTTLARLIAG--TTNAAFEALSAVT   83 (436)
T ss_pred             EECCCCCCHHHHHHHHHH--hhCCceEEecccc
Confidence            599999999999999987  4666676666544

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=96.37  E-value=0.00019  Score=71.37  Aligned_cols=115  Identities=28%  Similarity=0.287  Sum_probs=68.6

Q ss_pred             chhHHhcCCCCCCEEEecCCCCCCchhhh--ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc
Q 041097          246 LLSKSLCRLSCLESLKLANESKMPRRSNI--ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER  323 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~~lp~L~~L--lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~  323 (391)
                      .+-+++.-++.|+.|+++.       +++  ...+..+ +.|+.|+|++|.+...|--....+ .|+.|.++.|....  
T Consensus       178 ~mD~SLqll~ale~LnLsh-------Nk~~~v~~Lr~l-~~LkhLDlsyN~L~~vp~l~~~gc-~L~~L~lrnN~l~t--  246 (1096)
T KOG1859|consen  178 LMDESLQLLPALESLNLSH-------NKFTKVDNLRRL-PKLKHLDLSYNCLRHVPQLSMVGC-KLQLLNLRNNALTT--  246 (1096)
T ss_pred             hHHHHHHHHHHhhhhccch-------hhhhhhHHHHhc-ccccccccccchhccccccchhhh-hheeeeecccHHHh--
Confidence            5566777777788887776       111  1123346 778888888877665442222232 37888887443322  


Q ss_pred             ccCCCcccccceeeecccc--ccccchHhhcCCCCCCEEEeeCCcHHHHHH
Q 041097          324 TMGIRAMPKLECLIINPYA--HLKRIHEQLWCLKSLNKLELWWPEPELRQQ  372 (391)
Q Consensus       324 ~~~~~~~~~L~~L~l~~c~--~l~~lp~~~~~l~~L~~L~l~~~~~~l~~~  372 (391)
                      .-....+.+|+.|+++++.  +.+.+- -++.|..|+.|++.|+|-....|
T Consensus       247 L~gie~LksL~~LDlsyNll~~hseL~-pLwsLs~L~~L~LeGNPl~c~p~  296 (1096)
T KOG1859|consen  247 LRGIENLKSLYGLDLSYNLLSEHSELE-PLWSLSSLIVLWLEGNPLCCAPW  296 (1096)
T ss_pred             hhhHHhhhhhhccchhHhhhhcchhhh-HHHHHHHHHHHhhcCCccccCHH
Confidence            2223467788888888653  222221 24567888999999988543333

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

Probab=96.36  E-value=0.0034  Score=50.70  Aligned_cols=21  Identities=19%  Similarity=0.238  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |-|+|..|+||||+|+.+++.
T Consensus        22 v~i~G~~G~GKT~l~~~i~~~   42 (151)
T cd00009          22 LLLYGPPGTGKTTLARAIANE   42 (151)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999984

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.

>TIGR00235 udk uridine kinase

Probab=96.36  E-value=0.0019  Score=56.40  Aligned_cols=20  Identities=25%  Similarity=0.361  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+||||||+.+..
T Consensus         9 i~I~G~sGsGKSTl~~~l~~   28 (207)
T TIGR00235         9 IGIGGGSGSGKTTVARKIYE   28 (207)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999986

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

>PRK08233 hypothetical protein; Provisional

Probab=96.36  E-value=0.0019  Score=54.92  Aligned_cols=20  Identities=15%  Similarity=0.172  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|.+|+||||+|+.+..
T Consensus         6 I~I~G~~GsGKtTla~~L~~   25 (182)
T PRK08233          6 ITIAAVSGGGKTTLTERLTH   25 (182)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            68999999999999999886

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.34  E-value=0.002  Score=56.35  Aligned_cols=20  Identities=25%  Similarity=0.421  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||||+.++.
T Consensus         9 I~I~G~sGsGKTTl~~~l~~   28 (209)
T PRK05480          9 IGIAGGSGSGKTTVASTIYE   28 (209)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999887

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.34  E-value=0.0024  Score=45.01  Aligned_cols=20  Identities=20%  Similarity=0.258  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|+||||+|+.+-+
T Consensus         2 i~i~G~~gsGKst~~~~l~~   21 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAE   21 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999776

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.

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=96.27  E-value=0.00018  Score=64.32  Aligned_cols=117  Identities=18%  Similarity=0.157  Sum_probs=77.3

Q ss_pred             chhHHhcCCCCCCEEEecCCC--CCCchhhhccccccCCCCccEEEeecccCCCCChhhhc-CC-CCCCEEEcCCCCCcC
Q 041097          246 LLSKSLCRLSCLESLKLANES--KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALE-KL-SVLQVLKLKQNLYSE  321 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~--~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~-~l-~~L~~L~l~~~~~~~  321 (391)
                      .+...|.+=.+|+.|+++..+  .-..++-   -+.++ +.|..|+|+||.+..+....+- .. ++|..|+++++--+-
T Consensus       225 ~I~~~iAkN~~L~~lnlsm~sG~t~n~~~l---l~~sc-s~L~~LNlsWc~l~~~~Vtv~V~hise~l~~LNlsG~rrnl  300 (419)
T KOG2120|consen  225 PIVNTIAKNSNLVRLNLSMCSGFTENALQL---LLSSC-SRLDELNLSWCFLFTEKVTVAVAHISETLTQLNLSGYRRNL  300 (419)
T ss_pred             HHHHHHhccccceeeccccccccchhHHHH---HHHhh-hhHhhcCchHhhccchhhhHHHhhhchhhhhhhhhhhHhhh
Confidence            566778888899999998722  1001110   34567 8999999999987765443322 22 688899998433221


Q ss_pred             -ccccC--CCcccccceeeecccccccc-chHhhcCCCCCCEEEeeCCc
Q 041097          322 -ERTMG--IRAMPKLECLIINPYAHLKR-IHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       322 -~~~~~--~~~~~~L~~L~l~~c~~l~~-lp~~~~~l~~L~~L~l~~~~  366 (391)
                       ..-++  ....|+|.+|++++|..++. .-..+-.++.|++|.++.|-
T Consensus       301 ~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSlsRCY  349 (419)
T KOG2120|consen  301 QKSHLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLSRCY  349 (419)
T ss_pred             hhhHHHHHHHhCCceeeeccccccccCchHHHHHHhcchheeeehhhhc
Confidence             01111  13688999999999987764 22345678999999998775

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.26  E-value=0.019  Score=49.95  Aligned_cols=110  Identities=15%  Similarity=0.180  Sum_probs=55.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc-ccEEEEEEcCCCcChHH----------------HHHHHHHhhcCCCCC-CCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY-FDCHAWVQESLPYDADQ----------------ILYDIIKFVMPSPEG-FIP   62 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~-F~~~~~~~vs~~~~~~~----------------i~~~~~~~~~~~~eg-~~~   62 (391)
                      |+|+|-||+||||+|..+... -++.. ++..+. .-+.++++..                ++++..........+ ++.
T Consensus         3 IaI~GKGG~GKTtiaalll~~-l~~~~~~~VLvV-DaDpd~nL~~~LGve~~~~~lg~~~e~~~k~~~a~~~~~~~~~fk   80 (255)
T COG3640           3 IAITGKGGVGKTTIAALLLKR-LLSKGGYNVLVV-DADPDSNLPEALGVEEPMKYLGGKRELLKKRTGAEPGGPPGEMFK   80 (255)
T ss_pred             EEEecCCCccHHHHHHHHHHH-HHhcCCceEEEE-eCCCCCChHHhcCCCCCCcccccHHHHHHHHhccCCCCCcccccc
Confidence            689999999999998884331 11222 333332 2233444332                333222221111222 332


Q ss_pred             CC--hHHHHHHHHHHHHcCccEEeeeccCCCceeeEEcCcchHHHHHhhccc
Q 041097           63 DN--NEATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFE  112 (391)
Q Consensus        63 ~~--~~~~~~~~~~~L~~k~~l~~~~~~~~~~~~~~~~hdl~~~~~~~~~~~  112 (391)
                      ..  ..++-+.+..+--+-.++..-+....|.--+|-|-.++|.+...+..+
T Consensus        81 ~~~~~~di~~e~~~e~~~~~LLvmGkie~~GeGC~Cp~~allR~~l~~l~~~  132 (255)
T COG3640          81 ENPLVSDLPDEYLVENGDIDLLVMGKIEEGGEGCACPMNALLRRLLRHLILN  132 (255)
T ss_pred             cCcchhhhhHHHhhhcCCccEEEeccccCCCCcccchHHHHHHHHHHHHhcc
Confidence            22  344444555444443444333333233334788888999988877655

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

Probab=96.24  E-value=0.0051  Score=56.76  Aligned_cols=25  Identities=20%  Similarity=0.124  Sum_probs=20.5

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKH   26 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~   26 (391)
                      -.||.+|+||||||+.+.+...-..
T Consensus       166 IlWGppG~GKTtlArlia~tsk~~S  190 (554)
T KOG2028|consen  166 ILWGPPGTGKTTLARLIASTSKKHS  190 (554)
T ss_pred             EEecCCCCchHHHHHHHHhhcCCCc
Confidence            4799999999999999998644333

>PRK06762 hypothetical protein; Provisional

Probab=96.24  E-value=0.0023  Score=53.73  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+.+
T Consensus         5 i~i~G~~GsGKST~A~~L~~   24 (166)
T PRK06762          5 IIIRGNSGSGKTTIAKQLQE   24 (166)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>PRK03839 putative kinase; Provisional

Probab=96.23  E-value=0.0022  Score=54.59  Aligned_cols=20  Identities=20%  Similarity=0.257  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.||.|+||||+|+.+.+
T Consensus         3 I~l~G~pGsGKsT~~~~La~   22 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAE   22 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999987

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.16  E-value=0.003  Score=53.54  Aligned_cols=32  Identities=19%  Similarity=0.259  Sum_probs=24.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWV   34 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~   34 (391)
                      |.++|+.|+||||+|+.+++  .+...+....++
T Consensus        10 I~i~G~~GsGKst~a~~l~~--~l~~~~~~~~~~   41 (176)
T PRK05541         10 IWITGLAGSGKTTIAKALYE--RLKLKYSNVIYL   41 (176)
T ss_pred             EEEEcCCCCCHHHHHHHHHH--HHHHcCCcEEEE
Confidence            57899999999999999987  455555544444

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=96.14  E-value=0.035  Score=53.58  Aligned_cols=76  Identities=12%  Similarity=0.113  Sum_probs=42.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc--cEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHHHcC
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF--DCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLING   79 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F--~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~L~~k   79 (391)
                      -|+|..|+||||+++.++++  ++...  -.++++..........++..+...+............++....+...+..+
T Consensus        59 lI~G~~GtGKT~l~~~v~~~--l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~  136 (394)
T PRK00411         59 LIYGPPGTGKTTTVKKVFEE--LEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDER  136 (394)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhc
Confidence            48999999999999999984  33222  234444444444556666666665532111111112344555555555433

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.13  E-value=0.0033  Score=56.48  Aligned_cols=154  Identities=15%  Similarity=0.074  Sum_probs=84.4

Q ss_pred             CcccEEEcCCCccccCC--cccC-CCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCC
Q 041097          179 KFLRVLDLGSLVLIRYP--SGIE-NLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLS  255 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p--~~i~-~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~  255 (391)
                      ..+..|.+.++.+...-  ..|+ ...+++.++|.+|.|+..                           .++-..+.+|+
T Consensus        45 ra~ellvln~~~id~~gd~~~~~~~~~~v~elDL~~N~iSdW---------------------------seI~~ile~lP   97 (418)
T KOG2982|consen   45 RALELLVLNGSIIDNEGDVMLFGSSVTDVKELDLTGNLISDW---------------------------SEIGAILEQLP   97 (418)
T ss_pred             cchhhheecCCCCCcchhHHHHHHHhhhhhhhhcccchhccH---------------------------HHHHHHHhcCc
Confidence            34445666666665222  2232 244566666666655533                           25566678899


Q ss_pred             CCCEEEecCCCCCCchhhhccccccCC---CCccEEEeecccCCCCCh-hhhcCCCCCCEEEcCCCCCcCcccc---CCC
Q 041097          256 CLESLKLANESKMPRRSNIILAEYQFP---PSLTHLSFSNIELMDDPI-PALEKLSVLQVLKLKQNLYSEERTM---GIR  328 (391)
Q Consensus       256 ~L~~L~l~~~~~lp~L~~Llp~~~~l~---~~L~~L~l~~~~~~~~~~-~~l~~l~~L~~L~l~~~~~~~~~~~---~~~  328 (391)
                      .|++|+++...       |-|.|..+|   .+|+.|.|.++.+...-. ..+..+|.++.|.++.|++.....-   .+.
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~  170 (418)
T KOG2982|consen   98 ALTTLNLSCNS-------LSSDIKSLPLPLKNLRVLVLNGTGLSWTQSTSSLDDLPKVTELHMSDNSLRQLNLDDNCIED  170 (418)
T ss_pred             cceEeeccCCc-------CCCccccCcccccceEEEEEcCCCCChhhhhhhhhcchhhhhhhhccchhhhhccccccccc
Confidence            99999998721       111233331   699999999888776443 4567888888888887754321111   112


Q ss_pred             cccccceeeecccccc--ccchHhhcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHL--KRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l--~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .-+.++.|....|...  ..+..--.-++++..+.+..||
T Consensus       171 ~s~~v~tlh~~~c~~~~w~~~~~l~r~Fpnv~sv~v~e~P  210 (418)
T KOG2982|consen  171 WSTEVLTLHQLPCLEQLWLNKNKLSRIFPNVNSVFVCEGP  210 (418)
T ss_pred             cchhhhhhhcCCcHHHHHHHHHhHHhhcccchheeeecCc
Confidence            3334555555555311  1111111234555555555555

>PRK06696 uridine kinase; Validated

Probab=96.10  E-value=0.0053  Score=54.26  Aligned_cols=20  Identities=30%  Similarity=0.253  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|.+|+||||+|+.+..
T Consensus        25 I~I~G~sgsGKSTlA~~L~~   44 (223)
T PRK06696         25 VAIDGITASGKTTFADELAE   44 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999887

>PRK04040 adenylate kinase; Provisional

Probab=96.10  E-value=0.003  Score=54.14  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus         5 i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          5 VVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.10  E-value=0.025  Score=45.02  Aligned_cols=21  Identities=19%  Similarity=0.246  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      +.|+|.+|+||||+|+.+...
T Consensus         5 ~~l~G~~G~GKTtl~~~l~~~   25 (148)
T smart00382        5 ILIVGPPGSGKTTLARALARE   25 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            468999999999999998873

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.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.03  E-value=0.0036  Score=54.17  Aligned_cols=20  Identities=25%  Similarity=0.323  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||||+.+..
T Consensus         2 igi~G~~GsGKSTl~~~l~~   21 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIE   21 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999866

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK00625 shikimate kinase; Provisional

Probab=96.01  E-value=0.0035  Score=52.95  Aligned_cols=20  Identities=15%  Similarity=0.124  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++||.|+||||+++.+-+
T Consensus         3 I~LiG~pGsGKTT~~k~La~   22 (173)
T PRK00625          3 IFLCGLPTVGKTSFGKALAK   22 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>PRK06217 hypothetical protein; Validated

Probab=95.97  E-value=0.0039  Score=53.27  Aligned_cols=21  Identities=14%  Similarity=0.196  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|.|+.|+||||+|+.+...
T Consensus         4 I~i~G~~GsGKSTla~~L~~~   24 (183)
T PRK06217          4 IHITGASGSGTTTLGAALAER   24 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999999998874

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.97  E-value=0.0038  Score=53.35  Aligned_cols=20  Identities=15%  Similarity=0.076  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+..
T Consensus         2 i~i~G~sgsGKTtla~~l~~   21 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQR   21 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999887

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.

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.96  E-value=0.0035  Score=53.65  Aligned_cols=20  Identities=20%  Similarity=0.292  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|=||-|+||||||+.+.+
T Consensus         7 IvI~G~IG~GKSTLa~~La~   26 (216)
T COG1428           7 IVIEGMIGAGKSTLAQALAE   26 (216)
T ss_pred             EEEecccccCHHHHHHHHHH
Confidence            68999999999999999887

>PRK06547 hypothetical protein; Provisional

Probab=95.96  E-value=0.0041  Score=52.50  Aligned_cols=20  Identities=20%  Similarity=0.187  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|+||||+|+.+.+
T Consensus        18 i~i~G~~GsGKTt~a~~l~~   37 (172)
T PRK06547         18 VLIDGRSGSGKTTLAGALAA   37 (172)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.95  E-value=0.011  Score=53.30  Aligned_cols=83  Identities=14%  Similarity=0.117  Sum_probs=41.0

Q ss_pred             CCccEEEeecccCCCCC-hhhhcCCCCCCEEEcCCCCCcCccccC-CCcccccceeeeccccccccchH------hhcCC
Q 041097          283 PSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLKQNLYSEERTMG-IRAMPKLECLIINPYAHLKRIHE------QLWCL  354 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~~~~~~~~~~~~-~~~~~~L~~L~l~~c~~l~~lp~------~~~~l  354 (391)
                      +|+..+.+..|.+.... -.....+|.+..|++..+....-.-++ ...||.|+.|.+++.+-+..+-.      -++.|
T Consensus       199 pnv~sv~v~e~PlK~~s~ek~se~~p~~~~LnL~~~~idswasvD~Ln~f~~l~dlRv~~~Pl~d~l~~~err~llIaRL  278 (418)
T KOG2982|consen  199 PNVNSVFVCEGPLKTESSEKGSEPFPSLSCLNLGANNIDSWASVDALNGFPQLVDLRVSENPLSDPLRGGERRFLLIARL  278 (418)
T ss_pred             ccchheeeecCcccchhhcccCCCCCcchhhhhcccccccHHHHHHHcCCchhheeeccCCcccccccCCcceEEEEeec
Confidence            56666666555332211 123344555556666534333221222 24667777777766653333321      23667


Q ss_pred             CCCCEEEeeCC
Q 041097          355 KSLNKLELWWP  365 (391)
Q Consensus       355 ~~L~~L~l~~~  365 (391)
                      ++++.|+=+..
T Consensus       279 ~~v~vLNGskI  289 (418)
T KOG2982|consen  279 TKVQVLNGSKI  289 (418)
T ss_pred             cceEEecCccc
Confidence            77777765443

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.95  E-value=0.0043  Score=52.81  Aligned_cols=20  Identities=25%  Similarity=0.361  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||||+.+..
T Consensus         2 i~i~G~sgsGKttla~~l~~   21 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSN   21 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999876

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.94  E-value=0.0053  Score=53.15  Aligned_cols=25  Identities=20%  Similarity=0.157  Sum_probs=21.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY   27 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~   27 (391)
                      |||-|-+|.||||+|+.+++  .++..
T Consensus        11 IgIaG~SgSGKTTva~~l~~--~~~~~   35 (218)
T COG0572          11 IGIAGGSGSGKTTVAKELSE--QLGVE   35 (218)
T ss_pred             EEEeCCCCCCHHHHHHHHHH--HhCcC
Confidence            79999999999999999988  45433

>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=95.94  E-value=0.0038  Score=55.03  Aligned_cols=20  Identities=15%  Similarity=0.233  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+..
T Consensus         2 igI~G~sGSGKTTla~~L~~   21 (220)
T cd02025           2 IGIAGSVAVGKSTTARVLQA   21 (220)
T ss_pred             EEeeCCCCCCHHHHHHHHHH
Confidence            79999999999999999876

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

>PF05729 NACHT: NACHT domain

Probab=95.94  E-value=0.0048  Score=51.30  Aligned_cols=37  Identities=8%  Similarity=0.011  Sum_probs=25.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc----ccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY----FDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~----F~~~~~~~vs   37 (391)
                      +-|+|.+|+||||+++.++++-.-...    +.+.+|+...
T Consensus         3 l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~   43 (166)
T PF05729_consen    3 LWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLR   43 (166)
T ss_pred             EEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeeh
Confidence            458999999999999998874211221    4556665544

>PRK07667 uridine kinase; Provisional

Probab=95.90  E-value=0.0044  Score=53.45  Aligned_cols=20  Identities=20%  Similarity=0.155  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|.+|+||||+|+.+..
T Consensus        20 IgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667         20 LGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999886

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.89  E-value=0.04  Score=52.51  Aligned_cols=49  Identities=14%  Similarity=0.154  Sum_probs=31.9

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccccc-------ccEEEEEEcCCCcChHHHHHHHHHhh
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHY-------FDCHAWVQESLPYDADQILYDIIKFV   53 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~-------F~~~~~~~vs~~~~~~~i~~~~~~~~   53 (391)
                      -|+|++|+||||+++.++++  +...       |. .+++..........+...+...+
T Consensus        44 ~I~G~~GtGKT~l~~~~~~~--l~~~~~~~~~~~~-~v~in~~~~~~~~~~~~~i~~~l   99 (365)
T TIGR02928        44 FIYGKTGTGKTAVTKYVMKE--LEEAAEDRDVRVV-TVYVNCQILDTLYQVLVELANQL   99 (365)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHHhhccCCceE-EEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999873  2211       22 33444333345566777766665

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.

>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=95.87  E-value=0.0045  Score=50.31  Aligned_cols=20  Identities=15%  Similarity=0.184  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++|++|+||||+|+.+..
T Consensus         2 ii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999874

...

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=95.86  E-value=0.018  Score=49.00  Aligned_cols=35  Identities=23%  Similarity=0.312  Sum_probs=19.5

Q ss_pred             cCCCCccEEEeecccCCCCC---hhhhcCCCCCCEEEcC
Q 041097          280 QFPPSLTHLSFSNIELMDDP---IPALEKLSVLQVLKLK  315 (391)
Q Consensus       280 ~l~~~L~~L~l~~~~~~~~~---~~~l~~l~~L~~L~l~  315 (391)
                      .+ +.|++|.+-+|..+...   .-.+.++|+|+.|+..
T Consensus       111 ~~-p~L~~Ltll~Npv~~k~~YR~yvl~klp~l~~LDF~  148 (233)
T KOG1644|consen  111 SC-PKLEYLTLLGNPVEHKKNYRLYVLYKLPSLRTLDFQ  148 (233)
T ss_pred             cC-CccceeeecCCchhcccCceeEEEEecCcceEeehh
Confidence            45 56666666665443322   2345566666666665

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=95.83  E-value=0.0056  Score=53.71  Aligned_cols=21  Identities=24%  Similarity=0.325  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|++|+|||||+..+..+
T Consensus         8 ivv~G~~g~GKTtl~~~l~~~   28 (219)
T COG1100           8 IVVLGDGGVGKTTLLNRLVGD   28 (219)
T ss_pred             EEEEcCCCccHHHHHHHHhcC
Confidence            689999999999999998875

>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=95.82  E-value=0.0045  Score=49.37  Aligned_cols=21  Identities=19%  Similarity=0.153  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |=|+|..|+||||+|+.+.++
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            348999999999999999983

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 ....

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.81  E-value=0.0053  Score=48.12  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=19.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|..|+|||||.+.+.+..
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            5799999999999999988743

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=95.81  E-value=0.0062  Score=50.47  Aligned_cols=22  Identities=18%  Similarity=0.280  Sum_probs=19.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |+++|.+|+|||||++.+.++.
T Consensus         3 i~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           3 VIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6899999999999999988653

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>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=95.79  E-value=0.0083  Score=53.13  Aligned_cols=35  Identities=23%  Similarity=0.398  Sum_probs=29.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |+|+|..|.|||||++.+..  .+.++|.++.+++..
T Consensus        16 ~viIG~sGSGKT~li~~lL~--~~~~~f~~I~l~t~~   50 (241)
T PF04665_consen   16 MVIIGKSGSGKTTLIKSLLY--YLRHKFDHIFLITPE   50 (241)
T ss_pred             EEEECCCCCCHHHHHHHHHH--hhcccCCEEEEEecC
Confidence            57999999999999999886  488899888877653

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

>PRK13949 shikimate kinase; Provisional

Probab=95.76  E-value=0.0053  Score=51.70  Aligned_cols=20  Identities=15%  Similarity=0.248  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+||.|+||||+++.+..
T Consensus         4 I~liG~~GsGKstl~~~La~   23 (169)
T PRK13949          4 IFLVGYMGAGKTTLGKALAR   23 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999886

>PRK13947 shikimate kinase; Provisional

Probab=95.75  E-value=0.0052  Score=51.77  Aligned_cols=20  Identities=15%  Similarity=0.313  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+||.|+||||+|+.+-+
T Consensus         4 I~l~G~~GsGKst~a~~La~   23 (171)
T PRK13947          4 IVLIGFMGTGKTTVGKRVAT   23 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57899999999999999876

>PHA00729 NTP-binding motif containing protein

Probab=95.70  E-value=0.006  Score=53.42  Aligned_cols=20  Identities=20%  Similarity=0.317  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+||||||..+.+
T Consensus        20 IlItG~pGvGKT~LA~aLa~   39 (226)
T PHA00729         20 AVIFGKQGSGKTTYALKVAR   39 (226)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.69  E-value=0.0072  Score=50.48  Aligned_cols=20  Identities=15%  Similarity=0.258  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+-.
T Consensus         1 i~l~G~~GsGKSTla~~l~~   20 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAH   20 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999876

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.

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.69  E-value=0.0015  Score=55.24  Aligned_cols=85  Identities=19%  Similarity=0.208  Sum_probs=64.8

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC--CCcccccceeeeccccccccch-HhhcCCCCCCE
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG--IRAMPKLECLIINPYAHLKRIH-EQLWCLKSLNK  359 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~--~~~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~  359 (391)
                      ..++.++-+++.+..+...-+..++.++.|.+..|.+-..-.++  .+..|+|+.|+|++|+.+++-- .++..+++|+.
T Consensus       101 ~~IeaVDAsds~I~~eGle~L~~l~~i~~l~l~~ck~~dD~~L~~l~~~~~~L~~L~lsgC~rIT~~GL~~L~~lknLr~  180 (221)
T KOG3864|consen  101 VKIEAVDASDSSIMYEGLEHLRDLRSIKSLSLANCKYFDDWCLERLGGLAPSLQDLDLSGCPRITDGGLACLLKLKNLRR  180 (221)
T ss_pred             ceEEEEecCCchHHHHHHHHHhccchhhhheeccccchhhHHHHHhcccccchheeeccCCCeechhHHHHHHHhhhhHH
Confidence            46788888888887777788889999999999844443322221  1478899999999999887543 47789999999


Q ss_pred             EEeeCCcH
Q 041097          360 LELWWPEP  367 (391)
Q Consensus       360 L~l~~~~~  367 (391)
                      |.|.++|.
T Consensus       181 L~l~~l~~  188 (221)
T KOG3864|consen  181 LHLYDLPY  188 (221)
T ss_pred             HHhcCchh
Confidence            99998874

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=95.68  E-value=0.0027  Score=61.75  Aligned_cols=127  Identities=21%  Similarity=0.251  Sum_probs=81.6

Q ss_pred             cCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCC
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSC  256 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~  256 (391)
                      .+..++.+.+..+.+......++.+.+|.+|++.++.|+.+.                              ..+..|++
T Consensus        70 ~l~~l~~l~l~~n~i~~~~~~l~~~~~l~~l~l~~n~i~~i~------------------------------~~l~~~~~  119 (414)
T KOG0531|consen   70 SLTSLKELNLRQNLIAKILNHLSKLKSLEALDLYDNKIEKIE------------------------------NLLSSLVN  119 (414)
T ss_pred             HhHhHHhhccchhhhhhhhcccccccceeeeeccccchhhcc------------------------------cchhhhhc
Confidence            344555555666776665556777888888888888776543                              12556777


Q ss_pred             CCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc-cCCCcccccce
Q 041097          257 LESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT-MGIRAMPKLEC  335 (391)
Q Consensus       257 L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~-~~~~~~~~L~~  335 (391)
                      |++|++++.. +..    +..+..+ +.|+.|++.+|.+..  ...+..+++|+.+++.+|....... + ...+.+|+.
T Consensus       120 L~~L~ls~N~-I~~----i~~l~~l-~~L~~L~l~~N~i~~--~~~~~~l~~L~~l~l~~n~i~~ie~~~-~~~~~~l~~  190 (414)
T KOG0531|consen  120 LQVLDLSFNK-ITK----LEGLSTL-TLLKELNLSGNLISD--ISGLESLKSLKLLDLSYNRIVDIENDE-LSELISLEE  190 (414)
T ss_pred             chheeccccc-ccc----ccchhhc-cchhhheeccCcchh--ccCCccchhhhcccCCcchhhhhhhhh-hhhccchHH
Confidence            8888887621 000    1244566 778888888887765  3455557888888888555443211 1 367778888


Q ss_pred             eeecccc
Q 041097          336 LIINPYA  342 (391)
Q Consensus       336 L~l~~c~  342 (391)
                      +.+.++.
T Consensus       191 l~l~~n~  197 (414)
T KOG0531|consen  191 LDLGGNS  197 (414)
T ss_pred             HhccCCc
Confidence            8888774

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.68  E-value=0.0072  Score=53.86  Aligned_cols=30  Identities=20%  Similarity=0.162  Sum_probs=20.6

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccEEEEE
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWV   34 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~   34 (391)
                      |+||+|+||||+++.+.+  .+...-..++.+
T Consensus         1 ViGpaGSGKTT~~~~~~~--~~~~~~~~~~~v   30 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSE--WLESNGRDVYIV   30 (238)
T ss_dssp             -EESTTSSHHHHHHHHHH--HHTTT-S-EEEE
T ss_pred             CCCCCCCCHHHHHHHHHH--HHHhccCCceEE
Confidence            799999999999999987  344443444444

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.66  E-value=0.0059  Score=51.45  Aligned_cols=20  Identities=10%  Similarity=0.212  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|++|+||||+|+.+..
T Consensus         7 i~l~G~~GsGKstla~~La~   26 (175)
T PRK00131          7 IVLIGFMGAGKSTIGRLLAK   26 (175)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            56899999999999999886

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.65  E-value=0.006  Score=53.91  Aligned_cols=35  Identities=9%  Similarity=0.108  Sum_probs=24.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |-|+|..|+||||||+.+++.  .......+.++..+
T Consensus        41 lll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~~   75 (226)
T TIGR03420        41 LYLWGESGSGKSHLLQAACAA--AEERGKSAIYLPLA   75 (226)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeHH
Confidence            348999999999999999873  22223344555443

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.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=95.65  E-value=0.0067  Score=49.99  Aligned_cols=20  Identities=15%  Similarity=0.237  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus         2 i~l~G~~GsGKstla~~la~   21 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAK   21 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999876

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.

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

Probab=95.64  E-value=0.0079  Score=50.52  Aligned_cols=33  Identities=12%  Similarity=0.181  Sum_probs=24.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccc-cccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKH-YFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~-~F~~~~~~~   35 (391)
                      |-|.|..|+|||||++.+++  .++. -+....|++
T Consensus         2 i~iTG~pG~GKTTll~k~i~--~l~~~~~~v~Gf~t   35 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIE--ELKKKGLPVGGFYT   35 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHH--HHHHTCGGEEEEEE
T ss_pred             EEEECcCCCCHHHHHHHHHH--HhhccCCccceEEe
Confidence            46899999999999999987  4543 456666665

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

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.62  E-value=0.007  Score=50.11  Aligned_cols=19  Identities=21%  Similarity=0.263  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |.|.|-+|+||||.++.+-
T Consensus         3 I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           3 IAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             EEEeCCCCCchHHHHHHHH
Confidence            6899999999999999974

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

Probab=95.61  E-value=0.017  Score=46.70  Aligned_cols=40  Identities=15%  Similarity=0.127  Sum_probs=29.8

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccccccc-EEEEEEcCCCcChHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFD-CHAWVQESLPYDADQILY   47 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~-~~~~~~vs~~~~~~~i~~   47 (391)
                      =++|..|+|||+||+.+..  .+    . .+..+.++...+.++++.
T Consensus         3 lL~G~~G~GKt~l~~~la~--~~----~~~~~~i~~~~~~~~~dl~g   43 (139)
T PF07728_consen    3 LLVGPPGTGKTTLARELAA--LL----GRPVIRINCSSDTTEEDLIG   43 (139)
T ss_dssp             EEEESSSSSHHHHHHHHHH--HH----TCEEEEEE-TTTSTHHHHHC
T ss_pred             EEECCCCCCHHHHHHHHHH--Hh----hcceEEEEecccccccccee
Confidence            4799999999999999886  22    3 444567788788887655

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.52  E-value=0.0077  Score=51.18  Aligned_cols=21  Identities=19%  Similarity=0.205  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|+.|+||||+++.+...
T Consensus         4 ~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         4 IYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            579999999999999998763

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.49  E-value=0.01  Score=48.12  Aligned_cols=20  Identities=10%  Similarity=0.245  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         2 i~i~GpsGsGKstl~~~L~~   21 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLE   21 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999987

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.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=95.46  E-value=0.008  Score=51.94  Aligned_cols=19  Identities=21%  Similarity=0.246  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |||+|+.|+||||.|+.+-
T Consensus         5 IglTG~igsGKStva~~~~   23 (201)
T COG0237           5 IGLTGGIGSGKSTVAKILA   23 (201)
T ss_pred             EEEecCCCCCHHHHHHHHH
Confidence            7999999999999999854

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

Probab=95.43  E-value=0.011  Score=45.60  Aligned_cols=20  Identities=20%  Similarity=0.318  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |=|+|.+|+|||++|+.+..
T Consensus         1 I~i~G~~G~GKS~l~~~l~~   20 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAK   20 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999765

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

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=95.42  E-value=0.009  Score=49.09  Aligned_cols=20  Identities=15%  Similarity=0.219  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+.+
T Consensus         2 i~l~G~~GsGKST~a~~l~~   21 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAE   21 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHh
Confidence            46899999999999999876

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK13946 shikimate kinase; Provisional

Probab=95.40  E-value=0.0088  Score=51.16  Aligned_cols=20  Identities=10%  Similarity=0.253  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++||.|+||||+++.+.+
T Consensus        13 I~l~G~~GsGKsti~~~LA~   32 (184)
T PRK13946         13 VVLVGLMGAGKSTVGRRLAT   32 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999886

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.40  E-value=0.0087  Score=51.15  Aligned_cols=20  Identities=10%  Similarity=0.131  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+||||+|+.+..
T Consensus         6 i~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         6 IFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

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.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.39  E-value=0.0092  Score=50.53  Aligned_cols=20  Identities=20%  Similarity=0.076  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus         7 i~~~G~~GsGKST~a~~la~   26 (175)
T PRK00889          7 VWFTGLSGAGKTTIARALAE   26 (175)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999886

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.37  E-value=0.0097  Score=48.51  Aligned_cols=20  Identities=20%  Similarity=0.162  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+||||+|+.+-.
T Consensus         2 I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999875

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=95.36  E-value=0.0098  Score=46.47  Aligned_cols=21  Identities=10%  Similarity=0.210  Sum_probs=19.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|.|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            689999999999999999974

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.35  E-value=0.009  Score=54.71  Aligned_cols=20  Identities=15%  Similarity=0.230  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+-.
T Consensus        65 IGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        65 ISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999987643

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK06893 DNA replication initiation factor; Validated

Probab=95.33  E-value=0.0093  Score=52.96  Aligned_cols=34  Identities=6%  Similarity=-0.045  Sum_probs=24.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      -+||..|+|||+||+++.+.  +......+.|++.+
T Consensus        43 ~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~~   76 (229)
T PRK06893         43 YIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPLS   76 (229)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeHH
Confidence            48999999999999999984  32222344566553

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.32  E-value=0.0075  Score=53.50  Aligned_cols=21  Identities=29%  Similarity=0.338  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |-|+||+|.||||+.|.++..
T Consensus        22 ilVvGMAGSGKTTF~QrL~~h   42 (366)
T KOG1532|consen   22 ILVVGMAGSGKTTFMQRLNSH   42 (366)
T ss_pred             EEEEecCCCCchhHHHHHHHH
Confidence            458999999999999999873

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.31  E-value=0.01  Score=50.40  Aligned_cols=20  Identities=10%  Similarity=0.282  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||||+.+..
T Consensus         4 i~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         4 IVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            57999999999999999987

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=95.30  E-value=0.01  Score=50.48  Aligned_cols=20  Identities=20%  Similarity=0.237  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|+.|+||||+++.+-+
T Consensus         2 i~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999764

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>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=95.30  E-value=0.0085  Score=47.35  Aligned_cols=26  Identities=19%  Similarity=0.156  Sum_probs=17.0

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccccccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFD   29 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~   29 (391)
                      =++|.+|+||||+|+.+..  .+...|.
T Consensus         3 Lleg~PG~GKT~la~~lA~--~~~~~f~   28 (131)
T PF07726_consen    3 LLEGVPGVGKTTLAKALAR--SLGLSFK   28 (131)
T ss_dssp             EEES---HHHHHHHHHHHH--HTT--EE
T ss_pred             eeECCCccHHHHHHHHHHH--HcCCcee
Confidence            3799999999999999887  4555564

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.29  E-value=0.01  Score=51.43  Aligned_cols=20  Identities=15%  Similarity=0.059  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus        27 i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         27 LWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>PRK13695 putative NTPase; Provisional

Probab=95.27  E-value=0.012  Score=49.88  Aligned_cols=33  Identities=12%  Similarity=0.237  Sum_probs=24.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccc-ccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVK-HYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk-~~F~~~~~~~   35 (391)
                      |+|+|.+|+|||||++.+++.  ++ .-|..+.|++
T Consensus         3 i~ltG~~G~GKTTll~~i~~~--l~~~G~~~~g~~~   36 (174)
T PRK13695          3 IGITGPPGVGKTTLVLKIAEL--LKEEGYKVGGFYT   36 (174)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEc
Confidence            589999999999999998873  33 2344455554

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=95.26  E-value=0.017  Score=51.33  Aligned_cols=20  Identities=15%  Similarity=0.175  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|.|||||++.+..
T Consensus        36 igi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         36 VGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999886

>PF13173 AAA_14: AAA domain

Probab=95.22  E-value=0.0094  Score=47.63  Aligned_cols=21  Identities=14%  Similarity=0.230  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      +.|.|.-|+||||+++.++.+
T Consensus         5 ~~l~G~R~vGKTtll~~~~~~   25 (128)
T PF13173_consen    5 IILTGPRGVGKTTLLKQLAKD   25 (128)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999998863

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

Probab=95.22  E-value=0.015  Score=47.24  Aligned_cols=36  Identities=11%  Similarity=0.092  Sum_probs=25.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccc-ccccEEEEEEcCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVK-HYFDCHAWVQESL   38 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk-~~F~~~~~~~vs~   38 (391)
                      |+|+|.-|+|||||++.+.+  +++ .-....++.....
T Consensus         3 v~VvG~~~sGKTTl~~~Li~--~l~~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    3 VQVVGPKNSGKTTLIRKLIN--ELKRRGYRVAVIKHTDH   39 (140)
T ss_dssp             EEEEESTTSSHHHHHHHHHH--HHHHTT--EEEEEE-ST
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHhHcCCceEEEEEccC
Confidence            58999999999999999998  454 4444554555443

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.22  E-value=0.011  Score=49.95  Aligned_cols=20  Identities=10%  Similarity=0.285  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+.+
T Consensus         7 I~liG~~GaGKStl~~~La~   26 (172)
T PRK05057          7 IFLVGPMGAGKSTIGRQLAQ   26 (172)
T ss_pred             EEEECCCCcCHHHHHHHHHH
Confidence            57999999999999999876

>PRK14530 adenylate kinase; Provisional

Probab=95.21  E-value=0.011  Score=51.97  Aligned_cols=20  Identities=15%  Similarity=0.189  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|++|+||||+|+.+..
T Consensus         6 I~i~G~pGsGKsT~~~~La~   25 (215)
T PRK14530          6 ILLLGAPGAGKGTQSSNLAE   25 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999865

>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=95.21  E-value=0.0093  Score=31.49  Aligned_cols=22  Identities=27%  Similarity=0.276  Sum_probs=17.6

Q ss_pred             ccceeeeccccccccchHhhcCC
Q 041097          332 KLECLIINPYAHLKRIHEQLWCL  354 (391)
Q Consensus       332 ~L~~L~l~~c~~l~~lp~~~~~l  354 (391)
                      +|++|++++| +++.+|.++++|
T Consensus         1 ~L~~Ldls~n-~l~~ip~~~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGN-NLTSIPSSFSNL   22 (22)
T ss_dssp             TESEEEETSS-EESEEGTTTTT-
T ss_pred             CccEEECCCC-cCEeCChhhcCC
Confidence            5899999999 788999887653

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 ....

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.18  E-value=0.012  Score=50.43  Aligned_cols=21  Identities=14%  Similarity=0.181  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|+.|+|||||++.+...
T Consensus         5 i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          5 IWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            579999999999999999763

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.16  E-value=0.016  Score=48.02  Aligned_cols=20  Identities=10%  Similarity=0.169  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         2 i~i~G~~gsGKTtl~~~l~~   21 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVK   21 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999987

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

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.15  E-value=0.018  Score=47.62  Aligned_cols=37  Identities=16%  Similarity=0.100  Sum_probs=26.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLP   39 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~   39 (391)
                      +.|+|..|+||||+++.+...  ....-..+.|+.....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e~~   38 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIEEE   38 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECCcc
Confidence            469999999999999998762  3322346677665544

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.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.14  E-value=0.011  Score=51.29  Aligned_cols=20  Identities=10%  Similarity=0.210  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||||+.+..
T Consensus         8 i~i~G~sGsGKstl~~~l~~   27 (205)
T PRK00300          8 IVLSGPSGAGKSTLVKALLE   27 (205)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            68999999999999999987

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=95.14  E-value=0.012  Score=50.07  Aligned_cols=20  Identities=25%  Similarity=0.197  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|++|+||||+|+.+..
T Consensus         2 i~i~G~pGsGKst~a~~la~   21 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVE   21 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

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.

>TIGR01287 nifH nitrogenase iron protein

Probab=95.13  E-value=0.012  Score=53.80  Aligned_cols=20  Identities=15%  Similarity=0.263  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-|||||||++..+..
T Consensus         3 ia~~gKGGVGKTT~a~nLA~   22 (275)
T TIGR01287         3 IAIYGKGGIGKSTTTQNIAA   22 (275)
T ss_pred             eEEeCCCcCcHHHHHHHHHH
Confidence            68999999999998877643

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PRK13975 thymidylate kinase; Provisional

Probab=95.12  E-value=0.011  Score=50.97  Aligned_cols=20  Identities=20%  Similarity=-0.019  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+.+
T Consensus         5 I~ieG~~GsGKtT~~~~L~~   24 (196)
T PRK13975          5 IVFEGIDGSGKTTQAKLLAE   24 (196)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999887

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.12  E-value=0.028  Score=49.01  Aligned_cols=43  Identities=7%  Similarity=0.007  Sum_probs=31.3

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILY   47 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~   47 (391)
                      -|+|.+|+||||++..+..+  ....-..++|+.... |+.+++.+
T Consensus        16 ~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        16 QIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC-CCHHHHHH
Confidence            58999999999999987653  222345788887654 77776555

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

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=95.09  E-value=0.034  Score=51.68  Aligned_cols=74  Identities=12%  Similarity=0.011  Sum_probs=44.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHH-HhhcCCCCCCCCC--ChHHHHHHHHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDII-KFVMPSPEGFIPD--NNEATVEKYLEQLI   77 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~-~~~~~~~eg~~~~--~~~~~~~~~~~~L~   77 (391)
                      -+.|.|||||||.|-+.--  .+-........+.++...+..+++...+ ..-..+++.+...  +.+...++++.++.
T Consensus         6 ~f~GKGGVGKTT~aaA~A~--~lA~~g~kvLlvStDPAhsL~d~f~~elg~~~~~I~~nL~a~eiD~~~~l~ey~~~v~   82 (322)
T COG0003           6 FFTGKGGVGKTTIAAATAV--KLAESGKKVLLVSTDPAHSLGDVFDLELGHDPRKVGPNLDALELDPEKALEEYWDEVK   82 (322)
T ss_pred             EEecCCcccHHHHHHHHHH--HHHHcCCcEEEEEeCCCCchHhhhccccCCchhhcCCCCceeeecHHHHHHHHHHHHH
Confidence            3689999999999998322  1223335677888887777777666411 1112333332221  25666667776665

>PRK06620 hypothetical protein; Validated

Probab=95.08  E-value=0.014  Score=51.20  Aligned_cols=20  Identities=10%  Similarity=-0.107  Sum_probs=18.0

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      =|||..|+|||+|++.+.+.
T Consensus        48 ~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         48 LIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             EEECCCCCCHHHHHHHHHhc
Confidence            38999999999999998874

>cd01876 YihA_EngB The YihA (EngB) subfamily

Probab=95.07  E-value=0.015  Score=48.19  Aligned_cols=20  Identities=10%  Similarity=0.147  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||.+.+.+
T Consensus         2 i~l~G~~g~GKTtL~~~l~~   21 (170)
T cd01876           2 IAFAGRSNVGKSSLINALTN   21 (170)
T ss_pred             EEEEcCCCCCHHHHHHHHhc
Confidence            68999999999999999984

This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.

>cd01862 Rab7 Rab7 subfamily

Probab=95.05  E-value=0.014  Score=48.75  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||++.+.++
T Consensus         3 i~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           3 VIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            689999999999999998764

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>PRK13948 shikimate kinase; Provisional

Probab=95.03  E-value=0.013  Score=49.87  Aligned_cols=20  Identities=20%  Similarity=0.204  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++||.|+||||+++.+-+
T Consensus        13 I~LiG~~GsGKSTvg~~La~   32 (182)
T PRK13948         13 VALAGFMGTGKSRIGWELSR   32 (182)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=95.03  E-value=0.017  Score=47.98  Aligned_cols=22  Identities=9%  Similarity=0.212  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|.+|+|||||+..+.++.
T Consensus         3 i~~vG~~~vGKTsli~~l~~~~   24 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEGR   24 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5799999999999999987753

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>PRK06761 hypothetical protein; Provisional

Probab=95.02  E-value=0.029  Score=51.09  Aligned_cols=21  Identities=14%  Similarity=0.086  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|.|+.|+||||+++.+.+.
T Consensus         6 IvI~G~~GsGKTTla~~L~~~   26 (282)
T PRK06761          6 IIIEGLPGFGKSTTAKMLNDI   26 (282)
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            568999999999999999983

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=95.00  E-value=0.014  Score=47.08  Aligned_cols=20  Identities=15%  Similarity=0.233  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||.+.+..
T Consensus        14 ~~i~G~nGsGKStLl~~l~g   33 (137)
T PF00005_consen   14 VAIVGPNGSGKSTLLKALAG   33 (137)
T ss_dssp             EEEEESTTSSHHHHHHHHTT
T ss_pred             EEEEccCCCccccceeeecc
Confidence            58999999999999999987

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

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

Probab=94.99  E-value=0.03  Score=50.61  Aligned_cols=39  Identities=10%  Similarity=0.178  Sum_probs=29.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc-cEEEEEEcCCCcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF-DCHAWVQESLPYD   41 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F-~~~~~~~vs~~~~   41 (391)
                      ++|.|-.|+||||||+.++++  ++..| +.|+++-+.+...
T Consensus        72 ~~If~~~G~GKTtLa~~i~~~--i~~~~~~~~V~~~iGer~~  111 (274)
T cd01133          72 IGLFGGAGVGKTVLIMELINN--IAKAHGGYSVFAGVGERTR  111 (274)
T ss_pred             EEEecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcH
Confidence            589999999999999999984  55455 4666766665433

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.

>PRK12377 putative replication protein; Provisional

Probab=94.97  E-value=0.013  Score=52.52  Aligned_cols=35  Identities=14%  Similarity=-0.049  Sum_probs=25.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      +.++|..|+|||+||.++.+  .+.....-+.++++.
T Consensus       104 l~l~G~~GtGKThLa~AIa~--~l~~~g~~v~~i~~~  138 (248)
T PRK12377        104 FVFSGKPGTGKNHLAAAIGN--RLLAKGRSVIVVTVP  138 (248)
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHHcCCCeEEEEHH
Confidence            35899999999999999998  344333445665543

>cd04155 Arl3 Arl3 subfamily

Probab=94.96  E-value=0.015  Score=48.85  Aligned_cols=21  Identities=19%  Similarity=0.134  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||++.+.+.
T Consensus        17 v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          17 ILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             EEEEccCCCCHHHHHHHHhcC
Confidence            689999999999999999874

Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=94.95  E-value=0.015  Score=48.91  Aligned_cols=20  Identities=20%  Similarity=0.227  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         9 i~ivG~sgsGKTTLi~~li~   28 (173)
T PRK10751          9 LAIAAWSGTGKTTLLKKLIP   28 (173)
T ss_pred             EEEECCCCChHHHHHHHHHH
Confidence            58999999999999999886

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.94  E-value=0.003  Score=56.21  Aligned_cols=94  Identities=23%  Similarity=0.287  Sum_probs=61.0

Q ss_pred             ccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc-ccCCCcccccceeeeccccccccchH-----hhc
Q 041097          279 YQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER-TMGIRAMPKLECLIINPYAHLKRIHE-----QLW  352 (391)
Q Consensus       279 ~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~-~~~~~~~~~L~~L~l~~c~~l~~lp~-----~~~  352 (391)
                      .++ +.|+.|.|+-|++..  +..+..+++|+.|+|..|+..... ......+|+|+.|-|..++--..-+.     .+.
T Consensus        38 ~kM-p~lEVLsLSvNkIss--L~pl~rCtrLkElYLRkN~I~sldEL~YLknlpsLr~LWL~ENPCc~~ag~nYR~~VLR  114 (388)
T KOG2123|consen   38 EKM-PLLEVLSLSVNKISS--LAPLQRCTRLKELYLRKNCIESLDELEYLKNLPSLRTLWLDENPCCGEAGQNYRRKVLR  114 (388)
T ss_pred             Hhc-ccceeEEeecccccc--chhHHHHHHHHHHHHHhcccccHHHHHHHhcCchhhhHhhccCCcccccchhHHHHHHH
Confidence            356 778888888877665  556677788888888777765322 22235788888888876543333332     346


Q ss_pred             CCCCCCEEEeeCCcHH-HHHHhhh
Q 041097          353 CLKSLNKLELWWPEPE-LRQQLRE  375 (391)
Q Consensus       353 ~l~~L~~L~l~~~~~~-l~~~~~~  375 (391)
                      .||+|++|+=....++ +++-++.
T Consensus       115 ~LPnLkKLDnv~VteeEle~ALr~  138 (388)
T KOG2123|consen  115 VLPNLKKLDNVPVTEEELEEALRD  138 (388)
T ss_pred             HcccchhccCccccHHHHHHHHhc
Confidence            7888888887666655 4444443

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=94.93  E-value=0.018  Score=47.81  Aligned_cols=21  Identities=29%  Similarity=0.388  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.+.
T Consensus         3 i~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        3 LVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=94.92  E-value=0.017  Score=46.99  Aligned_cols=22  Identities=5%  Similarity=0.228  Sum_probs=19.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |+|+|..|+|||||+..+..+.
T Consensus         4 i~~~G~~~~GKstl~~~l~~~~   25 (161)
T TIGR00231         4 IVIVGDPNVGKSTLLNRLLGNK   25 (161)
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6899999999999999987754

This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

>PRK05439 pantothenate kinase; Provisional

Probab=94.91  E-value=0.014  Score=53.81  Aligned_cols=20  Identities=15%  Similarity=0.218  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+..
T Consensus        89 IgIaG~~gsGKSTla~~L~~  108 (311)
T PRK05439         89 IGIAGSVAVGKSTTARLLQA  108 (311)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999865

>PRK08084 DNA replication initiation factor; Provisional

Probab=94.90  E-value=0.016  Score=51.72  Aligned_cols=34  Identities=9%  Similarity=0.085  Sum_probs=24.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      -|||..|+|||+|++++++.  +...-..+.|++++
T Consensus        49 ~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~~   82 (235)
T PRK08084         49 YLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPLD   82 (235)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEHH
Confidence            58999999999999999873  22222345566654

>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases

Probab=94.90  E-value=0.017  Score=47.64  Aligned_cols=22  Identities=18%  Similarity=0.140  Sum_probs=19.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |+|+|..|+|||||++.+.+..
T Consensus         2 i~iiG~~~~GKssli~~~~~~~   23 (158)
T cd00878           2 ILILGLDGAGKTTILYKLKLGE   23 (158)
T ss_pred             EEEEcCCCCCHHHHHHHHhcCC
Confidence            6899999999999999998753

Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thu

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=94.89  E-value=0.011  Score=52.05  Aligned_cols=85  Identities=20%  Similarity=0.180  Sum_probs=54.8

Q ss_pred             ccCCCCccEEEeecc--cCCCCChhhhcCCCCCCEEEcCCCCCcCc-cccCCCcccccceeeeccccccccch----Hhh
Q 041097          279 YQFPPSLTHLSFSNI--ELMDDPIPALEKLSVLQVLKLKQNLYSEE-RTMGIRAMPKLECLIINPYAHLKRIH----EQL  351 (391)
Q Consensus       279 ~~l~~~L~~L~l~~~--~~~~~~~~~l~~l~~L~~L~l~~~~~~~~-~~~~~~~~~~L~~L~l~~c~~l~~lp----~~~  351 (391)
                      ..+ ++|++|.++.|  +..........++|+|++|+++.|..... ...+...+++|..|++.+|.-.. +-    .-+
T Consensus        62 P~L-p~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~pl~~l~nL~~Ldl~n~~~~~-l~dyre~vf  139 (260)
T KOG2739|consen   62 PKL-PKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRPLKELENLKSLDLFNCSVTN-LDDYREKVF  139 (260)
T ss_pred             CCc-chhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccchhhhhcchhhhhcccCCccc-cccHHHHHH
Confidence            346 78999999888  44433334445669999999996655422 22233577788899999886332 21    234


Q ss_pred             cCCCCCCEEEeeCC
Q 041097          352 WCLKSLNKLELWWP  365 (391)
Q Consensus       352 ~~l~~L~~L~l~~~  365 (391)
                      .-+++|++|+-..+
T Consensus       140 ~ll~~L~~LD~~dv  153 (260)
T KOG2739|consen  140 LLLPSLKYLDGCDV  153 (260)
T ss_pred             HHhhhhcccccccc
Confidence            56788888875543

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=94.88  E-value=0.026  Score=49.47  Aligned_cols=20  Identities=15%  Similarity=0.245  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|-.|+|||||++.+.-
T Consensus        36 lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          36 LGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             EEEEcCCCCCHHHHHHHHhc
Confidence            48999999999999999854

>cd03114 ArgK-like The function of this protein family is unkown

Probab=94.86  E-value=0.017  Score=47.47  Aligned_cols=20  Identities=10%  Similarity=0.212  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |++.|.+|+||||+++.+..
T Consensus         2 i~~~G~~GsGKTt~~~~l~~   21 (148)
T cd03114           2 IGITGVPGAGKSTLIDALIT   21 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            68999999999999999865

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=94.85  E-value=0.066  Score=43.25  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |=|.|-+|+||||+++.+..
T Consensus        10 ILvtGTPG~GKstl~~~lae   29 (176)
T KOG3347|consen   10 ILVTGTPGTGKSTLAERLAE   29 (176)
T ss_pred             EEEeCCCCCCchhHHHHHHH
Confidence            45899999999999999875

>KOG3308 consensus Uncharacterized protein of the uridine kinase family [Nucleotide transport and metabolism]

Probab=94.85  E-value=0.016  Score=49.04  Aligned_cols=38  Identities=13%  Similarity=0.247  Sum_probs=27.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      |||-|+.-.||||||+.+.      ..|..|..+..+.=|-.+.
T Consensus         7 vgiSG~TnsGKTTLak~l~------~~f~~~~lIhqDDFyKp~~   44 (225)
T KOG3308|consen    7 VGISGCTNSGKTTLAKSLH------RFFPGCSLIHQDDFYKPEN   44 (225)
T ss_pred             EEeecccCCCHhHHHHHHH------HHccCCeeeccccccCchh
Confidence            6888888899999999944      5787777666554444444

>cd04159 Arl10_like Arl10-like subfamily

Probab=94.82  E-value=0.021  Score=46.71  Aligned_cols=21  Identities=10%  Similarity=0.085  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||.+.+.+.
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            689999999999999998875

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>cd00154 Rab Rab family

Probab=94.81  E-value=0.018  Score=47.04  Aligned_cols=21  Identities=14%  Similarity=0.300  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|..|+|||||+..+.++
T Consensus         3 i~~~G~~~~GKStl~~~l~~~   23 (159)
T cd00154           3 IVLIGDSGVGKTSLLLRFVDG   23 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998775

Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=94.81  E-value=0.017  Score=48.66  Aligned_cols=20  Identities=15%  Similarity=0.187  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+-.
T Consensus         5 i~~~G~~GsGKst~~~~la~   24 (171)
T PRK03731          5 LFLVGARGCGKTTVGMALAQ   24 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999876

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=94.80  E-value=0.039  Score=49.06  Aligned_cols=54  Identities=7%  Similarity=0.083  Sum_probs=35.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc----ccEEEEEEcCCCcChHHHHHHHHHhhcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY----FDCHAWVQESLPYDADQILYDIIKFVMP   55 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~----F~~~~~~~vs~~~~~~~i~~~~~~~~~~   55 (391)
                      +.|+|.+|+||||||..+.-+...+..    -..++|+.-...|+.+++.+ +.....+
T Consensus        22 ~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~-~~~~~~~   79 (235)
T cd01123          22 TEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQ-IAERFGL   79 (235)
T ss_pred             EEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHH-HHHHhcc
Confidence            368999999999999998643222221    35788888777787766544 3333333

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 .

>cd00876 Ras Ras family

Probab=94.78  E-value=0.02  Score=47.16  Aligned_cols=21  Identities=24%  Similarity=0.335  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.+.
T Consensus         2 i~i~G~~~~GKTsli~~l~~~   22 (160)
T cd00876           2 VVVLGAGGVGKSAITIQFVKG   22 (160)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999998753

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m

>smart00175 RAB Rab subfamily of small GTPases

Probab=94.76  E-value=0.02  Score=47.46  Aligned_cols=21  Identities=10%  Similarity=0.294  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 v~v~G~~~~GKTtli~~l~~~   23 (164)
T smart00175        3 IILIGDSGVGKSSLLSRFTDG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999998764

Rab GTPases are implicated in vesicle trafficking.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=94.76  E-value=0.018  Score=48.82  Aligned_cols=20  Identities=15%  Similarity=0.109  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.+.|+.|+||||+|+.+.+
T Consensus         5 i~l~G~~gsGKst~a~~l~~   24 (175)
T cd00227           5 IILNGGSSAGKSSIARALQS   24 (175)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999876

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK13768 GTPase; Provisional

Probab=94.75  E-value=0.017  Score=52.13  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.||+||||++..+..
T Consensus         5 i~v~G~~G~GKTt~~~~~~~   24 (253)
T PRK13768          5 VFFLGTAGSGKTTLTKALSD   24 (253)
T ss_pred             EEEECCCCccHHHHHHHHHH
Confidence            57899999999998888654

>PLN02796 D-glycerate 3-kinase

Probab=94.73  E-value=0.017  Score=53.77  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+|||||++.+..
T Consensus       103 IGI~G~sGSGKSTLa~~L~~  122 (347)
T PLN02796        103 IGISAPQGCGKTTLVFALVY  122 (347)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            69999999999999999886

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=94.73  E-value=0.018  Score=55.04  Aligned_cols=25  Identities=20%  Similarity=0.169  Sum_probs=20.5

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF   28 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F   28 (391)
                      -+||.+|+||||+|+++++  ++...|
T Consensus       160 LL~GppGtGKT~lakaia~--~l~~~~  184 (364)
T TIGR01242       160 LLYGPPGTGKTLLAKAVAH--ETNATF  184 (364)
T ss_pred             EEECCCCCCHHHHHHHHHH--hCCCCE
Confidence            4799999999999999998  344443

Many proteins may score above the trusted cutoff because an internal

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

Probab=94.73  E-value=0.02  Score=42.70  Aligned_cols=20  Identities=30%  Similarity=0.345  Sum_probs=17.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|.+|+||||++..+..
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~   21 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAA   21 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999998866

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

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=94.71  E-value=0.016  Score=48.35  Aligned_cols=20  Identities=10%  Similarity=0.114  Sum_probs=16.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|-.|+|||||++.+..
T Consensus         2 I~i~G~~stGKTTL~~~L~~   21 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAA   21 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=94.71  E-value=0.019  Score=44.03  Aligned_cols=19  Identities=26%  Similarity=0.371  Sum_probs=17.3

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      ++|.|..|+|||||++.+.
T Consensus        18 v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          18 VLITGDSGIGKTELALELI   36 (107)
T ss_pred             EEEEcCCCCCHHHHHHHhh
Confidence            4799999999999999975

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

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

Probab=94.70  E-value=0.043  Score=47.13  Aligned_cols=20  Identities=15%  Similarity=0.026  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+-|+||||+++.+.+
T Consensus         3 I~ieG~~GsGKtT~~~~L~~   22 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAE   22 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999987

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

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=94.68  E-value=0.019  Score=48.73  Aligned_cols=21  Identities=19%  Similarity=0.305  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |-|.|.+|+||||+|+.+-+.
T Consensus         3 iiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           3 ILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999874

>PRK09087 hypothetical protein; Validated

Probab=94.67  E-value=0.019  Score=50.83  Aligned_cols=21  Identities=19%  Similarity=0.210  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      +.|||..|+|||+|++.++++
T Consensus        47 l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         47 VVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999998874

>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=94.67  E-value=0.024  Score=46.78  Aligned_cols=95  Identities=13%  Similarity=0.024  Sum_probs=46.9

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHH---HHHHHHHHHc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEAT---VEKYLEQLIN   78 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~---~~~~~~~L~~   78 (391)
                      =+.|+.|.||||||+.+..  .+...=..+.++.      .+.+-     ......-||-.++-++.   ....-..|.+
T Consensus         6 wltGlsGsGKtTlA~~L~~--~L~~~g~~~~~LD------gD~lR-----~~l~~dl~fs~~dR~e~~rr~~~~A~ll~~   72 (156)
T PF01583_consen    6 WLTGLSGSGKTTLARALER--RLFARGIKVYLLD------GDNLR-----HGLNADLGFSKEDREENIRRIAEVAKLLAD   72 (156)
T ss_dssp             EEESSTTSSHHHHHHHHHH--HHHHTTS-EEEEE------HHHHC-----TTTTTT--SSHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH--HHHHcCCcEEEec------Ccchh-----hccCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            3789999999999999987  4544433444433      22210     00111223322111111   2223455666


Q ss_pred             CccEEeeeccCCCceeeEEcCcchHHHHHhhccccCcee
Q 041097           79 GGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLI  117 (391)
Q Consensus        79 k~~l~~~~~~~~~~~~~~~~hdl~~~~~~~~~~~~~~~~  117 (391)
                      .+.+.+..        .+.+-.-.|+.+.....+..|..
T Consensus        73 ~G~ivIva--------~isp~~~~R~~~R~~~~~~~f~e  103 (156)
T PF01583_consen   73 QGIIVIVA--------FISPYREDREWARELIPNERFIE  103 (156)
T ss_dssp             TTSEEEEE------------SHHHHHHHHHHHHTTEEEE
T ss_pred             CCCeEEEe--------eccCchHHHHHHHHhCCcCceEE
Confidence            66665544        22344556777776666544554

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 ....

>cd00879 Sar1 Sar1 subfamily

Probab=94.67  E-value=0.021  Score=48.84  Aligned_cols=21  Identities=14%  Similarity=0.017  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||++.+.++
T Consensus        22 i~ilG~~~~GKStLi~~l~~~   42 (190)
T cd00879          22 ILFLGLDNAGKTTLLHMLKDD   42 (190)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.

>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=94.66  E-value=0.018  Score=45.08  Aligned_cols=20  Identities=30%  Similarity=0.278  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.+.|.||+||||++..+..
T Consensus         2 i~~~GkgG~GKTt~a~~la~   21 (116)
T cd02034           2 IAITGKGGVGKTTIAALLAR   21 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.66  E-value=0.019  Score=51.63  Aligned_cols=20  Identities=20%  Similarity=0.325  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++|++|+||||+|+.+..
T Consensus         2 Ivl~G~pGSGKST~a~~La~   21 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAK   21 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            56899999999999999875

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.

>cd04113 Rab4 Rab4 subfamily

Probab=94.64  E-value=0.025  Score=46.86  Aligned_cols=21  Identities=14%  Similarity=0.254  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 i~v~G~~~vGKTsli~~l~~~   23 (161)
T cd04113           3 FIIIGSSGTGKSCLLHRFVEN   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=94.63  E-value=0.024  Score=46.77  Aligned_cols=21  Identities=19%  Similarity=0.368  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         4 i~iiG~~~vGKTsl~~~~~~~   24 (162)
T cd04138           4 LVVVGAGGVGKSALTIQLIQN   24 (162)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999998764

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=94.62  E-value=0.02  Score=47.16  Aligned_cols=20  Identities=20%  Similarity=0.220  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+||||+.+.+-.
T Consensus         7 vvitGVpGvGKTTVl~~~~~   26 (189)
T COG2019           7 VVITGVPGVGKTTVLKIALK   26 (189)
T ss_pred             EEEEcCCCCChHHHHHHHHH
Confidence            46999999999999988665

>TIGR00101 ureG urease accessory protein UreG

Probab=94.62  E-value=0.044  Score=47.44  Aligned_cols=20  Identities=25%  Similarity=0.325  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|.|||||++.+..
T Consensus         4 i~i~G~~GsGKTTll~~l~~   23 (199)
T TIGR00101         4 IGVAGPVGSGKTALIEALTR   23 (199)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999987

This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.

>PRK08356 hypothetical protein; Provisional

Probab=94.62  E-value=0.02  Score=49.47  Aligned_cols=18  Identities=28%  Similarity=0.244  Sum_probs=17.0

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |+|+|+.|+||||+|+.+
T Consensus         8 i~~~G~~gsGK~t~a~~l   25 (195)
T PRK08356          8 VGVVGKIAAGKTTVAKFF   25 (195)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            579999999999999998

>PRK04182 cytidylate kinase; Provisional

Probab=94.59  E-value=0.02  Score=48.51  Aligned_cols=20  Identities=20%  Similarity=0.149  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+.+
T Consensus         3 I~i~G~~GsGKstia~~la~   22 (180)
T PRK04182          3 ITISGPPGSGKTTVARLLAE   22 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999886

>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=94.57  E-value=0.019  Score=30.25  Aligned_cols=19  Identities=37%  Similarity=0.448  Sum_probs=10.4

Q ss_pred             ccEEEcCCCccccCCcccC
Q 041097          181 LRVLDLGSLVLIRYPSGIE  199 (391)
Q Consensus       181 L~~L~l~~~~l~~~p~~i~  199 (391)
                      |++|++++|.+..+|+.++
T Consensus         2 L~~Ldls~n~l~~ip~~~~   20 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPSSFS   20 (22)
T ss_dssp             ESEEEETSSEESEEGTTTT
T ss_pred             ccEEECCCCcCEeCChhhc
Confidence            4555555555555555444

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 ....

>cd04177 RSR1 RSR1 subgroup

Probab=94.57  E-value=0.025  Score=47.31  Aligned_cols=21  Identities=24%  Similarity=0.388  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         4 i~liG~~~~GKTsli~~~~~~   24 (168)
T cd04177           4 IVVLGAGGVGKSALTVQFVQN   24 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999997654

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=94.53  E-value=0.023  Score=46.77  Aligned_cols=20  Identities=15%  Similarity=0.079  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|..|+||||+|+.+..
T Consensus         2 i~i~G~~GsGKSTla~~L~~   21 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEE   21 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999765

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK01184 hypothetical protein; Provisional

Probab=94.53  E-value=0.021  Score=48.67  Aligned_cols=17  Identities=24%  Similarity=0.315  Sum_probs=15.5

Q ss_pred             CcEEcCCCCcHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAE   17 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~   17 (391)
                      |+|+|+.|+||||+|+.
T Consensus         4 i~l~G~~GsGKsT~a~~   20 (184)
T PRK01184          4 IGVVGMPGSGKGEFSKI   20 (184)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999999984

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=94.53  E-value=0.018  Score=52.16  Aligned_cols=19  Identities=21%  Similarity=0.027  Sum_probs=17.2

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|.+|+||||+|+.+.+
T Consensus        46 ll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881        46 IFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             EEEcCCCCCHHHHHHHHHH
Confidence            4799999999999999875

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.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=94.53  E-value=0.03  Score=47.09  Aligned_cols=22  Identities=9%  Similarity=0.277  Sum_probs=19.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      +.|.|+.|+||+||++.++++.
T Consensus         7 ~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           7 IVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             EEEECCCCCCHHHHHHHHHhhc
Confidence            4689999999999999999853

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=94.51  E-value=0.022  Score=48.91  Aligned_cols=20  Identities=20%  Similarity=0.155  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         2 I~i~G~pGsGKst~a~~La~   21 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAK   21 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK08727 hypothetical protein; Validated

Probab=94.51  E-value=0.024  Score=50.49  Aligned_cols=35  Identities=14%  Similarity=0.137  Sum_probs=24.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |.|||..|+|||.|++++++.  +........|++..
T Consensus        44 l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~~~   78 (233)
T PRK08727         44 LYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLPLQ   78 (233)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEeHH
Confidence            468999999999999999873  33333345565543

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=94.49  E-value=0.022  Score=47.76  Aligned_cols=20  Identities=20%  Similarity=0.154  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|+||||+|+.+-+
T Consensus         3 I~i~G~~GSGKstia~~la~   22 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAE   22 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=94.47  E-value=0.017  Score=47.23  Aligned_cols=40  Identities=20%  Similarity=0.135  Sum_probs=28.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhh
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFV   53 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~   53 (391)
                      |.|-|.+|+||||+|+.+.+...++.             +....++++++...
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~-------------vsaG~iFR~~A~e~   42 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKL-------------VSAGTIFREMARER   42 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCce-------------eeccHHHHHHHHHc
Confidence            57899999999999999887433332             23446666666544

>cd01864 Rab19 Rab19 subfamily

Probab=94.44  E-value=0.029  Score=46.72  Aligned_cols=20  Identities=15%  Similarity=0.199  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+..+..
T Consensus         6 v~vvG~~~~GKTsli~~l~~   25 (165)
T cd01864           6 IILIGDSNVGKTCVVQRFKS   25 (165)
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            57999999999999999754

Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=94.43  E-value=0.022  Score=52.21  Aligned_cols=20  Identities=10%  Similarity=0.170  Sum_probs=16.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-|||||||+|-.+-.
T Consensus         4 i~~~gKGGVGKTT~a~nLA~   23 (279)
T PRK13230          4 FCFYGKGGIGKSTTVCNIAA   23 (279)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57899999999998877543

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=94.41  E-value=0.021  Score=53.02  Aligned_cols=19  Identities=26%  Similarity=0.253  Sum_probs=17.8

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|+.|+||||||+.+.+
T Consensus        34 ll~Gp~G~GKT~la~~ia~   52 (305)
T TIGR00635        34 LLYGPPGLGKTTLAHIIAN   52 (305)
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999999987

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.

>cd01898 Obg Obg subfamily

Probab=94.41  E-value=0.026  Score=47.09  Aligned_cols=20  Identities=5%  Similarity=0.099  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+.+
T Consensus         3 v~ivG~~~~GKStl~~~l~~   22 (170)
T cd01898           3 VGLVGLPNAGKSTLLSAISN   22 (170)
T ss_pred             eEEECCCCCCHHHHHHHHhc
Confidence            68999999999999999875

The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=94.38  E-value=0.036  Score=52.11  Aligned_cols=20  Identities=25%  Similarity=0.252  Sum_probs=18.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -|+|+.|+||||+|+.+.+.
T Consensus        55 ll~GppG~GKT~la~~ia~~   74 (328)
T PRK00080         55 LLYGPPGLGKTTLANIIANE   74 (328)
T ss_pred             EEECCCCccHHHHHHHHHHH
Confidence            48999999999999999883

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

Probab=94.37  E-value=0.022  Score=48.37  Aligned_cols=20  Identities=15%  Similarity=0.144  Sum_probs=16.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -|+|.+|+|||||++.++..
T Consensus        28 ll~G~~G~GKT~ll~~~~~~   47 (185)
T PF13191_consen   28 LLTGESGSGKTSLLRALLDR   47 (185)
T ss_dssp             EE-B-TTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            58999999999999998874

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=94.37  E-value=0.024  Score=49.79  Aligned_cols=20  Identities=15%  Similarity=0.177  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+..
T Consensus        33 ~~l~G~nGsGKSTLl~~i~G   52 (218)
T cd03255          33 VAIVGPSGSGKSTLLNILGG   52 (218)
T ss_pred             EEEEcCCCCCHHHHHHHHhC
Confidence            58999999999999999986

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

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

Probab=94.37  E-value=0.025  Score=50.73  Aligned_cols=25  Identities=20%  Similarity=0.174  Sum_probs=20.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF   28 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F   28 (391)
                      =.+|++|.||||||.-+.|  ++...+
T Consensus        56 Ll~GPPGlGKTTLA~IIA~--Emgvn~   80 (332)
T COG2255          56 LLFGPPGLGKTTLAHIIAN--ELGVNL   80 (332)
T ss_pred             EeeCCCCCcHHHHHHHHHH--HhcCCe
Confidence            3689999999999999998  444433

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=94.36  E-value=0.029  Score=45.43  Aligned_cols=21  Identities=19%  Similarity=0.291  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |-++|..|+|||||+|.+-..
T Consensus         4 imliG~~g~GKTTL~q~L~~~   24 (143)
T PF10662_consen    4 IMLIGPSGSGKTTLAQALNGE   24 (143)
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            458999999999999998764

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.35  E-value=0.025  Score=49.86  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||.+.+.-
T Consensus        32 vsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          32 VAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999864

>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily

Probab=94.33  E-value=0.033  Score=46.52  Aligned_cols=21  Identities=29%  Similarity=0.235  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.+.
T Consensus         2 i~ivG~~~vGKTsli~~~~~~   22 (164)
T cd04162           2 ILVLGLDGAGKTSLLHSLSSE   22 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.

>PTZ00088 adenylate kinase 1; Provisional

Probab=94.31  E-value=0.022  Score=50.44  Aligned_cols=20  Identities=20%  Similarity=0.333  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         9 Ivl~G~PGsGK~T~a~~La~   28 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSK   28 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999865

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=94.30  E-value=0.024  Score=48.90  Aligned_cols=20  Identities=15%  Similarity=0.049  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         6 i~i~G~~G~GKst~a~~l~~   25 (197)
T PRK12339          6 HFIGGIPGVGKTSISGYIAR   25 (197)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999877

>PRK13342 recombination factor protein RarA; Reviewed

Probab=94.28  E-value=0.027  Score=54.71  Aligned_cols=20  Identities=20%  Similarity=0.160  Sum_probs=18.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -++|.+|+||||+|+.+.+.
T Consensus        40 lL~GppGtGKTtLA~~ia~~   59 (413)
T PRK13342         40 ILWGPPGTGKTTLARIIAGA   59 (413)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999883

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=94.27  E-value=0.027  Score=47.73  Aligned_cols=20  Identities=10%  Similarity=0.184  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.||||+++.+..
T Consensus         6 i~l~G~sGsGKSTl~~~la~   25 (176)
T PRK09825          6 YILMGVSGSGKSLIGSKIAA   25 (176)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999987

>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=94.27  E-value=0.029  Score=46.48  Aligned_cols=21  Identities=19%  Similarity=0.360  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         2 i~vvG~~~vGKtsl~~~~~~~   22 (162)
T PF00071_consen    2 IVVVGDSGVGKTSLINRLING   22 (162)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhh
Confidence            579999999999999998775

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....

>cd01860 Rab5_related Rab5-related subfamily

Probab=94.25  E-value=0.03  Score=46.38  Aligned_cols=22  Identities=9%  Similarity=0.235  Sum_probs=19.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|.+|+|||||++.+.++.
T Consensus         4 i~v~G~~~~GKSsli~~l~~~~   25 (163)
T cd01860           4 LVLLGDSSVGKSSLVLRFVKNE   25 (163)
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            5799999999999999987753

This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=94.24  E-value=0.03  Score=45.29  Aligned_cols=21  Identities=19%  Similarity=0.346  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         3 v~liG~~~vGKSsL~~~l~~~   23 (142)
T TIGR02528         3 IMFIGSVGCGKTTLTQALQGE   23 (142)
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            579999999999999998764

This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=94.24  E-value=0.024  Score=50.18  Aligned_cols=21  Identities=5%  Similarity=0.128  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |-|+|..|+|||+||+.+++.
T Consensus        45 ~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         45 FYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999873

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.24  E-value=0.055  Score=48.33  Aligned_cols=33  Identities=12%  Similarity=-0.025  Sum_probs=23.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQE   36 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~v   36 (391)
                      -++|.+|+|||+||.++.+.  +...=..++++++
T Consensus       103 ~l~G~~GtGKThLa~aia~~--l~~~g~~v~~it~  135 (244)
T PRK07952        103 IFSGKPGTGKNHLAAAICNE--LLLRGKSVLIITV  135 (244)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEH
Confidence            47999999999999999883  3322234455443

>cd04136 Rap_like Rap-like subfamily

Probab=94.21  E-value=0.034  Score=45.99  Aligned_cols=21  Identities=29%  Similarity=0.384  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         4 i~i~G~~~vGKTsl~~~~~~~   24 (163)
T cd04136           4 VVVLGSGGVGKSALTVQFVQG   24 (163)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999887653

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=94.17  E-value=0.063  Score=47.42  Aligned_cols=42  Identities=7%  Similarity=0.064  Sum_probs=30.3

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQIL   46 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~   46 (391)
                      -|+|.+|+||||+|.++..+  ....-..++||... .++.+++.
T Consensus        27 ~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e-~~~~~r~~   68 (225)
T PRK09361         27 QIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTE-GLSPERFK   68 (225)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECC-CCCHHHHH
Confidence            58999999999999998753  22223577888766 66666643

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=94.17  E-value=0.032  Score=46.31  Aligned_cols=20  Identities=35%  Similarity=0.298  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+..+.+
T Consensus         3 i~vvG~~~~GKtsl~~~l~~   22 (164)
T cd04101           3 CAVVGDPAVGKTAFVQMFHS   22 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57999999999999998754

RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=94.16  E-value=0.029  Score=49.04  Aligned_cols=20  Identities=10%  Similarity=0.137  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        30 ~~l~G~nGsGKSTLl~~l~G   49 (211)
T cd03225          30 VLIVGPNGSGKSTLLRLLNG   49 (211)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999987

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=94.14  E-value=0.029  Score=49.22  Aligned_cols=20  Identities=15%  Similarity=0.235  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        32 ~~i~G~nGsGKSTLl~~l~G   51 (216)
T TIGR00960        32 VFLVGHSGAGKSTFLKLILG   51 (216)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

>PHA02575 1 deoxynucleoside monophosphate kinase; Provisional

Probab=94.14  E-value=0.029  Score=48.91  Aligned_cols=20  Identities=15%  Similarity=0.032  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+||.|+||+|.|+.+-.
T Consensus         3 I~i~G~~gsGKstva~~~~~   22 (227)
T PHA02575          3 IAISGKKRSGKDTVADFIIE   22 (227)
T ss_pred             EEEeCCCCCCHHHHHHHHHh
Confidence            79999999999999999743

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=94.13  E-value=0.03  Score=51.05  Aligned_cols=20  Identities=25%  Similarity=0.321  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+++.+..
T Consensus         2 igI~G~sGsGKSTl~~~L~~   21 (273)
T cd02026           2 IGVAGDSGCGKSTFLRRLTS   21 (273)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999875

This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>cd04123 Rab21 Rab21 subfamily

Probab=94.12  E-value=0.033  Score=45.93  Aligned_cols=21  Identities=14%  Similarity=0.162  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus         3 i~i~G~~~~GKStli~~l~~~   23 (162)
T cd04123           3 VVLLGEGRVGKTSLVLRYVEN   23 (162)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999988765

The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site

>cd04124 RabL2 RabL2 subfamily

Probab=94.12  E-value=0.032  Score=46.33  Aligned_cols=21  Identities=10%  Similarity=0.197  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         3 i~vvG~~~vGKTsli~~~~~~   23 (161)
T cd04124           3 IILLGDSAVGKSKLVERFLMD   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999887654

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=94.11  E-value=0.033  Score=46.34  Aligned_cols=21  Identities=10%  Similarity=0.243  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~i~G~~~vGKSsli~~~~~~   25 (166)
T cd01869           5 LLLIGDSGVGKSCLLLRFADD   25 (166)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=94.11  E-value=0.028  Score=51.28  Aligned_cols=20  Identities=15%  Similarity=0.262  Sum_probs=16.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-|||||||+|-.+-.
T Consensus         4 iav~gKGGVGKTT~a~nLA~   23 (273)
T PRK13232          4 IAIYGKGGIGKSTTTQNLTA   23 (273)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57889999999998887643

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=94.10  E-value=0.031  Score=47.46  Aligned_cols=20  Identities=20%  Similarity=0.218  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (178)
T cd03229          29 VALLGPSGSGKSTLLRCIAG   48 (178)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

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.

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=94.08  E-value=0.03  Score=49.06  Aligned_cols=20  Identities=15%  Similarity=0.270  Sum_probs=16.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|-||+||||.+-.+-.
T Consensus         3 iav~gKGGvGKTt~~~nLA~   22 (212)
T cd02117           3 IAIYGKGGIGKSTTSQNLSA   22 (212)
T ss_pred             EEEECCCcCcHHHHHHHHHH
Confidence            67999999999997777543

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=94.08  E-value=0.026  Score=54.29  Aligned_cols=20  Identities=15%  Similarity=0.220  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.||||||+++..
T Consensus       222 IvI~G~~gsGKTTL~~~La~  241 (399)
T PRK08099        222 VAILGGESSGKSTLVNKLAN  241 (399)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=94.08  E-value=0.033  Score=44.63  Aligned_cols=21  Identities=14%  Similarity=0.253  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.+.|.-|+||||++|.+...
T Consensus        25 i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150        25 VLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999873

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein

Probab=94.06  E-value=0.029  Score=51.07  Aligned_cols=19  Identities=21%  Similarity=0.298  Sum_probs=16.0

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|.|-|||||||++-.+-
T Consensus         3 i~~~gKGGVGKTT~~~nLA   21 (268)
T TIGR01281         3 LAVYGKGGIGKSTTSSNLS   21 (268)
T ss_pred             EEEEcCCcCcHHHHHHHHH
Confidence            6788999999999777753

The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit.

>cd01878 HflX HflX subfamily

Probab=94.05  E-value=0.032  Score=48.37  Aligned_cols=22  Identities=9%  Similarity=0.151  Sum_probs=19.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |+|+|.+|+|||||.+.+.++.
T Consensus        44 I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          44 VALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             EEEECCCCCCHHHHHHHHhcch
Confidence            6899999999999999988753

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=94.05  E-value=0.031  Score=46.56  Aligned_cols=20  Identities=20%  Similarity=0.219  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||||...+..
T Consensus         2 i~~vG~~~~GKstLi~~l~~   21 (167)
T cd04160           2 VLILGLDNAGKTTFLEQLKT   21 (167)
T ss_pred             EEEEecCCCCHHHHHHHHhh
Confidence            67999999999999998754

Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.

>cd00880 Era_like Era (E

Probab=94.05  E-value=0.029  Score=45.65  Aligned_cols=19  Identities=5%  Similarity=0.144  Sum_probs=17.3

Q ss_pred             EEcCCCCcHHHHHHHHhCC
Q 041097            3 VLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|.+|+|||||++.+++.
T Consensus         1 i~G~~gsGKstl~~~l~~~   19 (163)
T cd00880           1 LFGRTNAGKSSLLNALLGQ   19 (163)
T ss_pred             CcCCCCCCHHHHHHHHhCc
Confidence            6899999999999999874

coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the se

>PLN02348 phosphoribulokinase

Probab=94.05  E-value=0.027  Score=53.34  Aligned_cols=20  Identities=20%  Similarity=0.297  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|-.|+||||+|+.+.+
T Consensus        52 IGIaG~SGSGKSTfA~~L~~   71 (395)
T PLN02348         52 IGLAADSGCGKSTFMRRLTS   71 (395)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999876

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

Probab=94.04  E-value=0.037  Score=51.88  Aligned_cols=21  Identities=10%  Similarity=0.194  Sum_probs=19.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|||..|+|||.+|+++++.
T Consensus       151 llL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        151 LGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             EEeeCCCCCCHHHHHHHHHHH
Confidence            589999999999999999983

>cd04140 ARHI_like ARHI subfamily

Probab=94.04  E-value=0.039  Score=45.99  Aligned_cols=21  Identities=14%  Similarity=0.264  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus         4 v~~vG~~~vGKTsli~~~~~~   24 (165)
T cd04140           4 VVVFGAGGVGKSSLVLRFVKG   24 (165)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999987653

ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to

>cd04150 Arf1_5_like Arf1-Arf5-like subfamily

Probab=94.03  E-value=0.032  Score=46.33  Aligned_cols=20  Identities=10%  Similarity=-0.031  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++|.+|+|||||++.+..
T Consensus         3 v~~~G~~~~GKTsli~~l~~   22 (159)
T cd04150           3 ILMVGLDAAGKTTILYKLKL   22 (159)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57999999999999999743

This subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=94.02  E-value=0.032  Score=47.86  Aligned_cols=20  Identities=20%  Similarity=0.302  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        21 ~~i~G~nGsGKSTLl~~i~G   40 (190)
T TIGR01166        21 LALLGANGAGKSTLLLHLNG   40 (190)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>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=94.00  E-value=0.033  Score=47.18  Aligned_cols=20  Identities=20%  Similarity=0.252  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||.+.+..
T Consensus        24 ~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          24 VVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            58999999999999999853

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.

>PRK10536 hypothetical protein; Provisional

Probab=93.98  E-value=0.12  Score=46.19  Aligned_cols=21  Identities=19%  Similarity=0.145  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|.|.+|.|||+||.++..+
T Consensus        77 V~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         77 IFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999997653

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.98  E-value=0.031  Score=53.00  Aligned_cols=20  Identities=25%  Similarity=0.305  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+++|.+|+||||++.++..
T Consensus       244 I~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        244 IALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            58999999999999998865

>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

Probab=93.98  E-value=0.02  Score=50.88  Aligned_cols=45  Identities=27%  Similarity=0.138  Sum_probs=30.3

Q ss_pred             hHHhhccCCcccEEEcCCCccc-cCCc----ccCCCCcccEEEccCCCCC
Q 041097          171 CEKICKMFKFLRVLDLGSLVLI-RYPS----GIENLFLLRYLKLNIPSLK  215 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~-~~p~----~i~~l~~L~~L~l~~~~i~  215 (391)
                      +.+.+-+++.|+..+|+.|.+. ..|+    -|+.-..|.+|.+.+|.+.
T Consensus        84 Ll~aLlkcp~l~~v~LSDNAfg~~~~e~L~d~is~~t~l~HL~l~NnGlG  133 (388)
T COG5238          84 LLKALLKCPRLQKVDLSDNAFGSEFPEELGDLISSSTDLVHLKLNNNGLG  133 (388)
T ss_pred             HHHHHhcCCcceeeeccccccCcccchHHHHHHhcCCCceeEEeecCCCC
Confidence            3456677788888888888765 3443    3456667777777777654

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=93.97  E-value=0.033  Score=48.08  Aligned_cols=20  Identities=10%  Similarity=0.106  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|+.|+||||+|+.+.+
T Consensus         4 i~itG~~gsGKst~~~~l~~   23 (195)
T PRK14730          4 IGLTGGIASGKSTVGNYLAQ   23 (195)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999764

>cd04161 Arl2l1_Arl13_like Arl2l1/Arl13 subfamily

Probab=93.97  E-value=0.037  Score=46.37  Aligned_cols=21  Identities=10%  Similarity=0.067  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         2 i~~~G~~~~GKTsl~~~l~~~   22 (167)
T cd04161           2 LLTVGLDNAGKTTLVSALQGE   22 (167)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998653

Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.

>PRK14527 adenylate kinase; Provisional

Probab=93.96  E-value=0.032  Score=47.92  Aligned_cols=20  Identities=20%  Similarity=0.136  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+||||+|+.+.+
T Consensus         9 i~i~G~pGsGKsT~a~~La~   28 (191)
T PRK14527          9 VIFLGPPGAGKGTQAERLAQ   28 (191)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>PRK02496 adk adenylate kinase; Provisional

Probab=93.96  E-value=0.033  Score=47.52  Aligned_cols=20  Identities=20%  Similarity=0.119  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         4 i~i~G~pGsGKst~a~~la~   23 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAE   23 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999865

>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=93.95  E-value=0.034  Score=46.89  Aligned_cols=20  Identities=25%  Similarity=0.237  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +.++|++|+||||+++.+..
T Consensus         3 ~~~~G~~G~GKTt~~~~la~   22 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLAL   22 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999875

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.

>cd00157 Rho Rho (Ras homology) family

Probab=93.95  E-value=0.036  Score=46.25  Aligned_cols=21  Identities=14%  Similarity=0.169  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 i~i~G~~~~GKSsli~~l~~~   23 (171)
T cd00157           3 IVVVGDGAVGKTCLLISYTTG   23 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            569999999999999998765

Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho protein

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=93.95  E-value=0.033  Score=49.79  Aligned_cols=20  Identities=15%  Similarity=0.152  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.|..|+|||||.|.++.
T Consensus        31 ~~iiGpNG~GKSTLLk~l~g   50 (258)
T COG1120          31 TGILGPNGSGKSTLLKCLAG   50 (258)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            47999999999999999987

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=93.94  E-value=0.034  Score=48.98  Aligned_cols=20  Identities=15%  Similarity=0.197  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        33 ~~i~G~nGsGKSTLl~~l~G   52 (220)
T cd03293          33 VALVGPSGCGKSTLLRIIAG   52 (220)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

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.

>PRK14490 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional

Probab=93.93  E-value=0.046  Score=52.27  Aligned_cols=25  Identities=16%  Similarity=0.119  Sum_probs=22.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY   27 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~   27 (391)
                      |+|+|..|+|||||+..+..  .++..
T Consensus         8 i~i~G~~gsGKTTl~~~l~~--~l~~~   32 (369)
T PRK14490          8 IAFCGYSGSGKTTLITALVR--RLSER   32 (369)
T ss_pred             EEEEeCCCCCHHHHHHHHHH--HHhhC
Confidence            68999999999999999988  56666

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.93  E-value=0.034  Score=47.94  Aligned_cols=21  Identities=10%  Similarity=0.025  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G~   49 (195)
T PRK13541         29 TYIKGANGCGKSSLLRMIAGI   49 (195)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            589999999999999999873

>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily

Probab=93.92  E-value=0.042  Score=45.72  Aligned_cols=20  Identities=30%  Similarity=0.486  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+....+
T Consensus         2 i~vvG~~~~GKtsli~~~~~   21 (165)
T cd04146           2 IAVLGASGVGKSALVVRFLT   21 (165)
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            67999999999999977654

RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=93.92  E-value=0.15  Score=42.62  Aligned_cols=99  Identities=17%  Similarity=0.155  Sum_probs=56.0

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHH---HHHHHHHHHcC
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEAT---VEKYLEQLING   79 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~---~~~~~~~L~~k   79 (391)
                      ..|+.|.||||+|.+++.  .+... .+.+++-     |-+.+=.     -..-.-||..++-.+.   ...+-..+.+.
T Consensus        28 ~TGLSGsGKSTiA~ale~--~L~~~-G~~~y~L-----DGDnvR~-----gL~~dLgFs~edR~eniRRvaevAkll~da   94 (197)
T COG0529          28 FTGLSGSGKSTIANALEE--KLFAK-GYHVYLL-----DGDNVRH-----GLNRDLGFSREDRIENIRRVAEVAKLLADA   94 (197)
T ss_pred             eecCCCCCHHHHHHHHHH--HHHHc-CCeEEEe-----cChhHhh-----cccCCCCCChHHHHHHHHHHHHHHHHHHHC
Confidence            359999999999999987  22211 1333332     2222111     1112345544331111   22344567777


Q ss_pred             ccEEeeeccCCCceeeEEcCcchHHHHHhhccccCceeecccCC
Q 041097           80 GFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQ  123 (391)
Q Consensus        80 ~~l~~~~~~~~~~~~~~~~hdl~~~~~~~~~~~~~~~~~~~~~~  123 (391)
                      +++..+.        ....+.-.|+++.....+..|.. ++-+.
T Consensus        95 G~iviva--------~ISP~r~~R~~aR~~~~~~~FiE-VyV~~  129 (197)
T COG0529          95 GLIVIVA--------FISPYREDRQMARELLGEGEFIE-VYVDT  129 (197)
T ss_pred             CeEEEEE--------eeCccHHHHHHHHHHhCcCceEE-EEeCC
Confidence            7776554        34466677889988888777776 55444

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; 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=93.92  E-value=0.034  Score=49.52  Aligned_cols=20  Identities=15%  Similarity=0.262  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G   48 (235)
T cd03261          29 LAIIGPSGSGKSTLLRLIVG   48 (235)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

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.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=93.92  E-value=0.034  Score=48.66  Aligned_cols=20  Identities=20%  Similarity=0.270  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        31 ~~l~G~nGsGKSTLl~~i~G   50 (214)
T TIGR02673        31 LFLTGPSGAGKTTLLKLLYG   50 (214)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd04103 Centaurin_gamma Centaurin gamma

Probab=93.91  E-value=0.042  Score=45.62  Aligned_cols=20  Identities=10%  Similarity=0.287  Sum_probs=17.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+|||||.+....
T Consensus         3 i~vvG~~gvGKTsli~~~~~   22 (158)
T cd04103           3 LGIVGNLQSGKSALVHRYLT   22 (158)
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            67999999999999987543

The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues.

>cd04163 Era Era subfamily

Probab=93.90  E-value=0.039  Score=45.46  Aligned_cols=21  Identities=10%  Similarity=0.202  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+++|..|+|||||+..+...
T Consensus         6 i~~~G~~g~GKttl~~~l~~~   26 (168)
T cd04163           6 VAIVGRPNVGKSTLLNALVGQ   26 (168)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999998663

Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.

>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

Probab=93.90  E-value=0.032  Score=47.96  Aligned_cols=20  Identities=30%  Similarity=0.391  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+-|+||||+++.+.+
T Consensus         2 I~ieG~~GsGKSTl~~~L~~   21 (193)
T cd01673           2 IVVEGNIGAGKSTLAKELAE   21 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.

>cd04175 Rap1 Rap1 subgroup

Probab=93.88  E-value=0.042  Score=45.63  Aligned_cols=21  Identities=29%  Similarity=0.403  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||+..+.++
T Consensus         4 i~~~G~~~~GKTsli~~~~~~   24 (164)
T cd04175           4 LVVLGSGGVGKSALTVQFVQG   24 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999887653

The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n

>PRK14738 gmk guanylate kinase; Provisional

Probab=93.88  E-value=0.035  Score=48.37  Aligned_cols=20  Identities=20%  Similarity=0.250  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||||++.+.+
T Consensus        16 ivi~GpsG~GK~tl~~~L~~   35 (206)
T PRK14738         16 VVISGPSGVGKDAVLARMRE   35 (206)
T ss_pred             EEEECcCCCCHHHHHHHHHh
Confidence            46899999999999999876

>PRK15453 phosphoribulokinase; Provisional

Probab=93.88  E-value=0.035  Score=50.26  Aligned_cols=20  Identities=25%  Similarity=0.175  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|-.|+||||+|+.+.+
T Consensus         8 I~ItG~SGsGKTTva~~l~~   27 (290)
T PRK15453          8 IAVTGSSGAGTTTVKRAFEK   27 (290)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999998764

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=93.87  E-value=0.035  Score=48.55  Aligned_cols=20  Identities=25%  Similarity=0.268  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (213)
T cd03259          29 LALLGPSGCGKTTLLRLIAG   48 (213)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. 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.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=93.86  E-value=0.035  Score=48.80  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (220)
T cd03263          31 FGLLGHNGAGKTTTLKMLTG   50 (220)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

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.

>PLN02200 adenylate kinase family protein

Probab=93.84  E-value=0.035  Score=49.37  Aligned_cols=20  Identities=20%  Similarity=0.121  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus        46 i~I~G~PGSGKsT~a~~La~   65 (234)
T PLN02200         46 TFVLGGPGSGKGTQCEKIVE   65 (234)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999765

>PRK00454 engB GTP-binding protein YsxC; Reviewed

Probab=93.84  E-value=0.037  Score=47.53  Aligned_cols=21  Identities=10%  Similarity=0.137  Sum_probs=19.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||.+.+.++
T Consensus        27 v~ivG~~~~GKSsli~~l~~~   47 (196)
T PRK00454         27 IAFAGRSNVGKSSLINALTNR   47 (196)
T ss_pred             EEEEcCCCCCHHHHHHHHhCC
Confidence            689999999999999999874

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.84  E-value=0.052  Score=46.95  Aligned_cols=20  Identities=20%  Similarity=0.175  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|.||||+++.+..
T Consensus         4 ilI~GptGSGKTTll~~ll~   23 (198)
T cd01131           4 VLVTGPTGSGKSTTLAAMID   23 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999998765

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.

>PRK14532 adenylate kinase; Provisional

Probab=93.84  E-value=0.036  Score=47.48  Aligned_cols=20  Identities=10%  Similarity=0.061  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|.|++|+||||+|+.+..
T Consensus         3 i~~~G~pGsGKsT~a~~la~   22 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVE   22 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999875

>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=93.84  E-value=0.036  Score=46.99  Aligned_cols=20  Identities=15%  Similarity=0.152  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        28 ~~l~G~nGsGKSTLl~~l~G   47 (177)
T cd03222          28 IGIVGPNGTGKTTAVKILAG   47 (177)
T ss_pred             EEEECCCCChHHHHHHHHHc
Confidence            58999999999999999876

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.

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

Probab=93.84  E-value=0.034  Score=52.56  Aligned_cols=42  Identities=19%  Similarity=0.158  Sum_probs=26.6

Q ss_pred             CcEEcCCCCcHH-HHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKT-AFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKT-TLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      |..||+.||||| ||||...--.. ...=..+++++.+ +|.+..
T Consensus       206 i~LVGPTGVGKTTTlAKLAar~~~-~~~~~kVaiITtD-tYRIGA  248 (407)
T COG1419         206 IALVGPTGVGKTTTLAKLAARYVM-LKKKKKVAIITTD-TYRIGA  248 (407)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHh-hccCcceEEEEec-cchhhH
Confidence            468999999996 89988754211 1222467777765 345444

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=93.83  E-value=0.035  Score=46.34  Aligned_cols=20  Identities=10%  Similarity=0.258  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |..+||-|+||||+.|.+.+
T Consensus         5 IvLiG~mGaGKSTIGr~LAk   24 (172)
T COG0703           5 IVLIGFMGAGKSTIGRALAK   24 (172)
T ss_pred             EEEEcCCCCCHhHHHHHHHH
Confidence            45789999999999999876

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=93.82  E-value=0.037  Score=48.34  Aligned_cols=20  Identities=20%  Similarity=0.192  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (210)
T cd03269          29 FGLLGPNGAGKTTTIRMILG   48 (210)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. 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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=93.82  E-value=0.058  Score=45.99  Aligned_cols=33  Identities=12%  Similarity=0.106  Sum_probs=26.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      |.++|..|+|||||++.+..  ..+..|..++.-+
T Consensus         5 ivl~Gpsg~GK~~l~~~L~~--~~~~~~~~~v~~T   37 (183)
T PF00625_consen    5 IVLVGPSGSGKSTLAKRLIQ--EFPDKFGRVVSHT   37 (183)
T ss_dssp             EEEESSTTSSHHHHHHHHHH--HSTTTEEEEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH--hcccccccceeec
Confidence            46899999999999999988  5667776555444

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

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

Probab=93.82  E-value=0.035  Score=57.45  Aligned_cols=25  Identities=20%  Similarity=0.258  Sum_probs=20.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF   28 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F   28 (391)
                      -+||++|+||||+|+.+++.  .+..|
T Consensus        56 LL~GPpGtGKTTLA~aIA~~--~~~~f   80 (725)
T PRK13341         56 ILYGPPGVGKTTLARIIANH--TRAHF   80 (725)
T ss_pred             EEECCCCCCHHHHHHHHHHH--hcCcc
Confidence            37999999999999999973  44444

>CHL00072 chlL photochlorophyllide reductase subunit L

Probab=93.82  E-value=0.035  Score=51.17  Aligned_cols=20  Identities=20%  Similarity=0.250  Sum_probs=16.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|-|||||||.+-.+-.
T Consensus         3 ia~~gKGGVGKTTta~nLA~   22 (290)
T CHL00072          3 LAVYGKGGIGKSTTSCNISI   22 (290)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57899999999998887543

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=93.81  E-value=0.037  Score=48.36  Aligned_cols=20  Identities=20%  Similarity=0.197  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        28 ~~i~G~nGsGKSTLl~~l~G   47 (211)
T cd03264          28 YGLLGPNGAGKTTLMRILAT   47 (211)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. 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.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=93.79  E-value=0.037  Score=48.11  Aligned_cols=20  Identities=25%  Similarity=0.217  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (205)
T cd03226          29 IALTGKNGAGKTTLAKILAG   48 (205)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999987

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=93.79  E-value=0.035  Score=50.88  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=17.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+||||++..+..
T Consensus       197 i~~vGptGvGKTTt~~kLa~  216 (282)
T TIGR03499       197 IALVGPTGVGKTTTLAKLAA  216 (282)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999988765

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=93.79  E-value=0.038  Score=46.75  Aligned_cols=21  Identities=24%  Similarity=0.349  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         4 v~l~G~~g~GKTtl~~~~~~~   24 (180)
T cd04137           4 IAVLGSRSVGKSSLTVQFVEG   24 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998653

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=93.78  E-value=0.088  Score=44.89  Aligned_cols=83  Identities=24%  Similarity=0.189  Sum_probs=37.6

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc-ccCCCcccccceeeeccccccccch----HhhcCCCCC
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER-TMGIRAMPKLECLIINPYAHLKRIH----EQLWCLKSL  357 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~-~~~~~~~~~L~~L~l~~c~~l~~lp----~~~~~l~~L  357 (391)
                      +.|.+|.+.+|.+....+.....+|+|..|.+..|+..... .-+.-++|+|++|.+-+++ .+..+    -.+..+|+|
T Consensus        64 ~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Ltll~Np-v~~k~~YR~yvl~klp~l  142 (233)
T KOG1644|consen   64 PRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLTLLGNP-VEHKKNYRLYVLYKLPSL  142 (233)
T ss_pred             cccceEEecCCcceeeccchhhhccccceEEecCcchhhhhhcchhccCCccceeeecCCc-hhcccCceeEEEEecCcc
Confidence            55555555555554433222233455555555544332211 1112345555555555443 11111    123456666


Q ss_pred             CEEEeeCCc
Q 041097          358 NKLELWWPE  366 (391)
Q Consensus       358 ~~L~l~~~~  366 (391)
                      +.|+..+..
T Consensus       143 ~~LDF~kVt  151 (233)
T KOG1644|consen  143 RTLDFQKVT  151 (233)
T ss_pred             eEeehhhhh
Confidence            666666554

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

Probab=93.78  E-value=0.083  Score=46.60  Aligned_cols=44  Identities=7%  Similarity=0.138  Sum_probs=31.5

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc------cEEEEEEcCCCcChHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF------DCHAWVQESLPYDADQILY   47 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F------~~~~~~~vs~~~~~~~i~~   47 (391)
                      .|+|.+|+||||||..+.-+.  ...-      ..++|+.-...|+.+++.+
T Consensus        23 ~I~G~~GsGKT~l~~~ia~~~--~~~~~~~g~~~~v~yi~~e~~~~~~rl~~   72 (226)
T cd01393          23 EIFGEFGSGKTQLCLQLAVEA--QLPGELGGLEGKVVYIDTEGAFRPERLVQ   72 (226)
T ss_pred             EEeCCCCCChhHHHHHHHHHh--hcccccCCCcceEEEEecCCCCCHHHHHH
Confidence            589999999999999875421  1122      4667887777788776544

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.

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=93.77  E-value=0.038  Score=48.37  Aligned_cols=20  Identities=15%  Similarity=0.287  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (214)
T cd03292          30 VFLVGPSGAGKSTLLKLIYK   49 (214)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999987

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=93.76  E-value=0.084  Score=45.36  Aligned_cols=20  Identities=20%  Similarity=0.048  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|..|+||||+++.+.+
T Consensus         6 IvieG~~GsGKsT~~~~L~~   25 (195)
T TIGR00041         6 IVIEGIDGAGKTTQANLLKK   25 (195)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999886

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

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=93.76  E-value=0.038  Score=48.90  Aligned_cols=20  Identities=15%  Similarity=0.172  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~i~G   48 (227)
T cd03260          29 TALIGPSGCGKSTLLRLLNR   48 (227)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999976

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional

Probab=93.76  E-value=0.037  Score=50.74  Aligned_cols=19  Identities=16%  Similarity=0.027  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |.|.|+.|+||||+++.+-
T Consensus         9 i~i~G~~GsGKtt~~~~l~   27 (288)
T PRK05416          9 VIVTGLSGAGKSVALRALE   27 (288)
T ss_pred             EEEECCCCCcHHHHHHHHH
Confidence            5799999999999999984

>PTZ00202 tuzin; Provisional

Probab=93.75  E-value=0.27  Score=47.42  Aligned_cols=46  Identities=13%  Similarity=0.107  Sum_probs=33.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhhc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVM   54 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~   54 (391)
                      +.|.|++|+|||||++.+...  +.    ...+++.++  ..+++...++..+.
T Consensus       289 vvLtG~~G~GKTTLlR~~~~~--l~----~~qL~vNpr--g~eElLr~LL~ALG  334 (550)
T PTZ00202        289 VVFTGFRGCGKSSLCRSAVRK--EG----MPAVFVDVR--GTEDTLRSVVKALG  334 (550)
T ss_pred             EEEECCCCCCHHHHHHHHHhc--CC----ceEEEECCC--CHHHHHHHHHHHcC
Confidence            368999999999999998863  32    336666665  55777777776654

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=93.75  E-value=0.037  Score=50.33  Aligned_cols=31  Identities=10%  Similarity=-0.007  Sum_probs=23.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWV   34 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~   34 (391)
                      |+|+|..|+|||||+..+..  .++..- .++.+
T Consensus         4 i~i~G~~gSGKTTLi~~Li~--~L~~~G-~V~~I   34 (274)
T PRK14493          4 LSIVGYKATGKTTLVERLVD--RLSGRG-RVGTV   34 (274)
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHhCC-CEEEE
Confidence            68999999999999999887  455544 34443

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=93.74  E-value=0.038  Score=48.38  Aligned_cols=20  Identities=15%  Similarity=0.311  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        28 ~~l~G~nGsGKSTLl~~l~G   47 (213)
T cd03235          28 LAIVGPNGAGKSTLLKAILG   47 (213)
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            58999999999999999976

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>cd04120 Rab12 Rab12 subfamily

Probab=93.74  E-value=0.047  Score=47.41  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|||||||++...++
T Consensus         3 vvvlG~~gVGKTSli~r~~~~   23 (202)
T cd04120           3 VIIIGSRGVGKTSLMRRFTDD   23 (202)
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            578999999999999887654

Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=93.73  E-value=0.038  Score=49.45  Aligned_cols=20  Identities=15%  Similarity=0.238  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        31 ~~l~G~nGsGKSTLl~~l~G   50 (243)
T TIGR02315        31 VAIIGPSGAGKSTLLRCINR   50 (243)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=93.73  E-value=0.038  Score=49.35  Aligned_cols=20  Identities=15%  Similarity=0.220  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (241)
T cd03256          30 VALIGPSGAGKSTLLRCLNG   49 (241)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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.

>PRK08181 transposase; Validated

Probab=93.73  E-value=0.056  Score=49.07  Aligned_cols=33  Identities=12%  Similarity=-0.046  Sum_probs=23.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      |-++|..|+|||.||.++.+  ++-.....+.|++
T Consensus       109 lll~Gp~GtGKTHLa~Aia~--~a~~~g~~v~f~~  141 (269)
T PRK08181        109 LLLFGPPGGGKSHLAAAIGL--ALIENGWRVLFTR  141 (269)
T ss_pred             EEEEecCCCcHHHHHHHHHH--HHHHcCCceeeee
Confidence            35899999999999999876  2322333445544

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=93.72  E-value=0.039  Score=47.06  Aligned_cols=20  Identities=15%  Similarity=0.082  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|..|.||||+|+.+..
T Consensus        21 i~i~G~~GsGKstla~~l~~   40 (184)
T TIGR00455        21 IWLTGLSGSGKSTIANALEK   40 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=93.71  E-value=0.046  Score=52.64  Aligned_cols=19  Identities=21%  Similarity=0.179  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|.+|+|||++|+++.+
T Consensus       169 LL~GppGtGKT~lAkaia~  187 (389)
T PRK03992        169 LLYGPPGTGKTLLAKAVAH  187 (389)
T ss_pred             EEECCCCCChHHHHHHHHH
Confidence            4799999999999999988

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=93.70  E-value=0.036  Score=50.40  Aligned_cols=20  Identities=15%  Similarity=0.262  Sum_probs=16.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|-|||||||++-.+..
T Consensus         4 iav~~KGGvGKTT~~~nLA~   23 (270)
T cd02040           4 IAIYGKGGIGKSTTTQNLSA   23 (270)
T ss_pred             EEEEeCCcCCHHHHHHHHHH
Confidence            57889999999998888654

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.

>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases

Probab=93.70  E-value=0.043  Score=45.92  Aligned_cols=20  Identities=20%  Similarity=0.370  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||||.+.+.+
T Consensus         3 i~vvG~~~vGKTsli~~~~~   22 (166)
T cd00877           3 LVLVGDGGTGKTTFVKRHLT   22 (166)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999998764

Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is

>PLN03046 D-glycerate 3-kinase; Provisional

Probab=93.69  E-value=0.038  Score=52.75  Aligned_cols=20  Identities=15%  Similarity=0.079  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|.|||||++.+..
T Consensus       215 IGIsG~qGSGKSTLa~~L~~  234 (460)
T PLN03046        215 IGFSAPQGCGKTTLVFALDY  234 (460)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999854

>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2)

Probab=93.69  E-value=0.039  Score=47.94  Aligned_cols=18  Identities=6%  Similarity=0.248  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |||+|..|.|||||++.+
T Consensus         3 i~~~g~~~~GKttL~~~l   20 (203)
T cd01888           3 IGTIGHVAHGKSTLVKAL   20 (203)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            689999999999999987

eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the sel

>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily

Probab=93.68  E-value=0.05  Score=47.08  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 ivivG~~~vGKTsli~~l~~~   23 (201)
T cd04107           3 VLVIGDLGVGKTSIIKRYVHG   23 (201)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999987654

Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=93.68  E-value=0.05  Score=45.62  Aligned_cols=21  Identities=14%  Similarity=0.235  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+...
T Consensus         5 i~vvG~~~vGKTsli~~~~~~   25 (170)
T cd04115           5 IIVIGDSNVGKTCLTYRFCAG   25 (170)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998654

Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=93.67  E-value=0.04  Score=48.79  Aligned_cols=20  Identities=20%  Similarity=0.258  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        39 ~~i~G~nGsGKSTLl~~i~G   58 (228)
T PRK10584         39 IALIGESGSGKSTLLAILAG   58 (228)
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            58999999999999999986

>PRK09183 transposase/IS protein; Provisional

Probab=93.67  E-value=0.035  Score=50.20  Aligned_cols=20  Identities=25%  Similarity=0.285  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||+||..+.+
T Consensus       105 v~l~Gp~GtGKThLa~al~~  124 (259)
T PRK09183        105 IVLLGPSGVGKTHLAIALGY  124 (259)
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            46899999999999999865

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=93.66  E-value=0.041  Score=47.84  Aligned_cols=20  Identities=15%  Similarity=0.125  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        27 ~~i~G~nGsGKSTLl~~l~G   46 (206)
T TIGR03608        27 YAIIGESGSGKSTLLNIIGL   46 (206)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=93.64  E-value=0.042  Score=49.34  Aligned_cols=20  Identities=25%  Similarity=0.170  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|-.|+||||+|+.+..
T Consensus         2 IgItG~SGSGKTTv~~~l~~   21 (277)
T cd02029           2 IAVTGSSGAGTTTVKRAFEH   21 (277)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999998765

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>TIGR01351 adk adenylate kinases

Probab=93.63  E-value=0.042  Score=48.04  Aligned_cols=20  Identities=20%  Similarity=0.184  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~   21 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAE   21 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56999999999999999865

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=93.63  E-value=0.041  Score=48.17  Aligned_cols=20  Identities=10%  Similarity=0.165  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        26 ~~i~G~nGsGKSTLl~~l~G   45 (214)
T cd03297          26 TGIFGASGAGKSTLLRCIAG   45 (214)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=93.61  E-value=0.098  Score=48.89  Aligned_cols=52  Identities=8%  Similarity=0.018  Sum_probs=36.4

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccc----cEEEEEEcCCCcChHHHHHHHHHhhcC
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYF----DCHAWVQESLPYDADQILYDIIKFVMP   55 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F----~~~~~~~vs~~~~~~~i~~~~~~~~~~   55 (391)
                      |+|.+|+|||+++..+.-+...+...    ..++|+.....|+.+++.+. +..+.|
T Consensus       107 i~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~-~~~~g~  162 (317)
T PRK04301        107 FYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQM-AEALGL  162 (317)
T ss_pred             EECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHH-HHHcCC
Confidence            89999999999999986532222111    37889988888998886553 333334

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=93.61  E-value=0.041  Score=48.99  Aligned_cols=20  Identities=20%  Similarity=0.218  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+.-
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (236)
T TIGR03864        30 VALLGPNGAGKSTLFSLLTR   49 (236)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>PRK14531 adenylate kinase; Provisional

Probab=93.60  E-value=0.042  Score=46.88  Aligned_cols=20  Identities=25%  Similarity=0.232  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|++|.||||+++.+..
T Consensus         5 i~i~G~pGsGKsT~~~~la~   24 (183)
T PRK14531          5 LLFLGPPGAGKGTQAARLCA   24 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999865

>cd04122 Rab14 Rab14 subfamily

Probab=93.60  E-value=0.054  Score=45.12  Aligned_cols=21  Identities=10%  Similarity=0.311  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.+.
T Consensus         5 i~iiG~~~vGKTsli~~~~~~   25 (166)
T cd04122           5 YIIIGDMGVGKSCLLHQFTEK   25 (166)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999997664

Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GT

>PRK00279 adk adenylate kinase; Reviewed

Probab=93.58  E-value=0.042  Score=48.23  Aligned_cols=20  Identities=20%  Similarity=0.112  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         3 I~v~G~pGsGKsT~a~~la~   22 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAE   22 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999765

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=93.57  E-value=0.042  Score=49.06  Aligned_cols=20  Identities=25%  Similarity=0.238  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (239)
T cd03296          31 VALLGPSGSGKTTLLRLIAG   50 (239)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). 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.

>cd01394 radB RadB

Probab=93.57  E-value=0.079  Score=46.52  Aligned_cols=38  Identities=16%  Similarity=0.016  Sum_probs=26.3

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcC
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYD   41 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~   41 (391)
                      .|+|.+|+||||+|..+...  ....=..++|+.....++
T Consensus        23 ~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e~~~~   60 (218)
T cd01394          23 QVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTEGLSS   60 (218)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCCCCH
Confidence            58999999999999997652  211223667776655554

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

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=93.57  E-value=0.042  Score=48.57  Aligned_cols=20  Identities=15%  Similarity=0.313  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        34 ~~i~G~nGsGKSTLl~~l~G   53 (228)
T cd03257          34 LGLVGESGSGKSTLARAILG   53 (228)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=93.56  E-value=0.043  Score=47.98  Aligned_cols=20  Identities=20%  Similarity=0.154  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.|..|.|||||++.+..
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G   48 (213)
T cd03301          29 VVLLGPSGCGKTTTLRMIAG   48 (213)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=93.56  E-value=0.043  Score=48.80  Aligned_cols=20  Identities=25%  Similarity=0.242  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        38 ~~l~G~nGsGKSTLl~~l~G   57 (233)
T PRK11629         38 MAIVGSSGSGKSTLLHLLGG   57 (233)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

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

Probab=93.56  E-value=0.0096  Score=47.48  Aligned_cols=75  Identities=16%  Similarity=0.084  Sum_probs=36.7

Q ss_pred             cCCcccEEEcCCCccccCCcccCCC-CcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchhH
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENL-FLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSK  249 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l-~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~  249 (391)
                      +...|...++++|.+..+|+.+... +.+..|++.+|.++.+|.++-      .++++.|.+.             ..|.
T Consensus        51 ~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N~l~-------------~~p~  117 (177)
T KOG4579|consen   51 KGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFNPLN-------------AEPR  117 (177)
T ss_pred             CCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccCccc-------------cchH
Confidence            3344444455555555555444322 244455555555555554433      4444444444             4555


Q ss_pred             HhcCCCCCCEEEecC
Q 041097          250 SLCRLSCLESLKLAN  264 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~  264 (391)
                      -+.+|.+|-.|+..+
T Consensus       118 vi~~L~~l~~Lds~~  132 (177)
T KOG4579|consen  118 VIAPLIKLDMLDSPE  132 (177)
T ss_pred             HHHHHHhHHHhcCCC
Confidence            555566666665544

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=93.55  E-value=0.043  Score=48.27  Aligned_cols=20  Identities=20%  Similarity=0.175  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~i~G   48 (220)
T cd03265          29 FGLLGPNGAGKTTTIKMLTT   48 (220)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. 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.

>cd04158 ARD1 ARD1 subfamily

Probab=93.55  E-value=0.048  Score=45.69  Aligned_cols=21  Identities=19%  Similarity=0.126  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         2 vvlvG~~~~GKTsl~~~l~~~   22 (169)
T cd04158           2 VVTLGLDGAGKTTILFKLKQD   22 (169)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membra

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=93.54  E-value=0.045  Score=45.47  Aligned_cols=20  Identities=15%  Similarity=0.213  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         4 i~i~G~~gsGKTTli~~L~~   23 (159)
T cd03116           4 IGFVGYSGSGKTTLLEKLIP   23 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999886

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>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=93.54  E-value=0.036  Score=48.81  Aligned_cols=20  Identities=20%  Similarity=0.243  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||||++.+.+
T Consensus        23 ~~l~G~rg~GKTsLl~~~~~   42 (234)
T PF01637_consen   23 ILLYGPRGSGKTSLLKEFIN   42 (234)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEcCCcCCHHHHHHHHHH
Confidence            46899999999999999887

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

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=93.54  E-value=0.043  Score=48.27  Aligned_cols=20  Identities=20%  Similarity=0.197  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        34 ~~i~G~nGsGKSTLl~~i~G   53 (221)
T TIGR02211        34 VAIVGSSGSGKSTLLHLLGG   53 (221)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=93.54  E-value=0.044  Score=48.47  Aligned_cols=21  Identities=14%  Similarity=0.067  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        36 ~~i~G~nGsGKSTLl~~l~G~   56 (225)
T PRK10247         36 KLITGPSGCGKSTLLKIVASL   56 (225)
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            589999999999999999873

>cd04135 Tc10 TC10 subfamily

Probab=93.53  E-value=0.055  Score=45.38  Aligned_cols=21  Identities=14%  Similarity=0.104  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         3 i~i~G~~~~GKTsl~~~~~~~   23 (174)
T cd04135           3 CVVVGDGAVGKTCLLMSYAND   23 (174)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999887554

TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=93.52  E-value=0.042  Score=48.15  Aligned_cols=19  Identities=16%  Similarity=0.032  Sum_probs=16.6

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|||.+|+||||+|+.+-+
T Consensus        16 liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        16 LIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             EEECCCCCCHHHHHHhcCC
Confidence            4899999999999998743

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

>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD

Probab=93.52  E-value=0.043  Score=48.67  Aligned_cols=21  Identities=14%  Similarity=0.161  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|.|..|.|||||++.+.-.
T Consensus        15 ~~i~G~nGsGKSTLl~~l~Gl   35 (230)
T TIGR02770        15 LALVGESGSGKSLTCLAILGL   35 (230)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            589999999999999999873

This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous.

>cd04117 Rab15 Rab15 subfamily

Probab=93.51  E-value=0.057  Score=44.84  Aligned_cols=21  Identities=14%  Similarity=0.297  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.+.
T Consensus         3 i~vvG~~~~GKTsli~~~~~~   23 (161)
T cd04117           3 LLLIGDSGVGKTCLLCRFTDN   23 (161)
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999887553

Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to

>PF00142 Fer4_NifH: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family; InterPro: IPR000392 This entry represents members of the NifH/BchL/ChlL family

Probab=93.51  E-value=0.042  Score=48.98  Aligned_cols=20  Identities=20%  Similarity=0.313  Sum_probs=17.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|||-||+||+|.+..+--
T Consensus         3 IAiYGKGGIGKST~~~Nlsa   22 (273)
T PF00142_consen    3 IAIYGKGGIGKSTTASNLSA   22 (273)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCcccChhhhHHHH
Confidence            68999999999999988643

Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [, , ]. The nitrogenase enzyme complex consists of two components: Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits. Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene []. Component II has 2 ATP-binding domains and one 4Fe-4S cluster per homodimer: it supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component I for the reduction of molecular nitrogen to ammonia []. There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) IPR001687 from INTERPRO and in the central section there are two conserved cysteines which have been shown, in nifH, to be the ligands of the 4Fe-4S cluster. Protochlorophyllide reductase is involved in light-independent chlorophyll biosynthesis. The light-independent reaction uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This enzyme complex is composed of three subunits: ChlL, ChlN and ChlB. ChlL is present as a homodimer, and binds one 4Fe-4S cluster per dimer. The conserved domains, including the ATP-binding motif and the Fe-S binding motif found in the three subunits, are similar to those in nitrogenases []. ; GO: 0005524 ATP binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1CP2_A 2AFI_F 1N2C_F 1FP6_C 2AFK_G 1M34_M 1XD8_A 1NIP_A 1M1Y_N 1G21_H ....

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.51  E-value=0.044  Score=47.60  Aligned_cols=20  Identities=15%  Similarity=0.106  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        30 ~~l~G~nGsGKSTLl~~l~G   49 (204)
T PRK13538         30 VQIEGPNGAGKTSLLRILAG   49 (204)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            48999999999999999987

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=93.51  E-value=0.044  Score=48.01  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        16 ~~l~G~NGsGKSTLlk~i~G   35 (213)
T PRK15177         16 IGILAAPGSGKTTLTRLLCG   35 (213)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=93.50  E-value=0.044  Score=49.00  Aligned_cols=20  Identities=15%  Similarity=0.207  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.|..|.|||||++.+..
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (242)
T PRK11124         31 LVLLGPSGAGKSSLLRVLNL   50 (242)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=93.50  E-value=0.044  Score=49.48  Aligned_cols=20  Identities=25%  Similarity=0.262  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (255)
T PRK11248         30 LVVLGPSGCGKTTLLNLIAG   49 (255)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

>PRK14732 coaE dephospho-CoA kinase; Provisional

Probab=93.50  E-value=0.046  Score=47.20  Aligned_cols=19  Identities=16%  Similarity=0.083  Sum_probs=17.3

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |||+|..|+||||+++.+-
T Consensus         2 i~itG~~gsGKst~~~~l~   20 (196)
T PRK14732          2 IGITGMIGGGKSTALKILE   20 (196)
T ss_pred             EEEECCCCccHHHHHHHHH
Confidence            6999999999999999754

>PTZ00369 Ras-like protein; Provisional

Probab=93.48  E-value=0.057  Score=46.24  Aligned_cols=21  Identities=19%  Similarity=0.339  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||+..+.++
T Consensus         8 i~iiG~~~~GKTsLi~~~~~~   28 (189)
T PTZ00369          8 LVVVGGGGVGKSALTIQFIQN   28 (189)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999987664

>PRK14733 coaE dephospho-CoA kinase; Provisional

Probab=93.47  E-value=0.046  Score=47.41  Aligned_cols=20  Identities=10%  Similarity=0.086  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+||||+++.+..
T Consensus         9 IglTG~iGsGKStv~~~l~~   28 (204)
T PRK14733          9 IGITGGIASGKSTATRILKE   28 (204)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999999764

>cd04110 Rab35 Rab35 subfamily

Probab=93.46  E-value=0.05  Score=47.03  Aligned_cols=21  Identities=10%  Similarity=0.279  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (199)
T cd04110           9 LLIIGDSGVGKSSLLLRFADN   29 (199)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999987653

Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is

>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB

Probab=93.45  E-value=0.05  Score=46.15  Aligned_cols=22  Identities=9%  Similarity=0.143  Sum_probs=19.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |+|+|..|+|||||...+..+.
T Consensus        21 i~ivG~~~~GKStlin~l~~~~   42 (179)
T TIGR03598        21 IAFAGRSNVGKSSLINALTNRK   42 (179)
T ss_pred             EEEEcCCCCCHHHHHHHHhCCC
Confidence            6899999999999999998753

Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.

>cd01868 Rab11_like Rab11-like

Probab=93.44  E-value=0.052  Score=45.06  Aligned_cols=21  Identities=10%  Similarity=0.283  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus         6 i~vvG~~~~GKSsli~~l~~~   26 (165)
T cd01868           6 IVLIGDSGVGKSNLLSRFTRN   26 (165)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998754

Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=93.43  E-value=0.046  Score=48.49  Aligned_cols=20  Identities=10%  Similarity=0.205  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        14 ~~i~G~nGsGKSTLl~~l~G   33 (230)
T TIGR01184        14 ISLIGHSGCGKSTLLNLISG   33 (230)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=93.42  E-value=0.047  Score=48.52  Aligned_cols=20  Identities=10%  Similarity=0.214  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        34 ~~l~G~nGsGKSTLl~~l~G   53 (233)
T cd03258          34 FGIIGRSGAGKSTLIRCING   53 (233)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

Other members of this system include the MetP permease and the MetQ substrate binding protein. 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.

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=93.40  E-value=0.054  Score=44.67  Aligned_cols=21  Identities=10%  Similarity=0.041  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus         2 i~i~G~~~~GKTsl~~~~~~~   22 (160)
T cd04156           2 VLLLGLDSAGKSTLLYKLKHA   22 (160)
T ss_pred             EEEEcCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in h

>PRK14737 gmk guanylate kinase; Provisional

Probab=93.40  E-value=0.048  Score=46.64  Aligned_cols=20  Identities=10%  Similarity=0.121  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||||++.+..
T Consensus         7 ivl~GpsG~GK~tl~~~l~~   26 (186)
T PRK14737          7 FIISSVAGGGKSTIIQALLE   26 (186)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999987

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

Probab=93.39  E-value=0.048  Score=46.67  Aligned_cols=20  Identities=15%  Similarity=0.227  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.||||+++.+..
T Consensus        28 i~I~G~tGSGKTTll~aL~~   47 (186)
T cd01130          28 ILISGGTGSGKTTLLNALLA   47 (186)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999875

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

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=93.39  E-value=0.051  Score=46.99  Aligned_cols=20  Identities=15%  Similarity=0.125  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||+++++.
T Consensus        25 ~~i~G~nGsGKStll~al~~   44 (197)
T cd03278          25 TAIVGPNGSGKSNIIDAIRW   44 (197)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            47999999999999999873

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>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=93.38  E-value=0.05  Score=45.94  Aligned_cols=20  Identities=20%  Similarity=0.340  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        31 ~~i~G~nGsGKStLl~~l~G   50 (173)
T cd03246          31 LAIIGPSGSGKSTLARLILG   50 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999986

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

>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily

Probab=93.35  E-value=0.063  Score=45.11  Aligned_cols=21  Identities=14%  Similarity=0.271  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         3 i~ivG~~~vGKTsli~~~~~~   23 (170)
T cd04108           3 VIVVGDLSVGKTCLINRFCKD   23 (170)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998765

Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further re

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=93.35  E-value=0.049  Score=48.55  Aligned_cols=20  Identities=15%  Similarity=0.250  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|+.|.|||||.|.+..
T Consensus        33 ~~iiGPNGaGKSTLlK~iLG   52 (254)
T COG1121          33 TALIGPNGAGKSTLLKAILG   52 (254)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases

Probab=93.34  E-value=0.072  Score=44.66  Aligned_cols=21  Identities=14%  Similarity=0.181  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||...+.++
T Consensus         1 i~i~G~~~vGKTsli~~~~~~   21 (174)
T smart00174        1 LVVVGDGAVGKTCLLISYTTN   21 (174)
T ss_pred             CEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999987653

Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=93.34  E-value=0.048  Score=47.99  Aligned_cols=20  Identities=25%  Similarity=0.308  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (222)
T cd03224          29 VALLGRNGAGKTTLLKTIMG   48 (222)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999876

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). 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.

>cd04144 Ras2 Ras2 subfamily

Probab=93.33  E-value=0.054  Score=46.41  Aligned_cols=21  Identities=29%  Similarity=0.376  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         2 i~ivG~~~vGKTsli~~l~~~   22 (190)
T cd04144           2 LVVLGDGGVGKTALTIQLCLN   22 (190)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999997653

The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=93.33  E-value=0.049  Score=48.89  Aligned_cols=21  Identities=24%  Similarity=0.373  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|+|||||++.+...
T Consensus        28 ~~i~G~NGsGKSTLlk~L~G~   48 (246)
T cd03237          28 IGILGPNGIGKTTFIKMLAGV   48 (246)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999999773

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. 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 of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=93.33  E-value=0.049  Score=47.81  Aligned_cols=20  Identities=20%  Similarity=0.106  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        34 ~~i~G~nGsGKSTLl~~l~G   53 (218)
T cd03266          34 TGLLGPNGAGKTTTLRMLAG   53 (218)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>cd04106 Rab23_lke Rab23-like subfamily

Probab=93.32  E-value=0.064  Score=44.28  Aligned_cols=21  Identities=10%  Similarity=0.140  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         3 v~~vG~~~~GKTsl~~~~~~~   23 (162)
T cd04106           3 VIVVGNGNVGKSSMIQRFVKG   23 (162)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.32  E-value=0.05  Score=47.11  Aligned_cols=20  Identities=20%  Similarity=0.135  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        30 ~~l~G~nGsGKSTLl~~i~G   49 (200)
T PRK13540         30 LHLKGSNGAGKTTLLKLIAG   49 (200)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999987

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=93.32  E-value=0.048  Score=48.53  Aligned_cols=20  Identities=15%  Similarity=0.129  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G   48 (236)
T cd03219          29 HGLIGPNGAGKTTLFNLISG   48 (236)
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            58999999999999999986

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).

>PRK08116 hypothetical protein; Validated

Probab=93.32  E-value=0.05  Score=49.48  Aligned_cols=32  Identities=22%  Similarity=0.053  Sum_probs=23.4

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      -+||-.|+|||.||.++++  ++...-..+++++
T Consensus       118 ~l~G~~GtGKThLa~aia~--~l~~~~~~v~~~~  149 (268)
T PRK08116        118 LLWGSVGTGKTYLAACIAN--ELIEKGVPVIFVN  149 (268)
T ss_pred             EEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEE
Confidence            4899999999999999998  3433323455544

>PRK05642 DNA replication initiation factor; Validated

Probab=93.32  E-value=0.061  Score=47.87  Aligned_cols=33  Identities=6%  Similarity=0.050  Sum_probs=23.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQE   36 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~v   36 (391)
                      -|||..|+|||.|++++.+.  +...=..+.|++.
T Consensus        49 ~l~G~~G~GKTHLl~a~~~~--~~~~~~~v~y~~~   81 (234)
T PRK05642         49 YLWGKDGVGRSHLLQAACLR--FEQRGEPAVYLPL   81 (234)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhCCCcEEEeeH
Confidence            48999999999999999872  2221134556554

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=93.32  E-value=0.051  Score=46.09  Aligned_cols=21  Identities=19%  Similarity=0.229  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|.|..|.|||||++.+.-.
T Consensus        31 ~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          31 IALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            479999999999999999873

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.

>cd01861 Rab6 Rab6 subfamily

Probab=93.31  E-value=0.056  Score=44.59  Aligned_cols=21  Identities=14%  Similarity=0.194  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||...+...
T Consensus         3 i~liG~~~~GKSsli~~l~~~   23 (161)
T cd01861           3 LVFLGDQSVGKTSIITRFMYD   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999997654

Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=93.31  E-value=0.049  Score=48.51  Aligned_cols=20  Identities=10%  Similarity=0.197  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (237)
T cd03252          31 VGIVGRSGSGKSTLTKLIQR   50 (237)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>cd02032 Bchl_like This family of proteins contains bchL and chlL

Probab=93.31  E-value=0.047  Score=49.64  Aligned_cols=19  Identities=21%  Similarity=0.298  Sum_probs=16.1

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|.|-||+||||.|-.+-
T Consensus         3 i~v~gKGGvGKTT~a~nLA   21 (267)
T cd02032           3 LAVYGKGGIGKSTTSSNLS   21 (267)
T ss_pred             EEEecCCCCCHHHHHHHHH
Confidence            6789999999999877754

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.

>cd04118 Rab24 Rab24 subfamily

Probab=93.30  E-value=0.053  Score=46.45  Aligned_cols=21  Identities=14%  Similarity=0.203  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         3 i~vvG~~~vGKSsLi~~~~~~   23 (193)
T cd04118           3 VVMLGKESVGKTSLVERYVHH   23 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilita

>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily

Probab=93.30  E-value=0.062  Score=45.26  Aligned_cols=20  Identities=25%  Similarity=0.358  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|-+|+|||||++....
T Consensus         5 i~vvG~~~vGKTsL~~~~~~   24 (172)
T cd04141           5 IVMLGAGGVGKSAVTMQFIS   24 (172)
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            57999999999999988654

Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=93.28  E-value=0.047  Score=50.78  Aligned_cols=20  Identities=15%  Similarity=0.227  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+++||.|+||||+++.+..
T Consensus       136 I~l~G~~GsGKStvg~~La~  155 (309)
T PRK08154        136 IALIGLRGAGKSTLGRMLAA  155 (309)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>cd04127 Rab27A Rab27a subfamily

Probab=93.28  E-value=0.064  Score=45.28  Aligned_cols=21  Identities=24%  Similarity=0.338  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus         7 i~ivG~~~vGKTsli~~~~~~   27 (180)
T cd04127           7 FLALGDSGVGKTSFLYQYTDN   27 (180)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998664

The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated

>cd04114 Rab30 Rab30 subfamily

Probab=93.27  E-value=0.052  Score=45.25  Aligned_cols=20  Identities=15%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||.+.+..
T Consensus        10 v~v~G~~~~GKSsli~~l~~   29 (169)
T cd04114          10 IVLIGNAGVGKTCLVRRFTQ   29 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999764

Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>cd01866 Rab2 Rab2 subfamily

Probab=93.26  E-value=0.054  Score=45.30  Aligned_cols=21  Identities=10%  Similarity=0.260  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus         7 i~vvG~~~vGKSsLl~~l~~~   27 (168)
T cd01866           7 YIIIGDTGVGKSCLLLQFTDK   27 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur

>PRK00698 tmk thymidylate kinase; Validated

Probab=93.26  E-value=0.046  Score=47.38  Aligned_cols=20  Identities=10%  Similarity=-0.007  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+-|+||||+++.+.+
T Consensus         6 I~ieG~~gsGKsT~~~~L~~   25 (205)
T PRK00698          6 ITIEGIDGAGKSTQIELLKE   25 (205)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999876

>smart00763 AAA_PrkA PrkA AAA domain

Probab=93.26  E-value=0.045  Score=51.38  Aligned_cols=20  Identities=15%  Similarity=0.230  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++++|..|+||||||+.+.+
T Consensus        81 l~L~GPPGsGKStla~~La~  100 (361)
T smart00763       81 LYLLGPVGGGKSSLVECLKR  100 (361)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999877

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

>cd01865 Rab3 Rab3 subfamily

Probab=93.25  E-value=0.059  Score=44.88  Aligned_cols=22  Identities=14%  Similarity=0.262  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|.+|+|||||+..+.++.
T Consensus         4 i~i~G~~~~GKSsli~~l~~~~   25 (165)
T cd01865           4 LLIIGNSSVGKTSFLFRYADDS   25 (165)
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            5799999999999999987653

The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot

>TIGR01978 sufC FeS assembly ATPase SufC

Probab=93.25  E-value=0.051  Score=48.61  Aligned_cols=21  Identities=14%  Similarity=0.230  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        29 ~~i~G~nGsGKSTLl~~l~Gl   49 (243)
T TIGR01978        29 HAIMGPNGSGKSTLSKTIAGH   49 (243)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999999873

SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.

>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=93.24  E-value=0.054  Score=45.73  Aligned_cols=20  Identities=20%  Similarity=0.223  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKStLl~~l~G   48 (173)
T cd03230          29 YGLLGPNGAGKTTLIKIILG   48 (173)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            57999999999999999987

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.

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=93.24  E-value=0.053  Score=46.67  Aligned_cols=20  Identities=20%  Similarity=0.207  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        36 ~~l~G~nGsGKSTLl~~l~G   55 (192)
T cd03232          36 TALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

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.

>cd04125 RabA_like RabA-like subfamily

Probab=93.23  E-value=0.059  Score=46.03  Aligned_cols=21  Identities=10%  Similarity=0.305  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus         3 i~v~G~~~vGKSsli~~~~~~   23 (188)
T cd04125           3 VVIIGDYGVGKSSLLKRFTED   23 (188)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>PRK14526 adenylate kinase; Provisional

Probab=93.22  E-value=0.053  Score=47.41  Aligned_cols=20  Identities=20%  Similarity=0.174  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus         3 i~l~G~pGsGKsT~a~~La~   22 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSN   22 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999765

>PRK13235 nifH nitrogenase reductase; Reviewed

Probab=93.22  E-value=0.049  Score=49.72  Aligned_cols=19  Identities=16%  Similarity=0.286  Sum_probs=15.9

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|+|-|||||||.+-.+-
T Consensus         4 iav~~KGGVGKTT~~~nLA   22 (274)
T PRK13235          4 VAIYGKGGIGKSTTTQNTV   22 (274)
T ss_pred             EEEeCCCCccHHHHHHHHH
Confidence            5788999999999877653

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=93.21  E-value=0.054  Score=46.82  Aligned_cols=21  Identities=19%  Similarity=0.170  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G~   49 (198)
T TIGR01189        29 LQVTGPNGIGKTTLLRILAGL   49 (198)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999999873

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=93.20  E-value=0.05  Score=54.22  Aligned_cols=20  Identities=25%  Similarity=0.403  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|.||||||+.+..
T Consensus        68 IGIaGpSGSGKTTLAk~Lag   87 (656)
T PLN02318         68 VGVAGPSGAGKTVFTEKVLN   87 (656)
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            79999999999999999876

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=93.19  E-value=0.053  Score=48.11  Aligned_cols=20  Identities=20%  Similarity=0.122  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G   48 (232)
T cd03218          29 VGLLGPNGAGKTTTFYMIVG   48 (232)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=93.19  E-value=0.06  Score=45.84  Aligned_cols=21  Identities=10%  Similarity=-0.023  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+..+
T Consensus        20 v~lvG~~~vGKTsli~~~~~~   40 (182)
T PTZ00133         20 ILMVGLDAAGKTTILYKLKLG   40 (182)
T ss_pred             EEEEcCCCCCHHHHHHHHhcC
Confidence            578999999999999998553

>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=93.19  E-value=0.056  Score=44.15  Aligned_cols=21  Identities=10%  Similarity=0.156  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        29 ~~i~G~nGsGKStLl~~l~G~   49 (144)
T cd03221          29 IGLVGRNGAGKSTLLKLIAGE   49 (144)
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            479999999999999999773

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.

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=93.19  E-value=0.054  Score=47.43  Aligned_cols=21  Identities=14%  Similarity=0.188  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|.|..|.|||||++.++-.
T Consensus        27 ~~i~G~nGsGKSTLl~~l~G~   47 (213)
T TIGR01277        27 VAIMGPSGAGKSTLLNLIAGF   47 (213)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            589999999999999999873

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>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=93.19  E-value=0.056  Score=45.33  Aligned_cols=21  Identities=10%  Similarity=0.118  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+.--
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G~   50 (166)
T cd03223          30 LLITGPSGTGKSSLFRALAGL   50 (166)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            489999999999999999773

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

>cd04129 Rho2 Rho2 subfamily

Probab=93.18  E-value=0.064  Score=45.81  Aligned_cols=20  Identities=10%  Similarity=0.061  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||.+.+..
T Consensus         4 i~ivG~~g~GKStLl~~l~~   23 (187)
T cd04129           4 LVIVGDGACGKTSLLSVFTL   23 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999864

Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.17  E-value=0.052  Score=50.59  Aligned_cols=20  Identities=20%  Similarity=0.214  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+++|..|+||||++.++..
T Consensus       117 i~lvGpnGsGKTTt~~kLA~  136 (318)
T PRK10416        117 ILVVGVNGVGKTTTIGKLAH  136 (318)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57999999999999998865

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

Probab=93.17  E-value=0.051  Score=52.81  Aligned_cols=25  Identities=20%  Similarity=0.179  Sum_probs=20.7

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF   28 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F   28 (391)
                      -++|..|+|||++|+++.+  +....|
T Consensus       221 LL~GPPGTGKT~LAraIA~--el~~~f  245 (438)
T PTZ00361        221 ILYGPPGTGKTLLAKAVAN--ETSATF  245 (438)
T ss_pred             EEECCCCCCHHHHHHHHHH--hhCCCE
Confidence            4799999999999999998  444444

>PRK06526 transposase; Provisional

Probab=93.17  E-value=0.051  Score=48.94  Aligned_cols=20  Identities=25%  Similarity=0.165  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++|.+|+|||+||+.+.+
T Consensus       101 lll~Gp~GtGKThLa~al~~  120 (254)
T PRK06526        101 VVFLGPPGTGKTHLAIGLGI  120 (254)
T ss_pred             EEEEeCCCCchHHHHHHHHH
Confidence            35899999999999999876

>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans

Probab=93.16  E-value=0.06  Score=44.82  Aligned_cols=21  Identities=5%  Similarity=0.150  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         3 i~~~G~~~~GKssli~~l~~~   23 (168)
T cd01897           3 LVIAGYPNVGKSSLVNKLTRA   23 (168)
T ss_pred             EEEEcCCCCCHHHHHHHHhcC
Confidence            579999999999999998774

NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.

>cd04151 Arl1 Arl1 subfamily

Probab=93.16  E-value=0.056  Score=44.63  Aligned_cols=20  Identities=15%  Similarity=0.022  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+..+..
T Consensus         2 v~lvG~~~~GKTsl~~~l~~   21 (158)
T cd04151           2 ILILGLDNAGKTTILYRLQL   21 (158)
T ss_pred             EEEECCCCCCHHHHHHHHcc
Confidence            57999999999999999854

Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.

>PRK04213 GTP-binding protein; Provisional

Probab=93.16  E-value=0.061  Score=46.47  Aligned_cols=21  Identities=10%  Similarity=0.203  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||...+.++
T Consensus        12 i~i~G~~~~GKSsLin~l~~~   32 (201)
T PRK04213         12 IVFVGRSNVGKSTLVRELTGK   32 (201)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999998764

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=93.15  E-value=0.05  Score=49.69  Aligned_cols=20  Identities=15%  Similarity=0.287  Sum_probs=16.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-|||||||.|-.+-.
T Consensus         5 Iav~~KGGVGKTT~a~nLA~   24 (275)
T PRK13233          5 IAIYGKGGIGKSTTTQNTAA   24 (275)
T ss_pred             EEEEcCCCCcHHHHHHHHHH
Confidence            56789999999998887543

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=93.13  E-value=0.055  Score=48.92  Aligned_cols=21  Identities=19%  Similarity=0.240  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        34 ~~l~G~nGsGKSTLl~~i~G~   54 (257)
T PRK10619         34 ISIIGSSGSGKSTFLRCINFL   54 (257)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999999873

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

Probab=93.13  E-value=0.12  Score=46.74  Aligned_cols=51  Identities=14%  Similarity=0.031  Sum_probs=35.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhhcCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPS   56 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~   56 (391)
                      +-|+|-+|+|||++|.+.-.  +.......|.|+..+.  +.+.+.+.... +.|.
T Consensus        26 ~lI~G~pGsGKT~f~~qfl~--~~~~~ge~vlyvs~~e--~~~~l~~~~~~-~g~d   76 (260)
T COG0467          26 VLITGPPGTGKTIFALQFLY--EGAREGEPVLYVSTEE--SPEELLENARS-FGWD   76 (260)
T ss_pred             EEEEcCCCCcHHHHHHHHHH--HHHhcCCcEEEEEecC--CHHHHHHHHHH-cCCC
Confidence            35899999999999998755  2334478899998874  45555554433 5553

>smart00178 SAR Sar1p-like members of the Ras-family of small GTPases

Probab=93.12  E-value=0.06  Score=45.88  Aligned_cols=21  Identities=14%  Similarity=0.023  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+..+
T Consensus        20 i~ivG~~~~GKTsli~~l~~~   40 (184)
T smart00178       20 ILFLGLDNAGKTTLLHMLKND   40 (184)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.

>cd01858 NGP_1 NGP-1

Probab=93.12  E-value=0.061  Score=44.57  Aligned_cols=21  Identities=10%  Similarity=0.126  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+++|+.|+||+||...+..+
T Consensus       105 v~~~G~~nvGKStliN~l~~~  125 (157)
T cd01858         105 VGFIGYPNVGKSSIINTLRSK  125 (157)
T ss_pred             EEEEeCCCCChHHHHHHHhcC
Confidence            478999999999999998864

Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.

>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily

Probab=93.11  E-value=0.058  Score=44.64  Aligned_cols=20  Identities=20%  Similarity=0.341  Sum_probs=17.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-+|+|||||+..+.+
T Consensus         5 i~i~G~~~~GKtsl~~~~~~   24 (164)
T cd04145           5 LVVVGGGGVGKSALTIQFIQ   24 (164)
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            57999999999999988654

This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali

>PF13479 AAA_24: AAA domain

Probab=93.11  E-value=0.045  Score=47.95  Aligned_cols=18  Identities=28%  Similarity=0.353  Sum_probs=16.5

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |.|||-+|+||||+|..+
T Consensus         6 ~lIyG~~G~GKTt~a~~~   23 (213)
T PF13479_consen    6 ILIYGPPGSGKTTLAASL   23 (213)
T ss_pred             EEEECCCCCCHHHHHHhC
Confidence            469999999999999996

>TIGR00017 cmk cytidylate kinase

Probab=93.11  E-value=0.057  Score=47.44  Aligned_cols=20  Identities=20%  Similarity=0.230  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|+||||+|+.+..
T Consensus         5 i~i~G~~GsGKst~~~~la~   24 (217)
T TIGR00017         5 IAIDGPSGAGKSTVAKAVAE   24 (217)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=93.10  E-value=0.055  Score=48.72  Aligned_cols=20  Identities=20%  Similarity=0.252  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        35 ~~i~G~nGsGKSTLl~~l~G   54 (253)
T PRK14242         35 TALIGPSGCGKSTFLRCLNR   54 (253)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999974

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=93.10  E-value=0.054  Score=48.42  Aligned_cols=20  Identities=10%  Similarity=0.245  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +|++|-.|+||||++|.+.-
T Consensus        42 ~glVGESG~GKSTlgr~i~~   61 (268)
T COG4608          42 LGLVGESGCGKSTLGRLILG   61 (268)
T ss_pred             EEEEecCCCCHHHHHHHHHc
Confidence            58999999999999999986

>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL

Probab=93.10  E-value=0.056  Score=47.68  Aligned_cols=20  Identities=20%  Similarity=0.360  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        37 ~~l~G~nGsGKSTLl~~i~G   56 (224)
T TIGR02324        37 VALSGPSGAGKSTLLKSLYA   56 (224)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=93.09  E-value=0.056  Score=44.45  Aligned_cols=18  Identities=22%  Similarity=0.165  Sum_probs=16.9

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.+|+||||+|+.+..
T Consensus         1 i~G~PgsGK~t~~~~la~   18 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAK   18 (151)
T ss_dssp             EEESTTSSHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHH
Confidence            789999999999999886

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>PRK07429 phosphoribulokinase; Provisional

Probab=93.09  E-value=0.054  Score=50.63  Aligned_cols=20  Identities=25%  Similarity=0.290  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+..
T Consensus        11 IgI~G~SGSGKSTla~~L~~   30 (327)
T PRK07429         11 LGVAGDSGCGKTTFLRGLAD   30 (327)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            79999999999999999876

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=93.09  E-value=0.059  Score=45.01  Aligned_cols=20  Identities=20%  Similarity=0.180  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.|..|.|||||.+.+.-
T Consensus        29 ~~l~G~nGsGKSTLl~~i~G   48 (163)
T cd03216          29 HALLGENGAGKSTLMKILSG   48 (163)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            57999999999999999987

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.

>PRK14245 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.08  E-value=0.056  Score=48.61  Aligned_cols=19  Identities=21%  Similarity=0.261  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      +||+|..|.|||||++.+.
T Consensus        32 ~~i~G~nGsGKSTLl~~i~   50 (250)
T PRK14245         32 VAFIGPSGCGKSTFLRLFN   50 (250)
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5899999999999999985

>CHL00181 cbbX CbbX; Provisional

Probab=93.08  E-value=0.05  Score=49.98  Aligned_cols=19  Identities=26%  Similarity=0.202  Sum_probs=17.1

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|.+|+||||+|+.+.+
T Consensus        63 ll~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         63 SFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3689999999999999965

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=93.07  E-value=0.057  Score=47.19  Aligned_cols=20  Identities=10%  Similarity=0.154  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G   48 (213)
T cd03262          29 VVIIGPSGSGKSTLLRCINL   48 (213)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>cd04132 Rho4_like Rho4-like subfamily

Probab=93.07  E-value=0.07  Score=45.41  Aligned_cols=21  Identities=19%  Similarity=0.159  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus         3 i~vvG~~~vGKTsli~~l~~~   23 (187)
T cd04132           3 IVVVGDGGCGKTCLLIVYSQG   23 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998765

Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=93.07  E-value=0.05  Score=55.50  Aligned_cols=21  Identities=24%  Similarity=0.251  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+||||+|+.+++.
T Consensus       178 vlL~Gp~GtGKTTLAr~i~~~  198 (615)
T TIGR02903       178 IILYGPPGVGKTTAARLALEE  198 (615)
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999874

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.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=93.06  E-value=0.058  Score=45.94  Aligned_cols=20  Identities=15%  Similarity=0.360  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (182)
T cd03215          29 VGIAGLVGNGQTELAEALFG   48 (182)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            48999999999999999987

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.

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=93.06  E-value=0.055  Score=49.15  Aligned_cols=20  Identities=10%  Similarity=0.077  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        40 ~~i~G~nGsGKSTLl~~l~G   59 (265)
T PRK10575         40 TGLIGHNGSGKSTLLKMLGR   59 (265)
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            58999999999999999986

>smart00072 GuKc Guanylate kinase homologues

Probab=93.06  E-value=0.077  Score=45.29  Aligned_cols=21  Identities=19%  Similarity=0.279  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|+.|+||+|+++.+...
T Consensus         5 ivl~Gpsg~GK~tl~~~L~~~   25 (184)
T smart00072        5 IVLSGPSGVGKGTLLAELIQE   25 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999998873

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=93.06  E-value=0.057  Score=48.82  Aligned_cols=20  Identities=20%  Similarity=0.205  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        41 ~~I~G~NGsGKSTLlk~l~G   60 (257)
T PRK11247         41 VAVVGRSGCGKSTLLRLLAG   60 (257)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=93.06  E-value=0.057  Score=48.29  Aligned_cols=20  Identities=15%  Similarity=0.159  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (242)
T cd03295          30 LVLIGPSGSGKTTTMKMINR   49 (242)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

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. 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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=93.04  E-value=0.056  Score=50.53  Aligned_cols=20  Identities=15%  Similarity=0.247  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|.+|+|||||+..+..
T Consensus        59 igi~G~~GaGKSTl~~~l~~   78 (332)
T PRK09435         59 IGITGVPGVGKSTFIEALGM   78 (332)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999998755

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.04  E-value=0.059  Score=46.98  Aligned_cols=21  Identities=14%  Similarity=0.077  Sum_probs=19.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G~   51 (207)
T PRK13539         31 LVLTGPNGSGKTTLLRLIAGL   51 (207)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999999873

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=93.03  E-value=0.059  Score=46.96  Aligned_cols=20  Identities=20%  Similarity=0.127  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (208)
T cd03268          29 YGFLGPNGAGKTTTMKIILG   48 (208)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            47999999999999999986

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>PRK14247 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.03  E-value=0.057  Score=48.53  Aligned_cols=20  Identities=15%  Similarity=0.159  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        32 ~~i~G~nGsGKSTLl~~i~G   51 (250)
T PRK14247         32 TALMGPSGSGKSTLLRVFNR   51 (250)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=93.02  E-value=0.058  Score=47.01  Aligned_cols=20  Identities=20%  Similarity=0.292  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+++|..|+|||||.+.+..
T Consensus        25 i~~~G~~gsGKTTli~~l~~   44 (207)
T TIGR00073        25 LNFMSSPGSGKTTLIEKLID   44 (207)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999876

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK10908 cell division protein FtsE; Provisional

Probab=93.01  E-value=0.059  Score=47.49  Aligned_cols=20  Identities=10%  Similarity=0.054  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (222)
T PRK10908         31 AFLTGHSGAGKSTLLKLICG   50 (222)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

>cd01895 EngA2 EngA2 subfamily

Probab=93.01  E-value=0.061  Score=44.72  Aligned_cols=21  Identities=10%  Similarity=0.278  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||+..+.+.
T Consensus         5 i~i~G~~~~GKstli~~l~~~   25 (174)
T cd01895           5 IAIIGRPNVGKSSLVNALLGE   25 (174)
T ss_pred             EEEEcCCCCCHHHHHHHHhCc
Confidence            689999999999999998764

This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.

>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation

Probab=93.01  E-value=0.061  Score=41.01  Aligned_cols=20  Identities=30%  Similarity=0.312  Sum_probs=15.8

Q ss_pred             CcEEc-CCCCcHHHHHHHHhC
Q 041097            1 MAVLD-SIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~G-mgGvGKTTLa~~vy~   20 (391)
                      |+|+| -||+||||+|..+..
T Consensus         2 i~~~~~kgG~Gkst~~~~la~   22 (104)
T cd02042           2 IAVANQKGGVGKTTTAVNLAA   22 (104)
T ss_pred             EEEEeCCCCcCHHHHHHHHHH
Confidence            45666 799999999888654

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.01  E-value=0.15  Score=47.49  Aligned_cols=46  Identities=11%  Similarity=0.174  Sum_probs=33.7

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc----cEEEEEEcCCCcChHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF----DCHAWVQESLPYDADQILY   47 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F----~~~~~~~vs~~~~~~~i~~   47 (391)
                      -|+|.+|+||||++..++-+.......    ..++|+.....|+.+++.+
T Consensus        99 ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~~  148 (310)
T TIGR02236        99 EVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQ  148 (310)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHHH
Confidence            489999999999999986543332111    2788998888888887654

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=92.99  E-value=0.058  Score=49.15  Aligned_cols=35  Identities=14%  Similarity=0.053  Sum_probs=22.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |+++|.+|+||||.+.++..  .+...=..+.++..+
T Consensus        75 i~l~G~~G~GKTTt~akLA~--~l~~~g~~V~li~~D  109 (272)
T TIGR00064        75 ILFVGVNGVGKTTTIAKLAN--KLKKQGKSVLLAAGD  109 (272)
T ss_pred             EEEECCCCCcHHHHHHHHHH--HHHhcCCEEEEEeCC
Confidence            56899999999998877754  233222345555543

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.

>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=92.99  E-value=0.062  Score=49.84  Aligned_cols=17  Identities=29%  Similarity=0.151  Sum_probs=14.5

Q ss_pred             cEEcCCCCcHHHHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~v   18 (391)
                      -+.|-|||||||+|-+.
T Consensus         5 ~~~GKGGVGKTT~aaA~   21 (305)
T PF02374_consen    5 FFGGKGGVGKTTVAAAL   21 (305)
T ss_dssp             EEEESTTSSHHHHHHHH
T ss_pred             EEecCCCCCcHHHHHHH
Confidence            37899999999999664

...

>cd01874 Cdc42 Cdc42 subfamily

Probab=92.99  E-value=0.076  Score=44.85  Aligned_cols=21  Identities=14%  Similarity=0.123  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||+..+.++
T Consensus         4 i~vvG~~~vGKTsl~~~~~~~   24 (175)
T cd01874           4 CVVVGDGAVGKTCLLISYTTN   24 (175)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999997654

Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addi

>PRK14528 adenylate kinase; Provisional

Probab=92.99  E-value=0.06  Score=46.08  Aligned_cols=20  Identities=15%  Similarity=0.101  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|.+|+||||+|+.+..
T Consensus         4 i~i~G~pGsGKtt~a~~la~   23 (186)
T PRK14528          4 IIFMGPPGAGKGTQAKILCE   23 (186)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999865

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=92.98  E-value=0.06  Score=48.00  Aligned_cols=20  Identities=15%  Similarity=0.091  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        50 ~~i~G~NGsGKSTLl~~i~G   69 (236)
T cd03267          50 VGFIGPNGAGKTTTLKILSG   69 (236)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=92.96  E-value=0.063  Score=45.23  Aligned_cols=20  Identities=15%  Similarity=0.230  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        31 ~~l~G~nGsGKstLl~~i~G   50 (171)
T cd03228          31 VAIVGPSGSGKSTLLKLLLR   50 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            48999999999999999987

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=92.96  E-value=0.12  Score=46.90  Aligned_cols=40  Identities=10%  Similarity=0.093  Sum_probs=25.8

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQIL   46 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~   46 (391)
                      -++|.+|+||||+|+.+.+  ....   ....++.+.+.+..+++
T Consensus        25 LL~G~~GtGKT~lA~~la~--~lg~---~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640        25 HLRGPAGTGKTTLAMHVAR--KRDR---PVMLINGDAELTTSDLV   64 (262)
T ss_pred             EEEcCCCCCHHHHHHHHHH--HhCC---CEEEEeCCccCCHHHHh
Confidence            4789999999999999875  2222   23344444445555544

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).

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=92.94  E-value=0.061  Score=48.46  Aligned_cols=20  Identities=15%  Similarity=0.298  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        33 ~~I~G~NGsGKSTLl~~i~G   52 (251)
T PRK09544         33 LTLLGPNGAGKSTLVRVVLG   52 (251)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>PTZ00132 GTP-binding nuclear protein Ran; Provisional

Probab=92.94  E-value=0.063  Score=47.00  Aligned_cols=20  Identities=20%  Similarity=0.350  Sum_probs=16.6

Q ss_pred             CcEEcCCCCcHHHHHH-HHhC
Q 041097            1 MAVLDSIGLDKTAFAA-EAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~-~vy~   20 (391)
                      |+|+|.+|+|||||+. .+..
T Consensus        12 v~liG~~g~GKTtLi~~~~~~   32 (215)
T PTZ00132         12 LILVGDGGVGKTTFVKRHLTG   32 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            5799999999999995 5443

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=92.94  E-value=0.06  Score=48.11  Aligned_cols=20  Identities=20%  Similarity=0.137  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        32 ~~l~G~nGsGKSTLl~~l~G   51 (241)
T PRK10895         32 VGLLGPNGAGKTTTFYMVVG   51 (241)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999977

>cd01870 RhoA_like RhoA-like subfamily

Probab=92.92  E-value=0.079  Score=44.47  Aligned_cols=21  Identities=10%  Similarity=0.061  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|+|||||++.+.++
T Consensus         4 i~iiG~~~~GKTsl~~~~~~~   24 (175)
T cd01870           4 LVIVGDGACGKTCLLIVFSKD   24 (175)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl

>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional

Probab=92.92  E-value=0.061  Score=48.33  Aligned_cols=20  Identities=20%  Similarity=0.209  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        32 ~~i~G~nGsGKSTLl~~l~G   51 (250)
T PRK11264         32 VAIIGPSGSGKTTLLRCINL   51 (250)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein

Probab=92.91  E-value=0.061  Score=48.29  Aligned_cols=20  Identities=15%  Similarity=0.222  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (247)
T TIGR00972        30 TALIGPSGCGKSTLLRSLNR   49 (247)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999975

This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters.

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=92.91  E-value=0.067  Score=44.63  Aligned_cols=21  Identities=10%  Similarity=0.243  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 i~vvG~~~~GKSsl~~~~~~~   26 (167)
T cd01867           6 LLLIGDSGVGKSCLLLRFSED   26 (167)
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            579999999999999998664

Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=92.90  E-value=0.14  Score=46.22  Aligned_cols=48  Identities=8%  Similarity=0.164  Sum_probs=34.9

Q ss_pred             EEcCCCCcHHHHHHHHhCCcccccc---c-cEEEEEEcCCCcChHHHHHHHHH
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHY---F-DCHAWVQESLPYDADQILYDIIK   51 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~---F-~~~~~~~vs~~~~~~~i~~~~~~   51 (391)
                      |+|.+|+|||.|+..++-+.++...   . ..++|+.-...|+.+++.+ +.+
T Consensus        43 i~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~-i~~   94 (256)
T PF08423_consen   43 IVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQ-IAE   94 (256)
T ss_dssp             EEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHH-HHH
T ss_pred             EEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHH-Hhh
Confidence            8999999999999877644344322   2 3789999888999999765 443

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 ....

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.90  E-value=0.062  Score=48.04  Aligned_cols=20  Identities=10%  Similarity=0.175  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        32 ~~i~G~nGsGKSTLl~~l~G   51 (241)
T PRK14250         32 YTIVGPSGAGKSTLIKLINR   51 (241)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=92.89  E-value=0.11  Score=48.99  Aligned_cols=54  Identities=6%  Similarity=0.030  Sum_probs=38.2

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccc----cEEEEEEcCCCcChHHHHHHHHHhhcCCC
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYF----DCHAWVQESLPYDADQILYDIIKFVMPSP   57 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F----~~~~~~~vs~~~~~~~i~~~~~~~~~~~~   57 (391)
                      |+|.+|+|||+|+..++-+..+....    ..++|+.-...|+.+++.+ ++..+.|..
T Consensus       128 i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~q-ia~~~~~~~  185 (342)
T PLN03186        128 IYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQ-IAERFGLNG  185 (342)
T ss_pred             EECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHH-HHHHcCCCh
Confidence            89999999999998877533332221    2789999888899998654 455444433

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=92.89  E-value=0.061  Score=48.51  Aligned_cols=20  Identities=15%  Similarity=0.145  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        34 ~~l~G~nGsGKSTLl~~l~G   53 (255)
T PRK11300         34 VSLIGPNGAGKTTVFNCLTG   53 (255)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>TIGR00750 lao LAO/AO transport system ATPase

Probab=92.86  E-value=0.061  Score=49.84  Aligned_cols=20  Identities=10%  Similarity=0.134  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|.+|+|||||+..+..
T Consensus        37 i~i~G~~G~GKttl~~~l~~   56 (300)
T TIGR00750        37 VGITGTPGAGKSTLLEALGM   56 (300)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999765

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=92.85  E-value=0.083  Score=48.17  Aligned_cols=20  Identities=25%  Similarity=0.356  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||+..+.+
T Consensus       107 v~l~G~pGsGKTTLl~~l~~  126 (290)
T PRK10463        107 LNLVSSPGSGKTTLLTETLM  126 (290)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999887

>cd04154 Arl2 Arl2 subfamily

Probab=92.85  E-value=0.069  Score=44.87  Aligned_cols=21  Identities=14%  Similarity=0.132  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+...
T Consensus        17 v~ivG~~~~GKTsL~~~l~~~   37 (173)
T cd04154          17 ILILGLDNAGKTTILKKLLGE   37 (173)
T ss_pred             EEEECCCCCCHHHHHHHHccC
Confidence            568999999999999997653

Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.

>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=92.85  E-value=0.061  Score=46.41  Aligned_cols=76  Identities=17%  Similarity=0.175  Sum_probs=36.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHH--HHHHHHhhcCCC-CC-CCCCChHHHHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQI--LYDIIKFVMPSP-EG-FIPDNNEATVEKYLEQL   76 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i--~~~~~~~~~~~~-eg-~~~~~~~~~~~~~~~~L   76 (391)
                      |.++|..|+||||.+-++..  +.+..=..+++++.+ .|.....  ++....... ++ .. ....+..+.+.+.++..
T Consensus         4 i~lvGptGvGKTTt~aKLAa--~~~~~~~~v~lis~D-~~R~ga~eQL~~~a~~l~-vp~~~~~~~~~~~~~~~~~l~~~   79 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAA--RLKLKGKKVALISAD-TYRIGAVEQLKTYAEILG-VPFYVARTESDPAEIAREALEKF   79 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHH--HHHHTT--EEEEEES-TSSTHHHHHHHHHHHHHT-EEEEESSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCchHhHHHHHHH--HHhhccccceeecCC-CCCccHHHHHHHHHHHhc-cccchhhcchhhHHHHHHHHHHH
Confidence            46899999999855444433  233333356666654 3444432  122222221 11 00 11112456666677777


Q ss_pred             HcCc
Q 041097           77 INGG   80 (391)
Q Consensus        77 ~~k~   80 (391)
                      .+++
T Consensus        80 ~~~~   83 (196)
T PF00448_consen   80 RKKG   83 (196)
T ss_dssp             HHTT
T ss_pred             hhcC
Confidence            6644

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 ....

>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=92.83  E-value=0.065  Score=46.84  Aligned_cols=20  Identities=15%  Similarity=0.295  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.|||||.|.+--
T Consensus        33 VaiIG~SGaGKSTLLR~lng   52 (258)
T COG3638          33 VAIIGPSGAGKSTLLRSLNG   52 (258)
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            68999999999999999754

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=92.83  E-value=0.066  Score=46.42  Aligned_cols=20  Identities=20%  Similarity=0.132  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||.+.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (201)
T cd03231          29 LQVTGPNGSGKTTLLRILAG   48 (201)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>cd04149 Arf6 Arf6 subfamily

Probab=92.83  E-value=0.064  Score=44.98  Aligned_cols=20  Identities=15%  Similarity=0.006  Sum_probs=17.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||++.+..
T Consensus        12 v~i~G~~~~GKTsli~~l~~   31 (168)
T cd04149          12 ILMLGLDAAGKTTILYKLKL   31 (168)
T ss_pred             EEEECcCCCCHHHHHHHHcc
Confidence            57999999999999998754

Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed t

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=92.83  E-value=0.063  Score=46.58  Aligned_cols=20  Identities=15%  Similarity=0.117  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        36 ~~i~G~nGsGKSTLl~~l~G   55 (202)
T cd03233          36 VLVLGRPGSGCSTLLKALAN   55 (202)
T ss_pred             EEEECCCCCCHHHHHHHhcc
Confidence            58999999999999999876

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.

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=92.81  E-value=0.065  Score=47.36  Aligned_cols=20  Identities=10%  Similarity=0.167  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.|..|+|||||++.+..
T Consensus        51 ~~i~G~nGsGKSTLl~~l~G   70 (224)
T cd03220          51 IGLIGRNGAGKSTLLRLLAG   70 (224)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

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

Probab=92.79  E-value=0.068  Score=47.33  Aligned_cols=21  Identities=14%  Similarity=0.191  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|.|.+|.||||+.+.++.+
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~   21 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKD   21 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHh
Confidence            579999999999999999885

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

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=92.79  E-value=0.067  Score=46.87  Aligned_cols=20  Identities=15%  Similarity=0.175  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||...+..
T Consensus        34 vaI~GpSGSGKSTLLniig~   53 (226)
T COG1136          34 VAIVGPSGSGKSTLLNLLGG   53 (226)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999875

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=92.78  E-value=0.078  Score=44.66  Aligned_cols=21  Identities=10%  Similarity=0.015  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+...
T Consensus        18 v~~~G~~~~GKTsl~~~l~~~   38 (174)
T cd04153          18 VIIVGLDNAGKTTILYQFLLG   38 (174)
T ss_pred             EEEECCCCCCHHHHHHHHccC
Confidence            579999999999999998653

Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.

>PRK14256 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.78  E-value=0.065  Score=48.24  Aligned_cols=20  Identities=15%  Similarity=0.218  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        33 ~~i~G~nGsGKSTLl~~l~G   52 (252)
T PRK14256         33 TAIIGPSGCGKSTVLRSINR   52 (252)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999976

>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=92.78  E-value=0.068  Score=45.42  Aligned_cols=20  Identities=15%  Similarity=0.252  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        28 ~~l~G~nGsGKStLl~~i~G   47 (180)
T cd03214          28 VGILGPNGAGKSTLLKTLAG   47 (180)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            57999999999999999987

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.

>cd04171 SelB SelB subfamily

Probab=92.78  E-value=0.067  Score=44.16  Aligned_cols=20  Identities=15%  Similarity=0.142  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-.|+|||||...+.+
T Consensus         3 i~i~G~~~~GKssl~~~l~~   22 (164)
T cd04171           3 IGTAGHIDHGKTTLIKALTG   22 (164)
T ss_pred             EEEEecCCCCHHHHHHHHhC
Confidence            68999999999999999875

SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo

>PRK13231 nitrogenase reductase-like protein; Reviewed

Probab=92.77  E-value=0.064  Score=48.66  Aligned_cols=20  Identities=15%  Similarity=0.278  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|-||+||||++..+..
T Consensus         5 iav~~KGGvGKTT~a~nLA~   24 (264)
T PRK13231          5 IAIYGKGGIGKSTTVSNMAA   24 (264)
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            56889999999999999765

>PLN02165 adenylate isopentenyltransferase

Probab=92.75  E-value=0.065  Score=49.81  Aligned_cols=20  Identities=10%  Similarity=0.350  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||||..+..
T Consensus        46 ivIiGPTGSGKStLA~~LA~   65 (334)
T PLN02165         46 VVIMGATGSGKSRLSVDLAT   65 (334)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57999999999999999876

>TIGR03873 F420-0_ABC_ATP proposed F420-0 ABC transporter, ATP-binding protein

Probab=92.75  E-value=0.065  Score=48.38  Aligned_cols=21  Identities=14%  Similarity=0.142  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|+|..|.|||||++.+...
T Consensus        30 ~~i~G~nGsGKSTLl~~i~G~   50 (256)
T TIGR03873        30 TGLLGPNGSGKSTLLRLLAGA   50 (256)
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            589999999999999999863

This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.

>cd04121 Rab40 Rab40 subfamily

Probab=92.75  E-value=0.086  Score=45.24  Aligned_cols=21  Identities=10%  Similarity=0.118  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         9 ivviG~~~vGKTsll~~~~~~   29 (189)
T cd04121           9 FLLVGDSDVGKGEILASLQDG   29 (189)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide d

>PRK14239 phosphate transporter ATP-binding protein; Provisional

Probab=92.75  E-value=0.066  Score=48.18  Aligned_cols=20  Identities=15%  Similarity=0.219  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        34 ~~i~G~nGsGKSTLl~~l~G   53 (252)
T PRK14239         34 TALIGPSGSGKSTLLRSINR   53 (252)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999964

>PRK14241 phosphate transporter ATP-binding protein; Provisional

Probab=92.74  E-value=0.067  Score=48.37  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        33 ~~i~G~nGsGKSTLl~~laG   52 (258)
T PRK14241         33 TAFIGPSGCGKSTVLRTLNR   52 (258)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=92.73  E-value=0.068  Score=47.74  Aligned_cols=20  Identities=10%  Similarity=0.190  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        30 ~~l~G~nGsGKSTLl~~l~G   49 (240)
T PRK09493         30 VVIIGPSGSGKSTLLRCINK   49 (240)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>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=92.71  E-value=0.063  Score=48.78  Aligned_cols=20  Identities=20%  Similarity=-0.016  Sum_probs=16.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|.+|+||||+|+.+..
T Consensus         4 iil~G~P~SGKTt~a~~L~~   23 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKK   23 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHH
Confidence            46899999999999999776

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK06921 hypothetical protein; Provisional

Probab=92.70  E-value=0.093  Score=47.64  Aligned_cols=33  Identities=18%  Similarity=0.000  Sum_probs=24.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccccc-ccEEEEEEc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHY-FDCHAWVQE   36 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~-F~~~~~~~v   36 (391)
                      -++|..|+|||.||.++.+  ++... -..++|++.
T Consensus       121 ~l~G~~G~GKThLa~aia~--~l~~~~g~~v~y~~~  154 (266)
T PRK06921        121 ALLGQPGSGKTHLLTAAAN--ELMRKKGVPVLYFPF  154 (266)
T ss_pred             EEECCCCCcHHHHHHHHHH--HHhhhcCceEEEEEH
Confidence            5899999999999999988  34332 234556654

>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional

Probab=92.70  E-value=0.067  Score=48.71  Aligned_cols=20  Identities=20%  Similarity=0.255  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        36 ~~i~G~nGsGKSTLl~~l~G   55 (269)
T PRK11831         36 TAIMGPSGIGKTTLLRLIGG   55 (269)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

>cd04148 RGK RGK subfamily

Probab=92.70  E-value=0.076  Score=46.83  Aligned_cols=21  Identities=29%  Similarity=0.428  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||+..+..+
T Consensus         3 I~lvG~~gvGKTsLi~~~~~~   23 (221)
T cd04148           3 VVMLGSPGVGKSSLASQFTSG   23 (221)
T ss_pred             EEEECCCCCcHHHHHHHHhcC
Confidence            679999999999999998543

The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=92.70  E-value=0.14  Score=48.22  Aligned_cols=55  Identities=13%  Similarity=0.131  Sum_probs=39.0

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccc----cEEEEEEcCCCcChHHHHHHHHHhhcCCCC
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYF----DCHAWVQESLPYDADQILYDIIKFVMPSPE   58 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F----~~~~~~~vs~~~~~~~i~~~~~~~~~~~~e   58 (391)
                      |+|..|+|||+|+..++-+.+++...    ..++|+.--..|+.+++.+ ++..+.|..+
T Consensus       131 I~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~  189 (344)
T PLN03187        131 AFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDAD  189 (344)
T ss_pred             EecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChh
Confidence            89999999999999876433343221    4788998888899998765 4555555433

>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.69  E-value=0.067  Score=48.78  Aligned_cols=20  Identities=10%  Similarity=0.162  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        30 ~~i~G~nGsGKSTLl~~l~G   49 (271)
T PRK13638         30 TGLVGANGCGKSTLFMNLSG   49 (271)
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            58999999999999999876

>cd01873 RhoBTB RhoBTB subfamily

Probab=92.69  E-value=0.086  Score=45.47  Aligned_cols=20  Identities=20%  Similarity=0.245  Sum_probs=16.5

Q ss_pred             CcEEcCCCCcHHHHHH-HHhC
Q 041097            1 MAVLDSIGLDKTAFAA-EAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~-~vy~   20 (391)
                      |.|+|-+|||||+|+. ..++
T Consensus         5 iv~vG~~~vGKTsLi~~~~~~   25 (195)
T cd01873           5 CVVVGDNAVGKTRLICARACN   25 (195)
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            5799999999999994 5544

Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature.

>cd04104 p47_IIGP_like p47 (47-kDa) family

Probab=92.66  E-value=0.074  Score=45.96  Aligned_cols=20  Identities=25%  Similarity=0.336  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-+|+|||||...+..
T Consensus         4 I~i~G~~g~GKSSLin~L~g   23 (197)
T cd04104           4 IAVTGESGAGKSSFINALRG   23 (197)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            68999999999999999976

The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei

>PRK14274 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.65  E-value=0.07  Score=48.29  Aligned_cols=20  Identities=20%  Similarity=0.300  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+.-
T Consensus        41 ~~l~G~nGsGKSTLl~~l~G   60 (259)
T PRK14274         41 TAIIGPSGCGKSTFIKTLNL   60 (259)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999974

>COG4240 Predicted kinase [General function prediction only]

Probab=92.63  E-value=0.058  Score=46.74  Aligned_cols=20  Identities=15%  Similarity=0.205  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|.-|.||||++-++++
T Consensus        53 ~gisGpQGSGKStls~~i~~   72 (300)
T COG4240          53 VGISGPQGSGKSTLSALIVR   72 (300)
T ss_pred             EEeecCCCCchhhHHHHHHH
Confidence            69999999999999999998

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=92.63  E-value=0.071  Score=47.37  Aligned_cols=20  Identities=15%  Similarity=0.187  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (234)
T cd03251          31 VALVGPSGSGKSTLVNLIPR   50 (234)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

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.

>cd04134 Rho3 Rho3 subfamily

Probab=92.62  E-value=0.089  Score=45.02  Aligned_cols=21  Identities=19%  Similarity=0.093  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.+.
T Consensus         3 ivivG~~~vGKTsli~~~~~~   23 (189)
T cd04134           3 VVVLGDGACGKTSLLNVFTRG   23 (189)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999987653

Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.

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

Probab=92.61  E-value=0.071  Score=51.32  Aligned_cols=21  Identities=19%  Similarity=0.192  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |-++|..|+|||++|+++.+.
T Consensus       182 vLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        182 VLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            348999999999999999883

>PRK14731 coaE dephospho-CoA kinase; Provisional

Probab=92.60  E-value=0.072  Score=46.47  Aligned_cols=20  Identities=20%  Similarity=0.194  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+++.+-.
T Consensus         8 igitG~igsGKSt~~~~l~~   27 (208)
T PRK14731          8 VGVTGGIGSGKSTVCRFLAE   27 (208)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999764

>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=92.59  E-value=0.081  Score=44.74  Aligned_cols=21  Identities=19%  Similarity=0.199  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|.|+.|+||||+.+.+.+.
T Consensus        17 ililGl~~sGKTtll~~l~~~   37 (175)
T PF00025_consen   17 ILILGLDGSGKTTLLNRLKNG   37 (175)
T ss_dssp             EEEEESTTSSHHHHHHHHHSS
T ss_pred             EEEECCCccchHHHHHHhhhc
Confidence            468999999999999998764

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....

>TIGR03689 pup_AAA proteasome ATPase

Probab=92.59  E-value=0.099  Score=51.75  Aligned_cols=20  Identities=25%  Similarity=0.205  Sum_probs=18.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -+||.+|+|||++|+++++.
T Consensus       220 LLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       220 LLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             EEECCCCCcHHHHHHHHHHh
Confidence            47999999999999999983

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.

>PRK14238 phosphate transporter ATP-binding protein; Provisional

Probab=92.59  E-value=0.071  Score=48.62  Aligned_cols=20  Identities=15%  Similarity=0.300  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        53 ~~I~G~nGsGKSTLl~~i~G   72 (271)
T PRK14238         53 TAIIGPSGCGKSTYIKTLNR   72 (271)
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999975

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=92.59  E-value=0.078  Score=43.90  Aligned_cols=20  Identities=20%  Similarity=0.230  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||+||.|.|++
T Consensus        32 iaitGPSG~GKStllk~va~   51 (223)
T COG4619          32 IAITGPSGCGKSTLLKIVAS   51 (223)
T ss_pred             EEEeCCCCccHHHHHHHHHh
Confidence            57999999999999999998

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=92.59  E-value=0.075  Score=45.87  Aligned_cols=20  Identities=10%  Similarity=0.189  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|.|||||.|-+..
T Consensus        31 v~iiGpSGSGKSTlLRclN~   50 (240)
T COG1126          31 VVIIGPSGSGKSTLLRCLNG   50 (240)
T ss_pred             EEEECCCCCCHHHHHHHHHC
Confidence            57999999999999999754

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=92.58  E-value=0.072  Score=47.39  Aligned_cols=20  Identities=15%  Similarity=0.295  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        30 ~~l~G~nGsGKSTLl~~i~G   49 (236)
T cd03253          30 VAIVGPSGSGKSTILRLLFR   49 (236)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999987

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.

>cd04116 Rab9 Rab9 subfamily

Probab=92.57  E-value=0.096  Score=43.74  Aligned_cols=21  Identities=14%  Similarity=0.279  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         8 i~vvG~~~~GKTsli~~~~~~   28 (170)
T cd04116           8 VILLGDGGVGKSSLMNRYVTN   28 (170)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999987653

Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CX

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=92.57  E-value=0.072  Score=47.19  Aligned_cols=20  Identities=25%  Similarity=0.310  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~l~G~nGsGKSTLl~~l~G   48 (230)
T TIGR03410        29 TCVLGRNGVGKTTLLKTLMG   48 (230)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

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.

>PRK11701 phnK phosphonate C-P lyase system protein PhnK; Provisional

Probab=92.57  E-value=0.072  Score=48.15  Aligned_cols=20  Identities=15%  Similarity=0.270  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.|..|.|||||++.++.
T Consensus        35 ~~i~G~nGsGKSTLl~~l~G   54 (258)
T PRK11701         35 LGIVGESGSGKTTLLNALSA   54 (258)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

>TIGR03005 ectoine_ehuA ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Probab=92.57  E-value=0.072  Score=47.96  Aligned_cols=20  Identities=15%  Similarity=0.232  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G   48 (252)
T TIGR03005        29 VALIGPSGSGKSTILRILMT   48 (252)
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	391
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-08
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-05
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	7e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-05
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	7e-05
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	2e-04
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-04
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-04
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-04
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-04
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	3e-04

>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 = 53.8 bits (130), Expect = 3e-08
 Identities = 40/191 (20%), Positives = 72/191 (37%), Gaps = 22/191 (11%)

Query: 181 LRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLL 240
              L+L S+ L ++P     L  L+++ ++   L  LP +  + + +        L +L 
Sbjct: 83  RVALELRSVPLPQFPDQAFRLSHLQHMTIDAAGLMELPDT--MQQFA-------GLETLT 133

Query: 241 LYYQSL--LSKSLCRLSCLESLKLANESKMPR-----RSNIILAEYQFPPSLTHLSFSNI 293
           L    L  L  S+  L+ L  L +    ++        S     E+Q   +L  L     
Sbjct: 134 LARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWT 193

Query: 294 ELMDDPIPALEKLSVLQVLKLKQNLYSE--ERTMGIRAMPKLECLIINPYAHLKRIHEQL 351
            +   P  ++  L  L+ LK++ +  S        I  +PKLE L +     L+      
Sbjct: 194 GIRSLP-ASIANLQNLKSLKIRNSPLSALGP---AIHHLPKLEELDLRGCTALRNYPPIF 249

Query: 352 WCLKSLNKLEL 362
                L +L L
Sbjct: 250 GGRAPLKRLIL 260

>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 = 44.2 bits (105), Expect = 3e-05
 Identities = 26/208 (12%), Positives = 64/208 (30%), Gaps = 37/208 (17%)

Query: 172 EKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQ 231
                +    +                 N    +       +LK+     +     G   
Sbjct: 26  RPYHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRALKATADLLEDATQPG--- 82

Query: 232 FHFSLASLLLYYQSL--LSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPS----- 284
                 +L L    L        RLS L+ + +         + ++    + P +     
Sbjct: 83  ----RVALELRSVPLPQFPDQAFRLSHLQHMTIDA-------AGLM----ELPDTMQQFA 127

Query: 285 -LTHLSFSNIELMDDPIPALEKLSVLQVLKLKQN---------LYSEERTMGIRAMPKLE 334
            L  L+ +   L   P  ++  L+ L+ L ++           L S + +   + +  L+
Sbjct: 128 GLETLTLARNPLRALP-ASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQ 186

Query: 335 CLIINPYAHLKRIHEQLWCLKSLNKLEL 362
            L +  +  ++ +   +  L++L  L++
Sbjct: 187 SLRLE-WTGIRSLPASIANLQNLKSLKI 213

>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 = 43.4 bits (103), Expect = 7e-05
 Identities = 44/192 (22%), Positives = 71/192 (36%), Gaps = 22/192 (11%)

Query: 181 LRVLDLGSLVLIRYPSGIENLFLLRYLKL-NIPSLKSLPSSRKILRLSGNSQFHFSLASL 239
           L  L L    L   P+ I +L  LR L +   P L  LP        SG  Q   +L SL
Sbjct: 129 LETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSL 188

Query: 240 LLYYQSL--LSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPS------LTHLSFS 291
            L +  +  L  S+  L  L+SLK+        R++ +       P+      L  L   
Sbjct: 189 RLEWTGIRSLPASIANLQNLKSLKI--------RNSPLS---ALGPAIHHLPKLEELDLR 237

Query: 292 NIELMDDPIPA-LEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ 350
               + +  P      + L+ L LK         + I  + +LE L +    +L R+   
Sbjct: 238 GCTALRN-YPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSL 296

Query: 351 LWCLKSLNKLEL 362
           +  L +   + +
Sbjct: 297 IAQLPANCIILV 308

>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 = 50.6 bits (120), Expect = 7e-07
 Identities = 61/406 (15%), Positives = 108/406 (26%), Gaps = 137/406 (33%)

Query: 8   GLDKTAFAAEAYSSNYVKHYFDCHA-WVQESLPYDADQILYDIIKFVMPSPEGFIPDNNE 66
           G  KT  A +   S  V+   D    W                +              N 
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFW----------------LNL-----------KNC 192

Query: 67  ATVEKYLEQLINGGFVGAGKRSDIGRINTCSIPGRCSPALLTVVFEGEFLISPIMDQEVR 126
            + E  LE L             +      +   R   +            S I  +   
Sbjct: 193 NSPETVLEMLQK-----------LLYQIDPNWTSRSDHS------------SNIKLRIHS 229

Query: 127 LRENVKRFTAHRKL-NDFAFLDD------FDSFLHS--LLYLTSGSQYLDPTYCEKICKM 177
           ++  ++R    +   N    L +      +++F  S  +L  T   Q  D          
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD---------- 279

Query: 178 FKFLRVLDLGSLVLIRYPSGI---ENL-FLLRYLKLNIPSLKSLPSSRKILRLSGNSQFH 233
             FL       + L  +   +   E    LL+YL       + LP       +   +   
Sbjct: 280 --FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC---RPQDLPR-----EVLTTNPRR 329

Query: 234 FSLASLLL--------YYQSLLSKSLCRL--SCLESLKLANESKMPRRSNIILAEYQ--- 280
            S+ +  +         ++ +    L  +  S L  L+ A   KM          +    
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM----------FDRLS 379

Query: 281 -FPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIIN 339
            FPP                IP      +L ++     + S+   + +  + K   +   
Sbjct: 380 VFPP-------------SAHIPT----ILLSLI-WFDVIKSDVMVV-VNKLHKYSLVEKQ 420

Query: 340 PYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKEQYGIQ 385
           P      I      L+   KLE    E  L + +      + Y I 
Sbjct: 421 PKESTISIPSIY--LELKVKLEN---EYALHRSIV-----DHYNIP 456

>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 = 46.0 bits (109), Expect = 1e-05
 Identities = 28/221 (12%), Positives = 71/221 (32%), Gaps = 22/221 (9%)

Query: 181 LRVLDLGSLVLIRYPSGIENLFLLRYLKL---------------NIPSLKSLPSSRKILR 225
           +  + L +  L+     +     L +  L                   ++++ + + + +
Sbjct: 216 VTWISLRNNKLVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTV-AKQTVKK 274

Query: 226 LSGNSQFHFSLASLL----LYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQF 281
           L+G ++   ++ +L        + L +    RL  L+  + A  S     +  +  E + 
Sbjct: 275 LTGQNEEECTVPTLGHYGAYCCEDLPAPFADRLIALKRKEHALLSGQGSETERLECEREN 334

Query: 282 PPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLE--CLIIN 339
                 +     +          +      L+ K+    E+ + G RA  +L+       
Sbjct: 335 QARQREIDALKEQYRTVIDQVTLRKQAKITLEQKKKALDEQVSNGRRAHAELDGTLQQAV 394

Query: 340 PYAHLKRIHEQLWCLKSLNKLELWWPEPELRQQLREFEDKE 380
               L+   E+   L+ L  +   + E  + QQ  +     
Sbjct: 395 GQIELQHATEEQSPLQLLRAIVKRYEEMYVEQQSVQNNAIR 435

>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 = 43.6 bits (103), Expect = 7e-05
 Identities = 44/210 (20%), Positives = 73/210 (34%), Gaps = 34/210 (16%)

Query: 178 FKFLRVLDLGSLVLIRYPSGI-ENLFLLRYLKLNIPSLKSLP-------SSRKILRLSGN 229
           F  L  L+L   ++     G   NLF LR L L    LK +P       S+   L +S N
Sbjct: 55  FPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISEN 114

Query: 230 S-------QFH--FSLASLLLYY---QSLLSKSLCRLSCLESLKLANESKMPRRSNII-- 275
                    F   ++L SL +       +  ++   L+ LE L L            +  
Sbjct: 115 KIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEK--------CNLTS 166

Query: 276 LAEYQFP--PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKL 333
           +          L  L   ++ +      + ++L  L+VL++    Y +  T        L
Sbjct: 167 IPTEALSHLHGLIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNL 226

Query: 334 ECLIINPYAHLKRIHEQ-LWCLKSLNKLEL 362
             L I  + +L  +    +  L  L  L L
Sbjct: 227 TSLSIT-HCNLTAVPYLAVRHLVYLRFLNL 255

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 36/193 (18%), Positives = 65/193 (33%), Gaps = 11/193 (5%)

Query: 178 FKFLRVLDLGSLVLIRYPSGIENLFLLR-YLKLNIPSLKSLPSSRKILRLSGNSQFHFSL 236
              L+ +D     L ++   I++L L R  ++      + L  + ++L +SG      +L
Sbjct: 46  EYLLKRVDT-EADLGQFTDIIKSLSLKRLTVRAARIPSRILFGALRVLGISGLQ--ELTL 102

Query: 237 ASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELM 296
            +L +   +           L  L L N S   R + +   +    P L  LS +    +
Sbjct: 103 ENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSL 162

Query: 297 DDPIPALEKLSVLQVLKLKQNLYSEERTMGI----RAMPKLECLII--NPYAHLKRIHEQ 350
           +     +     L  L L  N    ER +         P L+ L +          +   
Sbjct: 163 NFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSA 222

Query: 351 LWC-LKSLNKLEL 362
           L      L  L+L
Sbjct: 223 LAAARVQLQGLDL 235

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 24/214 (11%), Positives = 67/214 (31%), Gaps = 35/214 (16%)

Query: 181 LRVLDLG--SLVLIRYPSGIENLFLLRYLKLN------IPSLKSLPSSRKILRLSGNS-- 230
           +++  +G  +L      + ++ +  L  L         + +  +       L+L  N   
Sbjct: 550 IQIFYMGYNNLEEFPASASLQKMVKLGLLDCVHNKVRHLEAFGTNVKLTD-LKLDYNQIE 608

Query: 231 -------QFHFSLASLLLYYQSLLS----KSLCRLSCLESLKLAN--ESKMPRRSNIILA 277
                   F   +  L   +  L       +   +  + S+  +        R  +  + 
Sbjct: 609 EIPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAKSVYVMGSVDFSYNKIGSEGRNISCSMD 668

Query: 278 EYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNL-------YSEERTMGIRAM 330
           +Y+   + + ++ S  E+   P       S +  + L  NL         + +    +  
Sbjct: 669 DYKGI-NASTVTLSYNEIQKFPTELFATGSPISTIILSNNLMTSIPENSLKPKDGNYKNT 727

Query: 331 PKLECLIINPYAHLKRIHEQLWC--LKSLNKLEL 362
             L  + +  +  L  + +      L  L+ +++
Sbjct: 728 YLLTTIDLR-FNKLTSLSDDFRATTLPYLSNMDV 760

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 22/184 (11%), Positives = 48/184 (26%), Gaps = 8/184 (4%)

Query: 179 KFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLAS 238
             L+VL  G+           +  L   +         +   +  L           L  
Sbjct: 347 TELKVLSFGTHSETVSGRLFGDEELTPDMSEERKHRIRMHYKKMFLDYDQRLNLSDLLQD 406

Query: 239 LLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDD 298
            +     +          L+  ++ N +    R   I    Q    L  + F+N      
Sbjct: 407 AINRNPEMKPIKKDSRISLKDTQIGNLTN---RITFISKAIQRLTKLQIIYFAN-----S 458

Query: 299 PIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLN 358
           P          +          E   +    +  L  + +    ++ ++ + L+ L  L 
Sbjct: 459 PFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQ 518

Query: 359 KLEL 362
            L +
Sbjct: 519 SLNI 522

>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 = 42.2 bits (99), Expect = 2e-04
 Identities = 43/203 (21%), Positives = 62/203 (30%), Gaps = 28/203 (13%)

Query: 181 LRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGN--SQFHFSLAS 238
           LR L++    L   P     L  L      +  L +LPS    L + GN  +        
Sbjct: 83  LRTLEVSGNQLTSLPVLPPGLLELSIFSNPLTHLPALPSGLCKLWIFGNQLTSLPVLPPG 142

Query: 239 L--LLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELM 296
           L  L    + L+      S L  L   N        N + +    P  L  LS S+ +L 
Sbjct: 143 LQELSVSDNQLASLPALPSELCKLWAYN--------NQLTSLPMLPSGLQELSVSDNQLA 194

Query: 297 DDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKS 356
             P     +L  L     +                 L+ LI++    L  +      LK 
Sbjct: 195 SLP-TLPSELYKLWAYNNRLTSLPAL-------PSGLKELIVS-GNRLTSLPVLPSELKE 245

Query: 357 L----NKLELWWPEPELRQQLRE 375
           L    N+L      P L   L  
Sbjct: 246 LMVSGNRLTSL---PMLPSGLLS 265

>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 = 41.9 bits (99), Expect = 3e-04
 Identities = 30/137 (21%), Positives = 48/137 (35%), Gaps = 24/137 (17%)

Query: 181 LRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLL 240
           L  L      L   P   ++L  L     N+ +L  LP   + L +S N      L  L 
Sbjct: 93  LESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNN-----QLEKL- 146

Query: 241 LYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPI 300
                     L   S L+ + +         +N +      PPSL  ++  N +L +  +
Sbjct: 147 --------PELQNSSFLKIIDV--------DNNSLKKLPDLPPSLEFIAAGNNQLEE--L 188

Query: 301 PALEKLSVLQVLKLKQN 317
           P L+ L  L  +    N
Sbjct: 189 PELQNLPFLTAIYADNN 205

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	391
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.82
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.8
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.73
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.72
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.7
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.68
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.68
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.67
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.67
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.66
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.66
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.66
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.65
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.65
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.65
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.64
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.63
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.63
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.63
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.63
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.63
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.63
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.63
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.62
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.62
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.61
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.61
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.61
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.61
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.61
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.6
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.6
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.59
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.59
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.58
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.58
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.58
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.57
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.57
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.56
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.56
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.55
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.55
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.55
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.55
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.55
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.55
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.54
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.54
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.54
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.54
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.53
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.53
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.53
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.53
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.52
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.52
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.51
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.51
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.5
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.5
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.49
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.49
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.49
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.49
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.49
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.47
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.47
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.47
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.46
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.46
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.45
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.45
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.44
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.44
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.42
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.42
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.41
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.41
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.41
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.38
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.37
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.37
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.37
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.37
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.37
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.36
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.36
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.36
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.35
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.35
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.35
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.34
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.33
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.31
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.31
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.3
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.3
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.29
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.27
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.27
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.27
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.26
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.26
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.25
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.24
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.23
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.22
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.22
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.22
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.21
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.2
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.18
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.16
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.13
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.11
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.08
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.07
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.06
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.04
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.03
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.0
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.98
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.97
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.96
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	98.94
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	98.91
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	98.88
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.84
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	98.83
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.81
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	98.8
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.79
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.79
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.77
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.76
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	98.74
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.68
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.55
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.51
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.45
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.43
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.41
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.37
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	98.23
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.16
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.09
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.99
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	97.95
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.9
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	97.86
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	97.82
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	97.63
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.16
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.12
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.0
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.96
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	96.92
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	96.9
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	96.63
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	96.51
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.42
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.31
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.29
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.27
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.21
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.11
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.08
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.05
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.96
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.94
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.82
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.82
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.8
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.8
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.77
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.77
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.76
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.75
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.74
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.71
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.67
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.67
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.66
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.65
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.64
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.63
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.62
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.61
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	95.61
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.6
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.6
1via_A	175	Shikimate kinase; structural genomics, transferase	95.6
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.6
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.59
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.59
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.58
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.58
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.53
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.52
3bos_A	242	Putative DNA replication factor; P-loop containing	95.51
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.51
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.49
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.49
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.46
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.43
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.41
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.4
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.38
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.37
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.35
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.34
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.32
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.32
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.28
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.28
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.26
2fna_A	357	Conserved hypothetical protein; structural genomic	95.26
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.25
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.25
2chg_A	226	Replication factor C small subunit; DNA-binding pr	95.23
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.22
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.21
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.2
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	95.15
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.13
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.12
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.11
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.11
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.11
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.11
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.11
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.1
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.1
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.08
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	95.08
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.07
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.07
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.06
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.06
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.06
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.01
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.01
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.95
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.94
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.94
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	94.94
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.94
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	94.93
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.91
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.91
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	94.91
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.89
2cvh_A	220	DNA repair and recombination protein RADB; filamen	94.87
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	94.87
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	94.86
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	94.85
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.85
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	94.84
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	94.83
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	94.81
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.79
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	94.78
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.72
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.7
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	94.7
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.63
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.63
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.6
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.59
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.59
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.58
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.57
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.55
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	94.54
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.52
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	94.52
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.51
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.51
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.48
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.47
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.46
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	94.46
3fwy_A	314	Light-independent protochlorophyllide reductase I	94.45
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.45
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.41
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	94.4
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.4
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.4
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.39
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.38
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	94.37
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.37
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.35
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.34
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	94.34
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.32
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	94.31
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.31
3co5_A	143	Putative two-component system transcriptional RES	94.3
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	94.29
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.28
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.27
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	94.26
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.25
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.23
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.21
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	94.2
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.19
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.19
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.19
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.19
1g6h_A	257	High-affinity branched-chain amino acid transport	94.15
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.11
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.11
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.1
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.08
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.07
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.07
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.06
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.05
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.04
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	94.03
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.02
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.02
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	94.0
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.98
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	93.97
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.96
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.96
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.95
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.95
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	93.94
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.94
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	93.94
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	93.93
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.92
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	93.92
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.91
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.89
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.86
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.86
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.85
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	93.85
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.84
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.83
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	93.82
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.81
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	93.8
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.78
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.77
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	93.76
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	93.74
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	93.73
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.73
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.73
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.72
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	93.71
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.7
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.7
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	93.69
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.69
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.67
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.66
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	93.64
2eyu_A	261	Twitching motility protein PILT; pilus retraction	93.63
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	93.63
1tue_A	212	Replication protein E1; helicase, replication, E1E	93.62
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.61
2og2_A	359	Putative signal recognition particle receptor; nuc	93.6
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.56
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	93.55
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.52
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.49
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	93.49
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	93.48
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	93.48
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	93.48
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	93.48
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	93.47
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.47
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.47
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.46
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.43
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.43
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.42
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	93.42
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	93.42
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	93.38
3llu_A	196	RAS-related GTP-binding protein C; structural geno	93.38
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.37
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	93.36
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	93.33
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	93.32
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.32
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	93.3
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.28
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.28
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	93.28
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	93.28
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.27
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	93.26
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.25
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	93.25
2qgz_A	308	Helicase loader, putative primosome component; str	93.24
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.24
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	93.22
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	93.22
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	93.21
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	93.21
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	93.2
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.2
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	93.2
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.19
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	93.19
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.18
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	93.18
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	93.16
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	93.16
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	93.15
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	93.15
2fh5_B	214	SR-beta, signal recognition particle receptor beta	93.14
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	93.12
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	93.11
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	93.11
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	93.09
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.08
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	93.08
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	93.08
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	93.07
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	93.07
3pvs_A	447	Replication-associated recombination protein A; ma	93.07
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.04
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	93.03
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	93.03
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.01
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	92.99
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	92.97
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.95
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	92.95
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.94
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.93
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	92.91
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.89
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	92.89
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	92.89
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.87
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	92.84
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	92.83
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	92.82
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.81
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	92.81
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	92.81
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	92.81
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	92.8
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	92.79
3end_A	307	Light-independent protochlorophyllide reductase ir	92.78
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	92.77
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.74
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	92.71
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	92.71
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	92.7
2z43_A	324	DNA repair and recombination protein RADA; archaea	92.7
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.68
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	92.67
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	92.66
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.65
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	92.63
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	92.62
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	92.59
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.58
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	92.58
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	92.57
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	92.56
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	92.54
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.53
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	92.52
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	92.48
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	92.48
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	92.47
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	92.46
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	92.42
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	92.42
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	92.38
3kta_A	182	Chromosome segregation protein SMC; structural mai	92.33
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	92.33
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	92.32
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	92.32
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	92.31
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	92.3
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	92.3
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	92.3
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	92.29
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	92.29
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	92.28
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.27
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	92.27
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	92.25
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	92.24
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	92.22

>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=99.82  E-value=1.3e-19  Score=169.04  Aligned_cols=223  Identities=22%  Similarity=0.171  Sum_probs=157.3

Q ss_pred             CceEEEEEeccCCCcccccCCC--CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDFD--SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRY  206 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~~--~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~  206 (391)
                      ..++.|.+....... ++..+.  ++++.|.+.++...     .++..+..++.|++|++++|.+..+|..++++.+|++
T Consensus        81 ~~l~~L~L~~n~l~~-lp~~l~~l~~L~~L~L~~n~l~-----~lp~~~~~l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~  154 (328)
T 4fcg_A           81 PGRVALELRSVPLPQ-FPDQAFRLSHLQHMTIDAAGLM-----ELPDTMQQFAGLETLTLARNPLRALPASIASLNRLRE  154 (328)
T ss_dssp             TTCCEEEEESSCCSS-CCSCGGGGTTCSEEEEESSCCC-----CCCSCGGGGTTCSEEEEESCCCCCCCGGGGGCTTCCE
T ss_pred             cceeEEEccCCCchh-cChhhhhCCCCCEEECCCCCcc-----chhHHHhccCCCCEEECCCCccccCcHHHhcCcCCCE
Confidence            456667776333332 333333  67777777665542     2345566777788888888877777777777888888


Q ss_pred             EEccCC-CCCccCCCCcEEEeeCCccCcc-eeeEEecc--cccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccC
Q 041097          207 LKLNIP-SLKSLPSSRKILRLSGNSQFHF-SLASLLLY--YQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQF  281 (391)
Q Consensus       207 L~l~~~-~i~~lp~~~~~L~l~~~~l~~L-~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l  281 (391)
                      |++++| ....+|..++..++.+. +..+ +|+.|+++  ....+|..++++++|++|++++..    +.. +| .++.+
T Consensus       155 L~L~~n~~~~~~p~~~~~~~~~~~-~~~l~~L~~L~L~~n~l~~lp~~l~~l~~L~~L~L~~N~----l~~-l~~~l~~l  228 (328)
T 4fcg_A          155 LSIRACPELTELPEPLASTDASGE-HQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSP----LSA-LGPAIHHL  228 (328)
T ss_dssp             EEEEEETTCCCCCSCSEEEC-CCC-EEESTTCCEEEEEEECCCCCCGGGGGCTTCCEEEEESSC----CCC-CCGGGGGC
T ss_pred             EECCCCCCccccChhHhhccchhh-hccCCCCCEEECcCCCcCcchHhhcCCCCCCEEEccCCC----CCc-CchhhccC
Confidence            888774 44567766542222111 0111 56666666  344889999999999999998722    000 55 77888


Q ss_pred             CCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEE
Q 041097          282 PPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLE  361 (391)
Q Consensus       282 ~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~  361 (391)
                       ++|+.|++++|.+....+..++.+++|+.|+++.|...+..+...+.+++|++|++++|..+..+|.+++++++|+.++
T Consensus       229 -~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~iP~~l~~L~~L~~l~  307 (328)
T 4fcg_A          229 -PKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIIL  307 (328)
T ss_dssp             -TTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEECTTCTTCCCCCGGGGGSCTTCEEE
T ss_pred             -CCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeCCCCCchhhccHHHhhccCceEEe
Confidence             9999999999887777667889999999999996666655444557899999999999998899999999999999998


Q ss_pred             eeC
Q 041097          362 LWW  364 (391)
Q Consensus       362 l~~  364 (391)
                      +..
T Consensus       308 l~~  310 (328)
T 4fcg_A          308 VPP  310 (328)
T ss_dssp             CCG
T ss_pred             CCH
Confidence            753

>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=99.80  E-value=4.4e-19  Score=165.50  Aligned_cols=191  Identities=20%  Similarity=0.204  Sum_probs=144.4

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------IL  224 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L  224 (391)
                      .+++.|.+.++...     .+++.+.+++.|++|++++|.+..+|..++++.+|++|++++|.+..+|..++      +|
T Consensus        81 ~~l~~L~L~~n~l~-----~lp~~l~~l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~L  155 (328)
T 4fcg_A           81 PGRVALELRSVPLP-----QFPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARNPLRALPASIASLNRLREL  155 (328)
T ss_dssp             TTCCEEEEESSCCS-----SCCSCGGGGTTCSEEEEESSCCCCCCSCGGGGTTCSEEEEESCCCCCCCGGGGGCTTCCEE
T ss_pred             cceeEEEccCCCch-----hcChhhhhCCCCCEEECCCCCccchhHHHhccCCCCEEECCCCccccCcHHHhcCcCCCEE
Confidence            55666666655443     23344556777777777777777777777777777777777777777776654      55


Q ss_pred             EeeCCccCcceeeEEecccccchhHHhcC---------CCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeecc
Q 041097          225 RLSGNSQFHFSLASLLLYYQSLLSKSLCR---------LSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNI  293 (391)
Q Consensus       225 ~l~~~~l~~L~L~~L~l~~~~~lp~~i~~---------l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~  293 (391)
                      ++++|++.            ..+|..++.         +++|++|++++.. .    .  +| .++.+ ++|+.|++++|
T Consensus       156 ~L~~n~~~------------~~~p~~~~~~~~~~~~~~l~~L~~L~L~~n~l~----~--lp~~l~~l-~~L~~L~L~~N  216 (328)
T 4fcg_A          156 SIRACPEL------------TELPEPLASTDASGEHQGLVNLQSLRLEWTGIR----S--LPASIANL-QNLKSLKIRNS  216 (328)
T ss_dssp             EEEEETTC------------CCCCSCSEEEC-CCCEEESTTCCEEEEEEECCC----C--CCGGGGGC-TTCCEEEEESS
T ss_pred             ECCCCCCc------------cccChhHhhccchhhhccCCCCCEEECcCCCcC----c--chHhhcCC-CCCCEEEccCC
Confidence            55554322            366666554         8899999988722 1    0  67 78899 99999999999


Q ss_pred             cCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          294 ELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       294 ~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .+...+ +.++.+++|+.|+++.|...+..+...+.+++|++|++++|.....+|.++..+++|++|++++|+
T Consensus       217 ~l~~l~-~~l~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L~~n~  288 (328)
T 4fcg_A          217 PLSALG-PAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCV  288 (328)
T ss_dssp             CCCCCC-GGGGGCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEECTTCT
T ss_pred             CCCcCc-hhhccCCCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeCCCCC
Confidence            988755 578999999999999777766555556889999999999999889999999999999999999986

>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=99.73  E-value=1.1e-17  Score=173.52  Aligned_cols=216  Identities=19%  Similarity=0.102  Sum_probs=143.1

Q ss_pred             HhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccCCCCC-ccCCCCc------EEEeeCCccCcc---------e
Q 041097          173 KICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNIPSLK-SLPSSRK------ILRLSGNSQFHF---------S  235 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~~~i~-~lp~~~~------~L~l~~~~l~~L---------~  235 (391)
                      ..+..++.|+.|++++|.+. ..|..++.+.+|++|++++|.+. .+|..++      .|++++|++...         +
T Consensus       436 ~~l~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~~l~~  515 (768)
T 3rgz_A          436 SSLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLEN  515 (768)
T ss_dssp             GGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTT
T ss_pred             HHHhcCCCCCEEECCCCcccCcCCHHHcCCCCceEEEecCCcccCcCCHHHhcCCCCCEEEccCCccCCcCChHHhcCCC
Confidence            45566666667777666665 56666666677777777776665 4555544      677777665522         6


Q ss_pred             eeEEecc---cccchhHHhcCCCCCCEEEecCCC---CCC-ch-------------------------------------
Q 041097          236 LASLLLY---YQSLLSKSLCRLSCLESLKLANES---KMP-RR-------------------------------------  271 (391)
Q Consensus       236 L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~~~---~lp-~L-------------------------------------  271 (391)
                      |+.|+++   -...+|..++.+++|+.|++++..   .+| .+                                     
T Consensus       516 L~~L~L~~N~l~~~~p~~l~~l~~L~~L~Ls~N~l~g~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  595 (768)
T 3rgz_A          516 LAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGNLLE  595 (768)
T ss_dssp             CCEEECCSSCCEEECCGGGGGCTTCCEEECCSSEEESBCCGGGGTTTTCBCCSTTCSCEEEEEECCSCCTTCCSSEEEEE
T ss_pred             CCEEECCCCcccCcCCHHHcCCCCCCEEECCCCccCCcCChHHhcccchhhhhccccccccccccccccccccccccccc
Confidence            7777777   223577778888888888877611   111 00                                     


Q ss_pred             ----------------------hhh---cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc
Q 041097          272 ----------------------SNI---IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM  325 (391)
Q Consensus       272 ----------------------~~L---lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~  325 (391)
                                            +.+   .| .++.+ ++|+.|++++|.+....+..++.+++|+.|+++.|...+..+.
T Consensus       596 ~~~~~~~~~~~l~~~~~~~l~~~~~~g~~~~~~~~l-~~L~~LdLs~N~l~g~ip~~l~~l~~L~~L~Ls~N~l~g~ip~  674 (768)
T 3rgz_A          596 FQGIRSEQLNRLSTRNPCNITSRVYGGHTSPTFDNN-GSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPD  674 (768)
T ss_dssp             CTTCCGGGGGGGGGTCCSCTTSCEEEEECCCSCSSS-BCCCEEECCSSCCBSCCCGGGGGCTTCCEEECCSSCCCSCCCG
T ss_pred             cccccchhhhccccccccccccceecccCchhhhcc-ccccEEECcCCcccccCCHHHhccccCCEEeCcCCccCCCCCh
Confidence                                  000   23 45567 7899999999998877778999999999999998888876666


Q ss_pred             CCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCcH---------------------------HHHHHhhhccc
Q 041097          326 GIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPEP---------------------------ELRQQLREFED  378 (391)
Q Consensus       326 ~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~~---------------------------~l~~~~~~~~~  378 (391)
                      ..+.+++|+.|++++|.--..+|..++.+++|++|++++++-                           .+ ..|....+
T Consensus       675 ~l~~L~~L~~LdLs~N~l~g~ip~~l~~l~~L~~L~ls~N~l~g~iP~~~~~~~~~~~~~~gN~~Lcg~~l-~~C~~~~~  753 (768)
T 3rgz_A          675 EVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTEIDLSNNNLSGPIPEMGQFETFPPAKFLNNPGLCGYPL-PRCDPSNA  753 (768)
T ss_dssp             GGGGCTTCCEEECCSSCCEECCCGGGGGCCCCSEEECCSSEEEEECCSSSSGGGSCGGGGCSCTEEESTTS-CCCCSCC-
T ss_pred             HHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECcCCcccccCCCchhhccCCHHHhcCCchhcCCCC-cCCCCCcc
Confidence            668999999999998864347899999999999999885421                           12 26788999


Q ss_pred             cccceeecCCCC
Q 041097          379 KEQYGIQLYPYG  390 (391)
Q Consensus       379 ~~~~~i~~~~~~  390 (391)
                      ++|++|+|+|.+
T Consensus       754 ~~~~~~~~~~~~  765 (768)
T 3rgz_A          754 DGYAHHQRSHHH  765 (768)
T ss_dssp             ------------
T ss_pred             CCCCCCCCcccc
Confidence            999999999975

>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=99.72  E-value=1.1e-16  Score=149.27  Aligned_cols=201  Identities=21%  Similarity=0.152  Sum_probs=130.1

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCCCc----EEE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSSRK----ILR  225 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~----~L~  225 (391)
                      +.++.|.+.++...    ...+..+..++.|++|++++|.+..+ |..++++.+|++|+++++.+..+|..+.    .|+
T Consensus        52 ~~l~~L~L~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~~~L~~L~  127 (330)
T 1xku_A           52 PDTALLDLQNNKIT----EIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELR  127 (330)
T ss_dssp             TTCCEEECCSSCCC----CBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEEE
T ss_pred             CCCeEEECCCCcCC----EeChhhhccCCCCCEEECCCCcCCeeCHHHhcCCCCCCEEECCCCcCCccChhhcccccEEE
Confidence            67777777655442    12224578899999999999998865 7889999999999999999998887765    999


Q ss_pred             eeCCccCcc---------eeeEEecc--cc---cchhHHhcCCCCCCEEEecCCC--CCCchhhhcc-ccccCCCCccEE
Q 041097          226 LSGNSQFHF---------SLASLLLY--YQ---SLLSKSLCRLSCLESLKLANES--KMPRRSNIIL-AEYQFPPSLTHL  288 (391)
Q Consensus       226 l~~~~l~~L---------~L~~L~l~--~~---~~lp~~i~~l~~L~~L~l~~~~--~lp~L~~Llp-~~~~l~~~L~~L  288 (391)
                      +++|.+..+         +|+.|+++  ..   ...+..++.+++|++|++++..  .       +| .+  . ++|+.|
T Consensus       128 l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~l~~-------l~~~~--~-~~L~~L  197 (330)
T 1xku_A          128 VHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITT-------IPQGL--P-PSLTEL  197 (330)
T ss_dssp             CCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCS-------CCSSC--C-TTCSEE
T ss_pred             CCCCcccccCHhHhcCCccccEEECCCCcCCccCcChhhccCCCCcCEEECCCCcccc-------CCccc--c-ccCCEE
Confidence            999987765         78888888  12   2446678888899999888722  1       22 11  2 455555


Q ss_pred             EeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          289 SFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       289 ~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ++++|.+...++..++.+++|+.|+++.|..........+.+++|++|++++| .+..+|.++..+++|++|++++++
T Consensus       198 ~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N-~l~~lp~~l~~l~~L~~L~l~~N~  274 (330)
T 1xku_A          198 HLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNN-KLVKVPGGLADHKYIQVVYLHNNN  274 (330)
T ss_dssp             ECTTSCCCEECTGGGTTCTTCCEEECCSSCCCEECTTTGGGSTTCCEEECCSS-CCSSCCTTTTTCSSCCEEECCSSC
T ss_pred             ECCCCcCCccCHHHhcCCCCCCEEECCCCcCceeChhhccCCCCCCEEECCCC-cCccCChhhccCCCcCEEECCCCc
Confidence            55555555444445555555555555544433211112234555555555555 345555555555555555555443

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.70  E-value=1e-16  Score=148.44  Aligned_cols=214  Identities=15%  Similarity=0.100  Sum_probs=137.9

Q ss_pred             CceEEEEEeccCCCc--ccccCCC--CCccEEEEEe-cCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCcccCCCC
Q 041097          129 ENVKRFTAHRKLNDF--AFLDDFD--SFLHSLLYLT-SGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLF  202 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~--~~~~~~~--~~lrsl~~~~-~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~  202 (391)
                      .+++.+.+.......  .+...+.  ++++.|.+.+ ....    ...+..+.+++.|++|++++|.+. .+|..++++.
T Consensus        50 ~~l~~L~L~~~~l~~~~~~~~~l~~l~~L~~L~L~~~n~l~----~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~  125 (313)
T 1ogq_A           50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLV----GPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIK  125 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEE----SCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCT
T ss_pred             ceEEEEECCCCCccCCcccChhHhCCCCCCeeeCCCCCccc----ccCChhHhcCCCCCEEECcCCeeCCcCCHHHhCCC
Confidence            456777766333222  1333333  6777777763 3221    123355677777888888777776 6777777777


Q ss_pred             cccEEEccCCCCC-ccCCCCc------EEEeeCCccCcceeeEEecccccchhHHhcCCC-CCCEEEecCCCCCCchhhh
Q 041097          203 LLRYLKLNIPSLK-SLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLS-CLESLKLANESKMPRRSNI  274 (391)
Q Consensus       203 ~L~~L~l~~~~i~-~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~-~L~~L~l~~~~~lp~L~~L  274 (391)
                      +|++|++++|.+. .+|..+.      +|++++|.+.            ..+|..++.++ +|++|++++..    +...
T Consensus       126 ~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~------------~~~p~~l~~l~~~L~~L~L~~N~----l~~~  189 (313)
T 1ogq_A          126 TLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRIS------------GAIPDSYGSFSKLFTSMTISRNR----LTGK  189 (313)
T ss_dssp             TCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCE------------EECCGGGGCCCTTCCEEECCSSE----EEEE
T ss_pred             CCCEEeCCCCccCCcCChHHhcCCCCCeEECcCCccc------------CcCCHHHhhhhhcCcEEECcCCe----eecc
Confidence            8888888777766 5665554      6666666554            36777788887 78888887611    0001


Q ss_pred             cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccc-cchHhhc
Q 041097          275 IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLK-RIHEQLW  352 (391)
Q Consensus       275 lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~-~lp~~~~  352 (391)
                      .| .+..+ + |+.|++++|.+....+..++.+++|+.|+++.|...+. ....+.+++|++|++++|. +. .+|.++.
T Consensus       190 ~~~~~~~l-~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~-~~~~~~l~~L~~L~Ls~N~-l~~~~p~~l~  265 (313)
T 1ogq_A          190 IPPTFANL-N-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFD-LGKVGLSKNLNGLDLRNNR-IYGTLPQGLT  265 (313)
T ss_dssp             CCGGGGGC-C-CSEEECCSSEEEECCGGGCCTTSCCSEEECCSSEECCB-GGGCCCCTTCCEEECCSSC-CEECCCGGGG
T ss_pred             CChHHhCC-c-ccEEECcCCcccCcCCHHHhcCCCCCEEECCCCceeee-cCcccccCCCCEEECcCCc-ccCcCChHHh
Confidence            44 56666 4 88888888777666667777788888888876655432 2224566778888888774 44 6777777


Q ss_pred             CCCCCCEEEeeCCc
Q 041097          353 CLKSLNKLELWWPE  366 (391)
Q Consensus       353 ~l~~L~~L~l~~~~  366 (391)
                      .+++|++|++++++
T Consensus       266 ~l~~L~~L~Ls~N~  279 (313)
T 1ogq_A          266 QLKFLHSLNVSFNN  279 (313)
T ss_dssp             GCTTCCEEECCSSE
T ss_pred             cCcCCCEEECcCCc
Confidence            78888888877664

>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=99.68  E-value=5.1e-16  Score=151.14  Aligned_cols=205  Identities=20%  Similarity=0.135  Sum_probs=152.7

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCCc-------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSRK-------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~~-------  222 (391)
                      +.++.|.+.++...    ...+..+..++.|+.|++++|.+..++ ..+.++.+|++|++++|.+..+|....       
T Consensus        75 ~~l~~L~L~~n~i~----~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  150 (452)
T 3zyi_A           75 SNTRYLNLMENNIQ----MIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLR  150 (452)
T ss_dssp             TTCSEEECCSSCCC----EECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSBCCTTTSSSCTTCC
T ss_pred             CCccEEECcCCcCc----eECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCCcCCccChhhhcccCCCC
Confidence            66777766655432    122355677888888888888877444 677788888888888888887776532       


Q ss_pred             EEEeeCCccCcc---------eeeEEecc---cccchhH-HhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEE
Q 041097          223 ILRLSGNSQFHF---------SLASLLLY---YQSLLSK-SLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLS  289 (391)
Q Consensus       223 ~L~l~~~~l~~L---------~L~~L~l~---~~~~lp~-~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~  289 (391)
                      +|++++|.+..+         +|+.|+++   ....++. .+.++++|++|++++..    +.. +|.+..+ ++|+.|+
T Consensus       151 ~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~----l~~-~~~~~~l-~~L~~L~  224 (452)
T 3zyi_A          151 ELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCN----IKD-MPNLTPL-VGLEELE  224 (452)
T ss_dssp             EEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSC----CSS-CCCCTTC-TTCCEEE
T ss_pred             EEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCc----ccc-ccccccc-ccccEEE
Confidence            788888776654         67777777   3344554 57888999999988722    000 4556778 9999999


Q ss_pred             eecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHh-hcCCCCCCEEEeeCCc
Q 041097          290 FSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLELWWPE  366 (391)
Q Consensus       290 l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l~~~~  366 (391)
                      +++|.+...++..+..+++|+.|+++.|............+++|+.|++++| +++.+|.. +..+++|++|+++++|
T Consensus       225 Ls~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~Np  301 (452)
T 3zyi_A          225 MSGNHFPEIRPGSFHGLSSLKKLWVMNSQVSLIERNAFDGLASLVELNLAHN-NLSSLPHDLFTPLRYLVELHLHHNP  301 (452)
T ss_dssp             CTTSCCSEECGGGGTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCSCCCTTSSTTCTTCCEEECCSSC
T ss_pred             CcCCcCcccCcccccCccCCCEEEeCCCcCceECHHHhcCCCCCCEEECCCC-cCCccChHHhccccCCCEEEccCCC
Confidence            9999998887788999999999999977665433333468899999999988 57888754 5889999999999866

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.68  E-value=2.9e-16  Score=146.61  Aligned_cols=208  Identities=14%  Similarity=0.135  Sum_probs=113.3

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCCCc----EEE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSSRK----ILR  225 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~----~L~  225 (391)
                      +.++.|.+.++...    ...+..+..++.|++|++++|.+..+ |..++++.+|++|+++++.+..+|..+.    +|+
T Consensus        54 ~~l~~L~l~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~L~~L~  129 (332)
T 2ft3_A           54 PDTTLLDLQNNDIS----ELRKDDFKGLQHLYALVLVNNKISKIHEKAFSPLRKLQKLYISKNHLVEIPPNLPSSLVELR  129 (332)
T ss_dssp             TTCCEEECCSSCCC----EECTTTTTTCTTCCEEECCSSCCCEECGGGSTTCTTCCEEECCSSCCCSCCSSCCTTCCEEE
T ss_pred             CCCeEEECCCCcCC----ccCHhHhhCCCCCcEEECCCCccCccCHhHhhCcCCCCEEECCCCcCCccCccccccCCEEE
Confidence            56777766554432    11224567788888888888887754 6678888888888888888887776664    788


Q ss_pred             eeCCccCcc---------eeeEEecc--cc---cchhHHhcCCCCCCEEEecCCC--CC-----Cchhhh----------
Q 041097          226 LSGNSQFHF---------SLASLLLY--YQ---SLLSKSLCRLSCLESLKLANES--KM-----PRRSNI----------  274 (391)
Q Consensus       226 l~~~~l~~L---------~L~~L~l~--~~---~~lp~~i~~l~~L~~L~l~~~~--~l-----p~L~~L----------  274 (391)
                      +++|.+..+         +|+.|+++  ..   ...|..++.+ +|++|++++..  .+     +.|+.|          
T Consensus       130 l~~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l-~L~~L~l~~n~l~~l~~~~~~~L~~L~l~~n~i~~~  208 (332)
T 2ft3_A          130 IHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGL-KLNYLRISEAKLTGIPKDLPETLNELHLDHNKIQAI  208 (332)
T ss_dssp             CCSSCCCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSC-CCSCCBCCSSBCSSCCSSSCSSCSCCBCCSSCCCCC
T ss_pred             CCCCccCccCHhHhCCCccCCEEECCCCccccCCCCcccccCC-ccCEEECcCCCCCccCccccCCCCEEECCCCcCCcc
Confidence            887766643         56666665  11   1234444445 55555555411  11     112211          


Q ss_pred             cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHh-hc
Q 041097          275 IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ-LW  352 (391)
Q Consensus       275 lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~-~~  352 (391)
                      .| .+..+ ++|+.|++++|.+...+...++.+++|+.|+++.|... ..+...+.+++|++|+++++ .++.+|.. +.
T Consensus       209 ~~~~l~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~-~lp~~l~~l~~L~~L~l~~N-~l~~~~~~~~~  285 (332)
T 2ft3_A          209 ELEDLLRY-SKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDNNKLS-RVPAGLPDLKLLQVVYLHTN-NITKVGVNDFC  285 (332)
T ss_dssp             CTTSSTTC-TTCSCCBCCSSCCCCCCTTGGGGCTTCCEEECCSSCCC-BCCTTGGGCTTCCEEECCSS-CCCBCCTTSSS
T ss_pred             CHHHhcCC-CCCCEEECCCCcCCcCChhHhhCCCCCCEEECCCCcCe-ecChhhhcCccCCEEECCCC-CCCccChhHcc
Confidence            12 34445 55555555555555444444555555555555544332 11111244555555555554 24444321 11


Q ss_pred             C------CCCCCEEEeeCCc
Q 041097          353 C------LKSLNKLELWWPE  366 (391)
Q Consensus       353 ~------l~~L~~L~l~~~~  366 (391)
                      .      .++|+.|++.++|
T Consensus       286 ~~~~~~~~~~l~~L~l~~N~  305 (332)
T 2ft3_A          286 PVGFGVKRAYYNGISLFNNP  305 (332)
T ss_dssp             CSSCCSSSCCBSEEECCSSS
T ss_pred             ccccccccccccceEeecCc
Confidence            1      2445555555555

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.67  E-value=6.2e-16  Score=150.02  Aligned_cols=203  Identities=21%  Similarity=0.124  Sum_probs=145.3

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCC-Cc------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSS-RK------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~-~~------  222 (391)
                      +.++.|.+..+...    ...+..+..++.|++|++++|.+..++ ..+.++.+|++|++++|.+..+|.. +.      
T Consensus        64 ~~l~~L~L~~n~i~----~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  139 (440)
T 3zyj_A           64 TNTRLLNLHENQIQ----IIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLK  139 (440)
T ss_dssp             TTCSEEECCSCCCC----EECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCSSCCSSCCTTTSCSCSSCC
T ss_pred             CCCcEEEccCCcCC----eeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCCCcCCeeCHhHhhccccCc
Confidence            55666655544332    112245566777777777777766444 5567777777777777777766653 22      


Q ss_pred             EEEeeCCccCcc---------eeeEEecc---cccchhH-HhcCCCCCCEEEecCCC--CCCchhhhccccccCCCCccE
Q 041097          223 ILRLSGNSQFHF---------SLASLLLY---YQSLLSK-SLCRLSCLESLKLANES--KMPRRSNIILAEYQFPPSLTH  287 (391)
Q Consensus       223 ~L~l~~~~l~~L---------~L~~L~l~---~~~~lp~-~i~~l~~L~~L~l~~~~--~lp~L~~Llp~~~~l~~~L~~  287 (391)
                      .|++++|.+..+         +|+.|+++   ....++. .+.++++|++|++++..  .       +|.+..+ ++|+.
T Consensus       140 ~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~-------~~~~~~l-~~L~~  211 (440)
T 3zyj_A          140 ELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLRE-------IPNLTPL-IKLDE  211 (440)
T ss_dssp             EEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEECTTSCCSS-------CCCCTTC-SSCCE
T ss_pred             eeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecCCCCcCcc-------ccccCCC-cccCE
Confidence            777777765543         67777776   2334544 67889999999998732  2       5556778 99999


Q ss_pred             EEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          288 LSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       288 L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      |+|++|.+...+...+..+++|+.|+++.|............+++|+.|++++| +++.+|. .+..+++|++|+++++|
T Consensus       212 L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~Np  290 (440)
T 3zyj_A          212 LDLSGNHLSAIRPGSFQGLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHN-NLTLLPHDLFTPLHHLERIHLHHNP  290 (440)
T ss_dssp             EECTTSCCCEECTTTTTTCTTCCEEECTTCCCCEECTTSSTTCTTCCEEECTTS-CCCCCCTTTTSSCTTCCEEECCSSC
T ss_pred             EECCCCccCccChhhhccCccCCEEECCCCceeEEChhhhcCCCCCCEEECCCC-CCCccChhHhccccCCCEEEcCCCC
Confidence            999999988877788999999999999977665433333468899999999988 5788875 46889999999999866

>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=99.67  E-value=3.7e-16  Score=144.09  Aligned_cols=219  Identities=22%  Similarity=0.185  Sum_probs=156.9

Q ss_pred             cCceEEEEEeccCCCccccc-CC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcc
Q 041097          128 RENVKRFTAHRKLNDFAFLD-DF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLL  204 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~-~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L  204 (391)
                      +.+++++.+..+.... +.. .. + ++++.|.+.++...  .....+..+..++.|++|++++|.+..+|..+..+.+|
T Consensus        27 ~~~l~~L~L~~n~l~~-i~~~~~~~l~~L~~L~L~~n~l~--~~~~~~~~~~~~~~L~~L~Ls~n~i~~l~~~~~~l~~L  103 (306)
T 2z66_A           27 PSSATRLELESNKLQS-LPHGVFDKLTQLTKLSLSSNGLS--FKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQL  103 (306)
T ss_dssp             CTTCCEEECCSSCCCC-CCTTTTTTCTTCSEEECCSSCCC--EEEEEEHHHHSCSCCCEEECCSCSEEEEEEEEETCTTC
T ss_pred             CCCCCEEECCCCccCc-cCHhHhhccccCCEEECCCCccC--cccCcccccccccccCEEECCCCccccChhhcCCCCCC
Confidence            3567777776333333 332 22 3 78888877655432  00011245556888999999998888888888888899


Q ss_pred             cEEEccCCCCCccCC--CCc------EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhh-hc
Q 041097          205 RYLKLNIPSLKSLPS--SRK------ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSN-II  275 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~--~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~-Ll  275 (391)
                      ++|+++++.+..+|.  .+.      +|++++|.+.            ...|..++.+++|++|++++..    +.. .+
T Consensus       104 ~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~------------~~~~~~~~~l~~L~~L~l~~n~----l~~~~~  167 (306)
T 2z66_A          104 EHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTR------------VAFNGIFNGLSSLEVLKMAGNS----FQENFL  167 (306)
T ss_dssp             CEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCE------------ECSTTTTTTCTTCCEEECTTCE----EGGGEE
T ss_pred             CEEECCCCcccccccchhhhhccCCCEEECCCCcCC------------ccchhhcccCcCCCEEECCCCc----cccccc
Confidence            999998888877664  222      6666666655            3456678899999999998721    111 15


Q ss_pred             c-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCC
Q 041097          276 L-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCL  354 (391)
Q Consensus       276 p-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l  354 (391)
                      | .+..+ ++|+.|++++|.+...++..++.+++|+.|+++.|............+++|++|++++|.--...|..+..+
T Consensus       168 ~~~~~~l-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~  246 (306)
T 2z66_A          168 PDIFTEL-RNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHF  246 (306)
T ss_dssp             CSCCTTC-TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCSBCCSGGGTTCTTCCEEECTTSCCCBCSSSSCCCC
T ss_pred             hhHHhhC-cCCCEEECCCCCcCCcCHHHhcCCCCCCEEECCCCccCccChhhccCcccCCEeECCCCCCcccCHHHHHhh
Confidence            6 77888 999999999999888766788999999999999777655333344678999999999985334456678888


Q ss_pred             C-CCCEEEeeCCc
Q 041097          355 K-SLNKLELWWPE  366 (391)
Q Consensus       355 ~-~L~~L~l~~~~  366 (391)
                      + +|++|+++++|
T Consensus       247 ~~~L~~L~L~~N~  259 (306)
T 2z66_A          247 PSSLAFLNLTQND  259 (306)
T ss_dssp             CTTCCEEECTTCC
T ss_pred             hccCCEEEccCCC
Confidence            4 99999998854

>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=99.66  E-value=3.7e-15  Score=146.00  Aligned_cols=232  Identities=21%  Similarity=0.166  Sum_probs=129.9

Q ss_pred             CceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcc-cCCCCccc
Q 041097          129 ENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSG-IENLFLLR  205 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~-i~~l~~L~  205 (391)
                      ..++.|.+..+.......... + ++++.|.+.++...    ...+..+..++.|++|++++|.+..+|.. ++++.+|+
T Consensus        32 ~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  107 (477)
T 2id5_A           32 TETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVS----AVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLT  107 (477)
T ss_dssp             TTCSEEECCSSCCCEECTTTTTTCTTCCEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCCSCCTTSSTTCTTCC
T ss_pred             CCCcEEECCCCccceECHhHccCCCCCCEEECCCCccC----EeChhhhhCCccCCEEECCCCcCCccCcccccCCCCCC
Confidence            456666665332222112222 2 66666666544332    11234566677777777777777766643 56777777


Q ss_pred             EEEccCCCCCccCC-CCc------EEEeeCCccCcc---------eeeEEecc--cccchh-HHhcCCCCCCEEEecCCC
Q 041097          206 YLKLNIPSLKSLPS-SRK------ILRLSGNSQFHF---------SLASLLLY--YQSLLS-KSLCRLSCLESLKLANES  266 (391)
Q Consensus       206 ~L~l~~~~i~~lp~-~~~------~L~l~~~~l~~L---------~L~~L~l~--~~~~lp-~~i~~l~~L~~L~l~~~~  266 (391)
                      +|++++|.+..++. .+.      .|++++|.+..+         +|+.|+++  ....+| ..+..+++|+.|++.+..
T Consensus       108 ~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~l~~n~  187 (477)
T 2id5_A          108 KLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLN  187 (477)
T ss_dssp             EEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCEEEEESCCCSSCCHHHHTTCTTCCEEEEESCC
T ss_pred             EEECCCCccccCChhHccccccCCEEECCCCccceeChhhccCCCCCCEEECCCCcCcccChhHhcccCCCcEEeCCCCc
Confidence            77777777665433 222      677776655443         56666666  333444 346666666666666511


Q ss_pred             -------CC---Cchhhh----------cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCc-----
Q 041097          267 -------KM---PRRSNI----------IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYS-----  320 (391)
Q Consensus       267 -------~l---p~L~~L----------lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~-----  320 (391)
                             .+   +.|+.|          +| ..... .+|+.|++++|.+...+...++.+++|+.|+++.|...     
T Consensus       188 i~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~~-~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~  266 (477)
T 2id5_A          188 INAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYG-LNLTSLSITHCNLTAVPYLAVRHLVYLRFLNLSYNPISTIEGS  266 (477)
T ss_dssp             CCEECTTCSCSCTTCCEEEEECCTTCCEECTTTTTT-CCCSEEEEESSCCCSCCHHHHTTCTTCCEEECCSSCCCEECTT
T ss_pred             CcEeChhhcccCcccceeeCCCCccccccCcccccC-ccccEEECcCCcccccCHHHhcCccccCeeECCCCcCCccChh
Confidence                   11   222222          22 22233 45666666666655555455566666666666644332     


Q ss_pred             -------------------CccccCCCcccccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          321 -------------------EERTMGIRAMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       321 -------------------~~~~~~~~~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                                         ...+.....+++|+.|++++| .++.+|. .+..+++|++|+++++|
T Consensus       267 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~  331 (477)
T 2id5_A          267 MLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRVLNVSGN-QLTTLEESVFHSVGNLETLILDSNP  331 (477)
T ss_dssp             SCTTCTTCCEEECCSSCCSEECTTTBTTCTTCCEEECCSS-CCSCCCGGGBSCGGGCCEEECCSSC
T ss_pred             hccccccCCEEECCCCccceECHHHhcCcccCCEEECCCC-cCceeCHhHcCCCcccCEEEccCCC
Confidence                               111122346678888888877 4677765 45778888888887654

>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=99.66  E-value=1.3e-15  Score=139.51  Aligned_cols=178  Identities=21%  Similarity=0.164  Sum_probs=139.7

Q ss_pred             CcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCCCc-----EEEeeCCccCcceeeEEecccccchhHHhc
Q 041097          179 KFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSSRK-----ILRLSGNSQFHFSLASLLLYYQSLLSKSLC  252 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~  252 (391)
                      +.+++|++++|.+..+ +..+..+.+|++|+++++.+..+|..-.     +|++++|.+.             .+|..+.
T Consensus        31 ~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~l~~L~~L~Ls~N~l~-------------~l~~~~~   97 (290)
T 1p9a_G           31 KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQ-------------SLPLLGQ   97 (290)
T ss_dssp             TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEECCSCCTTCCEEECCSSCCS-------------SCCCCTT
T ss_pred             CCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCCCccCcccCCCCCCcCCEEECCCCcCC-------------cCchhhc
Confidence            5788899999988854 4678888999999999988887765422     7777777776             8898899


Q ss_pred             CCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCccc
Q 041097          253 RLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMP  331 (391)
Q Consensus       253 ~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~  331 (391)
                      .+++|++|++++..    +..+.| .+..+ ++|+.|++++|.+...+...+..+++|+.|+++.|.......-....++
T Consensus        98 ~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           98 TLPALTVLDVSFNR----LTSLPLGALRGL-GELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLE  172 (290)
T ss_dssp             TCTTCCEEECCSSC----CCCCCSSTTTTC-TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCT
T ss_pred             cCCCCCEEECCCCc----CcccCHHHHcCC-CCCCEEECCCCCCCccChhhcccccCCCEEECCCCcCCccCHHHhcCcC
Confidence            99999999999822    111123 57889 9999999999999888877889999999999997766532211125689


Q ss_pred             ccceeeeccccccccchHhhcCCCCCCEEEeeCCc-------HHHHHHhhh
Q 041097          332 KLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE-------PELRQQLRE  375 (391)
Q Consensus       332 ~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~-------~~l~~~~~~  375 (391)
                      +|+.|+++++ .++.+|.++...++|++|++.++|       ..+.+|+++
T Consensus       173 ~L~~L~L~~N-~l~~ip~~~~~~~~L~~l~L~~Np~~C~c~~~~l~~wl~~  222 (290)
T 1p9a_G          173 NLDTLLLQEN-SLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQD  222 (290)
T ss_dssp             TCCEEECCSS-CCCCCCTTTTTTCCCSEEECCSCCBCCSGGGHHHHHHHHH
T ss_pred             CCCEEECCCC-cCCccChhhcccccCCeEEeCCCCccCcCccHHHHHHHHh
Confidence            9999999988 589999999999999999999765       124566654

>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=99.66  E-value=1.8e-15  Score=147.12  Aligned_cols=87  Identities=25%  Similarity=0.241  Sum_probs=67.1

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHh-hcCCC
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ-LWCLK  355 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~-~~~l~  355 (391)
                      .+..+ ++|+.|++++|.+...++..++.+++|+.|+++.|...+..+...+.+++|++|++++| .++.+|.. +..++
T Consensus       318 ~~~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~  395 (455)
T 3v47_A          318 AFWGL-THLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTN-QLKSVPDGIFDRLT  395 (455)
T ss_dssp             TTTTC-TTCCEEECCSSCCCEECGGGGTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCT
T ss_pred             HhcCc-ccCCEEECCCCccCCcChhHhcCcccCCEEECCCCcccccChhhccccccccEEECCCC-ccccCCHhHhccCC
Confidence            66777 88888888888877766677888888888888866654433334468899999999987 57788754 58899


Q ss_pred             CCCEEEeeCC
Q 041097          356 SLNKLELWWP  365 (391)
Q Consensus       356 ~L~~L~l~~~  365 (391)
                      +|++|+++++
T Consensus       396 ~L~~L~l~~N  405 (455)
T 3v47_A          396 SLQKIWLHTN  405 (455)
T ss_dssp             TCCEEECCSS
T ss_pred             cccEEEccCC
Confidence            9999999863

>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=99.65  E-value=6.6e-16  Score=155.84  Aligned_cols=204  Identities=19%  Similarity=0.090  Sum_probs=145.1

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC---CcccCCCCcccEEEccCCCCCccCCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY---PSGIENLFLLRYLKLNIPSLKSLPSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~---p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----  222 (391)
                      +.++.+.+..+...      ....+..++.|+.|++++|.+...   |..++.+.+|++|+++++.+..+|..+.     
T Consensus       328 ~~L~~L~l~~n~~~------~~~~~~~l~~L~~L~ls~n~l~~~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~l~~L  401 (606)
T 3vq2_A          328 PFLKSLTLTMNKGS------ISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEEL  401 (606)
T ss_dssp             SSCCEEEEESCSSC------EECCCCCCTTCCEEECCSSCEEEEEECCHHHHCCSCCCEEECCSCSEEEECCCCTTCTTC
T ss_pred             CccceeeccCCcCc------cchhhccCCCCCEEECcCCccCCCcchhhhhccCCcccEeECCCCccccchhhccCCCCC
Confidence            55555555544221      011344667777777777776633   6667777777777777777776665554     


Q ss_pred             -EEEeeCCccCcc----------eeeEEecc---cccchhHHhcCCCCCCEEEecCCCCCCchhh-hcc-ccccCCCCcc
Q 041097          223 -ILRLSGNSQFHF----------SLASLLLY---YQSLLSKSLCRLSCLESLKLANESKMPRRSN-IIL-AEYQFPPSLT  286 (391)
Q Consensus       223 -~L~l~~~~l~~L----------~L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~-Llp-~~~~l~~~L~  286 (391)
                       .|++++|.+...          +|+.|+++   .....|..++.+++|++|++++..    +.. .+| .++.+ ++|+
T Consensus       402 ~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~----l~~~~~~~~~~~l-~~L~  476 (606)
T 3vq2_A          402 QHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNS----FKDNTLSNVFANT-TNLT  476 (606)
T ss_dssp             CEEECTTSEEESTTTTTTTTTCTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCE----EGGGEECSCCTTC-TTCC
T ss_pred             CeeECCCCccCCccChhhhhccccCCEEECcCCCCCccchhhhcCCCCCCEEECCCCc----CCCcchHHhhccC-CCCC
Confidence             777777644322          67777776   122356677788888888887611    111 146 77889 9999


Q ss_pred             EEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCC-CCCEEEeeCC
Q 041097          287 HLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLK-SLNKLELWWP  365 (391)
Q Consensus       287 ~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~-~L~~L~l~~~  365 (391)
                      .|++++|.+...++..++.+++|+.|+++.|...+..+...+.+++|+.|++++|. ++.+|.++..++ +|++|+++++
T Consensus       477 ~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~p~~~~~l~~~L~~l~l~~N  555 (606)
T 3vq2_A          477 FLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNR-IETSKGILQHFPKSLAFFNLTNN  555 (606)
T ss_dssp             EEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSCEEGGGTTTCTTCCEEECTTSC-CCCEESCGGGSCTTCCEEECCSC
T ss_pred             EEECCCCcCCccChhhhcccccCCEEECCCCcCCCcCHHHccCCCcCCEEECCCCc-CcccCHhHhhhcccCcEEEccCC
Confidence            99999999888777789999999999999777665444445789999999999884 889999999997 5999999874


Q ss_pred             c
Q 041097          366 E  366 (391)
Q Consensus       366 ~  366 (391)
                      |
T Consensus       556 ~  556 (606)
T 3vq2_A          556 S  556 (606)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.65  E-value=2e-15  Score=143.96  Aligned_cols=86  Identities=20%  Similarity=0.189  Sum_probs=44.7

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCC
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKS  356 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~  356 (391)
                      ++..+ ++|+.|++++|.+...++..++.+++|+.|+++.|.... .....+.+++|++|++++| .+..+|.++..+++
T Consensus       243 ~l~~l-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~l~~  319 (390)
T 3o6n_A          243 WLLNY-PGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLVA-LNLYGQPIPTLKVLDLSHN-HLLHVERNQPQFDR  319 (390)
T ss_dssp             GGGGC-TTCSEEECCSSCCCEEESGGGTTCSSCCEEECCSSCCCE-EECSSSCCTTCCEEECCSS-CCCCCGGGHHHHTT
T ss_pred             HHcCC-CCccEEECCCCcCCCcChhHccccccCCEEECCCCcCcc-cCcccCCCCCCCEEECCCC-cceecCccccccCc
Confidence            44455 566666666665555444555566666666666443322 1112234556666666655 35555555544555


Q ss_pred             CCEEEeeCC
Q 041097          357 LNKLELWWP  365 (391)
Q Consensus       357 L~~L~l~~~  365 (391)
                      |++|+++++
T Consensus       320 L~~L~L~~N  328 (390)
T 3o6n_A          320 LENLYLDHN  328 (390)
T ss_dssp             CSEEECCSS
T ss_pred             CCEEECCCC
Confidence            555555444

>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=99.65  E-value=2e-15  Score=137.78  Aligned_cols=192  Identities=23%  Similarity=0.214  Sum_probs=145.4

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcccEEEccCCC-CCcc-CCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPS-LKSL-PSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~-i~~l-p~~~~-----  222 (391)
                      +.++.|.+.+....    ...+..+..++.|++|+++++.+..+ |..++.+.+|++|+++++. +..+ |..+.     
T Consensus        32 ~~l~~L~l~~n~i~----~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~l~~~~~~~~~~l~~L  107 (285)
T 1ozn_A           32 AASQRIFLHGNRIS----HVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRL  107 (285)
T ss_dssp             TTCSEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTC
T ss_pred             CCceEEEeeCCcCC----ccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCCCCCccccCHHHhcCCcCC
Confidence            66777766554432    11224567888899999999888855 6788888999999999886 7776 33333     


Q ss_pred             -EEEeeCCccCcceeeEEecccccch-hHHhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCC
Q 041097          223 -ILRLSGNSQFHFSLASLLLYYQSLL-SKSLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDD  298 (391)
Q Consensus       223 -~L~l~~~~l~~L~L~~L~l~~~~~l-p~~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~  298 (391)
                       +|++++|.+.             .+ |..++++++|++|++++..    +.. +|  .++.+ ++|+.|++++|.+...
T Consensus       108 ~~L~l~~n~l~-------------~~~~~~~~~l~~L~~L~l~~n~----l~~-~~~~~~~~l-~~L~~L~l~~n~l~~~  168 (285)
T 1ozn_A          108 HTLHLDRCGLQ-------------ELGPGLFRGLAALQYLYLQDNA----LQA-LPDDTFRDL-GNLTHLFLHGNRISSV  168 (285)
T ss_dssp             CEEECTTSCCC-------------CCCTTTTTTCTTCCEEECCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCEE
T ss_pred             CEEECCCCcCC-------------EECHhHhhCCcCCCEEECCCCc----ccc-cCHhHhccC-CCccEEECCCCccccc
Confidence             6777777666             44 6678999999999998722    011 33  47788 9999999999998877


Q ss_pred             ChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccch-HhhcCCCCCCEEEeeCCc
Q 041097          299 PIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       299 ~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~~~  366 (391)
                      +...+..+++|+.|+++.|......+...+.+++|+.|++++| .++.+| ..+..+++|++|+++++|
T Consensus       169 ~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~N~  236 (285)
T 1ozn_A          169 PERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFAN-NLSALPTEALAPLRALQYLRLNDNP  236 (285)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCSCCCHHHHTTCTTCCEEECCSSC
T ss_pred             CHHHhcCccccCEEECCCCcccccCHhHccCcccccEeeCCCC-cCCcCCHHHcccCcccCEEeccCCC
Confidence            7667899999999999977665543334578899999999988 477776 458999999999999864

>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=99.64  E-value=2.2e-15  Score=151.89  Aligned_cols=85  Identities=20%  Similarity=0.195  Sum_probs=40.4

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCC
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKS  356 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~  356 (391)
                      +++.+ ++|+.|++++|.+...++..++.+++|+.|+++.|...+ .+...+.+++|+.|++++| .+..+|.++..+++
T Consensus       249 ~l~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~-l~~~~~~l~~L~~L~Ls~N-~l~~i~~~~~~l~~  325 (597)
T 3oja_B          249 WLLNY-PGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLVA-LNLYGQPIPTLKVLDLSHN-HLLHVERNQPQFDR  325 (597)
T ss_dssp             GGGGC-TTCSEEECCSSCCCEEESGGGTTCSSCCEEECTTSCCCE-EECSSSCCTTCCEEECCSS-CCCCCGGGHHHHTT
T ss_pred             hhccC-CCCCEEECCCCccCCCCHHHhcCccCCCEEECCCCCCCC-CCcccccCCCCcEEECCCC-CCCccCcccccCCC
Confidence            34445 555555555555554444455555555555555443332 1112234555555555554 24455544444444


Q ss_pred             CCEEEeeC
Q 041097          357 LNKLELWW  364 (391)
Q Consensus       357 L~~L~l~~  364 (391)
                      |++|++++
T Consensus       326 L~~L~L~~  333 (597)
T 3oja_B          326 LENLYLDH  333 (597)
T ss_dssp             CSEEECCS
T ss_pred             CCEEECCC
Confidence            44444433

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.63  E-value=7.1e-15  Score=133.03  Aligned_cols=169  Identities=27%  Similarity=0.272  Sum_probs=127.0

Q ss_pred             CcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCccCCCCc-------EEEeeCCccCcceeeEEecccccchhH-
Q 041097          179 KFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKSLPSSRK-------ILRLSGNSQFHFSLASLLLYYQSLLSK-  249 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~lp~~~~-------~L~l~~~~l~~L~L~~L~l~~~~~lp~-  249 (391)
                      ..++.|+++++.+..+|. .++++.+|++|+++++.+..+|..+.       +|++++|.+.             .+|. 
T Consensus        37 ~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~l~-------------~~~~~  103 (270)
T 2o6q_A           37 ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNKLQ-------------ALPIG  103 (270)
T ss_dssp             TTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECCSSCCC-------------CCCTT
T ss_pred             CCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCEEECCCCcCC-------------cCCHh
Confidence            467788888888776654 67778888888888888777776542       6666666666             5553 


Q ss_pred             HhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC
Q 041097          250 SLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR  328 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  328 (391)
                      .+..+++|++|++++..    +..+.| .++.+ ++|+.|++++|.+...+...++.+++|+.|+++.|...........
T Consensus       104 ~~~~l~~L~~L~l~~n~----l~~~~~~~~~~l-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~  178 (270)
T 2o6q_A          104 VFDQLVNLAELRLDRNQ----LKSLPPRVFDSL-TKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNNQLKRVPEGAFD  178 (270)
T ss_dssp             TTTTCSSCCEEECCSSC----CCCCCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTT
T ss_pred             HcccccCCCEEECCCCc----cCeeCHHHhCcC-cCCCEEECCCCcCCccCHhHccCCcccceeEecCCcCcEeChhHhc
Confidence            56889999999998722    011023 56788 9999999999998887777789999999999996665543222245


Q ss_pred             cccccceeeeccccccccchHh-hcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l~~~~  366 (391)
                      .+++|++|++++| .++.+|.. +..+++|++|+++++|
T Consensus       179 ~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~  216 (270)
T 2o6q_A          179 KLTELKTLKLDNN-QLKRVPEGAFDSLEKLKMLQLQENP  216 (270)
T ss_dssp             TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             cCCCcCEEECCCC-cCCcCCHHHhccccCCCEEEecCCC
Confidence            7889999999988 57888764 7889999999998865

>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=99.63  E-value=1.3e-14  Score=136.11  Aligned_cols=84  Identities=23%  Similarity=0.229  Sum_probs=49.5

Q ss_pred             cccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCC
Q 041097          278 EYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSL  357 (391)
Q Consensus       278 ~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L  357 (391)
                      +..+ ++|+.|++++|.+..  .+.+..+++|+.|+++.|.....  ...+.+++|++|++++|.--...|..++.+++|
T Consensus       239 ~~~l-~~L~~L~l~~n~l~~--~~~~~~l~~L~~L~l~~n~l~~~--~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L  313 (347)
T 4fmz_A          239 LANL-SQLTWLEIGTNQISD--INAVKDLTKLKMLNVGSNQISDI--SVLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNL  313 (347)
T ss_dssp             GTTC-TTCCEEECCSSCCCC--CGGGTTCTTCCEEECCSSCCCCC--GGGGGCTTCSEEECCSSCCCGGGHHHHHTCTTC
T ss_pred             hhcC-CCCCEEECCCCccCC--ChhHhcCCCcCEEEccCCccCCC--hhhcCCCCCCEEECcCCcCCCcChhHhhccccC
Confidence            4455 666666666665544  24556666666666664443331  223456677777777664323345566677777


Q ss_pred             CEEEeeCCc
Q 041097          358 NKLELWWPE  366 (391)
Q Consensus       358 ~~L~l~~~~  366 (391)
                      ++|++++|+
T Consensus       314 ~~L~L~~n~  322 (347)
T 4fmz_A          314 TTLFLSQNH  322 (347)
T ss_dssp             SEEECCSSS
T ss_pred             CEEEccCCc
Confidence            777777665

>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=99.63  E-value=5.3e-15  Score=138.70  Aligned_cols=87  Identities=22%  Similarity=0.240  Sum_probs=70.4

Q ss_pred             ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCC
Q 041097          275 ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCL  354 (391)
Q Consensus       275 lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l  354 (391)
                      ++.+..+ ++|+.|++++|.+...  +.+..+++|+.|+++.|......+...+.+++|++|++++|. +..++. +..+
T Consensus       258 ~~~~~~l-~~L~~L~l~~n~l~~~--~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~L~~n~-l~~~~~-~~~l  332 (347)
T 4fmz_A          258 INAVKDL-TKLKMLNVGSNQISDI--SVLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNH-ITDIRP-LASL  332 (347)
T ss_dssp             CGGGTTC-TTCCEEECCSSCCCCC--GGGGGCTTCSEEECCSSCCCGGGHHHHHTCTTCSEEECCSSS-CCCCGG-GGGC
T ss_pred             ChhHhcC-CCcCEEEccCCccCCC--hhhcCCCCCCEEECcCCcCCCcChhHhhccccCCEEEccCCc-cccccC-hhhh
Confidence            3456778 9999999999988774  678999999999999666544332233678999999999996 777776 8899


Q ss_pred             CCCCEEEeeCCc
Q 041097          355 KSLNKLELWWPE  366 (391)
Q Consensus       355 ~~L~~L~l~~~~  366 (391)
                      ++|++|++++|+
T Consensus       333 ~~L~~L~l~~N~  344 (347)
T 4fmz_A          333 SKMDSADFANQV  344 (347)
T ss_dssp             TTCSEESSSCC-
T ss_pred             hccceeehhhhc
Confidence            999999999987

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.63  E-value=5.7e-16  Score=143.45  Aligned_cols=216  Identities=14%  Similarity=0.044  Sum_probs=158.8

Q ss_pred             ccCceEEEEEec-cCCCcccccCCC--CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCcccCCCC
Q 041097          127 LRENVKRFTAHR-KLNDFAFLDDFD--SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLF  202 (391)
Q Consensus       127 ~~~~~r~l~~~~-~~~~~~~~~~~~--~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~  202 (391)
                      .....+.|.+.. +......+..+.  ++++.|.+..+...    ...+..+.+++.|++|++++|.+. .+|..++++.
T Consensus        74 ~l~~L~~L~L~~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~----~~~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~  149 (313)
T 1ogq_A           74 NLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVS----GAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLP  149 (313)
T ss_dssp             GCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCE----EECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCT
T ss_pred             CCCCCCeeeCCCCCcccccCChhHhcCCCCCEEECcCCeeC----CcCCHHHhCCCCCCEEeCCCCccCCcCChHHhcCC
Confidence            345678888761 332222333343  89999998876542    124467889999999999999998 8899999999


Q ss_pred             cccEEEccCCCCC-ccCCCCc-------EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhh
Q 041097          203 LLRYLKLNIPSLK-SLPSSRK-------ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNI  274 (391)
Q Consensus       203 ~L~~L~l~~~~i~-~lp~~~~-------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~L  274 (391)
                      +|++|++++|.+. .+|..++       .|++++|.+.            ..+|..++.++ |++|++++..    +...
T Consensus       150 ~L~~L~L~~N~l~~~~p~~l~~l~~~L~~L~L~~N~l~------------~~~~~~~~~l~-L~~L~Ls~N~----l~~~  212 (313)
T 1ogq_A          150 NLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLT------------GKIPPTFANLN-LAFVDLSRNM----LEGD  212 (313)
T ss_dssp             TCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEE------------EECCGGGGGCC-CSEEECCSSE----EEEC
T ss_pred             CCCeEECcCCcccCcCCHHHhhhhhcCcEEECcCCeee------------ccCChHHhCCc-ccEEECcCCc----ccCc
Confidence            9999999999988 6776554       6777777665            46778888887 9999888721    1111


Q ss_pred             cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcC
Q 041097          275 IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWC  353 (391)
Q Consensus       275 lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~  353 (391)
                      .| .+..+ ++|+.|++++|.+...+ +.+..+++|++|+++.|...+..+...+.+++|++|++++|.--..+|.. +.
T Consensus       213 ~~~~~~~l-~~L~~L~L~~N~l~~~~-~~~~~l~~L~~L~Ls~N~l~~~~p~~l~~l~~L~~L~Ls~N~l~~~ip~~-~~  289 (313)
T 1ogq_A          213 ASVLFGSD-KNTQKIHLAKNSLAFDL-GKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQG-GN  289 (313)
T ss_dssp             CGGGCCTT-SCCSEEECCSSEECCBG-GGCCCCTTCCEEECCSSCCEECCCGGGGGCTTCCEEECCSSEEEEECCCS-TT
T ss_pred             CCHHHhcC-CCCCEEECCCCceeeec-CcccccCCCCEEECcCCcccCcCChHHhcCcCCCEEECcCCcccccCCCC-cc
Confidence            45 67778 88999999988876544 44778889999999877665544444567888999999888532367755 78


Q ss_pred             CCCCCEEEeeCCc
Q 041097          354 LKSLNKLELWWPE  366 (391)
Q Consensus       354 l~~L~~L~l~~~~  366 (391)
                      +++|+.+++.++|
T Consensus       290 l~~L~~l~l~~N~  302 (313)
T 1ogq_A          290 LQRFDVSAYANNK  302 (313)
T ss_dssp             GGGSCGGGTCSSS
T ss_pred             ccccChHHhcCCC
Confidence            8888888888877

>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=99.63  E-value=3.7e-15  Score=137.63  Aligned_cols=180  Identities=21%  Similarity=0.191  Sum_probs=138.9

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------IL  224 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L  224 (391)
                      ++++.|.+.++...     .+ +.+..++.|++|++++|.+..++. +..+.+|++|+++++.+..+|. +.      .|
T Consensus        41 ~~L~~L~l~~~~i~-----~l-~~~~~l~~L~~L~L~~n~i~~~~~-~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L  112 (308)
T 1h6u_A           41 DGITTLSAFGTGVT-----TI-EGVQYLNNLIGLELKDNQITDLAP-LKNLTKITELELSGNPLKNVSA-IAGLQSIKTL  112 (308)
T ss_dssp             HTCCEEECTTSCCC-----CC-TTGGGCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSCCCSCCGG-GTTCTTCCEE
T ss_pred             CCcCEEEeeCCCcc-----Cc-hhhhccCCCCEEEccCCcCCCChh-HccCCCCCEEEccCCcCCCchh-hcCCCCCCEE
Confidence            66777776655443     12 356788999999999999887777 8899999999999998887763 32      77


Q ss_pred             EeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCC--CCCchhhhccccccCCCCccEEEeecccCCCCChhh
Q 041097          225 RLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANES--KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPA  302 (391)
Q Consensus       225 ~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~--~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~  302 (391)
                      ++++|.+.             .++. ++.+++|++|++++..  .       +|.+..+ ++|+.|++++|.+...+  .
T Consensus       113 ~l~~n~l~-------------~~~~-l~~l~~L~~L~l~~n~l~~-------~~~l~~l-~~L~~L~l~~n~l~~~~--~  168 (308)
T 1h6u_A          113 DLTSTQIT-------------DVTP-LAGLSNLQVLYLDLNQITN-------ISPLAGL-TNLQYLSIGNAQVSDLT--P  168 (308)
T ss_dssp             ECTTSCCC-------------CCGG-GTTCTTCCEEECCSSCCCC-------CGGGGGC-TTCCEEECCSSCCCCCG--G
T ss_pred             ECCCCCCC-------------Cchh-hcCCCCCCEEECCCCccCc-------CccccCC-CCccEEEccCCcCCCCh--h
Confidence            77777766             6654 8899999999998722  1       3346678 99999999999877644  3


Q ss_pred             hcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          303 LEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       303 l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +..+++|+.|+++.|.....  .....+++|++|++++| .+..+| .+..+++|++|++++++
T Consensus       169 l~~l~~L~~L~l~~n~l~~~--~~l~~l~~L~~L~L~~N-~l~~~~-~l~~l~~L~~L~l~~N~  228 (308)
T 1h6u_A          169 LANLSKLTTLKADDNKISDI--SPLASLPNLIEVHLKNN-QISDVS-PLANTSNLFIVTLTNQT  228 (308)
T ss_dssp             GTTCTTCCEEECCSSCCCCC--GGGGGCTTCCEEECTTS-CCCBCG-GGTTCTTCCEEEEEEEE
T ss_pred             hcCCCCCCEEECCCCccCcC--hhhcCCCCCCEEEccCC-ccCccc-cccCCCCCCEEEccCCe
Confidence            88999999999997765542  23567889999999988 477887 48899999999998766

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.63  E-value=5.5e-15  Score=149.98  Aligned_cols=227  Identities=12%  Similarity=0.098  Sum_probs=138.2

Q ss_pred             cCceEEEEEeccCCCcccccCCC--CCccEEEEEecC-CcCCCchhhHHhhccC------CcccEEEcCCCccccCCc--
Q 041097          128 RENVKRFTAHRKLNDFAFLDDFD--SFLHSLLYLTSG-SQYLDPTYCEKICKMF------KFLRVLDLGSLVLIRYPS--  196 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~~--~~lrsl~~~~~~-~~~~~~~~~~~~~~~~------~~L~~L~l~~~~l~~~p~--  196 (391)
                      ..+.+.|.+..+.....++..+.  ++++.|.+..+. ..   ...++..+..+      +.|++|++++|.+..+|.  
T Consensus       248 l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~~l~---~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~~ip~~~  324 (636)
T 4eco_A          248 LKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGIS---GEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVET  324 (636)
T ss_dssp             CTTCCEEEEECCTTCSSCCTTTTTCSSCCEEECTTCTTSC---HHHHHHHHHHHHHSGGGGTCCEEECCSSCCSSCCCHH
T ss_pred             cCCCCEEEecCCcCCccChHHHhcCCCCCEEECcCCCCCc---cccchHHHHhhhccccCCCCCEEECCCCcCCccCchh
Confidence            45677888873332322444443  788888776654 31   21244555554      899999999999999998  


Q ss_pred             ccCCCCcccEEEccCCCCC-ccCCCCc------EEEeeCCccCcc--------e-eeEEecc--cccchhHHhcCCC--C
Q 041097          197 GIENLFLLRYLKLNIPSLK-SLPSSRK------ILRLSGNSQFHF--------S-LASLLLY--YQSLLSKSLCRLS--C  256 (391)
Q Consensus       197 ~i~~l~~L~~L~l~~~~i~-~lp~~~~------~L~l~~~~l~~L--------~-L~~L~l~--~~~~lp~~i~~l~--~  256 (391)
                      .++++.+|++|++++|.+. .+| .++      .|++++|.+..+        + |+.|+++  ....+|..++.++  +
T Consensus       325 ~l~~l~~L~~L~L~~N~l~g~ip-~~~~l~~L~~L~L~~N~l~~lp~~l~~l~~~L~~L~Ls~N~l~~lp~~~~~~~l~~  403 (636)
T 4eco_A          325 SLQKMKKLGMLECLYNQLEGKLP-AFGSEIKLASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLKYIPNIFDAKSVSV  403 (636)
T ss_dssp             HHTTCTTCCEEECCSCCCEEECC-CCEEEEEESEEECCSSEEEECCTTSEEECTTCCEEECCSSCCSSCCSCCCTTCSSC
T ss_pred             hhccCCCCCEEeCcCCcCccchh-hhCCCCCCCEEECCCCccccccHhhhhhcccCcEEEccCCcCcccchhhhhcccCc
Confidence            8999999999999999998 888 665      888888876654        5 8888888  4557777776655  7


Q ss_pred             CCEEEecCCCCCCchhhhcc-ccc-------cCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcC-------
Q 041097          257 LESLKLANESKMPRRSNIIL-AEY-------QFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSE-------  321 (391)
Q Consensus       257 L~~L~l~~~~~lp~L~~Llp-~~~-------~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~-------  321 (391)
                      |++|++++..    +....| .+.       .+ ++|+.|++++|.+...+...+..+++|+.|+++.|....       
T Consensus       404 L~~L~Ls~N~----l~~~~p~~l~~~~~~~~~~-~~L~~L~Ls~N~l~~lp~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~  478 (636)
T 4eco_A          404 MSAIDFSYNE----IGSVDGKNFDPLDPTPFKG-INVSSINLSNNQISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLK  478 (636)
T ss_dssp             EEEEECCSSC----TTTTTTCSSCTTCSSCCCC-CCEEEEECCSSCCCSCCTHHHHTTCCCSEEECCSSCCSBCCSSSSE
T ss_pred             cCEEECcCCc----CCCcchhhhcccccccccC-CCCCEEECcCCccCcCCHHHHccCCCCCEEECCCCCCCCcCHHHhc
Confidence            8888887611    000022 222       33 455555555555444443334445555555554333220       


Q ss_pred             -----------------------ccccCCC--cccccceeeeccccccccchHhhcCCCCCCEEEeeC
Q 041097          322 -----------------------ERTMGIR--AMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWW  364 (391)
Q Consensus       322 -----------------------~~~~~~~--~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~  364 (391)
                                             ..+....  .+++|+.|++++| .++.+|.++..+++|++|++++
T Consensus       479 ~~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N-~l~~ip~~~~~l~~L~~L~Ls~  545 (636)
T 4eco_A          479 DENENFKNTYLLTSIDLRFNKLTKLSDDFRATTLPYLVGIDLSYN-SFSKFPTQPLNSSTLKGFGIRN  545 (636)
T ss_dssp             ETTEECTTGGGCCEEECCSSCCCBCCGGGSTTTCTTCCEEECCSS-CCSSCCCGGGGCSSCCEEECCS
T ss_pred             cccccccccCCccEEECcCCcCCccChhhhhccCCCcCEEECCCC-CCCCcChhhhcCCCCCEEECCC
Confidence                                   1111112  4556666666655 3445565565666666666643

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.63  E-value=4.2e-15  Score=141.82  Aligned_cols=226  Identities=19%  Similarity=0.096  Sum_probs=140.8

Q ss_pred             CceEEEEEeccCCCcccccC-C-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCC-cccCCCCcc
Q 041097          129 ENVKRFTAHRKLNDFAFLDD-F-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLL  204 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~-~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L  204 (391)
                      .+.+.+.+....... ++.. . . ++++.|.+.++...    ...+..+..++.|++|++++|.+..++ ..++++.+|
T Consensus        45 ~~l~~l~l~~~~l~~-l~~~~~~~l~~L~~L~L~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L  119 (390)
T 3o6n_A           45 NNQKIVTFKNSTMRK-LPAALLDSFRQVELLNLNDLQIE----EIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLL  119 (390)
T ss_dssp             CCCSEEEEESCEESE-ECTHHHHHCCCCSEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTC
T ss_pred             CCceEEEecCCchhh-CChhHhcccccCcEEECCCCccc----ccChhhccCCCCcCEEECCCCCCCcCCHHHhcCCCCC
Confidence            456666666222222 2221 1 2 56666666544332    112235666777777777777777554 446777777


Q ss_pred             cEEEccCCCCCccCCCC-c------EEEeeCCccCcc---------eeeEEecc--cccchhHHhcCCCCCCEEEecCCC
Q 041097          205 RYLKLNIPSLKSLPSSR-K------ILRLSGNSQFHF---------SLASLLLY--YQSLLSKSLCRLSCLESLKLANES  266 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~~~-~------~L~l~~~~l~~L---------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~  266 (391)
                      ++|+++++.+..+|..+ .      +|++++|.+..+         +|+.|+++  ....+  .++.+++|++|++.+..
T Consensus       120 ~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~--~~~~l~~L~~L~l~~n~  197 (390)
T 3o6n_A          120 TVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHV--DLSLIPSLFHANVSYNL  197 (390)
T ss_dssp             CEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECCSSCCSBC--CGGGCTTCSEEECCSSC
T ss_pred             CEEECCCCccCcCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECCCCcCCcc--ccccccccceeeccccc
Confidence            77777777777777654 2      777777765533         45555555  22222  13444555555554411


Q ss_pred             -----CCCchhhh---------ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccc
Q 041097          267 -----KMPRRSNI---------ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPK  332 (391)
Q Consensus       267 -----~lp~L~~L---------lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~  332 (391)
                           ..+.++.|         +| .... ++|+.|++++|.+..  .+.++.+++|+.|+++.|...+..+...+.+++
T Consensus       198 l~~~~~~~~L~~L~l~~n~l~~~~-~~~~-~~L~~L~l~~n~l~~--~~~l~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~  273 (390)
T 3o6n_A          198 LSTLAIPIAVEELDASHNSINVVR-GPVN-VELTILKLQHNNLTD--TAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQR  273 (390)
T ss_dssp             CSEEECCSSCSEEECCSSCCCEEE-CCCC-SSCCEEECCSSCCCC--CGGGGGCTTCSEEECCSSCCCEEESGGGTTCSS
T ss_pred             ccccCCCCcceEEECCCCeeeecc-cccc-ccccEEECCCCCCcc--cHHHcCCCCccEEECCCCcCCCcChhHcccccc
Confidence                 01122222         22 1123 688899998888766  367899999999999977665433334478899


Q ss_pred             cceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          333 LECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       333 L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      |++|++++| .++.+|..+..+++|++|+++++.
T Consensus       274 L~~L~L~~n-~l~~~~~~~~~l~~L~~L~L~~n~  306 (390)
T 3o6n_A          274 LERLYISNN-RLVALNLYGQPIPTLKVLDLSHNH  306 (390)
T ss_dssp             CCEEECCSS-CCCEEECSSSCCTTCCEEECCSSC
T ss_pred             CCEEECCCC-cCcccCcccCCCCCCCEEECCCCc
Confidence            999999988 588899888899999999999875

>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=99.62  E-value=1.7e-15  Score=157.13  Aligned_cols=195  Identities=22%  Similarity=0.192  Sum_probs=141.4

Q ss_pred             hHHhhccCCcccEEEcCCCccc-cCCcc-cCCCCcccEEEccCCCCC-ccCCCCc-------EEEeeCCccCc-------
Q 041097          171 CEKICKMFKFLRVLDLGSLVLI-RYPSG-IENLFLLRYLKLNIPSLK-SLPSSRK-------ILRLSGNSQFH-------  233 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~-~~p~~-i~~l~~L~~L~l~~~~i~-~lp~~~~-------~L~l~~~~l~~-------  233 (391)
                      .+..+..++.|++|++++|.+. .+|.. ++++.+|++|++++|.+. .+|..+.       +|++++|.+..       
T Consensus       310 ~p~~~~~l~~L~~L~L~~n~l~~~ip~~~l~~l~~L~~L~Ls~n~l~~~~p~~l~~l~~~L~~L~Ls~N~l~~~~~~~~~  389 (768)
T 3rgz_A          310 VPPFFGSCSLLESLALSSNNFSGELPMDTLLKMRGLKVLDLSFNEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLC  389 (768)
T ss_dssp             CCGGGGGCTTCCEEECCSSEEEEECCHHHHTTCTTCCEEECCSSEEEECCCTTHHHHTTTCSEEECCSSEEEEECCTTTT
T ss_pred             cchHHhcCCCccEEECCCCcccCcCCHHHHhcCCCCCEEeCcCCccCccccHHHHhhhcCCcEEEccCCCcCCCcChhhh
Confidence            3356677888888888888876 77765 788888888888888776 5665443       78888776542       


Q ss_pred             ---c-eeeEEecc---cccchhHHhcCCCCCCEEEecCCC---C-------CCchhhh----------cc-ccccCCCCc
Q 041097          234 ---F-SLASLLLY---YQSLLSKSLCRLSCLESLKLANES---K-------MPRRSNI----------IL-AEYQFPPSL  285 (391)
Q Consensus       234 ---L-~L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~~~---~-------lp~L~~L----------lp-~~~~l~~~L  285 (391)
                         + +|+.|+++   -...+|..++++++|++|++++..   .       ++.|+.|          +| .++.+ ++|
T Consensus       390 ~~~~~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~N~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~~~~l-~~L  468 (768)
T 3rgz_A          390 QNPKNTLQELYLQNNGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMYV-KTL  468 (768)
T ss_dssp             CSTTCCCCEEECCSSEEEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGC-TTC
T ss_pred             hcccCCccEEECCCCccccccCHHHhcCCCCCEEECcCCcccCcccHHHhcCCCCCEEECCCCcccCcCCHHHcCC-CCc
Confidence               1 57777777   223567777778888888777611   1       1222222          56 67777 888


Q ss_pred             cEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCC
Q 041097          286 THLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       286 ~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~  365 (391)
                      +.|++++|.+....+..++.+++|++|+++.|...+..+...+.+++|++|++++|.-...+|.+++.+++|++|++++|
T Consensus       469 ~~L~L~~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~Ls~N  548 (768)
T 3rgz_A          469 ETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLNTN  548 (768)
T ss_dssp             CEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCCEEECCSS
T ss_pred             eEEEecCCcccCcCCHHHhcCCCCCEEEccCCccCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCCEEECCCC
Confidence            88888888887666678888888999988877666554444578889999999988644478888999999999999865


Q ss_pred             c
Q 041097          366 E  366 (391)
Q Consensus       366 ~  366 (391)
                      +
T Consensus       549 ~  549 (768)
T 3rgz_A          549 L  549 (768)
T ss_dssp             E
T ss_pred             c
Confidence            4

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.62  E-value=6e-15  Score=153.42  Aligned_cols=188  Identities=17%  Similarity=0.118  Sum_probs=99.8

Q ss_pred             hhccCCcccEEEcCCCccccCCcccCCCCc-ccEEEccCCCCCccCCCCc--------EEEeeCCccCcc----------
Q 041097          174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFL-LRYLKLNIPSLKSLPSSRK--------ILRLSGNSQFHF----------  234 (391)
Q Consensus       174 ~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~-L~~L~l~~~~i~~lp~~~~--------~L~l~~~~l~~L----------  234 (391)
                      .+..++.|+.|++++|.+..+|..+.++.+ |++|++++|.+..+|..+.        .|++++|.+...          
T Consensus       590 ~~~~L~~L~~L~Ls~N~l~~lp~~l~~l~~~L~~L~Ls~N~L~~lp~~~~~~~~~~L~~L~Ls~N~l~g~ip~l~~~l~~  669 (876)
T 4ecn_A          590 AFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAKSVYVMGSVDFSYNKIGSEGRNISCSMDD  669 (876)
T ss_dssp             CCCTTSEESEEECCSSCCSCCCTTSCEECTTCCEEECCSSCCCSCCSCCCTTCSSCEEEEECCSSCTTTTSSSCSSCTTT
T ss_pred             hhcCCCcceEEECcCCccccchHHHhhccccCCEEECcCCCCCcCchhhhccccCCCCEEECcCCcCCCccccchhhhcc
Confidence            344455555555555555555555555555 5555555555555554432        455555544211          


Q ss_pred             ----eeeEEecc--cccchhHHhc-CCCCCCEEEecCCC--CCC---------------chhhh---------cc-ccc-
Q 041097          235 ----SLASLLLY--YQSLLSKSLC-RLSCLESLKLANES--KMP---------------RRSNI---------IL-AEY-  279 (391)
Q Consensus       235 ----~L~~L~l~--~~~~lp~~i~-~l~~L~~L~l~~~~--~lp---------------~L~~L---------lp-~~~-  279 (391)
                          +|+.|+++  ....+|..+. .+++|+.|++++..  .+|               +|+.|         +| .+. 
T Consensus       670 ~~~~~L~~L~Ls~N~L~~lp~~~~~~l~~L~~L~Ls~N~L~~ip~~~~~~~~~~l~nl~~L~~L~Ls~N~L~~lp~~l~~  749 (876)
T 4ecn_A          670 YKGINASTVTLSYNEIQKFPTELFATGSPISTIILSNNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRA  749 (876)
T ss_dssp             CCCCCEEEEECCSSCCCSCCHHHHHTTCCCSEEECCSCCCSCCCTTSSSCTTSCCTTGGGCCEEECCSSCCCCCCGGGST
T ss_pred             ccCCCcCEEEccCCcCCccCHHHHccCCCCCEEECCCCcCCccChHHhccccccccccCCccEEECCCCCCccchHHhhh
Confidence                46666666  4446666554 77888888887621  111               22222         44 443 


Q ss_pred             -cCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCC------CCcCccccCCCcccccceeeeccccccccchHhhc
Q 041097          280 -QFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQN------LYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLW  352 (391)
Q Consensus       280 -~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~------~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~  352 (391)
                       .+ ++|+.|+|++|.+... +..++.+++|+.|+++.|      ...+..+...+.+++|+.|++++|. +..+|..+.
T Consensus       750 ~~l-~~L~~L~Ls~N~L~~l-p~~l~~L~~L~~L~Ls~N~~ls~N~l~~~ip~~l~~L~~L~~L~Ls~N~-L~~Ip~~l~  826 (876)
T 4ecn_A          750 TTL-PYLSNMDVSYNCFSSF-PTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSND-IRKVDEKLT  826 (876)
T ss_dssp             TTC-TTCCEEECCSSCCSSC-CCGGGGCTTCCEEECCCCBCTTCCBCCCCCCTTGGGCSSCCEEECCSSC-CCBCCSCCC
T ss_pred             ccC-CCcCEEEeCCCCCCcc-chhhhcCCCCCEEECCCCCCcccccccccChHHHhcCCCCCEEECCCCC-CCccCHhhc
Confidence             55 5666666666655543 244556666666666532      1222212223456666666666653 466665543


Q ss_pred             CCCCCCEEEeeCCc
Q 041097          353 CLKSLNKLELWWPE  366 (391)
Q Consensus       353 ~l~~L~~L~l~~~~  366 (391)
                        ++|+.|++++||
T Consensus       827 --~~L~~LdLs~N~  838 (876)
T 4ecn_A          827 --PQLYILDIADNP  838 (876)
T ss_dssp             --SSSCEEECCSCT
T ss_pred             --CCCCEEECCCCC
Confidence              466666666665

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.61  E-value=1.1e-15  Score=150.01  Aligned_cols=202  Identities=18%  Similarity=0.113  Sum_probs=150.5

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC--CcEEEeeC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS--RKILRLSG  228 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~--~~~L~l~~  228 (391)
                      ++++.|.+.++....    ..+..+..++.|++|++++|.+...+. ++.+.+|++|++++|.+..+|..  +.+|++++
T Consensus        34 ~~L~~L~Ls~n~l~~----~~~~~~~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~l~~l~~~~~L~~L~L~~  108 (487)
T 3oja_A           34 WNVKELDLSGNPLSQ----ISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLRTLDLNNNYVQELLVGPSIETLHAAN  108 (487)
T ss_dssp             GGCCEEECCSSCCCC----CCGGGGTTCTTCCEEECTTSCCEEEEE-CTTCTTCCEEECCSSEEEEEEECTTCCEEECCS
T ss_pred             CCccEEEeeCCcCCC----CCHHHHhCCCCCCEEEeeCCCCCCCcc-cccCCCCCEEEecCCcCCCCCCCCCcCEEECcC
Confidence            467777776655431    233567888889999999888875554 88888999999998888877644  33888888


Q ss_pred             CccCcc------eeeEEecc--cccch-hHHhcCCCCCCEEEecCCCCCCchhhhcc-ccc-cCCCCccEEEeecccCCC
Q 041097          229 NSQFHF------SLASLLLY--YQSLL-SKSLCRLSCLESLKLANESKMPRRSNIIL-AEY-QFPPSLTHLSFSNIELMD  297 (391)
Q Consensus       229 ~~l~~L------~L~~L~l~--~~~~l-p~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~-~l~~~L~~L~l~~~~~~~  297 (391)
                      |.+..+      +|+.|+++  ....+ |..++.+++|++|++++..    +....| .+. .+ ++|+.|+|++|.+..
T Consensus       109 N~l~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~----l~~~~~~~l~~~l-~~L~~L~Ls~N~l~~  183 (487)
T 3oja_A          109 NNISRVSCSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNE----IDTVNFAELAASS-DTLEHLNLQYNFIYD  183 (487)
T ss_dssp             SCCCCEEECCCSSCEEEECCSSCCCSGGGBCGGGGSSEEEEECTTSC----CCEEEGGGGGGGT-TTCCEEECTTSCCCE
T ss_pred             CcCCCCCccccCCCCEEECCCCCCCCCCchhhcCCCCCCEEECCCCC----CCCcChHHHhhhC-CcccEEecCCCcccc
Confidence            877765      78888888  33344 5578889999999998722    111134 443 68 899999999998776


Q ss_pred             CChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          298 DPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       298 ~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .  +....+++|+.|+++.|...+ .+...+.+++|+.|++++| .+..+|.++..+++|+.|++++++
T Consensus       184 ~--~~~~~l~~L~~L~Ls~N~l~~-~~~~~~~l~~L~~L~Ls~N-~l~~lp~~l~~l~~L~~L~l~~N~  248 (487)
T 3oja_A          184 V--KGQVVFAKLKTLDLSSNKLAF-MGPEFQSAAGVTWISLRNN-KLVLIEKALRFSQNLEHFDLRGNG  248 (487)
T ss_dssp             E--ECCCCCTTCCEEECCSSCCCE-ECGGGGGGTTCSEEECTTS-CCCEECTTCCCCTTCCEEECTTCC
T ss_pred             c--cccccCCCCCEEECCCCCCCC-CCHhHcCCCCccEEEecCC-cCcccchhhccCCCCCEEEcCCCC
Confidence            4  344568999999999776654 2333567889999999987 578899999999999999998876

>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=99.61  E-value=6.4e-15  Score=148.43  Aligned_cols=205  Identities=20%  Similarity=0.113  Sum_probs=127.7

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCccCCCC-c------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKSLPSSR-K------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~lp~~~-~------  222 (391)
                      +.++.|.+.++...    ...+..+..++.|++|++++|.+..+|. .++++.+|++|++++|.+..+|..+ +      
T Consensus        75 ~~L~~L~L~~n~l~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~  150 (597)
T 3oja_B           75 RQVELLNLNDLQIE----EIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLT  150 (597)
T ss_dssp             CCCSEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             CCCcEEECCCCCCC----CCChHHhcCCCCCCEEECCCCcCCCCCHHHHcCCCCCCEEEeeCCCCCCCCHHHhccCCCCC
Confidence            55666655444322    1122355666677777777777665443 3566777777777777776666554 2      


Q ss_pred             EEEeeCCccCcc---------eeeEEecc--cccchhHHhcCCCCCCEEEecCCC-----CCCchhhh---------ccc
Q 041097          223 ILRLSGNSQFHF---------SLASLLLY--YQSLLSKSLCRLSCLESLKLANES-----KMPRRSNI---------ILA  277 (391)
Q Consensus       223 ~L~l~~~~l~~L---------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~-----~lp~L~~L---------lp~  277 (391)
                      +|++++|.+..+         +|+.|+++  ....++  ++.+++|++|++++..     ..+.|+.|         +| 
T Consensus       151 ~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~--~~~l~~L~~L~l~~n~l~~l~~~~~L~~L~ls~n~l~~~~-  227 (597)
T 3oja_B          151 TLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVD--LSLIPSLFHANVSYNLLSTLAIPIAVEELDASHNSINVVR-  227 (597)
T ss_dssp             EEECCSSCCCBCCTTTTTTCTTCCEEECTTSCCSBCC--GGGCTTCSEEECCSSCCSEEECCTTCSEEECCSSCCCEEE-
T ss_pred             EEEeeCCcCCCCChhhhhcCCcCcEEECcCCCCCCcC--hhhhhhhhhhhcccCccccccCCchhheeeccCCcccccc-
Confidence            666666655532         44444444  112221  2334444444443310     00112211         12 


Q ss_pred             cccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCC
Q 041097          278 EYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSL  357 (391)
Q Consensus       278 ~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L  357 (391)
                       +..+++|+.|++++|.+..  ++.++.+++|+.|+++.|...+..+...+.+++|+.|++++| .+..+|..+..+++|
T Consensus       228 -~~~~~~L~~L~L~~n~l~~--~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~~L  303 (597)
T 3oja_B          228 -GPVNVELTILKLQHNNLTD--TAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNN-RLVALNLYGQPIPTL  303 (597)
T ss_dssp             -CSCCSCCCEEECCSSCCCC--CGGGGGCTTCSEEECCSSCCCEEESGGGTTCSSCCEEECTTS-CCCEEECSSSCCTTC
T ss_pred             -cccCCCCCEEECCCCCCCC--ChhhccCCCCCEEECCCCccCCCCHHHhcCccCCCEEECCCC-CCCCCCcccccCCCC
Confidence             1112678888888888766  477899999999999977766544444578999999999987 588899888889999


Q ss_pred             CEEEeeCCc
Q 041097          358 NKLELWWPE  366 (391)
Q Consensus       358 ~~L~l~~~~  366 (391)
                      ++|++++|+
T Consensus       304 ~~L~Ls~N~  312 (597)
T 3oja_B          304 KVLDLSHNH  312 (597)
T ss_dssp             CEEECCSSC
T ss_pred             cEEECCCCC
Confidence            999999875

>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=99.61  E-value=2.2e-14  Score=140.11  Aligned_cols=221  Identities=22%  Similarity=0.198  Sum_probs=109.9

Q ss_pred             CceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYL  207 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L  207 (391)
                      ..++.+.+....... +..... ++++.|.+.++...     ..++ +..++.|++|++++|.+..++. ++++.+|++|
T Consensus        46 ~~l~~L~l~~~~i~~-l~~~~~l~~L~~L~Ls~n~l~-----~~~~-~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L  117 (466)
T 1o6v_A           46 DQVTTLQADRLGIKS-IDGVEYLNNLTQINFSNNQLT-----DITP-LKNLTKLVDILMNNNQIADITP-LANLTNLTGL  117 (466)
T ss_dssp             HTCCEEECCSSCCCC-CTTGGGCTTCCEEECCSSCCC-----CCGG-GTTCTTCCEEECCSSCCCCCGG-GTTCTTCCEE
T ss_pred             ccccEEecCCCCCcc-CcchhhhcCCCEEECCCCccC-----Cchh-hhccccCCEEECCCCccccChh-hcCCCCCCEE
Confidence            345566555222222 222222 56666665544432     1212 5666777777777776665554 6667777777


Q ss_pred             EccCCCCCccCCCCc------EEEeeCCccCcc-------eeeEEecc-cccchhHHhcCCCCCCEEEecCCC--C----
Q 041097          208 KLNIPSLKSLPSSRK------ILRLSGNSQFHF-------SLASLLLY-YQSLLSKSLCRLSCLESLKLANES--K----  267 (391)
Q Consensus       208 ~l~~~~i~~lp~~~~------~L~l~~~~l~~L-------~L~~L~l~-~~~~lp~~i~~l~~L~~L~l~~~~--~----  267 (391)
                      +++++.+..+|. +.      +|++++|.+..+       +|+.|++. ....++ .++++++|++|++++..  .    
T Consensus       118 ~L~~n~l~~~~~-~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~~~~~~~-~~~~l~~L~~L~l~~n~l~~~~~l  195 (466)
T 1o6v_A          118 TLFNNQITDIDP-LKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLK-PLANLTTLERLDISSNKVSDISVL  195 (466)
T ss_dssp             ECCSSCCCCCGG-GTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCG-GGTTCTTCCEEECCSSCCCCCGGG
T ss_pred             ECCCCCCCCChH-HcCCCCCCEEECCCCccCCChhhccCCcccEeecCCcccCch-hhccCCCCCEEECcCCcCCCChhh
Confidence            777766666553 22      666666644432       44444444 111111 13444444444443311  0    


Q ss_pred             ------------------------CCchhhh---------ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEc
Q 041097          268 ------------------------MPRRSNI---------ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKL  314 (391)
Q Consensus       268 ------------------------lp~L~~L---------lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l  314 (391)
                                              ++.|+.|         ++.+..+ ++|+.|++++|.+...+  .++.+++|+.|++
T Consensus       196 ~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~l~~l-~~L~~L~l~~n~l~~~~--~~~~l~~L~~L~l  272 (466)
T 1o6v_A          196 AKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASL-TNLTDLDLANNQISNLA--PLSGLTKLTELKL  272 (466)
T ss_dssp             GGCTTCSEEECCSSCCCCCGGGGGCTTCCEEECCSSCCCCCGGGGGC-TTCSEEECCSSCCCCCG--GGTTCTTCSEEEC
T ss_pred             ccCCCCCEEEecCCcccccccccccCCCCEEECCCCCcccchhhhcC-CCCCEEECCCCccccch--hhhcCCCCCEEEC
Confidence                                    0111111         2233344 45555555555444322  2455555555555


Q ss_pred             CCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          315 KQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +.|...+.  ...+.+++|++|++++| .++.+|. +..+++|++|++++|.
T Consensus       273 ~~n~l~~~--~~~~~l~~L~~L~L~~n-~l~~~~~-~~~l~~L~~L~L~~n~  320 (466)
T 1o6v_A          273 GANQISNI--SPLAGLTALTNLELNEN-QLEDISP-ISNLKNLTYLTLYFNN  320 (466)
T ss_dssp             CSSCCCCC--GGGTTCTTCSEEECCSS-CCSCCGG-GGGCTTCSEEECCSSC
T ss_pred             CCCccCcc--ccccCCCccCeEEcCCC-cccCchh-hcCCCCCCEEECcCCc
Confidence            54433321  11345666777777766 3555554 6667777777777664

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.61  E-value=3.7e-15  Score=151.20  Aligned_cols=188  Identities=19%  Similarity=0.173  Sum_probs=122.8

Q ss_pred             hhccCCcccEEEcCCCccccCCcccCCCCc-ccEEEccCCCCCccCCCCc--------EEEeeCCccCcc----------
Q 041097          174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFL-LRYLKLNIPSLKSLPSSRK--------ILRLSGNSQFHF----------  234 (391)
Q Consensus       174 ~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~-L~~L~l~~~~i~~lp~~~~--------~L~l~~~~l~~L----------  234 (391)
                      .+..++.|++|++++|.+..+|..++.+.+ |++|++++|.+..+|..+.        .|++++|.+...          
T Consensus       348 ~~~~l~~L~~L~L~~N~l~~lp~~l~~l~~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N~l~~~~p~~l~~~~~  427 (636)
T 4eco_A          348 AFGSEIKLASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLKYIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDPLDP  427 (636)
T ss_dssp             CCEEEEEESEEECCSSEEEECCTTSEEECTTCCEEECCSSCCSSCCSCCCTTCSSCEEEEECCSSCTTTTTTCSSCTTCS
T ss_pred             hhCCCCCCCEEECCCCccccccHhhhhhcccCcEEEccCCcCcccchhhhhcccCccCEEECcCCcCCCcchhhhccccc
Confidence            556667777777777777777777777777 8888888888777776543        778887765431          


Q ss_pred             ------eeeEEecc--cccchhHHh-cCCCCCCEEEecCCC--CCC---------------chhhh---------cc-cc
Q 041097          235 ------SLASLLLY--YQSLLSKSL-CRLSCLESLKLANES--KMP---------------RRSNI---------IL-AE  278 (391)
Q Consensus       235 ------~L~~L~l~--~~~~lp~~i-~~l~~L~~L~l~~~~--~lp---------------~L~~L---------lp-~~  278 (391)
                            +|+.|+++  ....+|..+ ..+++|++|++++..  .+|               .|+.|         +| .+
T Consensus       428 ~~~~~~~L~~L~Ls~N~l~~lp~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~~  507 (636)
T 4eco_A          428 TPFKGINVSSINLSNNQISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDF  507 (636)
T ss_dssp             SCCCCCCEEEEECCSSCCCSCCTHHHHTTCCCSEEECCSSCCSBCCSSSSEETTEECTTGGGCCEEECCSSCCCBCCGGG
T ss_pred             ccccCCCCCEEECcCCccCcCCHHHHccCCCCCEEECCCCCCCCcCHHHhccccccccccCCccEEECcCCcCCccChhh
Confidence                  67888887  455677654 458888888887721  111               23333         55 44


Q ss_pred             c--cCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCC------CCCcCccccCCCcccccceeeeccccccccchHh
Q 041097          279 Y--QFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQ------NLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ  350 (391)
Q Consensus       279 ~--~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~------~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~  350 (391)
                      .  .+ ++|+.|++++|.+... +..++.+++|+.|+++.      |...+..+...+.+++|++|++++|. +..+|..
T Consensus       508 ~~~~l-~~L~~L~Ls~N~l~~i-p~~~~~l~~L~~L~Ls~N~~ls~N~l~~~~p~~l~~l~~L~~L~Ls~N~-l~~ip~~  584 (636)
T 4eco_A          508 RATTL-PYLVGIDLSYNSFSKF-PTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQIGSND-IRKVNEK  584 (636)
T ss_dssp             STTTC-TTCCEEECCSSCCSSC-CCGGGGCSSCCEEECCSCBCTTCCBCCCCCCTTGGGCSSCCEEECCSSC-CCBCCSC
T ss_pred             hhccC-CCcCEEECCCCCCCCc-ChhhhcCCCCCEEECCCCcccccCcccccChHHHhcCCCCCEEECCCCc-CCccCHh
Confidence            4  66 7777777777776663 35666777777777743      22222222233567777777777764 5777766


Q ss_pred             hcCCCCCCEEEeeCCc
Q 041097          351 LWCLKSLNKLELWWPE  366 (391)
Q Consensus       351 ~~~l~~L~~L~l~~~~  366 (391)
                      +.  ++|++|+++++|
T Consensus       585 ~~--~~L~~L~Ls~N~  598 (636)
T 4eco_A          585 IT--PNISVLDIKDNP  598 (636)
T ss_dssp             CC--TTCCEEECCSCT
T ss_pred             Hh--CcCCEEECcCCC
Confidence            54  677777777775

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.61  E-value=1.7e-15  Score=140.42  Aligned_cols=202  Identities=18%  Similarity=0.115  Sum_probs=140.7

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC--CcEEEeeC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS--RKILRLSG  228 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~--~~~L~l~~  228 (391)
                      ++++.|.+.++...    ...+..+..++.|++|++++|.+...+. +..+.+|++|++++|.+..+|..  +.+|++++
T Consensus        34 ~~L~~L~L~~n~l~----~~~~~~~~~l~~L~~L~Ls~n~l~~~~~-~~~l~~L~~L~Ls~n~l~~l~~~~~L~~L~l~~  108 (317)
T 3o53_A           34 WNVKELDLSGNPLS----QISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLRTLDLNNNYVQELLVGPSIETLHAAN  108 (317)
T ss_dssp             GGCSEEECTTSCCC----CCCHHHHTTCTTCCEEECTTSCCEEEEE-ETTCTTCCEEECCSSEEEEEEECTTCCEEECCS
T ss_pred             CCCCEEECcCCccC----cCCHHHhhCCCcCCEEECCCCcCCcchh-hhhcCCCCEEECcCCccccccCCCCcCEEECCC
Confidence            45666666554432    1233567788888888888888775554 78888888888888887766533  33888888


Q ss_pred             CccCcc------eeeEEecc--cccchh-HHhcCCCCCCEEEecCCCCCCchhhhcc-cc-ccCCCCccEEEeecccCCC
Q 041097          229 NSQFHF------SLASLLLY--YQSLLS-KSLCRLSCLESLKLANESKMPRRSNIIL-AE-YQFPPSLTHLSFSNIELMD  297 (391)
Q Consensus       229 ~~l~~L------~L~~L~l~--~~~~lp-~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~-~~l~~~L~~L~l~~~~~~~  297 (391)
                      |.+..+      +|+.|+++  ....++ ..++.+++|++|++++..    +..+.| .+ ..+ ++|+.|++++|.+..
T Consensus       109 n~l~~~~~~~~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~----l~~~~~~~~~~~l-~~L~~L~L~~N~l~~  183 (317)
T 3o53_A          109 NNISRVSCSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNE----IDTVNFAELAASS-DTLEHLNLQYNFIYD  183 (317)
T ss_dssp             SCCSEEEECCCSSCEEEECCSSCCCSGGGBCTGGGSSEEEEECTTSC----CCEEEGGGGGGGT-TTCCEEECTTSCCCE
T ss_pred             CccCCcCccccCCCCEEECCCCCCCCccchhhhccCCCCEEECCCCC----CCcccHHHHhhcc-CcCCEEECCCCcCcc
Confidence            877665      68888887  444454 367788888888888722    011122 33 467 888999998888765


Q ss_pred             CChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          298 DPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       298 ~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .  +....+++|+.|+++.|.... .+.....+++|++|++++| .++.+|..+..+++|++|++++++
T Consensus       184 ~--~~~~~l~~L~~L~Ls~N~l~~-l~~~~~~l~~L~~L~L~~N-~l~~l~~~~~~l~~L~~L~l~~N~  248 (317)
T 3o53_A          184 V--KGQVVFAKLKTLDLSSNKLAF-MGPEFQSAAGVTWISLRNN-KLVLIEKALRFSQNLEHFDLRGNG  248 (317)
T ss_dssp             E--ECCCCCTTCCEEECCSSCCCE-ECGGGGGGTTCSEEECTTS-CCCEECTTCCCCTTCCEEECTTCC
T ss_pred             c--ccccccccCCEEECCCCcCCc-chhhhcccCcccEEECcCC-cccchhhHhhcCCCCCEEEccCCC
Confidence            3  334458889999998665543 2223467788999999887 578888888888899999988776

>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=99.60  E-value=2.2e-14  Score=140.41  Aligned_cols=205  Identities=22%  Similarity=0.202  Sum_probs=147.6

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCCCc-------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSSRK-------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~-------  222 (391)
                      ..++.|.+.++...    ...+..+..++.|++|++++|.+..+ |..++++.+|++|+++++.+..+|....       
T Consensus        32 ~~l~~L~L~~n~l~----~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  107 (477)
T 2id5_A           32 TETRLLDLGKNRIK----TLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLT  107 (477)
T ss_dssp             TTCSEEECCSSCCC----EECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCSCCTTSSTTCTTCC
T ss_pred             CCCcEEECCCCccc----eECHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCCcCCccCcccccCCCCCC
Confidence            67888877665543    12235678899999999999998855 7889999999999999999999987542       


Q ss_pred             EEEeeCCccCcc---------eeeEEecc--cccch-hHHhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEE
Q 041097          223 ILRLSGNSQFHF---------SLASLLLY--YQSLL-SKSLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHL  288 (391)
Q Consensus       223 ~L~l~~~~l~~L---------~L~~L~l~--~~~~l-p~~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L  288 (391)
                      +|++++|.+..+         +|+.|+++  ....+ |..++.+++|++|++.+..    +.. +|  .+..+ ++|+.|
T Consensus       108 ~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~----l~~-~~~~~l~~l-~~L~~L  181 (477)
T 2id5_A          108 KLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCN----LTS-IPTEALSHL-HGLIVL  181 (477)
T ss_dssp             EEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCEEEEESCC----CSS-CCHHHHTTC-TTCCEE
T ss_pred             EEECCCCccccCChhHccccccCCEEECCCCccceeChhhccCCCCCCEEECCCCc----Ccc-cChhHhccc-CCCcEE
Confidence            899999877643         67777776  22222 3456677777777776622    000 23  45667 788888


Q ss_pred             EeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccch-HhhcCCCCCCEEEeeCCc
Q 041097          289 SFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       289 ~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~~~  366 (391)
                      ++.+|.+...+...+..+++|+.|+++.|...+..........+|++|++++| +++.+| ..+..+++|++|++++++
T Consensus       182 ~l~~n~i~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~  259 (477)
T 2id5_A          182 RLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHC-NLTAVPYLAVRHLVYLRFLNLSYNP  259 (477)
T ss_dssp             EEESCCCCEECTTCSCSCTTCCEEEEECCTTCCEECTTTTTTCCCSEEEEESS-CCCSCCHHHHTTCTTCCEEECCSSC
T ss_pred             eCCCCcCcEeChhhcccCcccceeeCCCCccccccCcccccCccccEEECcCC-cccccCHHHhcCccccCeeECCCCc
Confidence            88887776665566777888888888755544433333344558899999887 477887 467889999999998875

>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=99.60  E-value=1.1e-14  Score=141.67  Aligned_cols=234  Identities=18%  Similarity=0.141  Sum_probs=150.4

Q ss_pred             cCceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcc
Q 041097          128 RENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLL  204 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L  204 (391)
                      +..++.|.+..+.......... + ++++.|.+..+...   ....+..+..++.|++|++++|.+... |..++++.+|
T Consensus        29 ~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~~~---~~i~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L  105 (455)
T 3v47_A           29 PAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPG---LVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANL  105 (455)
T ss_dssp             CTTCCEEECCSSCCCEECTTTTSSCTTCCEEECCCCSTT---CEECTTTTTTCTTCCEEECTTCTTCEECTTTTTTCTTC
T ss_pred             CCccCEEEecCCccCcCChhHhccCccccEEECcCCccc---ceECcccccccccCCEEeCCCCccCccChhhccCcccC
Confidence            4678888887443333223333 3 88888887665431   112345678899999999999998854 7889999999


Q ss_pred             cEEEccCCCCCc-cCCC--Cc------EEEeeCCccCcc----------eeeEEecc--cccc-hhHHh-----------
Q 041097          205 RYLKLNIPSLKS-LPSS--RK------ILRLSGNSQFHF----------SLASLLLY--YQSL-LSKSL-----------  251 (391)
Q Consensus       205 ~~L~l~~~~i~~-lp~~--~~------~L~l~~~~l~~L----------~L~~L~l~--~~~~-lp~~i-----------  251 (391)
                      ++|++++|.+.. .|..  +.      +|++++|.+..+          +|+.|+++  .... .|..+           
T Consensus       106 ~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~~~L~~L  185 (455)
T 3v47_A          106 EVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLL  185 (455)
T ss_dssp             CEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSCCCCGGGGGCTTCCEEECTTCCBSCCCTTTSGGGTTCEEEEE
T ss_pred             CEEeCCCCCCCccccCcccccCcccCCEEECCCCccCccCcccccCCCCcccEEeCCCCcccccChhhhhcccccccccc
Confidence            999999998874 3322  22      888888865543          56666666  1111 12112           


Q ss_pred             -----------------------cCCCCCCEEEecCCC-C--C-------------------------------------
Q 041097          252 -----------------------CRLSCLESLKLANES-K--M-------------------------------------  268 (391)
Q Consensus       252 -----------------------~~l~~L~~L~l~~~~-~--l-------------------------------------  268 (391)
                                             ..+++|++|++++.. .  .                                     
T Consensus       186 ~l~~n~l~~~~~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~  265 (455)
T 3v47_A          186 RLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPD  265 (455)
T ss_dssp             ECTTCBCTTCSTTCTTHHHHCCTTTTCEEEEEECTTSCCCHHHHHHHHHHTTTCCEEEEECTTCTTTSCCTTCCSSCCCC
T ss_pred             ccccCcccccchhhccccccccccccceeeeEecCCCcccccchhhhhccccccceeeEeeccccccccccchhhhccCc
Confidence                                   123455555554410 0  0                                     


Q ss_pred             ---------Cchhhh----------cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC
Q 041097          269 ---------PRRSNI----------IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR  328 (391)
Q Consensus       269 ---------p~L~~L----------lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  328 (391)
                               +.|+.|          .| .++.+ ++|+.|++++|.+...++..++.+++|+.|+++.|..........+
T Consensus       266 ~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~  344 (455)
T 3v47_A          266 NFTFKGLEASGVKTCDLSKSKIFALLKSVFSHF-TDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFE  344 (455)
T ss_dssp             TTTTGGGTTSCCCEEECCSSCCCEECTTTTTTC-TTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECGGGGT
T ss_pred             ccccccccccCceEEEecCccccccchhhcccC-CCCCEEECCCCcccccChhHhcCcccCCEEECCCCccCCcChhHhc
Confidence                     112211          34 56677 7888888888877766666777888888888886655332222336


Q ss_pred             cccccceeeeccccccccc-hHhhcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~~~  366 (391)
                      .+++|++|++++|. +..+ |.++..+++|++|+++++.
T Consensus       345 ~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~  382 (455)
T 3v47_A          345 NLDKLEVLDLSYNH-IRALGDQSFLGLPNLKELALDTNQ  382 (455)
T ss_dssp             TCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSC
T ss_pred             CcccCCEEECCCCc-ccccChhhccccccccEEECCCCc
Confidence            77888888888774 5555 6778888888888888764

>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=99.59  E-value=5.1e-14  Score=141.65  Aligned_cols=212  Identities=20%  Similarity=0.089  Sum_probs=137.3

Q ss_pred             CceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYL  207 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L  207 (391)
                      .+++.|.+..+.... +..  . ++++.|.+.++...     .++.   .+++|++|++++|.+..+|.   .+.+|++|
T Consensus        61 ~~L~~L~L~~N~l~~-lp~--~l~~L~~L~Ls~N~l~-----~lp~---~l~~L~~L~Ls~N~l~~l~~---~l~~L~~L  126 (622)
T 3g06_A           61 AHITTLVIPDNNLTS-LPA--LPPELRTLEVSGNQLT-----SLPV---LPPGLLELSIFSNPLTHLPA---LPSGLCKL  126 (622)
T ss_dssp             TTCSEEEECSCCCSC-CCC--CCTTCCEEEECSCCCS-----CCCC---CCTTCCEEEECSCCCCCCCC---CCTTCCEE
T ss_pred             CCCcEEEecCCCCCC-CCC--cCCCCCEEEcCCCcCC-----cCCC---CCCCCCEEECcCCcCCCCCC---CCCCcCEE
Confidence            456666666332222 222  4 66777766655432     1111   55677777777777766665   44566777


Q ss_pred             EccCCCCCccCCCCc---EEEeeCCccCcc-----eeeEEecc--cccchhHHhcCCCCCCEEEecCCC--CC----Cch
Q 041097          208 KLNIPSLKSLPSSRK---ILRLSGNSQFHF-----SLASLLLY--YQSLLSKSLCRLSCLESLKLANES--KM----PRR  271 (391)
Q Consensus       208 ~l~~~~i~~lp~~~~---~L~l~~~~l~~L-----~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~--~l----p~L  271 (391)
                      ++++|.+..+|..+.   +|++++|.+..+     +|+.|+++  ....+|   ..+++|+.|++++..  .+    ++|
T Consensus       127 ~L~~N~l~~lp~~l~~L~~L~Ls~N~l~~l~~~~~~L~~L~L~~N~l~~l~---~~~~~L~~L~Ls~N~l~~l~~~~~~L  203 (622)
T 3g06_A          127 WIFGNQLTSLPVLPPGLQELSVSDNQLASLPALPSELCKLWAYNNQLTSLP---MLPSGLQELSVSDNQLASLPTLPSEL  203 (622)
T ss_dssp             ECCSSCCSCCCCCCTTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCSCCC---CCCTTCCEEECCSSCCSCCCCCCTTC
T ss_pred             ECCCCCCCcCCCCCCCCCEEECcCCcCCCcCCccCCCCEEECCCCCCCCCc---ccCCCCcEEECCCCCCCCCCCccchh
Confidence            777776666665444   777777766554     56666666  344455   445778888887722  11    233


Q ss_pred             hhh------ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccc
Q 041097          272 SNI------ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLK  345 (391)
Q Consensus       272 ~~L------lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~  345 (391)
                      +.|      +..+...+++|+.|++++|.+...+    ..+++|+.|+++.|....  ++.  .+++|+.|++++| .++
T Consensus       204 ~~L~L~~N~l~~l~~~~~~L~~L~Ls~N~L~~lp----~~l~~L~~L~Ls~N~L~~--lp~--~~~~L~~L~Ls~N-~L~  274 (622)
T 3g06_A          204 YKLWAYNNRLTSLPALPSGLKELIVSGNRLTSLP----VLPSELKELMVSGNRLTS--LPM--LPSGLLSLSVYRN-QLT  274 (622)
T ss_dssp             CEEECCSSCCSSCCCCCTTCCEEECCSSCCSCCC----CCCTTCCEEECCSSCCSC--CCC--CCTTCCEEECCSS-CCC
T ss_pred             hEEECcCCcccccCCCCCCCCEEEccCCccCcCC----CCCCcCcEEECCCCCCCc--CCc--ccccCcEEeCCCC-CCC
Confidence            333      1111112278999999998877644    567899999999665543  222  6789999999988 588


Q ss_pred             cchHhhcCCCCCCEEEeeCCc
Q 041097          346 RIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       346 ~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .+|.++..+++|+.|++++++
T Consensus       275 ~lp~~l~~l~~L~~L~L~~N~  295 (622)
T 3g06_A          275 RLPESLIHLSSETTVNLEGNP  295 (622)
T ss_dssp             SCCGGGGGSCTTCEEECCSCC
T ss_pred             cCCHHHhhccccCEEEecCCC
Confidence            999999999999999999986

>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=99.59  E-value=5.9e-15  Score=138.87  Aligned_cols=227  Identities=21%  Similarity=0.160  Sum_probs=127.7

Q ss_pred             CceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcc-cCCCCccc
Q 041097          129 ENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSG-IENLFLLR  205 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~-i~~l~~L~  205 (391)
                      ..++.+.+..+.......... + ++++.|.+.++...    ...+..+..++.|++|++++|.+..+|.. ++++.+|+
T Consensus        52 ~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~----~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~  127 (353)
T 2z80_A           52 EAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGIN----TIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLT  127 (353)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCSSCCHHHHTTCTTCS
T ss_pred             ccCcEEECCCCcCcccCHHHhccCCCCCEEECCCCccC----ccCHhhcCCCCCCCEEECCCCcCCcCCHhHhCCCccCC
Confidence            356666666333332112123 3 67777766554332    11224466777788888888877777655 67777888


Q ss_pred             EEEccCCCCCccCC--CCc------EEEeeCC-ccCcc---------eeeEEecc--cccc-hhHHhcCCCCCCEEEecC
Q 041097          206 YLKLNIPSLKSLPS--SRK------ILRLSGN-SQFHF---------SLASLLLY--YQSL-LSKSLCRLSCLESLKLAN  264 (391)
Q Consensus       206 ~L~l~~~~i~~lp~--~~~------~L~l~~~-~l~~L---------~L~~L~l~--~~~~-lp~~i~~l~~L~~L~l~~  264 (391)
                      +|++++|.+..+|.  .+.      +|++++| .+..+         +|+.|+++  .... .|..++++++|++|++++
T Consensus       128 ~L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~l~~  207 (353)
T 2z80_A          128 FLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLILHM  207 (353)
T ss_dssp             EEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCSEEEEEEEEC
T ss_pred             EEECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCCCCcCccCHHHHhccccCCeecCCC
Confidence            88888877777776  232      6777766 34322         45555554  1122 244455555555555544


Q ss_pred             CCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChh---hhcCCCCCCEEEcCCCCCcCcc---cc-CCCcccccce
Q 041097          265 ESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIP---ALEKLSVLQVLKLKQNLYSEER---TM-GIRAMPKLEC  335 (391)
Q Consensus       265 ~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~---~l~~l~~L~~L~l~~~~~~~~~---~~-~~~~~~~L~~  335 (391)
                      ..    +.. +|  .+..+ ++|+.|++++|.+...+..   .....+.++.+++..+...+..   .+ ..+.+++|++
T Consensus       208 n~----l~~-~~~~~~~~~-~~L~~L~L~~n~l~~~~~~~l~~~~~~~~l~~l~L~~~~l~~~~l~~l~~~l~~l~~L~~  281 (353)
T 2z80_A          208 KQ----HIL-LLEIFVDVT-SSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDESLFQVMKLLNQISGLLE  281 (353)
T ss_dssp             SC----STT-HHHHHHHHT-TTEEEEEEESCBCTTCCCC------CCCCCCEEEEESCBCCHHHHHHHHHHHHTCTTCCE
T ss_pred             Cc----ccc-chhhhhhhc-ccccEEECCCCccccccccccccccccchhhccccccccccCcchhhhHHHHhcccCCCE
Confidence            11    000 22  22234 5555555555555443221   1223445555555533222111   11 1246789999


Q ss_pred             eeeccccccccchHhh-cCCCCCCEEEeeCCc
Q 041097          336 LIINPYAHLKRIHEQL-WCLKSLNKLELWWPE  366 (391)
Q Consensus       336 L~l~~c~~l~~lp~~~-~~l~~L~~L~l~~~~  366 (391)
                      |++++| .++.+|.++ ..+++|++|+++++|
T Consensus       282 L~Ls~N-~l~~i~~~~~~~l~~L~~L~L~~N~  312 (353)
T 2z80_A          282 LEFSRN-QLKSVPDGIFDRLTSLQKIWLHTNP  312 (353)
T ss_dssp             EECCSS-CCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             EECCCC-CCCccCHHHHhcCCCCCEEEeeCCC
Confidence            999988 588999885 899999999999864

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.58  E-value=3e-14  Score=148.16  Aligned_cols=232  Identities=13%  Similarity=0.091  Sum_probs=146.3

Q ss_pred             cCceEEEEEeccCCCcccccCCC--CCccEEEEEecC-CcCCCchhhHHhhcc-------CCcccEEEcCCCccccCCc-
Q 041097          128 RENVKRFTAHRKLNDFAFLDDFD--SFLHSLLYLTSG-SQYLDPTYCEKICKM-------FKFLRVLDLGSLVLIRYPS-  196 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~~--~~lrsl~~~~~~-~~~~~~~~~~~~~~~-------~~~L~~L~l~~~~l~~~p~-  196 (391)
                      ..+.+.|.+..+.....++..+.  ++++.|.+..+. ..   ...++..+..       ++.|+.|++++|.+..+|. 
T Consensus       490 L~~L~~L~Ls~N~l~~~iP~~l~~L~~L~~L~Ls~N~~ls---g~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~L~~ip~~  566 (876)
T 4ecn_A          490 LKDLTDVELYNCPNMTQLPDFLYDLPELQSLNIACNRGIS---AAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPAS  566 (876)
T ss_dssp             CTTCCEEEEESCTTCCSCCGGGGGCSSCCEEECTTCTTSC---HHHHHHHHHHHHHCTTTTTTCCEEECCSSCCCBCCCH
T ss_pred             CCCCCEEECcCCCCCccChHHHhCCCCCCEEECcCCCCcc---cccchHHHHhhhhcccccCCccEEEeeCCcCCccCCh
Confidence            45678888873332322444343  788888776654 21   1123344443       4599999999999998998 


Q ss_pred             -ccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcc--------e-eeEEecc--cccchhHHhcCCCC--
Q 041097          197 -GIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHF--------S-LASLLLY--YQSLLSKSLCRLSC--  256 (391)
Q Consensus       197 -~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L--------~-L~~L~l~--~~~~lp~~i~~l~~--  256 (391)
                       .++++.+|++|++++|.+..+| .++      .|++++|.+..+        + |+.|+++  ....+|..++.++.  
T Consensus       567 ~~l~~L~~L~~L~Ls~N~l~~lp-~~~~L~~L~~L~Ls~N~l~~lp~~l~~l~~~L~~L~Ls~N~L~~lp~~~~~~~~~~  645 (876)
T 4ecn_A          567 ASLQKMVKLGLLDCVHNKVRHLE-AFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAKSVYV  645 (876)
T ss_dssp             HHHTTCTTCCEEECTTSCCCBCC-CCCTTSEESEEECCSSCCSCCCTTSCEECTTCCEEECCSSCCCSCCSCCCTTCSSC
T ss_pred             hhhhcCCCCCEEECCCCCcccch-hhcCCCcceEEECcCCccccchHHHhhccccCCEEECcCCCCCcCchhhhccccCC
Confidence             8999999999999999998888 555      889999877654        5 8888888  45577777766654  


Q ss_pred             CCEEEecCCC---CCC------------chhhh---------cc-cc-ccCCCCccEEEeecccCCCCChhhhc------
Q 041097          257 LESLKLANES---KMP------------RRSNI---------IL-AE-YQFPPSLTHLSFSNIELMDDPIPALE------  304 (391)
Q Consensus       257 L~~L~l~~~~---~lp------------~L~~L---------lp-~~-~~l~~~L~~L~l~~~~~~~~~~~~l~------  304 (391)
                      |+.|++++..   .+|            +|+.|         +| .+ ..+ ++|+.|+|++|.+...+...+.      
T Consensus       646 L~~L~Ls~N~l~g~ip~l~~~l~~~~~~~L~~L~Ls~N~L~~lp~~~~~~l-~~L~~L~Ls~N~L~~ip~~~~~~~~~~l  724 (876)
T 4ecn_A          646 MGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATG-SPISTIILSNNLMTSIPENSLKPKDGNY  724 (876)
T ss_dssp             EEEEECCSSCTTTTSSSCSSCTTTCCCCCEEEEECCSSCCCSCCHHHHHTT-CCCSEEECCSCCCSCCCTTSSSCTTSCC
T ss_pred             CCEEECcCCcCCCccccchhhhccccCCCcCEEEccCCcCCccCHHHHccC-CCCCEEECCCCcCCccChHHhccccccc
Confidence            8888887621   111            22222         44 22 245 6666666666665543322221      


Q ss_pred             -CCCCCCEEEcCCCCCcCccccCCC--cccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          305 -KLSVLQVLKLKQNLYSEERTMGIR--AMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       305 -~l~~L~~L~l~~~~~~~~~~~~~~--~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                       ++++|+.|+++.|... ..+....  .+++|+.|++++| .+..+|.++..+++|+.|++++++
T Consensus       725 ~nl~~L~~L~Ls~N~L~-~lp~~l~~~~l~~L~~L~Ls~N-~L~~lp~~l~~L~~L~~L~Ls~N~  787 (876)
T 4ecn_A          725 KNTYLLTTIDLRFNKLT-SLSDDFRATTLPYLSNMDVSYN-CFSSFPTQPLNSSQLKAFGIRHQR  787 (876)
T ss_dssp             TTGGGCCEEECCSSCCC-CCCGGGSTTTCTTCCEEECCSS-CCSSCCCGGGGCTTCCEEECCCCB
T ss_pred             cccCCccEEECCCCCCc-cchHHhhhccCCCcCEEEeCCC-CCCccchhhhcCCCCCEEECCCCC
Confidence             2236666666655443 1111223  5677777777766 356677777777777777776544

>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=99.58  E-value=3.7e-14  Score=129.25  Aligned_cols=170  Identities=18%  Similarity=0.130  Sum_probs=135.3

Q ss_pred             CCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCcc-CCCCc------EEEeeCCc-cCcceeeEEecccccch-
Q 041097          178 FKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSL-PSSRK------ILRLSGNS-QFHFSLASLLLYYQSLL-  247 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~l-p~~~~------~L~l~~~~-l~~L~L~~L~l~~~~~l-  247 (391)
                      .+.|+.|+++++.+..++ ..+.++.+|++|+++++.+..+ |..+.      +|++++|. +.             .+ 
T Consensus        31 ~~~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~l~-------------~~~   97 (285)
T 1ozn_A           31 PAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLR-------------SVD   97 (285)
T ss_dssp             CTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCC-------------CCC
T ss_pred             CCCceEEEeeCCcCCccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCCCCCcc-------------ccC
Confidence            468999999999999766 5689999999999999998876 44443      77777775 55             55 


Q ss_pred             hHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC
Q 041097          248 SKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG  326 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~  326 (391)
                      |..+..+++|++|++++..    +..+.| .+..+ ++|+.|++++|.+...+...++.+++|+.|+++.|.........
T Consensus        98 ~~~~~~l~~L~~L~l~~n~----l~~~~~~~~~~l-~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~  172 (285)
T 1ozn_A           98 PATFHGLGRLHTLHLDRCG----LQELGPGLFRGL-AALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVPERA  172 (285)
T ss_dssp             TTTTTTCTTCCEEECTTSC----CCCCCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCEECTTT
T ss_pred             HHHhcCCcCCCEEECCCCc----CCEECHhHhhCC-cCCCEEECCCCcccccCHhHhccCCCccEEECCCCcccccCHHH
Confidence            6789999999999998822    011134 67788 99999999999998877777899999999999976655322222


Q ss_pred             CCcccccceeeeccccccccc-hHhhcCCCCCCEEEeeCCc
Q 041097          327 IRAMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       327 ~~~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~~~  366 (391)
                      ...+++|++|++++|. +..+ |.++..+++|++|+++++.
T Consensus       173 ~~~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~l~~n~  212 (285)
T 1ozn_A          173 FRGLHSLDRLLLHQNR-VAHVHPHAFRDLGRLMTLYLFANN  212 (285)
T ss_dssp             TTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSC
T ss_pred             hcCccccCEEECCCCc-ccccCHhHccCcccccEeeCCCCc
Confidence            4678999999999985 5555 8889999999999998864

>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=99.58  E-value=1.3e-14  Score=131.57  Aligned_cols=190  Identities=20%  Similarity=0.121  Sum_probs=135.6

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCC-Cc------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSS-RK------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~-~~------  222 (391)
                      ..++.|.+.++...   . .....+..++.|++|++++|.+..++ ..+.++.+|++|+++++.+..+|.. +.      
T Consensus        28 ~~l~~L~ls~n~l~---~-~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  103 (276)
T 2z62_A           28 FSTKNLDLSFNPLR---H-LGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQ  103 (276)
T ss_dssp             TTCCEEECTTCCCC---E-ECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCC
T ss_pred             CCccEEECCCCccc---c-cCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCccCccChhhhcCCcccc
Confidence            56777766554432   1 12235677888899999888888655 4678888899999988888876633 32      


Q ss_pred             EEEeeCCccCcceeeEEecccccchhH-HhcCCCCCCEEEecCCCCCCchhhh-cc-ccccCCCCccEEEeecccCCCCC
Q 041097          223 ILRLSGNSQFHFSLASLLLYYQSLLSK-SLCRLSCLESLKLANESKMPRRSNI-IL-AEYQFPPSLTHLSFSNIELMDDP  299 (391)
Q Consensus       223 ~L~l~~~~l~~L~L~~L~l~~~~~lp~-~i~~l~~L~~L~l~~~~~lp~L~~L-lp-~~~~l~~~L~~L~l~~~~~~~~~  299 (391)
                      .|++++|.+.             .++. .++.+++|++|++++..    +..+ +| .++.+ ++|+.|++++|.+...+
T Consensus       104 ~L~l~~n~l~-------------~~~~~~~~~l~~L~~L~l~~n~----l~~~~l~~~~~~l-~~L~~L~Ls~N~l~~~~  165 (276)
T 2z62_A          104 KLVAVETNLA-------------SLENFPIGHLKTLKELNVAHNL----IQSFKLPEYFSNL-TNLEHLDLSSNKIQSIY  165 (276)
T ss_dssp             EEECTTSCCC-------------CSTTCCCTTCTTCCEEECCSSC----CCCCCCCGGGGGC-TTCCEEECCSSCCCEEC
T ss_pred             EEECCCCCcc-------------ccCchhcccCCCCCEEECcCCc----cceecCchhhccC-CCCCEEECCCCCCCcCC
Confidence            6666666655             5544 68899999999998722    0110 46 77889 99999999999988766


Q ss_pred             hhhhcCCCCCC----EEEcCCCCCcCccccCCCcccccceeeeccccccccchHh-hcCCCCCCEEEeeC
Q 041097          300 IPALEKLSVLQ----VLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLELWW  364 (391)
Q Consensus       300 ~~~l~~l~~L~----~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l~~  364 (391)
                      ...+..+++|+    .|+++.|.... .........+|++|++++|. ++.+|.. +..+++|++|++++
T Consensus       166 ~~~~~~l~~L~~l~l~L~ls~n~l~~-~~~~~~~~~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~l~~  233 (276)
T 2z62_A          166 CTDLRVLHQMPLLNLSLDLSLNPMNF-IQPGAFKEIRLKELALDTNQ-LKSVPDGIFDRLTSLQKIWLHT  233 (276)
T ss_dssp             GGGGHHHHTCTTCCEEEECCSSCCCE-ECTTSSCSCCEEEEECCSSC-CSCCCTTTTTTCCSCCEEECCS
T ss_pred             HHHhhhhhhccccceeeecCCCcccc-cCccccCCCcccEEECCCCc-eeecCHhHhcccccccEEEccC
Confidence            55666555555    88998666543 22223344589999999885 8888865 58899999999993

>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=99.57  E-value=3.9e-14  Score=142.79  Aligned_cols=191  Identities=25%  Similarity=0.281  Sum_probs=106.2

Q ss_pred             hhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCC-CCc------EEEeeCCccC-c--------c-ee
Q 041097          174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPS-SRK------ILRLSGNSQF-H--------F-SL  236 (391)
Q Consensus       174 ~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~-~~~------~L~l~~~~l~-~--------L-~L  236 (391)
                      .+..++.|+.|++++|.+..+|..++.+.+|++|+++++.+..+++ .+.      +|++++|.+. .        + +|
T Consensus       273 ~~~~l~~L~~L~l~~n~l~~lp~~l~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L  352 (606)
T 3t6q_A          273 TFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENL  352 (606)
T ss_dssp             TTTTCTTCSEEECTTSCCSCCCSSCCSCTTCCEEECTTCCCSBGGGGCGGGCTTCSEEECCSCSSCCBCCSSTTTTCTTC
T ss_pred             HhccccCCCEEeccCCccCCCChhhcccccCCEEECccCCcCcCchhhhhccCcCCEEECCCCCcccccchhhhhccCcC
Confidence            3555666666666666666666666666666666666666554422 222      5555555332 1        1 45


Q ss_pred             eEEecc--cccch---hHHhcCCCCCCEEEecCCC-------C---CCchhhh----------cc--ccccCCCCccEEE
Q 041097          237 ASLLLY--YQSLL---SKSLCRLSCLESLKLANES-------K---MPRRSNI----------IL--AEYQFPPSLTHLS  289 (391)
Q Consensus       237 ~~L~l~--~~~~l---p~~i~~l~~L~~L~l~~~~-------~---lp~L~~L----------lp--~~~~l~~~L~~L~  289 (391)
                      +.|+++  ....+   |..++.+++|++|++++..       .   ++.|+.|          .|  .+..+ ++|+.|+
T Consensus       353 ~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l-~~L~~L~  431 (606)
T 3t6q_A          353 RELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNL-HLLKVLN  431 (606)
T ss_dssp             CEEECCSSCCCEEEESTTTTTTCTTCCEEECCSCSCEEECTTTTTTCTTCSEEECTTCCEECCTTCCTTTTC-TTCCEEE
T ss_pred             CEEECCCCccccccCcchhcccCCCCCEEECCCCcCCcCCHHHhcCCccCCeEECCCCcCCCcccchhhhCc-ccCCEEE
Confidence            555555  11122   3445555555555555410       1   1222222          22  35667 7777777


Q ss_pred             eecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC---CCcccccceeeeccccccccc-hHhhcCCCCCCEEEeeCC
Q 041097          290 FSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG---IRAMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       290 l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~---~~~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~~  365 (391)
                      +++|.+...++..++.+++|+.|+++.|...+..+..   .+.+++|++|++++|. +..+ |..+..+++|++|+++++
T Consensus       432 l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~Ls~N  510 (606)
T 3t6q_A          432 LSHSLLDISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCD-LSSIDQHAFTSLKMMNHVDLSHN  510 (606)
T ss_dssp             CTTCCCBTTCTTTTTTCTTCCEEECTTCBCGGGEECSSCGGGGCTTCCEEECTTSC-CCEECTTTTTTCTTCCEEECCSS
T ss_pred             CCCCccCCcCHHHHhCCCCCCEEECCCCCCCccccccchhhccCCCccEEECCCCc-cCccChhhhccccCCCEEECCCC
Confidence            7777776666566777777777777766554422211   2456667777777663 4443 456666677777776665


Q ss_pred             c
Q 041097          366 E  366 (391)
Q Consensus       366 ~  366 (391)
                      .
T Consensus       511 ~  511 (606)
T 3t6q_A          511 R  511 (606)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.57  E-value=5.4e-14  Score=137.38  Aligned_cols=200  Identities=20%  Similarity=0.184  Sum_probs=132.9

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------IL  224 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L  224 (391)
                      .+++++.+.+....     .+ +.+..++.|++|++++|.+..+|. ++++.+|++|+++++.+..+|. +.      +|
T Consensus        46 ~~l~~L~l~~~~i~-----~l-~~~~~l~~L~~L~Ls~n~l~~~~~-~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L  117 (466)
T 1o6v_A           46 DQVTTLQADRLGIK-----SI-DGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIADITP-LANLTNLTGL  117 (466)
T ss_dssp             HTCCEEECCSSCCC-----CC-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGG-GTTCTTCCEE
T ss_pred             ccccEEecCCCCCc-----cC-cchhhhcCCCEEECCCCccCCchh-hhccccCCEEECCCCccccChh-hcCCCCCCEE
Confidence            67788877665543     13 346789999999999999998877 9999999999999999988875 43      99


Q ss_pred             EeeCCccCcc-------eeeEEecc--cccchhHHhcCCCCCCEEEecC--CC-----CCCchhhh---------ccccc
Q 041097          225 RLSGNSQFHF-------SLASLLLY--YQSLLSKSLCRLSCLESLKLAN--ES-----KMPRRSNI---------ILAEY  279 (391)
Q Consensus       225 ~l~~~~l~~L-------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~--~~-----~lp~L~~L---------lp~~~  279 (391)
                      ++++|.+..+       +|++|+++  ....++ .++.+++|++|++.+  ..     .++.|+.|         ++.+.
T Consensus       118 ~L~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~-~~~~l~~L~~L~l~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~l~  196 (466)
T 1o6v_A          118 TLFNNQITDIDPLKNLTNLNRLELSSNTISDIS-ALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLA  196 (466)
T ss_dssp             ECCSSCCCCCGGGTTCTTCSEEEEEEEEECCCG-GGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEECCSSCCCCCGGGG
T ss_pred             ECCCCCCCCChHHcCCCCCCEEECCCCccCCCh-hhccCCcccEeecCCcccCchhhccCCCCCEEECcCCcCCCChhhc
Confidence            9999987765       78888888  444454 488899999998875  11     11222222         22344


Q ss_pred             cCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCE
Q 041097          280 QFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNK  359 (391)
Q Consensus       280 ~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~  359 (391)
                      .+ ++|+.|++++|.+...+  .++.+++|+.|+++.|....  ......+++|++|++++|. +..++. +..+++|++
T Consensus       197 ~l-~~L~~L~l~~n~l~~~~--~~~~l~~L~~L~l~~n~l~~--~~~l~~l~~L~~L~l~~n~-l~~~~~-~~~l~~L~~  269 (466)
T 1o6v_A          197 KL-TNLESLIATNNQISDIT--PLGILTNLDELSLNGNQLKD--IGTLASLTNLTDLDLANNQ-ISNLAP-LSGLTKLTE  269 (466)
T ss_dssp             GC-TTCSEEECCSSCCCCCG--GGGGCTTCCEEECCSSCCCC--CGGGGGCTTCSEEECCSSC-CCCCGG-GTTCTTCSE
T ss_pred             cC-CCCCEEEecCCcccccc--cccccCCCCEEECCCCCccc--chhhhcCCCCCEEECCCCc-cccchh-hhcCCCCCE
Confidence            45 55555555555544422  24555666666665443332  1123456677777777663 555554 667777777


Q ss_pred             EEeeCCc
Q 041097          360 LELWWPE  366 (391)
Q Consensus       360 L~l~~~~  366 (391)
                      |+++++.
T Consensus       270 L~l~~n~  276 (466)
T 1o6v_A          270 LKLGANQ  276 (466)
T ss_dssp             EECCSSC
T ss_pred             EECCCCc
Confidence            7776654

>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=99.56  E-value=3.5e-14  Score=130.00  Aligned_cols=162  Identities=28%  Similarity=0.290  Sum_probs=92.0

Q ss_pred             cCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchhHH
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSKS  250 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~  250 (391)
                      .++.|+.|+++++.+..++ .++.+.+|++|+++++.+..+|. +.      .|++++|.+.             .+| .
T Consensus        44 ~l~~L~~L~l~~~~i~~~~-~~~~l~~L~~L~L~~n~l~~~~~-l~~l~~L~~L~l~~n~l~-------------~~~-~  107 (291)
T 1h6t_A           44 ELNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVK-------------DLS-S  107 (291)
T ss_dssp             HHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCC-------------CGG-G
T ss_pred             hcCcccEEEccCCCcccCh-hHhcCCCCCEEEccCCccCCCcc-cccCCCCCEEECCCCcCC-------------CCh-h
Confidence            3445555555555555443 25555555555555555555443 22      4444444444             333 3


Q ss_pred             hcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcc
Q 041097          251 LCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAM  330 (391)
Q Consensus       251 i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~  330 (391)
                      ++.+++|++|++++..    +.. +|.+..+ ++|+.|++++|.+...  +.++.+++|+.|+++.|......  ....+
T Consensus       108 l~~l~~L~~L~L~~n~----i~~-~~~l~~l-~~L~~L~l~~n~l~~~--~~l~~l~~L~~L~L~~N~l~~~~--~l~~l  177 (291)
T 1h6t_A          108 LKDLKKLKSLSLEHNG----ISD-INGLVHL-PQLESLYLGNNKITDI--TVLSRLTKLDTLSLEDNQISDIV--PLAGL  177 (291)
T ss_dssp             GTTCTTCCEEECTTSC----CCC-CGGGGGC-TTCCEEECCSSCCCCC--GGGGGCTTCSEEECCSSCCCCCG--GGTTC
T ss_pred             hccCCCCCEEECCCCc----CCC-ChhhcCC-CCCCEEEccCCcCCcc--hhhccCCCCCEEEccCCccccch--hhcCC
Confidence            6667777777776522    000 2344556 6777777777766553  56667777777777755544322  24566


Q ss_pred             cccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          331 PKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       331 ~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ++|++|++++| .++.+| .+..+++|+.|++++++
T Consensus       178 ~~L~~L~L~~N-~i~~l~-~l~~l~~L~~L~l~~n~  211 (291)
T 1h6t_A          178 TKLQNLYLSKN-HISDLR-ALAGLKNLDVLELFSQE  211 (291)
T ss_dssp             TTCCEEECCSS-CCCBCG-GGTTCTTCSEEEEEEEE
T ss_pred             CccCEEECCCC-cCCCCh-hhccCCCCCEEECcCCc
Confidence            67777777766 466665 36667777777776654

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.56  E-value=1e-13  Score=135.00  Aligned_cols=205  Identities=16%  Similarity=0.105  Sum_probs=120.8

Q ss_pred             cCceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccE
Q 041097          128 RENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRY  206 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~  206 (391)
                      ...++.+.+....... ...... ++++.|.+..+....     +  .+..++.|++|++++|.+..++  ++++.+|++
T Consensus        41 l~~L~~L~Ls~n~l~~-~~~l~~l~~L~~L~Ls~n~l~~-----~--~~~~l~~L~~L~Ls~N~l~~~~--~~~l~~L~~  110 (457)
T 3bz5_A           41 LATLTSLDCHNSSITD-MTGIEKLTGLTKLICTSNNITT-----L--DLSQNTNLTYLACDSNKLTNLD--VTPLTKLTY  110 (457)
T ss_dssp             HTTCCEEECCSSCCCC-CTTGGGCTTCSEEECCSSCCSC-----C--CCTTCTTCSEEECCSSCCSCCC--CTTCTTCCE
T ss_pred             cCCCCEEEccCCCccc-ChhhcccCCCCEEEccCCcCCe-----E--ccccCCCCCEEECcCCCCceee--cCCCCcCCE
Confidence            3556677766332222 222223 677777666554431     1  1567777888888888777654  777778888


Q ss_pred             EEccCCCCCccCCCCc------EEEeeCCccCcc------eeeEEeccc---ccchhHHhcCCCCCCEEEecCCCCCCch
Q 041097          207 LKLNIPSLKSLPSSRK------ILRLSGNSQFHF------SLASLLLYY---QSLLSKSLCRLSCLESLKLANESKMPRR  271 (391)
Q Consensus       207 L~l~~~~i~~lp~~~~------~L~l~~~~l~~L------~L~~L~l~~---~~~lp~~i~~l~~L~~L~l~~~~~lp~L  271 (391)
                      |+++++.+..+|  ++      .|++++|.+..+      +|+.|+++.   ...+  .++.+++|++|++++..    +
T Consensus       111 L~L~~N~l~~l~--~~~l~~L~~L~l~~N~l~~l~l~~l~~L~~L~l~~n~~~~~~--~~~~l~~L~~L~ls~n~----l  182 (457)
T 3bz5_A          111 LNCDTNKLTKLD--VSQNPLLTYLNCARNTLTEIDVSHNTQLTELDCHLNKKITKL--DVTPQTQLTTLDCSFNK----I  182 (457)
T ss_dssp             EECCSSCCSCCC--CTTCTTCCEEECTTSCCSCCCCTTCTTCCEEECTTCSCCCCC--CCTTCTTCCEEECCSSC----C
T ss_pred             EECCCCcCCeec--CCCCCcCCEEECCCCccceeccccCCcCCEEECCCCCccccc--ccccCCcCCEEECCCCc----c
Confidence            888887777665  22      777777766643      555665551   1222  35556666666665521    0


Q ss_pred             hhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhh
Q 041097          272 SNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQL  351 (391)
Q Consensus       272 ~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~  351 (391)
                      .. +| ++.+ ++|+.|++++|.+...   .++.+++|+.|+++.|...+   ++.+.+++|+.|++++| .++.+|  +
T Consensus       183 ~~-l~-l~~l-~~L~~L~l~~N~l~~~---~l~~l~~L~~L~Ls~N~l~~---ip~~~l~~L~~L~l~~N-~l~~~~--~  250 (457)
T 3bz5_A          183 TE-LD-VSQN-KLLNRLNCDTNNITKL---DLNQNIQLTFLDCSSNKLTE---IDVTPLTQLTYFDCSVN-PLTELD--V  250 (457)
T ss_dssp             CC-CC-CTTC-TTCCEEECCSSCCSCC---CCTTCTTCSEEECCSSCCSC---CCCTTCTTCSEEECCSS-CCSCCC--C
T ss_pred             ce-ec-cccC-CCCCEEECcCCcCCee---ccccCCCCCEEECcCCcccc---cCccccCCCCEEEeeCC-cCCCcC--H
Confidence            00 22 4456 6777777777766653   25667777777777665554   22566777777777766 356655  3


Q ss_pred             cCCCCCCEEEe
Q 041097          352 WCLKSLNKLEL  362 (391)
Q Consensus       352 ~~l~~L~~L~l  362 (391)
                      +.+++|+.|++
T Consensus       251 ~~l~~L~~L~l  261 (457)
T 3bz5_A          251 STLSKLTTLHC  261 (457)
T ss_dssp             TTCTTCCEEEC
T ss_pred             HHCCCCCEEec
Confidence            34555544443

>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=99.55  E-value=2.4e-14  Score=144.41  Aligned_cols=231  Identities=17%  Similarity=0.147  Sum_probs=143.6

Q ss_pred             cCceEEEEEeccCCCcccccCCC--CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCc-ccCCCCc
Q 041097          128 RENVKRFTAHRKLNDFAFLDDFD--SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPS-GIENLFL  203 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~~--~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~-~i~~l~~  203 (391)
                      ..+.+.+.+..+.... ++....  ++++.|.+.++...    ...+..+..++.|+.|++++|.+. .+|. .++.+.+
T Consensus       277 l~~L~~L~l~~n~l~~-lp~~l~~l~~L~~L~l~~n~l~----~~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~  351 (606)
T 3t6q_A          277 FSGLQELDLTATHLSE-LPSGLVGLSTLKKLVLSANKFE----NLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLEN  351 (606)
T ss_dssp             CTTCSEEECTTSCCSC-CCSSCCSCTTCCEEECTTCCCS----BGGGGCGGGCTTCSEEECCSCSSCCBCCSSTTTTCTT
T ss_pred             ccCCCEEeccCCccCC-CChhhcccccCCEEECccCCcC----cCchhhhhccCcCCEEECCCCCcccccchhhhhccCc
Confidence            3467777776333332 333333  77777777655432    122345667777777777777765 4443 3677777


Q ss_pred             ccEEEccCCCCCcc---CCCCc------EEEeeCCccCcc---------eeeEEecc--ccc-chh-HHhcCCCCCCEEE
Q 041097          204 LRYLKLNIPSLKSL---PSSRK------ILRLSGNSQFHF---------SLASLLLY--YQS-LLS-KSLCRLSCLESLK  261 (391)
Q Consensus       204 L~~L~l~~~~i~~l---p~~~~------~L~l~~~~l~~L---------~L~~L~l~--~~~-~lp-~~i~~l~~L~~L~  261 (391)
                      |++|+++++.+..+   |..+.      .|++++|.+..+         +|+.|+++  ... ..| ..++.+++|++|+
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            77777777776654   33333      777777654433         56666666  111 112 2356666666666


Q ss_pred             ecCCC-------C---CCchhhh-----------cc---ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCC
Q 041097          262 LANES-------K---MPRRSNI-----------IL---AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQN  317 (391)
Q Consensus       262 l~~~~-------~---lp~L~~L-----------lp---~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~  317 (391)
                      +++..       .   +|+|+.|           +|   .+..+ ++|+.|++++|.+...++..++.+++|+.|+++.|
T Consensus       432 l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~l-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N  510 (606)
T 3t6q_A          432 LSHSLLDISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTL-GRLEILVLSFCDLSSIDQHAFTSLKMMNHVDLSHN  510 (606)
T ss_dssp             CTTCCCBTTCTTTTTTCTTCCEEECTTCBCGGGEECSSCGGGGC-TTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSS
T ss_pred             CCCCccCCcCHHHHhCCCCCCEEECCCCCCCccccccchhhccC-CCccEEECCCCccCccChhhhccccCCCEEECCCC
Confidence            66511       0   1222222           12   46677 88888888888877766677888888888888876


Q ss_pred             CCcCccccCCCcccccceeeeccccccccc-hHhhcCCCCCCEEEeeCCc
Q 041097          318 LYSEERTMGIRAMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       318 ~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~~~  366 (391)
                      ...+..+.....+++| +|++++|. ++.+ |..+..+++|++|+++++|
T Consensus       511 ~l~~~~~~~l~~l~~L-~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N~  558 (606)
T 3t6q_A          511 RLTSSSIEALSHLKGI-YLNLASNH-ISIILPSLLPILSQQRTINLRQNP  558 (606)
T ss_dssp             CCCGGGGGGGTTCCSC-EEECCSSC-CCCCCGGGHHHHHTSSEEECTTCC
T ss_pred             ccCcCChhHhCccccc-EEECcCCc-ccccCHhhcccCCCCCEEeCCCCC
Confidence            6655433344677788 88888874 5554 5567888999999998754

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.55  E-value=2.1e-14  Score=132.73  Aligned_cols=182  Identities=23%  Similarity=0.169  Sum_probs=119.0

Q ss_pred             cCCcccEEEcCCCccc-cCCccc--CCCCcccEEEccCCCCCccCC-----------CCcEEEeeCCccCcc--------
Q 041097          177 MFKFLRVLDLGSLVLI-RYPSGI--ENLFLLRYLKLNIPSLKSLPS-----------SRKILRLSGNSQFHF--------  234 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~-~~p~~i--~~l~~L~~L~l~~~~i~~lp~-----------~~~~L~l~~~~l~~L--------  234 (391)
                      .++.|++|++++|.+. ..|..+  +.+.+|++|++++|.+..+|.           .+.+|++++|.+..+        
T Consensus        93 ~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~l~~~~~~~L~~L~L~~N~l~~~~~~~~~~l  172 (312)
T 1wwl_A           93 GISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVF  172 (312)
T ss_dssp             TTSCCCEEEEEEEBCBSCCCCCSSSCCSCCCSEEEEESCBCSSSSSHHHHHHTTCCTTCCEEEEESCSCCCCCTTTCCCC
T ss_pred             CcCCccEEEccCCcccchhHHHHHHhcCCCccEEEccCCCCcchhHHHHHHHHhhcCCCcEEEeeCCCCccchHHHhccC
Confidence            4667777777777766 566655  667777777777776665542           233667776655543        


Q ss_pred             -eeeEEecccc-----cchhHHh--cCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCC-hhhh
Q 041097          235 -SLASLLLYYQ-----SLLSKSL--CRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDP-IPAL  303 (391)
Q Consensus       235 -~L~~L~l~~~-----~~lp~~i--~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~-~~~l  303 (391)
                       +|+.|++++.     ..+|..+  +.+++|++|++++.. +..+.. +|  .+..+ ++|+.|++++|.+...+ .+.+
T Consensus       173 ~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~-~~~~~~~~l-~~L~~L~Ls~N~l~~~~~~~~~  249 (312)
T 1wwl_A          173 PALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAG-METPSG-VCSALAAAR-VQLQGLDLSHNSLRDAAGAPSC  249 (312)
T ss_dssp             SSCCEEECCSCTTCHHHHHHHHSCTTSCTTCCEEECTTSC-CCCHHH-HHHHHHHTT-CCCSEEECTTSCCCSSCCCSCC
T ss_pred             CCCCEEECCCCCcCcchHHHHHHHhccCCCCCEEECCCCc-CcchHH-HHHHHHhcC-CCCCEEECCCCcCCcccchhhh
Confidence             5666666611     1245555  788888888887722 000000 22  23467 88888888888877654 3556


Q ss_pred             cCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          304 EKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       304 ~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ..+++|++|+++.|....   ++...+++|++|+++++ +++.+|. +..+++|++|++++++
T Consensus       250 ~~l~~L~~L~Ls~N~l~~---ip~~~~~~L~~L~Ls~N-~l~~~p~-~~~l~~L~~L~L~~N~  307 (312)
T 1wwl_A          250 DWPSQLNSLNLSFTGLKQ---VPKGLPAKLSVLDLSYN-RLDRNPS-PDELPQVGNLSLKGNP  307 (312)
T ss_dssp             CCCTTCCEEECTTSCCSS---CCSSCCSEEEEEECCSS-CCCSCCC-TTTSCEEEEEECTTCT
T ss_pred             hhcCCCCEEECCCCccCh---hhhhccCCceEEECCCC-CCCCChh-HhhCCCCCEEeccCCC
Confidence            677888888888666541   22222378889999877 5777876 7888889999888876

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.55  E-value=5e-14  Score=131.31  Aligned_cols=226  Identities=17%  Similarity=0.163  Sum_probs=144.5

Q ss_pred             CceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRY  206 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~  206 (391)
                      ..++.+.+..+.......... + ++++.|.+.++...    ...+..+..++.|++|++++|.+..+|..+.  .+|++
T Consensus        54 ~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~----~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~--~~L~~  127 (332)
T 2ft3_A           54 PDTTLLDLQNNDISELRKDDFKGLQHLYALVLVNNKIS----KIHEKAFSPLRKLQKLYISKNHLVEIPPNLP--SSLVE  127 (332)
T ss_dssp             TTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCC----EECGGGSTTCTTCCEEECCSSCCCSCCSSCC--TTCCE
T ss_pred             CCCeEEECCCCcCCccCHhHhhCCCCCcEEECCCCccC----ccCHhHhhCcCCCCEEECCCCcCCccCcccc--ccCCE
Confidence            457777776333333122233 3 77888877655432    1223567788888888888888887777665  67888


Q ss_pred             EEccCCCCCccCCCC-c------EEEeeCCccCcc----------eeeEEecc--cccchh-------------------
Q 041097          207 LKLNIPSLKSLPSSR-K------ILRLSGNSQFHF----------SLASLLLY--YQSLLS-------------------  248 (391)
Q Consensus       207 L~l~~~~i~~lp~~~-~------~L~l~~~~l~~L----------~L~~L~l~--~~~~lp-------------------  248 (391)
                      |+++++.+..+|... .      .|++++|.+...          +|+.|+++  ....+|                   
T Consensus       128 L~l~~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~L~~L~l~~n~l~~l~~~~~~~L~~L~l~~n~i~~  207 (332)
T 2ft3_A          128 LRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGLKLNYLRISEAKLTGIPKDLPETLNELHLDHNKIQA  207 (332)
T ss_dssp             EECCSSCCCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSCCCSCCBCCSSBCSSCCSSSCSSCSCCBCCSSCCCC
T ss_pred             EECCCCccCccCHhHhCCCccCCEEECCCCccccCCCCcccccCCccCEEECcCCCCCccCccccCCCCEEECCCCcCCc
Confidence            888888777776542 2      777777766421          44444444  222233                   


Q ss_pred             ---HHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc
Q 041097          249 ---KSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT  324 (391)
Q Consensus       249 ---~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~  324 (391)
                         ..+.++++|++|++++..    +..+.| .+..+ ++|+.|++++|.+...+ ..++.+++|+.|+++.|.......
T Consensus       208 ~~~~~l~~l~~L~~L~L~~N~----l~~~~~~~~~~l-~~L~~L~L~~N~l~~lp-~~l~~l~~L~~L~l~~N~l~~~~~  281 (332)
T 2ft3_A          208 IELEDLLRYSKLYRLGLGHNQ----IRMIENGSLSFL-PTLRELHLDNNKLSRVP-AGLPDLKLLQVVYLHTNNITKVGV  281 (332)
T ss_dssp             CCTTSSTTCTTCSCCBCCSSC----CCCCCTTGGGGC-TTCCEEECCSSCCCBCC-TTGGGCTTCCEEECCSSCCCBCCT
T ss_pred             cCHHHhcCCCCCCEEECCCCc----CCcCChhHhhCC-CCCCEEECCCCcCeecC-hhhhcCccCCEEECCCCCCCccCh
Confidence               345555555555555411    000033 67788 99999999999988655 568999999999999776654321


Q ss_pred             cCC------Ccccccceeeecccccc--ccchHhhcCCCCCCEEEeeCCc
Q 041097          325 MGI------RAMPKLECLIINPYAHL--KRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       325 ~~~------~~~~~L~~L~l~~c~~l--~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      -..      ..++.|+.|++++++..  ...|..+..+++|+.++++++.
T Consensus       282 ~~~~~~~~~~~~~~l~~L~l~~N~~~~~~~~~~~~~~l~~L~~l~l~~n~  331 (332)
T 2ft3_A          282 NDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLAIQFGNYK  331 (332)
T ss_dssp             TSSSCSSCCSSSCCBSEEECCSSSSCGGGSCGGGGTTBCCSTTEEC----
T ss_pred             hHccccccccccccccceEeecCcccccccCcccccccchhhhhhccccc
Confidence            111      12578999999998632  3456778899999999998865

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.55  E-value=7.7e-14  Score=126.34  Aligned_cols=173  Identities=23%  Similarity=0.214  Sum_probs=89.7

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCc
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNS  230 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~  230 (391)
                      ..++.+.+.+....     .+ +.+..++.|++|++++|.+..+ ..++.+.+|++|++++|.+..+|..          
T Consensus        41 ~~L~~L~l~~~~i~-----~~-~~l~~l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~L~~n~l~~~~~~----------  103 (272)
T 3rfs_A           41 NSIDQIIANNSDIK-----SV-QGIQYLPNVRYLALGGNKLHDI-SALKELTNLTYLILTGNQLQSLPNG----------  103 (272)
T ss_dssp             TTCCEEECTTSCCC-----CC-TTGGGCTTCCEEECTTSCCCCC-GGGTTCTTCCEEECTTSCCCCCCTT----------
T ss_pred             cceeeeeeCCCCcc-----cc-cccccCCCCcEEECCCCCCCCc-hhhcCCCCCCEEECCCCccCccChh----------
Confidence            45555555444332     11 3355667777777777776654 3566677777777777766655432          


Q ss_pred             cCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCC
Q 041097          231 QFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVL  309 (391)
Q Consensus       231 l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L  309 (391)
                                         .++.+++|++|++++..    +..+.| .++.+ ++|+.|++++|.+...+...++.+++|
T Consensus       104 -------------------~~~~l~~L~~L~L~~n~----l~~~~~~~~~~l-~~L~~L~L~~n~l~~~~~~~~~~l~~L  159 (272)
T 3rfs_A          104 -------------------VFDKLTNLKELVLVENQ----LQSLPDGVFDKL-TNLTYLNLAHNQLQSLPKGVFDKLTNL  159 (272)
T ss_dssp             -------------------TTTTCTTCCEEECTTSC----CCCCCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTC
T ss_pred             -------------------HhcCCcCCCEEECCCCc----CCccCHHHhccC-CCCCEEECCCCccCccCHHHhccCccC
Confidence                               24555555555555411    000011 24455 556666666655555444445555666


Q ss_pred             CEEEcCCCCCcCccccCCCcccccceeeeccccccccchH-hhcCCCCCCEEEeeCC
Q 041097          310 QVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWP  365 (391)
Q Consensus       310 ~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~  365 (391)
                      +.|+++.|...+......+.+++|++|++++|. ++.+|. .+..+++|++|+++++
T Consensus       160 ~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~N  215 (272)
T 3rfs_A          160 TELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQ-LKSVPDGVFDRLTSLQYIWLHDN  215 (272)
T ss_dssp             CEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEECCSS
T ss_pred             CEEECCCCCcCccCHHHhcCCccCCEEECCCCc-CCccCHHHHhCCcCCCEEEccCC
Confidence            666665444332111112445566666665552 444433 2455566666665543

>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=99.55  E-value=1.2e-14  Score=133.79  Aligned_cols=193  Identities=17%  Similarity=0.122  Sum_probs=129.8

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC---CcccCCCCcccEEEccCCCCCccCCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY---PSGIENLFLLRYLKLNIPSLKSLPSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~---p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----  222 (391)
                      +.++.|.+.++...    ......+.+++.|++|++++|.+...   |..+..+.+|++|+++++.+..+|..+.     
T Consensus        28 ~~l~~L~L~~n~l~----~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~l~~~~~~l~~L  103 (306)
T 2z66_A           28 SSATRLELESNKLQ----SLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQL  103 (306)
T ss_dssp             TTCCEEECCSSCCC----CCCTTTTTTCTTCSEEECCSSCCCEEEEEEHHHHSCSCCCEEECCSCSEEEEEEEEETCTTC
T ss_pred             CCCCEEECCCCccC----ccCHhHhhccccCCEEECCCCccCcccCcccccccccccCEEECCCCccccChhhcCCCCCC
Confidence            45666655544332    11112355666777777777666533   4455556677777777776666554432     


Q ss_pred             -EEEeeCCccCcceeeEEecccccchh--HHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCC-
Q 041097          223 -ILRLSGNSQFHFSLASLLLYYQSLLS--KSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMD-  297 (391)
Q Consensus       223 -~L~l~~~~l~~L~L~~L~l~~~~~lp--~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~-  297 (391)
                       +|++++|.+.             .++  ..+..+++|++|++++..    +....| .+..+ ++|+.|++++|.+.. 
T Consensus       104 ~~L~l~~n~l~-------------~~~~~~~~~~l~~L~~L~l~~n~----l~~~~~~~~~~l-~~L~~L~l~~n~l~~~  165 (306)
T 2z66_A          104 EHLDFQHSNLK-------------QMSEFSVFLSLRNLIYLDISHTH----TRVAFNGIFNGL-SSLEVLKMAGNSFQEN  165 (306)
T ss_dssp             CEEECTTSEEE-------------SSTTTTTTTTCTTCCEEECTTSC----CEECSTTTTTTC-TTCCEEECTTCEEGGG
T ss_pred             CEEECCCCccc-------------ccccchhhhhccCCCEEECCCCc----CCccchhhcccC-cCCCEEECCCCccccc
Confidence             4444444444             554  478899999999998722    011134 56788 999999999998765 


Q ss_pred             CChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          298 DPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       298 ~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      ..+..++.+++|++|+++.|......+...+.+++|++|++++|. +..+|. .+..+++|++|++++++
T Consensus       166 ~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~  234 (306)
T 2z66_A          166 FLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNN-FFSLDTFPYKCLNSLQVLDYSLNH  234 (306)
T ss_dssp             EECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSC-CSBCCSGGGTTCTTCCEEECTTSC
T ss_pred             cchhHHhhCcCCCEEECCCCCcCCcCHHHhcCCCCCCEEECCCCc-cCccChhhccCcccCCEeECCCCC
Confidence            234678899999999999776654333334688999999999884 666654 67889999999999876

>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=99.55  E-value=1e-14  Score=137.22  Aligned_cols=207  Identities=17%  Similarity=0.085  Sum_probs=128.0

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCC-Cc------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSS-RK------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------  222 (391)
                      +.++.|.+.++...    ......+.+++.|++|++++|.+..+ |..++++.+|++|++++|.+..+|.. ++      
T Consensus        52 ~~L~~L~l~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~  127 (353)
T 2z80_A           52 EAVKSLDLSNNRIT----YISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLT  127 (353)
T ss_dssp             TTCCEEECTTSCCC----EECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSSCCHHHHTTCTTCS
T ss_pred             ccCcEEECCCCcCc----ccCHHHhccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCCcCCcCCHhHhCCCccCC
Confidence            67888877655442    12223578889999999999998855 46788999999999999999888765 22      


Q ss_pred             EEEeeCCccCcc----------eeeEEeccc---ccch-hHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccE
Q 041097          223 ILRLSGNSQFHF----------SLASLLLYY---QSLL-SKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTH  287 (391)
Q Consensus       223 ~L~l~~~~l~~L----------~L~~L~l~~---~~~l-p~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~  287 (391)
                      +|++++|.+..+          +|+.|+++.   ...+ |..++++++|++|++++..    +....| .+..+ ++|+.
T Consensus       128 ~L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~----l~~~~~~~l~~l-~~L~~  202 (353)
T 2z80_A          128 FLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASD----LQSYEPKSLKSI-QNVSH  202 (353)
T ss_dssp             EEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETT----CCEECTTTTTTC-SEEEE
T ss_pred             EEECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCCCC----cCccCHHHHhcc-ccCCe
Confidence            888888866522          455555551   2222 2345555555555555411    000024 55666 67777


Q ss_pred             EEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC---CCcccccceeeecccc----ccccchHhhcCCCCCCEE
Q 041097          288 LSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG---IRAMPKLECLIINPYA----HLKRIHEQLWCLKSLNKL  360 (391)
Q Consensus       288 L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~---~~~~~~L~~L~l~~c~----~l~~lp~~~~~l~~L~~L  360 (391)
                      |++++|.+...+...++.+++|+.|+++.|...+.....   ....+.++.++++++.    .+..+|.++..+++|++|
T Consensus       203 L~l~~n~l~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~~~~~~l~~l~L~~~~l~~~~l~~l~~~l~~l~~L~~L  282 (353)
T 2z80_A          203 LILHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDESLFQVMKLLNQISGLLEL  282 (353)
T ss_dssp             EEEECSCSTTHHHHHHHHTTTEEEEEEESCBCTTCCCC------CCCCCCEEEEESCBCCHHHHHHHHHHHHTCTTCCEE
T ss_pred             ecCCCCccccchhhhhhhcccccEEECCCCccccccccccccccccchhhccccccccccCcchhhhHHHHhcccCCCEE
Confidence            777776665444334455677777777755544321111   1123344455554432    234578889999999999


Q ss_pred             EeeCCc
Q 041097          361 ELWWPE  366 (391)
Q Consensus       361 ~l~~~~  366 (391)
                      +++++.
T Consensus       283 ~Ls~N~  288 (353)
T 2z80_A          283 EFSRNQ  288 (353)
T ss_dssp             ECCSSC
T ss_pred             ECCCCC
Confidence            999875

>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=99.54  E-value=5.7e-14  Score=136.66  Aligned_cols=180  Identities=22%  Similarity=0.191  Sum_probs=140.2

Q ss_pred             CcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcc---------eeeEEec
Q 041097          179 KFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHF---------SLASLLL  241 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L---------~L~~L~l  241 (391)
                      +.+++|++++|.+..+ |..++++.+|++|++++|.+..++.. +.      +|++++|.+..+         +|+.|++
T Consensus        75 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L  154 (452)
T 3zyi_A           75 SNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRELWL  154 (452)
T ss_dssp             TTCSEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSBCCTTTSSSCTTCCEEEC
T ss_pred             CCccEEECcCCcCceECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCCcCCccChhhhcccCCCCEEEC
Confidence            5899999999999855 67899999999999999999987643 33      999999987754         7888888


Q ss_pred             c--cccchhH-HhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCC
Q 041097          242 Y--YQSLLSK-SLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQ  316 (391)
Q Consensus       242 ~--~~~~lp~-~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~  316 (391)
                      +  ....+|. .+.++++|++|++.+.+.   +.. +|  .+..+ ++|+.|++++|.+...  +.+..+++|+.|+++.
T Consensus       155 ~~N~l~~~~~~~~~~l~~L~~L~l~~~~~---l~~-i~~~~~~~l-~~L~~L~L~~n~l~~~--~~~~~l~~L~~L~Ls~  227 (452)
T 3zyi_A          155 RNNPIESIPSYAFNRVPSLMRLDLGELKK---LEY-ISEGAFEGL-FNLKYLNLGMCNIKDM--PNLTPLVGLEELEMSG  227 (452)
T ss_dssp             CSCCCCEECTTTTTTCTTCCEEECCCCTT---CCE-ECTTTTTTC-TTCCEEECTTSCCSSC--CCCTTCTTCCEEECTT
T ss_pred             CCCCcceeCHhHHhcCCcccEEeCCCCCC---ccc-cChhhccCC-CCCCEEECCCCccccc--ccccccccccEEECcC
Confidence            8  4555554 677888888888876110   010 33  56778 9999999999988764  4688899999999997


Q ss_pred             CCCcCccccCCCcccccceeeeccccccccc-hHhhcCCCCCCEEEeeCCc
Q 041097          317 NLYSEERTMGIRAMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       317 ~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~~~  366 (391)
                      |...+..+.....+++|+.|++++|. +..+ |..+..+++|++|+++++.
T Consensus       228 N~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~N~  277 (452)
T 3zyi_A          228 NHFPEIRPGSFHGLSSLKKLWVMNSQ-VSLIERNAFDGLASLVELNLAHNN  277 (452)
T ss_dssp             SCCSEECGGGGTTCTTCCEEECTTSC-CCEECTTTTTTCTTCCEEECCSSC
T ss_pred             CcCcccCcccccCccCCCEEEeCCCc-CceECHHHhcCCCCCCEEECCCCc
Confidence            76655433344788999999999885 5555 5678899999999998864

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.54  E-value=2.4e-14  Score=140.52  Aligned_cols=178  Identities=19%  Similarity=0.116  Sum_probs=142.8

Q ss_pred             CCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcc----eeeEEecc--cc
Q 041097          178 FKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHF----SLASLLLY--YQ  244 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L----~L~~L~l~--~~  244 (391)
                      ++.|+.|++++|.+..++ ..++.+.+|++|++++|.+...++ ++      +|++++|.+..+    +|+.|+++  ..
T Consensus        33 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~l~~l~~~~~L~~L~L~~N~l  111 (487)
T 3oja_A           33 AWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLRTLDLNNNYVQELLVGPSIETLHAANNNI  111 (487)
T ss_dssp             GGGCCEEECCSSCCCCCCGGGGTTCTTCCEEECTTSCCEEEEE-CTTCTTCCEEECCSSEEEEEEECTTCCEEECCSSCC
T ss_pred             CCCccEEEeeCCcCCCCCHHHHhCCCCCCEEEeeCCCCCCCcc-cccCCCCCEEEecCCcCCCCCCCCCcCEEECcCCcC
Confidence            348999999999999665 689999999999999999886554 43      999999988776    78889888  34


Q ss_pred             cchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhc-CCCCCCEEEcCCCCCcCc
Q 041097          245 SLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALE-KLSVLQVLKLKQNLYSEE  322 (391)
Q Consensus       245 ~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~-~l~~L~~L~l~~~~~~~~  322 (391)
                      ..++.  ..+++|++|++++..    +..+.| .++.+ ++|+.|++++|.+...++..+. .+++|+.|+++.|...+.
T Consensus       112 ~~~~~--~~l~~L~~L~L~~N~----l~~~~~~~~~~l-~~L~~L~Ls~N~l~~~~~~~l~~~l~~L~~L~Ls~N~l~~~  184 (487)
T 3oja_A          112 SRVSC--SRGQGKKNIYLANNK----ITMLRDLDEGCR-SRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDV  184 (487)
T ss_dssp             CCEEE--CCCSSCEEEECCSSC----CCSGGGBCGGGG-SSEEEEECTTSCCCEEEGGGGGGGTTTCCEEECTTSCCCEE
T ss_pred             CCCCc--cccCCCCEEECCCCC----CCCCCchhhcCC-CCCCEEECCCCCCCCcChHHHhhhCCcccEEecCCCccccc
Confidence            44443  356889999998722    111145 67888 9999999999998876666665 799999999997776543


Q ss_pred             cccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          323 RTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       323 ~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                        .....+++|+.|++++| .++.+|..+..+++|+.|+++++.
T Consensus       185 --~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~l~~L~~L~Ls~N~  225 (487)
T 3oja_A          185 --KGQVVFAKLKTLDLSSN-KLAFMGPEFQSAAGVTWISLRNNK  225 (487)
T ss_dssp             --ECCCCCTTCCEEECCSS-CCCEECGGGGGGTTCSEEECTTSC
T ss_pred             --cccccCCCCCEEECCCC-CCCCCCHhHcCCCCccEEEecCCc
Confidence              34456899999999988 588998889999999999999875

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.54  E-value=1.4e-14  Score=134.23  Aligned_cols=185  Identities=18%  Similarity=0.111  Sum_probs=145.5

Q ss_pred             hHHhhccCCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcc----eeeEE
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHF----SLASL  239 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L----~L~~L  239 (391)
                      +...+..++.|+.|++++|.+..++ ..++.+.+|++|++++|.+..+++ +.      +|++++|.+..+    +|+.|
T Consensus        26 ~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~-~~~l~~L~~L~Ls~n~l~~l~~~~~L~~L  104 (317)
T 3o53_A           26 LASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLRTLDLNNNYVQELLVGPSIETL  104 (317)
T ss_dssp             HHHHHTTGGGCSEEECTTSCCCCCCHHHHTTCTTCCEEECTTSCCEEEEE-ETTCTTCCEEECCSSEEEEEEECTTCCEE
T ss_pred             HHHHhccCCCCCEEECcCCccCcCCHHHhhCCCcCCEEECCCCcCCcchh-hhhcCCCCEEECcCCccccccCCCCcCEE
Confidence            3355666789999999999999666 689999999999999999886554 33      999999988876    78888


Q ss_pred             ecc--cccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhh-cCCCCCCEEEcC
Q 041097          240 LLY--YQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPAL-EKLSVLQVLKLK  315 (391)
Q Consensus       240 ~l~--~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l-~~l~~L~~L~l~  315 (391)
                      +++  ....++.  ..+++|++|++++..    +..+.| .++.+ ++|+.|++++|.+...++..+ +.+++|++|+++
T Consensus       105 ~l~~n~l~~~~~--~~~~~L~~L~l~~N~----l~~~~~~~~~~l-~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~  177 (317)
T 3o53_A          105 HAANNNISRVSC--SRGQGKKNIYLANNK----ITMLRDLDEGCR-SRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQ  177 (317)
T ss_dssp             ECCSSCCSEEEE--CCCSSCEEEECCSSC----CCSGGGBCTGGG-SSEEEEECTTSCCCEEEGGGGGGGTTTCCEEECT
T ss_pred             ECCCCccCCcCc--cccCCCCEEECCCCC----CCCccchhhhcc-CCCCEEECCCCCCCcccHHHHhhccCcCCEEECC
Confidence            888  3444443  347889999998722    111134 67778 999999999999887665555 578999999999


Q ss_pred             CCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          316 QNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       316 ~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .|.....  .....+++|++|++++| .++.+|..+..+++|++|+++++.
T Consensus       178 ~N~l~~~--~~~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~~L~~L~L~~N~  225 (317)
T 3o53_A          178 YNFIYDV--KGQVVFAKLKTLDLSSN-KLAFMGPEFQSAAGVTWISLRNNK  225 (317)
T ss_dssp             TSCCCEE--ECCCCCTTCCEEECCSS-CCCEECGGGGGGTTCSEEECTTSC
T ss_pred             CCcCccc--ccccccccCCEEECCCC-cCCcchhhhcccCcccEEECcCCc
Confidence            7765542  33446899999999988 588998889999999999999876

>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=99.54  E-value=1e-13  Score=138.57  Aligned_cols=37  Identities=22%  Similarity=0.161  Sum_probs=23.8

Q ss_pred             cccccceeeeccccccccchHh-hcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l~~~~  366 (391)
                      .+++|++|++++| .++.+|.. +..+++|++|+++++|
T Consensus       471 ~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~L~l~~N~  508 (562)
T 3a79_B          471 HLQALQELNVASN-QLKSVPDGVFDRLTSLQYIWLHDNP  508 (562)
T ss_dssp             SSCCCSEEECCSS-CCCCCCTTSTTTCTTCCCEECCSCC
T ss_pred             CCCCCCEEECCCC-CCCCCCHHHHhcCCCCCEEEecCCC
Confidence            4556666666665 35666665 6667777777776643

>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=99.53  E-value=1.9e-13  Score=122.15  Aligned_cols=166  Identities=21%  Similarity=0.226  Sum_probs=114.7

Q ss_pred             cccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcceeeEEecccccchhHHhc
Q 041097          180 FLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHFSLASLLLYYQSLLSKSLC  252 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~  252 (391)
                      ..+.++++++.+..+|..+.  .++++|+++++.+..++.. +.      +|++++|.+.            ...|..+.
T Consensus        15 ~~~~l~~~~~~l~~~p~~~~--~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~------------~~~~~~~~   80 (251)
T 3m19_A           15 GKKEVDCQGKSLDSVPSGIP--ADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQ------------TLSAGVFD   80 (251)
T ss_dssp             GGTEEECTTCCCSSCCSCCC--TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCC------------CCCTTTTT
T ss_pred             CCeEEecCCCCccccCCCCC--CCCCEEEccCCCcCccCHhHhcCcccCCEEECCCCcCC------------ccCHhHhc
Confidence            45566777777766666655  3667777777766655442 22      5566655555            12244578


Q ss_pred             CCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcc
Q 041097          253 RLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAM  330 (391)
Q Consensus       253 ~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~  330 (391)
                      .+++|++|++++..    +.. +|  .+..+ ++|+.|++++|.+...+...++.+++|+.|+++.|..........+.+
T Consensus        81 ~l~~L~~L~L~~n~----l~~-~~~~~~~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l  154 (251)
T 3m19_A           81 DLTELGTLGLANNQ----LAS-LPLGVFDHL-TQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKL  154 (251)
T ss_dssp             TCTTCCEEECTTSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTC
T ss_pred             cCCcCCEEECCCCc----ccc-cChhHhccc-CCCCEEEcCCCcCCCcChhHhccCCcccEEECcCCcCCccCHHHcCcC
Confidence            88999999988722    011 23  56778 899999999998887776667889999999998666554222234678


Q ss_pred             cccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          331 PKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       331 ~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      ++|++|+++++ .++.+|. .+..+++|++|++++++
T Consensus       155 ~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~  190 (251)
T 3m19_A          155 TNLQTLSLSTN-QLQSVPHGAFDRLGKLQTITLFGNQ  190 (251)
T ss_dssp             TTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSCC
T ss_pred             cCCCEEECCCC-cCCccCHHHHhCCCCCCEEEeeCCc
Confidence            89999999987 4677764 67888999999998755

>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=99.53  E-value=1.7e-13  Score=127.58  Aligned_cols=179  Identities=18%  Similarity=0.152  Sum_probs=141.6

Q ss_pred             CcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCcc-CCCCc------EEEeeCCccCcc------eeeEEecc--
Q 041097          179 KFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKSL-PSSRK------ILRLSGNSQFHF------SLASLLLY--  242 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~l-p~~~~------~L~l~~~~l~~L------~L~~L~l~--  242 (391)
                      +.+++|+++++.+..++. .++++.+|++|+++++.+..+ |..+.      +|++++|.+..+      +|+.|+++  
T Consensus        52 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~~~L~~L~l~~n  131 (330)
T 1xku_A           52 PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHEN  131 (330)
T ss_dssp             TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEEECCSS
T ss_pred             CCCeEEECCCCcCCEeChhhhccCCCCCEEECCCCcCCeeCHHHhcCCCCCCEEECCCCcCCccChhhcccccEEECCCC
Confidence            689999999999997765 789999999999999999987 66665      999999988876      79999999  


Q ss_pred             cccchh-HHhcCCCCCCEEEecCCCCCCchhh--hcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCC
Q 041097          243 YQSLLS-KSLCRLSCLESLKLANESKMPRRSN--IIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNL  318 (391)
Q Consensus       243 ~~~~lp-~~i~~l~~L~~L~l~~~~~lp~L~~--Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  318 (391)
                      ....++ ..++++++|++|++++..    +..  ..| .+..+ ++|+.|++++|.+...+. .+  .++|+.|+++.|.
T Consensus       132 ~l~~~~~~~~~~l~~L~~L~l~~n~----l~~~~~~~~~~~~l-~~L~~L~l~~n~l~~l~~-~~--~~~L~~L~l~~n~  203 (330)
T 1xku_A          132 EITKVRKSVFNGLNQMIVVELGTNP----LKSSGIENGAFQGM-KKLSYIRIADTNITTIPQ-GL--PPSLTELHLDGNK  203 (330)
T ss_dssp             CCCBBCHHHHTTCTTCCEEECCSSC----CCGGGBCTTGGGGC-TTCCEEECCSSCCCSCCS-SC--CTTCSEEECTTSC
T ss_pred             cccccCHhHhcCCccccEEECCCCc----CCccCcChhhccCC-CCcCEEECCCCccccCCc-cc--cccCCEEECCCCc
Confidence            344444 568999999999998722    000  034 67788 999999999998876552 22  2899999999776


Q ss_pred             CcCccccCCCcccccceeeeccccccccch-HhhcCCCCCCEEEeeCCc
Q 041097          319 YSEERTMGIRAMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       319 ~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~~~  366 (391)
                      .....+...+.+++|++|++++|. ++.++ .++..+++|++|+++++.
T Consensus       204 l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~N~  251 (330)
T 1xku_A          204 ITKVDAASLKGLNNLAKLGLSFNS-ISAVDNGSLANTPHLRELHLNNNK  251 (330)
T ss_dssp             CCEECTGGGTTCTTCCEEECCSSC-CCEECTTTGGGSTTCCEEECCSSC
T ss_pred             CCccCHHHhcCCCCCCEEECCCCc-CceeChhhccCCCCCCEEECCCCc
Confidence            654333334688999999999885 66665 478899999999999875

>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=99.53  E-value=1.1e-13  Score=139.75  Aligned_cols=99  Identities=22%  Similarity=0.234  Sum_probs=74.2

Q ss_pred             cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccc-hHhhc
Q 041097          275 IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRI-HEQLW  352 (391)
Q Consensus       275 lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l-p~~~~  352 (391)
                      .| .+..+ ++|+.|+|++|.+...++..++.+++|+.|+++.|...+......+.+++|++|+++++. ++.+ |..+.
T Consensus       486 ~~~~~~~l-~~L~~L~Ls~N~L~~l~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~l~  563 (635)
T 4g8a_A          486 LPDIFTEL-RNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNH-IMTSKKQELQ  563 (635)
T ss_dssp             ECSCCTTC-TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCBCCCGGGTTCTTCCEEECTTSC-CCBCCSSCTT
T ss_pred             Cchhhhhc-cccCEEECCCCccCCcChHHHcCCCCCCEEECCCCcCCCCChhHHhCCCCCCEEECCCCc-CCCCCHHHHH
Confidence            44 56677 889999999988887777788999999999999776655433334678899999999884 6665 56677


Q ss_pred             CC-CCCCEEEeeCCc------H-HHHHHhhh
Q 041097          353 CL-KSLNKLELWWPE------P-ELRQQLRE  375 (391)
Q Consensus       353 ~l-~~L~~L~l~~~~------~-~l~~~~~~  375 (391)
                      .+ ++|++|+++++|      - .|.+|++.
T Consensus       564 ~l~~~L~~L~L~~Np~~C~C~~~~~~~wl~~  594 (635)
T 4g8a_A          564 HFPSSLAFLNLTQNDFACTCEHQSFLQWIKD  594 (635)
T ss_dssp             CCCTTCCEEECTTCCBCCSGGGHHHHHHHHH
T ss_pred             hhhCcCCEEEeeCCCCcccCCcHHHHHHHHh
Confidence            77 689999998633      2 24566654

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.53  E-value=2e-13  Score=143.02  Aligned_cols=234  Identities=21%  Similarity=0.190  Sum_probs=133.6

Q ss_pred             cCceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcc
Q 041097          128 RENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLL  204 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L  204 (391)
                      +..++.|.+..+.......... + ++++.|.+..+...   ....+..+..+++|++|++++|.+..+ |..++++.+|
T Consensus        23 p~~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdLs~n~~~---~~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L   99 (844)
T 3j0a_A           23 LNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTP---LTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHL   99 (844)
T ss_dssp             CTTCCEEEEESCCCCEECSSSCSSCCSCSEEEECTTCCC---CEECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSC
T ss_pred             CCCcCEEECCCCcCCccChhHCcccccCeEEeCCCCCCc---cccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCccc
Confidence            4567777776333333222233 3 67777766554221   112235566777777777777776633 6677777777


Q ss_pred             cEEEccCCCCCc-cCCC--Cc------EEEeeCCccCcc----------eeeEEecc--cc-cchhH-------------
Q 041097          205 RYLKLNIPSLKS-LPSS--RK------ILRLSGNSQFHF----------SLASLLLY--YQ-SLLSK-------------  249 (391)
Q Consensus       205 ~~L~l~~~~i~~-lp~~--~~------~L~l~~~~l~~L----------~L~~L~l~--~~-~~lp~-------------  249 (391)
                      ++|++++|.+.. +|..  ++      +||+++|.+..+          +|+.|+++  .. ...|.             
T Consensus       100 ~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~~~l~~l~~~~L~~L  179 (844)
T 3j0a_A          100 FELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFF  179 (844)
T ss_dssp             CCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCCCCCCSGGGHHHHHCSSCCC
T ss_pred             CEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcCCeeCHHHcccccCCccceE
Confidence            777777776654 3433  22      677776655432          56666655  11 01111             


Q ss_pred             -------------HhcCCCC------CCEEEecCCC---CC---------------------------------------
Q 041097          250 -------------SLCRLSC------LESLKLANES---KM---------------------------------------  268 (391)
Q Consensus       250 -------------~i~~l~~------L~~L~l~~~~---~l---------------------------------------  268 (391)
                                   .++.+++      |+.|++++..   ..                                       
T Consensus       180 ~L~~n~l~~~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~~l~~~~l~~L~l~~~~~~~~~~~~~l~~~~~~~  259 (844)
T 3j0a_A          180 SLAANSLYSRVSVDWGKCMNPFRNMVLEILDVSGNGWTVDITGNFSNAISKSQAFSLILAHHIMGAGFGFHNIKDPDQNT  259 (844)
T ss_dssp             EECCSBSCCCCCCCCCSSSCTTTTCCBSEEBCSSCCSSTTTTSGGGGTSCSCCBSEEECCSSCCBCSSSCSSSTTGGGTT
T ss_pred             ECCCCccccccccchhhcCCccccCceeEEecCCCcCchhHHHHHHhhcCcccccceecccccccccccccccCCCChhh
Confidence                         1222222      5555554310   00                                       


Q ss_pred             ------Cchhhh----------cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCccc
Q 041097          269 ------PRRSNI----------IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMP  331 (391)
Q Consensus       269 ------p~L~~L----------lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~  331 (391)
                            ++++.|          .| .+..+ ++|+.|++++|.+...+...++.+++|++|+++.|..........+.++
T Consensus       260 f~~l~~~~L~~L~Ls~n~l~~~~~~~~~~l-~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~  338 (844)
T 3j0a_A          260 FAGLARSSVRHLDLSHGFVFSLNSRVFETL-KDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSYNLLGELYSSNFYGLP  338 (844)
T ss_dssp             TTTTTTSCCCEEECTTCCCCEECSCCSSSC-CCCCEEEEESCCCCEECTTTTTTCSSCCEEEEESCCCSCCCSCSCSSCT
T ss_pred             hhccccCCccEEECCCCcccccChhhhhcC-CCCCEEECCCCcCCCCChHHhcCCCCCCEEECCCCCCCccCHHHhcCCC
Confidence                  111111          23 55667 7788888888777666556677788888888876655443333346777


Q ss_pred             ccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          332 KLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       332 ~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      +|++|++++| .+..+|. .+..+++|++|+++++.
T Consensus       339 ~L~~L~L~~N-~i~~~~~~~~~~l~~L~~L~Ls~N~  373 (844)
T 3j0a_A          339 KVAYIDLQKN-HIAIIQDQTFKFLEKLQTLDLRDNA  373 (844)
T ss_dssp             TCCEEECCSC-CCCCCCSSCSCSCCCCCEEEEETCC
T ss_pred             CCCEEECCCC-CCCccChhhhcCCCCCCEEECCCCC
Confidence            8888888877 4666653 46778888888887765

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.52  E-value=8.8e-14  Score=134.85  Aligned_cols=180  Identities=22%  Similarity=0.221  Sum_probs=140.2

Q ss_pred             CcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcc---------eeeEEec
Q 041097          179 KFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHF---------SLASLLL  241 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L---------~L~~L~l  241 (391)
                      ..+++|++++|.+..++ ..+.++.+|++|++++|.+..++.. +.      +|++++|++..+         +|+.|++
T Consensus        64 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L  143 (440)
T 3zyj_A           64 TNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELWL  143 (440)
T ss_dssp             TTCSEEECCSCCCCEECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCSSCCSSCCTTTSCSCSSCCEEEC
T ss_pred             CCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCCCcCCeeCHhHhhccccCceeeC
Confidence            67999999999999655 7899999999999999999887633 22      999999987755         7888888


Q ss_pred             c--cccchhH-HhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCC
Q 041097          242 Y--YQSLLSK-SLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQ  316 (391)
Q Consensus       242 ~--~~~~lp~-~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~  316 (391)
                      +  ....+|. .+.++++|++|++.+.+.+   .. +|  .+..+ ++|+.|++++|.+...  +.+..+++|+.|+++.
T Consensus       144 ~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l---~~-i~~~~~~~l-~~L~~L~L~~n~l~~~--~~~~~l~~L~~L~Ls~  216 (440)
T 3zyj_A          144 RNNPIESIPSYAFNRIPSLRRLDLGELKRL---SY-ISEGAFEGL-SNLRYLNLAMCNLREI--PNLTPLIKLDELDLSG  216 (440)
T ss_dssp             CSCCCCEECTTTTTTCTTCCEEECCCCTTC---CE-ECTTTTTTC-SSCCEEECTTSCCSSC--CCCTTCSSCCEEECTT
T ss_pred             CCCcccccCHHHhhhCcccCEeCCCCCCCc---ce-eCcchhhcc-cccCeecCCCCcCccc--cccCCCcccCEEECCC
Confidence            8  4555554 6788888888888761100   00 33  56778 9999999999988764  4688999999999997


Q ss_pred             CCCcCccccCCCcccccceeeeccccccccc-hHhhcCCCCCCEEEeeCCc
Q 041097          317 NLYSEERTMGIRAMPKLECLIINPYAHLKRI-HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       317 ~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l-p~~~~~l~~L~~L~l~~~~  366 (391)
                      |............+++|+.|+++++. ++.+ |..+..+++|++|+++++.
T Consensus       217 N~l~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~l~~L~~L~L~~N~  266 (440)
T 3zyj_A          217 NHLSAIRPGSFQGLMHLQKLWMIQSQ-IQVIERNAFDNLQSLVEINLAHNN  266 (440)
T ss_dssp             SCCCEECTTTTTTCTTCCEEECTTCC-CCEECTTSSTTCTTCCEEECTTSC
T ss_pred             CccCccChhhhccCccCCEEECCCCc-eeEEChhhhcCCCCCCEEECCCCC
Confidence            76654333344688999999999884 6666 4568899999999998864

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.52  E-value=2.8e-13  Score=122.46  Aligned_cols=166  Identities=25%  Similarity=0.218  Sum_probs=132.2

Q ss_pred             CcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcceeeEEecccccchhHH-
Q 041097          179 KFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHFSLASLLLYYQSLLSKS-  250 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~-  250 (391)
                      ...+.++++++.+..+|..+.  .++++|+++++.+..+|.. +.      +|++++|.+.             .+|.. 
T Consensus        16 ~~~~~l~~~~~~l~~ip~~~~--~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~-------------~i~~~~   80 (270)
T 2o6q_A           16 NNKNSVDCSSKKLTAIPSNIP--ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQ-------------TLPAGI   80 (270)
T ss_dssp             TTTTEEECTTSCCSSCCSCCC--TTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCCS-------------CCCTTT
T ss_pred             CCCCEEEccCCCCCccCCCCC--CCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCccC-------------eeChhh
Confidence            457899999999999998776  5899999999999988763 33      7777777776             77765 


Q ss_pred             hcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC
Q 041097          251 LCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR  328 (391)
Q Consensus       251 i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  328 (391)
                      +.++++|++|++++..    +.. +|  .+..+ ++|+.|++++|.+...+...++.+++|++|+++.|..........+
T Consensus        81 ~~~l~~L~~L~l~~n~----l~~-~~~~~~~~l-~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~  154 (270)
T 2o6q_A           81 FKELKNLETLWVTDNK----LQA-LPIGVFDQL-VNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFD  154 (270)
T ss_dssp             TSSCTTCCEEECCSSC----CCC-CCTTTTTTC-SSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT
T ss_pred             hcCCCCCCEEECCCCc----CCc-CCHhHcccc-cCCCEEECCCCccCeeCHHHhCcCcCCCEEECCCCcCCccCHhHcc
Confidence            5889999999998722    000 33  45778 9999999999999888877889999999999997765542222246


Q ss_pred             cccccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      .+++|++|++++| .++.+|. .+..+++|++|+++++.
T Consensus       155 ~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~N~  192 (270)
T 2o6q_A          155 KLTSLKELRLYNN-QLKRVPEGAFDKLTELKTLKLDNNQ  192 (270)
T ss_dssp             TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CCcccceeEecCC-cCcEeChhHhccCCCcCEEECCCCc
Confidence            7899999999988 4777775 47889999999998875

>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=99.51  E-value=1.6e-13  Score=136.67  Aligned_cols=90  Identities=19%  Similarity=0.143  Sum_probs=45.1

Q ss_pred             hccCCcccEEEcCCCccc--cCCcccCCCCcccEEEccCCC-CCccCC-CCc------EEEeeCCccCcc---------e
Q 041097          175 CKMFKFLRVLDLGSLVLI--RYPSGIENLFLLRYLKLNIPS-LKSLPS-SRK------ILRLSGNSQFHF---------S  235 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~--~~p~~i~~l~~L~~L~l~~~~-i~~lp~-~~~------~L~l~~~~l~~L---------~  235 (391)
                      +..++.|++|++++|.+.  ..|..++++.+|++|+++++. +..+|. .+.      .|++++|.+...         +
T Consensus        94 ~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~  173 (549)
T 2z81_A           94 FGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRD  173 (549)
T ss_dssp             HTTCTTCCEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCSE
T ss_pred             hccCCCCcEEECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCeeeccCCcccccChhhhhcccc
Confidence            444555555555555544  223444555555555555443 333432 222      455555444331         4


Q ss_pred             eeEEecc--cccchhHHh-cCCCCCCEEEecC
Q 041097          236 LASLLLY--YQSLLSKSL-CRLSCLESLKLAN  264 (391)
Q Consensus       236 L~~L~l~--~~~~lp~~i-~~l~~L~~L~l~~  264 (391)
                      |+.|++.  ....+|..+ +.+++|++|++++
T Consensus       174 L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~  205 (549)
T 2z81_A          174 IHHLTLHLSESAFLLEIFADILSSVRYLELRD  205 (549)
T ss_dssp             EEEEEEECSBSTTHHHHHHHSTTTBSEEEEES
T ss_pred             CceEecccCcccccchhhHhhcccccEEEccC
Confidence            5555555  333445433 5678888888876

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.51  E-value=4e-13  Score=130.76  Aligned_cols=125  Identities=15%  Similarity=0.053  Sum_probs=92.4

Q ss_pred             ccCceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCccc
Q 041097          127 LRENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLR  205 (391)
Q Consensus       127 ~~~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~  205 (391)
                      .....+.+.+..+.... + .... ++++.|.+..+....     .  .+..++.|++|++++|.+..+|  ++.+.+|+
T Consensus        62 ~l~~L~~L~Ls~n~l~~-~-~~~~l~~L~~L~Ls~N~l~~-----~--~~~~l~~L~~L~L~~N~l~~l~--~~~l~~L~  130 (457)
T 3bz5_A           62 KLTGLTKLICTSNNITT-L-DLSQNTNLTYLACDSNKLTN-----L--DVTPLTKLTYLNCDTNKLTKLD--VSQNPLLT  130 (457)
T ss_dssp             GCTTCSEEECCSSCCSC-C-CCTTCTTCSEEECCSSCCSC-----C--CCTTCTTCCEEECCSSCCSCCC--CTTCTTCC
T ss_pred             ccCCCCEEEccCCcCCe-E-ccccCCCCCEEECcCCCCce-----e--ecCCCCcCCEEECCCCcCCeec--CCCCCcCC
Confidence            45678888887333333 2 2234 889999887766541     2  2778999999999999998876  89999999


Q ss_pred             EEEccCCCCCccCCC----CcEEEeeCC-ccCcc------eeeEEecc--cccchhHHhcCCCCCCEEEecC
Q 041097          206 YLKLNIPSLKSLPSS----RKILRLSGN-SQFHF------SLASLLLY--YQSLLSKSLCRLSCLESLKLAN  264 (391)
Q Consensus       206 ~L~l~~~~i~~lp~~----~~~L~l~~~-~l~~L------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~  264 (391)
                      +|+++++.++.+|-.    +..|++++| .+..+      +|+.|+++  ....+|  ++.+++|+.|++++
T Consensus       131 ~L~l~~N~l~~l~l~~l~~L~~L~l~~n~~~~~~~~~~l~~L~~L~ls~n~l~~l~--l~~l~~L~~L~l~~  200 (457)
T 3bz5_A          131 YLNCARNTLTEIDVSHNTQLTELDCHLNKKITKLDVTPQTQLTTLDCSFNKITELD--VSQNKLLNRLNCDT  200 (457)
T ss_dssp             EEECTTSCCSCCCCTTCTTCCEEECTTCSCCCCCCCTTCTTCCEEECCSSCCCCCC--CTTCTTCCEEECCS
T ss_pred             EEECCCCccceeccccCCcCCEEECCCCCcccccccccCCcCCEEECCCCccceec--cccCCCCCEEECcC
Confidence            999999999887521    118899888 33332      78888888  455565  78888888888877

>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=99.50  E-value=9.5e-14  Score=139.41  Aligned_cols=161  Identities=28%  Similarity=0.299  Sum_probs=75.3

Q ss_pred             CCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchhHHh
Q 041097          178 FKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSKSL  251 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i  251 (391)
                      +..|+.|+++++.+..++ .++.+.+|++|+|++|.+..+|. +.      .|+|++|.+.             .+| .+
T Consensus        42 L~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~l~-------------~l~-~l  105 (605)
T 1m9s_A           42 LNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKLTDIKP-LTNLKNLGWLFLDENKIK-------------DLS-SL  105 (605)
T ss_dssp             HTTCCCCBCTTCCCCCCT-TGGGCTTCCEEECTTSCCCCCGG-GGGCTTCCEEECCSSCCC-------------CCT-TS
T ss_pred             CCCCCEEECcCCCCCCCh-HHccCCCCCEEEeeCCCCCCChh-hccCCCCCEEECcCCCCC-------------CCh-hh
Confidence            344444455544444433 34444455555555544444432 11      3333333333             222 35


Q ss_pred             cCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCccc
Q 041097          252 CRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMP  331 (391)
Q Consensus       252 ~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~  331 (391)
                      +.+++|++|++++..    +.. +|.+..+ ++|+.|+|++|.+...  +.++.+++|+.|+|+.|...+..+  ...++
T Consensus       106 ~~l~~L~~L~Ls~N~----l~~-l~~l~~l-~~L~~L~Ls~N~l~~l--~~l~~l~~L~~L~Ls~N~l~~~~~--l~~l~  175 (605)
T 1m9s_A          106 KDLKKLKSLSLEHNG----ISD-INGLVHL-PQLESLYLGNNKITDI--TVLSRLTKLDTLSLEDNQISDIVP--LAGLT  175 (605)
T ss_dssp             TTCTTCCEEECTTSC----CCC-CGGGGGC-TTCSEEECCSSCCCCC--GGGGSCTTCSEEECCSSCCCCCGG--GTTCT
T ss_pred             ccCCCCCEEEecCCC----CCC-CccccCC-CccCEEECCCCccCCc--hhhcccCCCCEEECcCCcCCCchh--hccCC
Confidence            555555555555411    000 2234445 5555555555554442  445555555555555444333211  34455


Q ss_pred             ccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          332 KLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       332 ~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +|+.|+|++| .+..+| .+..+++|+.|++++|+
T Consensus       176 ~L~~L~Ls~N-~i~~l~-~l~~l~~L~~L~L~~N~  208 (605)
T 1m9s_A          176 KLQNLYLSKN-HISDLR-ALAGLKNLDVLELFSQE  208 (605)
T ss_dssp             TCCEEECCSS-CCCBCG-GGTTCTTCSEEECCSEE
T ss_pred             CCCEEECcCC-CCCCCh-HHccCCCCCEEEccCCc
Confidence            5555555555 344444 35555555555555543

>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=99.50  E-value=2.9e-13  Score=133.92  Aligned_cols=108  Identities=19%  Similarity=0.157  Sum_probs=68.6

Q ss_pred             CceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRY  206 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~  206 (391)
                      .+++.+.+..+.......... + ++++.|.+.++...    ...+..+..++.|++|++++|.+..+|..  .+.+|++
T Consensus        21 ~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~   94 (520)
T 2z7x_B           21 QKTTILNISQNYISELWTSDILSLSKLRILIISHNRIQ----YLDISVFKFNQELEYLDLSHNKLVKISCH--PTVNLKH   94 (520)
T ss_dssp             TTCSEEECCSSCCCCCCHHHHTTCTTCCEEECCSSCCC----EEEGGGGTTCTTCCEEECCSSCCCEEECC--CCCCCSE
T ss_pred             ccccEEECCCCcccccChhhccccccccEEecCCCccC----CcChHHhhcccCCCEEecCCCceeecCcc--ccCCccE
Confidence            567777776333332111222 3 67777777655432    12345677788888888888888777766  7788888


Q ss_pred             EEccCCCCCc--cCCCCc------EEEeeCCccCcc------ee--eEEecc
Q 041097          207 LKLNIPSLKS--LPSSRK------ILRLSGNSQFHF------SL--ASLLLY  242 (391)
Q Consensus       207 L~l~~~~i~~--lp~~~~------~L~l~~~~l~~L------~L--~~L~l~  242 (391)
                      |++++|.+..  +|..++      +|++++|.+...      +|  +.|+++
T Consensus        95 L~L~~N~l~~~~~p~~~~~l~~L~~L~L~~n~l~~~~~~~l~~L~L~~L~l~  146 (520)
T 2z7x_B           95 LDLSFNAFDALPICKEFGNMSQLKFLGLSTTHLEKSSVLPIAHLNISKVLLV  146 (520)
T ss_dssp             EECCSSCCSSCCCCGGGGGCTTCCEEEEEESSCCGGGGGGGTTSCEEEEEEE
T ss_pred             EeccCCccccccchhhhccCCcceEEEecCcccchhhccccccceeeEEEee
Confidence            8888888775  455555      788887765432      33  777666

>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=99.49  E-value=5e-13  Score=133.62  Aligned_cols=108  Identities=19%  Similarity=0.132  Sum_probs=72.6

Q ss_pred             CceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRY  206 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~  206 (391)
                      .+++.+.+..+.......... + ++++.|.+.++...    ...+..+..++.|++|++++|.+..+|..  .+.+|++
T Consensus        52 ~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~----~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~  125 (562)
T 3a79_B           52 PRTKALSLSQNSISELRMPDISFLSELRVLRLSHNRIR----SLDFHVFLFNQDLEYLDVSHNRLQNISCC--PMASLRH  125 (562)
T ss_dssp             TTCCEEECCSSCCCCCCGGGTTTCTTCCEEECCSCCCC----EECTTTTTTCTTCCEEECTTSCCCEECSC--CCTTCSE
T ss_pred             CCcCEEECCCCCccccChhhhccCCCccEEECCCCCCC----cCCHHHhCCCCCCCEEECCCCcCCccCcc--ccccCCE
Confidence            567777777333333122233 3 77888777665442    12235577788888888888888888776  7888888


Q ss_pred             EEccCCCCCccC--CCCc------EEEeeCCccCcc--------eeeEEecc
Q 041097          207 LKLNIPSLKSLP--SSRK------ILRLSGNSQFHF--------SLASLLLY  242 (391)
Q Consensus       207 L~l~~~~i~~lp--~~~~------~L~l~~~~l~~L--------~L~~L~l~  242 (391)
                      |++++|.+..+|  ..++      +|++++|.+...        +|+.|+++
T Consensus       126 L~Ls~N~l~~l~~p~~~~~l~~L~~L~L~~n~l~~~~~~~l~~L~L~~L~L~  177 (562)
T 3a79_B          126 LDLSFNDFDVLPVCKEFGNLTKLTFLGLSAAKFRQLDLLPVAHLHLSCILLD  177 (562)
T ss_dssp             EECCSSCCSBCCCCGGGGGCTTCCEEEEECSBCCTTTTGGGTTSCEEEEEEE
T ss_pred             EECCCCCccccCchHhhcccCcccEEecCCCccccCchhhhhhceeeEEEee
Confidence            888888887765  4444      888888866532        44888877

>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=99.49  E-value=1.1e-13  Score=139.47  Aligned_cols=206  Identities=18%  Similarity=0.157  Sum_probs=119.7

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCC-CCccC----CCCcEEE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPS-LKSLP----SSRKILR  225 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~-i~~lp----~~~~~L~  225 (391)
                      +.++.+.+.+....     .++ .+..++.|+.|++++|.+..+| .+ .+.+|++|+++++. +...+    +.+..|+
T Consensus       285 ~~L~~L~l~~~~~~-----~l~-~l~~~~~L~~L~l~~n~l~~lp-~~-~l~~L~~L~l~~n~~~~~~~~~~l~~L~~L~  356 (606)
T 3vq2_A          285 ANVSAMSLAGVSIK-----YLE-DVPKHFKWQSLSIIRCQLKQFP-TL-DLPFLKSLTLTMNKGSISFKKVALPSLSYLD  356 (606)
T ss_dssp             TTCSEEEEESCCCC-----CCC-CCCTTCCCSEEEEESCCCSSCC-CC-CCSSCCEEEEESCSSCEECCCCCCTTCCEEE
T ss_pred             CCCCEEEecCccch-----hhh-hccccccCCEEEcccccCcccc-cC-CCCccceeeccCCcCccchhhccCCCCCEEE
Confidence            56666666554433     121 4455556666666666665555 33 55566666665552 21111    0111555


Q ss_pred             eeCCccCcc-----------eeeEEecc--cccchhHHhcCCCCCCEEEecCCC-----------CCCchhhh-------
Q 041097          226 LSGNSQFHF-----------SLASLLLY--YQSLLSKSLCRLSCLESLKLANES-----------KMPRRSNI-------  274 (391)
Q Consensus       226 l~~~~l~~L-----------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~-----------~lp~L~~L-------  274 (391)
                      +++|.+..+           +|+.|+++  ....+|..++.+++|++|++++..           .++.|+.|       
T Consensus       357 ls~n~l~~~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l  436 (606)
T 3vq2_A          357 LSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNT  436 (606)
T ss_dssp             CCSSCEEEEEECCHHHHCCSCCCEEECCSCSEEEECCCCTTCTTCCEEECTTSEEESTTTTTTTTTCTTCCEEECTTSCC
T ss_pred             CcCCccCCCcchhhhhccCCcccEeECCCCccccchhhccCCCCCCeeECCCCccCCccChhhhhccccCCEEECcCCCC
Confidence            555543321           45555555  233444455555555555555410           01112111       


Q ss_pred             ---cc-ccccCCCCccEEEeecccCCCC-ChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccc-h
Q 041097          275 ---IL-AEYQFPPSLTHLSFSNIELMDD-PIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRI-H  348 (391)
Q Consensus       275 ---lp-~~~~l~~~L~~L~l~~~~~~~~-~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l-p  348 (391)
                         .| .++.+ ++|+.|++++|.+... .+..++.+++|+.|+++.|...+..+...+.+++|++|++++|. +..+ |
T Consensus       437 ~~~~~~~~~~l-~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~  514 (606)
T 3vq2_A          437 KIDFDGIFLGL-TSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNN-LLFLDS  514 (606)
T ss_dssp             EECCTTTTTTC-TTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSC-CSCEEG
T ss_pred             CccchhhhcCC-CCCCEEECCCCcCCCcchHHhhccCCCCCEEECCCCcCCccChhhhcccccCCEEECCCCc-CCCcCH
Confidence               44 56777 8888888888876652 34567788888888888665544333334678889999999884 5554 7


Q ss_pred             HhhcCCCCCCEEEeeCCc
Q 041097          349 EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       349 ~~~~~l~~L~~L~l~~~~  366 (391)
                      .++..+++|++|+++++.
T Consensus       515 ~~~~~l~~L~~L~l~~N~  532 (606)
T 3vq2_A          515 SHYNQLYSLSTLDCSFNR  532 (606)
T ss_dssp             GGTTTCTTCCEEECTTSC
T ss_pred             HHccCCCcCCEEECCCCc
Confidence            888889999999988775

>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=99.49  E-value=1.5e-13  Score=118.14  Aligned_cols=151  Identities=19%  Similarity=0.227  Sum_probs=117.5

Q ss_pred             ccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCC
Q 041097          176 KMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLS  255 (391)
Q Consensus       176 ~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~  255 (391)
                      .+++.|+.|+++++.+..+| .+..+.+|++|+++++.+..+                               +.++.++
T Consensus        41 ~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l~~n~~~~~-------------------------------~~l~~l~   88 (197)
T 4ezg_A           41 AQMNSLTYITLANINVTDLT-GIEYAHNIKDLTINNIHATNY-------------------------------NPISGLS   88 (197)
T ss_dssp             HHHHTCCEEEEESSCCSCCT-TGGGCTTCSEEEEESCCCSCC-------------------------------GGGTTCT
T ss_pred             hhcCCccEEeccCCCccChH-HHhcCCCCCEEEccCCCCCcc-------------------------------hhhhcCC
Confidence            45667888899888888777 688888888888888755432                               3577889


Q ss_pred             CCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccc
Q 041097          256 CLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLE  334 (391)
Q Consensus       256 ~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~  334 (391)
                      +|++|++++..    +....| .++.+ ++|+.|++++|.+....+..++.+++|+.|+++.|..... ....+.+++|+
T Consensus        89 ~L~~L~l~~n~----l~~~~~~~l~~l-~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~-~~~l~~l~~L~  162 (197)
T 4ezg_A           89 NLERLRIMGKD----VTSDKIPNLSGL-TSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITD-IMPLKTLPELK  162 (197)
T ss_dssp             TCCEEEEECTT----CBGGGSCCCTTC-TTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCC-CGGGGGCSSCC
T ss_pred             CCCEEEeECCc----cCcccChhhcCC-CCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccc-cHhhcCCCCCC
Confidence            99999998722    111134 77788 9999999999998876678899999999999996652332 23457889999


Q ss_pred             eeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          335 CLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       335 ~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +|++++| .++.++ .+..+++|++|++++++
T Consensus       163 ~L~l~~n-~i~~~~-~l~~l~~L~~L~l~~N~  192 (197)
T 4ezg_A          163 SLNIQFD-GVHDYR-GIEDFPKLNQLYAFSQT  192 (197)
T ss_dssp             EEECTTB-CCCCCT-TGGGCSSCCEEEECBC-
T ss_pred             EEECCCC-CCcChH-HhccCCCCCEEEeeCcc
Confidence            9999988 478887 78899999999999876

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.49  E-value=3.9e-13  Score=121.68  Aligned_cols=197  Identities=19%  Similarity=0.148  Sum_probs=144.7

Q ss_pred             ccCceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcc-cCCCCcc
Q 041097          127 LRENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSG-IENLFLL  204 (391)
Q Consensus       127 ~~~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~-i~~l~~L  204 (391)
                      ....++.+.+....... +..... +.++.|.+.++...     .+ +.+..++.|++|++++|.+..++.. ++++.+|
T Consensus        39 ~l~~L~~L~l~~~~i~~-~~~l~~l~~L~~L~l~~n~l~-----~~-~~l~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L  111 (272)
T 3rfs_A           39 ELNSIDQIIANNSDIKS-VQGIQYLPNVRYLALGGNKLH-----DI-SALKELTNLTYLILTGNQLQSLPNGVFDKLTNL  111 (272)
T ss_dssp             HHTTCCEEECTTSCCCC-CTTGGGCTTCCEEECTTSCCC-----CC-GGGTTCTTCCEEECTTSCCCCCCTTTTTTCTTC
T ss_pred             cccceeeeeeCCCCccc-ccccccCCCCcEEECCCCCCC-----Cc-hhhcCCCCCCEEECCCCccCccChhHhcCCcCC
Confidence            34567777776332222 333334 88888887766543     12 4678899999999999999977654 6899999


Q ss_pred             cEEEccCCCCCccCCCC-c------EEEeeCCccCcceeeEEecccccchhH-HhcCCCCCCEEEecCCCCCCchhhhcc
Q 041097          205 RYLKLNIPSLKSLPSSR-K------ILRLSGNSQFHFSLASLLLYYQSLLSK-SLCRLSCLESLKLANESKMPRRSNIIL  276 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~~~-~------~L~l~~~~l~~L~L~~L~l~~~~~lp~-~i~~l~~L~~L~l~~~~~lp~L~~Llp  276 (391)
                      ++|++++|.+..+|... .      +|++++|.+.             .+|. .++.+++|++|++++..    +.. +|
T Consensus       112 ~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~-------------~~~~~~~~~l~~L~~L~l~~n~----l~~-~~  173 (272)
T 3rfs_A          112 KELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQ-------------SLPKGVFDKLTNLTELDLSYNQ----LQS-LP  173 (272)
T ss_dssp             CEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCC-------------CCCTTTTTTCTTCCEEECCSSC----CCC-CC
T ss_pred             CEEECCCCcCCccCHHHhccCCCCCEEECCCCccC-------------ccCHHHhccCccCCEEECCCCC----cCc-cC
Confidence            99999999999887653 2      7788777776             5554 46889999999998722    011 23


Q ss_pred             --ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCC
Q 041097          277 --AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCL  354 (391)
Q Consensus       277 --~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l  354 (391)
                        .++.+ ++|+.|++++|.+...+...++.+++|+.|+++.|.+.       +.+|+|+.|++..+.--..+|.+++.+
T Consensus       174 ~~~~~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~-------~~~~~l~~l~~~~n~~~g~ip~~~~~~  245 (272)
T 3rfs_A          174 EGVFDKL-TQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWD-------CTCPGIRYLSEWINKHSGVVRNSAGSV  245 (272)
T ss_dssp             TTTTTTC-TTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSCBC-------CCTTTTHHHHHHHHHTGGGBBCTTSCB
T ss_pred             HHHhcCC-ccCCEEECCCCcCCccCHHHHhCCcCCCEEEccCCCcc-------ccCcHHHHHHHHHHhCCCcccCccccc
Confidence              45778 89999999999888877677889999999999866554       446788888888775445788887766


Q ss_pred             CC
Q 041097          355 KS  356 (391)
Q Consensus       355 ~~  356 (391)
                      +.
T Consensus       246 ~~  247 (272)
T 3rfs_A          246 AP  247 (272)
T ss_dssp             CG
T ss_pred             CC
Confidence            54

>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=99.49  E-value=1.7e-13  Score=121.57  Aligned_cols=188  Identities=13%  Similarity=0.074  Sum_probs=119.2

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCc-cccCCc-ccCCCCcccEEEccC-CCCCccCCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLV-LIRYPS-GIENLFLLRYLKLNI-PSLKSLPSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-l~~~p~-~i~~l~~L~~L~l~~-~~i~~lp~~~~-----  222 (391)
                      ..++.|.+.+....    ...+..+..++.|+.|++++|. +..++. .+..+.+|++|++++ +.++.+|....     
T Consensus        31 ~~l~~L~l~~n~l~----~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~  106 (239)
T 2xwt_C           31 PSTQTLKLIETHLR----TIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPL  106 (239)
T ss_dssp             TTCCEEEEESCCCS----EECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTT
T ss_pred             CcccEEEEeCCcce----EECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCC
Confidence            56777776655442    1122356667777777877775 665554 567777777777776 77777664331     


Q ss_pred             --EEEeeCCccCcceeeEEecccccchhHHhcCCCCCC---EEEecCC-CCCCchhhhcc--ccccCCCCcc-EEEeecc
Q 041097          223 --ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLE---SLKLANE-SKMPRRSNIIL--AEYQFPPSLT-HLSFSNI  293 (391)
Q Consensus       223 --~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~---~L~l~~~-~~lp~L~~Llp--~~~~l~~~L~-~L~l~~~  293 (391)
                        .|++++|.+.             .+|. ++.+++|+   +|++++. .    +.. +|  .+..+ ++|+ .|++++|
T Consensus       107 L~~L~l~~n~l~-------------~lp~-~~~l~~L~~L~~L~l~~N~~----l~~-i~~~~~~~l-~~L~~~L~l~~n  166 (239)
T 2xwt_C          107 LKFLGIFNTGLK-------------MFPD-LTKVYSTDIFFILEITDNPY----MTS-IPVNAFQGL-CNETLTLKLYNN  166 (239)
T ss_dssp             CCEEEEEEECCC-------------SCCC-CTTCCBCCSEEEEEEESCTT----CCE-ECTTTTTTT-BSSEEEEECCSC
T ss_pred             CCEEeCCCCCCc-------------cccc-cccccccccccEEECCCCcc----hhh-cCcccccch-hcceeEEEcCCC
Confidence              5555555555             5665 77777777   8888762 2    111 33  46667 7888 8888888


Q ss_pred             cCCCCChhhhcCCCCCCEEEcCCCC-CcCccccCCCcc-cccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          294 ELMDDPIPALEKLSVLQVLKLKQNL-YSEERTMGIRAM-PKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       294 ~~~~~~~~~l~~l~~L~~L~l~~~~-~~~~~~~~~~~~-~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .+...+...+.. ++|+.|+++.|. ...........+ ++|+.|+++++ .++.+|..  .+++|++|++.+++
T Consensus       167 ~l~~i~~~~~~~-~~L~~L~L~~n~~l~~i~~~~~~~l~~~L~~L~l~~N-~l~~l~~~--~~~~L~~L~l~~~~  237 (239)
T 2xwt_C          167 GFTSVQGYAFNG-TKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLDVSQT-SVTALPSK--GLEHLKELIARNTW  237 (239)
T ss_dssp             CCCEECTTTTTT-CEEEEEECTTCTTCCEECTTTTTTCSBCCSEEECTTC-CCCCCCCT--TCTTCSEEECTTC-
T ss_pred             CCcccCHhhcCC-CCCCEEEcCCCCCcccCCHHHhhccccCCcEEECCCC-ccccCChh--HhccCceeeccCcc
Confidence            776544334444 788888888553 332111122456 78888888876 47777755  67788888887765

>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=99.47  E-value=4e-13  Score=122.81  Aligned_cols=169  Identities=23%  Similarity=0.169  Sum_probs=134.3

Q ss_pred             hccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcceeeEEecccccch
Q 041097          175 CKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHFSLASLLLYYQSLL  247 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L~L~~L~l~~~~~l  247 (391)
                      +.+++.++.++++++.+..+|..+.  .++++|+++++.+..++.. +.      .|++++|.+.             .+
T Consensus         6 ~~~l~~l~~l~~~~~~l~~ip~~~~--~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~n~l~-------------~~   70 (290)
T 1p9a_G            6 VSKVASHLEVNCDKRNLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELT-------------KL   70 (290)
T ss_dssp             EECSTTCCEEECTTSCCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCC-------------EE
T ss_pred             ccccCCccEEECCCCCCCcCCCCCC--CCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCCCccC-------------cc
Confidence            4677889999999999999998776  5899999999998876532 32      7777777766             56


Q ss_pred             hHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC
Q 041097          248 SKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG  326 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~  326 (391)
                      +.. +.+++|++|++++..    +.. +| .+..+ ++|+.|++++|.+...+...++.+++|+.|+++.|.........
T Consensus        71 ~~~-~~l~~L~~L~Ls~N~----l~~-l~~~~~~l-~~L~~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~~~~~~~  143 (290)
T 1p9a_G           71 QVD-GTLPVLGTLDLSHNQ----LQS-LPLLGQTL-PALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGL  143 (290)
T ss_dssp             ECC-SCCTTCCEEECCSSC----CSS-CCCCTTTC-TTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTT
T ss_pred             cCC-CCCCcCCEEECCCCc----CCc-CchhhccC-CCCCEEECCCCcCcccCHHHHcCCCCCCEEECCCCCCCccChhh
Confidence            554 789999999999832    000 56 67788 99999999999998887788999999999999977665422222


Q ss_pred             CCcccccceeeeccccccccchHh-hcCCCCCCEEEeeCCc
Q 041097          327 IRAMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLELWWPE  366 (391)
Q Consensus       327 ~~~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l~~~~  366 (391)
                      ...+++|+.|+++++ +++.+|.. +..+++|++|+++++.
T Consensus       144 ~~~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~L~L~~N~  183 (290)
T 1p9a_G          144 LTPTPKLEKLSLANN-NLTELPAGLLNGLENLDTLLLQENS  183 (290)
T ss_dssp             TTTCTTCCEEECTTS-CCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             cccccCCCEEECCCC-cCCccCHHHhcCcCCCCEEECCCCc
Confidence            357889999999988 58899865 4789999999998765

>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=99.47  E-value=5.3e-13  Score=123.12  Aligned_cols=188  Identities=18%  Similarity=0.132  Sum_probs=140.2

Q ss_pred             cCceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccE
Q 041097          128 RENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRY  206 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~  206 (391)
                      ..+++.+.+....... +..... ++++.|.+.++...     .+++ +..++.|++|++++|.+..++ .+..+.+|++
T Consensus        40 l~~L~~L~l~~~~i~~-l~~~~~l~~L~~L~L~~n~i~-----~~~~-~~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~~  111 (308)
T 1h6u_A           40 LDGITTLSAFGTGVTT-IEGVQYLNNLIGLELKDNQIT-----DLAP-LKNLTKITELELSGNPLKNVS-AIAGLQSIKT  111 (308)
T ss_dssp             HHTCCEEECTTSCCCC-CTTGGGCTTCCEEECCSSCCC-----CCGG-GTTCCSCCEEECCSCCCSCCG-GGTTCTTCCE
T ss_pred             cCCcCEEEeeCCCccC-chhhhccCCCCEEEccCCcCC-----CChh-HccCCCCCEEEccCCcCCCch-hhcCCCCCCE
Confidence            4567888877332222 333233 88888888766543     2323 889999999999999998765 7899999999


Q ss_pred             EEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcccccc
Q 041097          207 LKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQ  280 (391)
Q Consensus       207 L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~  280 (391)
                      |++++|.+..+|. +.      .|++++|.+.             .++. ++.+++|++|++++..    +.. +|.+..
T Consensus       112 L~l~~n~l~~~~~-l~~l~~L~~L~l~~n~l~-------------~~~~-l~~l~~L~~L~l~~n~----l~~-~~~l~~  171 (308)
T 1h6u_A          112 LDLTSTQITDVTP-LAGLSNLQVLYLDLNQIT-------------NISP-LAGLTNLQYLSIGNAQ----VSD-LTPLAN  171 (308)
T ss_dssp             EECTTSCCCCCGG-GTTCTTCCEEECCSSCCC-------------CCGG-GGGCTTCCEEECCSSC----CCC-CGGGTT
T ss_pred             EECCCCCCCCchh-hcCCCCCCEEECCCCccC-------------cCcc-ccCCCCccEEEccCCc----CCC-ChhhcC
Confidence            9999999988774 33      7777777776             6655 8899999999998722    000 334667


Q ss_pred             CCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchH
Q 041097          281 FPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHE  349 (391)
Q Consensus       281 l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~  349 (391)
                      + ++|+.|++++|.+...+  .+..+++|+.|+++.|...+..  +...+++|+.|++++|. +...|.
T Consensus       172 l-~~L~~L~l~~n~l~~~~--~l~~l~~L~~L~L~~N~l~~~~--~l~~l~~L~~L~l~~N~-i~~~~~  234 (308)
T 1h6u_A          172 L-SKLTTLKADDNKISDIS--PLASLPNLIEVHLKNNQISDVS--PLANTSNLFIVTLTNQT-ITNQPV  234 (308)
T ss_dssp             C-TTCCEEECCSSCCCCCG--GGGGCTTCCEEECTTSCCCBCG--GGTTCTTCCEEEEEEEE-EECCCE
T ss_pred             C-CCCCEEECCCCccCcCh--hhcCCCCCCEEEccCCccCccc--cccCCCCCCEEEccCCe-eecCCe
Confidence            8 99999999999887644  3889999999999977665433  35788999999999885 666554

>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=99.47  E-value=6.2e-13  Score=135.89  Aligned_cols=235  Identities=20%  Similarity=0.141  Sum_probs=138.9

Q ss_pred             cCceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCc-ccCCCCcc
Q 041097          128 RENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPS-GIENLFLL  204 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~-~i~~l~~L  204 (391)
                      +.+++.+.+..+.......... + ++++.|.+..+...    ...+..+.+++.|++|++++|.+..+|. .++++.+|
T Consensus        24 ~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L   99 (680)
T 1ziw_A           24 PTNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNTIS----KLEPELCQKLPMLKVLNLQHNELSQLSDKTFAFCTNL   99 (680)
T ss_dssp             CTTCSEEECCSSCCCCCCGGGGGGGTTCSEEECCSSCCC----CCCTTHHHHCTTCCEEECCSSCCCCCCTTTTTTCTTC
T ss_pred             CCCCcEEECCCCCCCCcCHHHHhCCCcCcEEECCCCccC----ccCHHHHhcccCcCEEECCCCccCccChhhhccCCCC
Confidence            3567788777333333122223 3 77888877655432    1233567788888888888888887776 58888888


Q ss_pred             cEEEccCCCCCccCC-CCc------EEEeeCCccCcc---------eeeEEecc--cccchh-HHh--cCCCCCCEEEec
Q 041097          205 RYLKLNIPSLKSLPS-SRK------ILRLSGNSQFHF---------SLASLLLY--YQSLLS-KSL--CRLSCLESLKLA  263 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~-~~~------~L~l~~~~l~~L---------~L~~L~l~--~~~~lp-~~i--~~l~~L~~L~l~  263 (391)
                      ++|+++++.+..+|+ .++      +|++++|.+...         +|++|+++  ....++ ..+  ..+++|++|+++
T Consensus       100 ~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~L~~L~L~  179 (680)
T 1ziw_A          100 TELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNNKIQALKSEELDIFANSSLKKLELS  179 (680)
T ss_dssp             SEEECCSSCCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSCCCCBCHHHHGGGTTCEESEEECT
T ss_pred             CEEECCCCccCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEEccCCcccccCHHHhhccccccccEEECC
Confidence            888888888887764 343      888888865543         67777777  233333 333  245677777776


Q ss_pred             CCC--C--------CCch---------------------------hhh----------cc-ccccCC-CCccEEEeeccc
Q 041097          264 NES--K--------MPRR---------------------------SNI----------IL-AEYQFP-PSLTHLSFSNIE  294 (391)
Q Consensus       264 ~~~--~--------lp~L---------------------------~~L----------lp-~~~~l~-~~L~~L~l~~~~  294 (391)
                      +..  .        ++.|                           +.|          .| ++..++ ++|+.|++++|.
T Consensus       180 ~n~l~~~~~~~~~~l~~L~~L~l~~~~l~~~~~~~~~~~l~~~~L~~L~L~~n~l~~~~~~~~~~l~~~~L~~L~Ls~n~  259 (680)
T 1ziw_A          180 SNQIKEFSPGCFHAIGRLFGLFLNNVQLGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNN  259 (680)
T ss_dssp             TCCCCCBCTTGGGGSSEECEEECTTCCCHHHHHHHHHHHHTTSCCCEEECTTSCCCEECTTTTGGGGGSCCCEEECTTSC
T ss_pred             CCcccccChhhhhhhhhhhhhhccccccChhhHHHHHHHhhhccccEEEccCCcccccChhHhhccCcCCCCEEECCCCC
Confidence            511  0        0111                           111          12 333330 236777777666


Q ss_pred             CCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecccccc-----ccchH----hhcCCCCCCEEEeeCC
Q 041097          295 LMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHL-----KRIHE----QLWCLKSLNKLELWWP  365 (391)
Q Consensus       295 ~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l-----~~lp~----~~~~l~~L~~L~l~~~  365 (391)
                      +...+...++.+++|++|+++.|...+..+...+.+++|++|+++++..-     ..+|.    .+..+++|++|+++++
T Consensus       260 l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~lp~i~~~~~~~l~~L~~L~l~~n  339 (680)
T 1ziw_A          260 LNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDN  339 (680)
T ss_dssp             CCEECTTTTTTCTTCCEEECCSCCBSEECTTTTTTCTTCCEEECTTCBCCC------CCEECTTTTTTCTTCCEEECCSC
T ss_pred             cCccCcccccCcccccEeeCCCCccCccChhhhcCCCCccEEeccchhhhcccccccccccChhhcccCCCCCEEECCCC
Confidence            65555556666777777777755444322223356667777777654311     12332    5566777777777765


Q ss_pred             c
Q 041097          366 E  366 (391)
Q Consensus       366 ~  366 (391)
                      .
T Consensus       340 ~  340 (680)
T 1ziw_A          340 D  340 (680)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.46  E-value=3.8e-14  Score=134.96  Aligned_cols=179  Identities=15%  Similarity=0.074  Sum_probs=116.0

Q ss_pred             hccCCcccEEEcCCCcccc-----CCcccCCCCcccEEEccCCCCC-----ccC---------------CCCcEEEeeCC
Q 041097          175 CKMFKFLRVLDLGSLVLIR-----YPSGIENLFLLRYLKLNIPSLK-----SLP---------------SSRKILRLSGN  229 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~~-----~p~~i~~l~~L~~L~l~~~~i~-----~lp---------------~~~~~L~l~~~  229 (391)
                      +..++.|++|++++|.+..     +|..+.++.+|++|++++|.+.     .++               ..+.+|++++|
T Consensus        90 l~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~~n  169 (386)
T 2ca6_A           90 LLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRN  169 (386)
T ss_dssp             HTTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSS
T ss_pred             HhhCCcccEEECCCCcCCHHHHHHHHHHHHhCCCCCEEECcCCCCCHHHHHHHHHHHHHHhhhhhcccCCCCcEEECCCC
Confidence            3455666666666665543     4445555566666666665553     122               12224444444


Q ss_pred             ccCcceeeEEecccccchh---HHhcCCCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeecccCC----CCCh
Q 041097          230 SQFHFSLASLLLYYQSLLS---KSLCRLSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIELM----DDPI  300 (391)
Q Consensus       230 ~l~~L~L~~L~l~~~~~lp---~~i~~l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~----~~~~  300 (391)
                      .+.           ...+|   ..+..+++|++|++++.. .-.....+.| .+..+ ++|+.|+|++|.+.    ...+
T Consensus       170 ~l~-----------~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~-~~L~~L~Ls~n~l~~~g~~~l~  237 (386)
T 2ca6_A          170 RLE-----------NGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYC-QELKVLDLQDNTFTHLGSSALA  237 (386)
T ss_dssp             CCT-----------GGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGC-TTCCEEECCSSCCHHHHHHHHH
T ss_pred             CCC-----------cHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcC-CCccEEECcCCCCCcHHHHHHH
Confidence            432           12444   578889999999998722 1001111256 77788 99999999999875    2234


Q ss_pred             hhhcCCCCCCEEEcCCCCCcCcc------ccCCCcccccceeeecccccccc-----chHhh-cCCCCCCEEEeeCCc
Q 041097          301 PALEKLSVLQVLKLKQNLYSEER------TMGIRAMPKLECLIINPYAHLKR-----IHEQL-WCLKSLNKLELWWPE  366 (391)
Q Consensus       301 ~~l~~l~~L~~L~l~~~~~~~~~------~~~~~~~~~L~~L~l~~c~~l~~-----lp~~~-~~l~~L~~L~l~~~~  366 (391)
                      ..+..+++|+.|+++.|......      .+..+.+++|++|++++|. +..     +|..+ .++++|++|++++|+
T Consensus       238 ~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~-i~~~g~~~l~~~l~~~l~~L~~L~l~~N~  314 (386)
T 2ca6_A          238 IALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGNR  314 (386)
T ss_dssp             HHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             HHHccCCCcCEEECCCCCCchhhHHHHHHHHhhccCCCeEEEECcCCc-CCHHHHHHHHHHHHhcCCCceEEEccCCc
Confidence            67789999999999977654431      1112458999999999885 665     88888 678999999998865

>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=99.46  E-value=1.4e-13  Score=133.81  Aligned_cols=163  Identities=23%  Similarity=0.188  Sum_probs=104.3

Q ss_pred             ccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc---EEEeeCCccCcc-----eeeEEecc--cccchhHH
Q 041097          181 LRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK---ILRLSGNSQFHF-----SLASLLLY--YQSLLSKS  250 (391)
Q Consensus       181 L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~---~L~l~~~~l~~L-----~L~~L~l~--~~~~lp~~  250 (391)
                      ++.|+++++.+..+|..   ..+|++|+++++.+..+|..+.   .|++++|.+..+     +|+.|+++  ....+| +
T Consensus        73 l~~L~l~~~~l~~lp~~---~~~L~~L~l~~n~l~~lp~~~~~L~~L~l~~n~l~~l~~~~~~L~~L~L~~n~l~~lp-~  148 (454)
T 1jl5_A           73 AHELELNNLGLSSLPEL---PPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLP-E  148 (454)
T ss_dssp             CSEEECTTSCCSCCCSC---CTTCSEEECCSSCCSSCCCCCTTCCEEECCSSCCSCCCSCCTTCCEEECCSSCCSSCC-C
T ss_pred             CCEEEecCCccccCCCC---cCCCCEEEccCCcCCccccccCCCcEEECCCCccCcccCCCCCCCEEECcCCCCCCCc-c
Confidence            47888888887777653   3578888888888887776554   888888877665     78999998  455677 5


Q ss_pred             hcCCCCCCEEEecCCC--CCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC
Q 041097          251 LCRLSCLESLKLANES--KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR  328 (391)
Q Consensus       251 i~~l~~L~~L~l~~~~--~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  328 (391)
                      ++++++|++|++++..  .       +|.  .. .+|+.|++++|.+...+  .++.+++|+.|+++.|...+..    .
T Consensus       149 ~~~l~~L~~L~l~~N~l~~-------lp~--~~-~~L~~L~L~~n~l~~l~--~~~~l~~L~~L~l~~N~l~~l~----~  212 (454)
T 1jl5_A          149 LQNSSFLKIIDVDNNSLKK-------LPD--LP-PSLEFIAAGNNQLEELP--ELQNLPFLTAIYADNNSLKKLP----D  212 (454)
T ss_dssp             CTTCTTCCEEECCSSCCSC-------CCC--CC-TTCCEEECCSSCCSSCC--CCTTCTTCCEEECCSSCCSSCC----C
T ss_pred             cCCCCCCCEEECCCCcCcc-------cCC--Cc-ccccEEECcCCcCCcCc--cccCCCCCCEEECCCCcCCcCC----C
Confidence            9999999999998722  1       221  12 56666777666655532  4666666666666655443211    1


Q ss_pred             cccccceeeeccccccccchHhhcCCCCCCEEEeeCC
Q 041097          329 AMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~  365 (391)
                      .+++|++|++++| .++.+| .++.+++|++|+++++
T Consensus       213 ~~~~L~~L~l~~n-~l~~lp-~~~~l~~L~~L~l~~N  247 (454)
T 1jl5_A          213 LPLSLESIVAGNN-ILEELP-ELQNLPFLTTIYADNN  247 (454)
T ss_dssp             CCTTCCEEECCSS-CCSSCC-CCTTCTTCCEEECCSS
T ss_pred             CcCcccEEECcCC-cCCccc-ccCCCCCCCEEECCCC
Confidence            1235555555555 344555 2455555555555443

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.45  E-value=4.6e-13  Score=133.78  Aligned_cols=190  Identities=19%  Similarity=0.136  Sum_probs=116.6

Q ss_pred             HhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc----E----------------------EEe
Q 041097          173 KICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK----I----------------------LRL  226 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~----~----------------------L~l  226 (391)
                      ..+..++.|+.|+++++.+..+|..+..+ +|++|+++++.+..+|....    .                      |++
T Consensus       276 ~~~~~l~~L~~L~l~~~~l~~l~~~~~~~-~L~~L~l~~n~~~~l~~~~l~~L~~L~l~~n~~~~~~~~~~~~~L~~L~l  354 (570)
T 2z63_A          276 DLFNCLTNVSSFSLVSVTIERVKDFSYNF-GWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDL  354 (570)
T ss_dssp             TTTGGGTTCSEEEEESCEECSCCBCCSCC-CCSEEEEESCBCSSCCBCBCSSCCEEEEESCBSCCBCCCCBCTTCCEEEC
T ss_pred             hhhcCcCcccEEEecCccchhhhhhhccC-CccEEeeccCcccccCcccccccCEEeCcCCccccccccccCCCCCEEeC
Confidence            45566778888888888888888877777 88888888877776665321    4                      444


Q ss_pred             eCCccCcc-----------eeeEEecc--cccchhHHhcCCCCCCEEEecCCC-----------CCCchhhh--------
Q 041097          227 SGNSQFHF-----------SLASLLLY--YQSLLSKSLCRLSCLESLKLANES-----------KMPRRSNI--------  274 (391)
Q Consensus       227 ~~~~l~~L-----------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~-----------~lp~L~~L--------  274 (391)
                      ++|.+...           +|+.|+++  ....+|..++.+++|++|++.+..           .+++|+.|        
T Consensus       355 ~~n~l~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~  434 (570)
T 2z63_A          355 SRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTR  434 (570)
T ss_dssp             CSSCCBEEEEEEHHHHTCSCCCEEECCSCSEEEEEEEEETCTTCCEEECTTSEEESCTTSCTTTTCTTCCEEECTTSCCE
T ss_pred             cCCccCccccccccccccCccCEEECCCCccccccccccccCCCCEEEccCCccccccchhhhhcCCCCCEEeCcCCccc
Confidence            44433321           45555555  233344445566666666665410           01222222        


Q ss_pred             --cc-ccccCCCCccEEEeecccCCC-CChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccch-H
Q 041097          275 --IL-AEYQFPPSLTHLSFSNIELMD-DPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIH-E  349 (391)
Q Consensus       275 --lp-~~~~l~~~L~~L~l~~~~~~~-~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp-~  349 (391)
                        .| .+..+ ++|+.|++.+|.+.. ..+..++.+++|+.|+++.|...+..+...+.+++|++|++++| +++.+| .
T Consensus       435 ~~~~~~~~~l-~~L~~L~l~~n~l~~~~~p~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~  512 (570)
T 2z63_A          435 VAFNGIFNGL-SSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMASN-QLKSVPDG  512 (570)
T ss_dssp             ECCTTTTTTC-TTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCSCCCTT
T ss_pred             ccchhhhhcC-CcCcEEECcCCcCccccchhhhhcccCCCEEECCCCccccCChhhhhcccCCCEEeCCCC-cCCCCCHH
Confidence              33 45556 666777776666542 22245666777777777755444322233467888999999887 466665 4


Q ss_pred             hhcCCCCCCEEEeeCC
Q 041097          350 QLWCLKSLNKLELWWP  365 (391)
Q Consensus       350 ~~~~l~~L~~L~l~~~  365 (391)
                      .+..+++|++|+++++
T Consensus       513 ~~~~l~~L~~L~l~~N  528 (570)
T 2z63_A          513 IFDRLTSLQKIWLHTN  528 (570)
T ss_dssp             TTTTCTTCCEEECCSS
T ss_pred             HhhcccCCcEEEecCC
Confidence            5788899999998874

>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=99.45  E-value=4.9e-13  Score=132.29  Aligned_cols=178  Identities=20%  Similarity=0.156  Sum_probs=109.5

Q ss_pred             CcccEEEcCCCccc-cCCccc-----CCCCcccEEEccCCCCCccC----------CCCc--------------------
Q 041097          179 KFLRVLDLGSLVLI-RYPSGI-----ENLFLLRYLKLNIPSLKSLP----------SSRK--------------------  222 (391)
Q Consensus       179 ~~L~~L~l~~~~l~-~~p~~i-----~~l~~L~~L~l~~~~i~~lp----------~~~~--------------------  222 (391)
                      ..|+.|++++|.+. .+|..+     +++.+|+.++++++.+ .+|          ..+.                    
T Consensus       247 ~~L~~L~l~~n~l~~~~p~~~~~~~~~~l~~L~~l~l~~n~~-~~p~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~l~~  325 (520)
T 2z7x_B          247 TTVWYFSISNVKLQGQLDFRDFDYSGTSLKALSIHQVVSDVF-GFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISP  325 (520)
T ss_dssp             SSCSEEEEEEEEEESCCCCCCCCCCSCCCCEEEEEEEEECCC-CSCTHHHHHHHHTCCCSEEEEESSCCCCCCCCSSCCC
T ss_pred             CcccEEEeecccccCccccchhhcccccCceeEeccccccce-ecchhhhhcccccCceeEEEcCCCccccccchhhCCc
Confidence            47888888888877 788888     7888888888877776 566          1222                    


Q ss_pred             --EEEeeCCccCcc---------eeeEEecc--ccc---chhHHhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCC
Q 041097          223 --ILRLSGNSQFHF---------SLASLLLY--YQS---LLSKSLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPS  284 (391)
Q Consensus       223 --~L~l~~~~l~~L---------~L~~L~l~--~~~---~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~  284 (391)
                        +|++++|.+...         +|+.|+++  ...   .+|..++.+++|++|++++..    +..-+|  .+..+ ++
T Consensus       326 L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~l~~L~~L~Ls~N~----l~~~l~~~~~~~l-~~  400 (520)
T 2z7x_B          326 FLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNS----VSYDEKKGDCSWT-KS  400 (520)
T ss_dssp             CCEEECCSSCCCTTTTTTCCCCSSCCEEECCSSCCCBHHHHHHHHTTCTTCCEEECCSSC----CBCCGGGCSCCCC-TT
T ss_pred             ccEEEeECCccChhhhhhhccCCCCCEEEccCCccCccccchHHHhhCCCCCEEECCCCc----CCcccccchhccC-cc
Confidence              455555444331         45555555  222   334455555555555555411    000033  24455 66


Q ss_pred             ccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHh-hcCCCCCCEEEee
Q 041097          285 LTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLELW  363 (391)
Q Consensus       285 L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l~  363 (391)
                      |+.|++++|.+....+..+.  ++|+.|+++.|... ..+.....+++|++|++++| .++.+|.. +..+++|++|+++
T Consensus       401 L~~L~Ls~N~l~~~~~~~l~--~~L~~L~Ls~N~l~-~ip~~~~~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~L~l~  476 (520)
T 2z7x_B          401 LLSLNMSSNILTDTIFRCLP--PRIKVLDLHSNKIK-SIPKQVVKLEALQELNVASN-QLKSVPDGIFDRLTSLQKIWLH  476 (520)
T ss_dssp             CCEEECCSSCCCGGGGGSCC--TTCCEEECCSSCCC-CCCGGGGGCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECC
T ss_pred             CCEEECcCCCCCcchhhhhc--ccCCEEECCCCccc-ccchhhhcCCCCCEEECCCC-cCCccCHHHhccCCcccEEECc
Confidence            77777776665432222221  57777777755444 22222357889999999988 58889876 7889999999998


Q ss_pred             CCc
Q 041097          364 WPE  366 (391)
Q Consensus       364 ~~~  366 (391)
                      ++|
T Consensus       477 ~N~  479 (520)
T 2z7x_B          477 TNP  479 (520)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            755

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.44  E-value=1.3e-12  Score=136.72  Aligned_cols=110  Identities=25%  Similarity=0.253  Sum_probs=88.2

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCc-cccC-CcccCCCCcccEEEccCCCCCcc-CCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLV-LIRY-PSGIENLFLLRYLKLNIPSLKSL-PSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~-l~~~-p~~i~~l~~L~~L~l~~~~i~~l-p~~~~-----  222 (391)
                      +.++.|.+..+...    ...+..+..++.|++|++++|. +..+ |..++++.+|++|++++|.+..+ |..++     
T Consensus        24 ~~l~~LdLs~N~i~----~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L   99 (844)
T 3j0a_A           24 NTTERLLLSFNYIR----TVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHL   99 (844)
T ss_dssp             TTCCEEEEESCCCC----EECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSC
T ss_pred             CCcCEEECCCCcCC----ccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCccc
Confidence            88999998876543    1234567899999999999995 4355 78899999999999999999876 66665     


Q ss_pred             -EEEeeCCccCc-------c----eeeEEecc--cccch--hHHhcCCCCCCEEEecC
Q 041097          223 -ILRLSGNSQFH-------F----SLASLLLY--YQSLL--SKSLCRLSCLESLKLAN  264 (391)
Q Consensus       223 -~L~l~~~~l~~-------L----~L~~L~l~--~~~~l--p~~i~~l~~L~~L~l~~  264 (391)
                       +|++++|.+..       +    +|++|+++  ....+  ++.++++++|++|++++
T Consensus       100 ~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~  157 (844)
T 3j0a_A          100 FELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSS  157 (844)
T ss_dssp             CCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEES
T ss_pred             CEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCC
Confidence             99999997654       2    89999999  33333  46799999999999988

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.44  E-value=3.6e-13  Score=134.61  Aligned_cols=164  Identities=21%  Similarity=0.155  Sum_probs=110.3

Q ss_pred             cCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCcc---CC------CCcEEEeeCCccCcc--------eeeEE
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSL---PS------SRKILRLSGNSQFHF--------SLASL  239 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~l---p~------~~~~L~l~~~~l~~L--------~L~~L  239 (391)
                      .++.|+.|+++++.+...... ..+.+|++|+++++.+...   |.      .+..|++++|.+..+        +|+.|
T Consensus       323 ~l~~L~~L~l~~n~~~~~~~~-~~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~l~~L~~L  401 (570)
T 2z63_A          323 KLKSLKRLTFTSNKGGNAFSE-VDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHL  401 (570)
T ss_dssp             BCSSCCEEEEESCBSCCBCCC-CBCTTCCEEECCSSCCBEEEEEEHHHHTCSCCCEEECCSCSEEEEEEEEETCTTCCEE
T ss_pred             cccccCEEeCcCCcccccccc-ccCCCCCEEeCcCCccCccccccccccccCccCEEECCCCccccccccccccCCCCEE
Confidence            445555555555554422211 5677888888888877654   22      223888888765543        67777


Q ss_pred             ecc--cccch-h-HHhcCCCCCCEEEecCCC----------CCCchhhh-----------cc-ccccCCCCccEEEeecc
Q 041097          240 LLY--YQSLL-S-KSLCRLSCLESLKLANES----------KMPRRSNI-----------IL-AEYQFPPSLTHLSFSNI  293 (391)
Q Consensus       240 ~l~--~~~~l-p-~~i~~l~~L~~L~l~~~~----------~lp~L~~L-----------lp-~~~~l~~~L~~L~l~~~  293 (391)
                      +++  ..... | ..+..+++|++|++++..          .+++|+.|           +| .++.+ ++|+.|++++|
T Consensus       402 ~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~p~~~~~l-~~L~~L~l~~n  480 (570)
T 2z63_A          402 DFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTEL-RNLTFLDLSQC  480 (570)
T ss_dssp             ECTTSEEESCTTSCTTTTCTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCEEGGGEECSCCTTC-TTCCEEECTTS
T ss_pred             EccCCccccccchhhhhcCCCCCEEeCcCCcccccchhhhhcCCcCcEEECcCCcCccccchhhhhcc-cCCCEEECCCC
Confidence            777  22222 2 356677777777776611          12333333           66 78889 99999999999


Q ss_pred             cCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecccc
Q 041097          294 ELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYA  342 (391)
Q Consensus       294 ~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~  342 (391)
                      .+....+..++.+++|+.|+++.|...+......+.+++|+.|++++++
T Consensus       481 ~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~N~  529 (570)
T 2z63_A          481 QLEQLSPTAFNSLSSLQVLNMASNQLKSVPDGIFDRLTSLQKIWLHTNP  529 (570)
T ss_dssp             CCCEECTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             ccccCChhhhhcccCCCEEeCCCCcCCCCCHHHhhcccCCcEEEecCCc
Confidence            9888767889999999999999776655322224688999999999885

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.42  E-value=1.1e-13  Score=127.80  Aligned_cols=180  Identities=23%  Similarity=0.252  Sum_probs=136.9

Q ss_pred             ccEEEcCCCccc--cCCcccC-------CCCcccEEEccCCCCC-ccCCCC--c------EEEeeCCccCcc--------
Q 041097          181 LRVLDLGSLVLI--RYPSGIE-------NLFLLRYLKLNIPSLK-SLPSSR--K------ILRLSGNSQFHF--------  234 (391)
Q Consensus       181 L~~L~l~~~~l~--~~p~~i~-------~l~~L~~L~l~~~~i~-~lp~~~--~------~L~l~~~~l~~L--------  234 (391)
                      |+.|+++++.+.  .+|..+.       ++.+|++|+++++.+. .+|..+  .      +|++++|.+..+        
T Consensus        65 L~~L~L~~n~l~~~~~~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~l~  144 (312)
T 1wwl_A           65 IKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQ  144 (312)
T ss_dssp             HHHCCCCEEEEEEEECBHHHHHHHHHHHTTSCCCEEEEEEEBCBSCCCCCSSSCCSCCCSEEEEESCBCSSSSSHHHHHH
T ss_pred             HhhcccccccccCCCcCHHHHHHHHHhcCcCCccEEEccCCcccchhHHHHHHhcCCCccEEEccCCCCcchhHHHHHHH
Confidence            788899998885  5666665       7899999999999988 678765  3      999999987642        


Q ss_pred             -----eeeEEecc--cccchh-HHhcCCCCCCEEEecCCCCCCchhhhcc-cc--ccCCCCccEEEeecccCCCCC---h
Q 041097          235 -----SLASLLLY--YQSLLS-KSLCRLSCLESLKLANESKMPRRSNIIL-AE--YQFPPSLTHLSFSNIELMDDP---I  300 (391)
Q Consensus       235 -----~L~~L~l~--~~~~lp-~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~--~~l~~~L~~L~l~~~~~~~~~---~  300 (391)
                           +|++|+++  ....++ ..++++++|++|++++........  +| .+  ..+ ++|+.|++++|.+...+   .
T Consensus       145 ~~~~~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~--~~~~~~~~~l-~~L~~L~L~~N~l~~~~~~~~  221 (312)
T 1wwl_A          145 QWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERG--LISALCPLKF-PTLQVLALRNAGMETPSGVCS  221 (312)
T ss_dssp             TTCCTTCCEEEEESCSCCCCCTTTCCCCSSCCEEECCSCTTCHHHH--HHHHSCTTSC-TTCCEEECTTSCCCCHHHHHH
T ss_pred             HhhcCCCcEEEeeCCCCccchHHHhccCCCCCEEECCCCCcCcchH--HHHHHHhccC-CCCCEEECCCCcCcchHHHHH
Confidence                 68899988  444555 788899999999998721000000  23 33  788 99999999999887422   2


Q ss_pred             hhhcCCCCCCEEEcCCCCCcCccccC-CCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          301 PALEKLSVLQVLKLKQNLYSEERTMG-IRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       301 ~~l~~l~~L~~L~l~~~~~~~~~~~~-~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ..+..+++|+.|+++.|...+..+.. ...+++|++|++++| .++.+|.++.  ++|++|+++++.
T Consensus       222 ~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~Ls~N-~l~~ip~~~~--~~L~~L~Ls~N~  285 (312)
T 1wwl_A          222 ALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFT-GLKQVPKGLP--AKLSVLDLSYNR  285 (312)
T ss_dssp             HHHHTTCCCSEEECTTSCCCSSCCCSCCCCCTTCCEEECTTS-CCSSCCSSCC--SEEEEEECCSSC
T ss_pred             HHHhcCCCCCEEECCCCcCCcccchhhhhhcCCCCEEECCCC-ccChhhhhcc--CCceEEECCCCC
Confidence            34468899999999988776644223 246789999999988 4889998876  899999999875

>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=99.42  E-value=9.5e-13  Score=131.00  Aligned_cols=195  Identities=19%  Similarity=0.105  Sum_probs=115.6

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCC-Cc------
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSS-RK------  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~-~~------  222 (391)
                      +.++.|.+.++...    ...+..+..++.|++|++++|.+..++ ..++++.+|++|++++|.+..+|.. ++      
T Consensus        26 ~~L~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~  101 (549)
T 2z81_A           26 AAMKSLDLSFNKIT----YIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLK  101 (549)
T ss_dssp             TTCCEEECCSSCCC----EECSSTTSSCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCSCCHHHHTTCTTCC
T ss_pred             CCccEEECcCCccC----ccChhhhhcCCcccEEECCCCCcCccChhhccccccCCEEECCCCccCccCHHHhccCCCCc
Confidence            45666655544432    111234566667777777777766443 5566777777777777766665543 22      


Q ss_pred             EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCCh
Q 041097          223 ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPI  300 (391)
Q Consensus       223 ~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~  300 (391)
                      +|++++|.+.           ...+|..++++++|++|++++...+   .. +|  .++.+ ++|+.|++++|.+....+
T Consensus       102 ~L~Ls~n~l~-----------~~~~~~~~~~l~~L~~L~L~~n~~~---~~-~~~~~~~~l-~~L~~L~L~~n~l~~~~~  165 (549)
T 2z81_A          102 YLNLMGNPYQ-----------TLGVTSLFPNLTNLQTLRIGNVETF---SE-IRRIDFAGL-TSLNELEIKALSLRNYQS  165 (549)
T ss_dssp             EEECTTCCCS-----------SSCSSCSCTTCTTCCEEEEEESSSC---CE-ECTTTTTTC-CEEEEEEEEETTCCEECT
T ss_pred             EEECCCCccc-----------ccchhhhhhccCCccEEECCCCccc---cc-cCHhhhhcc-cccCeeeccCCcccccCh
Confidence            5555555444           0123566777788888877761100   00 22  56677 788888888877766555


Q ss_pred             hhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccc---hHh-hcCCCCCCEEEeeCCc
Q 041097          301 PALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRI---HEQ-LWCLKSLNKLELWWPE  366 (391)
Q Consensus       301 ~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l---p~~-~~~l~~L~~L~l~~~~  366 (391)
                      ..++.+++|+.|+++.|..........+.+++|++|++++|. +..+   |.. ...+++|++|++.++.
T Consensus       166 ~~l~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~~~~~~~L~~L~l~~n~  234 (549)
T 2z81_A          166 QSLKSIRDIHHLTLHLSESAFLLEIFADILSSVRYLELRDTN-LARFQFSPLPVDEVSSPMKKLAFRGSV  234 (549)
T ss_dssp             TTTTTCSEEEEEEEECSBSTTHHHHHHHSTTTBSEEEEESCB-CTTCCCCCCSSCCCCCCCCEEEEESCE
T ss_pred             hhhhccccCceEecccCcccccchhhHhhcccccEEEccCCc-cccccccccchhhhhhcccceeccccc
Confidence            677778888888887444321111111347788888888774 5544   222 2456788888888764

>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=99.41  E-value=2.2e-12  Score=112.97  Aligned_cols=148  Identities=20%  Similarity=0.246  Sum_probs=78.2

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      +.++++++.+..+|..+.  .+++.|+++++.+..+|.                             ..+..+++|+.|+
T Consensus        14 ~~v~c~~~~l~~iP~~l~--~~l~~L~l~~n~i~~i~~-----------------------------~~~~~l~~L~~L~   62 (220)
T 2v9t_B           14 NIVDCRGKGLTEIPTNLP--ETITEIRLEQNTIKVIPP-----------------------------GAFSPYKKLRRID   62 (220)
T ss_dssp             TEEECTTSCCSSCCSSCC--TTCCEEECCSSCCCEECT-----------------------------TSSTTCTTCCEEE
T ss_pred             CEEEcCCCCcCcCCCccC--cCCCEEECCCCcCCCcCH-----------------------------hHhhCCCCCCEEE
Confidence            456777777777776654  466777777776665543                             2344555555555


Q ss_pred             ecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecc
Q 041097          262 LANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINP  340 (391)
Q Consensus       262 l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~  340 (391)
                      +++..    +..+.| .+..+ ++|++|+|++|.+...+...+..+++|+.|+++.|..........+.+++|++|++++
T Consensus        63 Ls~N~----i~~~~~~~~~~l-~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~  137 (220)
T 2v9t_B           63 LSNNQ----ISELAPDAFQGL-RSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYD  137 (220)
T ss_dssp             CCSSC----CCEECTTTTTTC-SSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS
T ss_pred             CCCCc----CCCcCHHHhhCC-cCCCEEECCCCcCCccCHhHccCCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCC
Confidence            55411    000023 44455 5555666555555554444455556666666654444332222234555566666665


Q ss_pred             ccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          341 YAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       341 c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      + .++.+|. .+..+++|++|++.++|
T Consensus       138 N-~l~~~~~~~~~~l~~L~~L~L~~N~  163 (220)
T 2v9t_B          138 N-KLQTIAKGTFSPLRAIQTMHLAQNP  163 (220)
T ss_dssp             S-CCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             C-cCCEECHHHHhCCCCCCEEEeCCCC
Confidence            5 2444443 35556666666665543

>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=99.41  E-value=2.3e-12  Score=112.82  Aligned_cols=149  Identities=17%  Similarity=0.178  Sum_probs=106.0

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      +.++++++.+..+|..+..  .+++|+++++.+..++.                            +..++.+++|++|+
T Consensus        14 ~~l~~s~n~l~~iP~~~~~--~~~~L~L~~N~l~~~~~----------------------------~~~~~~l~~L~~L~   63 (220)
T 2v70_A           14 TTVDCSNQKLNKIPEHIPQ--YTAELRLNNNEFTVLEA----------------------------TGIFKKLPQLRKIN   63 (220)
T ss_dssp             TEEECCSSCCSSCCSCCCT--TCSEEECCSSCCCEECC----------------------------CCCGGGCTTCCEEE
T ss_pred             CEeEeCCCCcccCccCCCC--CCCEEEcCCCcCCccCc----------------------------hhhhccCCCCCEEE
Confidence            4677777777777766643  34677777766665421                            12356788888888


Q ss_pred             ecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecc
Q 041097          262 LANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINP  340 (391)
Q Consensus       262 l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~  340 (391)
                      +++..    +..+.| .+..+ ++|+.|+|++|.+...+...++.+++|++|+++.|...+..+...+.+++|+.|++++
T Consensus        64 L~~N~----i~~i~~~~~~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~  138 (220)
T 2v70_A           64 FSNNK----ITDIEEGAFEGA-SGVNEILLTSNRLENVQHKMFKGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYD  138 (220)
T ss_dssp             CCSSC----CCEECTTTTTTC-TTCCEEECCSSCCCCCCGGGGTTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTT
T ss_pred             CCCCc----CCEECHHHhCCC-CCCCEEECCCCccCccCHhHhcCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCC
Confidence            87622    111123 56778 8899999998888887777788899999999987776654333446788899999987


Q ss_pred             ccccccc-hHhhcCCCCCCEEEeeCCc
Q 041097          341 YAHLKRI-HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       341 c~~l~~l-p~~~~~l~~L~~L~l~~~~  366 (391)
                      + .++.+ |..+..+++|++|+++++|
T Consensus       139 N-~l~~~~~~~~~~l~~L~~L~L~~N~  164 (220)
T 2v70_A          139 N-QITTVAPGAFDTLHSLSTLNLLANP  164 (220)
T ss_dssp             S-CCCCBCTTTTTTCTTCCEEECCSCC
T ss_pred             C-cCCEECHHHhcCCCCCCEEEecCcC
Confidence            7 46666 6778889999999988765

>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=99.41  E-value=1.8e-13  Score=127.48  Aligned_cols=175  Identities=18%  Similarity=0.142  Sum_probs=103.9

Q ss_pred             ccCCcccEEEcCCCccc-c-CCcccCCCCcccEEEccCCCCC-ccCCCCc------EEEeeCC-ccCcceeeEEeccccc
Q 041097          176 KMFKFLRVLDLGSLVLI-R-YPSGIENLFLLRYLKLNIPSLK-SLPSSRK------ILRLSGN-SQFHFSLASLLLYYQS  245 (391)
Q Consensus       176 ~~~~~L~~L~l~~~~l~-~-~p~~i~~l~~L~~L~l~~~~i~-~lp~~~~------~L~l~~~-~l~~L~L~~L~l~~~~  245 (391)
                      ..++.|+.|++++|.+. . +|..+..+.+|++|+++++.+. ..|..+.      +|++++| .+.           ..
T Consensus        90 ~~~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~L~~~~~l~-----------~~  158 (336)
T 2ast_B           90 FSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFS-----------EF  158 (336)
T ss_dssp             CCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCC-----------HH
T ss_pred             ccCCCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcCcccCHHHHHHHhcCCCCCEEECCCCCCCC-----------HH
Confidence            35566667777666655 2 5556666667777777666554 2222221      4444444 333           11


Q ss_pred             chhHHhcCCCCCCEEEecCC-CCCCchhhhcc-ccccCCC-CccEEEeeccc--CCC-CChhhhcCCCCCCEEEcCCCC-
Q 041097          246 LLSKSLCRLSCLESLKLANE-SKMPRRSNIIL-AEYQFPP-SLTHLSFSNIE--LMD-DPIPALEKLSVLQVLKLKQNL-  318 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~-~~lp~L~~Llp-~~~~l~~-~L~~L~l~~~~--~~~-~~~~~l~~l~~L~~L~l~~~~-  318 (391)
                      .++..++.+++|++|++++. . +..-.  +| .+..+ + +|+.|++++|.  +.. .....++.+++|+.|+++.|. 
T Consensus       159 ~l~~~~~~~~~L~~L~l~~~~~-l~~~~--~~~~~~~l-~~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L~l~~~~~  234 (336)
T 2ast_B          159 ALQTLLSSCSRLDELNLSWCFD-FTEKH--VQVAVAHV-SETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVM  234 (336)
T ss_dssp             HHHHHHHHCTTCCEEECCCCTT-CCHHH--HHHHHHHS-CTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTT
T ss_pred             HHHHHHhcCCCCCEEcCCCCCC-cChHH--HHHHHHhc-ccCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEEeCCCCCc
Confidence            36666777888888888762 2 00000  34 45667 6 88888888873  332 223456678888888888665 


Q ss_pred             CcCccccCCCcccccceeeecccccccc-chHhhcCCCCCCEEEeeCC
Q 041097          319 YSEERTMGIRAMPKLECLIINPYAHLKR-IHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       319 ~~~~~~~~~~~~~~L~~L~l~~c~~l~~-lp~~~~~l~~L~~L~l~~~  365 (391)
                      .....+...+.+++|++|++++|..+.. ....+..+++|++|++++|
T Consensus       235 l~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~l~~~~~L~~L~l~~~  282 (336)
T 2ast_B          235 LKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI  282 (336)
T ss_dssp             CCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             CCHHHHHHHhCCCCCCEeeCCCCCCCCHHHHHHHhcCCCCCEEeccCc
Confidence            3333333446678888888888853221 1124677888888888876

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.38  E-value=3.6e-12  Score=126.76  Aligned_cols=153  Identities=23%  Similarity=0.187  Sum_probs=98.7

Q ss_pred             CcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecc--cccchhHHhcCCCC
Q 041097          179 KFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLY--YQSLLSKSLCRLSC  256 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~--~~~~lp~~i~~l~~  256 (391)
                      +.|+.|++++|.+..+|   +.+.+|++|++++|.+..+|. +.          . +|+.|+++  ....+|.   .+++
T Consensus        80 ~~L~~L~Ls~N~l~~ip---~~l~~L~~L~Ls~N~l~~ip~-l~----------~-~L~~L~Ls~N~l~~lp~---~l~~  141 (571)
T 3cvr_A           80 PQITVLEITQNALISLP---ELPASLEYLDACDNRLSTLPE-LP----------A-SLKHLDVDNNQLTMLPE---LPAL  141 (571)
T ss_dssp             TTCSEEECCSSCCSCCC---CCCTTCCEEECCSSCCSCCCC-CC----------T-TCCEEECCSSCCSCCCC---CCTT
T ss_pred             CCCCEEECcCCCCcccc---cccCCCCEEEccCCCCCCcch-hh----------c-CCCEEECCCCcCCCCCC---cCcc
Confidence            34455555555544444   234445555555554444444 22          0 34444444  2226777   6899


Q ss_pred             CCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCccccc---
Q 041097          257 LESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKL---  333 (391)
Q Consensus       257 L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L---  333 (391)
                      |++|++++..    +.. +|.  .+ ++|+.|++++|.+...+.  +.  ++|+.|+++.|....  ++..  ..+|   
T Consensus       142 L~~L~Ls~N~----l~~-lp~--~l-~~L~~L~Ls~N~L~~lp~--l~--~~L~~L~Ls~N~L~~--lp~~--~~~L~~~  205 (571)
T 3cvr_A          142 LEYINADNNQ----LTM-LPE--LP-TSLEVLSVRNNQLTFLPE--LP--ESLEALDVSTNLLES--LPAV--PVRNHHS  205 (571)
T ss_dssp             CCEEECCSSC----CSC-CCC--CC-TTCCEEECCSSCCSCCCC--CC--TTCCEEECCSSCCSS--CCCC--C------
T ss_pred             ccEEeCCCCc----cCc-CCC--cC-CCcCEEECCCCCCCCcch--hh--CCCCEEECcCCCCCc--hhhH--HHhhhcc
Confidence            9999998722    000 343  35 899999999999887553  54  899999999776552  2221  1266   


Q ss_pred             ----ceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          334 ----ECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       334 ----~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                          +.|++++| .++.+|.++..+++|++|++++++
T Consensus       206 ~~~L~~L~Ls~N-~l~~lp~~l~~l~~L~~L~L~~N~  241 (571)
T 3cvr_A          206 EETEIFFRCREN-RITHIPENILSLDPTCTIILEDNP  241 (571)
T ss_dssp             --CCEEEECCSS-CCCCCCGGGGGSCTTEEEECCSSS
T ss_pred             cccceEEecCCC-cceecCHHHhcCCCCCEEEeeCCc
Confidence                99999987 588999999999999999999876

>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=99.37  E-value=1.7e-12  Score=117.53  Aligned_cols=194  Identities=17%  Similarity=0.041  Sum_probs=133.1

Q ss_pred             cCceEEEEEeccCCCcccccCC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCC-cccCCCCcc
Q 041097          128 RENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYP-SGIENLFLL  204 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L  204 (391)
                      +..++.+.+..+.......... + ++++.|.+.++...    ...+..+..++.|++|++++|.+..++ ..+.++.+|
T Consensus        27 ~~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n~l~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L  102 (276)
T 2z62_A           27 PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQ----TIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSL  102 (276)
T ss_dssp             CTTCCEEECTTCCCCEECTTTTTTCTTCSEEECTTCCCC----EECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTC
T ss_pred             CCCccEEECCCCcccccCHhHhccccCCcEEECCCCcCC----ccCHHHccCCcCCCEEECCCCccCccChhhhcCCccc
Confidence            4568888877333333122233 3 78888887665432    122346788999999999999998655 678999999


Q ss_pred             cEEEccCCCCCccCC-CCc------EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-
Q 041097          205 RYLKLNIPSLKSLPS-SRK------ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-  276 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~-~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-  276 (391)
                      ++|+++++.+..++. .++      +|++++|.+.           ...+|..++.+++|++|++++..    +..+.| 
T Consensus       103 ~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~-----------~~~l~~~~~~l~~L~~L~Ls~N~----l~~~~~~  167 (276)
T 2z62_A          103 QKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQ-----------SFKLPEYFSNLTNLEHLDLSSNK----IQSIYCT  167 (276)
T ss_dssp             CEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCC-----------CCCCCGGGGGCTTCCEEECCSSC----CCEECGG
T ss_pred             cEEECCCCCccccCchhcccCCCCCEEECcCCccc-----------eecCchhhccCCCCCEEECCCCC----CCcCCHH
Confidence            999999999988765 233      7777777766           11378899999999999998722    000012 


Q ss_pred             ccccCCCCcc----EEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecccc
Q 041097          277 AEYQFPPSLT----HLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYA  342 (391)
Q Consensus       277 ~~~~l~~~L~----~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~  342 (391)
                      .+..+ ++|+    .|++++|.+...+... ....+|+.|+++.|..........+.+++|+.|++++++
T Consensus       168 ~~~~l-~~L~~l~l~L~ls~n~l~~~~~~~-~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~N~  235 (276)
T 2z62_A          168 DLRVL-HQMPLLNLSLDLSLNPMNFIQPGA-FKEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNP  235 (276)
T ss_dssp             GGHHH-HTCTTCCEEEECCSSCCCEECTTS-SCSCCEEEEECCSSCCSCCCTTTTTTCCSCCEEECCSSC
T ss_pred             Hhhhh-hhccccceeeecCCCcccccCccc-cCCCcccEEECCCCceeecCHhHhcccccccEEEccCCc
Confidence            34444 4444    8999999887655333 344589999999776554221123678899999999764

>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=99.37  E-value=9.8e-12  Score=126.97  Aligned_cols=208  Identities=17%  Similarity=0.144  Sum_probs=144.0

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCC-cccCCCCcccEEEccCCCCCccCCC-------C
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYP-SGIENLFLLRYLKLNIPSLKSLPSS-------R  221 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p-~~i~~l~~L~~L~l~~~~i~~lp~~-------~  221 (391)
                      +.++.+.+..+...    ...+..+..++.|+.|++++|.+. .+| ..+..+.+|++|++++|.+..++..       +
T Consensus       381 ~~L~~L~L~~n~l~----~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~~L  456 (680)
T 1ziw_A          381 SPLHILNLTKNKIS----KIESDAFSWLGHLEVLDLGLNEIGQELTGQEWRGLENIFEIYLSYNKYLQLTRNSFALVPSL  456 (680)
T ss_dssp             SCCCEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCEEECCSGGGTTCTTCCEEECCSCSEEECCTTTTTTCTTC
T ss_pred             CcCceEECCCCCCC----eEChhhhhCCCCCCEEeCCCCcCccccCcccccCcccccEEecCCCCcceeChhhhhcCccc
Confidence            45666655444332    122355677888888888888876 455 5778888888888888876654332       2


Q ss_pred             cEEEeeCCccCcc-----------eeeEEecc--cccchhH-HhcCCCCCCEEEecCCC--CCCchhhhcc-----cccc
Q 041097          222 KILRLSGNSQFHF-----------SLASLLLY--YQSLLSK-SLCRLSCLESLKLANES--KMPRRSNIIL-----AEYQ  280 (391)
Q Consensus       222 ~~L~l~~~~l~~L-----------~L~~L~l~--~~~~lp~-~i~~l~~L~~L~l~~~~--~lp~L~~Llp-----~~~~  280 (391)
                      ..|++++|.+..+           +|+.|+++  ....+|+ .++.+++|++|++++..  .++.-.  +|     .+..
T Consensus       457 ~~L~l~~n~l~~~~~~p~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~Ls~N~l~~~~~~~--~~~~~~~~~~~  534 (680)
T 1ziw_A          457 QRLMLRRVALKNVDSSPSPFQPLRNLTILDLSNNNIANINDDMLEGLEKLEILDLQHNNLARLWKHA--NPGGPIYFLKG  534 (680)
T ss_dssp             CEEECTTSCCBCTTCSSCTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCGGGGSTT--STTSCCCTTTT
T ss_pred             ccchhccccccccccCCcccccCCCCCEEECCCCCCCcCChhhhccccccCEEeCCCCCccccchhh--ccCCcchhhcC
Confidence            2777777755421           67777777  3445554 57888999999888721  100000  11     3678


Q ss_pred             CCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHh-hc-CCCCCC
Q 041097          281 FPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ-LW-CLKSLN  358 (391)
Q Consensus       281 l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~-~~-~l~~L~  358 (391)
                      + ++|+.|++++|.+...+...++.+++|+.|+++.|.......-....+++|+.|++++| .++.+|.. +. .+++|+
T Consensus       535 l-~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~~~~~L~  612 (680)
T 1ziw_A          535 L-SHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQKN-LITSVEKKVFGPAFRNLT  612 (680)
T ss_dssp             C-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECTTS-CCCBCCHHHHHHHHTTCS
T ss_pred             C-CCCCEEECCCCCCCCCCHHHcccccCcceeECCCCCCCcCCHhHhCCCCCCCEEECCCC-cCCccChhHhcccccccC
Confidence            8 99999999999988777677899999999999977665322112357789999999988 57777654 45 689999


Q ss_pred             EEEeeCCc
Q 041097          359 KLELWWPE  366 (391)
Q Consensus       359 ~L~l~~~~  366 (391)
                      +|+++++|
T Consensus       613 ~l~l~~N~  620 (680)
T 1ziw_A          613 ELDMRFNP  620 (680)
T ss_dssp             EEECTTCC
T ss_pred             EEEccCCC
Confidence            99999865

>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=99.37  E-value=5e-12  Score=127.19  Aligned_cols=210  Identities=18%  Similarity=0.107  Sum_probs=140.1

Q ss_pred             ceEEEEEeccCCCcccccCCCCCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEc
Q 041097          130 NVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKL  209 (391)
Q Consensus       130 ~~r~l~~~~~~~~~~~~~~~~~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l  209 (391)
                      +.+.+.+....... ++....++++.|.+.++...     .++.   .++.|++|++++|.+..+|.   .+.+|++|++
T Consensus        41 ~l~~L~ls~n~L~~-lp~~l~~~L~~L~L~~N~l~-----~lp~---~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~L  108 (622)
T 3g06_A           41 GNAVLNVGESGLTT-LPDCLPAHITTLVIPDNNLT-----SLPA---LPPELRTLEVSGNQLTSLPV---LPPGLLELSI  108 (622)
T ss_dssp             CCCEEECCSSCCSC-CCSCCCTTCSEEEECSCCCS-----CCCC---CCTTCCEEEECSCCCSCCCC---CCTTCCEEEE
T ss_pred             CCcEEEecCCCcCc-cChhhCCCCcEEEecCCCCC-----CCCC---cCCCCCEEEcCCCcCCcCCC---CCCCCCEEEC
Confidence            35566665332222 33322278999988877653     1222   57899999999999998887   6789999999


Q ss_pred             cCCCCCccCCCCc---EEEeeCCccCcc-----eeeEEecc--cccchhHHhcCCCCCCEEEecCCC--CC----Cchhh
Q 041097          210 NIPSLKSLPSSRK---ILRLSGNSQFHF-----SLASLLLY--YQSLLSKSLCRLSCLESLKLANES--KM----PRRSN  273 (391)
Q Consensus       210 ~~~~i~~lp~~~~---~L~l~~~~l~~L-----~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~--~l----p~L~~  273 (391)
                      ++|.+..+|....   .|++++|.+..+     +|+.|+++  ....+|.   .+++|+.|++.+..  .+    ++|+.
T Consensus       109 s~N~l~~l~~~l~~L~~L~L~~N~l~~lp~~l~~L~~L~Ls~N~l~~l~~---~~~~L~~L~L~~N~l~~l~~~~~~L~~  185 (622)
T 3g06_A          109 FSNPLTHLPALPSGLCKLWIFGNQLTSLPVLPPGLQELSVSDNQLASLPA---LPSELCKLWAYNNQLTSLPMLPSGLQE  185 (622)
T ss_dssp             CSCCCCCCCCCCTTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCSCCCC---CCTTCCEEECCSSCCSCCCCCCTTCCE
T ss_pred             cCCcCCCCCCCCCCcCEEECCCCCCCcCCCCCCCCCEEECcCCcCCCcCC---ccCCCCEEECCCCCCCCCcccCCCCcE
Confidence            9999998877444   999999988765     78888888  4445554   35678888887722  22    22322


Q ss_pred             h------ccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccc
Q 041097          274 I------ILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRI  347 (391)
Q Consensus       274 L------lp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l  347 (391)
                      |      +..+...+++|+.|++.+|.+...+    ..+++|+.|+++.|...+   ++ ..+++|+.|++++| +++.+
T Consensus       186 L~Ls~N~l~~l~~~~~~L~~L~L~~N~l~~l~----~~~~~L~~L~Ls~N~L~~---lp-~~l~~L~~L~Ls~N-~L~~l  256 (622)
T 3g06_A          186 LSVSDNQLASLPTLPSELYKLWAYNNRLTSLP----ALPSGLKELIVSGNRLTS---LP-VLPSELKELMVSGN-RLTSL  256 (622)
T ss_dssp             EECCSSCCSCCCCCCTTCCEEECCSSCCSSCC----CCCTTCCEEECCSSCCSC---CC-CCCTTCCEEECCSS-CCSCC
T ss_pred             EECCCCCCCCCCCccchhhEEECcCCcccccC----CCCCCCCEEEccCCccCc---CC-CCCCcCcEEECCCC-CCCcC
Confidence            2      1111111255666666666554433    124778888888665543   11 56688999999987 57888


Q ss_pred             hHhhcCCCCCCEEEeeCCc
Q 041097          348 HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       348 p~~~~~l~~L~~L~l~~~~  366 (391)
                      |.   .+++|++|++++|.
T Consensus       257 p~---~~~~L~~L~Ls~N~  272 (622)
T 3g06_A          257 PM---LPSGLLSLSVYRNQ  272 (622)
T ss_dssp             CC---CCTTCCEEECCSSC
T ss_pred             Cc---ccccCcEEeCCCCC
Confidence            86   67889999998875

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.37  E-value=3.2e-12  Score=110.76  Aligned_cols=152  Identities=23%  Similarity=0.240  Sum_probs=108.4

Q ss_pred             CcccEEEcCCCccccCCcc-cCCCCcccEEEccCCCCCccCCCCc-------EEEeeCCccCcceeeEEecccccchhH-
Q 041097          179 KFLRVLDLGSLVLIRYPSG-IENLFLLRYLKLNIPSLKSLPSSRK-------ILRLSGNSQFHFSLASLLLYYQSLLSK-  249 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~~-i~~l~~L~~L~l~~~~i~~lp~~~~-------~L~l~~~~l~~L~L~~L~l~~~~~lp~-  249 (391)
                      +.|+.|+++++.+..++.. ++.+.+|++|+++++.+..+|....       +|++++|.+.             .+|. 
T Consensus        28 ~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~-------------~~~~~   94 (208)
T 2o6s_A           28 AQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQ-------------SLPNG   94 (208)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-------------CCCTT
T ss_pred             CCCcEEEcCCCccCcCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCCCcCC-------------ccCHh
Confidence            4667777777776655543 5667777777777777766665431       5666666555             4444 


Q ss_pred             HhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCC
Q 041097          250 SLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGI  327 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~  327 (391)
                      .++++++|++|++++..    +.. +|  .+..+ ++|+.|++++|.+...+...++.+++|+.|+++.|.+.       
T Consensus        95 ~~~~l~~L~~L~L~~N~----l~~-~~~~~~~~l-~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~-------  161 (208)
T 2o6s_A           95 VFDKLTQLKELALNTNQ----LQS-LPDGVFDKL-TQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWD-------  161 (208)
T ss_dssp             TTTTCTTCCEEECCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSCCBC-------
T ss_pred             HhcCccCCCEEEcCCCc----Ccc-cCHhHhccC-CcCCEEECCCCccceeCHHHhccCCCccEEEecCCCee-------
Confidence            46889999999998722    011 33  46778 99999999999888777667889999999999966543       


Q ss_pred             CcccccceeeeccccccccchHhhcCCCC
Q 041097          328 RAMPKLECLIINPYAHLKRIHEQLWCLKS  356 (391)
Q Consensus       328 ~~~~~L~~L~l~~c~~l~~lp~~~~~l~~  356 (391)
                      +.+++|+.|+++.+.--..+|.+++.++.
T Consensus       162 ~~~~~l~~L~~~~n~~~g~ip~~~~~l~~  190 (208)
T 2o6s_A          162 CTCPGIRYLSEWINKHSGVVRNSAGSVAP  190 (208)
T ss_dssp             CCTTTTHHHHHHHHHCTTTBBCTTSSBCT
T ss_pred             cCCCCHHHHHHHHHhCCceeeccCccccC
Confidence            45688999999887655578888877665

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.37  E-value=1e-12  Score=121.24  Aligned_cols=179  Identities=21%  Similarity=0.150  Sum_probs=100.3

Q ss_pred             CCcccEEEcCCCccc-cCCccc--CCCCcccEEEccCCCCCccC-----------CCCcEEEeeCCccCcc---------
Q 041097          178 FKFLRVLDLGSLVLI-RYPSGI--ENLFLLRYLKLNIPSLKSLP-----------SSRKILRLSGNSQFHF---------  234 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~-~~p~~i--~~l~~L~~L~l~~~~i~~lp-----------~~~~~L~l~~~~l~~L---------  234 (391)
                      +..|+.|++++|.+. ..|..+  +.+.+|++|++++|.+....           ..+.+|++++|.+..+         
T Consensus        90 ~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~  169 (310)
T 4glp_A           90 YSRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQAHSPAFSCEQVRAFP  169 (310)
T ss_dssp             HSCCCEEEEESCCCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEECCSSCCCCTTSCCCCT
T ss_pred             cCceeEEEeeCCEeccchhhhhhhccCCCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeCCCcchhhHHHhccCC
Confidence            355777888777766 555665  77777888888777766421           1223777777766522         


Q ss_pred             eeeEEecccc--cc---hhHH--hcCCCCCCEEEecCCC--CCCchhhhcc-c-cccCCCCccEEEeecccCCCCChhhh
Q 041097          235 SLASLLLYYQ--SL---LSKS--LCRLSCLESLKLANES--KMPRRSNIIL-A-EYQFPPSLTHLSFSNIELMDDPIPAL  303 (391)
Q Consensus       235 ~L~~L~l~~~--~~---lp~~--i~~l~~L~~L~l~~~~--~lp~L~~Llp-~-~~~l~~~L~~L~l~~~~~~~~~~~~l  303 (391)
                      +|+.|+++..  ..   ++..  ++.+++|++|++++..  .++.    .+ + ++.+ ++|+.|++++|.+....++.+
T Consensus       170 ~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~----~~~~l~~~l-~~L~~L~Ls~N~l~~~~p~~~  244 (310)
T 4glp_A          170 ALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMETPTG----VCAALAAAG-VQPHSLDLSHNSLRATVNPSA  244 (310)
T ss_dssp             TCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSSCCCCHHH----HHHHHHHHT-CCCSSEECTTSCCCCCCCSCC
T ss_pred             CCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCCCCCchHH----HHHHHHhcC-CCCCEEECCCCCCCccchhhH
Confidence            4444444411  11   2222  2456666666665521  0000    11 1 3456 677777777776665433344


Q ss_pred             cCC---CCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          304 EKL---SVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       304 ~~l---~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +.+   ++|++|+++.|....   ++.+.+++|++|++++| +++.+|. +..+++|++|++++++
T Consensus       245 ~~~~~~~~L~~L~Ls~N~l~~---lp~~~~~~L~~L~Ls~N-~l~~~~~-~~~l~~L~~L~L~~N~  305 (310)
T 4glp_A          245 PRCMWSSALNSLNLSFAGLEQ---VPKGLPAKLRVLDLSSN-RLNRAPQ-PDELPEVDNLTLDGNP  305 (310)
T ss_dssp             SSCCCCTTCCCEECCSSCCCS---CCSCCCSCCSCEECCSC-CCCSCCC-TTSCCCCSCEECSSTT
T ss_pred             HhccCcCcCCEEECCCCCCCc---hhhhhcCCCCEEECCCC-cCCCCch-hhhCCCccEEECcCCC
Confidence            444   577777776555441   12233467777777766 3566654 5666777777776665

>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=99.36  E-value=8.9e-12  Score=111.26  Aligned_cols=144  Identities=23%  Similarity=0.249  Sum_probs=84.5

Q ss_pred             cccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCC-c------EEEeeCCccCcceeeEEecccccchh-HH
Q 041097          180 FLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSR-K------ILRLSGNSQFHFSLASLLLYYQSLLS-KS  250 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~-~------~L~l~~~~l~~L~L~~L~l~~~~~lp-~~  250 (391)
                      .++.|+++++.+..++ ..++++.+|++|+++++.+..++... .      +|++++|.+.             .+| ..
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 DTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLA-------------SLPLGV  102 (251)
T ss_dssp             TCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCC-------------CCCTTT
T ss_pred             CCCEEEccCCCcCccCHhHhcCcccCCEEECCCCcCCccCHhHhccCCcCCEEECCCCccc-------------ccChhH
Confidence            4555555555555333 34555555555555555555444322 1      4444444444             333 34


Q ss_pred             hcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC
Q 041097          251 LCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR  328 (391)
Q Consensus       251 i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  328 (391)
                      ++.+++|++|++++..    +.. +|  .+..+ ++|+.|++++|.+...+...++.+++|+.|+++.|...........
T Consensus       103 ~~~l~~L~~L~L~~N~----l~~-~~~~~~~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~  176 (251)
T 3m19_A          103 FDHLTQLDKLYLGGNQ----LKS-LPSGVFDRL-TKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFD  176 (251)
T ss_dssp             TTTCTTCCEEECCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTT
T ss_pred             hcccCCCCEEEcCCCc----CCC-cChhHhccC-CcccEEECcCCcCCccCHHHcCcCcCCCEEECCCCcCCccCHHHHh
Confidence            5677788888777622    000 23  34667 7888888888877766655677788888888876655542222235


Q ss_pred             cccccceeeecccc
Q 041097          329 AMPKLECLIINPYA  342 (391)
Q Consensus       329 ~~~~L~~L~l~~c~  342 (391)
                      .+++|+.|++++++
T Consensus       177 ~l~~L~~L~l~~N~  190 (251)
T 3m19_A          177 RLGKLQTITLFGNQ  190 (251)
T ss_dssp             TCTTCCEEECCSCC
T ss_pred             CCCCCCEEEeeCCc
Confidence            67778888887664

>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=99.36  E-value=7.4e-12  Score=110.25  Aligned_cols=146  Identities=23%  Similarity=0.210  Sum_probs=88.7

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      +.++.+++.+..+|..+.  .+|++|+++++.+..++                             |..++.+++|++|+
T Consensus        22 ~~v~c~~~~l~~ip~~~~--~~L~~L~Ls~n~i~~~~-----------------------------~~~~~~l~~L~~L~   70 (229)
T 3e6j_A           22 TTVDCRSKRHASVPAGIP--TNAQILYLHDNQITKLE-----------------------------PGVFDSLINLKELY   70 (229)
T ss_dssp             TEEECTTSCCSSCCSCCC--TTCSEEECCSSCCCCCC-----------------------------TTTTTTCTTCCEEE
T ss_pred             CEeEccCCCcCccCCCCC--CCCCEEEcCCCccCccC-----------------------------HHHhhCccCCcEEE
Confidence            356666666666666554  46666666666555432                             34455666666666


Q ss_pred             ecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeec
Q 041097          262 LANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIIN  339 (391)
Q Consensus       262 l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~  339 (391)
                      +++..    +.. +|  .+..+ ++|+.|+|++|.+...+...++.+++|+.|+++.|.... .+...+.+++|++|+++
T Consensus        71 L~~N~----l~~-i~~~~~~~l-~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~L~Ls~N~l~~-lp~~~~~l~~L~~L~L~  143 (229)
T 3e6j_A           71 LGSNQ----LGA-LPVGVFDSL-TQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTE-LPRGIERLTHLTHLALD  143 (229)
T ss_dssp             CCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCS-CCTTGGGCTTCSEEECC
T ss_pred             CCCCC----CCC-cChhhcccC-CCcCEEECCCCcCCccChhHhCcchhhCeEeccCCcccc-cCcccccCCCCCEEECC
Confidence            66521    000 22  34566 777777777777766655556777777777777555441 12223566777777777


Q ss_pred             cccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          340 PYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       340 ~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      ++ .++.+|. .+..+++|++|++.++|
T Consensus       144 ~N-~l~~~~~~~~~~l~~L~~L~l~~N~  170 (229)
T 3e6j_A          144 QN-QLKSIPHGAFDRLSSLTHAYLFGNP  170 (229)
T ss_dssp             SS-CCCCCCTTTTTTCTTCCEEECTTSC
T ss_pred             CC-cCCccCHHHHhCCCCCCEEEeeCCC
Confidence            66 4666663 45677777777777654

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.36  E-value=1.6e-12  Score=119.85  Aligned_cols=182  Identities=17%  Similarity=0.158  Sum_probs=128.3

Q ss_pred             cccEEEcCCCccc--cCCc--ccCCCCcccEEEccCCCCC-ccCCCC--c------EEEeeCCccCc------------c
Q 041097          180 FLRVLDLGSLVLI--RYPS--GIENLFLLRYLKLNIPSLK-SLPSSR--K------ILRLSGNSQFH------------F  234 (391)
Q Consensus       180 ~L~~L~l~~~~l~--~~p~--~i~~l~~L~~L~l~~~~i~-~lp~~~--~------~L~l~~~~l~~------------L  234 (391)
                      .++.+.+.++.+.  .+..  ....+.+|++|+++++.+. ..|..+  .      +|++++|.+..            +
T Consensus        65 ~l~~l~l~~~~~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~  144 (310)
T 4glp_A           65 RVRRLTVGAAQVPAQLLVGALRVLAYSRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLK  144 (310)
T ss_dssp             CCCEEEECSCCCBHHHHHHHHHHHHHSCCCEEEEESCCCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHHHTTBC
T ss_pred             ceeEEEEeCCcCCHHHHHHHHHhcccCceeEEEeeCCEeccchhhhhhhccCCCCCEEEeecccccchhhhhHHHHhhhc
Confidence            4667777777654  1111  1223456999999999887 455554  3      99999998775            2


Q ss_pred             -eeeEEecc--cccch-hHHhcCCCCCCEEEecCCCCCCchhhh-cc-ccccCCCCccEEEeecccCCCCCh--h-hhcC
Q 041097          235 -SLASLLLY--YQSLL-SKSLCRLSCLESLKLANESKMPRRSNI-IL-AEYQFPPSLTHLSFSNIELMDDPI--P-ALEK  305 (391)
Q Consensus       235 -~L~~L~l~--~~~~l-p~~i~~l~~L~~L~l~~~~~lp~L~~L-lp-~~~~l~~~L~~L~l~~~~~~~~~~--~-~l~~  305 (391)
                       +|+.|+++  ....+ |..++.+++|++|++++.... ....+ .+ .++.+ ++|++|++++|.+...+.  . .++.
T Consensus       145 ~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~-~~~~~~~~~~~~~l-~~L~~L~Ls~N~l~~l~~~~~~l~~~  222 (310)
T 4glp_A          145 PGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGL-GERGLMAALCPHKF-PAIQNLALRNTGMETPTGVCAALAAA  222 (310)
T ss_dssp             SCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTC-HHHHHHTTSCTTSS-CCCCSCBCCSSCCCCHHHHHHHHHHH
T ss_pred             cCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCc-cchhhhHHHhhhcC-CCCCEEECCCCCCCchHHHHHHHHhc
Confidence             89999998  34444 467889999999999872100 00001 12 34678 999999999998864321  1 3578


Q ss_pred             CCCCCEEEcCCCCCcCccccCCCc---ccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          306 LSVLQVLKLKQNLYSEERTMGIRA---MPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       306 l~~L~~L~l~~~~~~~~~~~~~~~---~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +++|++|+++.|...+..+...+.   +++|++|++++| .++.+|.++.  ++|++|+++++.
T Consensus       223 l~~L~~L~Ls~N~l~~~~p~~~~~~~~~~~L~~L~Ls~N-~l~~lp~~~~--~~L~~L~Ls~N~  283 (310)
T 4glp_A          223 GVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFA-GLEQVPKGLP--AKLRVLDLSSNR  283 (310)
T ss_dssp             TCCCSSEECTTSCCCCCCCSCCSSCCCCTTCCCEECCSS-CCCSCCSCCC--SCCSCEECCSCC
T ss_pred             CCCCCEEECCCCCCCccchhhHHhccCcCcCCEEECCCC-CCCchhhhhc--CCCCEEECCCCc
Confidence            899999999988776543333344   379999999988 5889998774  899999999876

>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=99.35  E-value=5.9e-12  Score=115.09  Aligned_cols=165  Identities=24%  Similarity=0.207  Sum_probs=115.7

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------IL  224 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L  224 (391)
                      ++++.+.+.++...     .+ +.+..++.|+.|++++|.+..++. ++++.+|++|++++|.+..+|. +.      +|
T Consensus        46 ~~L~~L~l~~~~i~-----~~-~~~~~l~~L~~L~L~~n~l~~~~~-l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L  117 (291)
T 1h6t_A           46 NSIDQIIANNSDIK-----SV-QGIQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVKDLSS-LKDLKKLKSL  117 (291)
T ss_dssp             HTCCEEECTTSCCC-----CC-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCGGG-GTTCTTCCEE
T ss_pred             CcccEEEccCCCcc-----cC-hhHhcCCCCCEEEccCCccCCCcc-cccCCCCCEEECCCCcCCCChh-hccCCCCCEE
Confidence            45555555444332     12 346678888888888888887766 8888888888888888877664 22      67


Q ss_pred             EeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhc
Q 041097          225 RLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALE  304 (391)
Q Consensus       225 ~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~  304 (391)
                      ++++|.+.             .+ +.++.+++|++|++++..    +.. ++.+..+ ++|+.|++++|.+...+.  +.
T Consensus       118 ~L~~n~i~-------------~~-~~l~~l~~L~~L~l~~n~----l~~-~~~l~~l-~~L~~L~L~~N~l~~~~~--l~  175 (291)
T 1h6t_A          118 SLEHNGIS-------------DI-NGLVHLPQLESLYLGNNK----ITD-ITVLSRL-TKLDTLSLEDNQISDIVP--LA  175 (291)
T ss_dssp             ECTTSCCC-------------CC-GGGGGCTTCCEEECCSSC----CCC-CGGGGGC-TTCSEEECCSSCCCCCGG--GT
T ss_pred             ECCCCcCC-------------CC-hhhcCCCCCCEEEccCCc----CCc-chhhccC-CCCCEEEccCCccccchh--hc
Confidence            77777666             44 457888999999988722    000 2356678 899999999988776543  88


Q ss_pred             CCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccch
Q 041097          305 KLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIH  348 (391)
Q Consensus       305 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp  348 (391)
                      .+++|+.|+++.|....  ......+++|+.|+++++. +...|
T Consensus       176 ~l~~L~~L~L~~N~i~~--l~~l~~l~~L~~L~l~~n~-i~~~~  216 (291)
T 1h6t_A          176 GLTKLQNLYLSKNHISD--LRALAGLKNLDVLELFSQE-CLNKP  216 (291)
T ss_dssp             TCTTCCEEECCSSCCCB--CGGGTTCTTCSEEEEEEEE-EECCC
T ss_pred             CCCccCEEECCCCcCCC--ChhhccCCCCCEEECcCCc-ccCCc
Confidence            88999999998666554  2234678889999998774 44444

>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=99.35  E-value=1.5e-11  Score=119.54  Aligned_cols=110  Identities=20%  Similarity=0.207  Sum_probs=75.3

Q ss_pred             CceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYL  207 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L  207 (391)
                      ...+.+.+..+.... +..  . ..++.|.+..+....     ++   .-.+.|++|++++|.+..+| .++++.+|++|
T Consensus        91 ~~L~~L~l~~n~l~~-lp~--~~~~L~~L~l~~n~l~~-----l~---~~~~~L~~L~L~~n~l~~lp-~~~~l~~L~~L  158 (454)
T 1jl5_A           91 PHLESLVASCNSLTE-LPE--LPQSLKSLLVDNNNLKA-----LS---DLPPLLEYLGVSNNQLEKLP-ELQNSSFLKII  158 (454)
T ss_dssp             TTCSEEECCSSCCSS-CCC--CCTTCCEEECCSSCCSC-----CC---SCCTTCCEEECCSSCCSSCC-CCTTCTTCCEE
T ss_pred             CCCCEEEccCCcCCc-ccc--ccCCCcEEECCCCccCc-----cc---CCCCCCCEEECcCCCCCCCc-ccCCCCCCCEE
Confidence            456777766332222 211  2 677777776554321     11   11268999999999998888 59999999999


Q ss_pred             EccCCCCCccCCCCc---EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecC
Q 041097          208 KLNIPSLKSLPSSRK---ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLAN  264 (391)
Q Consensus       208 ~l~~~~i~~lp~~~~---~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~  264 (391)
                      +++++.+..+|..+.   +|++++|.+.             .+| .++++++|++|++.+
T Consensus       159 ~l~~N~l~~lp~~~~~L~~L~L~~n~l~-------------~l~-~~~~l~~L~~L~l~~  204 (454)
T 1jl5_A          159 DVDNNSLKKLPDLPPSLEFIAAGNNQLE-------------ELP-ELQNLPFLTAIYADN  204 (454)
T ss_dssp             ECCSSCCSCCCCCCTTCCEEECCSSCCS-------------SCC-CCTTCTTCCEEECCS
T ss_pred             ECCCCcCcccCCCcccccEEECcCCcCC-------------cCc-cccCCCCCCEEECCC
Confidence            999999888876655   8888888777             455 466677777776665

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.35  E-value=8.2e-13  Score=118.96  Aligned_cols=147  Identities=20%  Similarity=0.167  Sum_probs=92.5

Q ss_pred             hhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccch
Q 041097          174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLL  247 (391)
Q Consensus       174 ~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~l  247 (391)
                      .+..++.|++|+++++.+..++ .++.+.+|++|++++|.+..+|. +.      .|++++|.+.             .+
T Consensus        36 ~~~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~L~~N~i~~~~~-l~~l~~L~~L~L~~N~l~-------------~l  100 (263)
T 1xeu_A           36 SQKELSGVQNFNGDNSNIQSLA-GMQFFTNLKELHLSHNQISDLSP-LKDLTKLEELSVNRNRLK-------------NL  100 (263)
T ss_dssp             CHHHHTTCSEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSSCCS-------------CC
T ss_pred             chhhcCcCcEEECcCCCcccch-HHhhCCCCCEEECCCCccCCChh-hccCCCCCEEECCCCccC-------------Cc
Confidence            3566778888888888887776 67788888888888888777664 32      5566665555             44


Q ss_pred             hHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCC
Q 041097          248 SKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGI  327 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~  327 (391)
                      |... . ++|++|++++..    +.. +|.+..+ ++|+.|++++|.+...  +.++.+++|+.|+++.|...+.  ...
T Consensus       101 ~~~~-~-~~L~~L~L~~N~----l~~-~~~l~~l-~~L~~L~Ls~N~i~~~--~~l~~l~~L~~L~L~~N~i~~~--~~l  168 (263)
T 1xeu_A          101 NGIP-S-ACLSRLFLDNNE----LRD-TDSLIHL-KNLEILSIRNNKLKSI--VMLGFLSKLEVLDLHGNEITNT--GGL  168 (263)
T ss_dssp             TTCC-C-SSCCEEECCSSC----CSB-SGGGTTC-TTCCEEECTTSCCCBC--GGGGGCTTCCEEECTTSCCCBC--TTS
T ss_pred             Cccc-c-CcccEEEccCCc----cCC-ChhhcCc-ccccEEECCCCcCCCC--hHHccCCCCCEEECCCCcCcch--HHh
Confidence            4322 2 667777776622    000 2345566 7777777777766553  3566777777777775555442  233


Q ss_pred             Ccccccceeeeccccccccch
Q 041097          328 RAMPKLECLIINPYAHLKRIH  348 (391)
Q Consensus       328 ~~~~~L~~L~l~~c~~l~~lp  348 (391)
                      ..+++|+.|+++++. +...|
T Consensus       169 ~~l~~L~~L~l~~N~-~~~~~  188 (263)
T 1xeu_A          169 TRLKKVNWIDLTGQK-CVNEP  188 (263)
T ss_dssp             TTCCCCCEEEEEEEE-EECCC
T ss_pred             ccCCCCCEEeCCCCc-ccCCc
Confidence            566677777777663 33333

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.34  E-value=1.5e-12  Score=122.93  Aligned_cols=119  Identities=14%  Similarity=0.094  Sum_probs=72.8

Q ss_pred             chhHHhcCCC-CCCEEEecCCC--CCCchhhhcc-ccccCCCCccEEEeecccCCCCCh----hhhcCC-CCCCEEEcCC
Q 041097          246 LLSKSLCRLS-CLESLKLANES--KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPI----PALEKL-SVLQVLKLKQ  316 (391)
Q Consensus       246 ~lp~~i~~l~-~L~~L~l~~~~--~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~----~~l~~l-~~L~~L~l~~  316 (391)
                      .++..+..++ +|++|++++..  .... .. +. .+...|++|+.|+|++|.+.....    ..+..+ ++|+.|+++.
T Consensus       157 ~l~~~l~~~~~~L~~L~Ls~n~l~~~~~-~~-l~~~l~~~~~~L~~L~Ls~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls~  234 (362)
T 3goz_A          157 ELIQILAAIPANVNSLNLRGNNLASKNC-AE-LAKFLASIPASVTSLDLSANLLGLKSYAELAYIFSSIPNHVVSLNLCL  234 (362)
T ss_dssp             HHHHHHHTSCTTCCEEECTTSCGGGSCH-HH-HHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHHSCTTCCEEECCS
T ss_pred             HHHHHHhcCCccccEeeecCCCCchhhH-HH-HHHHHHhCCCCCCEEECCCCCCChhHHHHHHHHHhcCCCCceEEECcC
Confidence            4566667766 88888887722  0000 00 11 233443488888888888766442    334443 5888888886


Q ss_pred             CCCcCccc----cCCCcccccceeeecccc-------ccccchHhhcCCCCCCEEEeeCCc
Q 041097          317 NLYSEERT----MGIRAMPKLECLIINPYA-------HLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       317 ~~~~~~~~----~~~~~~~~L~~L~l~~c~-------~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      |.......    .....+++|++|++++|.       .+..++..+..+++|++|++++++
T Consensus       235 N~l~~~~~~~l~~~~~~l~~L~~L~L~~n~l~~i~~~~~~~l~~~~~~l~~L~~LdL~~N~  295 (362)
T 3goz_A          235 NCLHGPSLENLKLLKDSLKHLQTVYLDYDIVKNMSKEQCKALGAAFPNIQKIILVDKNGKE  295 (362)
T ss_dssp             SCCCCCCHHHHHHTTTTTTTCSEEEEEHHHHTTCCHHHHHHHHTTSTTCCEEEEECTTSCB
T ss_pred             CCCCcHHHHHHHHHHhcCCCccEEEeccCCccccCHHHHHHHHHHhccCCceEEEecCCCc
Confidence            66544321    112567788888888875       133455566778888888887754

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.33  E-value=1.9e-11  Score=105.77  Aligned_cols=146  Identities=26%  Similarity=0.258  Sum_probs=79.4

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      +.++.+++.+..+|..+.  .+|++|+++++.+..+|..                             .++.+++|++|+
T Consensus        10 ~~v~c~~~~l~~~p~~~~--~~l~~L~l~~n~l~~~~~~-----------------------------~~~~l~~L~~L~   58 (208)
T 2o6s_A           10 TTVECYSQGRTSVPTGIP--AQTTYLDLETNSLKSLPNG-----------------------------VFDELTSLTQLY   58 (208)
T ss_dssp             TEEECCSSCCSSCCSCCC--TTCSEEECCSSCCCCCCTT-----------------------------TTTTCTTCSEEE
T ss_pred             CEEEecCCCccCCCCCCC--CCCcEEEcCCCccCcCChh-----------------------------hhcccccCcEEE
Confidence            456777777777776654  4788888888887766543                             234555555555


Q ss_pred             ecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeec
Q 041097          262 LANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIIN  339 (391)
Q Consensus       262 l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~  339 (391)
                      +++..    +.. +|  .+..+ ++|++|++++|.+...+...++.+++|++|+++.|..........+.+++|++|+++
T Consensus        59 l~~n~----l~~-~~~~~~~~l-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~  132 (208)
T 2o6s_A           59 LGGNK----LQS-LPNGVFNKL-TSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLY  132 (208)
T ss_dssp             CCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECC
T ss_pred             CCCCc----cCc-cChhhcCCC-CCcCEEECCCCcCCccCHhHhcCccCCCEEEcCCCcCcccCHhHhccCCcCCEEECC
Confidence            55411    000 22  23445 566666666555554444445555666666665444332111112445566666665


Q ss_pred             cccccccchHh-hcCCCCCCEEEeeCC
Q 041097          340 PYAHLKRIHEQ-LWCLKSLNKLELWWP  365 (391)
Q Consensus       340 ~c~~l~~lp~~-~~~l~~L~~L~l~~~  365 (391)
                      ++ .++.+|.. +..+++|++|+++++
T Consensus       133 ~N-~l~~~~~~~~~~l~~L~~L~l~~N  158 (208)
T 2o6s_A          133 QN-QLKSVPDGVFDRLTSLQYIWLHDN  158 (208)
T ss_dssp             SS-CCSCCCTTTTTTCTTCCEEECCSC
T ss_pred             CC-ccceeCHHHhccCCCccEEEecCC
Confidence            55 34444433 455566666666553

>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=99.31  E-value=9e-12  Score=125.06  Aligned_cols=143  Identities=27%  Similarity=0.246  Sum_probs=91.5

Q ss_pred             hhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccch
Q 041097          174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLL  247 (391)
Q Consensus       174 ~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~l  247 (391)
                      .+..++.|+.|++++|.+..++. ++.+.+|++|+|++|.+..+| .+.      .|+|++|.+.             .+
T Consensus        60 ~l~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~Ls~N~l~-------------~l  124 (605)
T 1m9s_A           60 GIQYLPNVTKLFLNGNKLTDIKP-LTNLKNLGWLFLDENKIKDLS-SLKDLKKLKSLSLEHNGIS-------------DI  124 (605)
T ss_dssp             TGGGCTTCCEEECTTSCCCCCGG-GGGCTTCCEEECCSSCCCCCT-TSTTCTTCCEEECTTSCCC-------------CC
T ss_pred             HHccCCCCCEEEeeCCCCCCChh-hccCCCCCEEECcCCCCCCCh-hhccCCCCCEEEecCCCCC-------------CC
Confidence            45667777777777777776655 777777777777777777655 232      5666665555             44


Q ss_pred             hHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCC
Q 041097          248 SKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGI  327 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~  327 (391)
                       +.++.|++|+.|++++..    +.. ++.+..+ ++|+.|+|++|.+...++  +..+++|+.|+|+.|....  ....
T Consensus       125 -~~l~~l~~L~~L~Ls~N~----l~~-l~~l~~l-~~L~~L~Ls~N~l~~~~~--l~~l~~L~~L~Ls~N~i~~--l~~l  193 (605)
T 1m9s_A          125 -NGLVHLPQLESLYLGNNK----ITD-ITVLSRL-TKLDTLSLEDNQISDIVP--LAGLTKLQNLYLSKNHISD--LRAL  193 (605)
T ss_dssp             -GGGGGCTTCSEEECCSSC----CCC-CGGGGSC-TTCSEEECCSSCCCCCGG--GTTCTTCCEEECCSSCCCB--CGGG
T ss_pred             -ccccCCCccCEEECCCCc----cCC-chhhccc-CCCCEEECcCCcCCCchh--hccCCCCCEEECcCCCCCC--ChHH
Confidence             346777777777777622    000 2345566 777777777777665432  6777777777777555443  2334


Q ss_pred             Ccccccceeeecccc
Q 041097          328 RAMPKLECLIINPYA  342 (391)
Q Consensus       328 ~~~~~L~~L~l~~c~  342 (391)
                      ..+++|+.|++++|.
T Consensus       194 ~~l~~L~~L~L~~N~  208 (605)
T 1m9s_A          194 AGLKNLDVLELFSQE  208 (605)
T ss_dssp             TTCTTCSEEECCSEE
T ss_pred             ccCCCCCEEEccCCc
Confidence            567777777777664

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.31  E-value=8.6e-12  Score=117.58  Aligned_cols=164  Identities=23%  Similarity=0.214  Sum_probs=105.0

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCC---c-----EEEeeCCccCcceeeEEecccccchh-HHhc
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSR---K-----ILRLSGNSQFHFSLASLLLYYQSLLS-KSLC  252 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~---~-----~L~l~~~~l~~L~L~~L~l~~~~~lp-~~i~  252 (391)
                      ++++++++.+..+|..+..  .+++|++++|.+..+|...   .     .|++++|.+.             .++ ..+.
T Consensus        21 ~~l~c~~~~l~~iP~~~~~--~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N~i~-------------~i~~~~~~   85 (361)
T 2xot_A           21 NILSCSKQQLPNVPQSLPS--YTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLN-------------FISSEAFV   85 (361)
T ss_dssp             TEEECCSSCCSSCCSSCCT--TCSEEECCSSCCCEECTTSSSSCCTTCCEEECCSSCCC-------------EECTTTTT
T ss_pred             CEEEeCCCCcCccCccCCC--CCCEEECCCCCCCccChhhhhhcccccCEEECCCCcCC-------------ccChhhcc
Confidence            3455555555555554432  3555555555555544322   1     4444444444             443 4578


Q ss_pred             CCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc--cCC-C
Q 041097          253 RLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT--MGI-R  328 (391)
Q Consensus       253 ~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~--~~~-~  328 (391)
                      ++++|++|++++..    +..+.| .+..+ ++|+.|+|++|.+...+...+..+++|+.|+++.|.......  +.. +
T Consensus        86 ~l~~L~~L~Ls~N~----l~~~~~~~~~~l-~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~  160 (361)
T 2xot_A           86 PVPNLRYLDLSSNH----LHTLDEFLFSDL-QALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQISRFPVELIKDGN  160 (361)
T ss_dssp             TCTTCCEEECCSSC----CCEECTTTTTTC-TTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCSCCGGGTC---
T ss_pred             CCCCCCEEECCCCc----CCcCCHHHhCCC-cCCCEEECCCCcccEECHHHhCCcccCCEEECCCCcCCeeCHHHhcCcc
Confidence            88899999988722    111122 56778 899999999998887666788899999999999776554211  111 4


Q ss_pred             cccccceeeeccccccccch-HhhcCCCC--CCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRIH-EQLWCLKS--LNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp-~~~~~l~~--L~~L~l~~~~  366 (391)
                      .+++|+.|+++++ .++.+| ..+..++.  |+.|++.++|
T Consensus       161 ~l~~L~~L~L~~N-~l~~l~~~~~~~l~~~~l~~l~l~~N~  200 (361)
T 2xot_A          161 KLPKLMLLDLSSN-KLKKLPLTDLQKLPAWVKNGLYLHNNP  200 (361)
T ss_dssp             -CTTCCEEECCSS-CCCCCCHHHHHHSCHHHHTTEECCSSC
T ss_pred             cCCcCCEEECCCC-CCCccCHHHhhhccHhhcceEEecCCC
Confidence            6889999999977 577877 45677776  4889998754

>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=99.30  E-value=1.1e-11  Score=109.68  Aligned_cols=189  Identities=14%  Similarity=0.114  Sum_probs=139.4

Q ss_pred             cCceEEEEEeccCCCcccccCC-C-CCccEEEEEecC-CcCCCchhhHHhhccCCcccEEEcCC-CccccCC-cccCCCC
Q 041097          128 RENVKRFTAHRKLNDFAFLDDF-D-SFLHSLLYLTSG-SQYLDPTYCEKICKMFKFLRVLDLGS-LVLIRYP-SGIENLF  202 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~~~-~-~~lrsl~~~~~~-~~~~~~~~~~~~~~~~~~L~~L~l~~-~~l~~~p-~~i~~l~  202 (391)
                      +..++.+.+............. + ++++.|.+.++. ..    ...+..+..++.|++|++++ +.+..+| ..+..+.
T Consensus        30 ~~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~~l~----~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~  105 (239)
T 2xwt_C           30 PPSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQ----QLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELP  105 (239)
T ss_dssp             CTTCCEEEEESCCCSEECTTTTTTCTTCCEEEEECCSSCC----EECTTTEESCTTCCEEEEEEETTCCEECTTSEECCT
T ss_pred             CCcccEEEEeCCcceEECHHHccCCCCCcEEeCCCCCCcc----eeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCC
Confidence            4468888887444443222234 4 899999998775 32    12224678899999999998 8998776 5678999


Q ss_pred             cccEEEccCCCCCccCCCCc---------EEEeeCC-ccCcceeeEEecccccchhH-HhcCCCCCC-EEEecCCCCCCc
Q 041097          203 LLRYLKLNIPSLKSLPSSRK---------ILRLSGN-SQFHFSLASLLLYYQSLLSK-SLCRLSCLE-SLKLANESKMPR  270 (391)
Q Consensus       203 ~L~~L~l~~~~i~~lp~~~~---------~L~l~~~-~l~~L~L~~L~l~~~~~lp~-~i~~l~~L~-~L~l~~~~~lp~  270 (391)
                      +|++|+++++.+..+|. +.         .|++++| .+.             .+|. .+..+++|+ +|++++..    
T Consensus       106 ~L~~L~l~~n~l~~lp~-~~~l~~L~~L~~L~l~~N~~l~-------------~i~~~~~~~l~~L~~~L~l~~n~----  167 (239)
T 2xwt_C          106 LLKFLGIFNTGLKMFPD-LTKVYSTDIFFILEITDNPYMT-------------SIPVNAFQGLCNETLTLKLYNNG----  167 (239)
T ss_dssp             TCCEEEEEEECCCSCCC-CTTCCBCCSEEEEEEESCTTCC-------------EECTTTTTTTBSSEEEEECCSCC----
T ss_pred             CCCEEeCCCCCCccccc-cccccccccccEEECCCCcchh-------------hcCcccccchhcceeEEEcCCCC----
Confidence            99999999999998886 32         6677777 666             6665 588999999 99998722    


Q ss_pred             hhhhcc-ccccCCCCccEEEeeccc-CCCCChhhhcCC-CCCCEEEcCCCCCcCccccCCCcccccceeeeccccc
Q 041097          271 RSNIIL-AEYQFPPSLTHLSFSNIE-LMDDPIPALEKL-SVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAH  343 (391)
Q Consensus       271 L~~Llp-~~~~l~~~L~~L~l~~~~-~~~~~~~~l~~l-~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~  343 (391)
                      +.. +| ..... ++|+.|++++|. +...+...+..+ ++|+.|+++.|....   ++...+++|+.|.++++..
T Consensus       168 l~~-i~~~~~~~-~~L~~L~L~~n~~l~~i~~~~~~~l~~~L~~L~l~~N~l~~---l~~~~~~~L~~L~l~~~~~  238 (239)
T 2xwt_C          168 FTS-VQGYAFNG-TKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLDVSQTSVTA---LPSKGLEHLKELIARNTWT  238 (239)
T ss_dssp             CCE-ECTTTTTT-CEEEEEECTTCTTCCEECTTTTTTCSBCCSEEECTTCCCCC---CCCTTCTTCSEEECTTC--
T ss_pred             Ccc-cCHhhcCC-CCCCEEEcCCCCCcccCCHHHhhccccCCcEEECCCCcccc---CChhHhccCceeeccCccC
Confidence            000 45 44455 799999999994 877666778899 999999999766543   3334899999999998754

>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=99.30  E-value=3.8e-14  Score=141.35  Aligned_cols=174  Identities=21%  Similarity=0.158  Sum_probs=85.8

Q ss_pred             ccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCC--------------CCccCCCCc------EEE-eeCCccCcc
Q 041097          176 KMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPS--------------LKSLPSSRK------ILR-LSGNSQFHF  234 (391)
Q Consensus       176 ~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~--------------i~~lp~~~~------~L~-l~~~~l~~L  234 (391)
                      ...+.|+.|+++++.+..+|+.|+++.+|+.|+++++.              ....|..++      .|+ ++.+.+.. 
T Consensus       346 ~~~~~L~~L~Ls~n~L~~Lp~~i~~l~~L~~L~l~~n~~l~~l~~ll~~~~~~~~~~~~l~~l~~L~~L~~l~~n~~~~-  424 (567)
T 1dce_A          346 ATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDD-  424 (567)
T ss_dssp             STTTTSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHHHH-
T ss_pred             ccCccceeccCChhhHHhhHHHHHHHHHHHHhccccchhhhhHHHHHHhcccccCCHHHHHHHHhcccCcchhhcccch-
Confidence            44677888888888888888888888888888875542              111222222      333 22222111 


Q ss_pred             eeeEEecc--cccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEE
Q 041097          235 SLASLLLY--YQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVL  312 (391)
Q Consensus       235 ~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L  312 (391)
                       |+.+.+.  ....+|.     ..|+.|++++..    +.. +|.++.+ ++|+.|+|++|.+...| ..++.+++|+.|
T Consensus       425 -L~~l~l~~n~i~~l~~-----~~L~~L~Ls~n~----l~~-lp~~~~l-~~L~~L~Ls~N~l~~lp-~~~~~l~~L~~L  491 (567)
T 1dce_A          425 -LRSKFLLENSVLKMEY-----ADVRVLHLAHKD----LTV-LCHLEQL-LLVTHLDLSHNRLRALP-PALAALRCLEVL  491 (567)
T ss_dssp             -HHHHHHHHHHHHHHHH-----TTCSEEECTTSC----CSS-CCCGGGG-TTCCEEECCSSCCCCCC-GGGGGCTTCCEE
T ss_pred             -hhhhhhhcccccccCc-----cCceEEEecCCC----CCC-CcCcccc-ccCcEeecCcccccccc-hhhhcCCCCCEE
Confidence             1111111  0111111     135555555411    000 3334445 55555555555555332 455555555555


Q ss_pred             EcCCCCCcCccccCCCcccccceeeeccccccccc--hHhhcCCCCCCEEEeeCCc
Q 041097          313 KLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRI--HEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       313 ~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~l--p~~~~~l~~L~~L~l~~~~  366 (391)
                      +++.|...+  ++..+.+++|+.|++++| .++.+  |..++.+++|++|++++++
T Consensus       492 ~Ls~N~l~~--lp~l~~l~~L~~L~Ls~N-~l~~~~~p~~l~~l~~L~~L~L~~N~  544 (567)
T 1dce_A          492 QASDNALEN--VDGVANLPRLQELLLCNN-RLQQSAAIQPLVSCPRLVLLNLQGNS  544 (567)
T ss_dssp             ECCSSCCCC--CGGGTTCSSCCEEECCSS-CCCSSSTTGGGGGCTTCCEEECTTSG
T ss_pred             ECCCCCCCC--CcccCCCCCCcEEECCCC-CCCCCCCcHHHhcCCCCCEEEecCCc
Confidence            555444433  223345555555555554 34444  5555555555555555544

>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=99.29  E-value=2.7e-12  Score=119.50  Aligned_cols=174  Identities=18%  Similarity=0.148  Sum_probs=124.1

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccCC-CCCc--cCCCC-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNIP-SLKS--LPSSR-----  221 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~~-~i~~--lp~~~-----  221 (391)
                      ++++.|.+.++..   ....++..+..++.|+.|++++|.+. ..|..++++.+|++|++++| .+..  +|..+     
T Consensus        93 ~~L~~L~L~~~~l---~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~L~~~~~l~~~~l~~~~~~~~~  169 (336)
T 2ast_B           93 FRVQHMDLSNSVI---EVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSR  169 (336)
T ss_dssp             BCCCEEECTTCEE---CHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTT
T ss_pred             CCCCEEEccCCCc---CHHHHHHHHhhCCCCCEEeCcCcccCHHHHHHHhcCCCCCEEECCCCCCCCHHHHHHHHhcCCC
Confidence            7788887765442   23336677889999999999999987 67788899999999999998 5662  44322     


Q ss_pred             -cEEEeeCC-ccCcceeeEEecccccchhHHhcCCC-CCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeeccc-C
Q 041097          222 -KILRLSGN-SQFHFSLASLLLYYQSLLSKSLCRLS-CLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIE-L  295 (391)
Q Consensus       222 -~~L~l~~~-~l~~L~L~~L~l~~~~~lp~~i~~l~-~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~-~  295 (391)
                       ..|++++| .+..           ..++..++.++ +|++|++++.. .+..-.  +| .+..+ ++|+.|++++|. +
T Consensus       170 L~~L~l~~~~~l~~-----------~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~--l~~~~~~~-~~L~~L~l~~~~~l  235 (336)
T 2ast_B          170 LDELNLSWCFDFTE-----------KHVQVAVAHVSETITQLNLSGYRKNLQKSD--LSTLVRRC-PNLVHLDLSDSVML  235 (336)
T ss_dssp             CCEEECCCCTTCCH-----------HHHHHHHHHSCTTCCEEECCSCGGGSCHHH--HHHHHHHC-TTCSEEECTTCTTC
T ss_pred             CCEEcCCCCCCcCh-----------HHHHHHHHhcccCCCEEEeCCCcccCCHHH--HHHHHhhC-CCCCEEeCCCCCcC
Confidence             27777777 6651           12677788899 99999998721 010001  45 56678 899999999987 5


Q ss_pred             CCCChhhhcCCCCCCEEEcCCCCCcCcc-ccCCCcccccceeeeccc
Q 041097          296 MDDPIPALEKLSVLQVLKLKQNLYSEER-TMGIRAMPKLECLIINPY  341 (391)
Q Consensus       296 ~~~~~~~l~~l~~L~~L~l~~~~~~~~~-~~~~~~~~~L~~L~l~~c  341 (391)
                      ....+..++++++|+.|+++.|...... ....+.+++|++|++++|
T Consensus       236 ~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~l~~~~~L~~L~l~~~  282 (336)
T 2ast_B          236 KNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI  282 (336)
T ss_dssp             CGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             CHHHHHHHhCCCCCCEeeCCCCCCCCHHHHHHHhcCCCCCEEeccCc
Confidence            5555678888999999999865422111 212356889999999988

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.27  E-value=1.8e-11  Score=110.22  Aligned_cols=142  Identities=22%  Similarity=0.172  Sum_probs=104.9

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc----EEEe
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK----ILRL  226 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~----~L~l  226 (391)
                      ++++.|.+.++...     .+ +.+..++.|+.|++++|.+..++. ++++.+|++|++++|.++.+|....    .|++
T Consensus        41 ~~L~~L~l~~n~i~-----~l-~~l~~l~~L~~L~L~~N~i~~~~~-l~~l~~L~~L~L~~N~l~~l~~~~~~~L~~L~L  113 (263)
T 1xeu_A           41 SGVQNFNGDNSNIQ-----SL-AGMQFFTNLKELHLSHNQISDLSP-LKDLTKLEELSVNRNRLKNLNGIPSACLSRLFL  113 (263)
T ss_dssp             TTCSEEECTTSCCC-----CC-TTGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSSCCSCCTTCCCSSCCEEEC
T ss_pred             CcCcEEECcCCCcc-----cc-hHHhhCCCCCEEECCCCccCCChh-hccCCCCCEEECCCCccCCcCccccCcccEEEc
Confidence            67777777655443     12 256778899999999998887776 8888999999999988887765332    7777


Q ss_pred             eCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCC
Q 041097          227 SGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKL  306 (391)
Q Consensus       227 ~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l  306 (391)
                      ++|.+.             .++ .++.+++|++|++++..    +.. +|.++.+ ++|+.|++++|.+...  ..+..+
T Consensus       114 ~~N~l~-------------~~~-~l~~l~~L~~L~Ls~N~----i~~-~~~l~~l-~~L~~L~L~~N~i~~~--~~l~~l  171 (263)
T 1xeu_A          114 DNNELR-------------DTD-SLIHLKNLEILSIRNNK----LKS-IVMLGFL-SKLEVLDLHGNEITNT--GGLTRL  171 (263)
T ss_dssp             CSSCCS-------------BSG-GGTTCTTCCEEECTTSC----CCB-CGGGGGC-TTCCEEECTTSCCCBC--TTSTTC
T ss_pred             cCCccC-------------CCh-hhcCcccccEEECCCCc----CCC-ChHHccC-CCCCEEECCCCcCcch--HHhccC
Confidence            777766             554 58889999999988722    000 3456678 8999999999887764  677888


Q ss_pred             CCCCEEEcCCCCCcC
Q 041097          307 SVLQVLKLKQNLYSE  321 (391)
Q Consensus       307 ~~L~~L~l~~~~~~~  321 (391)
                      ++|+.|++++|....
T Consensus       172 ~~L~~L~l~~N~~~~  186 (263)
T 1xeu_A          172 KKVNWIDLTGQKCVN  186 (263)
T ss_dssp             CCCCEEEEEEEEEEC
T ss_pred             CCCCEEeCCCCcccC
Confidence            999999998665543

>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=99.27  E-value=1.1e-12  Score=127.72  Aligned_cols=213  Identities=15%  Similarity=0.057  Sum_probs=132.4

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCcccc-CCcccC-----CCCcccEEEccCCCCCc-----cCC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIR-YPSGIE-----NLFLLRYLKLNIPSLKS-----LPS  219 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~-~p~~i~-----~l~~L~~L~l~~~~i~~-----lp~  219 (391)
                      ++++.|.+..+.........+...+..++.|+.|++++|.+.. .+..+.     ...+|++|+++++.+..     +|.
T Consensus       142 ~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~  221 (461)
T 1z7x_W          142 CRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCG  221 (461)
T ss_dssp             CCCCEEECTTSCCBGGGHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHHHSCCCCCEEECTTSCCBTTHHHHHHH
T ss_pred             CcceEEECCCCCCCHHHHHHHHHHHhhCCCCCEEECcCCCcchHHHHHHHHHHhcCCCCceEEEccCCCCcHHHHHHHHH
Confidence            3566666544433211111334556667777777777777652 122222     24477777777777664     333


Q ss_pred             C------CcEEEeeCCccCcc--------------eeeEEecc--ccc-----chhHHhcCCCCCCEEEecCCC-CCCch
Q 041097          220 S------RKILRLSGNSQFHF--------------SLASLLLY--YQS-----LLSKSLCRLSCLESLKLANES-KMPRR  271 (391)
Q Consensus       220 ~------~~~L~l~~~~l~~L--------------~L~~L~l~--~~~-----~lp~~i~~l~~L~~L~l~~~~-~lp~L  271 (391)
                      .      +..|++++|.+...              +|+.|+++  ...     .++..+..+++|++|++++.. .-...
T Consensus       222 ~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~  301 (461)
T 1z7x_W          222 IVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGA  301 (461)
T ss_dssp             HHHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHH
T ss_pred             HHHhCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECcCCCCCHHHHHHHHHHHhhCCCcceEECCCCCCchHHH
Confidence            2      23777777765431              67777777  222     267778888888888887621 00000


Q ss_pred             hhhcc-ccc-cCCCCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCCCcCccccCC-----Ccccccceeeecc
Q 041097          272 SNIIL-AEY-QFPPSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNLYSEERTMGI-----RAMPKLECLIINP  340 (391)
Q Consensus       272 ~~Llp-~~~-~l~~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~~~~~-----~~~~~L~~L~l~~  340 (391)
                      .. ++ .+. .. ++|+.|++++|.+....    ...+..+++|+.|+++.|......+...     ...++|++|++++
T Consensus       302 ~~-l~~~l~~~~-~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~  379 (461)
T 1z7x_W          302 RL-LCETLLEPG-CQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLAD  379 (461)
T ss_dssp             HH-HHHHHTSTT-CCCCEEECTTSCCBGGGHHHHHHHHHHCSSCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTT
T ss_pred             HH-HHHHhccCC-ccceeeEcCCCCCchHHHHHHHHHHhhCCCccEEEccCCccccccHHHHHHHHcCCCCceEEEECCC
Confidence            00 22 121 23 69999999999876643    3556778999999999665443221111     1267999999999


Q ss_pred             ccccc-----cchHhhcCCCCCCEEEeeCCc
Q 041097          341 YAHLK-----RIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       341 c~~l~-----~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      |. +.     .+|.++..+++|++|++++++
T Consensus       380 n~-i~~~~~~~l~~~l~~~~~L~~L~l~~N~  409 (461)
T 1z7x_W          380 CD-VSDSSCSSLAATLLANHSLRELDLSNNC  409 (461)
T ss_dssp             SC-CCHHHHHHHHHHHHHCCCCCEEECCSSS
T ss_pred             CC-CChhhHHHHHHHHHhCCCccEEECCCCC
Confidence            84 66     688889899999999999886

>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=99.27  E-value=3.2e-12  Score=121.58  Aligned_cols=106  Identities=18%  Similarity=0.211  Sum_probs=74.3

Q ss_pred             CCCCEEEecCCC----CCCchhhhcc-ccccCCCCccEEEeecccCCCC----Chh-hhcCCCCCCEEEcCCCCCcC---
Q 041097          255 SCLESLKLANES----KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDD----PIP-ALEKLSVLQVLKLKQNLYSE---  321 (391)
Q Consensus       255 ~~L~~L~l~~~~----~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~----~~~-~l~~l~~L~~L~l~~~~~~~---  321 (391)
                      ++|++|++++..    .+|.    +. .+..+ ++|+.|++++|.+...    ..+ .+..+++|+.|+++.|....   
T Consensus       159 ~~L~~L~L~~n~l~~~~~~~----l~~~l~~~-~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~  233 (386)
T 2ca6_A          159 PPLRSIICGRNRLENGSMKE----WAKTFQSH-RLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGS  233 (386)
T ss_dssp             CCCCEEECCSSCCTGGGHHH----HHHHHHHC-TTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHH
T ss_pred             CCCcEEECCCCCCCcHHHHH----HHHHHHhC-CCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHH
Confidence            899999998721    1111    11 44567 8999999999987632    133 67889999999999766531   


Q ss_pred             -ccccCCCcccccceeeecccccccc-----chHhhc--CCCCCCEEEeeCCc
Q 041097          322 -ERTMGIRAMPKLECLIINPYAHLKR-----IHEQLW--CLKSLNKLELWWPE  366 (391)
Q Consensus       322 -~~~~~~~~~~~L~~L~l~~c~~l~~-----lp~~~~--~l~~L~~L~l~~~~  366 (391)
                       ..+.....+++|++|++++|. +..     +|.++.  .+++|++|++++|.
T Consensus       234 ~~l~~~l~~~~~L~~L~L~~n~-i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~  285 (386)
T 2ca6_A          234 SALAIALKSWPNLRELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNE  285 (386)
T ss_dssp             HHHHHHGGGCTTCCEEECTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSC
T ss_pred             HHHHHHHccCCCcCEEECCCCC-CchhhHHHHHHHHhhccCCCeEEEECcCCc
Confidence             111123577899999999885 543     477774  48999999999876

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=99.26  E-value=1.5e-11  Score=122.37  Aligned_cols=89  Identities=15%  Similarity=0.179  Sum_probs=69.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC--CccccccccEEEEEEcCCCc--ChHHHHHHHHHhhcCCCC--CC---CCCChHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYS--SNYVKHYFDCHAWVQESLPY--DADQILYDIIKFVMPSPE--GF---IPDNNEATVEK   71 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~--~~~lk~~F~~~~~~~vs~~~--~~~~i~~~~~~~~~~~~e--g~---~~~~~~~~~~~   71 (391)
                      |+||||||+||||||+.+|+  |..++.+|+.++|+++++.+  +...+++.++........  ..   .....++....
T Consensus       155 v~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~  234 (549)
T 2a5y_B          155 LFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRM  234 (549)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHHhcCcccccccccccccHHHHHHH
Confidence            68999999999999999998  77899999999999999885  888999988887653211  11   11124556777


Q ss_pred             HHHHHHcC-ccEEeeeccC
Q 041097           72 YLEQLING-GFVGAGKRSD   89 (391)
Q Consensus        72 ~~~~L~~k-~~l~~~~~~~   89 (391)
                      +...|.++ +++.+.++.+
T Consensus       235 l~~~L~~~kr~LlVLDdv~  253 (549)
T 2a5y_B          235 ICNALIDRPNTLFVFDDVV  253 (549)
T ss_dssp             HHHHHTTSTTEEEEEEEEC
T ss_pred             HHHHHcCCCcEEEEEECCC
Confidence            88888886 8888877643

>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=99.26  E-value=2.7e-12  Score=124.86  Aligned_cols=213  Identities=18%  Similarity=0.079  Sum_probs=122.0

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCcccc-CCcccC-CCC----cccEEEccCCCCC-----ccCC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIR-YPSGIE-NLF----LLRYLKLNIPSLK-----SLPS  219 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~-~p~~i~-~l~----~L~~L~l~~~~i~-----~lp~  219 (391)
                      ++++.+.+.++.........++..+..++.|++|++++|.+.. .+..+. .+.    +|++|++++|.+.     .+|.
T Consensus        28 ~~L~~L~L~~~~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~L~~n~i~~~~~~~l~~  107 (461)
T 1z7x_W           28 QQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSS  107 (461)
T ss_dssp             TTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHH
T ss_pred             CCccEEEccCCCCCHHHHHHHHHHHHhCCCcCEEeCCCCcCChHHHHHHHHHHhhCCCceeEEEccCCCCCHHHHHHHHH
Confidence            5666666665543210011344556666777777777776552 122221 233    5777777777665     2333


Q ss_pred             CCc------EEEeeCCccCcc--------------eeeEEecc-------cccchhHHhcCCCCCCEEEecCCC-CCCch
Q 041097          220 SRK------ILRLSGNSQFHF--------------SLASLLLY-------YQSLLSKSLCRLSCLESLKLANES-KMPRR  271 (391)
Q Consensus       220 ~~~------~L~l~~~~l~~L--------------~L~~L~l~-------~~~~lp~~i~~l~~L~~L~l~~~~-~lp~L  271 (391)
                      .+.      +|++++|.+...              +|++|+++       ....++..+..+++|++|++++.. .-...
T Consensus       108 ~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~  187 (461)
T 1z7x_W          108 TLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELTVSNNDINEAGV  187 (461)
T ss_dssp             HTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCTTCCEEECCSSBCHHHHH
T ss_pred             HHccCCceeEEECCCCcCchHHHHHHHHHHhcCCCcceEEECCCCCCCHHHHHHHHHHHhhCCCCCEEECcCCCcchHHH
Confidence            332      777777765431              37777777       112456777788888888887611 00000


Q ss_pred             hhhcc-ccc-cCCCCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCCCcCccc--c-C--CCcccccceeeecc
Q 041097          272 SNIIL-AEY-QFPPSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNLYSEERT--M-G--IRAMPKLECLIINP  340 (391)
Q Consensus       272 ~~Llp-~~~-~l~~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~~--~-~--~~~~~~L~~L~l~~  340 (391)
                      .. +. .+. .. ++|+.|++++|.+....    ...+..+++|+.|+++.|.......  + +  ...+++|++|++++
T Consensus       188 ~~-l~~~l~~~~-~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~~  265 (461)
T 1z7x_W          188 RV-LCQGLKDSP-CQLEALKLESCGVTSDNCRDLCGIVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWE  265 (461)
T ss_dssp             HH-HHHHHHHSC-CCCCEEECTTSCCBTTHHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTT
T ss_pred             HH-HHHHHhcCC-CCceEEEccCCCCcHHHHHHHHHHHHhCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECcC
Confidence            00 11 111 24 68888888888766543    3456677888888888554432211  0 0  12467788888887


Q ss_pred             cccccc-----chHhhcCCCCCCEEEeeCCc
Q 041097          341 YAHLKR-----IHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       341 c~~l~~-----lp~~~~~l~~L~~L~l~~~~  366 (391)
                      | .+..     +|..+..+++|++|+++++.
T Consensus       266 n-~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~  295 (461)
T 1z7x_W          266 C-GITAKGCGDLCRVLRAKESLKELSLAGNE  295 (461)
T ss_dssp             S-CCCHHHHHHHHHHHHHCTTCCEEECTTCC
T ss_pred             C-CCCHHHHHHHHHHHhhCCCcceEECCCCC
Confidence            7 4554     66677777778888777765

>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=99.25  E-value=5.1e-11  Score=99.38  Aligned_cols=41  Identities=20%  Similarity=0.082  Sum_probs=33.0

Q ss_pred             ccCCcccEEEcCCCccc--cCCcccCCCCcccEEEccCCCCCc
Q 041097          176 KMFKFLRVLDLGSLVLI--RYPSGIENLFLLRYLKLNIPSLKS  216 (391)
Q Consensus       176 ~~~~~L~~L~l~~~~l~--~~p~~i~~l~~L~~L~l~~~~i~~  216 (391)
                      ...+.|+.|++++|.+.  .+|..+..+.+|++|++++|.+..
T Consensus        21 ~~~~~L~~L~l~~n~l~~~~i~~~~~~l~~L~~L~l~~n~l~~   63 (168)
T 2ell_A           21 RTPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLIS   63 (168)
T ss_dssp             SCTTSCSEEECCSCBCBTTBCSSCCGGGGGCCEEEEESSCCCC
T ss_pred             CCcccCCEEECCCCCCChhhHHHHHHhCCCCCEEeCcCCCCCC
Confidence            34578889999999887  788888888888888888886654

>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=99.24  E-value=2.3e-11  Score=122.78  Aligned_cols=168  Identities=18%  Similarity=0.132  Sum_probs=121.4

Q ss_pred             CcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCC-c------EEEeeCCccCcceeeEEecccccchhH-
Q 041097          179 KFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSR-K------ILRLSGNSQFHFSLASLLLYYQSLLSK-  249 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~-~------~L~l~~~~l~~L~L~~L~l~~~~~lp~-  249 (391)
                      ..+++|+|++|.|..+| ..|.++.+|++|+|++|.++.+|+.. .      +|+|++|++.             .+|. 
T Consensus        52 ~~~~~LdLs~N~i~~l~~~~f~~l~~L~~L~Ls~N~i~~i~~~~f~~L~~L~~L~Ls~N~l~-------------~l~~~  118 (635)
T 4g8a_A           52 FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQ-------------SLALG  118 (635)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCC-------------EECGG
T ss_pred             cCCCEEEeeCCCCCCCCHHHHhCCCCCCEEECCCCcCCCcChhHhcCCCCCCEEEccCCcCC-------------CCCHH
Confidence            36888999999888776 46888999999999998888887643 2      7777777776             6664 


Q ss_pred             HhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCC-hhhhcCCCCCCEEEcCCCCCcCccccC
Q 041097          250 SLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLKQNLYSEERTMG  326 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~~~~~~~~~~~~  326 (391)
                      .++++++|++|++++..    +.. +|  .++.+ ++|+.|++++|.+.... +..++.+++|++|+++.|...+.....
T Consensus       119 ~f~~L~~L~~L~Ls~N~----l~~-l~~~~~~~L-~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~  192 (635)
T 4g8a_A          119 AFSGLSSLQKLVAVETN----LAS-LENFPIGHL-KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTD  192 (635)
T ss_dssp             GGTTCTTCCEEECTTSC----CCC-STTCCCTTC-TTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSCCCEECGGG
T ss_pred             HhcCCCCCCEEECCCCc----CCC-CChhhhhcC-cccCeeccccCccccCCCchhhccchhhhhhcccCcccccccccc
Confidence            68999999999998722    111 33  57889 99999999999887643 467789999999999977655432222


Q ss_pred             CCccccc----ceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          327 IRAMPKL----ECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       327 ~~~~~~L----~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ...+.++    ..++++.+ .+..++........++.+++.+..
T Consensus       193 l~~L~~l~~~~~~~~ls~n-~l~~i~~~~~~~~~~~~l~l~~n~  235 (635)
T 4g8a_A          193 LRVLHQMPLLNLSLDLSLN-PMNFIQPGAFKEIRLHKLTLRNNF  235 (635)
T ss_dssp             GHHHHTCTTCCCEEECTTC-CCCEECTTTTTTCEEEEEEEESCC
T ss_pred             ccchhhhhhhhhhhhcccC-cccccCcccccchhhhhhhhhccc
Confidence            2333333    34556654 467777666666677888887764

>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=99.23  E-value=5.5e-11  Score=111.53  Aligned_cols=200  Identities=16%  Similarity=0.091  Sum_probs=135.2

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCC-cccCCCCcccE-EEccCCCCCccCCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYP-SGIENLFLLRY-LKLNIPSLKSLPSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p-~~i~~l~~L~~-L~l~~~~i~~lp~~~~-----  222 (391)
                      ..++.|.+..+...    ......|.+++.|++|++++|.+. .+| ..+.++.+++. +.+..+++..+|+...     
T Consensus        30 ~~l~~L~Ls~N~i~----~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~~  105 (350)
T 4ay9_X           30 RNAIELRFVLTKLR----VIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPN  105 (350)
T ss_dssp             TTCSEEEEESCCCS----EECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCTT
T ss_pred             CCCCEEEccCCcCC----CcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCCcccccCchhhhhccc
Confidence            56777777665442    112235677888888888888764 454 34567777664 4556677777755432     


Q ss_pred             --EEEeeCCccCcc---------eeeEEecc---cccchhH-HhcCC-CCCCEEEecCCCCCCchhhhcc-ccccCCCCc
Q 041097          223 --ILRLSGNSQFHF---------SLASLLLY---YQSLLSK-SLCRL-SCLESLKLANESKMPRRSNIIL-AEYQFPPSL  285 (391)
Q Consensus       223 --~L~l~~~~l~~L---------~L~~L~l~---~~~~lp~-~i~~l-~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L  285 (391)
                        +|++++|.+..+         ++..|++.   ....+|. .+..+ ..++.|++++..    ++. +| ..... .+|
T Consensus       106 L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~----i~~-i~~~~f~~-~~L  179 (350)
T 4ay9_X          106 LQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNG----IQE-IHNSAFNG-TQL  179 (350)
T ss_dssp             CCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSC----CCE-ECTTSSTT-EEE
T ss_pred             cccccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhcccccc----ccC-CChhhccc-cch
Confidence              778887766543         45555554   3344443 33444 356777776521    010 44 44556 788


Q ss_pred             cEEEeec-ccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeC
Q 041097          286 THLSFSN-IELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWW  364 (391)
Q Consensus       286 ~~L~l~~-~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~  364 (391)
                      +.|.+.+ +.+...+...++.+++|+.|+++.|...   .++.+.+.+|+.|.+.++.+++.+| .+..+++|+.+++.+
T Consensus       180 ~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~l~---~lp~~~~~~L~~L~~l~~~~l~~lP-~l~~l~~L~~l~l~~  255 (350)
T 4ay9_X          180 DELNLSDNNNLEELPNDVFHGASGPVILDISRTRIH---SLPSYGLENLKKLRARSTYNLKKLP-TLEKLVALMEASLTY  255 (350)
T ss_dssp             EEEECTTCTTCCCCCTTTTTTEECCSEEECTTSCCC---CCCSSSCTTCCEEECTTCTTCCCCC-CTTTCCSCCEEECSC
T ss_pred             hHHhhccCCcccCCCHHHhccCcccchhhcCCCCcC---ccChhhhccchHhhhccCCCcCcCC-CchhCcChhhCcCCC
Confidence            9999875 6666666677899999999999966654   3345678899999999999999999 588999999999964

>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=99.22  E-value=9.2e-11  Score=102.55  Aligned_cols=123  Identities=17%  Similarity=0.163  Sum_probs=76.8

Q ss_pred             CcccEEEcCCCccccCC--cccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcceeeEEecccccchh-
Q 041097          179 KFLRVLDLGSLVLIRYP--SGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHFSLASLLLYYQSLLS-  248 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p--~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L~L~~L~l~~~~~lp-  248 (391)
                      ..++.|++++|.+..++  ..+..+.+|++|+++++.+..+|.. +.      .|++++|.+.             .++ 
T Consensus        32 ~~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N~l~-------------~~~~   98 (220)
T 2v70_A           32 QYTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTSNRLE-------------NVQH   98 (220)
T ss_dssp             TTCSEEECCSSCCCEECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCC-------------CCCG
T ss_pred             CCCCEEEcCCCcCCccCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEECCCCccC-------------ccCH
Confidence            45789999999999764  3478999999999999999877642 22      5555555554             333 


Q ss_pred             HHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCC
Q 041097          249 KSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLY  319 (391)
Q Consensus       249 ~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~  319 (391)
                      ..++.+++|++|++++..    +..+.| .+..+ ++|+.|+|++|.+...++..+..+++|+.|+++.|.+
T Consensus        99 ~~~~~l~~L~~L~Ls~N~----l~~~~~~~~~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l  165 (220)
T 2v70_A           99 KMFKGLESLKTLMLRSNR----ITCVGNDSFIGL-SSVRLLSLYDNQITTVAPGAFDTLHSLSTLNLLANPF  165 (220)
T ss_dssp             GGGTTCSSCCEEECTTSC----CCCBCTTSSTTC-TTCSEEECTTSCCCCBCTTTTTTCTTCCEEECCSCCE
T ss_pred             hHhcCCcCCCEEECCCCc----CCeECHhHcCCC-ccCCEEECCCCcCCEECHHHhcCCCCCCEEEecCcCC
Confidence            335566666666665511    000023 44555 6666666666665555445555666666666665443

>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=99.22  E-value=1.1e-10  Score=100.23  Aligned_cols=146  Identities=18%  Similarity=0.198  Sum_probs=79.8

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCc
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNS  230 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~  230 (391)
                      ++++.+.+.++...     .++ .+..++.|++|++++|.+..+ ..+..+.+|++|++++|.+..              
T Consensus        44 ~~L~~L~l~~n~i~-----~l~-~l~~l~~L~~L~l~~n~~~~~-~~l~~l~~L~~L~l~~n~l~~--------------  102 (197)
T 4ezg_A           44 NSLTYITLANINVT-----DLT-GIEYAHNIKDLTINNIHATNY-NPISGLSNLERLRIMGKDVTS--------------  102 (197)
T ss_dssp             HTCCEEEEESSCCS-----CCT-TGGGCTTCSEEEEESCCCSCC-GGGTTCTTCCEEEEECTTCBG--------------
T ss_pred             CCccEEeccCCCcc-----ChH-HHhcCCCCCEEEccCCCCCcc-hhhhcCCCCCEEEeECCccCc--------------
Confidence            55666666554432     122 467778888888888876544 477788888888888887764              


Q ss_pred             cCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeeccc-CCCCChhhhcCCCC
Q 041097          231 QFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIE-LMDDPIPALEKLSV  308 (391)
Q Consensus       231 l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~-~~~~~~~~l~~l~~  308 (391)
                                     ..|..++.+++|++|++++..    +....| .++.+ ++|+.|++++|. +...  +.++.+++
T Consensus       103 ---------------~~~~~l~~l~~L~~L~Ls~n~----i~~~~~~~l~~l-~~L~~L~L~~n~~i~~~--~~l~~l~~  160 (197)
T 4ezg_A          103 ---------------DKIPNLSGLTSLTLLDISHSA----HDDSILTKINTL-PKVNSIDLSYNGAITDI--MPLKTLPE  160 (197)
T ss_dssp             ---------------GGSCCCTTCTTCCEEECCSSB----CBGGGHHHHTTC-SSCCEEECCSCTBCCCC--GGGGGCSS
T ss_pred             ---------------ccChhhcCCCCCCEEEecCCc----cCcHhHHHHhhC-CCCCEEEccCCCCcccc--HhhcCCCC
Confidence                           112334445555555554411    000022 34455 555555555554 3332  24555566


Q ss_pred             CCEEEcCCCCCcCccccCCCcccccceeeeccc
Q 041097          309 LQVLKLKQNLYSEERTMGIRAMPKLECLIINPY  341 (391)
Q Consensus       309 L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c  341 (391)
                      |+.|+++.|....  ......+++|++|+++++
T Consensus       161 L~~L~l~~n~i~~--~~~l~~l~~L~~L~l~~N  191 (197)
T 4ezg_A          161 LKSLNIQFDGVHD--YRGIEDFPKLNQLYAFSQ  191 (197)
T ss_dssp             CCEEECTTBCCCC--CTTGGGCSSCCEEEECBC
T ss_pred             CCEEECCCCCCcC--hHHhccCCCCCEEEeeCc
Confidence            6666665444332  113345555666665544

>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=99.22  E-value=9.4e-11  Score=103.14  Aligned_cols=122  Identities=25%  Similarity=0.286  Sum_probs=75.8

Q ss_pred             CcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCCCc-------EEEeeCCccCcceeeEEecccccchhH-
Q 041097          179 KFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSSRK-------ILRLSGNSQFHFSLASLLLYYQSLLSK-  249 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~-------~L~l~~~~l~~L~L~~L~l~~~~~lp~-  249 (391)
                      ..|++|++++|.+..+ |..+..+.+|++|++++|.+..+|....       +|++++|.+.             .+|. 
T Consensus        40 ~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N~l~-------------~l~~~  106 (229)
T 3e6j_A           40 TNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLT-------------VLPSA  106 (229)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-------------CCCTT
T ss_pred             CCCCEEEcCCCccCccCHHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECCCCcCC-------------ccChh
Confidence            6788888888887755 5667788888888888888777764431       4555555444             3333 


Q ss_pred             HhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCC
Q 041097          250 SLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLY  319 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~  319 (391)
                      .++.+++|++|++++..    +.. +| .+..+ ++|+.|++++|.+...+...+..+++|+.|++..|.+
T Consensus       107 ~~~~l~~L~~L~Ls~N~----l~~-lp~~~~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~~  171 (229)
T 3e6j_A          107 VFDRLVHLKELFMCCNK----LTE-LPRGIERL-THLTHLALDQNQLKSIPHGAFDRLSSLTHAYLFGNPW  171 (229)
T ss_dssp             TTTTCTTCCEEECCSSC----CCS-CCTTGGGC-TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECTTSCB
T ss_pred             HhCcchhhCeEeccCCc----ccc-cCcccccC-CCCCEEECCCCcCCccCHHHHhCCCCCCEEEeeCCCc
Confidence            34566666666666522    000 44 55566 6666666666666655545566666666666665544

>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=99.21  E-value=9e-11  Score=102.61  Aligned_cols=39  Identities=15%  Similarity=0.196  Sum_probs=28.0

Q ss_pred             CcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCcc
Q 041097          179 KFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKSL  217 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~l  217 (391)
                      +.++.|+++++.+..++. .+..+.+|++|++++|.+..+
T Consensus        32 ~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~N~i~~~   71 (220)
T 2v9t_B           32 ETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISEL   71 (220)
T ss_dssp             TTCCEEECCSSCCCEECTTSSTTCTTCCEEECCSSCCCEE
T ss_pred             cCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCCCcCCCc
Confidence            467777888877775554 667777788888777777654

>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=9.5e-11  Score=110.41  Aligned_cols=143  Identities=26%  Similarity=0.207  Sum_probs=113.3

Q ss_pred             ccEEEccCCCCCccCCCCc----EEEeeCCccCcceeeEEecccccchhHH-hc-CCCCCCEEEecCCCCCCchhhhcc-
Q 041097          204 LRYLKLNIPSLKSLPSSRK----ILRLSGNSQFHFSLASLLLYYQSLLSKS-LC-RLSCLESLKLANESKMPRRSNIIL-  276 (391)
Q Consensus       204 L~~L~l~~~~i~~lp~~~~----~L~l~~~~l~~L~L~~L~l~~~~~lp~~-i~-~l~~L~~L~l~~~~~lp~L~~Llp-  276 (391)
                      -+.++++++.+..+|..+.    .|++++|.+.             .++.. +. ++++|++|++++..    +..+.| 
T Consensus        20 ~~~l~c~~~~l~~iP~~~~~~l~~L~Ls~N~l~-------------~l~~~~~~~~l~~L~~L~L~~N~----i~~i~~~   82 (361)
T 2xot_A           20 SNILSCSKQQLPNVPQSLPSYTALLDLSHNNLS-------------RLRAEWTPTRLTNLHSLLLSHNH----LNFISSE   82 (361)
T ss_dssp             TTEEECCSSCCSSCCSSCCTTCSEEECCSSCCC-------------EECTTSSSSCCTTCCEEECCSSC----CCEECTT
T ss_pred             CCEEEeCCCCcCccCccCCCCCCEEECCCCCCC-------------ccChhhhhhcccccCEEECCCCc----CCccChh
Confidence            3688999999998888776    9999999988             66554 55 89999999998722    111123 


Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhh----c
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQL----W  352 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~----~  352 (391)
                      .+..+ ++|+.|+|++|.+...+...+..+++|+.|+++.|............+++|++|+++++ .++.+|..+    .
T Consensus        83 ~~~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N-~l~~l~~~~~~~~~  160 (361)
T 2xot_A           83 AFVPV-PNLRYLDLSSNHLHTLDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQN-QISRFPVELIKDGN  160 (361)
T ss_dssp             TTTTC-TTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCCSCCGGGTC---
T ss_pred             hccCC-CCCCEEECCCCcCCcCCHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCC-cCCeeCHHHhcCcc
Confidence            57789 99999999999988877678899999999999977765433334478899999999988 588998775    5


Q ss_pred             CCCCCCEEEeeCC
Q 041097          353 CLKSLNKLELWWP  365 (391)
Q Consensus       353 ~l~~L~~L~l~~~  365 (391)
                      .+++|++|+++++
T Consensus       161 ~l~~L~~L~L~~N  173 (361)
T 2xot_A          161 KLPKLMLLDLSSN  173 (361)
T ss_dssp             -CTTCCEEECCSS
T ss_pred             cCCcCCEEECCCC
Confidence            7999999999875

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.18  E-value=3.2e-11  Score=113.66  Aligned_cols=204  Identities=15%  Similarity=0.082  Sum_probs=114.1

Q ss_pred             ccEEEEEecCCcCCCchhhHHhhccCC-cccEEEcCCCccccC-CcccCCC-----CcccEEEccCCCCCccC-------
Q 041097          153 LHSLLYLTSGSQYLDPTYCEKICKMFK-FLRVLDLGSLVLIRY-PSGIENL-----FLLRYLKLNIPSLKSLP-------  218 (391)
Q Consensus       153 lrsl~~~~~~~~~~~~~~~~~~~~~~~-~L~~L~l~~~~l~~~-p~~i~~l-----~~L~~L~l~~~~i~~lp-------  218 (391)
                      ++.|.+.++.........+...+..++ .|+.|++++|.+... +..+..+     .+|++|++++|.+...+       
T Consensus        24 L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~  103 (362)
T 3goz_A           24 VTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLSGNFLSYKSSDELVKT  103 (362)
T ss_dssp             CCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHH
T ss_pred             ceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECcCCcCChHHHHHHHHH
Confidence            555555444332111112224445555 566666666655522 3333332     55666666665554322       


Q ss_pred             -----CCCcEEEeeCCccCcceeeEEecccccchhHHhcCC-CCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEe
Q 041097          219 -----SSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRL-SCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSF  290 (391)
Q Consensus       219 -----~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l-~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l  290 (391)
                           ..+.+|++++|.+...        ....+...+..+ ++|++|++++.. .-..... ++ .+..+|++|+.|++
T Consensus       104 l~~~~~~L~~L~Ls~N~l~~~--------~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~-l~~~l~~~~~~L~~L~L  174 (362)
T 3goz_A          104 LAAIPFTITVLDLGWNDFSSK--------SSSEFKQAFSNLPASITSLNLRGNDLGIKSSDE-LIQILAAIPANVNSLNL  174 (362)
T ss_dssp             HHTSCTTCCEEECCSSCGGGS--------CHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHH-HHHHHHTSCTTCCEEEC
T ss_pred             HHhCCCCccEEECcCCcCCcH--------HHHHHHHHHHhCCCceeEEEccCCcCCHHHHHH-HHHHHhcCCccccEeee
Confidence                 2233555555544400        011222345554 699999998722 0000000 33 45566359999999


Q ss_pred             ecccCCCCChh----hhcCC-CCCCEEEcCCCCCcCcccc--C--CCc-ccccceeeeccccccccc-----hHhhcCCC
Q 041097          291 SNIELMDDPIP----ALEKL-SVLQVLKLKQNLYSEERTM--G--IRA-MPKLECLIINPYAHLKRI-----HEQLWCLK  355 (391)
Q Consensus       291 ~~~~~~~~~~~----~l~~l-~~L~~L~l~~~~~~~~~~~--~--~~~-~~~L~~L~l~~c~~l~~l-----p~~~~~l~  355 (391)
                      ++|.+......    .+..+ ++|+.|+++.|........  .  ... .++|++|++++|. +...     ...+..++
T Consensus       175 s~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~~~~~~l~~~~~~l~  253 (362)
T 3goz_A          175 RGNNLASKNCAELAKFLASIPASVTSLDLSANLLGLKSYAELAYIFSSIPNHVVSLNLCLNC-LHGPSLENLKLLKDSLK  253 (362)
T ss_dssp             TTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHHSCTTCCEEECCSSC-CCCCCHHHHHHTTTTTT
T ss_pred             cCCCCchhhHHHHHHHHHhCCCCCCEEECCCCCCChhHHHHHHHHHhcCCCCceEEECcCCC-CCcHHHHHHHHHHhcCC
Confidence            99998776644    34555 5999999997765442211  1  112 3589999999884 5543     34457889


Q ss_pred             CCCEEEeeCCc
Q 041097          356 SLNKLELWWPE  366 (391)
Q Consensus       356 ~L~~L~l~~~~  366 (391)
                      +|++|++++|.
T Consensus       254 ~L~~L~L~~n~  264 (362)
T 3goz_A          254 HLQTVYLDYDI  264 (362)
T ss_dssp             TCSEEEEEHHH
T ss_pred             CccEEEeccCC
Confidence            99999999875

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.16  E-value=3.6e-12  Score=130.93  Aligned_cols=114  Identities=22%  Similarity=0.153  Sum_probs=81.3

Q ss_pred             hHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccc
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQ  244 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~  244 (391)
                      .+..+..+..|++|+|++|.+..+|..+.++.+|++|+|++|.+..+|..++      +|+|++|.+.            
T Consensus       216 ~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~------------  283 (727)
T 4b8c_D          216 PKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLT------------  283 (727)
T ss_dssp             ------CCCCCCEEECTTSCCSCCCGGGGGCCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSCCS------------
T ss_pred             ChhhhccCCCCcEEECCCCCCCCCChhhcCCCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCcCC------------
Confidence            4567788899999999999999999888899999999999999888887665      6666666666            


Q ss_pred             cchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhh
Q 041097          245 SLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPAL  303 (391)
Q Consensus       245 ~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l  303 (391)
                       .+|.+++.|++|++|++++..    +.. +| .++.+ ++|+.|+|++|.+...++..+
T Consensus       284 -~lp~~~~~l~~L~~L~L~~N~----l~~-lp~~~~~l-~~L~~L~L~~N~l~~~~p~~~  336 (727)
T 4b8c_D          284 -SLPAELGSCFQLKYFYFFDNM----VTT-LPWEFGNL-CNLQFLGVEGNPLEKQFLKIL  336 (727)
T ss_dssp             -SCCSSGGGGTTCSEEECCSSC----CCC-CCSSTTSC-TTCCCEECTTSCCCSHHHHHH
T ss_pred             -ccChhhcCCCCCCEEECCCCC----CCc-cChhhhcC-CCccEEeCCCCccCCCChHHH
Confidence             677777777777777777622    000 56 66777 777777777777665444444

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.13  E-value=1.4e-10  Score=94.64  Aligned_cols=122  Identities=17%  Similarity=0.099  Sum_probs=73.4

Q ss_pred             ccCCcccEEEcCCCccc--cCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccch
Q 041097          176 KMFKFLRVLDLGSLVLI--RYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLL  247 (391)
Q Consensus       176 ~~~~~L~~L~l~~~~l~--~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~l  247 (391)
                      ...+.|+.|++++|.+.  .+|..++.+.+|++|++++|.+..+ ..++      +|++++|.+.            ..+
T Consensus        14 ~~~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~n~i~------------~~~   80 (149)
T 2je0_A           14 RTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSI-ANLPKLNKLKKLELSDNRVS------------GGL   80 (149)
T ss_dssp             CCGGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTSCCCCC-TTCCCCTTCCEEECCSSCCC------------SCT
T ss_pred             CCCccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCCCCCCc-hhhhcCCCCCEEECCCCccc------------chH
Confidence            34578999999999988  8888889999999999999988765 2222      5555555444            125


Q ss_pred             hHHhcCCCCCCEEEecCCCCCCchhhh-cc-ccccCCCCccEEEeecccCCCCCh---hhhcCCCCCCEEEcC
Q 041097          248 SKSLCRLSCLESLKLANESKMPRRSNI-IL-AEYQFPPSLTHLSFSNIELMDDPI---PALEKLSVLQVLKLK  315 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~~~~lp~L~~L-lp-~~~~l~~~L~~L~l~~~~~~~~~~---~~l~~l~~L~~L~l~  315 (391)
                      |..++.+++|++|++++..    +..+ .| .++.+ ++|+.|++++|.+...+.   ..++.+++|+.|+++
T Consensus        81 ~~~~~~l~~L~~L~ls~N~----i~~~~~~~~~~~l-~~L~~L~l~~N~l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A           81 EVLAEKCPNLTHLNLSGNK----IKDLSTIEPLKKL-ENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             HHHHHHCTTCCEEECTTSC----CCSHHHHGGGGGC-TTCCEEECTTCGGGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             HHHhhhCCCCCEEECCCCc----CCChHHHHHHhhC-CCCCEEeCcCCcccchHHHHHHHHHHCCCcccccCC
Confidence            5555555556665555411    0000 11 34455 555555555555544432   345555555555543

>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=99.11  E-value=6.3e-10  Score=95.02  Aligned_cols=126  Identities=20%  Similarity=0.127  Sum_probs=76.9

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      ++++++++.+..+|..+..  ++++|+++++.+..+|..                            ..++.+++|++|+
T Consensus        11 ~~l~~s~~~l~~ip~~~~~--~l~~L~l~~n~i~~~~~~----------------------------~~~~~l~~L~~L~   60 (192)
T 1w8a_A           11 TTVDCTGRGLKEIPRDIPL--HTTELLLNDNELGRISSD----------------------------GLFGRLPHLVKLE   60 (192)
T ss_dssp             TEEECTTSCCSSCCSCCCT--TCSEEECCSCCCCSBCCS----------------------------CSGGGCTTCCEEE
T ss_pred             CEEEcCCCCcCcCccCCCC--CCCEEECCCCcCCccCCc----------------------------cccccCCCCCEEE
Confidence            5677777777777776654  677777777766654421                            1255666777777


Q ss_pred             ecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecc
Q 041097          262 LANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINP  340 (391)
Q Consensus       262 l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~  340 (391)
                      +++..    +..+.| .+..+ ++|+.|+|++|.+...+...++.+++|++|+++.|...+..+...+.+++|++|++++
T Consensus        61 Ls~N~----l~~~~~~~~~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~  135 (192)
T 1w8a_A           61 LKRNQ----LTGIEPNAFEGA-SHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLAS  135 (192)
T ss_dssp             CCSSC----CCCBCTTTTTTC-TTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTT
T ss_pred             CCCCC----CCCcCHhHcCCc-ccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCC
Confidence            76521    011134 55666 7777777777776665555566777777777775555443222335566667777665


Q ss_pred             cc
Q 041097          341 YA  342 (391)
Q Consensus       341 c~  342 (391)
                      ++
T Consensus       136 N~  137 (192)
T 1w8a_A          136 NP  137 (192)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.08  E-value=3.8e-10  Score=94.91  Aligned_cols=133  Identities=14%  Similarity=0.071  Sum_probs=78.7

Q ss_pred             hccCCcccEEEcCCCccccCCcccCCCC-cccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcC
Q 041097          175 CKMFKFLRVLDLGSLVLIRYPSGIENLF-LLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCR  253 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~~~p~~i~~l~-~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~  253 (391)
                      +..+..|+.|++++|.+..+|. +..+. +|++|++++|.+..+                               +    
T Consensus        15 ~~~~~~L~~L~l~~n~l~~i~~-~~~~~~~L~~L~Ls~N~l~~~-------------------------------~----   58 (176)
T 1a9n_A           15 YTNAVRDRELDLRGYKIPVIEN-LGATLDQFDAIDFSDNEIRKL-------------------------------D----   58 (176)
T ss_dssp             EECTTSCEEEECTTSCCCSCCC-GGGGTTCCSEEECCSSCCCEE-------------------------------C----
T ss_pred             cCCcCCceEEEeeCCCCchhHH-hhhcCCCCCEEECCCCCCCcc-------------------------------c----
Confidence            3456677777777777776543 44444 677777666655432                               1    


Q ss_pred             CCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc-CCCcccc
Q 041097          254 LSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM-GIRAMPK  332 (391)
Q Consensus       254 l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~-~~~~~~~  332 (391)
                                             .++.+ ++|+.|++++|.+...+...++.+++|++|+++.|.......+ ..+.+++
T Consensus        59 -----------------------~l~~l-~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~  114 (176)
T 1a9n_A           59 -----------------------GFPLL-RRLKTLLVNNNRICRIGEGLDQALPDLTELILTNNSLVELGDLDPLASLKS  114 (176)
T ss_dssp             -----------------------CCCCC-SSCCEEECCSSCCCEECSCHHHHCTTCCEEECCSCCCCCGGGGGGGGGCTT
T ss_pred             -----------------------ccccC-CCCCEEECCCCcccccCcchhhcCCCCCEEECCCCcCCcchhhHhhhcCCC
Confidence                                   22334 5555555555555544333345666666666665544221111 2245667


Q ss_pred             cceeeeccccccccchHh----hcCCCCCCEEEeeCCcHH
Q 041097          333 LECLIINPYAHLKRIHEQ----LWCLKSLNKLELWWPEPE  368 (391)
Q Consensus       333 L~~L~l~~c~~l~~lp~~----~~~l~~L~~L~l~~~~~~  368 (391)
                      |++|++++|. +..+|..    +..+++|++|++++++.+
T Consensus       115 L~~L~l~~N~-i~~~~~~~~~~~~~l~~L~~Ld~~~n~~~  153 (176)
T 1a9n_A          115 LTYLCILRNP-VTNKKHYRLYVIYKVPQVRVLDFQKVKLK  153 (176)
T ss_dssp             CCEEECCSSG-GGGSTTHHHHHHHHCTTCSEETTEECCHH
T ss_pred             CCEEEecCCC-CCCcHhHHHHHHHHCCccceeCCCcCCHH
Confidence            7777777664 5666664    788889999998888754

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.07  E-value=5.5e-10  Score=111.08  Aligned_cols=184  Identities=18%  Similarity=0.156  Sum_probs=123.2

Q ss_pred             ceEEEEEeccCCCcccccCCCCCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEc
Q 041097          130 NVKRFTAHRKLNDFAFLDDFDSFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKL  209 (391)
Q Consensus       130 ~~r~l~~~~~~~~~~~~~~~~~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l  209 (391)
                      +++.|.+..+.... ++....++++.|.+.++...     .++   ..++.|++|++++|.+..+|. +++  +|++|++
T Consensus        60 ~L~~L~Ls~n~L~~-lp~~l~~~L~~L~Ls~N~l~-----~ip---~~l~~L~~L~Ls~N~l~~ip~-l~~--~L~~L~L  127 (571)
T 3cvr_A           60 QFSELQLNRLNLSS-LPDNLPPQITVLEITQNALI-----SLP---ELPASLEYLDACDNRLSTLPE-LPA--SLKHLDV  127 (571)
T ss_dssp             TCSEEECCSSCCSC-CCSCCCTTCSEEECCSSCCS-----CCC---CCCTTCCEEECCSSCCSCCCC-CCT--TCCEEEC
T ss_pred             CccEEEeCCCCCCc-cCHhHcCCCCEEECcCCCCc-----ccc---cccCCCCEEEccCCCCCCcch-hhc--CCCEEEC
Confidence            56667766332222 33222277888888776553     232   457899999999999998888 766  9999999


Q ss_pred             cCCCCCccCCCCc---EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCcc
Q 041097          210 NIPSLKSLPSSRK---ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLT  286 (391)
Q Consensus       210 ~~~~i~~lp~~~~---~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~  286 (391)
                      ++|.++.+|..+.   .|++++|.+.             .+|.   .+++|++|++++..    +.. +|.   ++++|+
T Consensus       128 s~N~l~~lp~~l~~L~~L~Ls~N~l~-------------~lp~---~l~~L~~L~Ls~N~----L~~-lp~---l~~~L~  183 (571)
T 3cvr_A          128 DNNQLTMLPELPALLEYINADNNQLT-------------MLPE---LPTSLEVLSVRNNQ----LTF-LPE---LPESLE  183 (571)
T ss_dssp             CSSCCSCCCCCCTTCCEEECCSSCCS-------------CCCC---CCTTCCEEECCSSC----CSC-CCC---CCTTCC
T ss_pred             CCCcCCCCCCcCccccEEeCCCCccC-------------cCCC---cCCCcCEEECCCCC----CCC-cch---hhCCCC
Confidence            9999999987332   8899998888             5665   57788888887722    000 333   226888


Q ss_pred             EEEeecccCCCCChhhhcCCCCC-------CEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCC
Q 041097          287 HLSFSNIELMDDPIPALEKLSVL-------QVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCL  354 (391)
Q Consensus       287 ~L~l~~~~~~~~~~~~l~~l~~L-------~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l  354 (391)
                      .|+|++|.+...+.  +..  +|       +.|+++.|.... .+.....+++|+.|++++|+--..+|..+..+
T Consensus       184 ~L~Ls~N~L~~lp~--~~~--~L~~~~~~L~~L~Ls~N~l~~-lp~~l~~l~~L~~L~L~~N~l~~~~p~~l~~l  253 (571)
T 3cvr_A          184 ALDVSTNLLESLPA--VPV--RNHHSEETEIFFRCRENRITH-IPENILSLDPTCTIILEDNPLSSRIRESLSQQ  253 (571)
T ss_dssp             EEECCSSCCSSCCC--CC----------CCEEEECCSSCCCC-CCGGGGGSCTTEEEECCSSSCCHHHHHHHHHH
T ss_pred             EEECcCCCCCchhh--HHH--hhhcccccceEEecCCCccee-cCHHHhcCCCCCEEEeeCCcCCCcCHHHHHHh
Confidence            88888888775443  333  56       888888665542 22223568888888888876434567666554

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.06  E-value=2.5e-10  Score=93.12  Aligned_cols=112  Identities=19%  Similarity=0.133  Sum_probs=86.2

Q ss_pred             chhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc-
Q 041097          246 LLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT-  324 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~-  324 (391)
                      .+|..++.+++|++|++++..    +.. ++.++.+ ++|+.|++++|.+....+..++.+++|++|+++.|...+... 
T Consensus        33 ~~~~~~~~l~~L~~L~l~~n~----l~~-~~~~~~l-~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~ls~N~i~~~~~~  106 (149)
T 2je0_A           33 KLEGLTDEFEELEFLSTINVG----LTS-IANLPKL-NKLKKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTI  106 (149)
T ss_dssp             BCCSCCTTCTTCCEEECTTSC----CCC-CTTCCCC-TTCCEEECCSSCCCSCTHHHHHHCTTCCEEECTTSCCCSHHHH
T ss_pred             HHHHHHhhcCCCcEEECcCCC----CCC-chhhhcC-CCCCEEECCCCcccchHHHHhhhCCCCCEEECCCCcCCChHHH
Confidence            345566788999999998722    000 2356778 999999999999887666777889999999999777655322 


Q ss_pred             cCCCcccccceeeeccccccccchH----hhcCCCCCCEEEeeC
Q 041097          325 MGIRAMPKLECLIINPYAHLKRIHE----QLWCLKSLNKLELWW  364 (391)
Q Consensus       325 ~~~~~~~~L~~L~l~~c~~l~~lp~----~~~~l~~L~~L~l~~  364 (391)
                      ...+.+++|++|++++| .+..+|.    .+..+++|++|++++
T Consensus       107 ~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~~~~l~~L~~L~l~d  149 (149)
T 2je0_A          107 EPLKKLENLKSLDLFNC-EVTNLNDYRENVFKLLPQLTYLDGYD  149 (149)
T ss_dssp             GGGGGCTTCCEEECTTC-GGGGSTTHHHHHHHHCTTCCEETTBC
T ss_pred             HHHhhCCCCCEEeCcCC-cccchHHHHHHHHHHCCCcccccCCC
Confidence            34478999999999988 4777775    678999999998864

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.04  E-value=9.5e-10  Score=94.00  Aligned_cols=119  Identities=24%  Similarity=0.231  Sum_probs=69.0

Q ss_pred             cEEEccCCCCCccCCCCc----EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccc
Q 041097          205 RYLKLNIPSLKSLPSSRK----ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEY  279 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~~~~----~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~  279 (391)
                      ++++++++.+..+|..+.    .|++++|.+.             .+|..+..+++|++|++++..    +..+.| .+.
T Consensus        13 ~~l~~~~~~l~~ip~~~~~~l~~L~L~~n~i~-------------~ip~~~~~l~~L~~L~Ls~N~----i~~i~~~~f~   75 (193)
T 2wfh_A           13 TVVRCSNKGLKVLPKGIPRDVTELYLDGNQFT-------------LVPKELSNYKHLTLIDLSNNR----ISTLSNQSFS   75 (193)
T ss_dssp             TEEECTTSCCSSCCSCCCTTCCEEECCSSCCC-------------SCCGGGGGCTTCCEEECCSSC----CCCCCTTTTT
T ss_pred             CEEEcCCCCCCcCCCCCCCCCCEEECCCCcCc-------------hhHHHhhcccCCCEEECCCCc----CCEeCHhHcc
Confidence            567788888887776554    6777777666             666666677777777766521    000012 355


Q ss_pred             cCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccc
Q 041097          280 QFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPY  341 (391)
Q Consensus       280 ~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c  341 (391)
                      .+ ++|+.|+|++|.+...+...++.+++|+.|+++.|.......-....+++|+.|+++++
T Consensus        76 ~l-~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N  136 (193)
T 2wfh_A           76 NM-TQLLTLILSYNRLRCIPPRTFDGLKSLRLLSLHGNDISVVPEGAFNDLSALSHLAIGAN  136 (193)
T ss_dssp             TC-TTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSS
T ss_pred             CC-CCCCEEECCCCccCEeCHHHhCCCCCCCEEECCCCCCCeeChhhhhcCccccEEEeCCC
Confidence            56 66666666666666555555666666666666644443211111234555566655544

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.03  E-value=2.1e-09  Score=91.81  Aligned_cols=119  Identities=24%  Similarity=0.201  Sum_probs=95.2

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchh-HHhcCC
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLS-KSLCRL  254 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp-~~i~~l  254 (391)
                      ++++++++.+..+|..+.  .+|++|+++++.+..+|..+.      .|++++|.+.             .++ ..+..+
T Consensus        13 ~~l~~~~~~l~~ip~~~~--~~l~~L~L~~n~i~~ip~~~~~l~~L~~L~Ls~N~i~-------------~i~~~~f~~l   77 (193)
T 2wfh_A           13 TVVRCSNKGLKVLPKGIP--RDVTELYLDGNQFTLVPKELSNYKHLTLIDLSNNRIS-------------TLSNQSFSNM   77 (193)
T ss_dssp             TEEECTTSCCSSCCSCCC--TTCCEEECCSSCCCSCCGGGGGCTTCCEEECCSSCCC-------------CCCTTTTTTC
T ss_pred             CEEEcCCCCCCcCCCCCC--CCCCEEECCCCcCchhHHHhhcccCCCEEECCCCcCC-------------EeCHhHccCC
Confidence            578999999998998775  489999999999999986665      8888888777             555 568999


Q ss_pred             CCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCc
Q 041097          255 SCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYS  320 (391)
Q Consensus       255 ~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~  320 (391)
                      ++|++|++++..    +..+.| .+..+ ++|+.|+|++|.+...+...+..+++|+.|++..|.+.
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----LRCIPPRTFDGL-KSLRLLSLHGNDISVVPEGAFNDLSALSHLAIGANPLY  139 (193)
T ss_dssp             TTCCEEECCSSC----CCBCCTTTTTTC-TTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSCEE
T ss_pred             CCCCEEECCCCc----cCEeCHHHhCCC-CCCCEEECCCCCCCeeChhhhhcCccccEEEeCCCCee
Confidence            999999998722    111133 57788 99999999999988877677889999999999977654

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.00  E-value=4.9e-09  Score=88.05  Aligned_cols=123  Identities=23%  Similarity=0.267  Sum_probs=66.6

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      +.++++++.+..+|..+.  .+|++|+++++.+..+|                             +..++.+++|++|+
T Consensus        10 ~~l~~~~~~l~~~p~~~~--~~l~~L~l~~n~l~~~~-----------------------------~~~~~~l~~L~~L~   58 (177)
T 2o6r_A           10 TEIRCNSKGLTSVPTGIP--SSATRLELESNKLQSLP-----------------------------HGVFDKLTQLTKLS   58 (177)
T ss_dssp             TEEECCSSCCSSCCTTCC--TTCSEEECCSSCCCCCC-----------------------------TTTTTTCTTCSEEE
T ss_pred             CEEEecCCCCccCCCCCC--CCCcEEEeCCCcccEeC-----------------------------HHHhcCcccccEEE
Confidence            456666666666665443  35666666666555443                             22345666666666


Q ss_pred             ecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC-CCcccccceeee
Q 041097          262 LANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG-IRAMPKLECLII  338 (391)
Q Consensus       262 l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~-~~~~~~L~~L~l  338 (391)
                      +++..    +.. +|  .+..+ ++|+.|++++|.+...+...++.+++|++|+++.|..... +.. ...+++|++|++
T Consensus        59 l~~n~----l~~-~~~~~~~~l-~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~-~~~~~~~l~~L~~L~l  131 (177)
T 2o6r_A           59 LSQNQ----IQS-LPDGVFDKL-TKLTILYLHENKLQSLPNGVFDKLTQLKELALDTNQLKSV-PDGIFDRLTSLQKIWL  131 (177)
T ss_dssp             CCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCC-CTTTTTTCTTCCEEEC
T ss_pred             CCCCc----ceE-eChhHccCC-CccCEEECCCCCccccCHHHhhCCcccCEEECcCCcceEe-CHHHhcCCcccCEEEe
Confidence            66511    000 22  34556 6666666666666655545556666666666665544321 111 134556666666


Q ss_pred             cccc
Q 041097          339 NPYA  342 (391)
Q Consensus       339 ~~c~  342 (391)
                      ++++
T Consensus       132 ~~N~  135 (177)
T 2o6r_A          132 HTNP  135 (177)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            6553

>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=98.98  E-value=3.9e-09  Score=98.87  Aligned_cols=212  Identities=15%  Similarity=0.093  Sum_probs=142.6

Q ss_pred             cCceEEEEEeccCCCccccc-CC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccE-EEcCCCccccC-CcccCCCC
Q 041097          128 RENVKRFTAHRKLNDFAFLD-DF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRV-LDLGSLVLIRY-PSGIENLF  202 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~-~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~-L~l~~~~l~~~-p~~i~~l~  202 (391)
                      +.+++.|.+..+.... +.. .. + ++++.|.+..+...   .......|..+..++. +.+.++++..+ |..+..+.
T Consensus        29 ~~~l~~L~Ls~N~i~~-i~~~~f~~l~~L~~L~Ls~N~i~---~~i~~~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~  104 (350)
T 4ay9_X           29 PRNAIELRFVLTKLRV-IQKGAFSGFGDLEKIEISQNDVL---EVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLP  104 (350)
T ss_dssp             CTTCSEEEEESCCCSE-ECTTSSTTCTTCCEEEEECCTTC---CEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCT
T ss_pred             CCCCCEEEccCCcCCC-cCHHHHcCCCCCCEEECcCCCCC---CccChhHhhcchhhhhhhcccCCcccccCchhhhhcc
Confidence            4567888887444444 333 33 4 88999988877542   1112245667776664 66777888866 46678999


Q ss_pred             cccEEEccCCCCCccCCCCc-------EEEeeC-CccCcc----------eeeEEecc--cccchhHHhcCCCCCCEEEe
Q 041097          203 LLRYLKLNIPSLKSLPSSRK-------ILRLSG-NSQFHF----------SLASLLLY--YQSLLSKSLCRLSCLESLKL  262 (391)
Q Consensus       203 ~L~~L~l~~~~i~~lp~~~~-------~L~l~~-~~l~~L----------~L~~L~l~--~~~~lp~~i~~l~~L~~L~l  262 (391)
                      +|++|+++++.+..+|....       .|++.+ +.+..+          .++.|+++  ....+|..+....+|++|.+
T Consensus       105 ~L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~i~~i~~~~f~~~~L~~l~l  184 (350)
T 4ay9_X          105 NLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNL  184 (350)
T ss_dssp             TCCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCCCEECTTSSTTEEEEEEEC
T ss_pred             ccccccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhccccccccCCChhhccccchhHHhh
Confidence            99999999999988876543       677765 345443          58888888  67788888888889999999


Q ss_pred             cCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecc
Q 041097          263 ANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINP  340 (391)
Q Consensus       263 ~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~  340 (391)
                      .+.+.   +.. +|  .+..+ ++|+.|++++|.+...+..   .+.+|+.|.+. +.......+....+++|+.+++.+
T Consensus       185 ~~~n~---l~~-i~~~~f~~l-~~L~~LdLs~N~l~~lp~~---~~~~L~~L~~l-~~~~l~~lP~l~~l~~L~~l~l~~  255 (350)
T 4ay9_X          185 SDNNN---LEE-LPNDVFHGA-SGPVILDISRTRIHSLPSY---GLENLKKLRAR-STYNLKKLPTLEKLVALMEASLTY  255 (350)
T ss_dssp             TTCTT---CCC-CCTTTTTTE-ECCSEEECTTSCCCCCCSS---SCTTCCEEECT-TCTTCCCCCCTTTCCSCCEEECSC
T ss_pred             ccCCc---ccC-CCHHHhccC-cccchhhcCCCCcCccChh---hhccchHhhhc-cCCCcCcCCCchhCcChhhCcCCC
Confidence            75210   000 45  45778 9999999999998876643   45667777766 233333455567899999999975


Q ss_pred             ccccccchHhhc
Q 041097          341 YAHLKRIHEQLW  352 (391)
Q Consensus       341 c~~l~~lp~~~~  352 (391)
                      ...-..+..|..
T Consensus       256 ~~~c~~~~~~~~  267 (350)
T 4ay9_X          256 PSHCCAFANWRR  267 (350)
T ss_dssp             HHHHHHHHHSCC
T ss_pred             Cccccchhhhhh
Confidence            432223333433

>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=98.97  E-value=5.2e-10  Score=112.13  Aligned_cols=41  Identities=12%  Similarity=0.063  Sum_probs=24.5

Q ss_pred             hhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEcc
Q 041097          170 YCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLN  210 (391)
Q Consensus       170 ~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~  210 (391)
                      .+...+..++.|+.|++++|.+..+|..+.++.+|++|+++
T Consensus       211 ~l~~~~~~~~~L~~L~L~~~~~~~l~~~~~~~~~L~~L~l~  251 (592)
T 3ogk_B          211 DLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGG  251 (592)
T ss_dssp             HHHHHHHHCTTCCEEECSSCBGGGGHHHHHHCTTCCEEEEC
T ss_pred             HHHHHHhhCCCCcEEeccCccHHHHHHHHhhhhHHHhhccc
Confidence            34455566677777777776665555555555555555554

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.96  E-value=1.2e-09  Score=108.84  Aligned_cols=147  Identities=24%  Similarity=0.311  Sum_probs=102.0

Q ss_pred             HHhhccCCcccEEE-cCCCccccCCc------ccCC--CCcccEEEccCCCCCccCCCCc------EEEeeCCccCccee
Q 041097          172 EKICKMFKFLRVLD-LGSLVLIRYPS------GIEN--LFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSL  236 (391)
Q Consensus       172 ~~~~~~~~~L~~L~-l~~~~l~~~p~------~i~~--l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L  236 (391)
                      +..+..++.|+.|+ ++.+.+..++.      .+..  ...|++|++++|.++.+|. ++      .|++++|.+.    
T Consensus       402 ~~~l~~l~~L~~L~~l~~n~~~~L~~l~l~~n~i~~l~~~~L~~L~Ls~n~l~~lp~-~~~l~~L~~L~Ls~N~l~----  476 (567)
T 1dce_A          402 KETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLR----  476 (567)
T ss_dssp             HHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHHHTTCSEEECTTSCCSSCCC-GGGGTTCCEEECCSSCCC----
T ss_pred             HHHHHHHHhcccCcchhhcccchhhhhhhhcccccccCccCceEEEecCCCCCCCcC-ccccccCcEeecCccccc----
Confidence            34556667777777 44443222221      1111  1247888888888888876 54      7777777777    


Q ss_pred             eEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCC-hhhhcCCCCCCEEEcC
Q 041097          237 ASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLK  315 (391)
Q Consensus       237 ~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~  315 (391)
                               .+|..++.|++|++|++++..    +.. +|.++.+ ++|+.|+|++|.+.... +..++.+++|+.|+++
T Consensus       477 ---------~lp~~~~~l~~L~~L~Ls~N~----l~~-lp~l~~l-~~L~~L~Ls~N~l~~~~~p~~l~~l~~L~~L~L~  541 (567)
T 1dce_A          477 ---------ALPPALAALRCLEVLQASDNA----LEN-VDGVANL-PRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQ  541 (567)
T ss_dssp             ---------CCCGGGGGCTTCCEEECCSSC----CCC-CGGGTTC-SSCCEEECCSSCCCSSSTTGGGGGCTTCCEEECT
T ss_pred             ---------ccchhhhcCCCCCEEECCCCC----CCC-CcccCCC-CCCcEEECCCCCCCCCCCcHHHhcCCCCCEEEec
Confidence                     888899999999999998732    000 5667788 99999999999988875 6889999999999999


Q ss_pred             CCCCcCccccCC---Ccccccceeee
Q 041097          316 QNLYSEERTMGI---RAMPKLECLII  338 (391)
Q Consensus       316 ~~~~~~~~~~~~---~~~~~L~~L~l  338 (391)
                      .|...+......   ..+|+|+.|++
T Consensus       542 ~N~l~~~~~~~~~l~~~lp~L~~L~l  567 (567)
T 1dce_A          542 GNSLCQEEGIQERLAEMLPSVSSILT  567 (567)
T ss_dssp             TSGGGGSSSCTTHHHHHCTTCSEEEC
T ss_pred             CCcCCCCccHHHHHHHHCcccCccCC
Confidence            777655322111   24788888853

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=98.94  E-value=6.8e-10  Score=113.99  Aligned_cols=111  Identities=20%  Similarity=0.160  Sum_probs=61.7

Q ss_pred             hhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc
Q 041097          247 LSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM  325 (391)
Q Consensus       247 lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~  325 (391)
                      .|..+..+++|+.|++++..    +.. +| .+..+ ++|+.|+|++|.+...| ..++.|++|++|+|+.|... ..+.
T Consensus       216 ~~~~~~~l~~L~~L~Ls~n~----l~~-l~~~~~~l-~~L~~L~Ls~N~l~~lp-~~~~~l~~L~~L~Ls~N~l~-~lp~  287 (727)
T 4b8c_D          216 PKDSKYDDQLWHALDLSNLQ----IFN-ISANIFKY-DFLTRLYLNGNSLTELP-AEIKNLSNLRVLDLSHNRLT-SLPA  287 (727)
T ss_dssp             ------CCCCCCEEECTTSC----CSC-CCGGGGGC-CSCSCCBCTTSCCSCCC-GGGGGGTTCCEEECTTSCCS-SCCS
T ss_pred             ChhhhccCCCCcEEECCCCC----CCC-CChhhcCC-CCCCEEEeeCCcCcccC-hhhhCCCCCCEEeCcCCcCC-ccCh
Confidence            34556666666666666521    000 34 44556 66667776666666333 55666667777777655544 2222


Q ss_pred             CCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          326 GIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       326 ~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ..+.+++|++|+|++| .++.+|.+++.+++|++|+|++++
T Consensus       288 ~~~~l~~L~~L~L~~N-~l~~lp~~~~~l~~L~~L~L~~N~  327 (727)
T 4b8c_D          288 ELGSCFQLKYFYFFDN-MVTTLPWEFGNLCNLQFLGVEGNP  327 (727)
T ss_dssp             SGGGGTTCSEEECCSS-CCCCCCSSTTSCTTCCCEECTTSC
T ss_pred             hhcCCCCCCEEECCCC-CCCccChhhhcCCCccEEeCCCCc
Confidence            2356666777777666 456666666666777777666544

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=98.91  E-value=3.1e-09  Score=88.42  Aligned_cols=127  Identities=20%  Similarity=0.167  Sum_probs=79.1

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCc
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNS  230 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~  230 (391)
                      +.++.|.+.++...   ...++..+..++.|++|++++|.+..+ ..++.+.+|++|++++|.+...             
T Consensus        24 ~~L~~L~l~~n~l~---~~~i~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~N~l~~~-------------   86 (168)
T 2ell_A           24 AAVRELVLDNCKSN---DGKIEGLTAEFVNLEFLSLINVGLISV-SNLPKLPKLKKLELSENRIFGG-------------   86 (168)
T ss_dssp             TSCSEEECCSCBCB---TTBCSSCCGGGGGCCEEEEESSCCCCC-SSCCCCSSCCEEEEESCCCCSC-------------
T ss_pred             ccCCEEECCCCCCC---hhhHHHHHHhCCCCCEEeCcCCCCCCh-hhhccCCCCCEEECcCCcCchH-------------
Confidence            56667766554432   112334567889999999999999877 7889999999999999877652             


Q ss_pred             cCcceeeEEecccccchhHHhcCCCCCCEEEecCCC--CCCchhhhccccccCCCCccEEEeecccCCCCCh---hhhcC
Q 041097          231 QFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANES--KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPI---PALEK  305 (391)
Q Consensus       231 l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~--~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~---~~l~~  305 (391)
                                      +|..++.+++|++|++++..  .+|.    ++.+..+ ++|+.|++++|.+...+.   ..+..
T Consensus        87 ----------------~~~~~~~l~~L~~L~Ls~N~l~~~~~----~~~l~~l-~~L~~L~l~~N~l~~~~~~~~~~~~~  145 (168)
T 2ell_A           87 ----------------LDMLAEKLPNLTHLNLSGNKLKDIST----LEPLKKL-ECLKSLDLFNCEVTNLNDYRESVFKL  145 (168)
T ss_dssp             ----------------CCHHHHHCTTCCEEECBSSSCCSSGG----GGGGSSC-SCCCEEECCSSGGGTSTTHHHHHHTT
T ss_pred             ----------------HHHHHhhCCCCCEEeccCCccCcchh----HHHHhcC-CCCCEEEeeCCcCcchHHHHHHHHHh
Confidence                            34445556666666666511  1100    0134455 566666666665554443   34555


Q ss_pred             CCCCCEEEcC
Q 041097          306 LSVLQVLKLK  315 (391)
Q Consensus       306 l~~L~~L~l~  315 (391)
                      +++|++|+++
T Consensus       146 l~~L~~L~l~  155 (168)
T 2ell_A          146 LPQLTYLDGY  155 (168)
T ss_dssp             CSSCCEETTE
T ss_pred             CccCcEecCC
Confidence            5666666555

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=98.88  E-value=1.3e-09  Score=112.69  Aligned_cols=52  Identities=19%  Similarity=0.183  Sum_probs=46.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccE-EEEEEcCCCcChHHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDC-HAWVQESLPYDADQILYDIIKF   52 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~-~~~~~vs~~~~~~~i~~~~~~~   52 (391)
                      |+||||||+||||||+.+|++.+++..|+. ++|+++++.++...+...+...
T Consensus       153 V~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~l  205 (1221)
T 1vt4_I          153 VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL  205 (1221)
T ss_dssp             EEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHH
T ss_pred             EEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            689999999999999999998788999996 9999999999988887776654

>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=98.84  E-value=2.2e-09  Score=107.59  Aligned_cols=127  Identities=13%  Similarity=0.068  Sum_probs=76.2

Q ss_pred             eeeEEecc--cccchhHHhcCCCCCCEEEecC-CC---------C---CCchhhh---------cc-ccccCCCCccEEE
Q 041097          235 SLASLLLY--YQSLLSKSLCRLSCLESLKLAN-ES---------K---MPRRSNI---------IL-AEYQFPPSLTHLS  289 (391)
Q Consensus       235 ~L~~L~l~--~~~~lp~~i~~l~~L~~L~l~~-~~---------~---lp~L~~L---------lp-~~~~l~~~L~~L~  289 (391)
                      +|+.|++.  ....+|..++++++|++|.+.. ..         .   +++|+.+         +| .+..+ ++|+.|+
T Consensus       221 ~L~~L~L~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~l~~~~~~~-~~L~~L~  299 (592)
T 3ogk_B          221 SLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFA-AQIRKLD  299 (592)
T ss_dssp             TCCEEECSSCBGGGGHHHHHHCTTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTCCTTTGGGGGGGG-GGCCEEE
T ss_pred             CCcEEeccCccHHHHHHHHhhhhHHHhhcccccccccchHHHHHHhhccccccccCccccchhHHHHHHhhc-CCCcEEe
Confidence            45555554  2334666666666677666653 00         0   0111111         45 55667 8889999


Q ss_pred             eecccCCCCCh-hhhcCCCCCCEEEcCCCCCcCccccCC-Ccccccceeeecc----------cccccc--chHhhcCCC
Q 041097          290 FSNIELMDDPI-PALEKLSVLQVLKLKQNLYSEERTMGI-RAMPKLECLIINP----------YAHLKR--IHEQLWCLK  355 (391)
Q Consensus       290 l~~~~~~~~~~-~~l~~l~~L~~L~l~~~~~~~~~~~~~-~~~~~L~~L~l~~----------c~~l~~--lp~~~~~l~  355 (391)
                      +++|.+..... ..++.+++|+.|++. ++......... ..+++|++|++++          |..+..  ++.....++
T Consensus       300 Ls~~~l~~~~~~~~~~~~~~L~~L~L~-~~~~~~~l~~~~~~~~~L~~L~L~~g~~~~~~~~~~~~~~~~~~~~l~~~~~  378 (592)
T 3ogk_B          300 LLYALLETEDHCTLIQKCPNLEVLETR-NVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGCQ  378 (592)
T ss_dssp             ETTCCCCHHHHHHHHTTCTTCCEEEEE-GGGHHHHHHHHHHHCTTCCEEEEECCCCSSTTSSTTCCCCHHHHHHHHHHCT
T ss_pred             cCCCcCCHHHHHHHHHhCcCCCEEecc-CccCHHHHHHHHHhCCCCCEEEeecCccccccccccCccCHHHHHHHHhhCc
Confidence            98887544333 346788899999887 44332222211 3578899999995          766653  344446688


Q ss_pred             CCCEEEee
Q 041097          356 SLNKLELW  363 (391)
Q Consensus       356 ~L~~L~l~  363 (391)
                      +|++|++.
T Consensus       379 ~L~~L~l~  386 (592)
T 3ogk_B          379 ELEYMAVY  386 (592)
T ss_dssp             TCSEEEEE
T ss_pred             cCeEEEee
Confidence            99999983

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=98.83  E-value=9.7e-09  Score=87.54  Aligned_cols=108  Identities=20%  Similarity=0.159  Sum_probs=83.2

Q ss_pred             cccEEEcCCCccccCCcc--cCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCC
Q 041097          180 FLRVLDLGSLVLIRYPSG--IENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCL  257 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p~~--i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L  257 (391)
                      .++.|+++++.+..++..  ++.+.+|++|++++|.+..++                             |..++.+++|
T Consensus        30 ~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~-----------------------------~~~~~~l~~L   80 (192)
T 1w8a_A           30 HTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIE-----------------------------PNAFEGASHI   80 (192)
T ss_dssp             TCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBC-----------------------------TTTTTTCTTC
T ss_pred             CCCEEECCCCcCCccCCccccccCCCCCEEECCCCCCCCcC-----------------------------HhHcCCcccC
Confidence            789999999999877753  889999999999998887643                             4566778888


Q ss_pred             CEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcC
Q 041097          258 ESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSE  321 (391)
Q Consensus       258 ~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~  321 (391)
                      ++|++++..    +..+.| .+..+ ++|+.|++++|.+...++..++.+++|++|+++.|.+..
T Consensus        81 ~~L~Ls~N~----l~~~~~~~~~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~c  140 (192)
T 1w8a_A           81 QELQLGENK----IKEISNKMFLGL-HQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNC  140 (192)
T ss_dssp             CEEECCSCC----CCEECSSSSTTC-TTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBCC
T ss_pred             CEEECCCCc----CCccCHHHhcCC-CCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCCccC
Confidence            888887722    111123 46778 899999999988877666778888999999998777654

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.81  E-value=3.2e-11  Score=103.60  Aligned_cols=77  Identities=27%  Similarity=0.280  Sum_probs=41.4

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc-cCCCcccccceeeeccccccccc-hH----------h
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT-MGIRAMPKLECLIINPYAHLKRI-HE----------Q  350 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~-~~~~~~~~L~~L~l~~c~~l~~l-p~----------~  350 (391)
                      ++|+.|++++|.+..  ++.++.+++|+.|+++.|....... .....+++|++|++++|. +... |.          .
T Consensus        93 ~~L~~L~L~~N~l~~--l~~~~~l~~L~~L~l~~N~i~~~~~~~~l~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~~~~~  169 (198)
T 1ds9_A           93 DTLEELWISYNQIAS--LSGIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLLLAGNP-LYNDYKENNATSEYRIEV  169 (198)
T ss_dssp             HHCSEEEEEEEECCC--HHHHHHHHHSSEEEESEEECCCHHHHHHHTTTTTCSEEEECSCH-HHHHHHTTTTHHHHHHHH
T ss_pred             CcCCEEECcCCcCCc--CCccccCCCCCEEECCCCcCCchhHHHHHhcCCCCCEEEecCCc-cccccccccchHHHHHHH
Confidence            556666666665544  3355566666666666444332111 112455666666666553 3222 21          2


Q ss_pred             hcCCCCCCEEEe
Q 041097          351 LWCLKSLNKLEL  362 (391)
Q Consensus       351 ~~~l~~L~~L~l  362 (391)
                      +..+++|++|+-
T Consensus       170 ~~~l~~L~~Ld~  181 (198)
T 1ds9_A          170 VKRLPNLKKLDG  181 (198)
T ss_dssp             HHHCSSCSEECC
T ss_pred             HHhCCCcEEECC
Confidence            677888888873

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=98.80  E-value=3.2e-08  Score=82.97  Aligned_cols=109  Identities=23%  Similarity=0.245  Sum_probs=84.3

Q ss_pred             CCcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCC
Q 041097          178 FKFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSC  256 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~  256 (391)
                      .+.|+.|+++++.+..+|. .++.+.+|++|+++++.+..+|.                             ..++.+++
T Consensus        27 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~-----------------------------~~~~~l~~   77 (177)
T 2o6r_A           27 PSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPD-----------------------------GVFDKLTK   77 (177)
T ss_dssp             CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCT-----------------------------TTTTTCTT
T ss_pred             CCCCcEEEeCCCcccEeCHHHhcCcccccEEECCCCcceEeCh-----------------------------hHccCCCc
Confidence            3689999999999987775 46889999999999998877653                             33567888


Q ss_pred             CCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcC
Q 041097          257 LESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSE  321 (391)
Q Consensus       257 L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~  321 (391)
                      |++|++++..    +.. +|  .+..+ ++|+.|++++|.+...+...+..+++|+.|+++.|.+.+
T Consensus        78 L~~L~l~~N~----l~~-~~~~~~~~l-~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~~  138 (177)
T 2o6r_A           78 LTILYLHENK----LQS-LPNGVFDKL-TQLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDC  138 (177)
T ss_dssp             CCEEECCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSCBCC
T ss_pred             cCEEECCCCC----ccc-cCHHHhhCC-cccCEEECcCCcceEeCHHHhcCCcccCEEEecCCCeec
Confidence            8888887722    011 33  45778 899999999998887776667889999999999776543

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.79  E-value=2.7e-08  Score=83.36  Aligned_cols=102  Identities=22%  Similarity=0.252  Sum_probs=71.2

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      +.++++++.+..+|..+.  .+|++|+++++.+..+|                             |..++.+++|++|+
T Consensus        15 ~~l~~~~n~l~~iP~~~~--~~L~~L~Ls~N~l~~~~-----------------------------~~~~~~l~~L~~L~   63 (174)
T 2r9u_A           15 TLVNCQNIRLASVPAGIP--TDKQRLWLNNNQITKLE-----------------------------PGVFDHLVNLQQLY   63 (174)
T ss_dssp             SEEECCSSCCSSCCSCCC--TTCSEEECCSSCCCCCC-----------------------------TTTTTTCTTCCEEE
T ss_pred             cEEEeCCCCCCccCCCcC--CCCcEEEeCCCCccccC-----------------------------HHHhcCCcCCCEEE
Confidence            567888888877777665  57777777777766543                             44567778888888


Q ss_pred             ecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCc
Q 041097          262 LANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYS  320 (391)
Q Consensus       262 l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~  320 (391)
                      +++..    +.. +|  .+..+ ++|+.|+|++|.+...+...++.+++|+.|+++.|.+.
T Consensus        64 Ls~N~----l~~-i~~~~~~~l-~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~~~  118 (174)
T 2r9u_A           64 FNSNK----LTA-IPTGVFDKL-TQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWD  118 (174)
T ss_dssp             CCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCBC
T ss_pred             CCCCC----CCc-cChhHhCCc-chhhEEECCCCccceeCHHHhccccCCCEEEeCCCCcc
Confidence            87622    000 34  34677 88888888888877766556788888888888866544

>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=98.79  E-value=2.7e-08  Score=82.97  Aligned_cols=103  Identities=24%  Similarity=0.259  Sum_probs=72.7

Q ss_pred             ccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEE
Q 041097          181 LRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESL  260 (391)
Q Consensus       181 L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L  260 (391)
                      .+.++++++.+..+|..+.  .+|++|++++|.++.++                             |..++.+++|++|
T Consensus        11 ~~~l~~s~n~l~~ip~~~~--~~l~~L~L~~N~i~~~~-----------------------------~~~~~~l~~L~~L   59 (170)
T 3g39_A           11 GTTVDCSGKSLASVPTGIP--TTTQVLYLYDNQITKLE-----------------------------PGVFDRLTQLTRL   59 (170)
T ss_dssp             TTEEECTTSCCSSCCSCCC--TTCSEEECCSSCCCCCC-----------------------------TTTTTTCTTCSEE
T ss_pred             CCEEEeCCCCcCccCccCC--CCCcEEEcCCCcCCccC-----------------------------hhhhcCcccCCEE
Confidence            4677888888887777664  57777777777766553                             4456778888888


Q ss_pred             EecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCc
Q 041097          261 KLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYS  320 (391)
Q Consensus       261 ~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~  320 (391)
                      ++++..    +.. +|  .+..+ ++|+.|+|++|.+...+...++.+++|++|+++.|.+.
T Consensus        60 ~Ls~N~----l~~-l~~~~f~~l-~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~~~  115 (170)
T 3g39_A           60 DLDNNQ----LTV-LPAGVFDKL-TQLTQLSLNDNQLKSIPRGAFDNLKSLTHIWLLNNPWD  115 (170)
T ss_dssp             ECCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCBC
T ss_pred             ECCCCC----cCc-cChhhccCC-CCCCEEECCCCccCEeCHHHhcCCCCCCEEEeCCCCCC
Confidence            887622    011 33  35677 88888888888887776666788888888888866543

>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=98.77  E-value=4e-09  Score=105.69  Aligned_cols=84  Identities=15%  Similarity=0.078  Sum_probs=49.7

Q ss_pred             cccCCCCccEEEeecccCCCCCh-hhhcCCCCCCEEEcCCCCCcCccccCC-Ccccccceeeecc--------cccccc-
Q 041097          278 EYQFPPSLTHLSFSNIELMDDPI-PALEKLSVLQVLKLKQNLYSEERTMGI-RAMPKLECLIINP--------YAHLKR-  346 (391)
Q Consensus       278 ~~~l~~~L~~L~l~~~~~~~~~~-~~l~~l~~L~~L~l~~~~~~~~~~~~~-~~~~~L~~L~l~~--------c~~l~~-  346 (391)
                      +..+ ++|+.|++++|.+....+ ..+..+++|+.|++..| ......... ..+++|++|++.+        |..+.. 
T Consensus       285 ~~~~-~~L~~L~L~~~~l~~~~l~~~~~~~~~L~~L~l~~~-~~~~~l~~l~~~~~~L~~L~L~~~~~~g~~~~~~l~~~  362 (594)
T 2p1m_B          285 YSVC-SRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLDY-IEDAGLEVLASTCKDLRELRVFPSEPFVMEPNVALTEQ  362 (594)
T ss_dssp             HHHH-TTCCEEECTTCCCCHHHHHHHHTTCTTCCEEEEEGG-GHHHHHHHHHHHCTTCCEEEEECSCTTCSSCSSCCCHH
T ss_pred             HHhh-CCCCEEEccCCCCCHHHHHHHHhcCCCcCEEeCcCc-cCHHHHHHHHHhCCCCCEEEEecCcccccccCCCCCHH
Confidence            3456 888888888887543322 33567888898888844 221111111 2478888888843        334432 


Q ss_pred             -chHhhcCCCCCCEEEee
Q 041097          347 -IHEQLWCLKSLNKLELW  363 (391)
Q Consensus       347 -lp~~~~~l~~L~~L~l~  363 (391)
                       +......+++|++|.+.
T Consensus       363 ~l~~l~~~~~~L~~L~~~  380 (594)
T 2p1m_B          363 GLVSVSMGCPKLESVLYF  380 (594)
T ss_dssp             HHHHHHHHCTTCCEEEEE
T ss_pred             HHHHHHHhchhHHHHHHh
Confidence             12222347888888664

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.76  E-value=2.4e-10  Score=98.09  Aligned_cols=48  Identities=17%  Similarity=0.195  Sum_probs=36.3

Q ss_pred             hHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCC
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPS  219 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~  219 (391)
                      ++..+..++.|++|++++|.+..+| .++.+.+|++|++++|.+..+|.
T Consensus        40 l~~~~~~l~~L~~L~ls~n~l~~l~-~~~~l~~L~~L~l~~n~l~~l~~   87 (198)
T 1ds9_A           40 MDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIEN   87 (198)
T ss_dssp             CHHHHHHTTTCSEEECSEEEESCCC-CHHHHTTCCEEEEEEEEECSCSS
T ss_pred             hhHHHhcCCCCCEEECCCCCCcccc-ccccCCCCCEEECCCCCcccccc
Confidence            3446777888888888888887777 77778888888888877766664

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=98.74  E-value=1.3e-08  Score=85.32  Aligned_cols=61  Identities=11%  Similarity=0.003  Sum_probs=44.1

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhcc-CCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKM-FKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLP  218 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~-~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp  218 (391)
                      ..++.|.+.++...     .+ +.+.. .+.|++|++++|.+..+ ..++.+.+|++|++++|.+..+|
T Consensus        19 ~~L~~L~l~~n~l~-----~i-~~~~~~~~~L~~L~Ls~N~l~~~-~~l~~l~~L~~L~Ls~N~l~~~~   80 (176)
T 1a9n_A           19 VRDRELDLRGYKIP-----VI-ENLGATLDQFDAIDFSDNEIRKL-DGFPLLRRLKTLLVNNNRICRIG   80 (176)
T ss_dssp             TSCEEEECTTSCCC-----SC-CCGGGGTTCCSEEECCSSCCCEE-CCCCCCSSCCEEECCSSCCCEEC
T ss_pred             CCceEEEeeCCCCc-----hh-HHhhhcCCCCCEEECCCCCCCcc-cccccCCCCCEEECCCCcccccC
Confidence            45666655554432     12 22333 34899999999999877 68899999999999999887765

>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=98.68  E-value=3.8e-08  Score=98.50  Aligned_cols=99  Identities=14%  Similarity=0.082  Sum_probs=55.0

Q ss_pred             CceEEEEEeccCCCcccccCC--C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCcccc-----CCcccCC
Q 041097          129 ENVKRFTAHRKLNDFAFLDDF--D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIR-----YPSGIEN  200 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~--~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~-----~p~~i~~  200 (391)
                      .+.+.|.+............+  . ++++.|.+.++...  ....+......++.|++|++++|.+..     ++.....
T Consensus       105 ~~L~~L~L~~~~~~~~~~~~l~~~~~~L~~L~L~~~~~~--~~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~~  182 (594)
T 2p1m_B          105 TWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGF--STDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDT  182 (594)
T ss_dssp             TTCCEEEEESCBCCHHHHHHHHHHCTTCCEEEEESCEEE--EHHHHHHHHHHCTTCCEEECTTCEEECCCGGGGGGSCTT
T ss_pred             CCCCeEEeeCcEEcHHHHHHHHHhCCCCcEEeCCCcCCC--CHHHHHHHHHhCCCCCEEeCcCCccCCcchHHHHHHhhc
Confidence            356677766322221111112  3 67788877655321  122344555678888888888887552     2233346


Q ss_pred             CCcccEEEccCCC--CC--ccC------CCCcEEEeeCC
Q 041097          201 LFLLRYLKLNIPS--LK--SLP------SSRKILRLSGN  229 (391)
Q Consensus       201 l~~L~~L~l~~~~--i~--~lp------~~~~~L~l~~~  229 (391)
                      +.+|++|+++++.  +.  .++      +.+..|++++|
T Consensus       183 ~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~  221 (594)
T 2p1m_B          183 YTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRA  221 (594)
T ss_dssp             CCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTT
T ss_pred             CCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCC
Confidence            6788888888775  21  111      23347888776

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.55  E-value=2e-07  Score=78.00  Aligned_cols=64  Identities=19%  Similarity=0.218  Sum_probs=29.3

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccc
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPY  341 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c  341 (391)
                      .++.+ ++|+.|+|++|.+...+...++.+++|++|+++.|.......-..+.+++|++|+++++
T Consensus        52 ~~~~l-~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N  115 (174)
T 2r9u_A           52 VFDHL-VNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNN  115 (174)
T ss_dssp             TTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSS
T ss_pred             HhcCC-cCCCEEECCCCCCCccChhHhCCcchhhEEECCCCccceeCHHHhccccCCCEEEeCCC
Confidence            34445 55555555555555444334455555555555544333211111234445555555444

>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=98.51  E-value=2.9e-07  Score=76.64  Aligned_cols=64  Identities=20%  Similarity=0.208  Sum_probs=29.7

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccc
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPY  341 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c  341 (391)
                      .+..+ ++|++|+|++|.+...+...+..+++|++|+++.|..........+.+++|++|+++++
T Consensus        49 ~~~~l-~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N  112 (170)
T 3g39_A           49 VFDRL-TQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQLKSIPRGAFDNLKSLTHIWLLNN  112 (170)
T ss_dssp             TTTTC-TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             hhcCc-ccCCEEECCCCCcCccChhhccCCCCCCEEECCCCccCEeCHHHhcCCCCCCEEEeCCC
Confidence            34445 55555555555555444444455555555555544333211111234445555555443

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.45  E-value=2.2e-07  Score=93.14  Aligned_cols=86  Identities=17%  Similarity=0.173  Sum_probs=55.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccc-cccc-cEEEEEEcCCCcChHHHHHHHHH---hhcC--CCCCCCCCChHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYV-KHYF-DCHAWVQESLPYDADQILYDIIK---FVMP--SPEGFIPDNNEATVEKYL   73 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~l-k~~F-~~~~~~~vs~~~~~~~i~~~~~~---~~~~--~~eg~~~~~~~~~~~~~~   73 (391)
                      |+|+||||+||||||+.+|++..+ +.+| +.++|++++.. +...+...+..   ....  ...+......+.....+.
T Consensus       150 v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~  228 (591)
T 1z6t_A          150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLR  228 (591)
T ss_dssp             EEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHH
Confidence            589999999999999999997666 7889 58999999865 44444444322   2111  000111222455666666


Q ss_pred             HHHHc--CccEEeeec
Q 041097           74 EQLIN--GGFVGAGKR   87 (391)
Q Consensus        74 ~~L~~--k~~l~~~~~   87 (391)
                      ..+.+  +.++.+.++
T Consensus       229 ~~l~~~~~~~LLVLDd  244 (591)
T 1z6t_A          229 ILMLRKHPRSLLILDD  244 (591)
T ss_dssp             HHHHHTCTTCEEEEEE
T ss_pred             HHHccCCCCeEEEEeC
Confidence            66665  457777665

>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=98.43  E-value=4.1e-07  Score=98.87  Aligned_cols=87  Identities=15%  Similarity=0.137  Sum_probs=55.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccc-cccc-cEEEEEEcCCCcChHH--HHHHHHHhhcCCC--CCCCCCChHHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYV-KHYF-DCHAWVQESLPYDADQ--ILYDIIKFVMPSP--EGFIPDNNEATVEKYLE   74 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~l-k~~F-~~~~~~~vs~~~~~~~--i~~~~~~~~~~~~--eg~~~~~~~~~~~~~~~   74 (391)
                      |+|+||||+||||||+.+|++... +.+| +.+.|+.+++..+...  .+..+...+....  ..-.....++....+..
T Consensus       150 v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~  229 (1249)
T 3sfz_A          150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRV  229 (1249)
T ss_dssp             EEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHH
Confidence            689999999999999999997543 5566 5888999998654332  2333333332211  11122235666666666


Q ss_pred             HHHcC--ccEEeeec
Q 041097           75 QLING--GFVGAGKR   87 (391)
Q Consensus        75 ~L~~k--~~l~~~~~   87 (391)
                      .|..+  +++.+.++
T Consensus       230 ~l~~~~~~~LlvlDd  244 (1249)
T 3sfz_A          230 LMLRKHPRSLLILDD  244 (1249)
T ss_dssp             HTSSSSCSCEEEEES
T ss_pred             HHhccCCCEEEEEec
Confidence            66665  77777665

>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=98.41  E-value=1.3e-06  Score=80.78  Aligned_cols=44  Identities=9%  Similarity=0.011  Sum_probs=28.1

Q ss_pred             CCcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCCc
Q 041097          178 FKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSRK  222 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~~  222 (391)
                      +..|+.+++.+ .+..++ ..|..+.+|+.+.+.++.+..++....
T Consensus       100 ~~~L~~l~L~~-~i~~I~~~aF~~~~~L~~l~l~~n~i~~i~~~aF  144 (329)
T 3sb4_A          100 KQTLEKVILSE-KIKNIEDAAFKGCDNLKICQIRKKTAPNLLPEAL  144 (329)
T ss_dssp             CTTCCC-CBCT-TCCEECTTTTTTCTTCCEEEBCCSSCCEECTTSS
T ss_pred             cCCCcEEECCc-cccchhHHHhhcCcccceEEcCCCCccccchhhh
Confidence            67777777766 665444 346677777777777776666555443

>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=98.37  E-value=1.1e-06  Score=81.93  Aligned_cols=34  Identities=18%  Similarity=0.028  Sum_probs=19.5

Q ss_pred             EEcCCC-ccccCCcccCCCCcccEEEccC-CCCCccC
Q 041097          184 LDLGSL-VLIRYPSGIENLFLLRYLKLNI-PSLKSLP  218 (391)
Q Consensus       184 L~l~~~-~l~~~p~~i~~l~~L~~L~l~~-~~i~~lp  218 (391)
                      ++++++ .+..+|. ++.+.+|++|+|++ |.+..+|
T Consensus        13 v~~~~~n~l~~ip~-l~~~~~L~~L~l~~~n~l~~~~   48 (347)
T 2ifg_A           13 LRCTRDGALDSLHH-LPGAENLTELYIENQQHLQHLE   48 (347)
T ss_dssp             EECCSSCCCTTTTT-SCSCSCCSEEECCSCSSCCEEC
T ss_pred             EEcCCCCCCCccCC-CCCCCCeeEEEccCCCCCCCcC
Confidence            355555 5555666 66666666666654 5555544

>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=98.23  E-value=9.8e-07  Score=73.29  Aligned_cols=84  Identities=13%  Similarity=0.110  Sum_probs=64.9

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccC-CCc----ccccceeeeccccccccch-HhhcCCCC
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMG-IRA----MPKLECLIINPYAHLKRIH-EQLWCLKS  356 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~-~~~----~~~L~~L~l~~c~~l~~lp-~~~~~l~~  356 (391)
                      .+|+.|++++|.++...+..+..+++|+.|+++.|......-+. ...    .++|++|+|++|.+++.-- ..+..+++
T Consensus        61 ~~L~~LDLs~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~~  140 (176)
T 3e4g_A           61 YKIQAIDATDSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFRN  140 (176)
T ss_dssp             CCEEEEEEESCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCTT
T ss_pred             ceEeEEeCcCCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCCC
Confidence            48999999999988777788899999999999965543322111 122    3589999999998776422 34678999


Q ss_pred             CCEEEeeCCc
Q 041097          357 LNKLELWWPE  366 (391)
Q Consensus       357 L~~L~l~~~~  366 (391)
                      |++|++++||
T Consensus       141 L~~L~L~~c~  150 (176)
T 3e4g_A          141 LKYLFLSDLP  150 (176)
T ss_dssp             CCEEEEESCT
T ss_pred             CCEEECCCCC
Confidence            9999999998

>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=98.16  E-value=2.7e-06  Score=79.20  Aligned_cols=89  Identities=18%  Similarity=0.123  Sum_probs=63.3

Q ss_pred             chhHHhcCCCCCCEEEecC-CCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcc
Q 041097          246 LLSKSLCRLSCLESLKLAN-ESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEER  323 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~-~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~  323 (391)
                      .+|. +..+++|++|++++ ..    +..+.| .++.+ ++|+.|+|++|.+...+...++.|++|+.|+|+.|......
T Consensus        23 ~ip~-l~~~~~L~~L~l~~~n~----l~~~~~~~~~~l-~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~   96 (347)
T 2ifg_A           23 SLHH-LPGAENLTELYIENQQH----LQHLELRDLRGL-GELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLS   96 (347)
T ss_dssp             TTTT-SCSCSCCSEEECCSCSS----CCEECGGGSCSC-CCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCC
T ss_pred             ccCC-CCCCCCeeEEEccCCCC----CCCcChhHhccc-cCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCccceeC
Confidence            8888 99999999999974 22    111123 67788 89999999998888777778888999999999877665421


Q ss_pred             ccCC-Ccccccceeeecccc
Q 041097          324 TMGI-RAMPKLECLIINPYA  342 (391)
Q Consensus       324 ~~~~-~~~~~L~~L~l~~c~  342 (391)
                       ... ..+ .|+.|++.++.
T Consensus        97 -~~~~~~~-~L~~l~l~~N~  114 (347)
T 2ifg_A           97 -WKTVQGL-SLQELVLSGNP  114 (347)
T ss_dssp             -STTTCSC-CCCEEECCSSC
T ss_pred             -HHHcccC-CceEEEeeCCC
Confidence             111 223 38888887663

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.09  E-value=1e-06  Score=82.99  Aligned_cols=36  Identities=33%  Similarity=0.349  Sum_probs=17.3

Q ss_pred             CCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCC
Q 041097          283 PSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNL  318 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~  318 (391)
                      ++|++|+|++|.+....    ...+...++|+.|+++.|.
T Consensus       183 ~~L~~L~Ls~N~l~~~g~~~L~~~L~~~~~L~~L~Ls~N~  222 (372)
T 3un9_A          183 TSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNG  222 (372)
T ss_dssp             SSCCEEECTTSSCHHHHHHHHHHHGGGCSCCCEEECCSSC
T ss_pred             CCcCEEeCCCCCCCcHHHHHHHHHHhcCCCcCeEECCCCC
Confidence            55555555555543322    1233444555555555443

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.99  E-value=1.3e-05  Score=74.95  Aligned_cols=192  Identities=17%  Similarity=0.171  Sum_probs=107.8

Q ss_pred             cCCC-CCccEEEEEecCCcCCCch----hhHHhhccCCcccEEEcCCCccc----------cCCcccCCCCcccEEEccC
Q 041097          147 DDFD-SFLHSLLYLTSGSQYLDPT----YCEKICKMFKFLRVLDLGSLVLI----------RYPSGIENLFLLRYLKLNI  211 (391)
Q Consensus       147 ~~~~-~~lrsl~~~~~~~~~~~~~----~~~~~~~~~~~L~~L~l~~~~l~----------~~p~~i~~l~~L~~L~l~~  211 (391)
                      .... ..++.|.+..........+    .+..+..++++|+.|.+.+...+          .+...+..+++|+.|.+++
T Consensus       102 ~~~~~~~v~~L~lg~~~~~~~~~~~~~~~L~~s~~~l~~L~~L~l~~~~~e~~~is~~~~~~L~~ll~~~P~L~~L~L~g  181 (362)
T 2ra8_A          102 KDKKLPSLKQITIGXWGYEGEDCSDIADGIVENKEKFAHFEGLFWGDIDFEEQEISWIEQVDLSPVLDAMPLLNNLKIKG  181 (362)
T ss_dssp             HCTTGGGCSEEEECCCCSSSCCSHHHHHHHHTTHHHHTTCSEEEECCCCTTTCCGGGCBCCBCHHHHHTCTTCCEEEEEC
T ss_pred             cCCCchhcceEEEcccccCCCcHHHHHHHHHHhhhhcchhhheeecCcchhhcccccccccCHHHHHhcCCCCcEEEEeC
Confidence            3445 6677787654332100111    22334556778888887654322          1222234456666666655


Q ss_pred             CCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhcccc--ccCCCCccEEE
Q 041097          212 PSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAE--YQFPPSLTHLS  289 (391)
Q Consensus       212 ~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~--~~l~~~L~~L~  289 (391)
                      +.-.                              .++. + .+++|++|.+.... ++. .. +..+  ..+ ++|+.|+
T Consensus       182 ~~~l------------------------------~l~~-~-~~~~L~~L~L~~~~-l~~-~~-l~~l~~~~l-p~L~~L~  225 (362)
T 2ra8_A          182 TNNL------------------------------SIGK-K-PRPNLKSLEIISGG-LPD-SV-VEDILGSDL-PNLEKLV  225 (362)
T ss_dssp             CBTC------------------------------BCCS-C-BCTTCSEEEEECSB-CCH-HH-HHHHHHSBC-TTCCEEE
T ss_pred             CCCc------------------------------eecc-c-cCCCCcEEEEecCC-CCh-HH-HHHHHHccC-CCCcEEE
Confidence            4101                              2222 3 37899999997521 000 00 1112  368 9999999


Q ss_pred             eecc--cCCCC-Ch----hhh--cCCCCCCEEEcCCCCCcCc---cccCCCcccccceeeecccccccc-----chHhhc
Q 041097          290 FSNI--ELMDD-PI----PAL--EKLSVLQVLKLKQNLYSEE---RTMGIRAMPKLECLIINPYAHLKR-----IHEQLW  352 (391)
Q Consensus       290 l~~~--~~~~~-~~----~~l--~~l~~L~~L~l~~~~~~~~---~~~~~~~~~~L~~L~l~~c~~l~~-----lp~~~~  352 (391)
                      |+.+  ..... .+    +.+  +.+|+|++|++..|.....   ...+.+.+|+|++|+|+.| .+..     ++.++.
T Consensus       226 L~~~~~~~~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n-~L~d~G~~~L~~~L~  304 (362)
T 2ra8_A          226 LYVGVEDYGFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAG-VLTDEGARLLLDHVD  304 (362)
T ss_dssp             EECBCGGGTCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSS-CCBHHHHHHHHTTHH
T ss_pred             EeccccccccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCC-CCChHHHHHHHhhcc
Confidence            9642  11111 11    122  3579999999985544321   1233467899999999866 4554     566667


Q ss_pred             CCCCCCEEEeeCCc--HHHHHHhhh
Q 041097          353 CLKSLNKLELWWPE--PELRQQLRE  375 (391)
Q Consensus       353 ~l~~L~~L~l~~~~--~~l~~~~~~  375 (391)
                      ++++|+.|++++|+  ++..+.+.+
T Consensus       305 ~l~~L~~L~L~~n~i~d~~~~~l~~  329 (362)
T 2ra8_A          305 KIKHLKFINMKYNYLSDEMKKELQK  329 (362)
T ss_dssp             HHTTCSEEECCSBBCCHHHHHHHHH
T ss_pred             cCCcceEEECCCCcCCHHHHHHHHH
Confidence            88999999998775  344444443

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=97.95  E-value=5.7e-06  Score=77.86  Aligned_cols=38  Identities=18%  Similarity=0.192  Sum_probs=26.2

Q ss_pred             CCcccEEEcCCCcccc-----CCcccC-CCCcccEEEccCCCCC
Q 041097          178 FKFLRVLDLGSLVLIR-----YPSGIE-NLFLLRYLKLNIPSLK  215 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~-----~p~~i~-~l~~L~~L~l~~~~i~  215 (391)
                      ++.|+.|++++|.+..     +...+. ...+|++|++++|.+.
T Consensus        71 ~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~l~  114 (372)
T 3un9_A           71 LSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLD  114 (372)
T ss_dssp             HTTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCCCC
T ss_pred             HhhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCCCC
Confidence            4678899999998762     222222 2368888888888765

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.90  E-value=3.5e-05  Score=72.08  Aligned_cols=180  Identities=14%  Similarity=0.129  Sum_probs=106.9

Q ss_pred             CCccEEEEEecCCcCCCc-h----hhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEE
Q 041097          151 SFLHSLLYLTSGSQYLDP-T----YCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILR  225 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~-~----~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~  225 (391)
                      +++++|.+.+........ |    .+...+..++.|+.|.++++.-..++. +. +.+|+.|.+..+.+..         
T Consensus       139 ~~L~~L~l~~~~~e~~~is~~~~~~L~~ll~~~P~L~~L~L~g~~~l~l~~-~~-~~~L~~L~L~~~~l~~---------  207 (362)
T 2ra8_A          139 AHFEGLFWGDIDFEEQEISWIEQVDLSPVLDAMPLLNNLKIKGTNNLSIGK-KP-RPNLKSLEIISGGLPD---------  207 (362)
T ss_dssp             TTCSEEEECCCCTTTCCGGGCBCCBCHHHHHTCTTCCEEEEECCBTCBCCS-CB-CTTCSEEEEECSBCCH---------
T ss_pred             chhhheeecCcchhhcccccccccCHHHHHhcCCCCcEEEEeCCCCceecc-cc-CCCCcEEEEecCCCCh---------
Confidence            789999886543211001 1    255677888999999998874223443 33 6788888877654321         


Q ss_pred             eeCCccCcceeeEEecccccchhHHhc--CCCCCCEEEecC------CC-CCCchhhhccccccCCCCccEEEeecccCC
Q 041097          226 LSGNSQFHFSLASLLLYYQSLLSKSLC--RLSCLESLKLAN------ES-KMPRRSNIILAEYQFPPSLTHLSFSNIELM  296 (391)
Q Consensus       226 l~~~~l~~L~L~~L~l~~~~~lp~~i~--~l~~L~~L~l~~------~~-~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~  296 (391)
                                          .....++  .+++|++|+++.      .+ .+..+..++ ....+ ++|+.|+|.+|.+.
T Consensus       208 --------------------~~l~~l~~~~lp~L~~L~L~~~~~~~~~~~~~~~l~~~l-~~~~~-p~Lr~L~L~~~~i~  265 (362)
T 2ra8_A          208 --------------------SVVEDILGSDLPNLEKLVLYVGVEDYGFDGDMNVFRPLF-SKDRF-PNLKWLGIVDAEEQ  265 (362)
T ss_dssp             --------------------HHHHHHHHSBCTTCCEEEEECBCGGGTCCSCGGGTGGGS-CTTTC-TTCCEEEEESCTTH
T ss_pred             --------------------HHHHHHHHccCCCCcEEEEeccccccccchhHHHHHHHH-hcCCC-CCcCEEeCCCCCCc
Confidence                                2223343  789999999853      11 111111101 12357 89999999998765


Q ss_pred             CCChhhh---cCCCCCCEEEcCCCCCcCcc---ccCC-CcccccceeeeccccccccchHhhcCCCC--CCEEEeeCCc
Q 041097          297 DDPIPAL---EKLSVLQVLKLKQNLYSEER---TMGI-RAMPKLECLIINPYAHLKRIHEQLWCLKS--LNKLELWWPE  366 (391)
Q Consensus       297 ~~~~~~l---~~l~~L~~L~l~~~~~~~~~---~~~~-~~~~~L~~L~l~~c~~l~~lp~~~~~l~~--L~~L~l~~~~  366 (391)
                      ......+   ..+++|++|+++.|......   .... ..+++|+.|++++|. +..  .....+..  ...+++++..
T Consensus       266 ~~~~~~la~a~~~~~L~~LdLs~n~L~d~G~~~L~~~L~~l~~L~~L~L~~n~-i~d--~~~~~l~~alg~~~~~~~~~  341 (362)
T 2ra8_A          266 NVVVEMFLESDILPQLETMDISAGVLTDEGARLLLDHVDKIKHLKFINMKYNY-LSD--EMKKELQKSLPMKIDVSDSQ  341 (362)
T ss_dssp             HHHHHHHHHCSSGGGCSEEECCSSCCBHHHHHHHHTTHHHHTTCSEEECCSBB-CCH--HHHHHHHHHCCSEEECCSBC
T ss_pred             hHHHHHHHhCccCCCCCEEECCCCCCChHHHHHHHhhcccCCcceEEECCCCc-CCH--HHHHHHHHHcCCEEEecCCc
Confidence            4222222   35799999999966544321   1222 467899999999884 432  22222222  3567776644

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=97.86  E-value=0.00036  Score=66.18  Aligned_cols=42  Identities=17%  Similarity=0.150  Sum_probs=25.6

Q ss_pred             cccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCCc
Q 041097          180 FLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSRK  222 (391)
Q Consensus       180 ~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~~  222 (391)
                      .|+.+.+.. .+..++ ..+..+.+|+.+.+..+++..+|....
T Consensus       158 ~L~~i~lp~-~l~~I~~~aF~~c~~L~~l~l~~n~l~~I~~~aF  200 (401)
T 4fdw_A          158 TVQEIVFPS-TLEQLKEDIFYYCYNLKKADLSKTKITKLPASTF  200 (401)
T ss_dssp             CCCEEECCT-TCCEECSSTTTTCTTCCEEECTTSCCSEECTTTT
T ss_pred             CceEEEeCC-CccEehHHHhhCcccCCeeecCCCcceEechhhE
Confidence            466666654 444333 456667777777777776766665543

>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=97.82  E-value=0.0001  Score=67.87  Aligned_cols=178  Identities=8%  Similarity=-0.003  Sum_probs=107.8

Q ss_pred             HhhccCCcccEEEcCCCccccCC-cccCCCCcccEEEccCCC----CCccCCCCc--------EEEeeCC-ccCc-----
Q 041097          173 KICKMFKFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPS----LKSLPSSRK--------ILRLSGN-SQFH-----  233 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~----i~~lp~~~~--------~L~l~~~-~l~~-----  233 (391)
                      ..|..+..|+.++++++.+..++ ..+..+.++.++......    ...+.....        ++++... .+..     
T Consensus       118 ~aF~~~~~L~~l~l~~n~i~~i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~~L~~~i~~~~~~~l~~~~~~~  197 (329)
T 3sb4_A          118 AAFKGCDNLKICQIRKKTAPNLLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGEPLETTIQVGAMGKLEDEIMKA  197 (329)
T ss_dssp             TTTTTCTTCCEEEBCCSSCCEECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESCCCEEEEEECTTCCHHHHHHHT
T ss_pred             HHhhcCcccceEEcCCCCccccchhhhcCCCceEEecCcchhhhhccccccccccccccccceeEEecCCCcHHHHHhhc
Confidence            56788999999999999876444 556666677776654421    111111111        1222111 0000     


Q ss_pred             ----ceeeEEeccc-c--cchhHHhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhc
Q 041097          234 ----FSLASLLLYY-Q--SLLSKSLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALE  304 (391)
Q Consensus       234 ----L~L~~L~l~~-~--~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~  304 (391)
                          -+++.+.+.. .  .........+++|+.+++.+..    +.. +|  .+..+ ++|+.|.+..+ +...+...+.
T Consensus       198 ~~~~~~~~~l~~~~~l~~~~~~~l~~~~~~L~~l~L~~n~----i~~-I~~~aF~~~-~~L~~l~l~~n-i~~I~~~aF~  270 (329)
T 3sb4_A          198 GLQPRDINFLTIEGKLDNADFKLIRDYMPNLVSLDISKTN----ATT-IPDFTFAQK-KYLLKIKLPHN-LKTIGQRVFS  270 (329)
T ss_dssp             TCCGGGCSEEEEEECCCHHHHHHHHHHCTTCCEEECTTBC----CCE-ECTTTTTTC-TTCCEEECCTT-CCEECTTTTT
T ss_pred             ccCccccceEEEeeeecHHHHHHHHHhcCCCeEEECCCCC----cce-ecHhhhhCC-CCCCEEECCcc-cceehHHHhh
Confidence                0233333330 0  0111111237899999998622    011 44  46678 99999999887 5666667889


Q ss_pred             CCCCCC-EEEcCCCCCcCccccCC---CcccccceeeeccccccccchH-hhcCCCCCCEEEe
Q 041097          305 KLSVLQ-VLKLKQNLYSEERTMGI---RAMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLEL  362 (391)
Q Consensus       305 ~l~~L~-~L~l~~~~~~~~~~~~~---~~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l  362 (391)
                      .+++|+ .+.+. +...   .++.   ..+++|+.+++.+. +++.++. .+.++++|++++.
T Consensus       271 ~~~~L~~~l~l~-~~l~---~I~~~aF~~c~~L~~l~l~~n-~i~~I~~~aF~~~~~L~~ly~  328 (329)
T 3sb4_A          271 NCGRLAGTLELP-ASVT---AIEFGAFMGCDNLRYVLATGD-KITTLGDELFGNGVPSKLIYK  328 (329)
T ss_dssp             TCTTCCEEEEEC-TTCC---EECTTTTTTCTTEEEEEECSS-CCCEECTTTTCTTCCCCEEEC
T ss_pred             CChhccEEEEEc-ccce---EEchhhhhCCccCCEEEeCCC-ccCccchhhhcCCcchhhhcc
Confidence            999999 99998 3221   2333   45678999998755 5788875 6789999999874

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=97.63  E-value=0.00083  Score=63.66  Aligned_cols=181  Identities=10%  Similarity=0.075  Sum_probs=95.8

Q ss_pred             HhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-------EEEeeCCccCcc--------eee
Q 041097          173 KICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-------ILRLSGNSQFHF--------SLA  237 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-------~L~l~~~~l~~L--------~L~  237 (391)
                      ..|..+..|+.+++.++.+..++...-...+|+.+.+..+ ++.++....       .+++..+ +..+        +|+
T Consensus       174 ~aF~~c~~L~~l~l~~n~l~~I~~~aF~~~~L~~l~lp~~-l~~I~~~aF~~~~~L~~l~l~~~-l~~I~~~aF~~~~L~  251 (401)
T 4fdw_A          174 DIFYYCYNLKKADLSKTKITKLPASTFVYAGIEEVLLPVT-LKEIGSQAFLKTSQLKTIEIPEN-VSTIGQEAFRESGIT  251 (401)
T ss_dssp             STTTTCTTCCEEECTTSCCSEECTTTTTTCCCSEEECCTT-CCEECTTTTTTCTTCCCEECCTT-CCEECTTTTTTCCCS
T ss_pred             HHhhCcccCCeeecCCCcceEechhhEeecccCEEEeCCc-hheehhhHhhCCCCCCEEecCCC-ccCccccccccCCcc
Confidence            5678899999999999888877765544678888888744 666655443       4444432 2211        455


Q ss_pred             EEecc-cccchh-HHhcCCCCCCEEEecCCC-CCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEE
Q 041097          238 SLLLY-YQSLLS-KSLCRLSCLESLKLANES-KMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVL  312 (391)
Q Consensus       238 ~L~l~-~~~~lp-~~i~~l~~L~~L~l~~~~-~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L  312 (391)
                      .+.+. ....++ ..+.++++|+.+.+.+.. .-..... ++  .+..+ ++|+.+.+.++ +.......+..+++|+.+
T Consensus       252 ~i~lp~~i~~I~~~aF~~c~~L~~l~l~~~~~~~~~~~~-I~~~aF~~c-~~L~~l~l~~~-i~~I~~~aF~~c~~L~~l  328 (401)
T 4fdw_A          252 TVKLPNGVTNIASRAFYYCPELAEVTTYGSTFNDDPEAM-IHPYCLEGC-PKLARFEIPES-IRILGQGLLGGNRKVTQL  328 (401)
T ss_dssp             EEEEETTCCEECTTTTTTCTTCCEEEEESSCCCCCTTCE-ECTTTTTTC-TTCCEECCCTT-CCEECTTTTTTCCSCCEE
T ss_pred             EEEeCCCccEEChhHhhCCCCCCEEEeCCccccCCcccE-ECHHHhhCC-ccCCeEEeCCc-eEEEhhhhhcCCCCccEE
Confidence            55544 333342 345566666666665410 0000000 22  33445 66666666532 333334455666667776


Q ss_pred             EcCCCCCcCccccCCCccc--ccceeeeccccccccch-HhhcCCC-CCCEEEee
Q 041097          313 KLKQNLYSEERTMGIRAMP--KLECLIINPYAHLKRIH-EQLWCLK-SLNKLELW  363 (391)
Q Consensus       313 ~l~~~~~~~~~~~~~~~~~--~L~~L~l~~c~~l~~lp-~~~~~l~-~L~~L~l~  363 (391)
                      .+. +...   .++.++|.  +|+.+.+.++. ...++ ..+..++ +++.|++-
T Consensus       329 ~lp-~~l~---~I~~~aF~~~~L~~l~l~~n~-~~~l~~~~F~~~~~~l~~l~vp  378 (401)
T 4fdw_A          329 TIP-ANVT---QINFSAFNNTGIKEVKVEGTT-PPQVFEKVWYGFPDDITVIRVP  378 (401)
T ss_dssp             EEC-TTCC---EECTTSSSSSCCCEEEECCSS-CCBCCCSSCCCSCTTCCEEEEC
T ss_pred             EEC-cccc---EEcHHhCCCCCCCEEEEcCCC-CcccccccccCCCCCccEEEeC
Confidence            665 2211   12222221  67777776552 34443 2334443 56666663

>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=97.16  E-value=0.0001  Score=61.04  Aligned_cols=68  Identities=9%  Similarity=0.173  Sum_probs=42.2

Q ss_pred             ccCCCCccEEEeeccc-CCCCChhhhcCC----CCCCEEEcCCCCCcCc-cccCCCcccccceeeeccccccccc
Q 041097          279 YQFPPSLTHLSFSNIE-LMDDPIPALEKL----SVLQVLKLKQNLYSEE-RTMGIRAMPKLECLIINPYAHLKRI  347 (391)
Q Consensus       279 ~~l~~~L~~L~l~~~~-~~~~~~~~l~~l----~~L~~L~l~~~~~~~~-~~~~~~~~~~L~~L~l~~c~~l~~l  347 (391)
                      ..+ ++|+.|+|++|. ++...+..+..+    ++|++|+++.|.-... .......+++|++|++++|++++..
T Consensus        82 ~~~-~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~~L~~L~L~~c~~Itd~  155 (176)
T 3e4g_A           82 EGL-QYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFRNLKYLFLSDLPGVKEK  155 (176)
T ss_dssp             TTC-SCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCTTCCEEEEESCTTCCCH
T ss_pred             cCC-CCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCCCCCEEECCCCCCCCch
Confidence            456 777777777774 444445666664    3688888874432222 1222245788888888888777653

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.12  E-value=0.00028  Score=59.25  Aligned_cols=46  Identities=7%  Similarity=0.018  Sum_probs=32.5

Q ss_pred             hhHHhhccCCcccEEEcCCC-ccc-----cCCcccCCCCcccEEEccCCCCC
Q 041097          170 YCEKICKMFKFLRVLDLGSL-VLI-----RYPSGIENLFLLRYLKLNIPSLK  215 (391)
Q Consensus       170 ~~~~~~~~~~~L~~L~l~~~-~l~-----~~p~~i~~l~~L~~L~l~~~~i~  215 (391)
                      .+...+...+.|+.|++++| .+.     .+.+.+....+|++|+|++|.+.
T Consensus        27 ~l~~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~   78 (185)
T 1io0_A           27 TLKRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSN   78 (185)
T ss_dssp             HHHHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCC
T ss_pred             HHHHHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCC
Confidence            34566777888999999888 765     34455566677888887777654

>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=97.00  E-value=2.8e-05  Score=77.07  Aligned_cols=79  Identities=18%  Similarity=0.089  Sum_probs=57.3

Q ss_pred             ccccccc-----------EEEEEEcCCCcChHHHHHHHHHhhcCCCC--CCCCCC-----hHHHHHHHHHHHHcCccEEe
Q 041097           23 YVKHYFD-----------CHAWVQESLPYDADQILYDIIKFVMPSPE--GFIPDN-----NEATVEKYLEQLINGGFVGA   84 (391)
Q Consensus        23 ~lk~~F~-----------~~~~~~vs~~~~~~~i~~~~~~~~~~~~e--g~~~~~-----~~~~~~~~~~~L~~k~~l~~   84 (391)
                      .++.||.           +|+.||.++.++          ...|+++  ||+...     .++.++ ++.+|+++++++.
T Consensus       377 ~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----------i~~w~a~~~G~i~~~~~~~~~~~~~~-~l~~L~~rsLl~~  445 (549)
T 2a5y_B          377 ALQRCVEVLSDEDRSALAFAVVMPPGVDIP----------VKLWSCVIPVDICSNEEEQLDDEVAD-RLKRLSKRGALLS  445 (549)
T ss_dssp             HHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----------HHHHHHHSCC-------CCCTHHHHH-HHHHTTTBSSCSE
T ss_pred             HHHHHHhccchhhhhHhhheeeeCCCCeee----------eeeeeeeccceeccCCCCCCHHHHHH-HHHHHHHcCCeeE
Confidence            4577887           999999887766          2246677  776532     466666 9999999999987


Q ss_pred             eeccCCCceeeEEcCcchHHHHHhhccccCc
Q 041097           85 GKRSDIGRINTCSIPGRCSPALLTVVFEGEF  115 (391)
Q Consensus        85 ~~~~~~~~~~~~~~hdl~~~~~~~~~~~~~~  115 (391)
                      ...+   ...+|+|||++|++|..++.++.+
T Consensus       446 ~~~~---~~~~~~mHdlv~~~a~~~~~~~~~  473 (549)
T 2a5y_B          446 GKRM---PVLTFKIDHIIHMFLKHVVDAQTI  473 (549)
T ss_dssp             EECS---SSCEEECCHHHHHHHHTTSCTHHH
T ss_pred             ecCC---CceEEEeChHHHHHHHHHHHHHHH
Confidence            7643   445899999999999998876543

>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=96.96  E-value=0.0011  Score=62.10  Aligned_cols=84  Identities=12%  Similarity=-0.077  Sum_probs=48.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc--------ccEEEEEEcCCCc-ChHHHHHHHHHhhcCCCCCCCCCChHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY--------FDCHAWVQESLPY-DADQILYDIIKFVMPSPEGFIPDNNEATVEK   71 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~--------F~~~~~~~vs~~~-~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~   71 (391)
                      |-|+|++|+||||+|+.+++.  +...        ...++++..+... +...+...+...+.....+.......+....
T Consensus        48 vll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~  125 (384)
T 2qby_B           48 NLFLGLTGTGKTFVSKYIFNE--IEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDK  125 (384)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH--HHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHH
Confidence            458999999999999999873  3221        2345566554444 6666666666554322222222223555555


Q ss_pred             HHHHHHcCccEEeee
Q 041097           72 YLEQLINGGFVGAGK   86 (391)
Q Consensus        72 ~~~~L~~k~~l~~~~   86 (391)
                      +...+..+..+.+.+
T Consensus       126 l~~~l~~~~~vlilD  140 (384)
T 2qby_B          126 IKNGTRNIRAIIYLD  140 (384)
T ss_dssp             HHHHHSSSCEEEEEE
T ss_pred             HHHHhccCCCEEEEE
Confidence            666665555333333

>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=96.92  E-value=0.002  Score=60.96  Aligned_cols=50  Identities=20%  Similarity=0.216  Sum_probs=35.8

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccccc-----cc-EEEEEEcCCCcChHHHHHHHHHhh
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHY-----FD-CHAWVQESLPYDADQILYDIIKFV   53 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~-----F~-~~~~~~vs~~~~~~~i~~~~~~~~   53 (391)
                      ||+|++|+||||||+.+++.  +...     |. .++|+......+...+...+....
T Consensus        56 ~i~G~~G~GKT~L~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l  111 (412)
T 1w5s_A           56 GSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQT  111 (412)
T ss_dssp             ECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHH
T ss_pred             eCcCcCCCCHHHHHHHHHHH--HHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHh
Confidence            56999999999999999973  3321     23 356666555667777777776655

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=96.90  E-value=0.00038  Score=58.42  Aligned_cols=119  Identities=18%  Similarity=0.135  Sum_probs=79.3

Q ss_pred             chhHHhcCCCCCCEEEecCC-C-CCCchhhhcc-ccccCCCCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCC
Q 041097          246 LLSKSLCRLSCLESLKLANE-S-KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNL  318 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~-~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~  318 (391)
                      .+...+...++|++|++++. . .-..... +. .+... ++|+.|+|++|.+....    ...+...++|++|+++.|.
T Consensus        27 ~l~~~l~~~~~L~~L~L~~n~~i~~~g~~~-l~~~L~~~-~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~  104 (185)
T 1io0_A           27 TLKRIQNNDPDLEEVNLNNIMNIPVPTLKA-CAEALKTN-TYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNF  104 (185)
T ss_dssp             HHHHHHTTCTTCCEEECTTCTTCCHHHHHH-HHHHHTTC-CSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSC
T ss_pred             HHHHHHhcCCCCCEEEecCCCCCCHHHHHH-HHHHHHhC-CCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCCc
Confidence            45567788999999999873 2 0000011 22 44556 89999999999876543    2345566899999999766


Q ss_pred             CcCccc---c-CCCcccccceeee--ccccccc-----cchHhhcCCCCCCEEEeeCCcH
Q 041097          319 YSEERT---M-GIRAMPKLECLII--NPYAHLK-----RIHEQLWCLKSLNKLELWWPEP  367 (391)
Q Consensus       319 ~~~~~~---~-~~~~~~~L~~L~l--~~c~~l~-----~lp~~~~~l~~L~~L~l~~~~~  367 (391)
                      ......   . .....++|++|++  ++| .+.     .+...+...++|++|+++++.-
T Consensus       105 i~~~g~~~l~~~L~~n~~L~~L~L~~~~N-~i~~~g~~~l~~~L~~n~~L~~L~L~~n~i  163 (185)
T 1io0_A          105 ISGSGILALVEALQSNTSLIELRIDNQSQ-PLGNNVEMEIANMLEKNTTLLKFGYHFTQQ  163 (185)
T ss_dssp             CCHHHHHHHHHGGGGCSSCCEEECCCCSS-CCCHHHHHHHHHHHHHCSSCCEEECCCSSH
T ss_pred             CCHHHHHHHHHHHHhCCCceEEEecCCCC-CCCHHHHHHHHHHHHhCCCcCEEeccCCCC
Confidence            543221   1 1134568999999  555 343     2556667789999999998874

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=96.63  E-value=0.002  Score=57.20  Aligned_cols=82  Identities=23%  Similarity=0.212  Sum_probs=41.8

Q ss_pred             CCccEEEeecccCCCCC--hhhhcCCCCCCEEEcCCCCCcCccccCCCccc--ccceeeeccccccccch-------Hhh
Q 041097          283 PSLTHLSFSNIELMDDP--IPALEKLSVLQVLKLKQNLYSEERTMGIRAMP--KLECLIINPYAHLKRIH-------EQL  351 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~--~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~--~L~~L~l~~c~~l~~lp-------~~~  351 (391)
                      ++|+.|+|++|.+....  ...++.+++|+.|+|+.|...+...+  +.+.  +|++|.+++++--..+|       ..+
T Consensus       170 ~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N~i~~~~~l--~~l~~l~L~~L~L~~Npl~~~~~~~~~y~~~il  247 (267)
T 3rw6_A          170 PELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSEREL--DKIKGLKLEELWLDGNSLCDTFRDQSTYISAIR  247 (267)
T ss_dssp             TTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTSCCCSGGGG--GGGTTSCCSEEECTTSTTGGGCSSHHHHHHHHH
T ss_pred             CCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCCccCCchhh--hhcccCCcceEEccCCcCccccCcchhHHHHHH
Confidence            55555555555554422  13344566666666665554432111  1222  66666666654222232       235


Q ss_pred             cCCCCCCEEEeeCCc
Q 041097          352 WCLKSLNKLELWWPE  366 (391)
Q Consensus       352 ~~l~~L~~L~l~~~~  366 (391)
                      ..+++|+.|+=...+
T Consensus       248 ~~~P~L~~LDg~~v~  262 (267)
T 3rw6_A          248 ERFPKLLRLDGHELP  262 (267)
T ss_dssp             HHCTTCCEESSCBCC
T ss_pred             HHCcccCeECCcCCC
Confidence            677788777654443

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=96.51  E-value=0.0019  Score=57.35  Aligned_cols=13  Identities=31%  Similarity=0.324  Sum_probs=6.4

Q ss_pred             CCCcChHHHHHHH
Q 041097           37 SLPYDADQILYDI   49 (391)
Q Consensus        37 s~~~~~~~i~~~~   49 (391)
                      .+.++.+.++..+
T Consensus        32 g~ky~k~~ll~~i   44 (267)
T 3rw6_A           32 GRKYDKAWLLSMI   44 (267)
T ss_dssp             GGGSCHHHHHHHH
T ss_pred             ccccCHHHHHHHH
Confidence            4445555555443

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.42  E-value=0.0011  Score=54.51  Aligned_cols=18  Identities=22%  Similarity=0.252  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |+|+|+.|+||||+|+.+
T Consensus         4 I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            4 ILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            689999999999999998

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.31  E-value=0.011  Score=55.16  Aligned_cols=75  Identities=15%  Similarity=0.038  Sum_probs=43.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc------cEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF------DCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLE   74 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F------~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~   74 (391)
                      |.|+|++|+||||+|+.+++.  +...+      -.++++......+...+...+...+.. ..........+....+..
T Consensus        47 vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~l~~  123 (387)
T 2v1u_A           47 ALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGV-RVPFTGLSVGEVYERLVK  123 (387)
T ss_dssp             EEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSC-CCCSSCCCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCC-CCCCCCCCHHHHHHHHHH
Confidence            458999999999999999873  32211      244556555556666777776665522 111111123444555555


Q ss_pred             HHHc
Q 041097           75 QLIN   78 (391)
Q Consensus        75 ~L~~   78 (391)
                      .+..
T Consensus       124 ~l~~  127 (387)
T 2v1u_A          124 RLSR  127 (387)
T ss_dssp             HHTT
T ss_pred             HHhc
Confidence            5543

>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=96.29  E-value=0.0011  Score=55.17  Aligned_cols=20  Identities=25%  Similarity=0.395  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+||||||+.+++
T Consensus        41 ~~l~G~~G~GKTtL~~~i~~   60 (180)
T 3ec2_A           41 LTFVGSPGVGKTHLAVATLK   60 (180)
T ss_dssp             EEECCSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999987

>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=96.27  E-value=0.0063  Score=56.69  Aligned_cols=50  Identities=18%  Similarity=0.203  Sum_probs=32.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc---cEEEEEEcCCCcChHHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF---DCHAWVQESLPYDADQILYDIIKF   52 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F---~~~~~~~vs~~~~~~~i~~~~~~~   52 (391)
                      |.|+|++|+||||||+.+++  .++..+   ..++++......+...+...+...
T Consensus        48 vli~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~  100 (386)
T 2qby_A           48 IFIYGLTGTGKTAVVKFVLS--KLHKKFLGKFKHVYINTRQIDTPYRVLADLLES  100 (386)
T ss_dssp             EEEEECTTSSHHHHHHHHHH--HHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTT
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHHHhcCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            46999999999999999987  343332   245565544444555555555443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.21  E-value=0.0015  Score=55.24  Aligned_cols=33  Identities=18%  Similarity=0.102  Sum_probs=23.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      |-|+|.+|+||||||+.+++.  +......+.++.
T Consensus        57 ~~l~G~~GtGKT~la~~i~~~--~~~~~~~~~~~~   89 (202)
T 2w58_A           57 LYLHGSFGVGKTYLLAAIANE--LAKRNVSSLIVY   89 (202)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEE
Confidence            358999999999999999983  333333444544

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.11  E-value=0.002  Score=53.00  Aligned_cols=20  Identities=10%  Similarity=0.285  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus         7 i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            7 IFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999876

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.08  E-value=0.0021  Score=52.64  Aligned_cols=20  Identities=15%  Similarity=-0.034  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         4 i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            4 IILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.05  E-value=0.002  Score=53.86  Aligned_cols=20  Identities=15%  Similarity=0.159  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus        12 i~l~G~~GsGKSTl~~~La~   31 (191)
T 1zp6_A           12 LLLSGHPGSGKSTIAEALAN   31 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999986

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.96  E-value=0.0025  Score=53.89  Aligned_cols=20  Identities=15%  Similarity=0.179  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus        28 i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           28 IFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>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=95.94  E-value=0.0026  Score=52.49  Aligned_cols=20  Identities=10%  Similarity=0.011  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+.+
T Consensus         6 i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            6 IILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999876

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.82  E-value=0.0032  Score=52.01  Aligned_cols=20  Identities=20%  Similarity=0.313  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         5 I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            5 ILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEecCCCCCHHHHHHHHHh
Confidence            57899999999999999875

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.82  E-value=0.003  Score=53.54  Aligned_cols=20  Identities=20%  Similarity=0.258  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus         4 i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            4 IGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHH
Confidence            68999999999999999865

>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=95.80  E-value=0.0092  Score=55.76  Aligned_cols=51  Identities=14%  Similarity=0.135  Sum_probs=35.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc-cEEEEEEcCCCcChHHHHHHHHHhh
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF-DCHAWVQESLPYDADQILYDIIKFV   53 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F-~~~~~~~vs~~~~~~~i~~~~~~~~   53 (391)
                      |.|+|..|+||||+|+.+.+.  +.... ..++++..+...+...+...+...+
T Consensus        47 ~li~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l   98 (389)
T 1fnn_A           47 ATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAIIGEIARSL   98 (389)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HhhhcCeeEEEEeCccCCCHHHHHHHHHHHh
Confidence            468999999999999999873  33221 2455666566666667777666554

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.80  E-value=0.0033  Score=52.26  Aligned_cols=20  Identities=10%  Similarity=0.297  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+|||||++.+..
T Consensus         8 i~i~GpsGsGKSTL~~~L~~   27 (180)
T 1kgd_A            8 LVLLGAHGVGRRHIKNTLIT   27 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999876

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.77  E-value=0.0036  Score=51.55  Aligned_cols=20  Identities=25%  Similarity=0.522  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++..+.
T Consensus        12 ~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A           12 VVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             EEEECCTTSCHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHcc
Confidence            58999999999999998665

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.77  E-value=0.0035  Score=52.09  Aligned_cols=20  Identities=15%  Similarity=0.288  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         3 i~l~G~nGsGKTTLl~~l~g   22 (178)
T 1ye8_A            3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999876

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.76  E-value=0.0035  Score=52.13  Aligned_cols=20  Identities=15%  Similarity=0.298  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus         8 i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            8 IYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999865

>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=95.75  E-value=0.0036  Score=51.59  Aligned_cols=20  Identities=25%  Similarity=0.308  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus        11 i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A           11 YVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.74  E-value=0.0036  Score=53.01  Aligned_cols=20  Identities=15%  Similarity=0.240  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus        21 I~l~G~~GsGKSTla~~L~~   40 (202)
T 3t61_A           21 IVVMGVSGSGKSSVGEAIAE   40 (202)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.71  E-value=0.0037  Score=52.75  Aligned_cols=20  Identities=25%  Similarity=0.517  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus         3 I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            3 IAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCccCHHHHHHHHHH
Confidence            68999999999999999876

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.67  E-value=0.0024  Score=51.44  Aligned_cols=20  Identities=15%  Similarity=0.119  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+++
T Consensus        39 ~~l~G~~G~GKTtL~~~i~~   58 (149)
T 2kjq_A           39 IYVWGEEGAGKSHLLQAWVA   58 (149)
T ss_dssp             EEEESSSTTTTCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            47999999999999999987

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.67  E-value=0.004  Score=52.05  Aligned_cols=20  Identities=10%  Similarity=0.174  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus         5 i~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            5 YIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            57999999999999999864

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.66  E-value=0.0041  Score=50.90  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus        10 i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A           10 LVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             EEEESCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=95.65  E-value=0.0041  Score=51.50  Aligned_cols=20  Identities=25%  Similarity=0.336  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus        14 i~i~G~~GsGKst~~~~l~~   33 (180)
T 3iij_A           14 ILLTGTPGVGKTTLGKELAS   33 (180)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            56999999999999999875

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=95.64  E-value=0.0041  Score=51.83  Aligned_cols=20  Identities=20%  Similarity=0.242  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+.+
T Consensus        13 I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A           13 ILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999875

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.63  E-value=0.0042  Score=52.56  Aligned_cols=20  Identities=25%  Similarity=0.273  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus        32 i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           32 VVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>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=95.62  E-value=0.0042  Score=52.51  Aligned_cols=20  Identities=20%  Similarity=0.162  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus        28 i~l~G~sGsGKSTl~~~La~   47 (200)
T 3uie_A           28 IWVTGLSGSGKSTLACALNQ   47 (200)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=95.61  E-value=0.0043  Score=51.73  Aligned_cols=20  Identities=20%  Similarity=0.169  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         6 I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            6 VVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=95.61  E-value=0.0038  Score=51.71  Aligned_cols=20  Identities=20%  Similarity=0.230  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|..|+||||+|+.+.+
T Consensus        46 ~ll~G~~G~GKT~l~~~~~~   65 (195)
T 1jbk_A           46 PVLIGEPGVGKTAIVEGLAQ   65 (195)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             eEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999877

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.60  E-value=0.0042  Score=53.48  Aligned_cols=20  Identities=10%  Similarity=0.144  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus         8 i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            8 ITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=95.60  E-value=0.0044  Score=51.52  Aligned_cols=20  Identities=10%  Similarity=0.107  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus         5 I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            5 AVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999865

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.60  E-value=0.0044  Score=51.11  Aligned_cols=20  Identities=15%  Similarity=0.263  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus         7 i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            7 IVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57899999999999999875

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.60  E-value=0.0036  Score=53.36  Aligned_cols=20  Identities=15%  Similarity=0.205  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|.|||||++.+..
T Consensus        25 v~I~G~sGsGKSTl~~~l~~   44 (208)
T 3c8u_A           25 VALSGAPGSGKSTLSNPLAA   44 (208)
T ss_dssp             EEEECCTTSCTHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=95.59  E-value=0.0044  Score=52.59  Aligned_cols=20  Identities=25%  Similarity=0.245  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|+.|+||||+++.+..
T Consensus         5 i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            5 VGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEECSTTSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999864

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.59  E-value=0.0044  Score=52.43  Aligned_cols=20  Identities=10%  Similarity=0.272  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus         9 i~l~G~~GsGKSTl~~~L~~   28 (207)
T 2j41_A            9 IVLSGPSGVGKGTVRKRIFE   28 (207)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999876

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.58  E-value=0.0045  Score=52.33  Aligned_cols=20  Identities=15%  Similarity=0.197  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||++.+..
T Consensus        10 i~l~Gp~GsGKSTl~~~L~~   29 (205)
T 3tr0_A           10 FIISAPSGAGKTSLVRALVK   29 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHh
Confidence            58999999999999999876

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.58  E-value=0.0042  Score=52.78  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||+|+.+..
T Consensus        24 i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           24 IGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.53  E-value=0.0049  Score=50.30  Aligned_cols=20  Identities=5%  Similarity=0.029  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            3 IYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEESCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.52  E-value=0.0048  Score=52.34  Aligned_cols=20  Identities=20%  Similarity=0.318  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+++.+..
T Consensus        15 i~l~G~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           15 LVVCGPSGVGKGTLIKKVLS   34 (204)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>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=95.51  E-value=0.0048  Score=53.35  Aligned_cols=35  Identities=6%  Similarity=0.064  Sum_probs=23.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |-|+|..|+||||+|+.+.+.  +......+.++..+
T Consensus        55 ~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~   89 (242)
T 3bos_A           55 IYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLG   89 (242)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGG
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHH
Confidence            358999999999999999873  32222334555543

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.51  E-value=0.0049  Score=51.85  Aligned_cols=20  Identities=20%  Similarity=0.260  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|+.|+||||+|+.+-.
T Consensus        15 IgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           15 IGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999764

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.49  E-value=0.0047  Score=51.55  Aligned_cols=20  Identities=20%  Similarity=0.136  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         4 I~i~G~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            4 GIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.49  E-value=0.0047  Score=52.59  Aligned_cols=20  Identities=15%  Similarity=0.172  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||++.+..
T Consensus         9 i~i~G~~GsGKSTl~~~l~~   28 (211)
T 3asz_A            9 IGIAGGTASGKTTLAQALAR   28 (211)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.46  E-value=0.0052  Score=51.06  Aligned_cols=20  Identities=20%  Similarity=0.154  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+.+
T Consensus         7 I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            7 VIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=95.43  E-value=0.0055  Score=50.22  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+.+
T Consensus         5 I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            5 IFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             EEEESCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.41  E-value=0.0056  Score=51.02  Aligned_cols=20  Identities=20%  Similarity=0.107  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+++.+..
T Consensus        16 i~l~G~~GsGKsT~~~~L~~   35 (186)
T 2yvu_A           16 VWLTGLPGSGKTTIATRLAD   35 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>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=95.40  E-value=0.0049  Score=53.12  Aligned_cols=20  Identities=20%  Similarity=0.132  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+||||+|+.+++
T Consensus        48 ~ll~G~~G~GKT~l~~~~~~   67 (250)
T 1njg_A           48 YLFSGTRGVGKTSIARLLAK   67 (250)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999986

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.38  E-value=0.0057  Score=51.10  Aligned_cols=20  Identities=25%  Similarity=0.199  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus         6 I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            6 VFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999765

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.37  E-value=0.0058  Score=51.64  Aligned_cols=20  Identities=10%  Similarity=0.278  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         7 i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            7 VVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999865

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=95.35  E-value=0.0056  Score=51.13  Aligned_cols=20  Identities=15%  Similarity=0.130  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         8 I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            8 IIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.32  E-value=0.0062  Score=50.87  Aligned_cols=20  Identities=30%  Similarity=0.252  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+.+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.32  E-value=0.0061  Score=53.38  Aligned_cols=20  Identities=15%  Similarity=0.164  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+|||||++.+..
T Consensus        30 i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           30 AVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999883

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.28  E-value=0.006  Score=51.23  Aligned_cols=20  Identities=10%  Similarity=0.140  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus        15 I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           15 IFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=95.28  E-value=0.0064  Score=51.34  Aligned_cols=20  Identities=20%  Similarity=0.172  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus        23 I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           23 VLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.26  E-value=0.0062  Score=51.56  Aligned_cols=20  Identities=15%  Similarity=0.082  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+++.+..
T Consensus        25 i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A           25 LGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>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=95.26  E-value=0.015  Score=53.44  Aligned_cols=32  Identities=9%  Similarity=0.015  Sum_probs=23.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |.|+|++|+|||||++.+.+.  ...   ...|+...
T Consensus        33 v~i~G~~G~GKT~L~~~~~~~--~~~---~~~~~~~~   64 (357)
T 2fna_A           33 TLVLGLRRTGKSSIIKIGINE--LNL---PYIYLDLR   64 (357)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH--HTC---CEEEEEGG
T ss_pred             EEEECCCCCCHHHHHHHHHHh--cCC---CEEEEEch
Confidence            469999999999999999873  322   24566544

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.25  E-value=0.0065  Score=54.71  Aligned_cols=20  Identities=15%  Similarity=0.193  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+||||||+.+..
T Consensus        34 i~I~G~sGsGKSTla~~L~~   53 (290)
T 1odf_A           34 IFFSGPQGSGKSFTSIQIYN   53 (290)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999765

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.25  E-value=0.0063  Score=50.97  Aligned_cols=20  Identities=15%  Similarity=0.135  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus        12 I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A           12 IFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999865

>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=95.23  E-value=0.013  Score=49.61  Aligned_cols=20  Identities=25%  Similarity=0.116  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|.+|+||||+|+.+++
T Consensus        41 ~ll~G~~G~GKT~l~~~l~~   60 (226)
T 2chg_A           41 LLFSGPPGTGKTATAIALAR   60 (226)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999887

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.22  E-value=0.0065  Score=51.20  Aligned_cols=20  Identities=30%  Similarity=0.351  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+|+.+..
T Consensus        11 I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A           11 IGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.21  E-value=0.005  Score=50.84  Aligned_cols=19  Identities=26%  Similarity=0.260  Sum_probs=17.5

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+.+
T Consensus        47 ll~G~~G~GKT~la~~~~~   65 (187)
T 2p65_A           47 ILLGDPGVGKTAIVEGLAI   65 (187)
T ss_dssp             EEESCGGGCHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999999876

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.20  E-value=0.007  Score=51.53  Aligned_cols=20  Identities=10%  Similarity=0.285  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+|||||++.+..
T Consensus        11 i~l~GpsGsGKsTl~~~L~~   30 (208)
T 3tau_A           11 IVLSGPSGVGKGTVREAVFK   30 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHh
Confidence            57999999999999999876

>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=95.15  E-value=0.0064  Score=55.97  Aligned_cols=20  Identities=30%  Similarity=0.268  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +.++|..|+||||||+.+.+
T Consensus        54 ~ll~Gp~G~GKTTLa~~ia~   73 (334)
T 1in4_A           54 VLLAGPPGLGKTTLAHIIAS   73 (334)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            46899999999999999987

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.13  E-value=0.0074  Score=53.16  Aligned_cols=20  Identities=15%  Similarity=0.069  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||||+.+..
T Consensus         4 i~I~G~~GSGKSTla~~La~   23 (253)
T 2ze6_A            4 HLIYGPTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            47999999999999999875

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.12  E-value=0.0075  Score=54.92  Aligned_cols=20  Identities=20%  Similarity=0.238  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||++.+..
T Consensus        93 vgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           93 IGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCchHHHHHHHHHh
Confidence            68999999999999999876

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.11  E-value=0.0078  Score=50.83  Aligned_cols=20  Identities=20%  Similarity=0.179  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+.+
T Consensus        18 I~l~G~~GsGKsT~~~~L~~   37 (203)
T 1ukz_A           18 IFVLGGPGAGKGTQCEKLVK   37 (203)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.11  E-value=0.0077  Score=51.08  Aligned_cols=20  Identities=20%  Similarity=0.034  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         7 I~i~G~~GsGKsT~~~~L~~   26 (213)
T 2plr_A            7 IAFEGIDGSGKSSQATLLKD   26 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.11  E-value=0.0077  Score=53.75  Aligned_cols=20  Identities=20%  Similarity=0.192  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+++|..|+||||||+.+..
T Consensus        47 vlL~Gp~GtGKTtLakala~   66 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVAN   66 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            47899999999999999987

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.11  E-value=0.0076  Score=53.05  Aligned_cols=20  Identities=15%  Similarity=0.140  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus        30 I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           30 ITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999874

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=95.11  E-value=0.0075  Score=53.33  Aligned_cols=20  Identities=15%  Similarity=0.280  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|++|+||||+|+.+..
T Consensus         7 Ivl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            7 IILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.10  E-value=0.0055  Score=50.72  Aligned_cols=20  Identities=20%  Similarity=0.169  Sum_probs=14.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         8 I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            8 IWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             EEEECCC----CHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999865

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.10  E-value=0.0079  Score=51.36  Aligned_cols=20  Identities=15%  Similarity=0.185  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=95.08  E-value=0.0076  Score=50.23  Aligned_cols=20  Identities=25%  Similarity=0.185  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus         9 I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            9 VFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>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=95.08  E-value=0.007  Score=53.20  Aligned_cols=20  Identities=20%  Similarity=0.292  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+||||||+.+.+
T Consensus        52 ~ll~G~~G~GKTtl~~~i~~   71 (254)
T 1ixz_A           52 VLLVGPPGVGKTHLARAVAG   71 (254)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999987

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=95.07  E-value=0.008  Score=51.33  Aligned_cols=20  Identities=10%  Similarity=0.131  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999764

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.07  E-value=0.008  Score=52.60  Aligned_cols=20  Identities=10%  Similarity=0.152  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+|||||++.+..
T Consensus        28 igI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           28 IGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.06  E-value=0.008  Score=52.84  Aligned_cols=20  Identities=15%  Similarity=0.185  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|+.|+||||+|+.+..
T Consensus        25 I~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           25 IGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.06  E-value=0.0082  Score=51.58  Aligned_cols=20  Identities=10%  Similarity=0.270  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        26 ~~lvGpsGsGKSTLl~~L~g   45 (218)
T 1z6g_A           26 LVICGPSGVGKGTLIKKLLN   45 (218)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999875

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.06  E-value=0.0086  Score=50.22  Aligned_cols=20  Identities=20%  Similarity=0.248  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         4 i~i~G~nG~GKTTll~~l~g   23 (189)
T 2i3b_A            4 VFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             EEEESCCSSCHHHHHHHHHH
T ss_pred             EEEECCCCChHHHHHHHHHh
Confidence            58999999999999999876

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.01  E-value=0.0069  Score=50.64  Aligned_cols=20  Identities=10%  Similarity=0.328  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+|||||++.+..
T Consensus         4 IVi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            4 IVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=94.95  E-value=0.0093  Score=49.29  Aligned_cols=20  Identities=15%  Similarity=0.057  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+++.+..
T Consensus         8 i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            8 VWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=94.94  E-value=0.0086  Score=47.74  Aligned_cols=20  Identities=10%  Similarity=-0.117  Sum_probs=18.3

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -|+|..|+|||++|+.+++.
T Consensus        28 ll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A           28 WLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             EEESSTTSSHHHHHHHHHHS
T ss_pred             EEECCCCCCHHHHHHHHHHh
Confidence            48999999999999999874

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=94.94  E-value=0.0093  Score=50.69  Aligned_cols=20  Identities=5%  Similarity=0.029  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        23 ~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           23 VVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            58999999999999999875

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=94.94  E-value=0.0093  Score=53.78  Aligned_cols=19  Identities=11%  Similarity=0.158  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -+||.+|+|||+||+.+.+
T Consensus        40 Ll~GppGtGKT~la~aiA~   58 (293)
T 3t15_A           40 GIWGGKGQGKSFQCELVFR   58 (293)
T ss_dssp             EEEECTTSCHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4789999999999999998

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.94  E-value=0.0092  Score=52.42  Aligned_cols=20  Identities=20%  Similarity=0.205  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus        51 i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           51 MYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=94.93  E-value=0.0079  Score=55.23  Aligned_cols=21  Identities=10%  Similarity=0.091  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|++|+|||||++.+.+.
T Consensus        34 v~i~G~~G~GKT~Ll~~~~~~   54 (350)
T 2qen_A           34 TLLLGIRRVGKSSLLRAFLNE   54 (350)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHHHHH
Confidence            469999999999999999873

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=94.91  E-value=0.0086  Score=53.64  Aligned_cols=19  Identities=16%  Similarity=0.179  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|.|+.|+||||+|+.+-
T Consensus        78 I~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           78 LGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             EEEEECTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            6899999999999999976

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.91  E-value=0.01  Score=53.00  Aligned_cols=19  Identities=21%  Similarity=0.209  Sum_probs=17.8

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|.+|+||||+|+.+.+
T Consensus        55 ll~G~~GtGKT~la~~la~   73 (285)
T 3h4m_A           55 LLYGPPGTGKTLLAKAVAT   73 (285)
T ss_dssp             EEESSSSSSHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            4899999999999999987

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=94.91  E-value=0.009  Score=50.73  Aligned_cols=20  Identities=5%  Similarity=-0.170  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus        13 I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A           13 IVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=94.89  E-value=0.0096  Score=50.95  Aligned_cols=20  Identities=25%  Similarity=0.287  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+++.+..
T Consensus         7 I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            7 VALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999853

>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=94.87  E-value=0.023  Score=48.40  Aligned_cols=42  Identities=14%  Similarity=0.090  Sum_probs=29.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILY   47 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~   47 (391)
                      ++|+|.+|+||||||+.+..    + .=..++|+.....++.+.+..
T Consensus        23 ~~i~G~~GsGKTtl~~~l~~----~-~~~~v~~i~~~~~~~~~~~~~   64 (220)
T 2cvh_A           23 TQVYGPYASGKTTLALQTGL----L-SGKKVAYVDTEGGFSPERLVQ   64 (220)
T ss_dssp             EEEECSTTSSHHHHHHHHHH----H-HCSEEEEEESSCCCCHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH----H-cCCcEEEEECCCCCCHHHHHH
Confidence            47999999999999999875    1 113677777665556665443

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=94.87  E-value=0.0092  Score=51.49  Aligned_cols=20  Identities=10%  Similarity=0.214  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus        10 I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A           10 AVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=94.86  E-value=0.0093  Score=50.70  Aligned_cols=20  Identities=5%  Similarity=-0.045  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+.+
T Consensus        12 I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A           12 IVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=94.85  E-value=0.068  Score=48.54  Aligned_cols=69  Identities=12%  Similarity=0.124  Sum_probs=39.7

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccc--------cccEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHH
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKH--------YFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLE   74 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~--------~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~   74 (391)
                      |+|.+|+|||++|+.|.+.  ++.        .|.++ ++.-....+...+...++..+..  +........+..+.++.
T Consensus        50 i~GpPGTGKT~~v~~v~~~--L~~~~~~~~~~~~~~v-~INc~~~~t~~~~~~~I~~~L~g--~~~~~~~~~~~L~~~f~  124 (318)
T 3te6_A           50 ITNADDSTKFQLVNDVMDE--LITSSARKELPIFDYI-HIDALELAGMDALYEKIWFAISK--ENLCGDISLEALNFYIT  124 (318)
T ss_dssp             EECCCSHHHHHHHHHHHHH--HHHTTTTTSSCCEEEE-EEETTCCC--HHHHHHHHHHHSC--CC--CCCCHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHH--HHHHhhhccCCceEEE-EEeccccCCHHHHHHHHHHHhcC--CCCCchHHHHHHHHHHH
Confidence            8999999999999999883  321        24333 33322334556677777766532  22222224555666776


Q ss_pred             HH
Q 041097           75 QL   76 (391)
Q Consensus        75 ~L   76 (391)
                      .+
T Consensus       125 ~~  126 (318)
T 3te6_A          125 NV  126 (318)
T ss_dssp             HS
T ss_pred             Hh
Confidence            65

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=94.85  E-value=0.011  Score=48.05  Aligned_cols=20  Identities=15%  Similarity=0.237  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|.-|.|||||+|.+..
T Consensus        36 v~L~G~nGaGKTTLlr~l~g   55 (158)
T 1htw_A           36 VYLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=94.84  E-value=0.0089  Score=52.62  Aligned_cols=20  Identities=20%  Similarity=0.219  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+||||+|+.+.+
T Consensus        48 vll~G~~GtGKT~la~~la~   67 (257)
T 1lv7_A           48 VLMVGPPGTGKTLLAKAIAG   67 (257)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHH
Confidence            35899999999999999987

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=94.83  E-value=0.01  Score=50.90  Aligned_cols=20  Identities=20%  Similarity=0.225  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         7 I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            7 MVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999875

>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=94.81  E-value=0.009  Score=54.58  Aligned_cols=19  Identities=26%  Similarity=0.289  Sum_probs=17.9

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|||..|+||||||+.+.+
T Consensus        41 ll~G~~GtGKT~la~~i~~   59 (324)
T 1l8q_A           41 FIYGSVGTGKTHLLQAAGN   59 (324)
T ss_dssp             EEECSSSSSHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            4899999999999999987

>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=94.79  E-value=0.011  Score=52.10  Aligned_cols=19  Identities=26%  Similarity=0.275  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|.+|+||||+|+.+.+
T Consensus        43 ll~G~~GtGKT~la~~la~   61 (262)
T 2qz4_A           43 LLLGPPGCGKTLLAKAVAT   61 (262)
T ss_dssp             EEESCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999999987

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=94.78  E-value=0.011  Score=49.89  Aligned_cols=20  Identities=10%  Similarity=-0.087  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+++.+.+
T Consensus         7 I~l~G~~GsGKsT~~~~L~~   26 (204)
T 2v54_A            7 IVFEGLDKSGKTTQCMNIME   26 (204)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            68999999999999999876

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=94.72  E-value=0.006  Score=51.92  Aligned_cols=20  Identities=15%  Similarity=0.172  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|+||||+|+.+..
T Consensus         3 I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>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=94.70  E-value=0.011  Score=53.36  Aligned_cols=20  Identities=20%  Similarity=0.169  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++|..|+||||||+.+.+
T Consensus        52 vLL~Gp~GtGKT~la~ala~   71 (301)
T 3cf0_A           52 VLFYGPPGCGKTLLAKAIAN   71 (301)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHH
Confidence            35899999999999999997

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=94.70  E-value=0.01  Score=53.01  Aligned_cols=20  Identities=20%  Similarity=0.292  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+||||||+.+..
T Consensus        76 vll~Gp~GtGKTtl~~~i~~   95 (278)
T 1iy2_A           76 VLLVGPPGVGKTHLARAVAG   95 (278)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCcChHHHHHHHHHH
Confidence            47999999999999999987

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=94.63  E-value=0.012  Score=53.26  Aligned_cols=20  Identities=25%  Similarity=0.200  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||+++.+..
T Consensus       105 i~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          105 VLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57999999999999999875

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=94.60  E-value=0.014  Score=48.39  Aligned_cols=20  Identities=15%  Similarity=0.323  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+|||||++.+..
T Consensus         5 v~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            5 LMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEESCTTSSHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57999999999999999876

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.59  E-value=0.013  Score=48.00  Aligned_cols=20  Identities=15%  Similarity=0.034  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||+..+..
T Consensus         7 i~i~G~sGsGKTTl~~~L~~   26 (169)
T 1xjc_A            7 WQVVGYKHSGKTTLMEKWVA   26 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.59  E-value=0.014  Score=47.36  Aligned_cols=21  Identities=10%  Similarity=0.183  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||.+.+...
T Consensus         6 v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            6 IALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999998764

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=94.58  E-value=0.013  Score=50.35  Aligned_cols=20  Identities=15%  Similarity=0.165  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        19 i~l~GpsGsGKSTLlk~L~g   38 (219)
T 1s96_A           19 YIVSAPSGAGKSSLIQALLK   38 (219)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57999999999999999876

>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=94.57  E-value=0.034  Score=48.11  Aligned_cols=45  Identities=4%  Similarity=0.037  Sum_probs=30.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccc----cccEEEEEEcCCCcChHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKH----YFDCHAWVQESLPYDADQI   45 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~----~F~~~~~~~vs~~~~~~~i   45 (391)
                      ++|+|..|+|||||++.+..+...+.    .-..++|+.-...++.+.+
T Consensus        27 ~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~   75 (243)
T 1n0w_A           27 TEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL   75 (243)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH
Confidence            47999999999999999875322221    1246777776555565554

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=94.55  E-value=0.013  Score=49.44  Aligned_cols=20  Identities=10%  Similarity=0.096  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus         5 i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            5 VTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999865

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=94.54  E-value=0.013  Score=52.65  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|..|+||||+|+.+.+
T Consensus        57 vll~Gp~GtGKT~la~~la~   76 (297)
T 3b9p_A           57 LLLFGPPGNGKTLLARAVAT   76 (297)
T ss_dssp             EEEESSSSSCHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHH
Confidence            35899999999999999987

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.52  E-value=0.013  Score=48.96  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||++.+...
T Consensus        32 v~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           32 VVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            589999999999999998764

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=94.52  E-value=0.014  Score=49.76  Aligned_cols=20  Identities=15%  Similarity=0.059  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus        28 i~~~G~~GsGKsT~~~~l~~   47 (211)
T 1m7g_A           28 IWLTGLSASGKSTLAVELEH   47 (211)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999875

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=94.51  E-value=0.013  Score=50.03  Aligned_cols=20  Identities=15%  Similarity=-0.009  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=94.51  E-value=0.014  Score=49.15  Aligned_cols=20  Identities=10%  Similarity=0.336  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus        22 ivl~GPSGaGKsTL~~~L~~   41 (197)
T 3ney_A           22 LVLIGASGVGRSHIKNALLS   41 (197)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHh
Confidence            57999999999999999875

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.48  E-value=0.014  Score=48.93  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||.+.+...
T Consensus         8 v~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            8 VVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            589999999999999998764

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=94.47  E-value=0.014  Score=50.70  Aligned_cols=20  Identities=10%  Similarity=0.167  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        34 ~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           34 VSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            58999999999999999875

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.46  E-value=0.014  Score=50.45  Aligned_cols=20  Identities=10%  Similarity=0.111  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        33 ~~iiG~nGsGKSTLl~~l~G   52 (224)
T 2pcj_A           33 VSIIGASGSGKSTLLYILGL   52 (224)
T ss_dssp             EEEEECTTSCHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=94.46  E-value=0.37  Score=45.00  Aligned_cols=79  Identities=23%  Similarity=0.191  Sum_probs=51.1

Q ss_pred             cccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCc---ccccceeeeccccccccch-HhhcC
Q 041097          278 EYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRA---MPKLECLIINPYAHLKRIH-EQLWC  353 (391)
Q Consensus       278 ~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~---~~~L~~L~l~~c~~l~~lp-~~~~~  353 (391)
                      +... .+|+.+.+..+ +.......+..+.+|+.+.+. +..   ..++.++   +.+|+.+.+...  ++.++ ..+..
T Consensus       293 F~~~-~~L~~i~l~~~-i~~I~~~aF~~c~~L~~i~lp-~~v---~~I~~~aF~~c~~L~~i~lp~~--l~~I~~~aF~~  364 (394)
T 4fs7_A          293 FYGC-SSLTEVKLLDS-VKFIGEEAFESCTSLVSIDLP-YLV---EEIGKRSFRGCTSLSNINFPLS--LRKIGANAFQG  364 (394)
T ss_dssp             TTTC-TTCCEEEECTT-CCEECTTTTTTCTTCCEECCC-TTC---CEECTTTTTTCTTCCEECCCTT--CCEECTTTBTT
T ss_pred             cccc-ccccccccccc-cceechhhhcCCCCCCEEEeC-Ccc---cEEhHHhccCCCCCCEEEECcc--ccEehHHHhhC
Confidence            3445 77888877553 333334566778888888886 222   1233343   457888888643  66775 35788


Q ss_pred             CCCCCEEEeeC
Q 041097          354 LKSLNKLELWW  364 (391)
Q Consensus       354 l~~L~~L~l~~  364 (391)
                      +++|+.+++.+
T Consensus       365 C~~L~~i~lp~  375 (394)
T 4fs7_A          365 CINLKKVELPK  375 (394)
T ss_dssp             CTTCCEEEEEG
T ss_pred             CCCCCEEEECC
Confidence            99999998854

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=94.45  E-value=0.014  Score=53.15  Aligned_cols=19  Identities=21%  Similarity=0.277  Sum_probs=16.3

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|+|-|||||||.|-.+-
T Consensus        51 IAIaGKGGVGKTTtavNLA   69 (314)
T 3fwy_A           51 FAVYGKGGIGKSTTSSNLS   69 (314)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCccCHHHHHHHHH
Confidence            6899999999999887753

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.45  E-value=0.014  Score=53.24  Aligned_cols=20  Identities=10%  Similarity=0.205  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+..
T Consensus        95 igI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           95 IGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999854

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.41  E-value=0.013  Score=53.13  Aligned_cols=20  Identities=15%  Similarity=0.243  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+|||||++.+..
T Consensus        83 igI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           83 ISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=94.40  E-value=0.014  Score=50.09  Aligned_cols=20  Identities=5%  Similarity=-0.074  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         8 I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            8 VMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.40  E-value=0.015  Score=50.60  Aligned_cols=20  Identities=20%  Similarity=0.424  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        34 ~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           34 VAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.40  E-value=0.015  Score=49.71  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        38 ~~iiG~NGsGKSTLlk~l~G   57 (214)
T 1sgw_A           38 VNFHGPNGIGKTTLLKTIST   57 (214)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>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=94.39  E-value=0.014  Score=50.07  Aligned_cols=44  Identities=14%  Similarity=0.220  Sum_probs=27.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccc---c-cccEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVK---H-YFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk---~-~F~~~~~~~vs~~~~~~~   44 (391)
                      ++|+|..|+|||||++.+.-.....   . .-...+|+.-...++.+.
T Consensus        28 ~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~   75 (231)
T 4a74_A           28 TEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER   75 (231)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH
Confidence            4799999999999999986421111   1 123566666444444443

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.38  E-value=0.015  Score=50.01  Aligned_cols=20  Identities=10%  Similarity=0.081  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         3 I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=94.37  E-value=0.0095  Score=49.07  Aligned_cols=20  Identities=10%  Similarity=0.247  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         5 v~IvG~SGsGKSTL~~~L~~   24 (171)
T 2f1r_A            5 LSIVGTSDSGKTTLITRMMP   24 (171)
T ss_dssp             EEEEESCHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999865

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.37  E-value=0.015  Score=50.66  Aligned_cols=20  Identities=20%  Similarity=0.262  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        27 ~~liG~nGsGKSTLl~~l~G   46 (240)
T 2onk_A           27 CVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999876

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.35  E-value=0.017  Score=47.80  Aligned_cols=21  Identities=10%  Similarity=0.183  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||.+.+.++
T Consensus        10 i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A           10 IALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEECSTTSSHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999998874

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=94.34  E-value=0.017  Score=46.28  Aligned_cols=21  Identities=19%  Similarity=0.368  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+..+
T Consensus         6 i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>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=94.34  E-value=0.014  Score=52.59  Aligned_cols=20  Identities=25%  Similarity=0.298  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+||||++..+..
T Consensus       108 i~lvG~~GsGKTTl~~~LA~  127 (296)
T 2px0_A          108 IVLFGSTGAGKTTTLAKLAA  127 (296)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999764

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.32  E-value=0.015  Score=49.79  Aligned_cols=20  Identities=10%  Similarity=0.064  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         8 I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            8 LILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999865

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=94.31  E-value=0.018  Score=47.68  Aligned_cols=21  Identities=19%  Similarity=0.368  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        24 i~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           24 LVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>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=94.31  E-value=0.014  Score=55.96  Aligned_cols=20  Identities=20%  Similarity=0.330  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +-|||..|+||||||+.+.+
T Consensus       133 lll~Gp~G~GKTtLa~aia~  152 (440)
T 2z4s_A          133 LFIYGGVGLGKTHLLQSIGN  152 (440)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999988

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.30  E-value=0.0096  Score=47.34  Aligned_cols=20  Identities=10%  Similarity=-0.091  Sum_probs=18.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -|+|..|+|||++|+.+++.
T Consensus        31 ll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A           31 FLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             EEEEETTCCHHHHHGGGCCT
T ss_pred             EEECCCCccHHHHHHHHHHh
Confidence            48999999999999999874

>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=94.29  E-value=0.013  Score=51.74  Aligned_cols=20  Identities=20%  Similarity=0.237  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++|..|+||||+|+.+.+
T Consensus        47 vll~G~~GtGKT~la~~la~   66 (268)
T 2r62_A           47 VLLVGPPGTGKTLLAKAVAG   66 (268)
T ss_dssp             CCCBCSSCSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            35899999999999999987

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.28  E-value=0.011  Score=51.25  Aligned_cols=20  Identities=20%  Similarity=0.260  Sum_probs=14.0

Q ss_pred             CcEEcCCCCcHHHHHHHHh-C
Q 041097            1 MAVLDSIGLDKTAFAAEAY-S   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy-~   20 (391)
                      |||+|..|+|||||++.+. .
T Consensus        30 i~l~Gp~GsGKSTl~~~L~~~   50 (231)
T 3lnc_A           30 LVLSSPSGCGKTTVANKLLEK   50 (231)
T ss_dssp             EEEECSCC----CHHHHHHC-
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            5899999999999999988 5

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.27  E-value=0.012  Score=50.05  Aligned_cols=20  Identities=25%  Similarity=0.134  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        25 ~~liG~nGsGKSTLl~~l~G   44 (208)
T 3b85_A           25 VFGLGPAGSGKTYLAMAKAV   44 (208)
T ss_dssp             EEEECCTTSSTTHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999875

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=94.26  E-value=0.016  Score=50.56  Aligned_cols=20  Identities=15%  Similarity=0.069  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+.+
T Consensus        32 I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           32 YIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.25  E-value=0.017  Score=52.34  Aligned_cols=20  Identities=15%  Similarity=0.097  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||+++.+..
T Consensus       103 i~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A          103 IMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.23  E-value=0.017  Score=50.33  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        35 ~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           35 VTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999976

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.21  E-value=0.017  Score=46.22  Aligned_cols=21  Identities=5%  Similarity=0.173  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         4 i~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            4 VVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998764

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=94.20  E-value=0.02  Score=46.58  Aligned_cols=21  Identities=24%  Similarity=0.311  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.+.
T Consensus         7 i~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            7 VVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCccHHHHHHHHhcC
Confidence            579999999999999998764

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.19  E-value=0.018  Score=51.40  Aligned_cols=20  Identities=20%  Similarity=0.293  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        37 ~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           37 TAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            58999999999999999875

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.19  E-value=0.018  Score=51.03  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        35 ~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           35 ISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999876

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.19  E-value=0.018  Score=49.87  Aligned_cols=20  Identities=30%  Similarity=0.317  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus        37 ~~i~G~nGsGKSTLl~~l~G   56 (229)
T 2pze_A           37 LAVAGSTGAGKTSLLMMIMG   56 (229)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=94.19  E-value=0.017  Score=46.49  Aligned_cols=21  Identities=14%  Similarity=0.210  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         8 i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            8 MVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.15  E-value=0.018  Score=50.76  Aligned_cols=20  Identities=10%  Similarity=0.142  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        36 ~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           36 TLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999876

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=94.11  E-value=0.022  Score=45.87  Aligned_cols=21  Identities=29%  Similarity=0.403  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=94.11  E-value=0.022  Score=45.79  Aligned_cols=21  Identities=19%  Similarity=0.268  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         7 i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.10  E-value=0.019  Score=50.19  Aligned_cols=20  Identities=15%  Similarity=0.052  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        31 ~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           31 IAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999875

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.08  E-value=0.019  Score=50.80  Aligned_cols=20  Identities=20%  Similarity=0.235  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        53 ~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           53 VVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEcCCCCcHHHHHHHHHc
Confidence            58999999999999999876

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.07  E-value=0.019  Score=50.36  Aligned_cols=20  Identities=15%  Similarity=0.179  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        32 ~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           32 HALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             EEEECSTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.07  E-value=0.02  Score=50.24  Aligned_cols=20  Identities=10%  Similarity=0.212  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        38 ~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           38 IGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.06  E-value=0.019  Score=50.87  Aligned_cols=20  Identities=15%  Similarity=0.220  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+..
T Consensus        40 ~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           40 VAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             EEEECCTTSCHHHHHHHHTS
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            58999999999999999876

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.05  E-value=0.02  Score=50.64  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        49 ~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           49 CALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=94.04  E-value=0.019  Score=49.66  Aligned_cols=20  Identities=20%  Similarity=0.157  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+.+
T Consensus        19 I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           19 AVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999875

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.03  E-value=0.023  Score=45.90  Aligned_cols=21  Identities=19%  Similarity=0.300  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            6 VAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.02  E-value=0.02  Score=50.86  Aligned_cols=20  Identities=20%  Similarity=0.285  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        49 ~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           49 HAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999987

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.02  E-value=0.02  Score=50.46  Aligned_cols=20  Identities=15%  Similarity=0.140  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        44 ~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           44 FGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999986

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=94.00  E-value=0.023  Score=46.40  Aligned_cols=21  Identities=10%  Similarity=0.279  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        12 i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           12 LLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEECCTTSCHHHHHHHHCSC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.98  E-value=0.021  Score=50.14  Aligned_cols=20  Identities=15%  Similarity=0.255  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        29 ~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           29 LHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            58999999999999999986

>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=93.97  E-value=0.021  Score=50.72  Aligned_cols=19  Identities=26%  Similarity=0.101  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+.+
T Consensus        68 Ll~G~~GtGKT~la~~ia~   86 (272)
T 1d2n_A           68 LLEGPPHSGKTALAAKIAE   86 (272)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            4899999999999999987

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.96  E-value=0.024  Score=45.77  Aligned_cols=21  Identities=14%  Similarity=0.156  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus         9 i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            9 VVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998754

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.96  E-value=0.021  Score=50.66  Aligned_cols=20  Identities=15%  Similarity=0.174  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+.-
T Consensus        36 ~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           36 LLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            58999999999999999876

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.95  E-value=0.02  Score=49.07  Aligned_cols=20  Identities=20%  Similarity=0.326  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+..+..
T Consensus        41 i~ivG~~gvGKTtl~~~l~~   60 (226)
T 2hf9_A           41 FDFMGAIGSGKTLLIEKLID   60 (226)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999775

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.95  E-value=0.022  Score=45.90  Aligned_cols=20  Identities=25%  Similarity=0.262  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||.+.+.+
T Consensus         5 i~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            5 VLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            57999999999999999865

>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=93.94  E-value=0.018  Score=52.30  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|..|+||||+|+.+++
T Consensus        41 vll~G~~GtGKT~la~~i~~   60 (324)
T 1hqc_A           41 LLLFGPPGLGKTTLAHVIAH   60 (324)
T ss_dssp             CEEECCTTCCCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999987

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.94  E-value=0.021  Score=50.77  Aligned_cols=20  Identities=25%  Similarity=0.220  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        48 ~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           48 TALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999976

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=93.94  E-value=0.021  Score=50.24  Aligned_cols=20  Identities=20%  Similarity=0.260  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +.+.|.||+||||++..+..
T Consensus        17 ~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           17 VVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEeCCCCCCHHHHHHHHHH
Confidence            36899999999999999864

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=93.93  E-value=0.021  Score=49.44  Aligned_cols=20  Identities=20%  Similarity=0.177  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+|+.+..
T Consensus        12 i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A           12 VAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999865

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.92  E-value=0.021  Score=47.48  Aligned_cols=21  Identities=10%  Similarity=0.080  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus        51 i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           51 IIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=93.92  E-value=0.021  Score=52.30  Aligned_cols=20  Identities=15%  Similarity=0.260  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||||+.+..
T Consensus        10 I~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A           10 IVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCcCcHHHHHHHHHH
Confidence            68999999999999999876

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.91  E-value=0.023  Score=46.49  Aligned_cols=21  Identities=5%  Similarity=0.055  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||.+.+...
T Consensus         7 i~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            7 VVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999998764

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.89  E-value=0.02  Score=50.85  Aligned_cols=20  Identities=20%  Similarity=0.454  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||.+.++.
T Consensus         5 v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            5 IMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEESSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.86  E-value=0.024  Score=45.76  Aligned_cols=20  Identities=15%  Similarity=0.263  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+..+..
T Consensus         5 i~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            5 VMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999864

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.86  E-value=0.022  Score=50.86  Aligned_cols=20  Identities=15%  Similarity=0.057  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        50 ~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           50 WILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            58999999999999999876

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.85  E-value=0.022  Score=45.96  Aligned_cols=21  Identities=14%  Similarity=0.265  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus         9 i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            9 VCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=93.85  E-value=0.017  Score=49.88  Aligned_cols=20  Identities=20%  Similarity=0.263  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|.-|+||||+++.+..
T Consensus        23 i~i~G~~GsGKSTl~~~L~~   42 (230)
T 2vp4_A           23 VLIEGNIGSGKTTYLNHFEK   42 (230)
T ss_dssp             EEEECSTTSCHHHHHHTTGG
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            68999999999999999876

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=93.84  E-value=0.024  Score=46.75  Aligned_cols=21  Identities=19%  Similarity=0.105  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus        10 i~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A           10 IVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.83  E-value=0.023  Score=50.00  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        34 ~~l~G~nGsGKSTLl~~l~G   53 (253)
T 2nq2_C           34 LAVLGQNGCGKSTLLDLLLG   53 (253)
T ss_dssp             EEEECCSSSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=93.82  E-value=0.019  Score=51.62  Aligned_cols=20  Identities=15%  Similarity=0.233  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|.|+.|+||||+|+.+..
T Consensus        36 ivl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           36 FLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             EEEECCTTSCTHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999875

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.81  E-value=0.023  Score=45.81  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=93.80  E-value=0.024  Score=46.72  Aligned_cols=20  Identities=20%  Similarity=0.177  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         9 i~i~G~sGsGKTTl~~~l~~   28 (174)
T 1np6_A            9 LAFAAWSGTGKTTLLKKLIP   28 (174)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            57999999999999999886

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=93.78  E-value=0.021  Score=47.40  Aligned_cols=20  Identities=20%  Similarity=-0.037  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||++.+.+
T Consensus        17 i~vvG~~~~GKssL~~~l~~   36 (198)
T 3t1o_A           17 IVYYGPGLSGKTTNLKWIYS   36 (198)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999988765

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=93.77  E-value=0.027  Score=46.23  Aligned_cols=21  Identities=19%  Similarity=0.420  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        21 i~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           21 LVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>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=93.76  E-value=0.025  Score=51.67  Aligned_cols=19  Identities=16%  Similarity=0.174  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|.+|+|||++|+++.+
T Consensus        55 Ll~GppGtGKT~la~aia~   73 (322)
T 3eie_A           55 LLYGPPGTGKSYLAKAVAT   73 (322)
T ss_dssp             EEECSSSSCHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            4799999999999999987

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=93.74  E-value=0.024  Score=49.19  Aligned_cols=20  Identities=15%  Similarity=0.067  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|+.|+||||+++.+..
T Consensus        19 i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           19 IAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             EEEECSSCSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999765

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=93.73  E-value=0.016  Score=50.97  Aligned_cols=20  Identities=15%  Similarity=0.067  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus        35 i~l~G~~GsGKSTla~~L~~   54 (253)
T 2p5t_B           35 ILLGGQSGAGKTTIHRIKQK   54 (253)
T ss_dssp             EEEESCGGGTTHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999865

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=93.73  E-value=0.021  Score=47.89  Aligned_cols=21  Identities=14%  Similarity=0.042  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||++.+.++
T Consensus        28 i~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           28 LVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             EEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998763

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.73  E-value=0.021  Score=52.16  Aligned_cols=19  Identities=16%  Similarity=0.209  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+|||+||+++.+
T Consensus        49 LL~GppGtGKT~la~ala~   67 (322)
T 1xwi_A           49 LLFGPPGTGKSYLAKAVAT   67 (322)
T ss_dssp             EEESSSSSCHHHHHHHHHH
T ss_pred             EEECCCCccHHHHHHHHHH
Confidence            4799999999999999987

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=93.72  E-value=0.028  Score=46.64  Aligned_cols=21  Identities=24%  Similarity=0.407  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus        24 i~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           24 LAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCcHHHHHHHHHhC
Confidence            579999999999999887654

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=93.71  E-value=0.024  Score=52.14  Aligned_cols=20  Identities=25%  Similarity=0.326  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+++.+..
T Consensus        27 i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A           27 VILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57899999999999999886

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=93.70  E-value=0.029  Score=45.00  Aligned_cols=21  Identities=29%  Similarity=0.404  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus         6 i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999887654

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=93.70  E-value=0.026  Score=46.57  Aligned_cols=21  Identities=19%  Similarity=0.129  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus        19 i~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           19 ILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998774

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=93.69  E-value=0.025  Score=48.50  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        26 ~~i~G~~GsGKTtl~~~l~~   45 (235)
T 2w0m_A           26 IALTGEPGTGKTIFSLHFIA   45 (235)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            47999999999999999875

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=93.69  E-value=0.025  Score=51.14  Aligned_cols=20  Identities=10%  Similarity=0.160  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.|||||++.+..
T Consensus       129 vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          129 LAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHhh
Confidence            58999999999999999865

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.67  E-value=0.034  Score=45.28  Aligned_cols=21  Identities=14%  Similarity=0.249  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        11 i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A           11 VTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             EEEESCTTTTHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998764

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.66  E-value=0.025  Score=46.23  Aligned_cols=21  Identities=19%  Similarity=0.335  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        11 i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A           11 VIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999988664

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=93.64  E-value=0.028  Score=46.09  Aligned_cols=21  Identities=14%  Similarity=0.265  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         9 i~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            9 IAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998754

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=93.63  E-value=0.026  Score=49.90  Aligned_cols=20  Identities=20%  Similarity=0.200  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus        28 v~i~Gp~GsGKSTll~~l~g   47 (261)
T 2eyu_A           28 ILVTGPTGSGKSTTIASMID   47 (261)
T ss_dssp             EEEECSTTCSHHHHHHHHHH
T ss_pred             EEEECCCCccHHHHHHHHHH
Confidence            57999999999999999865

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=93.63  E-value=0.029  Score=46.16  Aligned_cols=21  Identities=19%  Similarity=0.379  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         7 i~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            7 LVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=93.62  E-value=0.019  Score=48.51  Aligned_cols=20  Identities=10%  Similarity=0.114  Sum_probs=17.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +-|+|.+|.||||+|..+.+
T Consensus        61 ili~GPPGtGKTt~a~ala~   80 (212)
T 1tue_A           61 LVFCGPANTGKSYFGMSFIH   80 (212)
T ss_dssp             EEEESCGGGCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35899999999999988876

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=93.61  E-value=0.028  Score=45.86  Aligned_cols=21  Identities=24%  Similarity=0.360  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus        12 i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           12 LVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=93.60  E-value=0.026  Score=52.32  Aligned_cols=20  Identities=15%  Similarity=0.097  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||+++.+..
T Consensus       160 i~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          160 IMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCChHHHHHHHHHh
Confidence            57999999999999999876

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=93.56  E-value=0.031  Score=45.48  Aligned_cols=21  Identities=10%  Similarity=0.311  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        18 i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           18 YIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=93.55  E-value=0.029  Score=46.32  Aligned_cols=21  Identities=5%  Similarity=0.052  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus         4 i~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            4 IIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            579999999999999998774

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.52  E-value=0.028  Score=46.72  Aligned_cols=21  Identities=14%  Similarity=0.265  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        26 i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           26 IALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             EEEEEBTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998775

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.49  E-value=0.022  Score=51.52  Aligned_cols=20  Identities=15%  Similarity=0.308  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.|||||++.+.-
T Consensus        83 vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           83 LALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             EEEESSSCHHHHHHHHHHTT
T ss_pred             EEEECCCCchHHHHHHHHHc
Confidence            58999999999999999865

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=93.49  E-value=0.023  Score=51.32  Aligned_cols=19  Identities=21%  Similarity=0.177  Sum_probs=17.0

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+.+
T Consensus        71 ll~G~~GtGKT~la~~la~   89 (309)
T 3syl_A           71 SFTGNPGTGKTTVALKMAG   89 (309)
T ss_dssp             EEEECTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999998766

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=93.48  E-value=0.032  Score=46.15  Aligned_cols=21  Identities=10%  Similarity=0.283  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        23 i~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           23 VGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999876553

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=93.48  E-value=0.033  Score=45.73  Aligned_cols=21  Identities=19%  Similarity=0.268  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        21 i~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           21 VIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            579999999999999998764

>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=93.48  E-value=0.026  Score=52.33  Aligned_cols=19  Identities=16%  Similarity=0.174  Sum_probs=17.8

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||||+++.+
T Consensus        88 LL~GppGtGKT~la~ala~  106 (355)
T 2qp9_X           88 LLYGPPGTGKSYLAKAVAT  106 (355)
T ss_dssp             EEECSTTSCHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            4799999999999999988

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=93.48  E-value=0.026  Score=47.23  Aligned_cols=20  Identities=15%  Similarity=0.263  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||++.+.+
T Consensus        26 i~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           26 VMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             EEEECSTTSSHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999753

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=93.47  E-value=0.033  Score=45.73  Aligned_cols=21  Identities=14%  Similarity=0.123  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus         8 i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            8 CVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999988654

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.47  E-value=0.03  Score=45.68  Aligned_cols=21  Identities=19%  Similarity=0.121  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         9 i~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            9 IVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=93.47  E-value=0.029  Score=45.23  Aligned_cols=21  Identities=10%  Similarity=0.221  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus         9 i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998753

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=93.46  E-value=0.028  Score=45.75  Aligned_cols=21  Identities=14%  Similarity=0.279  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        10 i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A           10 VILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998754

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.43  E-value=0.031  Score=46.32  Aligned_cols=21  Identities=10%  Similarity=0.275  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        26 i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           26 VAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             EEEEEBTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998775

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.43  E-value=0.027  Score=47.98  Aligned_cols=20  Identities=20%  Similarity=0.388  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+|||||+..+..
T Consensus        33 i~i~G~~g~GKTTl~~~l~~   52 (221)
T 2wsm_A           33 VNIMGAIGSGKTLLIERTIE   52 (221)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999998765

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.42  E-value=0.029  Score=49.58  Aligned_cols=20  Identities=20%  Similarity=0.242  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        33 ~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           33 VIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            58999999999999999986

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=93.42  E-value=0.014  Score=52.52  Aligned_cols=20  Identities=15%  Similarity=0.132  Sum_probs=15.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+.+
T Consensus         8 IgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            8 ISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             EEEESCC---CCTHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            69999999999999999765

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=93.42  E-value=0.028  Score=51.40  Aligned_cols=20  Identities=20%  Similarity=0.122  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+||||+++.+..
T Consensus       132 i~lvG~nGaGKTTll~~Lag  151 (328)
T 3e70_C          132 IMFVGFNGSGKTTTIAKLAN  151 (328)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999875

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=93.38  E-value=0.029  Score=50.51  Aligned_cols=20  Identities=20%  Similarity=0.313  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         5 I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            5 ILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=93.38  E-value=0.03  Score=46.75  Aligned_cols=20  Identities=5%  Similarity=0.132  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||++.+.+
T Consensus        23 i~~vG~~~vGKTsLi~~l~~   42 (196)
T 3llu_A           23 ILLMGLRRSGKSSIQKVVFH   42 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999998776

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=93.37  E-value=0.028  Score=45.33  Aligned_cols=21  Identities=10%  Similarity=0.271  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            6 ILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999998754

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=93.36  E-value=0.034  Score=46.56  Aligned_cols=21  Identities=19%  Similarity=0.268  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        17 i~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           17 VIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998654

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=93.33  E-value=0.029  Score=46.73  Aligned_cols=21  Identities=14%  Similarity=0.028  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||.+.+.++
T Consensus        26 i~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           26 LLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998763

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=93.32  E-value=0.029  Score=46.17  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        13 i~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           13 FLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998754

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=93.32  E-value=0.031  Score=45.15  Aligned_cols=21  Identities=19%  Similarity=0.143  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        10 i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A           10 ILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998654

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=93.30  E-value=0.031  Score=46.41  Aligned_cols=21  Identities=14%  Similarity=0.279  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||+..+.++
T Consensus        28 i~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           28 VVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=93.28  E-value=0.03  Score=53.84  Aligned_cols=20  Identities=15%  Similarity=0.184  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus       296 I~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          296 ILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCcccHHHHHHHHHH
Confidence            58999999999999999875

>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=93.28  E-value=0.031  Score=50.60  Aligned_cols=20  Identities=20%  Similarity=0.187  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+||||++..+..
T Consensus       107 i~ivG~~GsGKTTl~~~LA~  126 (306)
T 1vma_A          107 IMVVGVNGTGKTTSCGKLAK  126 (306)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCChHHHHHHHHHH
Confidence            57999999999999999865

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=93.28  E-value=0.033  Score=50.99  Aligned_cols=19  Identities=26%  Similarity=0.183  Sum_probs=17.6

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+.+
T Consensus        59 ll~G~~GtGKT~la~~ia~   77 (338)
T 3pfi_A           59 LFSGPAGLGKTTLANIISY   77 (338)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECcCCCCHHHHHHHHHH
Confidence            4899999999999999977

>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=93.28  E-value=0.031  Score=51.79  Aligned_cols=19  Identities=21%  Similarity=0.137  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+.+
T Consensus       121 Ll~GppGtGKT~la~aia~  139 (357)
T 3d8b_A          121 LLFGPPGTGKTLIGKCIAS  139 (357)
T ss_dssp             EEESSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999999987

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.27  E-value=0.031  Score=47.47  Aligned_cols=21  Identities=10%  Similarity=0.080  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus        15 i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           15 IIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>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=93.26  E-value=0.024  Score=61.39  Aligned_cols=79  Identities=13%  Similarity=0.124  Sum_probs=61.2

Q ss_pred             HhC--CccccccccEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHHHcCccEEeeeccCCCceee
Q 041097           18 AYS--SNYVKHYFDCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLINGGFVGAGKRSDIGRINT   95 (391)
Q Consensus        18 vy~--~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~L~~k~~l~~~~~~~~~~~~~   95 (391)
                      .|+  +++.+.||.+++.|+.+..++.+.++.      .|.++       ++.++.++.+|++++++....   .+...+
T Consensus       371 s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~------~~~~~-------~~~~~~~l~~L~~~sl~~~~~---~~~~~~  434 (1249)
T 3sfz_A          371 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCV------LWDLE-------TEEVEDILQEFVNKSLLFCNR---NGKSFC  434 (1249)
T ss_dssp             HHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHH------HHTCC-------HHHHHHHHHHHHHTTSCEEEE---SSSSEE
T ss_pred             HHHhCCHHHHHHHHHhCccCCCCeeCHHHHHH------HhCCC-------HHHHHHHHHHHHhccceEEec---CCCceE
Confidence            355  357789999999999888888877655      34332       577899999999999998654   344457


Q ss_pred             EEcCcchHHHHHhhccc
Q 041097           96 CSIPGRCSPALLTVVFE  112 (391)
Q Consensus        96 ~~~hdl~~~~~~~~~~~  112 (391)
                      |+||+++|+++...+.+
T Consensus       435 ~~~h~l~~~~~~~~~~~  451 (1249)
T 3sfz_A          435 YYLHDLQVDFLTEKNRS  451 (1249)
T ss_dssp             EECCHHHHHHHHHHTGG
T ss_pred             EEecHHHHHHHHhhhhH
Confidence            99999999999887654

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=93.25  E-value=0.031  Score=50.31  Aligned_cols=20  Identities=25%  Similarity=0.096  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+||||+++.+..
T Consensus       101 i~i~g~~G~GKTT~~~~la~  120 (295)
T 1ls1_A          101 WFLVGLQGSGKTTTAAKLAL  120 (295)
T ss_dssp             EEEECCTTTTHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999875

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=93.25  E-value=0.026  Score=50.99  Aligned_cols=20  Identities=20%  Similarity=0.413  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||.+.++.
T Consensus        21 I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           21 LMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEETTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            47999999999999999886

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.24  E-value=0.028  Score=50.94  Aligned_cols=19  Identities=16%  Similarity=0.261  Sum_probs=17.8

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -+||..|+|||+||+++++
T Consensus       156 ll~G~~GtGKT~La~aia~  174 (308)
T 2qgz_A          156 YLYGDMGIGKSYLLAAMAH  174 (308)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999999988

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=93.24  E-value=0.032  Score=45.62  Aligned_cols=21  Identities=14%  Similarity=0.080  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus        11 i~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D           11 CVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=93.22  E-value=0.028  Score=50.70  Aligned_cols=20  Identities=25%  Similarity=0.338  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++|..|+||||+|+.+.+
T Consensus        50 ~ll~G~~GtGKt~la~~la~   69 (311)
T 4fcw_A           50 FLFLGPTGVGKTELAKTLAA   69 (311)
T ss_dssp             EEEESCSSSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHH
Confidence            35899999999999999887

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=93.22  E-value=0.048  Score=47.11  Aligned_cols=20  Identities=25%  Similarity=0.325  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+++.+.+
T Consensus        29 i~i~G~~GsGKsT~~~~l~~   48 (229)
T 4eaq_A           29 ITFEGPEGSGKTTVINEVYH   48 (229)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57899999999999999987

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=93.21  E-value=0.031  Score=50.28  Aligned_cols=46  Identities=13%  Similarity=0.128  Sum_probs=28.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccccc-EEEEEEcCCCcChHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFD-CHAWVQESLPYDADQILYDII   50 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~-~~~~~~vs~~~~~~~i~~~~~   50 (391)
                      ++|+|..|+|||||++.+...  +...-. .+.|+..  +.+.+.+.+++.
T Consensus        38 ~~i~G~~G~GKTTl~~~ia~~--~~~~~G~~v~~~~~--e~~~~~~~~r~~   84 (296)
T 1cr0_A           38 IMVTSGSGMGKSTFVRQQALQ--WGTAMGKKVGLAML--EESVEETAEDLI   84 (296)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH--HHHTSCCCEEEEES--SSCHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH--HHHHcCCeEEEEeC--cCCHHHHHHHHH
Confidence            479999999999999998763  221112 3555543  334445544443

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=93.21  E-value=0.036  Score=46.22  Aligned_cols=21  Identities=10%  Similarity=-0.023  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        32 i~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           32 ILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             EEEEESTTSSHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=93.20  E-value=0.038  Score=46.10  Aligned_cols=21  Identities=19%  Similarity=0.428  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        31 i~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           31 LAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=93.20  E-value=0.032  Score=46.81  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||+..+.++
T Consensus        11 i~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A           11 VIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=93.20  E-value=0.033  Score=45.56  Aligned_cols=21  Identities=14%  Similarity=0.354  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+..+
T Consensus        15 i~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           15 LVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998754

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.19  E-value=0.038  Score=46.02  Aligned_cols=21  Identities=10%  Similarity=0.031  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        20 i~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           20 VVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             EEEECCTTSCHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998774

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=93.19  E-value=0.031  Score=44.85  Aligned_cols=20  Identities=10%  Similarity=-0.031  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+|||||+..+.+
T Consensus         3 i~~~G~~~~GKssl~~~l~~   22 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKL   22 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            57999999999999999865

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=93.18  E-value=0.033  Score=51.97  Aligned_cols=20  Identities=25%  Similarity=0.177  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus       172 i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          172 WLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999886

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=93.18  E-value=0.039  Score=46.24  Aligned_cols=21  Identities=14%  Similarity=0.256  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.+.
T Consensus        11 i~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A           11 ILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEECSTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=93.16  E-value=0.04  Score=45.40  Aligned_cols=22  Identities=14%  Similarity=0.104  Sum_probs=19.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|..|+|||||...+.++.
T Consensus        21 i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           21 LLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            5799999999999999988653

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=93.16  E-value=0.027  Score=46.06  Aligned_cols=21  Identities=14%  Similarity=0.219  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus        10 i~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A           10 LGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=93.15  E-value=0.031  Score=46.48  Aligned_cols=21  Identities=14%  Similarity=0.343  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||+..+.++
T Consensus        26 i~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           26 VCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEECTTSSHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            679999999999999998764

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=93.15  E-value=0.036  Score=46.12  Aligned_cols=21  Identities=19%  Similarity=0.325  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        29 i~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           29 VIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=93.14  E-value=0.039  Score=46.70  Aligned_cols=21  Identities=10%  Similarity=0.045  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus        10 i~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B           10 VLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998764

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=93.12  E-value=0.034  Score=50.70  Aligned_cols=20  Identities=20%  Similarity=0.170  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+||||++..+..
T Consensus       108 I~ivG~~G~GKTT~~~~LA~  127 (320)
T 1zu4_A          108 FMLVGVNGTGKTTSLAKMAN  127 (320)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999998765

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=93.11  E-value=0.04  Score=45.72  Aligned_cols=21  Identities=10%  Similarity=0.243  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        19 i~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           19 LLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>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=93.11  E-value=0.03  Score=50.78  Aligned_cols=19  Identities=21%  Similarity=0.102  Sum_probs=17.6

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+++
T Consensus        50 ll~G~~G~GKT~la~~l~~   68 (327)
T 1iqp_A           50 LFAGPPGVGKTTAALALAR   68 (327)
T ss_dssp             EEESCTTSSHHHHHHHHHH
T ss_pred             EEECcCCCCHHHHHHHHHH
Confidence            4899999999999999987

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=93.09  E-value=0.038  Score=46.70  Aligned_cols=21  Identities=19%  Similarity=0.105  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus        31 i~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           31 IVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=93.08  E-value=0.033  Score=49.61  Aligned_cols=20  Identities=20%  Similarity=0.185  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        33 ~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           33 GALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            47999999999999998764

>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=93.08  E-value=0.031  Score=50.61  Aligned_cols=19  Identities=16%  Similarity=0.038  Sum_probs=17.6

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|.+|+||||+|+.+.+
T Consensus        46 ll~G~~G~GKt~la~~l~~   64 (323)
T 1sxj_B           46 IISGMPGIGKTTSVHCLAH   64 (323)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECcCCCCHHHHHHHHHH
Confidence            4899999999999999987

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=93.08  E-value=0.038  Score=46.19  Aligned_cols=21  Identities=10%  Similarity=0.142  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        23 i~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           23 CVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             EEEECSTTSSHHHHHHHHHC-
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=93.07  E-value=0.021  Score=48.20  Aligned_cols=21  Identities=10%  Similarity=0.006  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||.+.+...
T Consensus        29 v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           29 VAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             EEEEECTTSSHHHHHTTTCCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            589999999999999998764

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=93.07  E-value=0.035  Score=50.48  Aligned_cols=20  Identities=15%  Similarity=0.174  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||||+.+..
T Consensus         8 i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            8 IFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=93.07  E-value=0.038  Score=52.94  Aligned_cols=19  Identities=21%  Similarity=0.163  Sum_probs=17.8

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -+||..|+||||+|+.+.+
T Consensus        54 LL~GppGtGKTtlAr~ia~   72 (447)
T 3pvs_A           54 ILWGPPGTGKTTLAEVIAR   72 (447)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            4899999999999999987

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=93.04  E-value=0.036  Score=45.77  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        14 i~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           14 FLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.03  E-value=0.029  Score=46.05  Aligned_cols=21  Identities=19%  Similarity=0.131  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||...+.++
T Consensus        21 i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           21 ILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             EEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999997753

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=93.03  E-value=0.037  Score=46.44  Aligned_cols=21  Identities=19%  Similarity=0.295  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        28 i~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           28 FLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHC-
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=93.01  E-value=0.035  Score=49.85  Aligned_cols=20  Identities=30%  Similarity=0.317  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||++.+..
T Consensus        67 ~~i~G~NGsGKSTLlk~l~G   86 (290)
T 2bbs_A           67 LAVAGSTGAGKTSLLMMIMG   86 (290)
T ss_dssp             EEEEESTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            58999999999999999976

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=92.99  E-value=0.037  Score=47.15  Aligned_cols=20  Identities=20%  Similarity=0.179  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|+.|+||||+++.+..
T Consensus         6 i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            6 IALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999764

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=92.97  E-value=0.035  Score=45.16  Aligned_cols=21  Identities=14%  Similarity=0.205  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        17 i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           17 LVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998653

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=92.95  E-value=0.043  Score=47.57  Aligned_cols=21  Identities=14%  Similarity=0.256  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||...+...
T Consensus        32 i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           32 IVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            689999999999999998874

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=92.95  E-value=0.039  Score=46.45  Aligned_cols=21  Identities=14%  Similarity=0.123  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        33 i~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           33 CVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999887754

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.94  E-value=0.038  Score=45.09  Aligned_cols=21  Identities=14%  Similarity=0.252  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.+.
T Consensus        13 i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           13 VMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=92.93  E-value=0.038  Score=45.76  Aligned_cols=21  Identities=19%  Similarity=0.128  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        25 i~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           25 LTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998754

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=92.91  E-value=0.044  Score=47.03  Aligned_cols=21  Identities=10%  Similarity=0.169  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        32 I~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           32 IILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             EEEECSTTSSHHHHHHHHTTT
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998774

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=92.89  E-value=0.045  Score=45.48  Aligned_cols=21  Identities=14%  Similarity=0.135  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        26 i~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           26 IVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=92.89  E-value=0.042  Score=46.04  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        27 i~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           27 VVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999998764

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=92.89  E-value=0.039  Score=45.78  Aligned_cols=21  Identities=10%  Similarity=0.260  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        24 i~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           24 YIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=92.87  E-value=0.039  Score=45.63  Aligned_cols=21  Identities=14%  Similarity=0.240  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        25 i~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           25 LLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.84  E-value=0.044  Score=45.26  Aligned_cols=21  Identities=10%  Similarity=0.004  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus        19 i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           19 VIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             EEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998864

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=92.83  E-value=0.037  Score=51.30  Aligned_cols=19  Identities=26%  Similarity=0.197  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|..|+||||+|+.+.+
T Consensus        74 Ll~GppGtGKT~la~~la~   92 (368)
T 3uk6_A           74 LIAGQPGTGKTAIAMGMAQ   92 (368)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4899999999999999987

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=92.82  E-value=0.04  Score=46.10  Aligned_cols=21  Identities=10%  Similarity=0.256  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        31 i~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           31 IVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEESSTTSSHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.81  E-value=0.04  Score=45.87  Aligned_cols=21  Identities=10%  Similarity=0.156  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||+..+..+
T Consensus        10 i~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A           10 TVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998765

>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=92.81  E-value=0.11  Score=47.32  Aligned_cols=47  Identities=9%  Similarity=0.070  Sum_probs=33.6

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccc---------cc-----cEEEEEEcCCCcChHHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKH---------YF-----DCHAWVQESLPYDADQILYD   48 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~---------~F-----~~~~~~~vs~~~~~~~i~~~   48 (391)
                      -|+|.+|+||||||..+.-+..+..         ..     ..++|+.....|+.+.+.+.
T Consensus       102 ~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~  162 (322)
T 2i1q_A          102 EFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQM  162 (322)
T ss_dssp             EEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHH
Confidence            5899999999999998765322221         11     47888888877887776643

>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=92.81  E-value=0.032  Score=48.46  Aligned_cols=20  Identities=35%  Similarity=0.338  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|-||+||||+|..+-.
T Consensus         3 I~vs~kGGvGKTt~a~~LA~   22 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIK   22 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHH
T ss_pred             EEEecCCCCCHHHHHHHHHH
Confidence            57899999999999998754

>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=92.81  E-value=0.035  Score=50.99  Aligned_cols=19  Identities=16%  Similarity=0.034  Sum_probs=17.6

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||+|+.+.+
T Consensus        62 ll~G~~G~GKT~la~~la~   80 (353)
T 1sxj_D           62 LFYGPPGTGKTSTILALTK   80 (353)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            5899999999999999887

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=92.80  E-value=0.041  Score=46.74  Aligned_cols=21  Identities=14%  Similarity=0.129  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        37 i~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           37 VVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEECTTSSHHHHHHHHHC-
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=92.79  E-value=0.034  Score=48.30  Aligned_cols=20  Identities=15%  Similarity=0.298  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|..|+||||+++.+.+
T Consensus         5 i~~~G~~g~GKtt~~~~l~~   24 (241)
T 2ocp_A            5 LSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>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=92.77  E-value=0.098  Score=48.26  Aligned_cols=44  Identities=14%  Similarity=0.196  Sum_probs=28.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc----cEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF----DCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F----~~~~~~~vs~~~~~~~   44 (391)
                      ++|+|..|+|||||++.+.-....+...    ..++|+.-...+..+.
T Consensus       134 ~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~  181 (349)
T 1pzn_A          134 TEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER  181 (349)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHH
Confidence            4799999999999999987632222222    2557776554454444

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.74  E-value=0.12  Score=46.83  Aligned_cols=48  Identities=15%  Similarity=0.083  Sum_probs=32.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKF   52 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~   52 (391)
                      +-|.|.+|+||||||..+..+.-.+.  ..++||..  +.+.+.+..++...
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~sl--E~s~~~l~~R~~~~  118 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSL--EMGKKENIKRLIVT  118 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEES--SSCHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEEC--CCCHHHHHHHHHHH
Confidence            35899999999999999765322222  46777653  36677777766543

>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=92.71  E-value=0.11  Score=47.89  Aligned_cols=47  Identities=6%  Similarity=0.036  Sum_probs=33.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccc----cccEEEEEEcCCCcChHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKH----YFDCHAWVQESLPYDADQILY   47 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~----~F~~~~~~~vs~~~~~~~i~~   47 (391)
                      +.|+|..|+||||||..+..+.....    .=..++||.-...|+.+.+.+
T Consensus       125 ~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~  175 (343)
T 1v5w_A          125 TEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD  175 (343)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH
Confidence            35899999999999999875422221    123788888877788777654

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.71  E-value=0.048  Score=51.77  Aligned_cols=18  Identities=22%  Similarity=0.235  Sum_probs=17.2

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      .||++|.|||+||+++.+
T Consensus       220 LyGPPGTGKTllAkAiA~  237 (434)
T 4b4t_M          220 MYGPPGTGKTLLARACAA  237 (434)
T ss_dssp             EESCTTSSHHHHHHHHHH
T ss_pred             EECcCCCCHHHHHHHHHH
Confidence            699999999999999988

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.70  E-value=0.039  Score=46.50  Aligned_cols=21  Identities=14%  Similarity=0.325  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        29 i~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           29 IVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            579999999999999987653

>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=92.70  E-value=0.1  Score=47.56  Aligned_cols=47  Identities=9%  Similarity=0.070  Sum_probs=33.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc----ccEEEEEEcCCCcChHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY----FDCHAWVQESLPYDADQILY   47 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~----F~~~~~~~vs~~~~~~~i~~   47 (391)
                      +.|+|.+|+||||||..+..+......    =..++|+.....|+.+.+.+
T Consensus       110 ~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~  160 (324)
T 2z43_A          110 TEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN  160 (324)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH
T ss_pred             EEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH
Confidence            358999999999999998653222211    13788888877787777654

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=92.68  E-value=0.043  Score=45.40  Aligned_cols=21  Identities=14%  Similarity=0.235  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        23 i~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           23 IIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998653

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=92.67  E-value=0.043  Score=45.41  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        18 i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           18 ILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999998764

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=92.66  E-value=0.042  Score=45.16  Aligned_cols=21  Identities=10%  Similarity=0.004  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||...+.++
T Consensus        24 i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           24 VIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEETTSSHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>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=92.65  E-value=0.043  Score=49.33  Aligned_cols=19  Identities=21%  Similarity=0.303  Sum_probs=17.5

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||+|+.+.+
T Consensus        54 ll~G~~GtGKT~la~~la~   72 (310)
T 1ofh_A           54 LMIGPTGVGKTEIARRLAK   72 (310)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4799999999999999987

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.63  E-value=0.049  Score=51.61  Aligned_cols=18  Identities=17%  Similarity=0.198  Sum_probs=17.1

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      .||++|+|||+||+++.+
T Consensus       211 L~GPPGtGKT~lakAiA~  228 (428)
T 4b4t_K          211 LYGPPGTGKTMLVKAVAN  228 (428)
T ss_dssp             EESCTTTTHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            699999999999999988

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=92.62  E-value=0.043  Score=50.83  Aligned_cols=20  Identities=10%  Similarity=0.077  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+|+|||||+..+..
T Consensus        82 I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           82 VGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999998754

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.59  E-value=0.051  Score=50.90  Aligned_cols=18  Identities=22%  Similarity=0.207  Sum_probs=17.1

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      .||++|.|||+||+++.+
T Consensus       187 L~GPPGTGKTllAkAiA~  204 (405)
T 4b4t_J          187 LYGPPGTGKTLLARAVAH  204 (405)
T ss_dssp             EESCSSSSHHHHHHHHHH
T ss_pred             EeCCCCCCHHHHHHHHHH
Confidence            589999999999999988

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=92.58  E-value=0.041  Score=51.14  Aligned_cols=20  Identities=15%  Similarity=0.215  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|.|||||++.+..
T Consensus       173 ~~IvG~nGsGKSTLlk~L~g  192 (365)
T 1lw7_A          173 VAILGGESSGKSVLVNKLAA  192 (365)
T ss_dssp             EEEECCTTSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            47999999999999999764

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=92.58  E-value=0.04  Score=45.62  Aligned_cols=22  Identities=23%  Similarity=0.116  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|..|+|||||.+.+.++.
T Consensus        24 i~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           24 VLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            5799999999999999987653

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=92.57  E-value=0.042  Score=48.47  Aligned_cols=20  Identities=20%  Similarity=0.265  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|-||+||||+|..+..
T Consensus         4 I~vs~KGGvGKTT~a~nLA~   23 (269)
T 1cp2_A            4 VAIYGKGGIGKSTTTQNLTS   23 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEecCCCCcHHHHHHHHHH
Confidence            56789999999999988754

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.56  E-value=0.042  Score=45.69  Aligned_cols=21  Identities=14%  Similarity=0.264  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus        11 i~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A           11 VVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCcHHHHHHHHHcC
Confidence            579999999999999998653

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=92.54  E-value=0.054  Score=45.92  Aligned_cols=21  Identities=24%  Similarity=0.328  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        28 i~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           28 LLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999998765

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.53  E-value=0.04  Score=45.71  Aligned_cols=21  Identities=14%  Similarity=0.260  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        26 i~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           26 LLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            579999999999999998764

>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=92.52  E-value=0.047  Score=48.10  Aligned_cols=20  Identities=15%  Similarity=0.125  Sum_probs=18.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      -|+|..|+|||++|+.+++.
T Consensus        33 ll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A           33 LIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             EEECCTTSCHHHHHHHHHHT
T ss_pred             EEECCCCCcHHHHHHHHHHh
Confidence            48999999999999999873

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.48  E-value=0.044  Score=46.21  Aligned_cols=21  Identities=14%  Similarity=0.066  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        28 i~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           28 LVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=92.48  E-value=0.047  Score=50.55  Aligned_cols=20  Identities=15%  Similarity=0.184  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        57 ~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           57 YGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEcCCCchHHHHHHHHhc
Confidence            58999999999999999875

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=92.47  E-value=0.056  Score=46.58  Aligned_cols=20  Identities=20%  Similarity=0.127  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      .||.|+.|+||||+|+.+.+
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~   30 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKE   30 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             eeeECCCCCCHHHHHHHHHH
Confidence            48999999999999999865

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.46  E-value=0.052  Score=45.07  Aligned_cols=21  Identities=14%  Similarity=0.104  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus        21 i~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           21 CVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>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=92.42  E-value=0.051  Score=50.67  Aligned_cols=19  Identities=21%  Similarity=0.226  Sum_probs=17.5

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||+|+.+.+
T Consensus        76 ll~Gp~GtGKT~la~~la~   94 (376)
T 1um8_A           76 LLIGPTGSGKTLMAQTLAK   94 (376)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4799999999999999987

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=92.42  E-value=0.046  Score=50.54  Aligned_cols=20  Identities=15%  Similarity=0.194  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||.+.+.-
T Consensus        33 ~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           33 LFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCchHHHHHHHHhc
Confidence            47999999999999999865

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=92.38  E-value=0.044  Score=50.83  Aligned_cols=19  Identities=21%  Similarity=0.232  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||+|+.+.+
T Consensus        55 ll~GppGtGKT~la~~ia~   73 (363)
T 3hws_A           55 LLIGPTGSGKTLLAETLAR   73 (363)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4799999999999999987

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=92.33  E-value=0.057  Score=44.46  Aligned_cols=19  Identities=16%  Similarity=0.218  Sum_probs=17.3

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      +|+|..|.|||||+++++-
T Consensus        30 ~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           30 AIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             EEEECTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            6999999999999999863

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=92.33  E-value=0.11  Score=44.24  Aligned_cols=20  Identities=10%  Similarity=0.001  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+++.+.+
T Consensus         9 i~~eG~~gsGKsT~~~~l~~   28 (213)
T 4edh_A            9 VTLEGPEGAGKSTNRDYLAE   28 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            56889999999999999876

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=92.32  E-value=0.059  Score=45.78  Aligned_cols=21  Identities=14%  Similarity=0.183  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus        30 i~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           30 LVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            579999999999999998764

>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=92.32  E-value=0.059  Score=48.84  Aligned_cols=19  Identities=16%  Similarity=-0.038  Sum_probs=17.4

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|++|+||||||.++..
T Consensus       127 LI~GpPGsGKTtLAlqlA~  145 (331)
T 2vhj_A          127 IVTGKGNSGKTPLVHALGE  145 (331)
T ss_dssp             EEECSCSSSHHHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHH
Confidence            4899999999999999876

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=92.31  E-value=0.058  Score=52.29  Aligned_cols=20  Identities=20%  Similarity=0.292  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|..|+||||||+.+.+
T Consensus        67 vLL~GppGtGKTtLaraIa~   86 (499)
T 2dhr_A           67 VLLVGPPGVGKTHLARAVAG   86 (499)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999987

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.30  E-value=0.058  Score=51.25  Aligned_cols=18  Identities=22%  Similarity=0.235  Sum_probs=17.2

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      .||++|.|||+||+++.+
T Consensus       220 L~GPPGtGKTllAkAiA~  237 (437)
T 4b4t_L          220 LYGPPGTGKTLLAKAVAA  237 (437)
T ss_dssp             EESCTTSSHHHHHHHHHH
T ss_pred             EECCCCCcHHHHHHHHHH
Confidence            699999999999999988

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=92.30  E-value=0.05  Score=51.57  Aligned_cols=20  Identities=20%  Similarity=0.283  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus       261 Iil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          261 VVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             EEEESCTTSSHHHHHHHHTG
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999876

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=92.30  E-value=0.052  Score=50.16  Aligned_cols=20  Identities=20%  Similarity=0.190  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+|..|+|||||.+.+.-
T Consensus        44 ~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           44 VGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             EEEECSTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            47999999999999999865

>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=92.29  E-value=0.043  Score=50.55  Aligned_cols=20  Identities=10%  Similarity=0.102  Sum_probs=17.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +.|+|..|+||||+|+.+..
T Consensus        39 ~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           39 LLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             EEEECSTTSSHHHHHHTHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35899999999999998765

>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=92.29  E-value=0.054  Score=52.15  Aligned_cols=20  Identities=20%  Similarity=0.248  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++|..|+||||||+.+.+
T Consensus        52 vLL~GppGtGKT~Laraia~   71 (476)
T 2ce7_A           52 ILLVGPPGTGKTLLARAVAG   71 (476)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999987

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=92.28  E-value=0.056  Score=45.26  Aligned_cols=21  Identities=10%  Similarity=0.061  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        28 i~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           28 LVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999998764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.27  E-value=0.05  Score=50.49  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.|||||++.+..
T Consensus       178 i~ivG~sGsGKSTll~~l~~  197 (361)
T 2gza_A          178 IVVAGETGSGKTTLMKALMQ  197 (361)
T ss_dssp             EEEEESSSSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999876

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=92.27  E-value=0.057  Score=45.59  Aligned_cols=21  Identities=14%  Similarity=0.023  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus        12 i~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           12 CVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998754

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=92.25  E-value=0.049  Score=45.77  Aligned_cols=21  Identities=10%  Similarity=0.254  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus        11 i~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y           11 LLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998754

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=92.24  E-value=0.055  Score=45.09  Aligned_cols=19  Identities=16%  Similarity=0.272  Sum_probs=17.3

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |.|+|-+|+|||||...+.
T Consensus         9 v~lvG~~~vGKSsL~~~~~   27 (192)
T 2cjw_A            9 VVLIGEQGVGKSTLANIFA   27 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5799999999999999875

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=92.22  E-value=0.033  Score=45.69  Aligned_cols=21  Identities=14%  Similarity=0.211  Sum_probs=8.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus        11 i~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C           11 LLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999997654

---

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	391
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	0.002

>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 = 37.7 bits (86), Expect = 0.002
 Identities = 40/198 (20%), Positives = 69/198 (34%), Gaps = 15/198 (7%)

Query: 178 FKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLP------------SSRKIL 224
            K L  L L +  + +  P     L  L  L L+   LK LP               +I 
Sbjct: 54  LKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEIT 113

Query: 225 RLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPS 284
           ++  +     +   ++    + L  S       + +K  +  ++   +NI       PPS
Sbjct: 114 KVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRI-ADTNITTIPQGLPPS 172

Query: 285 LTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHL 344
           LT L     ++      +L+ L+ L  L L  N  S      +   P L  L +N    L
Sbjct: 173 LTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLN-NNKL 231

Query: 345 KRIHEQLWCLKSLNKLEL 362
            ++   L   K +  + L
Sbjct: 232 VKVPGGLADHKYIQVVYL 249

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	391
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.63
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.53
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.49
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.49
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.48
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.45
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.44
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.44
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.44
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.41
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.36
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.35
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.32
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.27
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.22
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.2
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.19
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.18
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.16
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.15
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.04
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.03
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.0
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.92
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	98.88
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	98.8
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.78
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.69
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.68
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.65
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.61
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.44
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	98.41
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.27
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.25
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	97.89
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.18
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.01
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.9
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.84
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.84
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.74
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.73
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.7
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.69
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.65
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.62
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.57
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.56
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.55
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.39
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.38
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	96.32
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.25
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.18
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.17
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.15
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.12
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.06
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.05
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	96.02
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.01
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.98
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	95.92
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.92
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	95.78
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.65
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.65
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.6
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.59
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.55
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	95.55
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.51
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.39
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.38
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	95.37
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.33
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.29
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.29
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.27
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.22
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.2
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.18
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	95.11
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.1
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.09
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.08
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.02
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.01
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	94.99
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.92
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.82
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	94.82
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.81
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.81
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	94.75
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	94.73
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.73
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	94.73
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.72
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.71
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.69
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.69
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.68
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.67
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	94.65
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.58
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.57
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.54
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.53
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.53
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.52
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.5
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.49
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.47
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.45
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.43
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.41
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.33
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.33
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.32
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	94.32
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.31
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	94.3
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.29
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.28
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.26
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	94.2
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.2
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.19
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.18
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	94.15
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.15
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.14
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.14
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.12
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.1
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.1
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.08
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.06
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.06
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.01
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.96
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	93.94
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	93.9
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.85
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	93.82
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.8
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	93.8
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.79
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.79
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	93.79
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.73
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	93.7
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.7
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.63
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	93.6
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.6
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	93.57
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	93.54
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	93.53
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.53
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	93.53
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	93.49
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.48
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	93.47
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.46
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.45
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.45
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	93.42
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	93.4
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.4
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.39
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.35
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	93.34
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.33
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	93.33
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.21
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	93.19
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.15
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.14
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.14
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.13
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.1
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.09
d1j8yf2	211	GTPase domain of the signal sequence recognition p	93.08
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.06
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.01
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.97
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	92.97
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.91
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.91
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.85
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.8
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	92.79
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	92.79
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.77
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	92.73
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.72
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	92.7
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.65
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	92.61
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	92.59
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	92.51
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.47
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	92.46
d2fh5b1	207	Signal recognition particle receptor beta-subunit	92.36
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.27
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.17
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	92.03
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	91.98
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	91.9
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.89
d1nrjb_	209	Signal recognition particle receptor beta-subunit	91.88
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	91.87
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	91.8
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	91.79
d1ls1a2	207	GTPase domain of the signal sequence recognition p	91.67
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	91.55
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	91.25
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	91.14
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	91.07
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	90.92
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	90.88
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	90.84
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.84
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	90.63
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	90.56
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	90.19
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	90.01
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	89.9
d1okkd2	207	GTPase domain of the signal recognition particle r	89.83
d2qy9a2	211	GTPase domain of the signal recognition particle r	89.65
d1vmaa2	213	GTPase domain of the signal recognition particle r	89.62
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	89.52
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	89.48
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	89.39
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	89.11
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	88.48
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	88.36
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	88.3
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.23
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	88.2
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	87.6
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.46
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	87.23
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	87.15
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	86.97
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	86.92
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	86.82
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	86.8
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	86.31
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	86.03
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	85.75
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	85.58
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	84.98
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	84.75
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	84.64
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	84.54
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	84.26
d1xpua3	289	Transcription termination factor Rho, ATPase domai	84.24
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	83.99
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	83.52
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	83.48
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.25
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	82.62
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	82.46
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	82.25
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	82.16
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	81.55
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	80.96
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	80.75
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	80.66

>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=99.63  E-value=2.4e-15  Score=133.70  Aligned_cols=176  Identities=22%  Similarity=0.170  Sum_probs=139.8

Q ss_pred             CcccEEEcCCCccccCC-cccCCCCcccEEEccCCCCCccCCCCc-----EEEeeCCccCcceeeEEecccccchhHHhc
Q 041097          179 KFLRVLDLGSLVLIRYP-SGIENLFLLRYLKLNIPSLKSLPSSRK-----ILRLSGNSQFHFSLASLLLYYQSLLSKSLC  252 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p-~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~  252 (391)
                      +.+++|+|++|.+..+| ..+.++.+|++|++++|+++.+|..-.     +|++++|++.             ..+..+.
T Consensus        31 ~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~~l~~~~~l~~L~~L~Ls~N~l~-------------~~~~~~~   97 (266)
T d1p9ag_          31 KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQ-------------SLPLLGQ   97 (266)
T ss_dssp             TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEECCSCCTTCCEEECCSSCCS-------------SCCCCTT
T ss_pred             cCCCEEECcCCcCCCcCHHHhhcccccccccccccccccccccccccccccccccccccc-------------ccccccc
Confidence            47889999999988776 568899999999999998887775322     7777777776             6778889


Q ss_pred             CCCCCCEEEecCCC--CCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCc
Q 041097          253 RLSCLESLKLANES--KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRA  329 (391)
Q Consensus       253 ~l~~L~~L~l~~~~--~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~  329 (391)
                      .+++|+.|++++..  .+      .+ .+..+ .+++.|.+.+|.+...+...+..+++|+.|+++.|.......-..+.
T Consensus        98 ~l~~L~~L~l~~~~~~~~------~~~~~~~l-~~l~~L~l~~n~l~~l~~~~~~~l~~l~~l~l~~N~l~~~~~~~~~~  170 (266)
T d1p9ag_          98 TLPALTVLDVSFNRLTSL------PLGALRGL-GELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNG  170 (266)
T ss_dssp             TCTTCCEEECCSSCCCCC------CSSTTTTC-TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTT
T ss_pred             ccccccccccccccccee------eccccccc-cccccccccccccceeccccccccccchhcccccccccccCcccccc
Confidence            99999999998722  21      12 45667 99999999999988887778889999999999977665432222467


Q ss_pred             ccccceeeeccccccccchHhhcCCCCCCEEEeeCCc-------HHHHHHhhh
Q 041097          330 MPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE-------PELRQQLRE  375 (391)
Q Consensus       330 ~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~-------~~l~~~~~~  375 (391)
                      +++|++|+++++ +++.+|+++..+++|+.|+++++|       ..|.+|+++
T Consensus       171 l~~L~~L~Ls~N-~L~~lp~~~~~~~~L~~L~L~~Np~~CdC~~~~l~~wl~~  222 (266)
T d1p9ag_         171 LENLDTLLLQEN-SLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQD  222 (266)
T ss_dssp             CTTCCEEECCSS-CCCCCCTTTTTTCCCSEEECCSCCBCCSGGGHHHHHHHHH
T ss_pred             ccccceeecccC-CCcccChhHCCCCCCCEEEecCCCCCCCcchHHHHHHHHh
Confidence            899999999988 589999999999999999999876       335556553

>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=99.53  E-value=9.6e-14  Score=125.57  Aligned_cols=209  Identities=16%  Similarity=0.119  Sum_probs=130.1

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccC-CcccCCCCcccEEEccCCCCCccCCCCc----EEE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRY-PSGIENLFLLRYLKLNIPSLKSLPSSRK----ILR  225 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~----~L~  225 (391)
                      +.++.|.+..+...    ...+..|..+..|+.|+++++.+..+ |..+.++.+|++|++++++++.+|....    .|+
T Consensus        31 ~~l~~L~Ls~N~i~----~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~n~l~~l~~~~~~~l~~L~  106 (305)
T d1xkua_          31 PDTALLDLQNNKIT----EIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELR  106 (305)
T ss_dssp             TTCCEEECCSSCCC----CBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEEE
T ss_pred             CCCCEEECcCCcCC----CcChhHhhccccccccccccccccccchhhhhCCCccCEecccCCccCcCccchhhhhhhhh
Confidence            56777776655432    11223577888999999999998866 5678899999999999999998887776    788


Q ss_pred             eeCCccCcc---------eeeEEecc-----cccchhHHhcCCCCCCEEEecCCC--C-----CCchhhh----------
Q 041097          226 LSGNSQFHF---------SLASLLLY-----YQSLLSKSLCRLSCLESLKLANES--K-----MPRRSNI----------  274 (391)
Q Consensus       226 l~~~~l~~L---------~L~~L~l~-----~~~~lp~~i~~l~~L~~L~l~~~~--~-----lp~L~~L----------  274 (391)
                      +..+.+..+         .++.+...     .....+..+..+++|+.+.+.+.+  .     +++++.|          
T Consensus       107 ~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~~~~L~~L~l~~n~~~~~  186 (305)
T d1xkua_         107 VHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKV  186 (305)
T ss_dssp             CCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSCCTTCSEEECTTSCCCEE
T ss_pred             ccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCcccCCccCEEECCCCcCCCC
Confidence            888777665         34444444     111223456667777777776611  1     1122222          


Q ss_pred             cc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHh---
Q 041097          275 IL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQ---  350 (391)
Q Consensus       275 lp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~---  350 (391)
                      .| .+..+ ++++.|.+++|.+...+...+..+++|++|+++.|.... .+.....+++|++|+++++ +++.++..   
T Consensus       187 ~~~~~~~~-~~l~~L~~s~n~l~~~~~~~~~~l~~L~~L~L~~N~L~~-lp~~l~~l~~L~~L~Ls~N-~i~~i~~~~f~  263 (305)
T d1xkua_         187 DAASLKGL-NNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVK-VPGGLADHKYIQVVYLHNN-NISAIGSNDFC  263 (305)
T ss_dssp             CTGGGTTC-TTCCEEECCSSCCCEECTTTGGGSTTCCEEECCSSCCSS-CCTTTTTCSSCCEEECCSS-CCCCCCTTSSS
T ss_pred             ChhHhhcc-ccccccccccccccccccccccccccceeeecccccccc-cccccccccCCCEEECCCC-ccCccChhhcc
Confidence            22 44555 666777776666665555566666777777776544332 1122345667777777765 46666432   


Q ss_pred             ----hcCCCCCCEEEeeCCc
Q 041097          351 ----LWCLKSLNKLELWWPE  366 (391)
Q Consensus       351 ----~~~l~~L~~L~l~~~~  366 (391)
                          ....++|+.|+++++|
T Consensus       264 ~~~~~~~~~~L~~L~L~~N~  283 (305)
T d1xkua_         264 PPGYNTKKASYSGVSLFSNP  283 (305)
T ss_dssp             CSSCCTTSCCCSEEECCSSS
T ss_pred             CcchhcccCCCCEEECCCCc
Confidence                1345667777777666

>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=99.49  E-value=2.1e-13  Score=116.55  Aligned_cols=158  Identities=28%  Similarity=0.321  Sum_probs=115.3

Q ss_pred             CCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-----EEEeeCCccCcceeeEEecccccchhHHhc
Q 041097          178 FKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-----ILRLSGNSQFHFSLASLLLYYQSLLSKSLC  252 (391)
Q Consensus       178 ~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~  252 (391)
                      +..|+.|+++++.+..++ ++..+.+|++|+++++.++.++..-.     .|++++|++.             .+| .++
T Consensus        45 L~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~L~~n~i~~l~~~~~l~~L~~L~l~~n~i~-------------~l~-~l~  109 (210)
T d1h6ta2          45 LNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVK-------------DLS-SLK  109 (210)
T ss_dssp             HHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSSCCC-------------CGG-GGT
T ss_pred             hcCccEEECcCCCCCCch-hHhhCCCCCEEeCCCccccCccccccCcccccccccccccc-------------ccc-ccc
Confidence            345666677777666544 46666677777777776665552111     5555555555             555 588


Q ss_pred             CCCCCCEEEecCCC--CCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcc
Q 041097          253 RLSCLESLKLANES--KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAM  330 (391)
Q Consensus       253 ~l~~L~~L~l~~~~--~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~  330 (391)
                      ++++|+.|++.+..  .       ++.+..+ ++++.+++.++.+..  ......+++|+.++++.|....  +.+.+.+
T Consensus       110 ~l~~L~~L~l~~~~~~~-------~~~l~~l-~~l~~l~~~~n~l~~--~~~~~~l~~L~~l~l~~n~l~~--i~~l~~l  177 (210)
T d1h6ta2         110 DLKKLKSLSLEHNGISD-------INGLVHL-PQLESLYLGNNKITD--ITVLSRLTKLDTLSLEDNQISD--IVPLAGL  177 (210)
T ss_dssp             TCTTCCEEECTTSCCCC-------CGGGGGC-TTCCEEECCSSCCCC--CGGGGGCTTCSEEECCSSCCCC--CGGGTTC
T ss_pred             ccccccccccccccccc-------ccccccc-ccccccccccccccc--cccccccccccccccccccccc--cccccCC
Confidence            99999999998722  2       3356678 999999999988765  3567889999999999666543  3345789


Q ss_pred             cccceeeeccccccccchHhhcCCCCCCEEEeeC
Q 041097          331 PKLECLIINPYAHLKRIHEQLWCLKSLNKLELWW  364 (391)
Q Consensus       331 ~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~  364 (391)
                      ++|++|++++| .++.+| .+..+++|++|+|++
T Consensus       178 ~~L~~L~Ls~N-~i~~l~-~l~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         178 TKLQNLYLSKN-HISDLR-ALAGLKNLDVLELFS  209 (210)
T ss_dssp             TTCCEEECCSS-CCCBCG-GGTTCTTCSEEEEEE
T ss_pred             CCCCEEECCCC-CCCCCh-hhcCCCCCCEEEccC
Confidence            99999999988 588998 699999999999975

>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=99.49  E-value=3.5e-13  Score=125.36  Aligned_cols=82  Identities=13%  Similarity=-0.014  Sum_probs=53.6

Q ss_pred             CceEEEEEeccCCCcccccCCC-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEE
Q 041097          129 ENVKRFTAHRKLNDFAFLDDFD-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYL  207 (391)
Q Consensus       129 ~~~r~l~~~~~~~~~~~~~~~~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L  207 (391)
                      .+++.|.+....... +...-. ++++.|.+.++...     .+ +.+.+++.|++|++++|.+..++ .++++.+|++|
T Consensus        44 ~~l~~L~l~~~~I~~-l~gl~~L~nL~~L~Ls~N~l~-----~l-~~l~~L~~L~~L~L~~n~i~~i~-~l~~l~~L~~L  115 (384)
T d2omza2          44 DQVTTLQADRLGIKS-IDGVEYLNNLTQINFSNNQLT-----DI-TPLKNLTKLVDILMNNNQIADIT-PLANLTNLTGL  115 (384)
T ss_dssp             TTCCEEECCSSCCCC-CTTGGGCTTCCEEECCSSCCC-----CC-GGGTTCTTCCEEECCSSCCCCCG-GGTTCTTCCEE
T ss_pred             CCCCEEECCCCCCCC-ccccccCCCCCEEeCcCCcCC-----CC-ccccCCccccccccccccccccc-ccccccccccc
Confidence            457777776333322 222223 77777777665543     12 34778888889999888887655 37888888888


Q ss_pred             EccCCCCCccC
Q 041097          208 KLNIPSLKSLP  218 (391)
Q Consensus       208 ~l~~~~i~~lp  218 (391)
                      +++++.+..++
T Consensus       116 ~~~~~~~~~~~  126 (384)
T d2omza2         116 TLFNNQITDID  126 (384)
T ss_dssp             ECCSSCCCCCG
T ss_pred             ccccccccccc
Confidence            88877665443

>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=99.48  E-value=7.5e-14  Score=126.83  Aligned_cols=204  Identities=17%  Similarity=0.147  Sum_probs=105.3

Q ss_pred             CccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCC-Cccc-cCCcccCCCCcccEEEccCCCCCccCCCCc-------
Q 041097          152 FLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGS-LVLI-RYPSGIENLFLLRYLKLNIPSLKSLPSSRK-------  222 (391)
Q Consensus       152 ~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~-~~l~-~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-------  222 (391)
                      +++.|.+.+....  ....+++.+.+++.|++|++++ +.+. .+|..|+++.+|++|+++++++..++....       
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~~~~~~~~~~~~~L~  128 (313)
T d1ogqa_          51 RVNNLDLSGLNLP--KPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLV  128 (313)
T ss_dssp             CEEEEEEECCCCS--SCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCC
T ss_pred             EEEEEECCCCCCC--CCCCCChHHhcCccccccccccccccccccccccccccccchhhhccccccccccccccchhhhc
Confidence            4556655554332  0112456777888888888876 5665 778888888888888888887776544422       


Q ss_pred             EEEeeCCccCc--------c-eeeEEecc---cccchhHHhcCCCCC-CEEEecCCCCCCchhhhcc-ccccCCCCccEE
Q 041097          223 ILRLSGNSQFH--------F-SLASLLLY---YQSLLSKSLCRLSCL-ESLKLANESKMPRRSNIIL-AEYQFPPSLTHL  288 (391)
Q Consensus       223 ~L~l~~~~l~~--------L-~L~~L~l~---~~~~lp~~i~~l~~L-~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L  288 (391)
                      .++++.|.+..        + +|+.++++   ....+|..++.+.++ +.+.+....    +....| .+..+  +...+
T Consensus       129 ~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~----l~~~~~~~~~~l--~~~~l  202 (313)
T d1ogqa_         129 TLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNR----LTGKIPPTFANL--NLAFV  202 (313)
T ss_dssp             EEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSE----EEEECCGGGGGC--CCSEE
T ss_pred             ccccccccccccCchhhccCcccceeecccccccccccccccccccccccccccccc----cccccccccccc--ccccc
Confidence            66666654331        0 23333333   112344444444443 333333200    000022 22332  22234


Q ss_pred             EeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccc-cchHhhcCCCCCCEEEeeCC
Q 041097          289 SFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLK-RIHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       289 ~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~-~lp~~~~~l~~L~~L~l~~~  365 (391)
                      ++.++.........++.+++|+.+++..+...+. +...+.+++|+.|++++|. ++ .+|.+++++++|++|+++++
T Consensus       203 ~l~~~~~~~~~~~~~~~~~~l~~l~~~~~~l~~~-~~~~~~~~~L~~L~Ls~N~-l~g~iP~~l~~L~~L~~L~Ls~N  278 (313)
T d1ogqa_         203 DLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFD-LGKVGLSKNLNGLDLRNNR-IYGTLPQGLTQLKFLHSLNVSFN  278 (313)
T ss_dssp             ECCSSEEEECCGGGCCTTSCCSEEECCSSEECCB-GGGCCCCTTCCEEECCSSC-CEECCCGGGGGCTTCCEEECCSS
T ss_pred             cccccccccccccccccccccccccccccccccc-ccccccccccccccCccCe-ecccCChHHhCCCCCCEEECcCC
Confidence            4444443333444455556666666654443332 2233555666666666553 44 56666666666666666553

>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=99.45  E-value=1.9e-12  Score=120.33  Aligned_cols=76  Identities=20%  Similarity=0.201  Sum_probs=35.0

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEe
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLEL  362 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l  362 (391)
                      ++++.|++++|.+...  ..++.+++|+.|+++.|....  +...+.+++|++|++++| +++.+|. +.++++|++|+|
T Consensus       307 ~~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~~L~L  380 (384)
T d2omza2         307 KNLTYLTLYFNNISDI--SPVSSLTKLQRLFFANNKVSD--VSSLANLTNINWLSAGHN-QISDLTP-LANLTRITQLGL  380 (384)
T ss_dssp             TTCSEEECCSSCCSCC--GGGGGCTTCCEEECCSSCCCC--CGGGGGCTTCCEEECCSS-CCCBCGG-GTTCTTCSEEEC
T ss_pred             cccCeEECCCCCCCCC--cccccCCCCCEEECCCCCCCC--ChhHcCCCCCCEEECCCC-cCCCChh-hccCCCCCEeeC
Confidence            4555555555544432  234455555555555333222  112234455555555544 3444442 445555555555


Q ss_pred             eC
Q 041097          363 WW  364 (391)
Q Consensus       363 ~~  364 (391)
                      ++
T Consensus       381 ~~  382 (384)
T d2omza2         381 ND  382 (384)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.44  E-value=9.3e-13  Score=117.76  Aligned_cols=179  Identities=22%  Similarity=0.158  Sum_probs=124.2

Q ss_pred             CcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCccCCCCc-------EEEee-CCccCcc---------eeeEEe
Q 041097          179 KFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKSLPSSRK-------ILRLS-GNSQFHF---------SLASLL  240 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~lp~~~~-------~L~l~-~~~l~~L---------~L~~L~  240 (391)
                      ..+++|++++|.+..+|. .+.++.+|++|+++++.+..++....       .++.. .+.+..+         +|+.|+
T Consensus        32 ~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L~  111 (284)
T d1ozna_          32 AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLH  111 (284)
T ss_dssp             TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEE
T ss_pred             CCCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccccccccccchhhcccccCCEEe
Confidence            457888888888887774 57888888888888888876655553       44433 2233321         455555


Q ss_pred             cc--cccch-hHHhcCCCCCCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcC
Q 041097          241 LY--YQSLL-SKSLCRLSCLESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLK  315 (391)
Q Consensus       241 l~--~~~~l-p~~i~~l~~L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~  315 (391)
                      +.  ....+ +..++.+.+|+.+++.+..    +.. +|  .+..+ ++|+.|++.+|.+...+...+..+++|+.+.+.
T Consensus       112 l~~n~~~~~~~~~~~~~~~L~~l~l~~N~----l~~-i~~~~f~~~-~~L~~L~l~~N~l~~l~~~~f~~l~~L~~l~l~  185 (284)
T d1ozna_         112 LDRCGLQELGPGLFRGLAALQYLYLQDNA----LQA-LPDDTFRDL-GNLTHLFLHGNRISSVPERAFRGLHSLDRLLLH  185 (284)
T ss_dssp             CTTSCCCCCCTTTTTTCTTCCEEECCSSC----CCC-CCTTTTTTC-TTCCEEECCSSCCCEECTTTTTTCTTCCEEECC
T ss_pred             cCCcccccccccccchhcccchhhhcccc----ccc-cChhHhccc-cchhhcccccCcccccchhhhccccccchhhhh
Confidence            55  22222 2345556666666665511    000 33  56677 899999999999887777788899999999999


Q ss_pred             CCCCcCccccCCCcccccceeeeccccccccch-HhhcCCCCCCEEEeeC
Q 041097          316 QNLYSEERTMGIRAMPKLECLIINPYAHLKRIH-EQLWCLKSLNKLELWW  364 (391)
Q Consensus       316 ~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp-~~~~~l~~L~~L~l~~  364 (391)
                      .|...+..+-..+.+++|++|+++++. +..+| .+++.+++|++|++++
T Consensus       186 ~N~l~~i~~~~f~~l~~L~~L~l~~N~-i~~~~~~~~~~~~~L~~L~l~~  234 (284)
T d1ozna_         186 QNRVAHVHPHAFRDLGRLMTLYLFANN-LSALPTEALAPLRALQYLRLND  234 (284)
T ss_dssp             SSCCCEECTTTTTTCTTCCEEECCSSC-CSCCCHHHHTTCTTCCEEECCS
T ss_pred             hccccccChhHhhhhhhcccccccccc-cccccccccccccccCEEEecC
Confidence            666654333334788999999999885 55654 6789999999999987

>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=99.44  E-value=9.8e-13  Score=113.61  Aligned_cols=81  Identities=22%  Similarity=0.243  Sum_probs=64.2

Q ss_pred             ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCC
Q 041097          277 AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKS  356 (391)
Q Consensus       277 ~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~  356 (391)
                      .+... ++|+.|.+.+|.+..  ...++++++|+.|++++|....  +.+.+.+++|++|++++| +++.+| .++++++
T Consensus       146 ~~~~~-~~L~~L~l~~n~~~~--~~~l~~l~~L~~L~Ls~n~l~~--l~~l~~l~~L~~L~Ls~N-~lt~i~-~l~~l~~  218 (227)
T d1h6ua2         146 PLAGL-TNLQYLSIGNAQVSD--LTPLANLSKLTTLKADDNKISD--ISPLASLPNLIEVHLKNN-QISDVS-PLANTSN  218 (227)
T ss_dssp             GGGGC-TTCCEEECCSSCCCC--CGGGTTCTTCCEEECCSSCCCC--CGGGGGCTTCCEEECTTS-CCCBCG-GGTTCTT
T ss_pred             hhccc-ccccccccccccccc--chhhcccccceecccCCCccCC--ChhhcCCCCCCEEECcCC-cCCCCc-ccccCCC
Confidence            34566 889999999988655  3458899999999999665443  334578899999999998 588888 4889999


Q ss_pred             CCEEEeeC
Q 041097          357 LNKLELWW  364 (391)
Q Consensus       357 L~~L~l~~  364 (391)
                      |++|++++
T Consensus       219 L~~L~lsn  226 (227)
T d1h6ua2         219 LFIVTLTN  226 (227)
T ss_dssp             CCEEEEEE
T ss_pred             CCEEEeeC
Confidence            99999864

>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=99.44  E-value=9.1e-13  Score=111.45  Aligned_cols=155  Identities=24%  Similarity=0.265  Sum_probs=104.6

Q ss_pred             cCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EEEeeCCccCcceeeEEecccccchhHH
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------ILRLSGNSQFHFSLASLLLYYQSLLSKS  250 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~~  250 (391)
                      .+..++.|+++++.+..+. +++.+++|++|++++|.++.++. ++      +|++++|.+.             .++ .
T Consensus        38 ~l~~l~~L~l~~~~i~~l~-~l~~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n~~~-------------~~~-~  101 (199)
T d2omxa2          38 DLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIA-------------DIT-P  101 (199)
T ss_dssp             HHTTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCC-------------CCG-G
T ss_pred             HhcCCCEEECCCCCCCCcc-ccccCCCcCcCccccccccCccc-ccCCcccccccccccccc-------------ccc-c
Confidence            3456667777777666543 46666777777777776665542 21      4444444433             444 3


Q ss_pred             hcCCCCCCEEEecCCC-CCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCc
Q 041097          251 LCRLSCLESLKLANES-KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRA  329 (391)
Q Consensus       251 i~~l~~L~~L~l~~~~-~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~  329 (391)
                      ++.+++|+.|++.+.. .-      .+.+..+ ++|+.|++++|.+..  ++.+..+++|+.|++..|....  ..+.+.
T Consensus       102 l~~l~~L~~L~l~~~~~~~------~~~~~~l-~~L~~L~l~~n~l~~--~~~l~~~~~L~~L~l~~n~l~~--l~~l~~  170 (199)
T d2omxa2         102 LANLTNLTGLTLFNNQITD------IDPLKNL-TNLNRLELSSNTISD--ISALSGLTSLQQLNFSSNQVTD--LKPLAN  170 (199)
T ss_dssp             GTTCTTCSEEECCSSCCCC------CGGGTTC-TTCSEEECCSSCCCC--CGGGTTCTTCSEEECCSSCCCC--CGGGTT
T ss_pred             ccccccccccccccccccc------ccccchh-hhhHHhhhhhhhhcc--cccccccccccccccccccccC--CccccC
Confidence            7788889998887622 10      2245678 889999998887654  3567888999999998665443  233467


Q ss_pred             ccccceeeeccccccccchHhhcCCCCCCEE
Q 041097          330 MPKLECLIINPYAHLKRIHEQLWCLKSLNKL  360 (391)
Q Consensus       330 ~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L  360 (391)
                      +++|++|++++| +++.+| .++.+++|++|
T Consensus       171 l~~L~~L~ls~N-~i~~i~-~l~~L~~L~~L  199 (199)
T d2omxa2         171 LTTLERLDISSN-KVSDIS-VLAKLTNLESL  199 (199)
T ss_dssp             CTTCCEEECCSS-CCCCCG-GGGGCTTCSEE
T ss_pred             CCCCCEEECCCC-CCCCCc-cccCCCCCCcC
Confidence            889999999988 478886 57788888876

>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=99.41  E-value=3.5e-13  Score=122.28  Aligned_cols=225  Identities=13%  Similarity=0.049  Sum_probs=130.3

Q ss_pred             ceEEEEEeccCCCc--ccccCCC--CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCcccc-CCcccCCCCcc
Q 041097          130 NVKRFTAHRKLNDF--AFLDDFD--SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIR-YPSGIENLFLL  204 (391)
Q Consensus       130 ~~r~l~~~~~~~~~--~~~~~~~--~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~-~p~~i~~l~~L  204 (391)
                      ++..+.+.......  .++..+.  ++++.|.+.+...-   ...+++.+.+++.|++|++++|++.. .+..+..+.+|
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~~~~~~~~~~~~~L  127 (313)
T d1ogqa_          51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNL---VGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTL  127 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTE---ESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTC
T ss_pred             EEEEEECCCCCCCCCCCCChHHhcCcccccccccccccc---ccccccccccccccchhhhccccccccccccccchhhh
Confidence            46666666222221  1333343  78888877652211   00245667888888888888888773 44556777778


Q ss_pred             cEEEccCCCCC-ccCCCCc------EEEeeCCccCc-c--------e-eeEEecc---cccchhHHhcCCCCCCEEEecC
Q 041097          205 RYLKLNIPSLK-SLPSSRK------ILRLSGNSQFH-F--------S-LASLLLY---YQSLLSKSLCRLSCLESLKLAN  264 (391)
Q Consensus       205 ~~L~l~~~~i~-~lp~~~~------~L~l~~~~l~~-L--------~-L~~L~l~---~~~~lp~~i~~l~~L~~L~l~~  264 (391)
                      ++++++.+.+. .+|..++      ++++++|.+.. +        + ++.+.+.   -....|..++.+..+ .+++..
T Consensus       128 ~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~~~-~l~l~~  206 (313)
T d1ogqa_         128 VTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLA-FVDLSR  206 (313)
T ss_dssp             CEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCCS-EEECCS
T ss_pred             cccccccccccccCchhhccCcccceeeccccccccccccccccccccccccccccccccccccccccccccc-cccccc
Confidence            88887776544 4565555      67777765442 1        2 3444444   112345555555444 455554


Q ss_pred             CCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccc
Q 041097          265 ESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAH  343 (391)
Q Consensus       265 ~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~  343 (391)
                      ..    .....| .++.+ ++++.+++.++.+...+ +.++.+++|+.|+++.|...+..+...+.+++|++|+++++. 
T Consensus       207 ~~----~~~~~~~~~~~~-~~l~~l~~~~~~l~~~~-~~~~~~~~L~~L~Ls~N~l~g~iP~~l~~L~~L~~L~Ls~N~-  279 (313)
T d1ogqa_         207 NM----LEGDASVLFGSD-KNTQKIHLAKNSLAFDL-GKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNN-  279 (313)
T ss_dssp             SE----EEECCGGGCCTT-SCCSEEECCSSEECCBG-GGCCCCTTCCEEECCSSCCEECCCGGGGGCTTCCEEECCSSE-
T ss_pred             cc----cccccccccccc-ccccccccccccccccc-cccccccccccccCccCeecccCChHHhCCCCCCEEECcCCc-
Confidence            11    000034 55566 77777777777655443 566677777777777666655443344667777777777663 


Q ss_pred             cc-cchHhhcCCCCCCEEEeeCCc
Q 041097          344 LK-RIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       344 l~-~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      ++ .+|. ++++++|+.+++.+++
T Consensus       280 l~g~iP~-~~~L~~L~~l~l~~N~  302 (313)
T d1ogqa_         280 LCGEIPQ-GGNLQRFDVSAYANNK  302 (313)
T ss_dssp             EEEECCC-STTGGGSCGGGTCSSS
T ss_pred             ccccCCC-cccCCCCCHHHhCCCc
Confidence            54 5663 4566777777666654

>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=99.36  E-value=4e-12  Score=112.49  Aligned_cols=167  Identities=23%  Similarity=0.161  Sum_probs=128.7

Q ss_pred             cCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcceeeEEecccccchhH
Q 041097          177 MFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHFSLASLLLYYQSLLSK  249 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L~L~~L~l~~~~~lp~  249 (391)
                      +...+...+.+++.+..+|+.+.  .++++|+|++|.++.+|.. +.      .|++++|++.             .+|.
T Consensus         8 ~~~~~~~v~C~~~~L~~iP~~lp--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~-------------~l~~   72 (266)
T d1p9ag_           8 KVASHLEVNCDKRNLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELT-------------KLQV   72 (266)
T ss_dssp             CSTTCCEEECTTSCCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCC-------------EEEC
T ss_pred             ccCCCeEEEccCCCCCeeCcCcC--cCCCEEECcCCcCCCcCHHHhhcccccccccccccccc-------------cccc
Confidence            34455667899999999998876  4789999999999988754 32      7777777666             6664


Q ss_pred             HhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCC
Q 041097          250 SLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIR  328 (391)
Q Consensus       250 ~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  328 (391)
                       ++.+++|++|++++..    +.. .| .+..+ ++|+.|+++++.+...+......+++++.|.+..|...........
T Consensus        73 -~~~l~~L~~L~Ls~N~----l~~-~~~~~~~l-~~L~~L~l~~~~~~~~~~~~~~~l~~l~~L~l~~n~l~~l~~~~~~  145 (266)
T d1p9ag_          73 -DGTLPVLGTLDLSHNQ----LQS-LPLLGQTL-PALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLT  145 (266)
T ss_dssp             -CSCCTTCCEEECCSSC----CSS-CCCCTTTC-TTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTT
T ss_pred             -cccccccccccccccc----ccc-cccccccc-cccccccccccccceeeccccccccccccccccccccceecccccc
Confidence             5789999999998722    000 34 66778 9999999999988877777888999999999996665432222235


Q ss_pred             cccccceeeeccccccccchH-hhcCCCCCCEEEeeCCc
Q 041097          329 AMPKLECLIINPYAHLKRIHE-QLWCLKSLNKLELWWPE  366 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~lp~-~~~~l~~L~~L~l~~~~  366 (391)
                      .+++|+.|+++++ +++.+|. .+..+++|++|+++++.
T Consensus       146 ~l~~l~~l~l~~N-~l~~~~~~~~~~l~~L~~L~Ls~N~  183 (266)
T d1p9ag_         146 PTPKLEKLSLANN-NLTELPAGLLNGLENLDTLLLQENS  183 (266)
T ss_dssp             TCTTCCEEECTTS-CCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             ccccchhcccccc-cccccCccccccccccceeecccCC
Confidence            7889999999987 5778764 57889999999998864

>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=99.35  E-value=6.9e-13  Score=118.08  Aligned_cols=88  Identities=11%  Similarity=0.034  Sum_probs=59.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcc--ccccccEEEEEEcCCCcChHHHHHHHHHhhcCCC----CCCCCC---ChHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNY--VKHYFDCHAWVQESLPYDADQILYDIIKFVMPSP----EGFIPD---NNEATVEK   71 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~--lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~~~~~----eg~~~~---~~~~~~~~   71 (391)
                      |+||||||+||||||+.+|++..  .+.+|++++|+++++.++...+...+........    .+....   ........
T Consensus        47 v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (277)
T d2a5yb3          47 LFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRM  126 (277)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHH
Confidence            68999999999999999998643  6788999999999999999988777654432111    111111   12222233


Q ss_pred             -HHHHHHcCccEEeeecc
Q 041097           72 -YLEQLINGGFVGAGKRS   88 (391)
Q Consensus        72 -~~~~L~~k~~l~~~~~~   88 (391)
                       ....|.+++++.+.++.
T Consensus       127 ~~~~~L~~kr~LlVLDDv  144 (277)
T d2a5yb3         127 ICNALIDRPNTLFVFDDV  144 (277)
T ss_dssp             HHHHHTTSTTEEEEEEEE
T ss_pred             HHHHHhccCCeeEecchh
Confidence             33445667777776653

>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=99.32  E-value=2.3e-11  Score=108.49  Aligned_cols=175  Identities=19%  Similarity=0.143  Sum_probs=134.3

Q ss_pred             EEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCC-Cc------EEEeeCCccCcc---------eeeEEecc---c
Q 041097          183 VLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSS-RK------ILRLSGNSQFHF---------SLASLLLY---Y  243 (391)
Q Consensus       183 ~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~-~~------~L~l~~~~l~~L---------~L~~L~l~---~  243 (391)
                      ++..+++++..+|..+.  ..+++|++++|+++.+|.. +.      +||++++.+..+         .++.+.+.   .
T Consensus        15 ~v~c~~~~L~~iP~~ip--~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~   92 (284)
T d1ozna_          15 TTSCPQQGLQAVPVGIP--AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQ   92 (284)
T ss_dssp             EEECCSSCCSSCCTTCC--TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTT
T ss_pred             EEEcCCCCCCccCCCCC--CCCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccccc
Confidence            45677788888998776  4689999999999999875 33      999999987765         56666655   3


Q ss_pred             ccch-hHHhcCCCCCCEEEecCCC--CCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCC
Q 041097          244 QSLL-SKSLCRLSCLESLKLANES--KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLY  319 (391)
Q Consensus       244 ~~~l-p~~i~~l~~L~~L~l~~~~--~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~  319 (391)
                      ...+ |..++++++|++|++.+..  .+      .+ .+... .+|+.+.+.+|.+...+...+..+++|+.|+++.|..
T Consensus        93 ~~~l~~~~~~~l~~L~~L~l~~n~~~~~------~~~~~~~~-~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~~N~l  165 (284)
T d1ozna_          93 LRSVDPATFHGLGRLHTLHLDRCGLQEL------GPGLFRGL-AALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRI  165 (284)
T ss_dssp             CCCCCTTTTTTCTTCCEEECTTSCCCCC------CTTTTTTC-TTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCC
T ss_pred             cccccchhhcccccCCEEecCCcccccc------cccccchh-cccchhhhccccccccChhHhccccchhhcccccCcc
Confidence            4444 5678999999999998722  11      12 44556 8999999999999887777888999999999997765


Q ss_pred             cCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          320 SEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       320 ~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      .....-....+++|+++.++++.-..-.|.++..+++|++|+++++.
T Consensus       166 ~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~  212 (284)
T d1ozna_         166 SSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANN  212 (284)
T ss_dssp             CEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             cccchhhhccccccchhhhhhccccccChhHhhhhhhcccccccccc
Confidence            43222223567899999999886434447899999999999998754

>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=99.27  E-value=4.5e-11  Score=107.56  Aligned_cols=202  Identities=20%  Similarity=0.170  Sum_probs=129.2

Q ss_pred             cCceEEEEEeccCCCccccc-CC-C-CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcc
Q 041097          128 RENVKRFTAHRKLNDFAFLD-DF-D-SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLL  204 (391)
Q Consensus       128 ~~~~r~l~~~~~~~~~~~~~-~~-~-~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L  204 (391)
                      +..+++|.+..+.... +.. .. + ++++.+.+......    ...+..+..++.|++|++++|++..+|..+.  .++
T Consensus        30 ~~~l~~L~Ls~N~i~~-l~~~~f~~l~~L~~L~l~~n~~~----~i~~~~f~~l~~L~~L~l~~n~l~~l~~~~~--~~l  102 (305)
T d1xkua_          30 PPDTALLDLQNNKITE-IKDGDFKNLKNLHTLILINNKIS----KISPGAFAPLVKLERLYLSKNQLKELPEKMP--KTL  102 (305)
T ss_dssp             CTTCCEEECCSSCCCC-BCTTTTTTCTTCCEEECCSSCCC----CBCTTTTTTCTTCCEEECCSSCCSBCCSSCC--TTC
T ss_pred             CCCCCEEECcCCcCCC-cChhHhhcccccccccccccccc----ccchhhhhCCCccCEecccCCccCcCccchh--hhh
Confidence            4678899988444333 332 33 3 88888887766543    1223567889999999999999998887554  477


Q ss_pred             cEEEccCCCCCccCCCCc-------EEEeeCC--------------------------ccCcc------eeeEEecc---
Q 041097          205 RYLKLNIPSLKSLPSSRK-------ILRLSGN--------------------------SQFHF------SLASLLLY---  242 (391)
Q Consensus       205 ~~L~l~~~~i~~lp~~~~-------~L~l~~~--------------------------~l~~L------~L~~L~l~---  242 (391)
                      +.|.+..+.+..++....       .++...+                          .+..+      +|+.|++.   
T Consensus       103 ~~L~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~~~~L~~L~l~~n~  182 (305)
T d1xkua_         103 QELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNK  182 (305)
T ss_dssp             CEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSCCTTCSEEECTTSC
T ss_pred             hhhhccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCcccCCccCEEECCCCc
Confidence            888888877776653322       3444333                          22221      44444444   


Q ss_pred             cccchhHHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcC
Q 041097          243 YQSLLSKSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSE  321 (391)
Q Consensus       243 ~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~  321 (391)
                      .....+..+.+++.++.|++++..    +..+.| ++..+ ++|++|+|++|.+...+ ..+..+++|++|+++.|....
T Consensus       183 ~~~~~~~~~~~~~~l~~L~~s~n~----l~~~~~~~~~~l-~~L~~L~L~~N~L~~lp-~~l~~l~~L~~L~Ls~N~i~~  256 (305)
T d1xkua_         183 ITKVDAASLKGLNNLAKLGLSFNS----ISAVDNGSLANT-PHLRELHLNNNKLVKVP-GGLADHKYIQVVYLHNNNISA  256 (305)
T ss_dssp             CCEECTGGGTTCTTCCEEECCSSC----CCEECTTTGGGS-TTCCEEECCSSCCSSCC-TTTTTCSSCCEEECCSSCCCC
T ss_pred             CCCCChhHhhcccccccccccccc----cccccccccccc-ccceeeecccccccccc-cccccccCCCEEECCCCccCc
Confidence            122233445555555555554411    011123 67788 99999999999988765 578999999999999765432


Q ss_pred             c--ccc-C---CCcccccceeeecccc
Q 041097          322 E--RTM-G---IRAMPKLECLIINPYA  342 (391)
Q Consensus       322 ~--~~~-~---~~~~~~L~~L~l~~c~  342 (391)
                      -  ..+ .   ...+++|+.|+|++++
T Consensus       257 i~~~~f~~~~~~~~~~~L~~L~L~~N~  283 (305)
T d1xkua_         257 IGSNDFCPPGYNTKKASYSGVSLFSNP  283 (305)
T ss_dssp             CCTTSSSCSSCCTTSCCCSEEECCSSS
T ss_pred             cChhhccCcchhcccCCCCEEECCCCc
Confidence            1  111 1   1356789999999886

>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=5.9e-11  Score=100.91  Aligned_cols=141  Identities=27%  Similarity=0.269  Sum_probs=104.0

Q ss_pred             hhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-----EEEeeCCccCcceeeEEecccccchh
Q 041097          174 ICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-----ILRLSGNSQFHFSLASLLLYYQSLLS  248 (391)
Q Consensus       174 ~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~l~~~~l~~L~L~~L~l~~~~~lp  248 (391)
                      .+..+++|+.|++++|++..++ .++.+.+|++|++++|+++.+|.-..     .|+++++.+.             .++
T Consensus        63 ~l~~l~~L~~L~L~~n~i~~l~-~~~~l~~L~~L~l~~n~i~~l~~l~~l~~L~~L~l~~~~~~-------------~~~  128 (210)
T d1h6ta2          63 GIQYLPNVTKLFLNGNKLTDIK-PLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGIS-------------DIN  128 (210)
T ss_dssp             TGGGCTTCCEEECCSSCCCCCG-GGTTCTTCCEEECCSSCCCCGGGGTTCTTCCEEECTTSCCC-------------CCG
T ss_pred             hHhhCCCCCEEeCCCccccCcc-ccccCcccccccccccccccccccccccccccccccccccc-------------ccc
Confidence            3567888999999999888766 46888899999999888887763211     5555555544             443


Q ss_pred             HHhcCCCCCCEEEecCCC-CCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCC
Q 041097          249 KSLCRLSCLESLKLANES-KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGI  327 (391)
Q Consensus       249 ~~i~~l~~L~~L~l~~~~-~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~  327 (391)
                       .+..+++|+.+.+.+.. .  .    .+.+..+ ++|+.+++++|.+..  ++.++++++|+.|+++.|....  +...
T Consensus       129 -~l~~l~~l~~l~~~~n~l~--~----~~~~~~l-~~L~~l~l~~n~l~~--i~~l~~l~~L~~L~Ls~N~i~~--l~~l  196 (210)
T d1h6ta2         129 -GLVHLPQLESLYLGNNKIT--D----ITVLSRL-TKLDTLSLEDNQISD--IVPLAGLTKLQNLYLSKNHISD--LRAL  196 (210)
T ss_dssp             -GGGGCTTCCEEECCSSCCC--C----CGGGGGC-TTCSEEECCSSCCCC--CGGGTTCTTCCEEECCSSCCCB--CGGG
T ss_pred             -ccccccccccccccccccc--c----ccccccc-ccccccccccccccc--cccccCCCCCCEEECCCCCCCC--Chhh
Confidence             57889999999987622 1  0    2256678 999999999998765  3458899999999999665543  3345


Q ss_pred             Ccccccceeeecc
Q 041097          328 RAMPKLECLIINP  340 (391)
Q Consensus       328 ~~~~~L~~L~l~~  340 (391)
                      ..+++|++|+|++
T Consensus       197 ~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         197 AGLKNLDVLELFS  209 (210)
T ss_dssp             TTCTTCSEEEEEE
T ss_pred             cCCCCCCEEEccC
Confidence            6788999999874

>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=99.20  E-value=1.2e-10  Score=100.20  Aligned_cols=158  Identities=20%  Similarity=0.176  Sum_probs=101.0

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc-----EEE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK-----ILR  225 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~-----~L~  225 (391)
                      ++++.+.+.++...     .+ ..+.+++.+++++++++.+..++ .+..+.+|+++.++++....++....     .+.
T Consensus        63 ~~L~~L~ls~n~i~-----~~-~~l~~l~~l~~l~~~~n~~~~i~-~l~~l~~L~~l~l~~~~~~~~~~~~~~~~~~~l~  135 (227)
T d1h6ua2          63 NNLIGLELKDNQIT-----DL-APLKNLTKITELELSGNPLKNVS-AIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVLY  135 (227)
T ss_dssp             TTCCEEECCSSCCC-----CC-GGGTTCCSCCEEECCSCCCSCCG-GGTTCTTCCEEECTTSCCCCCGGGTTCTTCCEEE
T ss_pred             CCCcEeecCCceee-----cc-ccccccccccccccccccccccc-cccccccccccccccccccccchhccccchhhhh
Confidence            56666655544332     11 23566666677776666665433 45666667777666665443322111     445


Q ss_pred             eeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCC-CCCchhhhccccccCCCCccEEEeecccCCCCChhhhc
Q 041097          226 LSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANES-KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALE  304 (391)
Q Consensus       226 l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~-~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~  304 (391)
                      ++.+.+.             . ...+..+++|++|++.+.. .  .    .+.++.+ ++|+.|++++|.+..  ++.++
T Consensus       136 ~~~~~~~-------------~-~~~~~~~~~L~~L~l~~n~~~--~----~~~l~~l-~~L~~L~Ls~n~l~~--l~~l~  192 (227)
T d1h6ua2         136 LDLNQIT-------------N-ISPLAGLTNLQYLSIGNAQVS--D----LTPLANL-SKLTTLKADDNKISD--ISPLA  192 (227)
T ss_dssp             CCSSCCC-------------C-CGGGGGCTTCCEEECCSSCCC--C----CGGGTTC-TTCCEEECCSSCCCC--CGGGG
T ss_pred             chhhhhc-------------h-hhhhccccccccccccccccc--c----chhhccc-ccceecccCCCccCC--Chhhc
Confidence            5444443             2 2346788999999998722 0  0    2256788 999999999998765  35688


Q ss_pred             CCCCCCEEEcCCCCCcCccccCCCcccccceeeecc
Q 041097          305 KLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINP  340 (391)
Q Consensus       305 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~  340 (391)
                      .+++|++|+++.|....  ..+.+.+++|+.|++++
T Consensus       193 ~l~~L~~L~Ls~N~lt~--i~~l~~l~~L~~L~lsn  226 (227)
T d1h6ua2         193 SLPNLIEVHLKNNQISD--VSPLANTSNLFIVTLTN  226 (227)
T ss_dssp             GCTTCCEEECTTSCCCB--CGGGTTCTTCCEEEEEE
T ss_pred             CCCCCCEEECcCCcCCC--CcccccCCCCCEEEeeC
Confidence            99999999999665443  33457889999999874

>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=99.19  E-value=2.9e-11  Score=98.35  Aligned_cols=86  Identities=15%  Similarity=0.063  Sum_probs=50.2

Q ss_pred             CCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccc-cCCCcccccceeeeccccccccchH----hhcCCCCC
Q 041097          283 PSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERT-MGIRAMPKLECLIINPYAHLKRIHE----QLWCLKSL  357 (391)
Q Consensus       283 ~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~-~~~~~~~~L~~L~l~~c~~l~~lp~----~~~~l~~L  357 (391)
                      ++|+.|++++|.+...+...+..+++|+.|++++|....... .....+++|++|++++|+ +...|.    .+..+++|
T Consensus        63 ~~L~~L~ls~N~i~~l~~~~~~~l~~L~~L~L~~N~i~~~~~l~~l~~l~~L~~L~l~~N~-i~~~~~~r~~~i~~lp~L  141 (162)
T d1a9na_          63 RRLKTLLVNNNRICRIGEGLDQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCILRNP-VTNKKHYRLYVIYKVPQV  141 (162)
T ss_dssp             SSCCEEECCSSCCCEECSCHHHHCTTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECCSSG-GGGSTTHHHHHHHHCTTC
T ss_pred             cchhhhhcccccccCCCccccccccccccceeccccccccccccccccccccchhhcCCCc-cccccchHHHHHHHCCCc
Confidence            555555555555554443344556666666666554432211 122456677777777664 455553    46788999


Q ss_pred             CEEEeeCCcHHH
Q 041097          358 NKLELWWPEPEL  369 (391)
Q Consensus       358 ~~L~l~~~~~~l  369 (391)
                      ++|+-....++=
T Consensus       142 ~~LD~~~i~~~e  153 (162)
T d1a9na_         142 RVLDFQKVKLKE  153 (162)
T ss_dssp             SEETTEECCHHH
T ss_pred             CeeCCCCCCHHH
Confidence            999877766443

>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=99.18  E-value=1.2e-10  Score=98.09  Aligned_cols=154  Identities=21%  Similarity=0.248  Sum_probs=107.8

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCc------EE
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRK------IL  224 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~------~L  224 (391)
                      .+++.|.+.+....     .+ +.+..+++|++|++++|++..++. ++++++|++|+++++.+..+|. +.      .|
T Consensus        40 ~~l~~L~l~~~~i~-----~l-~~l~~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n~~~~~~~-l~~l~~L~~L  111 (199)
T d2omxa2          40 DQVTTLQADRLGIK-----SI-DGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIADITP-LANLTNLTGL  111 (199)
T ss_dssp             TTCCEEECTTSCCC-----CC-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGG-GTTCTTCSEE
T ss_pred             cCCCEEECCCCCCC-----Cc-cccccCCCcCcCccccccccCccc-ccCCcccccccccccccccccc-cccccccccc
Confidence            45555555444332     12 345678999999999999887664 8899999999999998887763 22      56


Q ss_pred             EeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhc
Q 041097          225 RLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALE  304 (391)
Q Consensus       225 ~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~  304 (391)
                      +++++...             .+ ..+..+++|+.|++++.. +..    +|.+..+ ++|+.|++.+|.+..  ++.++
T Consensus       112 ~l~~~~~~-------------~~-~~~~~l~~L~~L~l~~n~-l~~----~~~l~~~-~~L~~L~l~~n~l~~--l~~l~  169 (199)
T d2omxa2         112 TLFNNQIT-------------DI-DPLKNLTNLNRLELSSNT-ISD----ISALSGL-TSLQQLNFSSNQVTD--LKPLA  169 (199)
T ss_dssp             ECCSSCCC-------------CC-GGGTTCTTCSEEECCSSC-CCC----CGGGTTC-TTCSEEECCSSCCCC--CGGGT
T ss_pred             cccccccc-------------cc-cccchhhhhHHhhhhhhh-hcc----ccccccc-ccccccccccccccC--Ccccc
Confidence            66555444             33 357889999999998732 000    3356677 999999999998766  35688


Q ss_pred             CCCCCCEEEcCCCCCcCccccCCCccccccee
Q 041097          305 KLSVLQVLKLKQNLYSEERTMGIRAMPKLECL  336 (391)
Q Consensus       305 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L  336 (391)
                      ++++|+.|+++.|....  ....+.+++|++|
T Consensus       170 ~l~~L~~L~ls~N~i~~--i~~l~~L~~L~~L  199 (199)
T d2omxa2         170 NLTTLERLDISSNKVSD--ISVLAKLTNLESL  199 (199)
T ss_dssp             TCTTCCEEECCSSCCCC--CGGGGGCTTCSEE
T ss_pred             CCCCCCEEECCCCCCCC--CccccCCCCCCcC
Confidence            99999999999665433  2223566777664

>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=99.16  E-value=6.6e-11  Score=91.62  Aligned_cols=101  Identities=31%  Similarity=0.420  Sum_probs=67.9

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      |+|+++++.+..++ .++.+.+|++|++++|.++.+|                              ++++.+++|++|+
T Consensus         1 R~L~Ls~n~l~~l~-~l~~l~~L~~L~ls~N~l~~lp------------------------------~~~~~l~~L~~L~   49 (124)
T d1dcea3           1 RVLHLAHKDLTVLC-HLEQLLLVTHLDLSHNRLRALP------------------------------PALAALRCLEVLQ   49 (124)
T ss_dssp             SEEECTTSCCSSCC-CGGGGTTCCEEECCSSCCCCCC------------------------------GGGGGCTTCCEEE
T ss_pred             CEEEcCCCCCCCCc-ccccCCCCCEEECCCCccCcch------------------------------hhhhhhhcccccc
Confidence            68899999988776 4788888999888888777654                              3455667777777


Q ss_pred             ecCCCCCCchhhhccccccCCCCccEEEeecccCCCCC-hhhhcCCCCCCEEEcCCCCC
Q 041097          262 LANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLKQNLY  319 (391)
Q Consensus       262 l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~~~~~  319 (391)
                      +++..    +.. +|.++.+ ++|+.|++++|.+...+ +..++.+++|+.|++++|..
T Consensus        50 l~~N~----i~~-l~~~~~l-~~L~~L~l~~N~i~~~~~~~~l~~~~~L~~L~l~~N~i  102 (124)
T d1dcea3          50 ASDNA----LEN-VDGVANL-PRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNSL  102 (124)
T ss_dssp             CCSSC----CCC-CGGGTTC-SSCCEEECCSSCCCSSSTTGGGGGCTTCCEEECTTSGG
T ss_pred             ccccc----ccc-cCccccc-cccCeEECCCCccCCCCCchhhcCCCCCCEEECCCCcC
Confidence            76521    000 3345566 77777777777666543 35566777777777775554

>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=99.15  E-value=4.2e-10  Score=102.52  Aligned_cols=31  Identities=23%  Similarity=0.224  Sum_probs=18.9

Q ss_pred             ccccceeeeccccccccchHhhcCCCCCCEEEeeC
Q 041097          330 MPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWW  364 (391)
Q Consensus       330 ~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~  364 (391)
                      +++|++|++++| +++.+|.+   +++|++|++++
T Consensus       283 ~~~L~~L~Ls~N-~l~~lp~~---~~~L~~L~L~~  313 (353)
T d1jl5a_         283 PPSLEELNVSNN-KLIELPAL---PPRLERLIASF  313 (353)
T ss_dssp             CTTCCEEECCSS-CCSCCCCC---CTTCCEEECCS
T ss_pred             CCCCCEEECCCC-ccCccccc---cCCCCEEECCC
Confidence            457777777766 46666643   34555555544

>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=99.04  E-value=7.3e-10  Score=100.92  Aligned_cols=53  Identities=26%  Similarity=0.301  Sum_probs=32.6

Q ss_pred             CCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEEeeCCc
Q 041097          306 LSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       306 l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~l~~~~  366 (391)
                      +++|++|+++.|....  .+  ..+++|+.|++++| +++.+|.   .+++|++|++++|+
T Consensus       283 ~~~L~~L~Ls~N~l~~--lp--~~~~~L~~L~L~~N-~L~~l~~---~~~~L~~L~L~~N~  335 (353)
T d1jl5a_         283 PPSLEELNVSNNKLIE--LP--ALPPRLERLIASFN-HLAEVPE---LPQNLKQLHVEYNP  335 (353)
T ss_dssp             CTTCCEEECCSSCCSC--CC--CCCTTCCEEECCSS-CCSCCCC---CCTTCCEEECCSSC
T ss_pred             CCCCCEEECCCCccCc--cc--cccCCCCEEECCCC-cCCcccc---ccCCCCEEECcCCc
Confidence            4677777777544321  11  24667777777765 4667764   24567777777765

>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=99.03  E-value=3.5e-10  Score=100.71  Aligned_cols=59  Identities=17%  Similarity=-0.020  Sum_probs=41.3

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-cCCcccCCCCcccEEEccCC
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-RYPSGIENLFLLRYLKLNIP  212 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-~~p~~i~~l~~L~~L~l~~~  212 (391)
                      .+++.+.+.++..   ....+...+..+++|+.|+++++.+. ..+..++++++|++|+++++
T Consensus        46 ~~L~~LdLs~~~i---~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c  105 (284)
T d2astb2          46 FRVQHMDLSNSVI---EVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC  105 (284)
T ss_dssp             BCCCEEECTTCEE---CHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTC
T ss_pred             CCCCEEECCCCcc---CHHHHHHHHHhCCCcccccccccCCCcHHHHHHhcCCCCcCcccccc
Confidence            5666665543322   23345566788889999999988876 55667788888999988875

>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=99.00  E-value=1.5e-09  Score=90.53  Aligned_cols=126  Identities=20%  Similarity=0.140  Sum_probs=72.6

Q ss_pred             cEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEE
Q 041097          182 RVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLK  261 (391)
Q Consensus       182 ~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~  261 (391)
                      ++++.+++.+..+|..+.  .++++|+|++|.+...+.                            +..++.+++|++|+
T Consensus        11 ~~v~Cs~~~L~~iP~~lp--~~l~~L~Ls~N~i~~~~~----------------------------~~~f~~l~~L~~L~   60 (192)
T d1w8aa_          11 TTVDCTGRGLKEIPRDIP--LHTTELLLNDNELGRISS----------------------------DGLFGRLPHLVKLE   60 (192)
T ss_dssp             TEEECTTSCCSSCCSCCC--TTCSEEECCSCCCCSBCC----------------------------SCSGGGCTTCCEEE
T ss_pred             CEEEEeCCCcCccCCCCC--CCCCEEEeCCCCCccccc----------------------------ccccCCCceEeeee
Confidence            467777777777777664  467777777776654211                            23355667777777


Q ss_pred             ecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeecc
Q 041097          262 LANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINP  340 (391)
Q Consensus       262 l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~  340 (391)
                      +++..    +..+.+ .+..+ ++|+.|+|++|.+...+...+.++++|+.|+|+.|.......-....+++|++|++++
T Consensus        61 L~~N~----i~~~~~~~~~~~-~~L~~L~Ls~N~l~~l~~~~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~  135 (192)
T d1w8aa_          61 LKRNQ----LTGIEPNAFEGA-SHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLAS  135 (192)
T ss_dssp             CCSSC----CCCBCTTTTTTC-TTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTT
T ss_pred             ccccc----cccccccccccc-cccceeeeccccccccCHHHHhCCCcccccccCCccccccCHHHhcCCcccccccccc
Confidence            76511    000012 44556 6777777777776665555666677777777765544332111123556666666665


Q ss_pred             cc
Q 041097          341 YA  342 (391)
Q Consensus       341 c~  342 (391)
                      ++
T Consensus       136 N~  137 (192)
T d1w8aa_         136 NP  137 (192)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=98.92  E-value=7.1e-09  Score=89.45  Aligned_cols=74  Identities=12%  Similarity=0.090  Sum_probs=52.4

Q ss_pred             CcccEEEcCCCccccCCc-ccCCCCcccEEEccCCCCCc-cCCCCc-------EEEeeC-CccCcceeeEEecccccchh
Q 041097          179 KFLRVLDLGSLVLIRYPS-GIENLFLLRYLKLNIPSLKS-LPSSRK-------ILRLSG-NSQFHFSLASLLLYYQSLLS  248 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~~p~-~i~~l~~L~~L~l~~~~i~~-lp~~~~-------~L~l~~-~~l~~L~L~~L~l~~~~~lp  248 (391)
                      ..++.|+++++.+..+|. .+.++.+|++|+++++.+.. +|....       .+++.. +.+.            ...+
T Consensus        29 ~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~------------~~~~   96 (242)
T d1xwdc1          29 RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLL------------YINP   96 (242)
T ss_dssp             SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCC------------EECT
T ss_pred             CCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeecccccccccccccccccccccc------------cccc
Confidence            478999999999998876 57899999999999988765 443221       454443 3333            1234


Q ss_pred             HHhcCCCCCCEEEecC
Q 041097          249 KSLCRLSCLESLKLAN  264 (391)
Q Consensus       249 ~~i~~l~~L~~L~l~~  264 (391)
                      ..+..+++|+++.+.+
T Consensus        97 ~~~~~l~~L~~l~l~~  112 (242)
T d1xwdc1          97 EAFQNLPNLQYLLISN  112 (242)
T ss_dssp             TSEECCTTCCEEEEES
T ss_pred             ccccccccccccccch
Confidence            5567888888888877

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.88  E-value=3.3e-09  Score=81.79  Aligned_cols=101  Identities=23%  Similarity=0.230  Sum_probs=62.4

Q ss_pred             hcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc-CCC
Q 041097          251 LCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM-GIR  328 (391)
Q Consensus       251 i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~-~~~  328 (391)
                      ++.+++|++|++++..    +.. +| .++.+ ++|+.|++++|.+...  +.++.+++|+.|+++.|.......+ ..+
T Consensus        16 l~~l~~L~~L~ls~N~----l~~-lp~~~~~l-~~L~~L~l~~N~i~~l--~~~~~l~~L~~L~l~~N~i~~~~~~~~l~   87 (124)
T d1dcea3          16 LEQLLLVTHLDLSHNR----LRA-LPPALAAL-RCLEVLQASDNALENV--DGVANLPRLQELLLCNNRLQQSAAIQPLV   87 (124)
T ss_dssp             GGGGTTCCEEECCSSC----CCC-CCGGGGGC-TTCCEEECCSSCCCCC--GGGTTCSSCCEEECCSSCCCSSSTTGGGG
T ss_pred             cccCCCCCEEECCCCc----cCc-chhhhhhh-hccccccccccccccc--CccccccccCeEECCCCccCCCCCchhhc
Confidence            6677788888887622    000 55 56677 8888888888877653  4577888888888876655432222 235


Q ss_pred             cccccceeeecccccccc---chHh-hcCCCCCCEE
Q 041097          329 AMPKLECLIINPYAHLKR---IHEQ-LWCLKSLNKL  360 (391)
Q Consensus       329 ~~~~L~~L~l~~c~~l~~---lp~~-~~~l~~L~~L  360 (391)
                      .+++|+.|++++++ +..   .+.. ...+|+|+.|
T Consensus        88 ~~~~L~~L~l~~N~-i~~~~~~~~~l~~~lp~L~~L  122 (124)
T d1dcea3          88 SCPRLVLLNLQGNS-LCQEEGIQERLAEMLPSVSSI  122 (124)
T ss_dssp             GCTTCCEEECTTSG-GGGSSSCTTHHHHHCTTCSEE
T ss_pred             CCCCCCEEECCCCc-CCcCccHHHHHHHHCcCcceE
Confidence            67778888877653 332   2222 2446666654

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=3.5e-09  Score=85.72  Aligned_cols=127  Identities=20%  Similarity=0.187  Sum_probs=76.7

Q ss_pred             hccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCC
Q 041097          175 CKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRL  254 (391)
Q Consensus       175 ~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l  254 (391)
                      +.....+|.|++++|++..++..+..+.+|++|++++|.+++++.                               +..+
T Consensus        14 ~~n~~~lr~L~L~~n~I~~i~~~~~~l~~L~~L~Ls~N~i~~l~~-------------------------------~~~l   62 (162)
T d1a9na_          14 YTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDG-------------------------------FPLL   62 (162)
T ss_dssp             EECTTSCEEEECTTSCCCSCCCGGGGTTCCSEEECCSSCCCEECC-------------------------------CCCC
T ss_pred             ccCcCcCcEEECCCCCCCccCccccccccCCEEECCCCCCCccCC-------------------------------cccC
Confidence            456668899999999999888766788999999999998876641                               3445


Q ss_pred             CCCCEEEecCCCCCCchhhhcc-c-cccCCCCccEEEeecccCCCCC-hhhhcCCCCCCEEEcCCCCCcCccc---cCCC
Q 041097          255 SCLESLKLANESKMPRRSNIIL-A-EYQFPPSLTHLSFSNIELMDDP-IPALEKLSVLQVLKLKQNLYSEERT---MGIR  328 (391)
Q Consensus       255 ~~L~~L~l~~~~~lp~L~~Llp-~-~~~l~~~L~~L~l~~~~~~~~~-~~~l~~l~~L~~L~l~~~~~~~~~~---~~~~  328 (391)
                      ++|++|++++..    +.. +| . ...+ ++|+.|++++|.+...+ +..+..+++|++|++++|.......   .-..
T Consensus        63 ~~L~~L~ls~N~----i~~-l~~~~~~~l-~~L~~L~L~~N~i~~~~~l~~l~~l~~L~~L~l~~N~i~~~~~~r~~~i~  136 (162)
T d1a9na_          63 RRLKTLLVNNNR----ICR-IGEGLDQAL-PDLTELILTNNSLVELGDLDPLASLKSLTYLCILRNPVTNKKHYRLYVIY  136 (162)
T ss_dssp             SSCCEEECCSSC----CCE-ECSCHHHHC-TTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECCSSGGGGSTTHHHHHHH
T ss_pred             cchhhhhccccc----ccC-CCccccccc-cccccceeccccccccccccccccccccchhhcCCCccccccchHHHHHH
Confidence            556666665511    000 22 1 2345 66666666666655432 2445666666666666544322110   0113


Q ss_pred             cccccceeee
Q 041097          329 AMPKLECLII  338 (391)
Q Consensus       329 ~~~~L~~L~l  338 (391)
                      .+|+|+.|+-
T Consensus       137 ~lp~L~~LD~  146 (162)
T d1a9na_         137 KVPQVRVLDF  146 (162)
T ss_dssp             HCTTCSEETT
T ss_pred             HCCCcCeeCC
Confidence            4566666653

>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=98.78  E-value=2e-09  Score=95.62  Aligned_cols=178  Identities=16%  Similarity=0.119  Sum_probs=113.4

Q ss_pred             cCCcccEEEcCCCccc--cCCcccCCCCcccEEEccCCCCCc-cCCCCcEEEeeCCccCcceeeEEecccc-----cchh
Q 041097          177 MFKFLRVLDLGSLVLI--RYPSGIENLFLLRYLKLNIPSLKS-LPSSRKILRLSGNSQFHFSLASLLLYYQ-----SLLS  248 (391)
Q Consensus       177 ~~~~L~~L~l~~~~l~--~~p~~i~~l~~L~~L~l~~~~i~~-lp~~~~~L~l~~~~l~~L~L~~L~l~~~-----~~lp  248 (391)
                      ....|+.|+++++.+.  .+...+.++.+|++|+++++.+.. .+..+.       +..  +|++|+++..     ..+.
T Consensus        44 ~~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l~-------~~~--~L~~L~Ls~c~~itd~~l~  114 (284)
T d2astb2          44 SPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLA-------KNS--NLVRLNLSGCSGFSEFALQ  114 (284)
T ss_dssp             CCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHT-------TCT--TCSEEECTTCBSCCHHHHH
T ss_pred             cCCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCCCcHHHHHHh-------cCC--CCcCccccccccccccccc
Confidence            3457889999998875  344556788999999999887541 111111       001  3444444411     1233


Q ss_pred             HHhcCCCCCCEEEecCCCCCCchhhhcc-ccccCCCCccEEEeeccc--CCCCChh-hhcCCCCCCEEEcCCCCCcC-cc
Q 041097          249 KSLCRLSCLESLKLANESKMPRRSNIIL-AEYQFPPSLTHLSFSNIE--LMDDPIP-ALEKLSVLQVLKLKQNLYSE-ER  323 (391)
Q Consensus       249 ~~i~~l~~L~~L~l~~~~~lp~L~~Llp-~~~~l~~~L~~L~l~~~~--~~~~~~~-~l~~l~~L~~L~l~~~~~~~-~~  323 (391)
                      .-...+++|++|++++...+.. .. ++ .+...+++|+.|++.+|.  +....+. ....+|+|+.|++++|.... ..
T Consensus       115 ~l~~~~~~L~~L~ls~c~~~~~-~~-~~~~~~~~~~~L~~L~l~~~~~~i~~~~l~~l~~~~~~L~~L~L~~~~~itd~~  192 (284)
T d2astb2         115 TLLSSCSRLDELNLSWCFDFTE-KH-VQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDC  192 (284)
T ss_dssp             HHHHHCTTCCEEECCCCTTCCH-HH-HHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGG
T ss_pred             hhhHHHHhcccccccccccccc-cc-chhhhcccccccchhhhcccccccccccccccccccccccccccccccCCCchh
Confidence            4456789999999987210000 00 12 223333799999999863  3332233 34678999999998554333 33


Q ss_pred             ccCCCcccccceeeecccccccc-chHhhcCCCCCCEEEeeCC
Q 041097          324 TMGIRAMPKLECLIINPYAHLKR-IHEQLWCLKSLNKLELWWP  365 (391)
Q Consensus       324 ~~~~~~~~~L~~L~l~~c~~l~~-lp~~~~~l~~L~~L~l~~~  365 (391)
                      +.....+++|++|++++|..+.. -...++++++|++|++++|
T Consensus       193 ~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~  235 (284)
T d2astb2         193 FQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI  235 (284)
T ss_dssp             GGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             hhhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeeeCC
Confidence            33346789999999999987753 3345788999999999987

>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=98.69  E-value=2e-10  Score=96.61  Aligned_cols=48  Identities=17%  Similarity=0.195  Sum_probs=39.8

Q ss_pred             hHHhhccCCcccEEEcCCCccccCCcccCCCCcccEEEccCCCCCccCC
Q 041097          171 CEKICKMFKFLRVLDLGSLVLIRYPSGIENLFLLRYLKLNIPSLKSLPS  219 (391)
Q Consensus       171 ~~~~~~~~~~L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~~i~~lp~  219 (391)
                      ++..+..+.+|+.|++++|.+..++ .+..+.+|++|++++|.++.+|.
T Consensus        40 l~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~   87 (198)
T d1m9la_          40 MDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIEN   87 (198)
T ss_dssp             CHHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEEEECSCSS
T ss_pred             hhhHHhcccccceeECcccCCCCcc-cccCCccccChhhcccccccccc
Confidence            4467888899999999999988775 58888999999999988877763

>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=98.68  E-value=2.6e-08  Score=82.77  Aligned_cols=107  Identities=20%  Similarity=0.145  Sum_probs=78.9

Q ss_pred             CcccEEEcCCCcccc-C-CcccCCCCcccEEEccCCCCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCC
Q 041097          179 KFLRVLDLGSLVLIR-Y-PSGIENLFLLRYLKLNIPSLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSC  256 (391)
Q Consensus       179 ~~L~~L~l~~~~l~~-~-p~~i~~l~~L~~L~l~~~~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~  256 (391)
                      ..++.|++++|.|.. . +..++.+.+|+.|+++++.+..+|                             +..+..+++
T Consensus        29 ~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~-----------------------------~~~~~~~~~   79 (192)
T d1w8aa_          29 LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIE-----------------------------PNAFEGASH   79 (192)
T ss_dssp             TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBC-----------------------------TTTTTTCTT
T ss_pred             CCCCEEEeCCCCCcccccccccCCCceEeeeecccccccccc-----------------------------ccccccccc
Confidence            578899999999963 4 356688999999999999887755                             344566777


Q ss_pred             CCEEEecCCCCCCchhhhcc--ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCc
Q 041097          257 LESLKLANESKMPRRSNIIL--AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYS  320 (391)
Q Consensus       257 L~~L~l~~~~~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~  320 (391)
                      |++|++++..    +.. +|  .+..+ ++|+.|+|++|.+...+...+..+++|++|+++.|.+.
T Consensus        80 L~~L~Ls~N~----l~~-l~~~~F~~l-~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~~~  139 (192)
T d1w8aa_          80 IQELQLGENK----IKE-ISNKMFLGL-HQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             CCEEECCSCC----CCE-ECSSSSTTC-TTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cceeeecccc----ccc-cCHHHHhCC-CcccccccCCccccccCHHHhcCCcccccccccccccc
Confidence            7777777621    111 33  56678 88888888888887777677788888888888866554

>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=98.65  E-value=3.4e-08  Score=85.06  Aligned_cols=188  Identities=14%  Similarity=0.064  Sum_probs=100.9

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCcccc-C-CcccCCCCcccEEEccC-CCCCccCCCCc-----
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLIR-Y-PSGIENLFLLRYLKLNI-PSLKSLPSSRK-----  222 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~~-~-p~~i~~l~~L~~L~l~~-~~i~~lp~~~~-----  222 (391)
                      ..+++|.+.+....    ......|.++++|++|+++++.+.. + +..+..+..++++.+.. +.+..++....     
T Consensus        29 ~~l~~L~Ls~n~i~----~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~l~~  104 (242)
T d1xwdc1          29 RNAIELRFVLTKLR----VIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPN  104 (242)
T ss_dssp             SCCSEEEEESCCCC----EECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCCEECTTSEECCTT
T ss_pred             CCCCEEECcCCcCC----ccChhHhhccchhhhhhhccccccceeecccccccccccccccccccccccccccccccccc
Confidence            57888888766543    1222467889999999999998763 3 34678899999998765 46666554432     


Q ss_pred             --EEEeeCCccCcceeeEEecccccchhHHhcCCCCCCEEEecC-CC-CCCchhhhcc--ccccCCCCccEEEeecccCC
Q 041097          223 --ILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLESLKLAN-ES-KMPRRSNIIL--AEYQFPPSLTHLSFSNIELM  296 (391)
Q Consensus       223 --~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~L~l~~-~~-~lp~L~~Llp--~~~~l~~~L~~L~l~~~~~~  296 (391)
                        .++++++.+.             ..+. ...+.+++.+.... .+ .+..    ++  .+..++..++.|.+.++.+.
T Consensus       105 L~~l~l~~~~l~-------------~~~~-~~~~~~l~~l~~~~~~n~~l~~----i~~~~~~~~~~~l~~L~l~~n~l~  166 (242)
T d1xwdc1         105 LQYLLISNTGIK-------------HLPD-VHKIHSLQKVLLDIQDNINIHT----IERNSFVGLSFESVILWLNKNGIQ  166 (242)
T ss_dssp             CCEEEEESCCCC-------------SCCC-CTTTCBSSCEEEEEESCTTCCE----ECTTSSTTSBSSCEEEECCSSCCC
T ss_pred             ccccccchhhhc-------------cccc-cccccccccccccccccccccc----ccccccccccccceeeeccccccc
Confidence              6777776655             3222 23333344333222 10 1000    11  22233246667777666655


Q ss_pred             CCChhhhcCCCCCCEEEcCCCCCcCccccC-CCcccccceeeeccccccccchHh-hcCCCCCCEEEe
Q 041097          297 DDPIPALEKLSVLQVLKLKQNLYSEERTMG-IRAMPKLECLIINPYAHLKRIHEQ-LWCLKSLNKLEL  362 (391)
Q Consensus       297 ~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~-~~~~~~L~~L~l~~c~~l~~lp~~-~~~l~~L~~L~l  362 (391)
                      ..+. .....+++..+....+......... ...+++|++|+++++. ++.+|.+ +.++++|+.+++
T Consensus       167 ~i~~-~~~~~~~l~~~~~l~~n~l~~l~~~~f~~l~~L~~L~Ls~N~-l~~l~~~~~~~l~~L~~l~~  232 (242)
T d1xwdc1         167 EIHN-CAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPSYGLENLKKLRARST  232 (242)
T ss_dssp             EECT-TTTTTCCEEEEECTTCTTCCCCCTTTTTTSCCCSEEECTTSC-CCCCCSSSCTTCCEEESSSE
T ss_pred             cccc-ccccchhhhccccccccccccccHHHhcCCCCCCEEECCCCc-CCccCHHHHcCCcccccCcC
Confidence            4332 2234455554443322221111111 2456677777777663 6666643 344444444433

>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=98.61  E-value=2.4e-09  Score=89.78  Aligned_cols=111  Identities=18%  Similarity=0.158  Sum_probs=73.8

Q ss_pred             chhHHhcCCCCCCEEEecCCCCCCchhhhccccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCCcCcccc
Q 041097          246 LLSKSLCRLSCLESLKLANESKMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLYSEERTM  325 (391)
Q Consensus       246 ~lp~~i~~l~~L~~L~l~~~~~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~  325 (391)
                      .+|.+++.|++|++|++++..    +.. ++.+..+ ++|+.|++++|.+...+ .....+++|+.|+++.|....  +.
T Consensus        39 ~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_          39 KMDATLSTLKACKHLALSTNN----IEK-ISSLSGM-ENLRILSLGRNLIKKIE-NLDAVADTLEELWISYNQIAS--LS  109 (198)
T ss_dssp             CCHHHHHHTTTCCEEECSEEE----ESC-CCCHHHH-TTCCEEECCEEEECSCS-SHHHHHHHCCEEECSEEECCC--HH
T ss_pred             hhhhHHhcccccceeECcccC----CCC-cccccCC-ccccChhhccccccccc-ccccccccccccccccccccc--cc
Confidence            667788888888888887621    000 3345567 78888888888776543 233345678888887554432  22


Q ss_pred             CCCcccccceeeeccccccccch--HhhcCCCCCCEEEeeCCc
Q 041097          326 GIRAMPKLECLIINPYAHLKRIH--EQLWCLKSLNKLELWWPE  366 (391)
Q Consensus       326 ~~~~~~~L~~L~l~~c~~l~~lp--~~~~~l~~L~~L~l~~~~  366 (391)
                      ....+++|+.|++++| +++.++  ..+..+++|++|+++++|
T Consensus       110 ~~~~l~~L~~L~L~~N-~i~~~~~~~~l~~l~~L~~L~L~~N~  151 (198)
T d1m9la_         110 GIEKLVNLRVLYMSNN-KITNWGEIDKLAALDKLEDLLLAGNP  151 (198)
T ss_dssp             HHHHHHHSSEEEESEE-ECCCHHHHHHHTTTTTCSEEEECSSH
T ss_pred             cccccccccccccccc-hhccccccccccCCCccceeecCCCc
Confidence            2346778888888876 466665  357788888888888876

>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=98.44  E-value=1.4e-07  Score=85.55  Aligned_cols=214  Identities=14%  Similarity=0.062  Sum_probs=128.5

Q ss_pred             CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-----------cCCcccCCCCcccEEEccCCCCCc---
Q 041097          151 SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-----------RYPSGIENLFLLRYLKLNIPSLKS---  216 (391)
Q Consensus       151 ~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-----------~~p~~i~~l~~L~~L~l~~~~i~~---  216 (391)
                      ..++.|.+.++.........+...+...+.|+.++++++...           .+...+....+|+.|+++++.+..   
T Consensus        31 ~~l~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~  110 (344)
T d2ca6a1          31 DSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQ  110 (344)
T ss_dssp             SCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSCCCCTTTH
T ss_pred             CCCCEEECcCCcCCHHHHHHHHHHHHhCCCCCEEECCCCcccccccccchHHHHHHHHHhhCCCcccccccccccccccc
Confidence            556666654432210001134455677788888888766532           122345567788888888876653   


Q ss_pred             --cC------CCCcEEEeeCCccCcc----------------------eeeEEecc-------cccchhHHhcCCCCCCE
Q 041097          217 --LP------SSRKILRLSGNSQFHF----------------------SLASLLLY-------YQSLLSKSLCRLSCLES  259 (391)
Q Consensus       217 --lp------~~~~~L~l~~~~l~~L----------------------~L~~L~l~-------~~~~lp~~i~~l~~L~~  259 (391)
                        +.      ..+..|++++|.+..-                      .|+.|.+.       ....+...+...++|+.
T Consensus       111 ~~l~~~l~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l~l~~n~i~~~~~~~l~~~l~~~~~L~~  190 (344)
T d2ca6a1         111 EPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHT  190 (344)
T ss_dssp             HHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCE
T ss_pred             cchhhhhcccccchheecccccccccccccccccccccccccccccCcccceeecccccccccccccccchhhhhhhhcc
Confidence              11      1222788887765321                      56777766       22345566777888888


Q ss_pred             EEecCCC-CCCchhhhcc-ccccCCCCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCCCcCcc------ccCC
Q 041097          260 LKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNLYSEER------TMGI  327 (391)
Q Consensus       260 L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~------~~~~  327 (391)
                      |++.... .-.....++. .+... ++|+.|++++|.+....    ...+..+++|+.|+++.|......      .+..
T Consensus       191 L~L~~n~i~~~g~~~~l~~~l~~~-~~L~~L~Ls~N~i~~~g~~~L~~~l~~~~~L~~L~Ls~n~i~~~g~~~l~~~l~~  269 (344)
T d2ca6a1         191 VKMVQNGIRPEGIEHLLLEGLAYC-QELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSK  269 (344)
T ss_dssp             EECCSSCCCHHHHHHHHHTTGGGC-TTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHT
T ss_pred             cccccccccccccccchhhhhcch-hhhcccccccccccccccccccccccccccchhhhhhcCccCchhhHHHHHHhhh
Confidence            8887621 0000011122 45567 88999999888764322    345678899999999866543321      1112


Q ss_pred             Ccccccceeeeccccccc-----cchHhhc-CCCCCCEEEeeCCc
Q 041097          328 RAMPKLECLIINPYAHLK-----RIHEQLW-CLKSLNKLELWWPE  366 (391)
Q Consensus       328 ~~~~~L~~L~l~~c~~l~-----~lp~~~~-~l~~L~~L~l~~~~  366 (391)
                      ...+.|++|++++|. +.     .+...+. ++++|++|+++++.
T Consensus       270 ~~~~~L~~L~ls~N~-i~~~~~~~l~~~l~~~~~~L~~L~l~~N~  313 (344)
T d2ca6a1         270 LENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGNR  313 (344)
T ss_dssp             CSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             ccCCCCCEEECCCCc-CChHHHHHHHHHHHccCCCCCEEECCCCc
Confidence            345689999999874 43     3455553 67899999998754

>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=98.41  E-value=4.3e-08  Score=91.95  Aligned_cols=104  Identities=16%  Similarity=0.043  Sum_probs=64.5

Q ss_pred             ceEEEEEeccCCCcc-cccCCC--CCccEEEEEecCCcCCCchhhHHhhccCCcccEEEcCCCccc-----cCCcccC-C
Q 041097          130 NVKRFTAHRKLNDFA-FLDDFD--SFLHSLLYLTSGSQYLDPTYCEKICKMFKFLRVLDLGSLVLI-----RYPSGIE-N  200 (391)
Q Consensus       130 ~~r~l~~~~~~~~~~-~~~~~~--~~lrsl~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~l~-----~~p~~i~-~  200 (391)
                      +++.|.+.+...... +.....  ++++++.+.++...+.....+...+..++.|+.|++++|.+.     .+.+.+. .
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~~   82 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTP   82 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCST
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHHHhcC
Confidence            345566664443331 223233  788999888775431111134566788999999999999875     2233333 2


Q ss_pred             CCcccEEEccCCCCCc-----cCCC------CcEEEeeCCccCc
Q 041097          201 LFLLRYLKLNIPSLKS-----LPSS------RKILRLSGNSQFH  233 (391)
Q Consensus       201 l~~L~~L~l~~~~i~~-----lp~~------~~~L~l~~~~l~~  233 (391)
                      ..+|++|++++|.+..     ++..      +..|++++|.+..
T Consensus        83 ~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~i~~  126 (460)
T d1z7xw1          83 SCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGD  126 (460)
T ss_dssp             TCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHH
T ss_pred             CCCCCEEECCCCCccccccccccchhhccccccccccccccchh
Confidence            3479999999998753     2322      2389999887543

>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=98.27  E-value=1.8e-06  Score=68.81  Aligned_cols=103  Identities=19%  Similarity=0.064  Sum_probs=60.5

Q ss_pred             ccEEEcCCCccccCCcccCCCCcccEEEccCC-CCCccCCCCcEEEeeCCccCcceeeEEecccccchhHHhcCCCCCCE
Q 041097          181 LRVLDLGSLVLIRYPSGIENLFLLRYLKLNIP-SLKSLPSSRKILRLSGNSQFHFSLASLLLYYQSLLSKSLCRLSCLES  259 (391)
Q Consensus       181 L~~L~l~~~~l~~~p~~i~~l~~L~~L~l~~~-~i~~lp~~~~~L~l~~~~l~~L~L~~L~l~~~~~lp~~i~~l~~L~~  259 (391)
                      ...++..+..+...|..+..+.+|++|++.++ .++.++                             +..+.++++|+.
T Consensus        10 ~~~l~c~~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~-----------------------------~~~f~~l~~L~~   60 (156)
T d2ifga3          10 SSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLE-----------------------------LRDLRGLGELRN   60 (156)
T ss_dssp             SSCEECCSSCCCTTTTTSCSCSCCSEEECCSCSSCCEEC-----------------------------GGGSCSCCCCSE
T ss_pred             CCeEEecCCCCccCcccccCccccCeeecCCCccccccC-----------------------------chhhccccccCc
Confidence            34566666666667777777777777777554 355443                             234566666666


Q ss_pred             EEecCCCCCCchhhhc-c-ccccCCCCccEEEeecccCCCCChhhhcCCCCCCEEEcCCCCC
Q 041097          260 LKLANESKMPRRSNII-L-AEYQFPPSLTHLSFSNIELMDDPIPALEKLSVLQVLKLKQNLY  319 (391)
Q Consensus       260 L~l~~~~~lp~L~~Ll-p-~~~~l~~~L~~L~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~  319 (391)
                      |++++..    +.. + | .+..+ ++|++|+|++|.+...+...+.. .+|+.|++++|.+
T Consensus        61 L~Ls~N~----l~~-i~~~~f~~l-~~L~~L~Ls~N~l~~l~~~~~~~-~~l~~L~L~~Np~  115 (156)
T d2ifga3          61 LTIVKSG----LRF-VAPDAFHFT-PRLSRLNLSFNALESLSWKTVQG-LSLQELVLSGNPL  115 (156)
T ss_dssp             EECCSSC----CCE-ECTTGGGSC-SCCCEEECCSSCCSCCCSTTTCS-CCCCEEECCSSCC
T ss_pred             ceeeccc----cCC-ccccccccc-ccccceeccCCCCcccChhhhcc-ccccccccCCCcc
Confidence            6666521    011 2 2 45566 67777777777766555444433 3577777765544

>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=98.25  E-value=8.1e-07  Score=70.83  Aligned_cols=83  Identities=20%  Similarity=0.099  Sum_probs=37.2

Q ss_pred             CCccEEEeecc-cCCCCChhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccchHhhcCCCCCCEEE
Q 041097          283 PSLTHLSFSNI-ELMDDPIPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIHEQLWCLKSLNKLE  361 (391)
Q Consensus       283 ~~L~~L~l~~~-~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp~~~~~l~~L~~L~  361 (391)
                      ++|+.|++.++ .+...+...+..+++|+.|+++.|.......-....+++|++|+|+++ +++.+|.......+|++|+
T Consensus        31 ~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N-~l~~l~~~~~~~~~l~~L~  109 (156)
T d2ifga3          31 ENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFN-ALESLSWKTVQGLSLQELV  109 (156)
T ss_dssp             SCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSS-CCSCCCSTTTCSCCCCEEE
T ss_pred             cccCeeecCCCccccccCchhhccccccCcceeeccccCCcccccccccccccceeccCC-CCcccChhhhccccccccc
Confidence            44555555432 244333444555555555555533322211111134445555555544 3555554433333455666


Q ss_pred             eeCCc
Q 041097          362 LWWPE  366 (391)
Q Consensus       362 l~~~~  366 (391)
                      |++.|
T Consensus       110 L~~Np  114 (156)
T d2ifga3         110 LSGNP  114 (156)
T ss_dssp             CCSSC
T ss_pred             cCCCc
Confidence            65443

>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=97.89  E-value=3.9e-06  Score=75.75  Aligned_cols=168  Identities=19%  Similarity=0.122  Sum_probs=94.4

Q ss_pred             HhhccCCcccEEEcCCCcccc-----CCcccCCCCcccEEEccCCCCCc--------------------cCCCCcEEEee
Q 041097          173 KICKMFKFLRVLDLGSLVLIR-----YPSGIENLFLLRYLKLNIPSLKS--------------------LPSSRKILRLS  227 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~~-----~p~~i~~l~~L~~L~l~~~~i~~--------------------lp~~~~~L~l~  227 (391)
                      ..+...+.|+.|++++|.+..     +...+....+|+.|+++++.+..                    -...+..++++
T Consensus        87 ~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l~l~  166 (344)
T d2ca6a1          87 QALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICG  166 (344)
T ss_dssp             HHHTTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECC
T ss_pred             HHHhhCCCcccccccccccccccccchhhhhcccccchheecccccccccccccccccccccccccccccCcccceeecc
Confidence            334455566666666655431     22233344556666666554321                    01122255555


Q ss_pred             CCccCcc-------------eeeEEeccc--c------cchhHHhcCCCCCCEEEecCCC-CCCchhhhcc-ccccCCCC
Q 041097          228 GNSQFHF-------------SLASLLLYY--Q------SLLSKSLCRLSCLESLKLANES-KMPRRSNIIL-AEYQFPPS  284 (391)
Q Consensus       228 ~~~l~~L-------------~L~~L~l~~--~------~~lp~~i~~l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~  284 (391)
                      .+.+..-             .|+.|+++.  .      ..+...+..+++|++|++++.. .-..... +. .+... ++
T Consensus       167 ~n~i~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~~g~~~-L~~~l~~~-~~  244 (344)
T d2ca6a1         167 RNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSA-LAIALKSW-PN  244 (344)
T ss_dssp             SSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHH-HHHHGGGC-TT
T ss_pred             cccccccccccccchhhhhhhhcccccccccccccccccchhhhhcchhhhccccccccccccccccc-cccccccc-cc
Confidence            5544321             566776661  1      1134457789999999998721 0000010 22 55677 89


Q ss_pred             ccEEEeecccCCCCChh----hhcC--CCCCCEEEcCCCCCcCccc--cCC---Ccccccceeeecccc
Q 041097          285 LTHLSFSNIELMDDPIP----ALEK--LSVLQVLKLKQNLYSEERT--MGI---RAMPKLECLIINPYA  342 (391)
Q Consensus       285 L~~L~l~~~~~~~~~~~----~l~~--l~~L~~L~l~~~~~~~~~~--~~~---~~~~~L~~L~l~~c~  342 (391)
                      |+.|++++|.+......    .+..  .+.|+.|++++|....+..  +..   ...++|++|+++++.
T Consensus       245 L~~L~Ls~n~i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~i~~~~~~~l~~~l~~~~~~L~~L~l~~N~  313 (344)
T d2ca6a1         245 LRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNR  313 (344)
T ss_dssp             CCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             chhhhhhcCccCchhhHHHHHHhhhccCCCCCEEECCCCcCChHHHHHHHHHHHccCCCCCEEECCCCc
Confidence            99999999988764333    3333  3679999999776443221  111   246789999999764

>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=97.18  E-value=5.9e-05  Score=69.78  Aligned_cols=183  Identities=27%  Similarity=0.117  Sum_probs=94.8

Q ss_pred             HhhccCCcccEEEcCCCccc------cCCcccCCCCcccEEEccCCCCCccC-----------CCCcEEEeeCCccCcce
Q 041097          173 KICKMFKFLRVLDLGSLVLI------RYPSGIENLFLLRYLKLNIPSLKSLP-----------SSRKILRLSGNSQFHFS  235 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~~l~------~~p~~i~~l~~L~~L~l~~~~i~~lp-----------~~~~~L~l~~~~l~~L~  235 (391)
                      ..+.....++.+++.++.+.      ...........++.++++++.+...+           ..+..+++++|.+... 
T Consensus       220 ~~l~~~~~~~~l~~~~n~~~~~~~~~~~~~~~~~~~~l~~l~l~~n~i~~~~~~~~~~~l~~~~~l~~l~l~~n~i~~~-  298 (460)
T d1z7xw1         220 GIVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDE-  298 (460)
T ss_dssp             HHHHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHH-
T ss_pred             ccccccccccccchhhccccccccchhhccccccccccccccccccccccccccccccccccccccccccccccccccc-
Confidence            44556677777777776643      12233344567777777777654211           1111555555544310 


Q ss_pred             eeEEecccccchhHHhc-CCCCCCEEEecCCC-CCCchhhhcc-ccccCCCCccEEEeecccCCCCCh----hhhc-CCC
Q 041097          236 LASLLLYYQSLLSKSLC-RLSCLESLKLANES-KMPRRSNIIL-AEYQFPPSLTHLSFSNIELMDDPI----PALE-KLS  307 (391)
Q Consensus       236 L~~L~l~~~~~lp~~i~-~l~~L~~L~l~~~~-~lp~L~~Llp-~~~~l~~~L~~L~l~~~~~~~~~~----~~l~-~l~  307 (391)
                             ....+...+. ....|+.+++.+.. .-..... +. .+... ++|+.|+|++|.+.....    ..+. ..+
T Consensus       299 -------~~~~l~~~l~~~~~~L~~l~l~~~~l~~~~~~~-l~~~~~~~-~~L~~L~Ls~N~i~~~g~~~l~~~l~~~~~  369 (460)
T d1z7xw1         299 -------GARLLCETLLEPGCQLESLWVKSCSFTAACCSH-FSSVLAQN-RFLLELQISNNRLEDAGVRELCQGLGQPGS  369 (460)
T ss_dssp             -------HHHHHHHHHTSTTCCCCEEECTTSCCBGGGHHH-HHHHHHHC-SSCCEEECCSSBCHHHHHHHHHHHHTSTTC
T ss_pred             -------ccchhhccccccccccccccccccchhhhhhhh-cccccccc-cchhhhheeeecccCcccchhhhhhhcccC
Confidence                   0012222222 34567777776611 0000000 11 22344 678888888877654322    2232 346


Q ss_pred             CCCEEEcCCCCCcCccc--cCC--Ccccccceeeeccccccc-----cchHhhc-CCCCCCEEEeeCCc
Q 041097          308 VLQVLKLKQNLYSEERT--MGI--RAMPKLECLIINPYAHLK-----RIHEQLW-CLKSLNKLELWWPE  366 (391)
Q Consensus       308 ~L~~L~l~~~~~~~~~~--~~~--~~~~~L~~L~l~~c~~l~-----~lp~~~~-~l~~L~~L~l~~~~  366 (391)
                      .|++|++++|.......  +..  ...++|++|+|+++. +.     .+.+.+. +.+.|++|++.++.
T Consensus       370 ~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~N~-i~~~g~~~l~~~l~~~~~~L~~l~l~~~~  437 (460)
T d1z7xw1         370 VLRVLWLADCDVSDSSCSSLAATLLANHSLRELDLSNNC-LGDAGILQLVESVRQPGCLLEQLVLYDIY  437 (460)
T ss_dssp             CCCEEECTTSCCCHHHHHHHHHHHHHCCCCCEEECCSSS-CCHHHHHHHHHHHTSTTCCCCEEECTTCC
T ss_pred             CCCEEECCCCCCChHHHHHHHHHHhcCCCCCEEECCCCc-CCHHHHHHHHHHHHhCCCccCEEECCCCC
Confidence            78888888665443211  111  235778888888763 43     2333443 34578888887755

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.01  E-value=8.2e-05  Score=59.95  Aligned_cols=20  Identities=15%  Similarity=0.215  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||||+++.+
T Consensus        10 I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2          10 VAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             EEEECCTTSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999776

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=96.90  E-value=0.00013  Score=57.42  Aligned_cols=20  Identities=10%  Similarity=0.285  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-+.|+.|+||||+||.+.+
T Consensus         5 I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           5 IFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45889999999999999876

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.84  E-value=0.00018  Score=57.21  Aligned_cols=20  Identities=25%  Similarity=0.336  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         7 I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           7 ILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.84  E-value=0.00015  Score=57.64  Aligned_cols=20  Identities=10%  Similarity=0.107  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++||.|+||||+|+.+.+
T Consensus         4 IvliG~~G~GKSTig~~La~   23 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAK   23 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999987

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.74  E-value=0.00019  Score=56.86  Aligned_cols=20  Identities=15%  Similarity=0.263  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.+.||+|+||||+|+.+..
T Consensus         3 I~liG~~GsGKsTi~k~La~   22 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAK   22 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.73  E-value=0.00024  Score=55.22  Aligned_cols=20  Identities=20%  Similarity=0.313  Sum_probs=17.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus         5 Iii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999998754

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.70  E-value=0.00026  Score=56.11  Aligned_cols=20  Identities=10%  Similarity=0.174  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         5 I~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           5 YIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999765

>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=96.69  E-value=0.0023  Score=54.34  Aligned_cols=75  Identities=13%  Similarity=0.096  Sum_probs=41.6

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccccccc-EEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHHHcC
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFD-CHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLING   79 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~-~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~L~~k   79 (391)
                      -|+|++|+||||+|+.+.+  +++..+. ...++................... .................+...+...
T Consensus        47 ll~GppGtGKT~l~~~l~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  122 (276)
T d1fnna2          47 TLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNFTAIIGEIARSL-NIPFPRRGLSRDEFLALLVEHLRER  122 (276)
T ss_dssp             EEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSHHHHHHHHHHHT-TCCCCSSCCCHHHHHHHHHHHHHHT
T ss_pred             EEECCCCCCHHHHHHHHHH--HHhcccCCcEEEecchhhhhhhhhhhhhHHhh-hhhhhhhccchhHHHHHHHHHHhhc
Confidence            4899999999999999987  4544444 233444444455555555544432 1111111122455555555555443

>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=96.65  E-value=0.0003  Score=55.65  Aligned_cols=26  Identities=15%  Similarity=-0.004  Sum_probs=21.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF   28 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F   28 (391)
                      |+|+|..|+|||||++.+.+  +++...
T Consensus         5 i~itG~~GSGKTTL~~~L~~--~l~~~g   30 (170)
T d1np6a_           5 LAFAAWSGTGKTTLLKKLIP--ALCARG   30 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHH--HHHHTT
T ss_pred             EEEEcCCCCCHHHHHHHHHH--HHHHCC
Confidence            58999999999999999986  444443

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.62  E-value=0.00032  Score=56.13  Aligned_cols=20  Identities=20%  Similarity=0.248  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||++.+..
T Consensus         4 v~ItG~~GtGKTtl~~~i~~   23 (189)
T d2i3ba1           4 VFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             EEEESCCSSCHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            57999999999999999986

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.57  E-value=0.00036  Score=55.65  Aligned_cols=32  Identities=9%  Similarity=-0.029  Sum_probs=22.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccc-cccEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKH-YFDCHAWV   34 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~-~F~~~~~~   34 (391)
                      |-++|+.|+||||+|+.+..  .+.. .++...++
T Consensus         9 I~l~G~~GsGKTTia~~La~--~L~~~~~~~~~~~   41 (183)
T d1m8pa3           9 IFLTGYMNSGKDAIARALQV--TLNQQGGRSVSLL   41 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHH--HHHHHCSSCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHhhcCCCchhhh
Confidence            34779999999999999986  4433 33444443

>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=96.56  E-value=0.00043  Score=56.13  Aligned_cols=33  Identities=9%  Similarity=-0.054  Sum_probs=24.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      |||.|..|+||||||+.+..  .+......+..+.
T Consensus        25 IgI~G~~GSGKSTla~~L~~--~l~~~~~~~~~~~   57 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQ--TLREQGISVCVFH   57 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH--Hhccccccceecc
Confidence            79999999999999999876  3444444444444

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.55  E-value=0.00034  Score=55.58  Aligned_cols=20  Identities=20%  Similarity=0.242  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         8 I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           8 ILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            57899999999999999876

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.39  E-value=0.00054  Score=54.66  Aligned_cols=20  Identities=15%  Similarity=0.288  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         3 i~I~G~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHh
Confidence            68999999999999999986

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.38  E-value=0.00043  Score=55.10  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++||.|+||||+|+.+.+
T Consensus         5 Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           5 IFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             EEEESCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45889999999999999876

>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=96.32  E-value=0.00048  Score=54.42  Aligned_cols=85  Identities=22%  Similarity=0.163  Sum_probs=48.6

Q ss_pred             ccCCCCccEEEeecccCCCCC--hhhhcCCCCCCEEEcCCCCCcCccccCCCcccccceeeeccccccccch-------H
Q 041097          279 YQFPPSLTHLSFSNIELMDDP--IPALEKLSVLQVLKLKQNLYSEERTMGIRAMPKLECLIINPYAHLKRIH-------E  349 (391)
Q Consensus       279 ~~l~~~L~~L~l~~~~~~~~~--~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~c~~l~~lp-------~  349 (391)
                      ..+ ++|++|+|++|.+....  ...++.+++|+.|++++|..............+|+.|++++++-.....       .
T Consensus        62 ~~~-~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~~~~~~~~~y~~~  140 (162)
T d1koha1          62 ENI-PELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLSDTFRDQSTYISA  140 (162)
T ss_dssp             HHC-TTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTSSSSSSHHHHHHH
T ss_pred             HhC-CCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccccchhhhhhhccccceeecCCCCcCcCcccchhHHHH
Confidence            346 67777777777766533  2345667777777777665543222222234467777777764211111       2


Q ss_pred             hhcCCCCCCEEEeeC
Q 041097          350 QLWCLKSLNKLELWW  364 (391)
Q Consensus       350 ~~~~l~~L~~L~l~~  364 (391)
                      -+..+|+|+.|+=..
T Consensus       141 i~~~~P~L~~LDg~~  155 (162)
T d1koha1         141 IRERFPKLLRLDGHE  155 (162)
T ss_dssp             HHTTSTTCCEETTEE
T ss_pred             HHHHCCCCCEECcCC
Confidence            246678888876433

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.25  E-value=0.00043  Score=56.08  Aligned_cols=29  Identities=14%  Similarity=-0.105  Sum_probs=21.3

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccEEEE
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDCHAW   33 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~   33 (391)
                      ++|+.|+||||+|+.+..  ++...+..+.+
T Consensus        24 L~G~pGSGKTTiAk~La~--~l~~~~~~~~~   52 (195)
T d1x6va3          24 LTGLSGAGKTTVSMALEE--YLVCHGIPCYT   52 (195)
T ss_dssp             EESSCHHHHHHHHHHHHH--HHHHTTCCEEE
T ss_pred             EECCCCCCHHHHHHHHHH--HHHhcCCCccc
Confidence            679999999999999876  44444444444

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.18  E-value=0.00083  Score=53.05  Aligned_cols=31  Identities=10%  Similarity=-0.041  Sum_probs=23.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc-ccEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY-FDCHAW   33 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~-F~~~~~   33 (391)
                      |||+|..|+|||||+..+..  +++.. +...+.
T Consensus         4 i~I~G~~gSGKTTli~~l~~--~L~~~g~~v~vi   35 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVA--AAVREGWRVGTV   35 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH--HHHHTTCCEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHH--HHHhCCCeEEEE
Confidence            58999999999999999876  45544 334443

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.17  E-value=0.00083  Score=55.12  Aligned_cols=26  Identities=12%  Similarity=0.096  Sum_probs=20.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYF   28 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F   28 (391)
                      |.++|.+|+||||+|+++..  .+....
T Consensus         5 i~l~GlpgsGKSTla~~L~~--~l~~~~   30 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTR--YLNFIG   30 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHH--HHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHhcC
Confidence            46899999999999999986  444443

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.15  E-value=0.0008  Score=53.32  Aligned_cols=20  Identities=10%  Similarity=0.011  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|..|+||||+|+.+..
T Consensus         6 I~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           6 IILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>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=96.12  E-value=0.0011  Score=55.64  Aligned_cols=18  Identities=33%  Similarity=0.290  Sum_probs=17.0

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|++|+||||+|+.+.+
T Consensus        40 ~~GPpGtGKT~lA~~la~   57 (238)
T d1in4a2          40 LAGPPGLGKTTLAHIIAS   57 (238)
T ss_dssp             EESSTTSSHHHHHHHHHH
T ss_pred             EECCCCCcHHHHHHHHHh
Confidence            799999999999999987

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.06  E-value=0.001  Score=53.20  Aligned_cols=20  Identities=20%  Similarity=0.169  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+++.+..
T Consensus         4 I~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           4 VVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.05  E-value=0.001  Score=54.91  Aligned_cols=20  Identities=15%  Similarity=0.185  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+.+
T Consensus         5 IgI~G~~gSGKSTla~~L~~   24 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQ   24 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999998765

>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=96.02  E-value=0.00033  Score=55.45  Aligned_cols=48  Identities=27%  Similarity=0.148  Sum_probs=38.8

Q ss_pred             HHhhccCCcccEEEcCCCccccCC---cccCCCCcccEEEccCCCCCccCC
Q 041097          172 EKICKMFKFLRVLDLGSLVLIRYP---SGIENLFLLRYLKLNIPSLKSLPS  219 (391)
Q Consensus       172 ~~~~~~~~~L~~L~l~~~~l~~~p---~~i~~l~~L~~L~l~~~~i~~lp~  219 (391)
                      ......++.|++|++++|++..++   ..+..+++|++|++++|.++.++.
T Consensus        58 ~~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~  108 (162)
T d1koha1          58 RIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERE  108 (162)
T ss_dssp             HHHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGG
T ss_pred             HHHHHhCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccccchh
Confidence            345567899999999999988554   446678999999999999987763

>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=96.01  E-value=0.0013  Score=55.17  Aligned_cols=18  Identities=28%  Similarity=0.320  Sum_probs=17.0

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|++|+||||+|+.+.+
T Consensus        40 l~GPpG~GKTtla~~la~   57 (239)
T d1ixsb2          40 LFGPPGLGKTTLAHVIAH   57 (239)
T ss_dssp             EECCTTSCHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            699999999999999987

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.98  E-value=0.0011  Score=53.71  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=16.9

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |||+|+.|+||||+|+.+
T Consensus         6 IgitG~~gSGKstva~~l   23 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALL   23 (191)
T ss_dssp             EEEEECTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            799999999999999985

>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=95.98  E-value=0.0012  Score=52.11  Aligned_cols=20  Identities=25%  Similarity=0.308  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+||||+|+.+..
T Consensus         9 ivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           9 YVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999876

>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=95.92  E-value=0.0013  Score=52.37  Aligned_cols=20  Identities=20%  Similarity=0.283  Sum_probs=17.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-++|++|+||||+|+.+..
T Consensus        17 iil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          17 VVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHTG
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999765

>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=95.92  E-value=0.0018  Score=51.21  Aligned_cols=20  Identities=15%  Similarity=0.159  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         7 I~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           7 LLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             EEEEECTTSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>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=95.78  E-value=0.0012  Score=56.31  Aligned_cols=20  Identities=15%  Similarity=0.046  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||++.+.+
T Consensus        32 i~i~G~~G~GKTsLl~~~~~   51 (283)
T d2fnaa2          32 TLVLGLRRTGKSSIIKIGIN   51 (283)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHH
Confidence            46899999999999999876

>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=95.65  E-value=0.0018  Score=51.92  Aligned_cols=20  Identities=20%  Similarity=0.136  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+..
T Consensus         4 ivi~G~~GsGKTT~~~~La~   23 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999876

>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=95.65  E-value=0.0017  Score=55.57  Aligned_cols=20  Identities=20%  Similarity=0.265  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-||+||||+|-.+-.
T Consensus         4 Iai~gKGGvGKTT~a~nLA~   23 (269)
T d1cp2a_           4 VAIYGKGGIGKSTTTQNLTS   23 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHHHH
Confidence            68999999999999987644

>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=95.60  E-value=0.0017  Score=54.85  Aligned_cols=19  Identities=11%  Similarity=0.059  Sum_probs=17.2

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|++|+||||+|+.+.+
T Consensus        37 ll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2          37 LLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             EEECSTTSSHHHHHHTHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3899999999999999876

>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=95.59  E-value=0.0017  Score=52.53  Aligned_cols=20  Identities=25%  Similarity=0.185  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|++|+||||+|+.+.+
T Consensus         9 I~i~G~pGSGKsT~a~~La~   28 (194)
T d1qf9a_           9 VFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.55  E-value=0.0022  Score=51.66  Aligned_cols=29  Identities=10%  Similarity=0.229  Sum_probs=22.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCH   31 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~   31 (391)
                      |.|+|+.|+|||||++.+.+  +....|...
T Consensus         4 Ivl~GpsG~GK~tl~~~L~~--~~~~~~~~~   32 (186)
T d1gkya_           4 IVISGPSGTGKSTLLKKLFA--EYPDSFGFS   32 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHH--HCTTTEEEC
T ss_pred             EEEECCCCCCHHHHHHHHHH--hCCcceeEE
Confidence            57999999999999999876  333445433

>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=95.55  E-value=0.0018  Score=55.20  Aligned_cols=18  Identities=17%  Similarity=0.252  Sum_probs=17.2

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|++|+||||||+++.+
T Consensus        37 L~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          37 LGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             EECCTTSCTHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            699999999999999987

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.51  E-value=0.0021  Score=51.32  Aligned_cols=20  Identities=15%  Similarity=0.190  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~   22 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVA   22 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999865

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=95.39  E-value=0.0027  Score=51.30  Aligned_cols=20  Identities=15%  Similarity=0.229  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+..
T Consensus         9 IiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           9 AAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999876

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=95.38  E-value=0.0023  Score=51.60  Aligned_cols=20  Identities=5%  Similarity=-0.074  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|+.|+||||+|+.+.+
T Consensus         6 I~i~GppGsGKsT~a~~La~   25 (189)
T d1zaka1           6 VMISGAPASGKGTQCELIKT   25 (189)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>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=95.37  E-value=0.0058  Score=51.42  Aligned_cols=19  Identities=21%  Similarity=0.167  Sum_probs=17.5

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||+|+++.+
T Consensus        56 ll~GPpG~GKTt~a~~la~   74 (253)
T d1sxja2          56 MLYGPPGIGKTTAAHLVAQ   74 (253)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3799999999999999987

>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=95.33  E-value=0.0026  Score=51.58  Aligned_cols=20  Identities=20%  Similarity=0.179  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus        11 I~i~GppGSGKsT~a~~La~   30 (196)
T d1ukza_          11 IFVLGGPGAGKGTQCEKLVK   30 (196)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=95.29  E-value=0.0021  Score=53.04  Aligned_cols=20  Identities=10%  Similarity=0.144  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|++|+||||+|+.+.+
T Consensus         6 I~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67889999999999999877

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.29  E-value=0.0027  Score=50.72  Aligned_cols=20  Identities=20%  Similarity=0.172  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         3 I~i~G~pGsGKsT~a~~La~   22 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAE   22 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999886

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=95.27  E-value=0.0028  Score=50.73  Aligned_cols=20  Identities=15%  Similarity=0.152  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~   22 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVE   22 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999886

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.22  E-value=0.0025  Score=51.57  Aligned_cols=20  Identities=20%  Similarity=0.263  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|-|.-|+||||+|+.+..
T Consensus        12 I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1          12 VLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             EEEECSTTSCHHHHHHTTGG
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999765

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.20  E-value=0.0027  Score=51.32  Aligned_cols=20  Identities=10%  Similarity=0.278  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+|||||++.+..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999876

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=95.18  E-value=0.0031  Score=54.94  Aligned_cols=35  Identities=9%  Similarity=0.179  Sum_probs=25.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccccc--EEEEEEcC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFD--CHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~--~~~~~~vs   37 (391)
                      |||.|..|+||||+|+.+..  .++..+.  .+..++.+
T Consensus        83 IGIaG~sgSGKSTla~~L~~--lL~~~~~~~~v~~Is~D  119 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQA--LLSRWPEHRRVELITTD  119 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHH--HHTTSTTCCCEEEEEGG
T ss_pred             EEEeCCCCCCCcHHHHHHHH--HHhhhcCCCceEEEeee
Confidence            79999999999999999876  4544442  34455544

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.11  E-value=0.0039  Score=50.80  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||.+.+..
T Consensus        30 ~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          30 VNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCChHHHHHHHHhc
Confidence            58999999999999999976

>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=95.10  E-value=0.0037  Score=52.02  Aligned_cols=18  Identities=22%  Similarity=0.130  Sum_probs=16.9

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|+||||+|+.+.+
T Consensus        50 l~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          50 FAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             EESCTTSSHHHHHHHHHH
T ss_pred             EECCCCCcHHHHHHHHHH
Confidence            799999999999999876

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=95.09  E-value=0.0037  Score=51.60  Aligned_cols=20  Identities=15%  Similarity=0.067  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|-|.+|+||||.|+.+..
T Consensus         6 IaIdGp~GsGKgT~ak~La~   25 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAK   25 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999876

>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=95.08  E-value=0.0023  Score=54.78  Aligned_cols=18  Identities=22%  Similarity=0.377  Sum_probs=16.8

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      |+|++|+||||+|+.+.+
T Consensus        51 l~GppGtGKT~l~~~l~~   68 (287)
T d1w5sa2          51 SIGRVGIGKTTLAKFTVK   68 (287)
T ss_dssp             CTTCCSSSHHHHHHHHHH
T ss_pred             eECCCCCCHHHHHHHHHH
Confidence            579999999999999987

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=95.02  E-value=0.0036  Score=54.11  Aligned_cols=19  Identities=16%  Similarity=0.211  Sum_probs=16.3

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|+|-|||||||+|-.+-
T Consensus         5 IaisgKGGVGKTT~a~NLA   23 (289)
T d2afhe1           5 CAIYGKGGIGKSTTTQNLV   23 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5789999999999887763

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=95.01  E-value=0.0044  Score=48.29  Aligned_cols=22  Identities=18%  Similarity=0.151  Sum_probs=19.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|.+|+|||||.+.+.++.
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            5799999999999999987753

>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=94.99  E-value=0.0037  Score=50.43  Aligned_cols=20  Identities=25%  Similarity=0.199  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|.|++|+||||.|+.+.+
T Consensus         4 I~i~GppGSGKsT~a~~La~   23 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIVE   23 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999886

>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=94.92  E-value=0.004  Score=49.68  Aligned_cols=20  Identities=20%  Similarity=0.225  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~   24 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQE   24 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999876

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.82  E-value=0.0041  Score=49.46  Aligned_cols=20  Identities=15%  Similarity=-0.009  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||.|+.+.+
T Consensus         3 I~i~G~pGSGKsT~~~~La~   22 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIME   22 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999876

>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=94.82  E-value=0.0067  Score=50.15  Aligned_cols=18  Identities=17%  Similarity=0.071  Sum_probs=16.9

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|+.|+||||+|+.+.+
T Consensus        40 l~Gp~G~GKttl~~~la~   57 (227)
T d1sxjc2          40 FYGPPGTGKTSTIVALAR   57 (227)
T ss_dssp             EECSSSSSHHHHHHHHHH
T ss_pred             EECCCCCChhHHHHHHHH
Confidence            799999999999999877

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=94.81  E-value=0.0049  Score=50.48  Aligned_cols=18  Identities=28%  Similarity=0.350  Sum_probs=16.5

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |||+|+.|+||||.|+.+
T Consensus         6 IgitG~igSGKStv~~~l   23 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHH
Confidence            799999999999999864

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=94.81  E-value=0.0039  Score=48.16  Aligned_cols=21  Identities=10%  Similarity=-0.023  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998654

>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=94.75  E-value=0.0052  Score=50.82  Aligned_cols=18  Identities=17%  Similarity=0.054  Sum_probs=16.5

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|+||||+|+.+.+
T Consensus        41 l~Gp~G~GKTt~a~~la~   58 (224)
T d1sxjb2          41 ISGMPGIGKTTSVHCLAH   58 (224)
T ss_dssp             EECSTTSSHHHHHHHHHH
T ss_pred             EECCCCCCchhhHHHHHH
Confidence            799999999999998876

>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=94.73  E-value=0.0053  Score=51.06  Aligned_cols=19  Identities=16%  Similarity=0.034  Sum_probs=17.3

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -++|..|+||||+|+.+.+
T Consensus        37 ll~Gp~G~GKTtl~~~i~~   55 (237)
T d1sxjd2          37 LFYGPPGTGKTSTILALTK   55 (237)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCChHHHHHHHHH
Confidence            3799999999999999987

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.73  E-value=0.0061  Score=47.59  Aligned_cols=21  Identities=14%  Similarity=0.235  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999988764

>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=94.73  E-value=0.0051  Score=51.86  Aligned_cols=18  Identities=28%  Similarity=0.128  Sum_probs=17.3

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.+|+|||++|+++.+
T Consensus        45 L~GppGtGKT~la~alA~   62 (246)
T d1d2na_          45 LEGPPHSGKTALAAKIAE   62 (246)
T ss_dssp             EECSTTSSHHHHHHHHHH
T ss_pred             EECcCCCCHHHHHHHHhh
Confidence            799999999999999998

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.72  E-value=0.0072  Score=47.51  Aligned_cols=21  Identities=19%  Similarity=0.300  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999987664

>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=94.71  E-value=0.0044  Score=54.20  Aligned_cols=19  Identities=21%  Similarity=0.303  Sum_probs=17.4

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -.+|++|+|||.|||++.+
T Consensus        53 Ll~GPpG~GKT~lAkalA~   71 (309)
T d1ofha_          53 LMIGPTGVGKTEIARRLAK   71 (309)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHhh
Confidence            4689999999999999986

>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=94.69  E-value=0.0055  Score=49.21  Aligned_cols=20  Identities=20%  Similarity=0.157  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|.|++|+||||+|+.+.+
T Consensus         6 iil~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           6 AVLLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999875

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.69  E-value=0.0064  Score=47.53  Aligned_cols=21  Identities=14%  Similarity=0.210  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|..|+|||||+..+.++
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999876653

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.68  E-value=0.0055  Score=51.33  Aligned_cols=20  Identities=10%  Similarity=0.212  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|.|||||++.+..
T Consensus        32 vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          32 IGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            68999999999999999865

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.67  E-value=0.0053  Score=51.91  Aligned_cols=20  Identities=20%  Similarity=0.242  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||++.+..
T Consensus        44 iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          44 VALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             EEEEECTTSSHHHHHHHHTT
T ss_pred             EEEECCCCChHHHHHHHHhc
Confidence            58999999999999999864

>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=94.65  E-value=0.0066  Score=49.70  Aligned_cols=19  Identities=16%  Similarity=0.018  Sum_probs=17.1

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      =+.|+.|+||||+|+.+..
T Consensus        28 wltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          28 WLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3789999999999999876

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=94.58  E-value=0.0061  Score=51.12  Aligned_cols=20  Identities=15%  Similarity=0.052  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|.|||||++.+.-
T Consensus        31 vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          31 IAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            58999999999999999854

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.57  E-value=0.006  Score=52.37  Aligned_cols=76  Identities=8%  Similarity=0.085  Sum_probs=39.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc--cc-EEEEEEcCCC-cChHHHHHHHHHhh----cCCCCCCCCCChHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY--FD-CHAWVQESLP-YDADQILYDIIKFV----MPSPEGFIPDNNEATVEKY   72 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~--F~-~~~~~~vs~~-~~~~~i~~~~~~~~----~~~~eg~~~~~~~~~~~~~   72 (391)
                      |||-|..|+||||||+.+..  .+...  +. .++.++.+.= .+.++ ..+.....    .....|.-....-+++.+.
T Consensus        30 IGi~G~qGSGKSTl~~~l~~--~L~~~~~~~~~v~~iS~DdfY~t~~~-r~~L~~~~~~~pl~~~RG~PgThD~~ll~~~  106 (286)
T d1odfa_          30 IFFSGPQGSGKSFTSIQIYN--HLMEKYGGEKSIGYASIDDFYLTHED-QLKLNEQFKNNKLLQGRGLPGTHDMKLLQEV  106 (286)
T ss_dssp             EEEECCTTSSHHHHHHHHHH--HHHHHHGGGSCEEEEEGGGGBCCHHH-HHHHHHHTTTCGGGSSSCSTTSBCHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHH--HHHHHhCCCcceEeeccCCCCCCHHH-HHHHhhhccccccceecCCCcchhHHHHHHH
Confidence            69999999999999998865  33222  22 3455554422 12221 11111111    1111222222246777788


Q ss_pred             HHHHHcC
Q 041097           73 LEQLING   79 (391)
Q Consensus        73 ~~~L~~k   79 (391)
                      +..|.+.
T Consensus       107 l~~l~~~  113 (286)
T d1odfa_         107 LNTIFNN  113 (286)
T ss_dssp             HHHHTC-
T ss_pred             HHHHHhh
Confidence            8888654

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.54  E-value=0.0064  Score=50.44  Aligned_cols=20  Identities=10%  Similarity=0.167  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        34 ~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          34 VSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCcchhhHhccC
Confidence            58999999999999999875

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.53  E-value=0.0063  Score=51.35  Aligned_cols=20  Identities=25%  Similarity=0.220  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||++.+..
T Consensus        43 vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          43 TALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            58999999999999999865

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=94.53  E-value=0.0075  Score=47.06  Aligned_cols=21  Identities=14%  Similarity=0.074  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            579999999999999997663

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.52  E-value=0.0065  Score=50.74  Aligned_cols=20  Identities=25%  Similarity=0.184  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.++-
T Consensus        32 ~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          32 MILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             EEEECSTTSSHHHHHHHHHT
T ss_pred             EEEECCCCChHHHHHHHHhc
Confidence            58999999999999999865

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.50  E-value=0.006  Score=52.39  Aligned_cols=20  Identities=25%  Similarity=0.285  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||++.+.-
T Consensus        65 vaivG~nGsGKSTLl~~i~G   84 (281)
T d1r0wa_          65 LAITGSTGSGKTSLLMLILG   84 (281)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCChHHHHHHHHhC
Confidence            68999999999999999965

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.49  E-value=0.0075  Score=47.24  Aligned_cols=21  Identities=14%  Similarity=0.265  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999997664

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=94.47  E-value=0.0066  Score=50.60  Aligned_cols=20  Identities=20%  Similarity=0.260  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|.|..|.|||||.+.+-.
T Consensus         3 i~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHH
Confidence            68999999999999999854

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=94.45  E-value=0.0065  Score=50.74  Aligned_cols=20  Identities=15%  Similarity=0.184  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        34 ~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          34 YGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             EEEEESTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            58999999999999999876

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.43  E-value=0.0075  Score=47.04  Aligned_cols=21  Identities=14%  Similarity=0.205  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999997654

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.41  E-value=0.0075  Score=47.57  Aligned_cols=21  Identities=10%  Similarity=0.260  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            579999999999999997654

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.33  E-value=0.0075  Score=49.17  Aligned_cols=18  Identities=28%  Similarity=0.298  Sum_probs=16.7

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |||+|.-|+||||+|+.+
T Consensus         5 IgITG~igSGKStv~~~l   22 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEECSTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            799999999999999975

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.33  E-value=0.0075  Score=51.05  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+.-
T Consensus        31 ~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          31 ISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHHc
Confidence            58999999999999999875

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.32  E-value=0.0076  Score=50.01  Aligned_cols=20  Identities=10%  Similarity=0.142  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||.+.+.-
T Consensus        29 ~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          29 VVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCChHHHHHHHHhc
Confidence            58999999999999999865

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.32  E-value=0.0063  Score=48.36  Aligned_cols=20  Identities=10%  Similarity=0.116  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|..|+|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999875

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.31  E-value=0.025  Score=46.75  Aligned_cols=46  Identities=2%  Similarity=0.049  Sum_probs=32.1

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccc----cEEEEEEcCCCcChHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYF----DCHAWVQESLPYDADQILY   47 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F----~~~~~~~vs~~~~~~~i~~   47 (391)
                      -|+|.+|+||||||..+..+......+    ..++|+.....++......
T Consensus        38 li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~   87 (251)
T d1szpa2          38 ELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVS   87 (251)
T ss_dssp             EEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGGGHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHHHHH
Confidence            489999999999998876543333222    3788888777776655433

>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=94.30  E-value=0.0088  Score=49.11  Aligned_cols=33  Identities=18%  Similarity=0.093  Sum_probs=25.0

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQE   36 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~v   36 (391)
                      -|||..|+|||-|++++++.  .......+++++.
T Consensus        40 ~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~~~   72 (213)
T d1l8qa2          40 FIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSSA   72 (213)
T ss_dssp             EEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEEH
T ss_pred             EEECCCCCcHHHHHHHHHHH--hccCccceEEech
Confidence            48999999999999999984  4444445666554

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.29  E-value=0.0082  Score=47.34  Aligned_cols=21  Identities=19%  Similarity=0.129  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus        19 I~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999998664

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.28  E-value=0.0079  Score=47.94  Aligned_cols=20  Identities=5%  Similarity=0.029  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+|||||++.+.+
T Consensus         5 ivl~GpsG~GK~tl~~~L~~   24 (182)
T d1znwa1           5 VVLSGPSAVGKSTVVRCLRE   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999876

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.26  E-value=0.0085  Score=47.09  Aligned_cols=20  Identities=5%  Similarity=0.145  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||++.+..
T Consensus         3 V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999999875

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.20  E-value=0.0088  Score=47.02  Aligned_cols=21  Identities=14%  Similarity=0.325  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999987764

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.20  E-value=0.0095  Score=46.72  Aligned_cols=22  Identities=18%  Similarity=0.413  Sum_probs=19.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSN   22 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~   22 (391)
                      |.|+|-+|+|||+|.+...++.
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5789999999999999987653

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.19  E-value=0.0083  Score=50.01  Aligned_cols=20  Identities=20%  Similarity=0.174  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        35 ~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          35 LVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCChHHHHHHHHHc
Confidence            58999999999999999865

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.18  E-value=0.0097  Score=46.69  Aligned_cols=21  Identities=14%  Similarity=0.256  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            579999999999999987553

>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=94.15  E-value=0.028  Score=43.94  Aligned_cols=116  Identities=16%  Similarity=0.170  Sum_probs=64.5

Q ss_pred             cCCCCCCEEEecCCCCC--CchhhhccccccCCCCccEEEeecccCCCCC----hhhhcCCCCCCEEEcCCCCCcCcccc
Q 041097          252 CRLSCLESLKLANESKM--PRRSNIILAEYQFPPSLTHLSFSNIELMDDP----IPALEKLSVLQVLKLKQNLYSEERTM  325 (391)
Q Consensus       252 ~~l~~L~~L~l~~~~~l--p~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~~~  325 (391)
                      .+.++|++|++++...+  ..+..+...+..- ++|+.|+|++|.+....    ...+...+.|+.|+++.|........
T Consensus        12 ~n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n-~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~   90 (167)
T d1pgva_          12 EDDTDLKEVNINNMKRVSKERIRSLIEAACNS-KHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLA   90 (167)
T ss_dssp             TTCSSCCEEECTTCCSSCHHHHHHHHHHHTTC-SCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHH
T ss_pred             hCCCCCcEEEeCCCCCCCHHHHHHHHHHHhhC-CccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHH
Confidence            44567777777651100  0111111133445 67788888777665321    23455567788888875554332211


Q ss_pred             C----CCcccccceeeecccc--cc-----ccchHhhcCCCCCCEEEeeCCcHH
Q 041097          326 G----IRAMPKLECLIINPYA--HL-----KRIHEQLWCLKSLNKLELWWPEPE  368 (391)
Q Consensus       326 ~----~~~~~~L~~L~l~~c~--~l-----~~lp~~~~~l~~L~~L~l~~~~~~  368 (391)
                      .    ...-+.|++|+++++.  .+     ..+...+..-++|++|+++.+...
T Consensus        91 ~l~~aL~~n~sL~~L~l~~n~~~~~g~~~~~~l~~~L~~n~sL~~l~l~~~~~~  144 (167)
T d1pgva_          91 RLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFASME  144 (167)
T ss_dssp             HHHHHTTTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECCCCCHH
T ss_pred             HHHHHHHhCCcCCEEECCCCcCCCccHHHHHHHHHHHHhCCCccEeeCcCCCch
Confidence            1    1233568888887652  11     234556667789999999776644

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=94.15  E-value=0.0087  Score=52.55  Aligned_cols=37  Identities=14%  Similarity=-0.031  Sum_probs=26.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLP   39 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~   39 (391)
                      |||.|.+|+|||||.-.+..  .+...-..++.+.++..
T Consensus        57 IgitG~pGaGKSTLi~~l~~--~~~~~g~~vavlavDps   93 (327)
T d2p67a1          57 LGVTGTPGAGKSTFLEAFGM--LLIREGLKVAVIAVDPS   93 (327)
T ss_dssp             EEEEECTTSCHHHHHHHHHH--HHHHTTCCEEEEEECCC
T ss_pred             EEeeCCCCCCHHHHHHHHHH--HHHhcCCceeeecCCCc
Confidence            79999999999999988764  23333345566666533

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.14  E-value=0.0097  Score=46.86  Aligned_cols=21  Identities=19%  Similarity=0.335  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+.++
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            579999999999999987654

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.14  E-value=0.0087  Score=46.78  Aligned_cols=21  Identities=10%  Similarity=0.271  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999998764

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.12  E-value=0.01  Score=46.37  Aligned_cols=21  Identities=10%  Similarity=0.311  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999887553

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.10  E-value=0.0095  Score=46.82  Aligned_cols=21  Identities=24%  Similarity=0.360  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999987654

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.10  E-value=0.009  Score=49.75  Aligned_cols=20  Identities=20%  Similarity=0.262  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||.|..|+|||||++.+.-
T Consensus        27 ~~liGpnGaGKSTll~~i~G   46 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCChHHHHHHHHHc
Confidence            47999999999999999876

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.08  E-value=0.009  Score=48.52  Aligned_cols=20  Identities=15%  Similarity=0.172  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|-|+-|+||||+++.+.+
T Consensus         3 I~ieG~dGsGKST~~~~L~~   22 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSG   22 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999876

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.06  E-value=0.01  Score=46.50  Aligned_cols=21  Identities=10%  Similarity=0.221  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987643

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.06  E-value=0.01  Score=46.35  Aligned_cols=21  Identities=14%  Similarity=0.156  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987653

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.01  E-value=0.011  Score=46.42  Aligned_cols=21  Identities=24%  Similarity=0.234  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            579999999999999997663

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.96  E-value=0.012  Score=46.99  Aligned_cols=21  Identities=24%  Similarity=0.328  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||+..+.++
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            579999999999999998765

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.94  E-value=0.0092  Score=47.47  Aligned_cols=20  Identities=10%  Similarity=0.297  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+|||||++.+..
T Consensus         6 ivl~Gpsg~GK~tl~~~L~~   25 (178)
T d1kgda_           6 LVLLGAHGVGRRHIKNTLIT   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999875

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.90  E-value=0.0086  Score=49.02  Aligned_cols=25  Identities=4%  Similarity=-0.118  Sum_probs=20.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY   27 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~   27 (391)
                      |+|-|+-|+||||+++.+.+  .++..
T Consensus         6 I~ieG~dGsGKsT~~~~L~~--~L~~~   30 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVE--ALCAA   30 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHH--HHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHHC
Confidence            57889999999999999987  45433

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.85  E-value=0.011  Score=46.48  Aligned_cols=20  Identities=15%  Similarity=0.273  Sum_probs=17.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|.+|+|||||+..+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57999999999999998654

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.82  E-value=0.0069  Score=50.44  Aligned_cols=20  Identities=15%  Similarity=0.245  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|-|+-|+||||+|+.+.+
T Consensus         5 I~ieG~dGsGKST~~~~L~~   24 (241)
T d1p5zb_           5 ISIEGNIAAGKSTFVNILKQ   24 (241)
T ss_dssp             EEEECSTTSSHHHHHTTTGG
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999665

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.80  E-value=0.012  Score=45.99  Aligned_cols=21  Identities=19%  Similarity=0.368  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||+..+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999988764

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.80  E-value=0.012  Score=46.40  Aligned_cols=21  Identities=24%  Similarity=0.360  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987654

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.79  E-value=0.013  Score=45.84  Aligned_cols=21  Identities=29%  Similarity=0.403  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|||||+|++.+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            579999999999999997654

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=93.79  E-value=0.0091  Score=47.16  Aligned_cols=21  Identities=14%  Similarity=0.042  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|.+|+|||||...+..+
T Consensus        16 I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          16 LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999997553

>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=93.79  E-value=0.014  Score=49.14  Aligned_cols=18  Identities=22%  Similarity=0.316  Sum_probs=17.2

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|+|||++|+++.+
T Consensus        47 l~GppGtGKT~la~aia~   64 (247)
T d1ixza_          47 LVGPPGVGKTHLARAVAG   64 (247)
T ss_dssp             EECCTTSSHHHHHHHHHH
T ss_pred             EecCCCCChhHHHHHHHH
Confidence            699999999999999997

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.73  E-value=0.012  Score=46.91  Aligned_cols=21  Identities=14%  Similarity=0.104  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            579999999999999987664

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.70  E-value=0.012  Score=47.29  Aligned_cols=21  Identities=10%  Similarity=0.254  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||++.+.++
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            579999999999999987654

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.70  E-value=0.013  Score=45.81  Aligned_cols=21  Identities=14%  Similarity=0.265  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|+|||||+..+.++
T Consensus         7 v~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           7 IAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999997654

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=93.63  E-value=0.01  Score=49.15  Aligned_cols=20  Identities=25%  Similarity=0.320  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        29 ~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          29 FVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             EEEECCCTHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            58999999999999999876

>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=93.60  E-value=0.029  Score=43.70  Aligned_cols=120  Identities=18%  Similarity=0.123  Sum_probs=74.5

Q ss_pred             hHHhcCCCCCCEEEecC-CC-CCCchhhhccccccCCCCccEEEeecccCCCCCh----hhhcCCCCCCEEEcCCCCCcC
Q 041097          248 SKSLCRLSCLESLKLAN-ES-KMPRRSNIILAEYQFPPSLTHLSFSNIELMDDPI----PALEKLSVLQVLKLKQNLYSE  321 (391)
Q Consensus       248 p~~i~~l~~L~~L~l~~-~~-~lp~L~~Llp~~~~l~~~L~~L~l~~~~~~~~~~----~~l~~l~~L~~L~l~~~~~~~  321 (391)
                      .....+.++|++|++.+ .. .-..+..+...+... ++|+.|++++|.+.....    ..+...+.++.+++..+....
T Consensus        10 ~~~~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n-~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~   88 (166)
T d1io0a_          10 KRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTN-TYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISG   88 (166)
T ss_dssp             HHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTC-CSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCH
T ss_pred             HHHHhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcC-CccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccccc
Confidence            34456778999999986 22 101111111134566 899999999998765432    345667899999998555432


Q ss_pred             ccc---c-CCCcccccceeeecccc-ccc-----cchHhhcCCCCCCEEEeeCCcHH
Q 041097          322 ERT---M-GIRAMPKLECLIINPYA-HLK-----RIHEQLWCLKSLNKLELWWPEPE  368 (391)
Q Consensus       322 ~~~---~-~~~~~~~L~~L~l~~c~-~l~-----~lp~~~~~l~~L~~L~l~~~~~~  368 (391)
                      +..   . .....++|+.+.|..|. .+.     .+...+...++|++|++......
T Consensus        89 ~g~~~l~~~l~~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~~~~~~  145 (166)
T d1io0a_          89 SGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQQG  145 (166)
T ss_dssp             HHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSSHH
T ss_pred             hhHHHHHHHHHhCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCcCCCCc
Confidence            221   1 11345678877776443 232     35556678899999999876643

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.60  E-value=0.015  Score=46.02  Aligned_cols=21  Identities=10%  Similarity=0.219  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|..|+|||||...+.+.
T Consensus         8 I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           8 VAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999998864

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.57  E-value=0.015  Score=46.28  Aligned_cols=21  Identities=14%  Similarity=0.123  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|||||||++.+.++
T Consensus         8 ivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999887654

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=93.54  E-value=0.01  Score=47.31  Aligned_cols=20  Identities=10%  Similarity=0.142  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|.+|+|||||...+.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            79999999999999999865

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=93.53  E-value=0.015  Score=45.51  Aligned_cols=21  Identities=19%  Similarity=0.268  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999987554

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.53  E-value=0.015  Score=45.38  Aligned_cols=21  Identities=29%  Similarity=0.404  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|||||||++.+.++
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987664

>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=93.53  E-value=0.021  Score=44.70  Aligned_cols=82  Identities=16%  Similarity=0.239  Sum_probs=57.2

Q ss_pred             CCccEEEeecc-cCCCCC----hhhhcCCCCCCEEEcCCCCCcCccccCC----Ccccccceeeeccccccc-----cch
Q 041097          283 PSLTHLSFSNI-ELMDDP----IPALEKLSVLQVLKLKQNLYSEERTMGI----RAMPKLECLIINPYAHLK-----RIH  348 (391)
Q Consensus       283 ~~L~~L~l~~~-~~~~~~----~~~l~~l~~L~~L~l~~~~~~~~~~~~~----~~~~~L~~L~l~~c~~l~-----~lp  348 (391)
                      ++|+.|+|+++ .+....    ...+...++|+.|+++.|..........    ...+.|++|++++|. +.     .+-
T Consensus        15 ~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~-i~~~g~~~l~   93 (167)
T d1pgva_          15 TDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNF-LTPELLARLL   93 (167)
T ss_dssp             SSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSB-CCHHHHHHHH
T ss_pred             CCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhh-cchHHHHHHH
Confidence            89999999875 344332    3456777999999999665443221111    245689999999884 43     344


Q ss_pred             HhhcCCCCCCEEEeeCC
Q 041097          349 EQLWCLKSLNKLELWWP  365 (391)
Q Consensus       349 ~~~~~l~~L~~L~l~~~  365 (391)
                      ..+..-++|++|+++++
T Consensus        94 ~aL~~n~sL~~L~l~~n  110 (167)
T d1pgva_          94 RSTLVTQSIVEFKADNQ  110 (167)
T ss_dssp             HHTTTTCCCSEEECCCC
T ss_pred             HHHHhCCcCCEEECCCC
Confidence            56778899999999865

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=93.49  E-value=0.013  Score=51.35  Aligned_cols=20  Identities=15%  Similarity=0.134  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|.+|+|||||.-.+..
T Consensus        54 igitG~pGaGKSTli~~l~~   73 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGS   73 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EeeeCCCCCCHHHHHHHHHH
Confidence            79999999999999988764

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.48  E-value=0.014  Score=45.89  Aligned_cols=20  Identities=10%  Similarity=0.262  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-.|+|||||..++.+
T Consensus         8 I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           8 IAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEECSSSSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            57999999999999999986

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=93.47  E-value=0.013  Score=47.18  Aligned_cols=20  Identities=15%  Similarity=0.135  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|.|++|+||||+|+.+.+
T Consensus        11 I~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_          11 IFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999876

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.46  E-value=0.015  Score=45.88  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||+..+.++
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987554

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.45  E-value=0.016  Score=45.40  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987654

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=93.45  E-value=0.014  Score=48.71  Aligned_cols=20  Identities=15%  Similarity=0.140  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||.+.+..
T Consensus        31 ~glvG~nGaGKSTLl~~l~G   50 (238)
T d1vpla_          31 FGLIGPNGAGKTTTLRIIST   50 (238)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            58999999999999999876

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.42  E-value=0.015  Score=45.88  Aligned_cols=21  Identities=10%  Similarity=0.093  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|+|||||+..+.++
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999887654

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=93.40  E-value=0.0066  Score=52.05  Aligned_cols=20  Identities=15%  Similarity=0.132  Sum_probs=15.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||+|+.+-+
T Consensus         7 IgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           7 ISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             EEEESCC---CCTHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            79999999999999998654

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.40  E-value=0.014  Score=48.69  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||.|..|.|||||.+.+.-
T Consensus        35 ~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          35 VTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            58999999999999999876

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.39  E-value=0.0088  Score=50.48  Aligned_cols=20  Identities=15%  Similarity=0.076  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|.|||||++.+..
T Consensus        47 vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          47 VAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             EEEECSTTSSHHHHHTTTTT
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            58999999999999999864

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.35  E-value=0.015  Score=49.12  Aligned_cols=20  Identities=10%  Similarity=0.142  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||++.+.-
T Consensus        33 ~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          33 TLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHHC
Confidence            58999999999999999976

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.34  E-value=0.01  Score=46.65  Aligned_cols=21  Identities=19%  Similarity=0.358  Sum_probs=17.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||++.+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987664

>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=93.33  E-value=0.014  Score=49.72  Aligned_cols=19  Identities=26%  Similarity=0.358  Sum_probs=15.1

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |.++|-|||||||+|-.+-
T Consensus        23 ii~sGKGGVGKTT~a~nLA   41 (279)
T d1ihua2          23 IMLMGKGGVGKTTMAAAIA   41 (279)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            3568999999999866653

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=93.33  E-value=0.014  Score=46.85  Aligned_cols=20  Identities=15%  Similarity=0.282  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|..|+|||||...+.+
T Consensus        26 I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          26 IALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHhcC
Confidence            68999999999999999986

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.21  E-value=0.015  Score=45.96  Aligned_cols=21  Identities=5%  Similarity=0.052  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|.+|+|||||...+.+.
T Consensus         3 I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           3 IIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999999863

>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=93.19  E-value=0.034  Score=45.99  Aligned_cols=42  Identities=12%  Similarity=0.014  Sum_probs=30.0

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILY   47 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~   47 (391)
                      -|+|.+|+||||+|..+..+  ....-..++|++..  .+.+.+.+
T Consensus        30 li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e--~~~~~~~~   71 (242)
T d1tf7a2          30 LATGATGTGKTLLVSRFVEN--ACANKERAILFAYE--ESRAQLLR   71 (242)
T ss_dssp             EEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESS--SCHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHH--HHHhccccceeecc--CCHHHHHH
Confidence            48999999999999998763  44556677887754  34444433

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.15  E-value=0.011  Score=49.41  Aligned_cols=20  Identities=25%  Similarity=0.336  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|+|||||++.+.-
T Consensus        34 ~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          34 FGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             EEEECSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHc
Confidence            58999999999999999854

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=93.14  E-value=0.018  Score=45.21  Aligned_cols=21  Identities=10%  Similarity=0.004  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||...+-++
T Consensus        18 I~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          18 VIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            579999999999999997664

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.14  E-value=0.018  Score=45.68  Aligned_cols=21  Identities=19%  Similarity=0.105  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|..|+|||||++.+.++
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999987664

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.13  E-value=0.019  Score=45.32  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+-++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987553

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.10  E-value=0.019  Score=45.57  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|+|||||++.+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987653

>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=93.09  E-value=0.016  Score=49.70  Aligned_cols=19  Identities=16%  Similarity=0.120  Sum_probs=15.3

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -+.|-||+||||+|-.+-.
T Consensus        12 ~~sGKGGVGKTTvaa~lA~   30 (296)
T d1ihua1          12 FFTGKGGVGKTSISCATAI   30 (296)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCcChHHHHHHHHHH
Confidence            3689999999997777543

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=93.08  E-value=0.015  Score=47.41  Aligned_cols=40  Identities=18%  Similarity=0.078  Sum_probs=21.2

Q ss_pred             CcEEcCCCCcHH-HHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKT-AFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKT-TLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      |..+|..|+||| |+||..+.   .+..=..+++++.+ .|....
T Consensus        15 i~lvGptGvGKTTTiAKLA~~---~~~~g~kV~lit~D-t~R~ga   55 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYF---YKKKGFKVGLVGAD-VYRPAA   55 (211)
T ss_dssp             EEEECSCCC----HHHHHHHH---HHHTTCCEEEEECC-CSSHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH---HHHCCCceEEEEee-ccccch
Confidence            356899999997 56666543   22111256777765 344444

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.06  E-value=0.02  Score=44.82  Aligned_cols=21  Identities=14%  Similarity=0.252  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||++.+.++
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999987553

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=93.01  E-value=0.015  Score=45.74  Aligned_cols=21  Identities=14%  Similarity=0.012  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||.+.+.++
T Consensus        15 IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          15 ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             EEEEEETTSSHHHHHHHTTCC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999998764

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.97  E-value=0.02  Score=44.75  Aligned_cols=21  Identities=19%  Similarity=0.420  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|-.|+|||||++.+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            468999999999999997764

>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=92.97  E-value=0.02  Score=48.28  Aligned_cols=18  Identities=22%  Similarity=0.235  Sum_probs=17.0

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.+|+|||++|+.+.+
T Consensus        50 L~GppGtGKT~la~~iA~   67 (256)
T d1lv7a_          50 MVGPPGTGKTLLAKAIAG   67 (256)
T ss_dssp             EECCTTSCHHHHHHHHHH
T ss_pred             eeCCCCCCccHHHHHHHH
Confidence            689999999999999987

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.91  E-value=0.019  Score=45.75  Aligned_cols=20  Identities=10%  Similarity=0.076  Sum_probs=17.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++|-+|+|||||.+..-.
T Consensus         5 ivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            46899999999999998644

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.91  E-value=0.019  Score=44.03  Aligned_cols=21  Identities=14%  Similarity=0.028  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|.+|+|||||+..+-++
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999997664

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.85  E-value=0.017  Score=47.95  Aligned_cols=20  Identities=15%  Similarity=0.298  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|-|+-|+||||+++.+.+
T Consensus         5 IviEG~~GsGKST~~~~L~~   24 (241)
T d2ocpa1           5 LSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            67899999999999999875

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.80  E-value=0.02  Score=45.93  Aligned_cols=18  Identities=17%  Similarity=0.237  Sum_probs=16.4

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |.|+|.+|+|||||++.+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            568999999999999986

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.79  E-value=0.041  Score=44.92  Aligned_cols=25  Identities=12%  Similarity=0.005  Sum_probs=20.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCcccccc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHY   27 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~   27 (391)
                      |+|-|+-|+||||+++.+.+  .++..
T Consensus         6 I~iEG~DGsGKST~~~~L~~--~L~~~   30 (214)
T d1tmka_           6 ILIEGLDRTGKTTQCNILYK--KLQPN   30 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHH--HTTTS
T ss_pred             EEEECCCCCcHHHHHHHHHH--HHHhC
Confidence            67999999999999999886  45443

>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=92.79  E-value=0.022  Score=48.08  Aligned_cols=18  Identities=22%  Similarity=0.209  Sum_probs=17.0

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|+|||++|+++.+
T Consensus        43 L~GppGtGKT~l~~ala~   60 (258)
T d1e32a2          43 LYGPPGTGKTLIARAVAN   60 (258)
T ss_dssp             EECCTTSSHHHHHHHHHH
T ss_pred             EecCCCCCchHHHHHHHH
Confidence            689999999999999887

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.77  E-value=0.021  Score=45.24  Aligned_cols=21  Identities=10%  Similarity=0.215  Sum_probs=18.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+|-.|+|||||..++.+.
T Consensus        11 V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            689999999999999988763

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=92.73  E-value=0.02  Score=46.51  Aligned_cols=20  Identities=15%  Similarity=0.165  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|+.|+|||||.+.+..
T Consensus         5 ivi~GPSG~GK~tl~~~L~~   24 (205)
T d1s96a_           5 YIVSAPSGAGKSSLIQALLK   24 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999876

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.72  E-value=0.022  Score=44.75  Aligned_cols=20  Identities=15%  Similarity=0.278  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|-+|+|||||+..+.+
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57999999999999977654

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=92.70  E-value=0.016  Score=48.08  Aligned_cols=20  Identities=15%  Similarity=0.255  Sum_probs=18.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      +||+|..|.|||||.+.+.-
T Consensus        28 ~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          28 LHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             EECBCCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            58999999999999999876

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=92.65  E-value=0.022  Score=44.25  Aligned_cols=21  Identities=19%  Similarity=0.128  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||+..+..+
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            578999999999999987553

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.61  E-value=0.023  Score=45.42  Aligned_cols=21  Identities=14%  Similarity=0.123  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|+|||||++.+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            579999999999999886554

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=92.59  E-value=0.017  Score=45.78  Aligned_cols=21  Identities=19%  Similarity=0.131  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|..|+|||||.+.+.++
T Consensus        20 I~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          20 ILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             EEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            568999999999999997553

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.51  E-value=0.098  Score=43.20  Aligned_cols=44  Identities=7%  Similarity=0.029  Sum_probs=32.2

Q ss_pred             cEEcCCCCcHHHHHHHHhCCc----cccccccEEEEEEcCCCcChHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSN----YVKHYFDCHAWVQESLPYDADQI   45 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~----~lk~~F~~~~~~~vs~~~~~~~i   45 (391)
                      -|+|.+|+||||+|.++..+.    .....+..+.|+.....+.....
T Consensus        41 ~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (258)
T d1v5wa_          41 EAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRL   88 (258)
T ss_dssp             EEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHH
Confidence            489999999999999875421    22345678889888877775543

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.47  E-value=0.025  Score=44.39  Aligned_cols=20  Identities=15%  Similarity=0.265  Sum_probs=17.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.++|-+|+|||||++.+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            56899999999999998754

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.46  E-value=0.022  Score=44.92  Aligned_cols=21  Identities=14%  Similarity=0.219  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-.|+|||||++.+.++
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            579999999999999987553

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.36  E-value=0.027  Score=45.53  Aligned_cols=21  Identities=10%  Similarity=0.045  Sum_probs=18.6

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus         3 V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           3 VLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            679999999999999998664

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=92.27  E-value=0.026  Score=43.50  Aligned_cols=20  Identities=5%  Similarity=0.061  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-+|+|||||..++..
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999999864

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=92.17  E-value=0.015  Score=45.86  Aligned_cols=20  Identities=10%  Similarity=0.003  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|.+++|||||..++..
T Consensus        19 I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          19 VAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             EEEEECTTSSHHHHHTTTCC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999998865

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.03  E-value=0.094  Score=43.33  Aligned_cols=45  Identities=16%  Similarity=0.233  Sum_probs=30.4

Q ss_pred             cEEcCCCCcHHHHHHHHhCCcccc----ccccEEEEEEcCCCcChHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVK----HYFDCHAWVQESLPYDADQIL   46 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk----~~F~~~~~~~vs~~~~~~~i~   46 (391)
                      -|+|.+|+||||+|.++..+...+    ..-..+.|+.....++.....
T Consensus        40 li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (254)
T d1pzna2          40 EVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIR   88 (254)
T ss_dssp             EEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHHH
Confidence            489999999999999875432111    123477888777666665543

>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=91.98  E-value=0.028  Score=46.19  Aligned_cols=35  Identities=17%  Similarity=0.054  Sum_probs=22.9

Q ss_pred             CcEE-cCCCCcHHHHHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVL-DSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~-GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |+|+ |-||+||||+|..+..  .+...=..++++..+
T Consensus         4 Iav~s~KGGvGKTtia~nlA~--~la~~g~~VlliD~D   39 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGV--ALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHH--HHHHTTCCEEEEECC
T ss_pred             EEEECCCCCChHHHHHHHHHH--HHHhCCCCEEEEeCC
Confidence            4566 8999999999998765  233332345555443

>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=91.90  E-value=0.03  Score=47.47  Aligned_cols=18  Identities=22%  Similarity=0.180  Sum_probs=17.1

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|.|||+||+++.+
T Consensus        46 L~Gp~GtGKT~l~~ala~   63 (265)
T d1r7ra3          46 FYGPPGCGKTLLAKAIAN   63 (265)
T ss_dssp             EBCCTTSSHHHHHHHHHH
T ss_pred             EECCCCCcchhHHHHHHH
Confidence            799999999999999987

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.89  E-value=0.028  Score=44.84  Aligned_cols=20  Identities=15%  Similarity=0.172  Sum_probs=17.4

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|+|-+|||||||.+.+.+
T Consensus         5 iv~lG~~~vGKTsll~r~~~   24 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRI   24 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999744

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.88  E-value=0.029  Score=45.25  Aligned_cols=21  Identities=10%  Similarity=0.080  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|.+|+|||||...+.++
T Consensus         6 V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           6 IIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            579999999999999998764

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=91.87  E-value=0.025  Score=45.97  Aligned_cols=20  Identities=15%  Similarity=0.071  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|-|+-|+||||+++.+.+
T Consensus         5 IviEG~dGsGKsT~~~~L~~   24 (210)
T d4tmka_           5 IVIEGLEGAGKTTARNVVVE   24 (210)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57889999999999999876

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=91.80  E-value=0.024  Score=50.42  Aligned_cols=19  Identities=26%  Similarity=0.204  Sum_probs=17.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -+||++|+||||+|+.+.+
T Consensus       158 ~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         158 LFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4799999999999999987

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=91.79  E-value=0.03  Score=46.46  Aligned_cols=20  Identities=15%  Similarity=-0.082  Sum_probs=18.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||.|..|+||||.|+.+.+
T Consensus         4 IgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999999998754

>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=91.67  E-value=0.035  Score=45.07  Aligned_cols=39  Identities=18%  Similarity=-0.038  Sum_probs=23.3

Q ss_pred             cEEcCCCCcHH-HHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            2 AVLDSIGLDKT-AFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         2 gI~GmgGvGKT-TLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      .++|..|+||| |+||..+.   ++..-..++.++.+ .|....
T Consensus        14 ~lvGp~GvGKTTTiaKLA~~---~~~~g~kV~lit~D-t~R~gA   53 (207)
T d1ls1a2          14 FLVGLQGSGKTTTAAKLALY---YKGKGRRPLLVAAD-TQRPAA   53 (207)
T ss_dssp             EEECCTTTTHHHHHHHHHHH---HHHTTCCEEEEECC-SSCHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH---HHHCCCcEEEEecc-cccchH
Confidence            46899999997 55555553   33332345666654 344444

>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=91.55  E-value=0.034  Score=46.21  Aligned_cols=18  Identities=22%  Similarity=0.172  Sum_probs=16.2

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|+||||+|+.+.+
T Consensus        39 l~Gp~G~GKtt~a~~~~~   56 (239)
T d1njfa_          39 FSGTRGVGKTSIARLLAK   56 (239)
T ss_dssp             EECSTTSSHHHHHHHHHH
T ss_pred             EECCCCCcHHHHHHHHHH
Confidence            789999999999999754

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.25  E-value=0.038  Score=45.33  Aligned_cols=21  Identities=10%  Similarity=0.044  Sum_probs=17.8

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|.+|+|||||++.+..+
T Consensus         9 illlG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           9 LLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999997543

>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=91.14  E-value=0.039  Score=45.35  Aligned_cols=34  Identities=15%  Similarity=0.015  Sum_probs=22.9

Q ss_pred             CcEE-cCCCCcHHHHHHHHhCCccccccccEEEEEEc
Q 041097            1 MAVL-DSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQE   36 (391)
Q Consensus         1 igI~-GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~v   36 (391)
                      |+|+ +-||+||||+|..+..  .+...-..++.+.-
T Consensus         5 Iav~~~kGGvGKTtia~nLA~--~la~~g~~VlliD~   39 (237)
T d1g3qa_           5 ISIVSGKGGTGKTTVTANLSV--ALGDRGRKVLAVDG   39 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHH--HHHHTTCCEEEEEC
T ss_pred             EEEECCCCCCcHHHHHHHHHH--HHHhCCCCEEEEeC
Confidence            4677 7799999999999865  34433334555543

>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=91.07  E-value=0.041  Score=44.63  Aligned_cols=18  Identities=11%  Similarity=0.087  Sum_probs=15.9

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|..|+||||+|+.+.+
T Consensus        29 l~Gp~G~GKtt~a~~~a~   46 (207)
T d1a5ta2          29 IQALPGMGDDALIYALSR   46 (207)
T ss_dssp             EECCTTSCHHHHHHHHHH
T ss_pred             EECCCCCcHHHHHHHHHH
Confidence            699999999999997654

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=90.92  E-value=0.072  Score=46.49  Aligned_cols=32  Identities=9%  Similarity=-0.018  Sum_probs=23.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEE
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQ   35 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~   35 (391)
                      |.|=|.-|+||||+++.+.+  .+..... ..+++
T Consensus         9 I~iEG~iGsGKSTl~~~L~~--~l~~~~~-v~~~~   40 (333)
T d1p6xa_           9 IYLDGVYGIGKSTTGRVMAS--AASGGSP-TLYFP   40 (333)
T ss_dssp             EEEECSTTSSHHHHHHHHHS--GGGCSSC-EEEEC
T ss_pred             EEEECCccCCHHHHHHHHHH--HhccCCC-eEEEe
Confidence            57889999999999999988  3444333 33444

>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=90.88  E-value=0.052  Score=43.40  Aligned_cols=70  Identities=13%  Similarity=0.124  Sum_probs=37.8

Q ss_pred             cEEcCCCCcHHHHHHHHhC---Ccccccccc-EEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYS---SNYVKHYFD-CHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLI   77 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~---~~~lk~~F~-~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~L~   77 (391)
                      -++|-+|||||+++..+..   +.++..... ..+| .    .+...++.         +-.+ ....++....+++++.
T Consensus        47 lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~-~----ld~~~LiA---------g~~~-rG~~E~rl~~il~e~~  111 (195)
T d1jbka_          47 VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVL-A----LDMGALVA---------GAKY-RGEFEERLKGVLNDLA  111 (195)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEE-E----ECHHHHHT---------TTCS-HHHHHHHHHHHHHHHH
T ss_pred             EEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEE-E----eeHHHHhc---------cCCc-cHHHHHHHHHHHHHHh
Confidence            4799999999998776644   123433333 4443 2    33444322         0111 1115777788888885


Q ss_pred             cC--ccEEeee
Q 041097           78 NG--GFVGAGK   86 (391)
Q Consensus        78 ~k--~~l~~~~   86 (391)
                      .+  ..+...+
T Consensus       112 ~~~~~iILfID  122 (195)
T d1jbka_         112 KQEGNVILFID  122 (195)
T ss_dssp             HSTTTEEEEEE
T ss_pred             cCCCcEEEEcc
Confidence            43  3344443

>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=90.84  E-value=0.049  Score=47.27  Aligned_cols=18  Identities=17%  Similarity=-0.025  Sum_probs=16.7

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      ++|.+|+|||.||+.+..
T Consensus       128 ~~G~pG~GKT~la~ala~  145 (321)
T d1w44a_         128 VTGKGNSGKTPLVHALGE  145 (321)
T ss_dssp             EECSSSSCHHHHHHHHHH
T ss_pred             EECCCCccHHHHHHHHHH
Confidence            489999999999999987

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.84  E-value=0.027  Score=44.17  Aligned_cols=21  Identities=14%  Similarity=0.211  Sum_probs=8.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.|+|-+|+|||||+..+..+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999876553

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.63  E-value=0.016  Score=44.74  Aligned_cols=20  Identities=10%  Similarity=0.253  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+++|.+|+|||||+..+.+
T Consensus         3 I~liG~~n~GKSSLin~l~g   22 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLN   22 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999999865

>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=90.56  E-value=0.055  Score=45.71  Aligned_cols=64  Identities=19%  Similarity=0.234  Sum_probs=35.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC---Ccccccccc-EEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYS---SNYVKHYFD-CHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQLI   77 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~---~~~lk~~F~-~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~L~   77 (391)
                      -+||.+|||||+++..+..   +..+...+. ..+| .++    ...++.         +-.+ ....++....++.++.
T Consensus        43 lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~-~l~----~~~lia---------g~~~-~g~~e~r~~~i~~~~~  107 (268)
T d1r6bx2          43 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIY-SLD----IGSLLA---------GTKY-RGDFEKRFKALLKQLE  107 (268)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEE-ECC----CC---C---------CCCC-SSCHHHHHHHHHHHHS
T ss_pred             EEECCCCCcHHHHHHHHHHHHHhCCcccccccceeE-Eee----echHhc---------cCcc-chhHHHHHHHHHHHhh
Confidence            4799999999988877654   123344443 3333 222    111111         1112 2337888888888886


Q ss_pred             cCc
Q 041097           78 NGG   80 (391)
Q Consensus        78 ~k~   80 (391)
                      ..+
T Consensus       108 ~~~  110 (268)
T d1r6bx2         108 QDT  110 (268)
T ss_dssp             SSS
T ss_pred             ccC
Confidence            554

>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=90.19  E-value=0.24  Score=38.11  Aligned_cols=43  Identities=7%  Similarity=0.036  Sum_probs=25.6

Q ss_pred             HhhccCCcccEEEcCCC-ccc-----cCCcccCCCCcccEEEccCCCCC
Q 041097          173 KICKMFKFLRVLDLGSL-VLI-----RYPSGIENLFLLRYLKLNIPSLK  215 (391)
Q Consensus       173 ~~~~~~~~L~~L~l~~~-~l~-----~~p~~i~~l~~L~~L~l~~~~i~  215 (391)
                      ......+.|+.|+++++ .+.     .+-..+....+|+.|+++++.+.
T Consensus        11 ~~~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~   59 (166)
T d1io0a_          11 RIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSN   59 (166)
T ss_dssp             HHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCC
T ss_pred             HHHhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCccc
Confidence            34455677777777763 343     23344556667777777776554

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.01  E-value=0.064  Score=43.09  Aligned_cols=43  Identities=5%  Similarity=0.022  Sum_probs=26.8

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccc----cccEEEEEEcCCCcChHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKH----YFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~----~F~~~~~~~vs~~~~~~~   44 (391)
                      -|+|.+|+||||||..+..+.....    .+....++.....+....
T Consensus        27 ~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (242)
T d1n0wa_          27 EMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPER   73 (242)
T ss_dssp             EEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHHH
Confidence            4899999999999988754322221    123455555555555444

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=89.90  E-value=0.057  Score=45.94  Aligned_cols=20  Identities=5%  Similarity=0.067  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|++.+|||||-.++=+
T Consensus         5 ~GivG~Pn~GKSTlf~~lt~   24 (278)
T d1jala1           5 CGIVGLPNVGKSTLFNALTK   24 (278)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHC
Confidence            69999999999999998765

>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=89.83  E-value=0.061  Score=43.51  Aligned_cols=34  Identities=15%  Similarity=0.083  Sum_probs=20.0

Q ss_pred             CcEEcCCCCcHHH-HHHHHhCCccccccccEEEEEEcC
Q 041097            1 MAVLDSIGLDKTA-FAAEAYSSNYVKHYFDCHAWVQES   37 (391)
Q Consensus         1 igI~GmgGvGKTT-La~~vy~~~~lk~~F~~~~~~~vs   37 (391)
                      |.++|+.|+|||| +||....   .+..=..+++++.+
T Consensus         9 i~lvGptGvGKTTTiaKLA~~---~~~~g~kV~lit~D   43 (207)
T d1okkd2           9 VLVVGVNGVGKTTTIAKLGRY---YQNLGKKVMFCAGD   43 (207)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH---HHTTTCCEEEECCC
T ss_pred             EEEECCCCCCHHHHHHHHHHH---HHHCCCcEEEEEec
Confidence            3569999999985 5555432   22111356666655

>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=89.65  E-value=0.064  Score=43.48  Aligned_cols=40  Identities=13%  Similarity=0.082  Sum_probs=23.0

Q ss_pred             CcEEcCCCCcHH-HHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKT-AFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKT-TLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      |..+|+.|+||| |+||..+.   ++..=..++.++. ..|....
T Consensus        12 i~lvGptGvGKTTTiAKLA~~---~~~~g~kV~lit~-Dt~R~gA   52 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQ---FEQQGKSVMLAAG-DTFRAAA   52 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH---HHTTTCCEEEECC-CTTCHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH---HHHCCCcEEEEec-ccccccc
Confidence            356999999997 56666543   3311024445444 4566654

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=89.62  E-value=0.067  Score=43.46  Aligned_cols=40  Identities=18%  Similarity=0.181  Sum_probs=23.9

Q ss_pred             CcEEcCCCCcHH-HHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            1 MAVLDSIGLDKT-AFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         1 igI~GmgGvGKT-TLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      |..+|+.|+||| |+||..+.  ..++. ..++.++.+ .|....
T Consensus        14 i~lvGptGvGKTTTiAKLAa~--~~~~~-~kV~lit~D-t~R~gA   54 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKM--FVDEG-KSVVLAAAD-TFRAAA   54 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--HHHTT-CCEEEEEEC-TTCHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHCC-CceEEEeec-ccccch
Confidence            356999999997 55555543  12222 356777765 344444

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=89.52  E-value=0.069  Score=43.14  Aligned_cols=18  Identities=17%  Similarity=0.097  Sum_probs=15.0

Q ss_pred             EEcCC-CCcHHHHHHHHhC
Q 041097            3 VLDSI-GLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~Gmg-GvGKTTLa~~vy~   20 (391)
                      |.|-| ||||||++-.+..
T Consensus         6 i~gt~~GVGKTtvs~~La~   24 (224)
T d1byia_           6 VTGTDTEVGKTVASCALLQ   24 (224)
T ss_dssp             EEESSTTSCHHHHHHHHHH
T ss_pred             EEECCCCccHHHHHHHHHH
Confidence            88998 9999998777654

>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=89.48  E-value=0.063  Score=41.31  Aligned_cols=19  Identities=16%  Similarity=0.221  Sum_probs=16.7

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      ...|-=|+||||++|.+..
T Consensus        37 ~L~G~LGaGKTtfvr~~~~   55 (158)
T d1htwa_          37 YLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEecCCCccHHHHHHHHHh
Confidence            4579999999999999876

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=89.39  E-value=0.058  Score=47.08  Aligned_cols=34  Identities=18%  Similarity=0.069  Sum_probs=25.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEc
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQE   36 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~v   36 (391)
                      |.|=|.-|+||||+++.+.+  .+...-..+.++++
T Consensus         8 I~IEG~iGsGKSTl~~~L~~--~l~~~g~~v~~~~E   41 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLH--HFAITPNRILLIGE   41 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHH--TTTTSGGGEEEECC
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHhhcCCceEEEeC
Confidence            57889999999999999877  34444345556554

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=89.11  E-value=0.07  Score=46.46  Aligned_cols=20  Identities=20%  Similarity=0.282  Sum_probs=18.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|..|.||||+++++..
T Consensus       169 ili~G~tgSGKTT~l~al~~  188 (323)
T d1g6oa_         169 VIVCGGTGSGKTTYIKSIME  188 (323)
T ss_dssp             EEEEESTTSSHHHHHHHHGG
T ss_pred             EEEEeeccccchHHHHHHhh
Confidence            46899999999999999876

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=88.48  E-value=0.078  Score=45.53  Aligned_cols=21  Identities=14%  Similarity=0.196  Sum_probs=18.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |||+|++.+|||||-.++-+.
T Consensus        13 iGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          13 TGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             EEEEECSSSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            699999999999999998753

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.36  E-value=0.071  Score=43.67  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=17.5

Q ss_pred             cEEcCCCCcHHHHHHHHhCC
Q 041097            2 AVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~   21 (391)
                      .|.|.-|.|||||.+.+..+
T Consensus         7 iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           7 LLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEESSSSSCHHHHHHHHHS
T ss_pred             EEeeCCCCCHHHHHHHHHhc
Confidence            48899999999999998763

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=88.30  E-value=0.059  Score=47.12  Aligned_cols=17  Identities=18%  Similarity=0.161  Sum_probs=15.4

Q ss_pred             EEcCCCCcHHHHHHHHh
Q 041097            3 VLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy   19 (391)
                      ++|..|+|||||||.+-
T Consensus        33 l~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_          33 VFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             EECCGGGCTTHHHHHHH
T ss_pred             EECCCCccHHHHHHHHH
Confidence            68999999999999874

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=88.23  E-value=0.22  Score=41.84  Aligned_cols=49  Identities=14%  Similarity=0.079  Sum_probs=29.9

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHHHHHHHHhh
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQILYDIIKFV   53 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i~~~~~~~~   53 (391)
                      .|.|.+|+||||+|..+.-+.-.++-+. +++|  |-+.+.+.+..++....
T Consensus        39 vi~G~~G~GKT~~~~~la~~~a~~~g~~-v~~~--s~E~~~~~~~~r~~~~~   87 (277)
T d1cr2a_          39 MVTSGSGMGKSTFVRQQALQWGTAMGKK-VGLA--MLEESVEETAEDLIGLH   87 (277)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHTSCCC-EEEE--ESSSCHHHHHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHhhhhhcccc-eeEe--eeccchhhHHhHHHHHh
Confidence            4789999999999888754211223333 3343  34466777766655443

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=88.20  E-value=0.097  Score=44.03  Aligned_cols=18  Identities=22%  Similarity=0.250  Sum_probs=15.5

Q ss_pred             cEEcCCCCcHHHHHHHHh
Q 041097            2 AVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy   19 (391)
                      -|+|.+|+||||||..+.
T Consensus        33 ~i~G~~G~GKS~l~l~la   50 (274)
T d1nlfa_          33 ALVSPGGAGKSMLALQLA   50 (274)
T ss_dssp             EEEESTTSSHHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHH
Confidence            389999999999997764

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=87.60  E-value=0.29  Score=39.89  Aligned_cols=19  Identities=16%  Similarity=0.176  Sum_probs=16.9

Q ss_pred             cEEcCCCCcHHHHHHHHhC
Q 041097            2 AVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~   20 (391)
                      -|+|-+|+||||+|..+..
T Consensus        38 ~i~G~~G~GKT~~~l~~a~   56 (258)
T d2i1qa2          38 EFAGVFGSGKTQIMHQSCV   56 (258)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHH
Confidence            4899999999999999854

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.23  E-value=0.11  Score=44.08  Aligned_cols=20  Identities=15%  Similarity=0.165  Sum_probs=18.0

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-+|.|||||+-++..
T Consensus         9 i~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           9 IGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            68999999999999999853

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=87.15  E-value=0.063  Score=42.60  Aligned_cols=18  Identities=17%  Similarity=0.093  Sum_probs=16.3

Q ss_pred             cEEcCCCCcHHHHHHHHh
Q 041097            2 AVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy   19 (391)
                      .|+|..|+||||+..+++
T Consensus        28 vi~G~NGsGKStil~Ai~   45 (222)
T d1qhla_          28 TLSGGNGAGKSTTMAAFV   45 (222)
T ss_dssp             HHHSCCSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            478999999999999985

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=86.97  E-value=0.11  Score=45.23  Aligned_cols=20  Identities=15%  Similarity=0.116  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |.|=|.-|+||||+++.+.+
T Consensus         7 I~IEG~iGsGKTTl~~~La~   26 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVA   26 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC
T ss_pred             EEEECCcCCCHHHHHHHHHH
Confidence            57889999999999999875

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=86.92  E-value=0.13  Score=43.11  Aligned_cols=21  Identities=14%  Similarity=0.230  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |.++|..|+|||||...++..
T Consensus        35 I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          35 ILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            579999999999999999874

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=86.82  E-value=0.12  Score=40.56  Aligned_cols=20  Identities=15%  Similarity=0.248  Sum_probs=18.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|-.++|||||..++..
T Consensus         8 IaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           8 LGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEeCCCCcHHHHHHHHHH
Confidence            68999999999999999864

>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=86.80  E-value=0.14  Score=44.36  Aligned_cols=18  Identities=17%  Similarity=0.233  Sum_probs=16.3

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      .+|+.|+|||.||+.+..
T Consensus        57 f~Gp~GvGKT~lak~la~   74 (315)
T d1r6bx3          57 FAGPTGVGKTEVTVQLSK   74 (315)
T ss_dssp             EECSTTSSHHHHHHHHHH
T ss_pred             EECCCcchhHHHHHHHHh
Confidence            589999999999999875

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.31  E-value=0.19  Score=40.93  Aligned_cols=23  Identities=9%  Similarity=0.108  Sum_probs=18.9

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccc
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYV   24 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~l   24 (391)
                      .++|..|||||||..++..+..+
T Consensus        99 ~~~G~SGVGKSTLiN~L~~~~~~  121 (225)
T d1u0la2          99 TMAGLSGVGKSSLLNAINPGLKL  121 (225)
T ss_dssp             EEECSTTSSHHHHHHHHSTTCCC
T ss_pred             EEECCCCCCHHHHHHhhcchhhh
Confidence            47899999999999998765333

>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=86.03  E-value=0.21  Score=44.46  Aligned_cols=62  Identities=11%  Similarity=0.168  Sum_probs=32.4

Q ss_pred             cEEcCCCCcHHHHH----HHHhCCccccccc-cEEEEEEcCCCcChHHHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHH
Q 041097            2 AVLDSIGLDKTAFA----AEAYSSNYVKHYF-DCHAWVQESLPYDADQILYDIIKFVMPSPEGFIPDNNEATVEKYLEQL   76 (391)
Q Consensus         2 gI~GmgGvGKTTLa----~~vy~~~~lk~~F-~~~~~~~vs~~~~~~~i~~~~~~~~~~~~eg~~~~~~~~~~~~~~~~L   76 (391)
                      -++|.+|||||+++    +.+.+. ++.... ++.+|.-     +...++.         +-++ ....++....++.++
T Consensus        47 llvG~~GvGKtaiv~~la~~i~~~-~vp~~l~~~~i~~l-----d~~~l~a---------g~~~-~g~~e~r~~~i~~~~  110 (387)
T d1qvra2          47 VLIGEPGVGKTAIVEGLAQRIVKG-DVPEGLKGKRIVSL-----QMGSLLA---------GAKY-RGEFEERLKAVIQEV  110 (387)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHT-CSCTTSTTCEEEEE-----CC---------------------CHHHHHHHHHHHH
T ss_pred             eEECCCCCCHHHHHHHHHHHHHhC-CCCHHHcCceEEEe-----eHhhhhc---------ccCc-chhHHHHHHHHHHHh
Confidence            47999999999976    444443 344333 3555422     2223221         1111 123677778888887


Q ss_pred             HcC
Q 041097           77 ING   79 (391)
Q Consensus        77 ~~k   79 (391)
                      ...
T Consensus       111 ~~~  113 (387)
T d1qvra2         111 VQS  113 (387)
T ss_dssp             HTT
T ss_pred             ccC
Confidence            654

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=85.75  E-value=0.16  Score=41.23  Aligned_cols=17  Identities=29%  Similarity=0.325  Sum_probs=14.9

Q ss_pred             cEEcCCCCcHHHHHHHH
Q 041097            2 AVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~v   18 (391)
                      -|+|..|+||||+|..+
T Consensus        30 ~I~G~~G~GKT~la~~~   46 (242)
T d1tf7a1          30 LVSGTSGTGKTLFSIQF   46 (242)
T ss_dssp             EEEESTTSSHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHH
Confidence            48999999999999764

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=85.58  E-value=0.15  Score=42.98  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=17.0

Q ss_pred             CcEEcCCCCcHHHHHHHH
Q 041097            1 MAVLDSIGLDKTAFAAEA   18 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~v   18 (391)
                      |+|+|-.|.|||||+..+
T Consensus         5 v~iiGh~~~GKTtL~e~l   22 (267)
T d2dy1a2           5 VALVGHAGSGKTTLTEAL   22 (267)
T ss_dssp             EEEEESTTSSHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHH
Confidence            689999999999999987

>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=84.98  E-value=0.41  Score=40.12  Aligned_cols=41  Identities=17%  Similarity=0.150  Sum_probs=31.2

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHHH
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQI   45 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~i   45 (391)
                      |+|..|+||||+|-.++.+.+-.  =..++|+..-..|+.+..
T Consensus        65 ~~G~~~~GKT~l~l~~~~~~q~~--g~~~vyIDtE~~~~~e~a  105 (269)
T d1mo6a1          65 IYGPESSGKTTVALHAVANAQAA--GGVAAFIDAEHALDPDYA  105 (269)
T ss_dssp             EECSSSSSHHHHHHHHHHHHHHT--TCEEEEEESSCCCCHHHH
T ss_pred             EecCCCcHHHHHHHHHHHHHhcC--CCEEEEEECCccCCHHHH
Confidence            79999999999997776643322  247899988778888763

>d1wxqa1 c.37.1.8 (A:1-319) GTP-binding protein PH0525 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein PH0525
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=84.75  E-value=0.16  Score=43.83  Aligned_cols=20  Identities=20%  Similarity=0.295  Sum_probs=18.5

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |||+|.+.+|||||-.++-+
T Consensus         3 v~lvG~pn~GKStlfn~lt~   22 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATL   22 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC
T ss_pred             EeEECCCCCCHHHHHHHHHC
Confidence            79999999999999999865

>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=84.64  E-value=0.32  Score=40.80  Aligned_cols=41  Identities=12%  Similarity=0.065  Sum_probs=31.0

Q ss_pred             cEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      -|+|..|.||||+|-.+.-+.+-..  ..++|+..-..|+.+.
T Consensus        61 ei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~~  101 (268)
T d1xp8a1          61 EIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPVY  101 (268)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHH
T ss_pred             EEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHHH
Confidence            4899999999999998876433222  3688888777788864

>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=84.54  E-value=0.35  Score=38.53  Aligned_cols=44  Identities=11%  Similarity=-0.108  Sum_probs=29.0

Q ss_pred             cEEcCCCCcHHHHHHHHhCCc--cccccccEEEEEEcCCCcChHHH
Q 041097            2 AVLDSIGLDKTAFAAEAYSSN--YVKHYFDCHAWVQESLPYDADQI   45 (391)
Q Consensus         2 gI~GmgGvGKTTLa~~vy~~~--~lk~~F~~~~~~~vs~~~~~~~i   45 (391)
                      =++|..|.||||+|+.+.+.-  .-..|-|....-+.+....++.+
T Consensus        19 l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~I   64 (198)
T d2gnoa2          19 LINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDI   64 (198)
T ss_dssp             EEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHH
Confidence            379999999999999876521  11234466555566555666654

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=84.26  E-value=0.19  Score=44.27  Aligned_cols=18  Identities=22%  Similarity=0.261  Sum_probs=15.4

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      -+|+.|||||-|||.+..
T Consensus        73 fiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          73 LIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             EECCTTSSHHHHHHHHHH
T ss_pred             eeCCCCccHHHHHHHHHh
Confidence            479999999999998754

>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=84.24  E-value=0.19  Score=42.64  Aligned_cols=21  Identities=14%  Similarity=0.025  Sum_probs=18.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      ++|.|-.|+|||||+..+.++
T Consensus        46 ~~I~g~~g~GKT~l~~~i~~~   66 (289)
T d1xpua3          46 GLIVAPPKAGKTMLLQNIAQS   66 (289)
T ss_dssp             EEEEECSSSSHHHHHHHHHHH
T ss_pred             eeEeCCCCCCHHHHHHHHHHH
Confidence            489999999999999998774

>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=83.99  E-value=0.42  Score=39.92  Aligned_cols=40  Identities=10%  Similarity=0.110  Sum_probs=30.2

Q ss_pred             EEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCCcChHH
Q 041097            3 VLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLPYDADQ   44 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~~~~~~   44 (391)
                      |+|..|+||||+|-.+..+.+-+.  ..++|+..-..|+.+.
T Consensus        59 i~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~~   98 (263)
T d1u94a1          59 IYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY   98 (263)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHH
T ss_pred             EecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHHH
Confidence            899999999999999877543332  3577887777787765

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=83.52  E-value=0.23  Score=45.01  Aligned_cols=18  Identities=22%  Similarity=0.342  Sum_probs=16.0

Q ss_pred             EEcCCCCcHHHHHHHHhC
Q 041097            3 VLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         3 I~GmgGvGKTTLa~~vy~   20 (391)
                      .+|+.|+|||-|||.+..
T Consensus        54 liGPTGvGKTlLAr~LAk   71 (443)
T d1g41a_          54 MIGPTGVGKTEIARRLAK   71 (443)
T ss_dssp             EECCTTSSHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            689999999999998765

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=83.48  E-value=0.24  Score=41.69  Aligned_cols=21  Identities=5%  Similarity=0.088  Sum_probs=19.2

Q ss_pred             CcEEcCCCCcHHHHHHHHhCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSS   21 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~   21 (391)
                      |+|+||+.|||+||+..+...
T Consensus       115 v~vvG~PNvGKSsliN~L~~~  135 (273)
T d1puja_         115 ALIIGIPNVGKSTLINRLAKK  135 (273)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEecCccchhhhhhhhhcc
Confidence            589999999999999998874

>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=82.62  E-value=0.33  Score=40.77  Aligned_cols=38  Identities=13%  Similarity=0.131  Sum_probs=27.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLP   39 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~   39 (391)
                      ++|.|-.|+|||||+..+.++. .+.+=+.++|+-+.+.
T Consensus        71 ~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iGer  108 (276)
T d2jdid3          71 IGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGER  108 (276)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEESCC
T ss_pred             EEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEEeccC
Confidence            5899999999999999987642 2233356778777755

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=82.46  E-value=0.27  Score=38.38  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|.|..|+||||+|-.+..
T Consensus        17 vl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          17 VLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            35889999999999988765

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=82.25  E-value=0.27  Score=39.44  Aligned_cols=19  Identities=16%  Similarity=0.254  Sum_probs=17.3

Q ss_pred             CcEEcCCCCcHHHHHHHHh
Q 041097            1 MAVLDSIGLDKTAFAAEAY   19 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy   19 (391)
                      |+|+|=++.|||||+.++.
T Consensus         6 i~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHH
Confidence            6899999999999998874

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=82.16  E-value=0.27  Score=38.33  Aligned_cols=20  Identities=15%  Similarity=0.257  Sum_probs=17.1

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|.|..|+||||+|-.+..
T Consensus        18 vli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          18 VLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            35789999999999988765

>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=80.96  E-value=0.31  Score=40.32  Aligned_cols=20  Identities=15%  Similarity=0.145  Sum_probs=17.9

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |-|+|-.|+|||++|+.++.
T Consensus        26 vlI~Ge~GtGK~~~A~~ih~   45 (247)
T d1ny5a2          26 VLITGESGVGKEVVARLIHK   45 (247)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHH
Confidence            34899999999999999986

>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=80.75  E-value=0.87  Score=38.11  Aligned_cols=37  Identities=14%  Similarity=0.027  Sum_probs=26.3

Q ss_pred             CcEEcCCCCcHHHHHHHHhCCccccccccEEEEEEcCCC
Q 041097            1 MAVLDSIGLDKTAFAAEAYSSNYVKHYFDCHAWVQESLP   39 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~~~~lk~~F~~~~~~~vs~~   39 (391)
                      ++|.|-.|+|||+|++.+-.+  .+..-+.|+++-+...
T Consensus        70 ~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer  106 (276)
T d1fx0a3          70 ELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQK  106 (276)
T ss_dssp             CBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCC
T ss_pred             EeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecch
Confidence            589999999999999875442  2334457777766644

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=80.66  E-value=0.32  Score=39.58  Aligned_cols=20  Identities=20%  Similarity=0.275  Sum_probs=17.7

Q ss_pred             CcEEcCCCCcHHHHHHHHhC
Q 041097            1 MAVLDSIGLDKTAFAAEAYS   20 (391)
Q Consensus         1 igI~GmgGvGKTTLa~~vy~   20 (391)
                      |+|+|=.++|||||+..+..
T Consensus         8 IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           8 VSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEeCCCccHHHHHHHHHh
Confidence            68999999999999988754