Citrus Sinensis ID: 044412

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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-
Protein Sequence
MFVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccHHHHHHHccccccccEEEEHHHHcccccHHHHHHHHHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHcccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHcHHHHHHHHHHccccHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEEHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEHHHHHHHHHHHcccHHHccEEHcccccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MFVKYVRAIITSfkknsfptsvSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFctsrfhfidytilvfpqmqepnvFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHgqvwkngfsspvFVQTAmvdnysysnkffeSRRVSRRLfdemperkfATWNTMIDAYARLAELLFnkmpawdirSWTTMITSYSQNKQFREALDAFNktkksgtgsdqVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG
Flexible Loop (DISEMBL)
MFVKYVRAIitsfkknsfptsvSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFdemperkfatWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG
Low Complexity Region (SEG)
MFVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG
Disordered region (IsUnstruct)
*FVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREAL**************QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY*******
Disordered Region (DISOPRED)
MFVKYVRAII************SFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN*
Disordered Region (DISEMBL)
MFVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG
Disordered Region (DISPRO)
MFVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYEN*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	311	2.2.26 [Sep-21-2011]
Q56X05	577	Pentatricopeptide repeat-	no	no	0.877	0.473	0.398	1e-65
Q9FG16	622	Pentatricopeptide repeat-	no	no	0.852	0.426	0.272	4e-34
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.877	0.440	0.277	7e-34
P0C8Q7	534	Pentatricopeptide repeat-	no	no	0.919	0.535	0.272	1e-33
Q38959	455	Pentatricopeptide repeat-	no	no	0.839	0.573	0.291	9e-32
Q9FIF7	544	Putative pentatricopeptid	no	no	0.948	0.542	0.264	3e-31
O49399	545	Pentatricopeptide repeat-	no	no	0.890	0.508	0.267	5e-31
Q9SIL5	534	Pentatricopeptide repeat-	no	no	0.877	0.511	0.265	5e-31
Q9FMA1	530	Pentatricopeptide repeat-	no	no	0.938	0.550	0.297	7e-31
Q9LN01	741	Pentatricopeptide repeat-	no	no	0.884	0.371	0.262	9e-31

>sp|Q56X05|PPR15_ARATH Pentatricopeptide repeat-containing protein At1g06145 OS=Arabidopsis thaliana GN=EMB1444 PE=2 SV=2

 Score =  249 bits (637), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 143/359 (39%), Positives = 190/359 (52%), Gaps = 86/359 (23%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV 93
           +K+CS+ K LE   A ++KT+ N DC L  QFI+ CTS F  +D  +    QMQEPNVFV
Sbjct: 35  IKQCSTPKLLESALAAMIKTSLNQDCRLMNQFITACTS-FKRLDLAVSTMTQMQEPNVFV 93

Query: 94  YHA----FSSLRHPLQAIAFYLYMLRAEVLLTT-------------------VHGQVWKN 130
           Y+A    F +  HP++++  Y+ MLR  V  ++                   +   +WK 
Sbjct: 94  YNALFKGFVTCSHPIRSLELYVRMLRDSVSPSSYTYSSLVKASSFASRFGESLQAHIWKF 153

Query: 131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL------ 184
           GF   V +QT ++D YS + +  E+R+V    FDEMPER    W TM+ AY R+      
Sbjct: 154 GFGFHVKIQTTLIDFYSATGRIREARKV----FDEMPERDDIAWTTMVSAYRRVLDMDSA 209

Query: 185 ------------------------------AELLFNKMPAWDIRSWTTMITSYSQNKQFR 214
                                         AE LFN+MP  DI SWTTMI  YSQNK++R
Sbjct: 210 NSLANQMSEKNEATSNCLINGYMGLGNLEQAESLFNQMPVKDIISWTTMIKGYSQNKRYR 269

Query: 215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------- 257
           EA+  F K  + G   D+VTM+TV+SACAHLG L++G+ + +Y                 
Sbjct: 270 EAIAVFYKMMEEGIIPDEVTMSTVISACAHLGVLEIGKEVHMYTLQNGFVLDVYIGSALV 329

Query: 258 -----CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
                C SL R+LLVFF L +KNL CWNSI E LA HGFA EAL MF +M  E+V+PN 
Sbjct: 330 DMYSKCGSLERALLVFFNLPKKNLFCWNSIIEGLAAHGFAQEALKMFAKMEMESVKPNA 388

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FG16|PP367_ARATH Pentatricopeptide repeat-containing protein At5g06540 OS=Arabidopsis thaliana GN=PCMP-H88 PE=2 SV=1

 Score =  145 bits (366), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 89/327 (27%), Positives = 161/327 (49%), Gaps = 62/327 (18%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHF------IDYTILVFPQMQ 87
           L+ CSS  +L+ ++  +++T+   D F+A + ++ C     F      + Y   +F Q+Q
Sbjct: 19  LQSCSSFSDLKIIHGFLLRTHLISDVFVASRLLALCVDDSTFNKPTNLLGYAYGIFSQIQ 78

Query: 88  EPNVFVYH----AFSSLRHPLQAIAFYLYMLRAEVLLTTV-------------------- 123
            PN+FV++     FS+   P +A  FY  ML++ +    +                    
Sbjct: 79  NPNLFVFNLLIRCFSTGAEPSKAFGFYTQMLKSRIWPDNITFPFLIKASSEMECVLVGEQ 138

Query: 124 -HGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA 182
            H Q+ + GF + V+V+ ++V  + Y+N  F +   + R+F +M  R   +W +M+  Y 
Sbjct: 139 THSQIVRFGFQNDVYVENSLV--HMYANCGFIA--AAGRIFGQMGFRDVVSWTSMVAGYC 194

Query: 183 RL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMAT 237
           +      A  +F++MP  ++ +W+ MI  Y++N  F +A+D F   K+ G  +++  M +
Sbjct: 195 KCGMVENAREMFDEMPHRNLFTWSIMINGYAKNNCFEKAIDLFEFMKREGVVANETVMVS 254

Query: 238 VLSACAHLGALDLGRGIQIY----------------------CRSLGRSLLVFFKLREKN 275
           V+S+CAHLGAL+ G     Y                      C  + +++ VF  L E +
Sbjct: 255 VISSCAHLGALEFGERAYEYVVKSHMTVNLILGTALVDMFWRCGDIEKAIHVFEGLPETD 314

Query: 276 LLCWNSITEALAIHGFAHEALGMFDRM 302
            L W+SI + LA+HG AH+A+  F +M
Sbjct: 315 SLSWSSIIKGLAVHGHAHKAMHYFSQM 341

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJY7|PP449_ARATH Pentatricopeptide repeat-containing protein At5g66520 OS=Arabidopsis thaliana GN=PCMP-H61 PE=2 SV=1

 Score =  144 bits (364), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 157/331 (47%), Gaps = 58/331 (17%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRF--HFIDYTILVFPQMQEPNV 91
           L++CS  +EL+ ++A ++KT    D +   +F+SFC S     F+ Y  +VF     P+ 
Sbjct: 21  LQRCSKQEELKQIHARMLKTGLMQDSYAITKFLSFCISSTSSDFLPYAQIVFDGFDRPDT 80

Query: 92  FVYH----AFSSLRHPLQAIAFYLYMLRAEV---------LL------------TTVHGQ 126
           F+++     FS    P +++  Y  ML +           LL            T +H Q
Sbjct: 81  FLWNLMIRGFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACSNLSAFEETTQIHAQ 140

Query: 127 VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAE 186
           + K G+ + V+   +++++Y+ +  F    +++  LFD +PE    +WN++I  Y +  +
Sbjct: 141 ITKLGYENDVYAVNSLINSYAVTGNF----KLAHLLFDRIPEPDDVSWNSVIKGYVKAGK 196

Query: 187 L-----LFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSA 241
           +     LF KM   +  SWTTMI+ Y Q    +EAL  F++ + S    D V++A  LSA
Sbjct: 197 MDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPDNVSLANALSA 256

Query: 242 CAHLGALDLGRGIQIY----------------------CRSLGRSLLVFFKLREKNLLCW 279
           CA LGAL+ G+ I  Y                      C  +  +L VF  +++K++  W
Sbjct: 257 CAQLGALEQGKWIHSYLNKTRIRMDSVLGCVLIDMYAKCGEMEEALEVFKNIKKKSVQAW 316

Query: 280 NSITEALAIHGFAHEALGMFDRMTYENVRPN 310
            ++    A HG   EA+  F  M    ++PN
Sbjct: 317 TALISGYAYHGHGREAISKFMEMQKMGIKPN 347

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8Q7|PP369_ARATH Pentatricopeptide repeat-containing protein At5g08305 OS=Arabidopsis thaliana GN=PCMP-E105 PE=2 SV=1

 Score =  144 bits (362), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 95/349 (27%), Positives = 170/349 (48%), Gaps = 63/349 (18%)

Query: 18  FPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCT-SRFHFI 76
             +S S +   I+ +Q   C S+ EL  ++  ++    + +     Q +SF   S    +
Sbjct: 2   LKSSSSLVAKSILRHQ---CKSMSELYKIHTLLITLGLSEEEPFVSQTLSFSALSSSGDV 58

Query: 77  DYTILVFPQMQEPNV----FVYHAFSSLRHPLQAIAFYLYMLRAEVLLT----------- 121
           DY      ++ +P      FV   FS+ R+P ++I+ Y+ MLR  +L             
Sbjct: 59  DYAYKFLSKLSDPPNYGWNFVIRGFSNSRNPEKSISVYIQMLRFGLLPDHMTYPFLMKSS 118

Query: 122 ----------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF 171
                     ++H  V K+G    +F+   ++  Y      F  +  +R+LFDEMP +  
Sbjct: 119 SRLSNRKLGGSLHCSVVKSGLEWDLFICNTLIHMYGS----FRDQASARKLFDEMPHKNL 174

Query: 172 ATWNTMIDAYAR-----LAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKS 226
            TWN+++DAYA+      A L+F++M   D+ +W++MI  Y +  ++ +AL+ F++  + 
Sbjct: 175 VTWNSILDAYAKSGDVVSARLVFDEMSERDVVTWSSMIDGYVKRGEYNKALEIFDQMMRM 234

Query: 227 GTG-SDQVTMATVLSACAHLGALDLGRGIQIY----------------------CRSLGR 263
           G+  +++VTM +V+ ACAHLGAL+ G+ +  Y                      C S+G 
Sbjct: 235 GSSKANEVTMVSVICACAHLGALNRGKTVHRYILDVHLPLTVILQTSLIDMYAKCGSIGD 294

Query: 264 SLLVFFK--LREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
           +  VF++  ++E + L WN+I   LA HGF  E+L +F +M    + P+
Sbjct: 295 AWSVFYRASVKETDALMWNAIIGGLASHGFIRESLQLFHKMRESKIDPD 343

Arabidopsis thaliana (taxid: 3702)

>sp|Q38959|PP257_ARATH Pentatricopeptide repeat-containing protein At3g26630, chloroplastic OS=Arabidopsis thaliana GN=PCMP-A6 PE=2 SV=1

 Score =  137 bits (345), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 93/319 (29%), Positives = 148/319 (46%), Gaps = 58/319 (18%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV 93
           L+ CS+  +L+ ++  I+K N   D  L +Q IS  +S F    Y  LVF Q+Q P+ F 
Sbjct: 27  LRTCSNFSQLKQIHTKIIKHNLTNDQLLVRQLIS-VSSSFGETQYASLVFNQLQSPSTFT 85

Query: 94  YH----AFSSLRHPLQAIAFYLYMLRAEV----------------------LLTTVHGQV 127
           ++    + S    P +A+  ++ M+ +                        L T VHG  
Sbjct: 86  WNLMIRSLSVNHKPREALLLFILMMISHQSQFDKFTFPFVIKACLASSSIRLGTQVHGLA 145

Query: 128 WKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI-----DAYA 182
            K GF + VF Q  ++D Y    K    R+V    FD+MP R   +W TM+     ++  
Sbjct: 146 IKAGFFNDVFFQNTLMDLYFKCGKPDSGRKV----FDKMPGRSIVSWTTMLYGLVSNSQL 201

Query: 183 RLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSAC 242
             AE++FN+MP  ++ SWT MIT+Y +N++  EA   F + +      ++ T+  +L A 
Sbjct: 202 DSAEIVFNQMPMRNVVSWTAMITAYVKNRRPDEAFQLFRRMQVDDVKPNEFTIVNLLQAS 261

Query: 243 AHLGALDLGRGIQIY----------------------CRSLGRSLLVFFKLREKNLLCWN 280
             LG+L +GR +  Y                      C SL  +  VF  ++ K+L  WN
Sbjct: 262 TQLGSLSMGRWVHDYAHKNGFVLDCFLGTALIDMYSKCGSLQDARKVFDVMQGKSLATWN 321

Query: 281 SITEALAIHGFAHEALGMF 299
           S+  +L +HG   EAL +F
Sbjct: 322 SMITSLGVHGCGEEALSLF 340

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIF7|PP435_ARATH Putative pentatricopeptide repeat-containing protein At5g59200, chloroplastic OS=Arabidopsis thaliana GN=PCMP-E41 PE=3 SV=1

 Score =  135 bits (341), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 92/348 (26%), Positives = 160/348 (45%), Gaps = 53/348 (15%)

Query: 11  TSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCT 70
           ++F+++    ++   R   + + L+ C +I  +  ++A I++T  + D F+  + I  C+
Sbjct: 13  STFRRDPDSNTLRLSRRKTLISVLRSCKNIAHVPSIHAKIIRTFHDQDAFVVFELIRVCS 72

Query: 71  SRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVL-----LT 121
           +    +DY   VF  +  PNV++Y A    F S       ++ Y  M+   VL     +T
Sbjct: 73  T-LDSVDYAYDVFSYVSNPNVYLYTAMIDGFVSSGRSADGVSLYHRMIHNSVLPDNYVIT 131

Query: 122 TV------------HGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPER 169
           +V            H QV K GF S   V   M++ Y  S +   +++    +FDEMP+R
Sbjct: 132 SVLKACDLKVCREIHAQVLKLGFGSSRSVGLKMMEIYGKSGELVNAKK----MFDEMPDR 187

Query: 170 KFATWNTMIDAYA-----RLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTK 224
                  MI+ Y+     + A  LF  +   D   WT MI    +NK+  +AL+ F + +
Sbjct: 188 DHVAATVMINCYSECGFIKEALELFQDVKIKDTVCWTAMIDGLVRNKEMNKALELFREMQ 247

Query: 225 KSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------------CRSLG 262
                +++ T   VLSAC+ LGAL+LGR +  +                      C  + 
Sbjct: 248 MENVSANEFTAVCVLSACSDLGALELGRWVHSFVENQRMELSNFVGNALINMYSRCGDIN 307

Query: 263 RSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
            +  VF  +R+K+++ +N++   LA+HG + EA+  F  M     RPN
Sbjct: 308 EARRVFRVMRDKDVISYNTMISGLAMHGASVEAINEFRDMVNRGFRPN 355

Arabidopsis thaliana (taxid: 3702)

>sp|O49399|PP321_ARATH Pentatricopeptide repeat-containing protein At4g18840 OS=Arabidopsis thaliana GN=PCMP-E101 PE=3 SV=2

 Score =  135 bits (339), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 96/359 (26%), Positives = 154/359 (42%), Gaps = 82/359 (22%)

Query: 35  KKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFH--FIDYTILVFPQMQEPNVF 92
           ++  S+ E++  +A ++KT    D F A + ++F  +      + Y   +  ++  PN F
Sbjct: 47  ERAKSLTEIQQAHAFMLKTGLFHDTFSASKLVAFAATNPEPKTVSYAHSILNRIGSPNGF 106

Query: 93  ----VYHAFSSLRHPLQAIAFYLYMLRAEVLLTT---------------------VHGQV 127
               V  A+++   P  A+  +  ML   V                         +HG  
Sbjct: 107 THNSVIRAYANSSTPEVALTVFREMLLGPVFPDKYSFTFVLKACAAFCGFEEGRQIHGLF 166

Query: 128 WKNGFSSPVFVQTAMVDNYSYSNKFFESRRV---------------------------SR 160
            K+G  + VFV+  +V+ Y  S  F  +R+V                           +R
Sbjct: 167 IKSGLVTDVFVENTLVNVYGRSGYFEIARKVLDRMPVRDAVSWNSLLSAYLEKGLVDEAR 226

Query: 161 RLFDEMPERKFATWNTMIDAYA-----RLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE 215
            LFDEM ER   +WN MI  YA     + A+ +F+ MP  D+ SW  M+T+Y+    + E
Sbjct: 227 ALFDEMEERNVESWNFMISGYAAAGLVKEAKEVFDSMPVRDVVSWNAMVTAYAHVGCYNE 286

Query: 216 ALDAFNKTKKSGT-GSDQVTMATVLSACAHLGALDLGRGIQIY----------------- 257
            L+ FNK     T   D  T+ +VLSACA LG+L  G  + +Y                 
Sbjct: 287 VLEVFNKMLDDSTEKPDGFTLVSVLSACASLGSLSQGEWVHVYIDKHGIEIEGFLATALV 346

Query: 258 -----CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
                C  + ++L VF    ++++  WNSI   L++HG   +AL +F  M YE  +PNG
Sbjct: 347 DMYSKCGKIDKALEVFRATSKRDVSTWNSIISDLSVHGLGKDALEIFSEMVYEGFKPNG 405

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIL5|PP165_ARATH Pentatricopeptide repeat-containing protein At2g20540 OS=Arabidopsis thaliana GN=PCMP-E78 PE=2 SV=1

 Score =  135 bits (339), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 88/331 (26%), Positives = 155/331 (46%), Gaps = 58/331 (17%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV 93
           L++  S  E + + A+I+    +   F+  + + FC  +   +DY   +F Q+  PNVF+
Sbjct: 17  LQRVKSRNEWKKINASIIIHGLSQSSFMVTKMVDFC-DKIEDMDYATRLFNQVSNPNVFL 75

Query: 94  YH----AFSSLRHPLQAIAFYLYMLRAEVLLTT----------------------VHGQV 127
           Y+    A++        I  Y  +LR    L                        VHG +
Sbjct: 76  YNSIIRAYTHNSLYCDVIRIYKQLLRKSFELPDRFTFPFMFKSCASLGSCYLGKQVHGHL 135

Query: 128 WKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAEL 187
            K G    V  + A++D Y   +   ++ +V    FDEM ER   +WN+++  YARL ++
Sbjct: 136 CKFGPRFHVVTENALIDMYMKFDDLVDAHKV----FDEMYERDVISWNSLLSGYARLGQM 191

Query: 188 -----LFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSAC 242
                LF+ M    I SWT MI+ Y+    + EA+D F + + +G   D++++ +VL +C
Sbjct: 192 KKAKGLFHLMLDKTIVSWTAMISGYTGIGCYVEAMDFFREMQLAGIEPDEISLISVLPSC 251

Query: 243 AHLGALDLGRGIQIY----------------------CRSLGRSLLVFFKLREKNLLCWN 280
           A LG+L+LG+ I +Y                      C  + +++ +F ++  K+++ W+
Sbjct: 252 AQLGSLELGKWIHLYAERRGFLKQTGVCNALIEMYSKCGVISQAIQLFGQMEGKDVISWS 311

Query: 281 SITEALAIHGFAHEALGMFDRMTYENVRPNG 311
           ++    A HG AH A+  F+ M    V+PNG
Sbjct: 312 TMISGYAYHGNAHGAIETFNEMQRAKVKPNG 342

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FMA1|PP433_ARATH Pentatricopeptide repeat-containing protein At5g56310 OS=Arabidopsis thaliana GN=PCMP-E13 PE=2 SV=1

 Score =  134 bits (338), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 109/367 (29%), Positives = 171/367 (46%), Gaps = 75/367 (20%)

Query: 2   FVKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFL 61
            ++ + A+  S   N F TS   ++IH   N LK   ++K+  C    ++ T  N D   
Sbjct: 1   MIQRINALSLSSGLNWFVTS---LKIH--GNNLK---TLKQSHCY---MIITGLNRDNLN 49

Query: 62  AKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYH----AFSSLRHP-LQAIAFYLY---- 112
             +FI  C++  H + Y   VF     PN ++++    A S L  P   +IA  +Y    
Sbjct: 50  VAKFIEACSNAGH-LRYAYSVFTHQPCPNTYLHNTMIRALSLLDEPNAHSIAITVYRKLW 108

Query: 113 -------------MLRAEVLLTTV------HGQVWKNGFSSPVFVQTAMVDNYSYSNKFF 153
                        +L+  V ++ V      HGQV   GF S V V T ++  Y       
Sbjct: 109 ALCAKPDTFTFPFVLKIAVRVSDVWFGRQIHGQVVVFGFDSSVHVVTGLIQMYFSCGGLG 168

Query: 154 ESRRVSRRLFDEMPERKFATWNTMIDAYARLAEL-----LFNKMPAWDIR---SWTTMIT 205
           ++R+    +FDEM  +    WN ++  Y ++ E+     L   MP W +R   SWT +I+
Sbjct: 169 DARK----MFDEMLVKDVNVWNALLAGYGKVGEMDEARSLLEMMPCW-VRNEVSWTCVIS 223

Query: 206 SYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLG---------RG--- 253
            Y+++ +  EA++ F +        D+VT+  VLSACA LG+L+LG         RG   
Sbjct: 224 GYAKSGRASEAIEVFQRMLMENVEPDEVTLLAVLSACADLGSLELGERICSYVDHRGMNR 283

Query: 254 --------IQIYCRS--LGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMT 303
                   I +Y +S  + ++L VF  + E+N++ W +I   LA HG   EAL MF+RM 
Sbjct: 284 AVSLNNAVIDMYAKSGNITKALDVFECVNERNVVTWTTIIAGLATHGHGAEALAMFNRMV 343

Query: 304 YENVRPN 310
              VRPN
Sbjct: 344 KAGVRPN 350

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LN01|PPR21_ARATH Pentatricopeptide repeat-containing protein At1g08070 OS=Arabidopsis thaliana GN=PCMP-H12 PE=2 SV=1

 Score =  134 bits (337), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 91/347 (26%), Positives = 158/347 (45%), Gaps = 72/347 (20%)

Query: 25  IRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHF--IDYTILV 82
           IR H   + L  C +++ L  ++A ++K   +   +   + I FC    HF  + Y I V
Sbjct: 31  IRNHPSLSLLHNCKTLQSLRIIHAQMIKIGLHNTNYALSKLIEFCILSPHFEGLPYAISV 90

Query: 83  FPQMQEPNVFVY------HAFSSLRHPLQAIAFYLYMLRAEVLLTT-------------- 122
           F  +QEPN+ ++      HA SS   P+ A+  Y+ M+   +L  +              
Sbjct: 91  FKTIQEPNLLIWNTMFRGHALSS--DPVSALKLYVCMISLGLLPNSYTFPFVLKSCAKSK 148

Query: 123 -------VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN 175
                  +HG V K G    ++V T+++  Y  + +  ++ +V    FD+ P R   ++ 
Sbjct: 149 AFKEGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKV----FDKSPHRDVVSYT 204

Query: 176 TMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS 230
            +I  YA       A+ LF+++P  D+ SW  MI+ Y++   ++EAL+ F    K+    
Sbjct: 205 ALIKGYASRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRP 264

Query: 231 DQVTMATVLSACAHLGALDLGRGIQIY----------------------CRSLGRSLLVF 268
           D+ TM TV+SACA  G+++LGR + ++                      C  L  +  +F
Sbjct: 265 DESTMVTVVSACAQSGSIELGRQVHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLF 324

Query: 269 FKLREKNLLCWNSITEALAIHGFAH-----EALGMFDRMTYENVRPN 310
            +L  K+++ WN++     I G+ H     EAL +F  M      PN
Sbjct: 325 ERLPYKDVISWNTL-----IGGYTHMNLYKEALLLFQEMLRSGETPN 366

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	311
224065565	933	predicted protein [Populus trichocarpa]	0.852	0.284	0.486	4e-80
449468660	697	PREDICTED: pentatricopeptide repeat-cont	0.932	0.416	0.418	2e-69
449517761	600	PREDICTED: pentatricopeptide repeat-cont	0.932	0.483	0.415	7e-69
302142959	494	unnamed protein product [Vitis vinifera]	0.749	0.471	0.433	1e-64
334182333	1322	uncharacterized basic helix-loop-helix p	0.874	0.205	0.399	7e-64
193806402	577	RecName: Full=Pentatricopeptide repeat-c	0.877	0.473	0.398	9e-64
62321090	577	hypothetical protein [Arabidopsis thalia	0.877	0.473	0.398	2e-63
297848882	1329	hypothetical protein ARALYDRAFT_311694 [	0.903	0.211	0.389	6e-63
359493640	464	PREDICTED: pentatricopeptide repeat-cont	0.610	0.409	0.508	5e-61
356524477	529	PREDICTED: pentatricopeptide repeat-cont	0.839	0.493	0.392	4e-58

>gi|224065565|ref|XP_002301860.1| predicted protein [Populus trichocarpa] gi|222843586|gb|EEE81133.1| predicted protein [Populus trichocarpa]

 Score =  304 bits (778), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 168/345 (48%), Positives = 201/345 (58%), Gaps = 80/345 (23%)

Query: 46  VYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSLR 101
           +YA +VKTN N DC+L  QFIS   S F+ +DY +L + QM+ PNVFVY+A    F    
Sbjct: 1   MYAVMVKTNTNQDCYLMNQFIS-ALSTFNRMDYAVLAYTQMEIPNVFVYNAMIKGFVQSY 59

Query: 102 HPLQAIAFYLYMLRAEVLLTT---------------------VHGQVWKNGFSSPVFVQT 140
            P+QA+  Y+ MLRA V  T+                     VHG VW+NGF S VFVQT
Sbjct: 60  QPVQALELYVQMLRANVSPTSYTFPSLIKACGLVSQLRFAEAVHGHVWRNGFDSHVFVQT 119

Query: 141 AMVDNYSYSNKFFESRRV---------------------------SRRLFDEMPERKFAT 173
           ++VD YS   +  ES RV                           + RLFD MP+R  AT
Sbjct: 120 SLVDFYSSMGRIEESVRVFDEMPERDVFAWTTMVSGLVRVGDMSSAGRLFDMMPDRNLAT 179

Query: 174 WNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGT 228
           WNT+ID YARL     AELLFN+MPA DI SWTTMI  YSQNK+FREAL  FN+  K G 
Sbjct: 180 WNTLIDGYARLREVDVAELLFNQMPARDIISWTTMINCYSQNKRFREALGVFNEMAKHGI 239

Query: 229 GSDQVTMATVLSACAHLGALDLGRGIQIY----------------------CRSLGRSLL 266
             D+VTMATV+SACAHLGALDLG+ I  Y                      C SL RSLL
Sbjct: 240 SPDEVTMATVISACAHLGALDLGKEIHYYIMQHGFNLDVYIGSALIDMYAKCGSLDRSLL 299

Query: 267 VFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
           +FFKLREKNL CWNS+ E LA+HG+A EAL MFD+M  E ++PNG
Sbjct: 300 MFFKLREKNLFCWNSVIEGLAVHGYAEEALAMFDKMEREKIKPNG 344

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468660|ref|XP_004152039.1| PREDICTED: pentatricopeptide repeat-containing protein At1g06145-like [Cucumis sativus]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 156/373 (41%), Positives = 208/373 (55%), Gaps = 83/373 (22%)

Query: 19  PTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDY 78
           P+  SF +   + N++K CS+I EL  + A+++KTNA  DCFL  QFIS  +   + + Y
Sbjct: 130 PSCPSFKQT--LLNRIKNCSTINELHGLCASMIKTNAIQDCFLVHQFIS-ASFALNSVHY 186

Query: 79  TILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTT------------ 122
            +  F QM+ PNVFVY+A    F    +P +A+  Y++ML    +L T            
Sbjct: 187 PVFAFTQMENPNVFVYNAMIKGFVYCGYPFRALQCYVHMLEESNVLPTSYTFSSLVKACT 246

Query: 123 ----------VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV-------------- 158
                     VH  +WK GF S +FVQTA+VD YS      E+R+V              
Sbjct: 247 FMCAVELGQMVHCHIWKKGFESHLFVQTALVDFYSKLEILSEARKVFDEMCERDAFAWTA 306

Query: 159 -------------SRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPAWDIRSW 200
                        +R+LF+EMPER  ATWNTMID YARL     AELLFN+MP  DI SW
Sbjct: 307 MVSALARVGDMDSARKLFEEMPERNTATWNTMIDGYARLGNVESAELLFNQMPTKDIISW 366

Query: 201 TTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY--- 257
           TTMIT YSQNKQ+++AL  +++ + +G   D+VTM+TV SACAH+GAL+LG+ I  Y   
Sbjct: 367 TTMITCYSQNKQYQDALAIYSEMRLNGIIPDEVTMSTVASACAHIGALELGKEIHHYVMS 426

Query: 258 -------------------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGM 298
                              C SL  SLL+FFKL +KNL CWN++ E LA+HG+A +AL M
Sbjct: 427 QGLNLDVYIGSALVDMYAKCGSLDLSLLIFFKLTDKNLYCWNAVIEGLAVHGYAEKALRM 486

Query: 299 FDRMTYENVRPNG 311
           F  M  E + PNG
Sbjct: 487 FAIMEREKIMPNG 499

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449517761|ref|XP_004165913.1| PREDICTED: pentatricopeptide repeat-containing protein At1g06145-like [Cucumis sativus]

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 155/373 (41%), Positives = 207/373 (55%), Gaps = 83/373 (22%)

Query: 19  PTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDY 78
           P+  SF +   + N++K CS+I EL  + A+++KTNA  DCFL  QFIS  +   + + Y
Sbjct: 33  PSRPSFKQT--LLNRIKNCSTINELHGLCASMIKTNAIQDCFLVHQFIS-ASFALNSVHY 89

Query: 79  TILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTT------------ 122
            +  F QM+ PNVFVY+A    F    +P +A+  Y++ML    +L T            
Sbjct: 90  PVFAFTQMENPNVFVYNAMIKGFVYCGYPFRALQCYVHMLEESNVLPTSYTFSSLVKACT 149

Query: 123 ----------VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV-------------- 158
                     VH  +WK GF S +FVQTA+VD YS      E+R+V              
Sbjct: 150 FMCAVELGQMVHCHIWKKGFESHLFVQTALVDFYSKLEILSEARKVFDEMCERDAFAWTA 209

Query: 159 -------------SRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPAWDIRSW 200
                        +R+LF+EMPER  ATWNTMID Y RL     AELLFN+MP  DI SW
Sbjct: 210 MLSALARVGDMDSARKLFEEMPERNTATWNTMIDGYTRLGNVESAELLFNQMPTKDIISW 269

Query: 201 TTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY--- 257
           TTMIT YSQNKQ+++AL  +++ + +G   D+VTM+TV SACAH+GAL+LG+ I  Y   
Sbjct: 270 TTMITCYSQNKQYQDALAIYSEMRLNGIIPDEVTMSTVASACAHIGALELGKEIHHYVMS 329

Query: 258 -------------------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGM 298
                              C SL  SLL+FFKL +KNL CWN++ E LA+HG+A +AL M
Sbjct: 330 QGLNLDVYIGSALVDMYAKCGSLDLSLLIFFKLTDKNLYCWNAVIEGLAVHGYAEKALRM 389

Query: 299 FDRMTYENVRPNG 311
           F  M  E + PNG
Sbjct: 390 FAIMEREKIMPNG 402

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142959|emb|CBI20254.3| unnamed protein product [Vitis vinifera]

 Score =  253 bits (645), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 147/339 (43%), Positives = 178/339 (52%), Gaps = 106/339 (31%)

Query: 30  IANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEP 89
           +A Q+KKCS +KELE VYA+++K NAN DCFL  QFI+ C S FH IDY IL F  MQEP
Sbjct: 15  LAQQIKKCSMVKELESVYASMIKANANQDCFLMNQFIAAC-SIFHRIDYAILAFTHMQEP 73

Query: 90  NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTT---------------------VH 124
           NVFVY+A         HP+QA+  YL M++A+V  T+                     VH
Sbjct: 74  NVFVYNAMIRALVQCYHPVQALDCYLDMVQAQVSPTSFTFSSLVKACSLVSELGFGEAVH 133

Query: 125 GQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV-------------------------- 158
           G +WK GF S VFVQTA+VD Y  + K  E+RRV                          
Sbjct: 134 GHIWKYGFDSHVFVQTALVDFYGNAGKIVEARRVFDEMSERDVFAWTTMISVHARTGDMS 193

Query: 159 -SRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQ 212
            +R+LFDEMP R  A+WN MID Y+RL     AELLF++MP  DI SWTTMI  YSQNK 
Sbjct: 194 SARQLFDEMPVRNTASWNAMIDGYSRLRNVESAELLFSQMPNRDIISWTTMIACYSQNKH 253

Query: 213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR 272
                                                           L +SL+VFFKLR
Sbjct: 254 ------------------------------------------------LDKSLVVFFKLR 265

Query: 273 EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
           +KNL CWNSI E LA+HG+A EAL MF RM  E ++PNG
Sbjct: 266 KKNLFCWNSIIEGLAVHGYAEEALAMFSRMQREKIKPNG 304

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334182333|ref|NP_172105.4| uncharacterized basic helix-loop-helix protein [Arabidopsis thaliana] gi|8810477|gb|AAF80138.1|AC024174_20 Contains similarity to an unknown protein T5J8.5 gi|4263522 from Arabidopsis thaliana BAC T5J8 gb|AC004044 and contains multiple PPR PF|01535 repeats. ESTs gb|AV565358, gb|AV558710, gb|AV524184 come from this gene [Arabidopsis thaliana] gi|332189826|gb|AEE27947.1| uncharacterized basic helix-loop-helix protein [Arabidopsis thaliana]

 Score =  250 bits (638), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 143/358 (39%), Positives = 190/358 (53%), Gaps = 86/358 (24%)

Query: 34   LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV 93
            +K+CS+ K LE   A ++KT+ N DC L  QFI+ CTS F  +D  +    QMQEPNVFV
Sbjct: 780  IKQCSTPKLLESALAAMIKTSLNQDCRLMNQFITACTS-FKRLDLAVSTMTQMQEPNVFV 838

Query: 94   YHA----FSSLRHPLQAIAFYLYMLRAEVLLTT-------------------VHGQVWKN 130
            Y+A    F +  HP++++  Y+ MLR  V  ++                   +   +WK 
Sbjct: 839  YNALFKGFVTCSHPIRSLELYVRMLRDSVSPSSYTYSSLVKASSFASRFGESLQAHIWKF 898

Query: 131  GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL------ 184
            GF   V +QT ++D YS + +  E+R+V    FDEMPER    W TM+ AY R+      
Sbjct: 899  GFGFHVKIQTTLIDFYSATGRIREARKV----FDEMPERDDIAWTTMVSAYRRVLDMDSA 954

Query: 185  ------------------------------AELLFNKMPAWDIRSWTTMITSYSQNKQFR 214
                                          AE LFN+MP  DI SWTTMI  YSQNK++R
Sbjct: 955  NSLANQMSEKNEATSNCLINGYMGLGNLEQAESLFNQMPVKDIISWTTMIKGYSQNKRYR 1014

Query: 215  EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------- 257
            EA+  F K  + G   D+VTM+TV+SACAHLG L++G+ + +Y                 
Sbjct: 1015 EAIAVFYKMMEEGIIPDEVTMSTVISACAHLGVLEIGKEVHMYTLQNGFVLDVYIGSALV 1074

Query: 258  -----CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
                 C SL R+LLVFF L +KNL CWNSI E LA HGFA EAL MF +M  E+V+PN
Sbjct: 1075 DMYSKCGSLERALLVFFNLPKKNLFCWNSIIEGLAAHGFAQEALKMFAKMEMESVKPN 1132

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|193806402|sp|Q56X05.2|PPR15_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At1g06145; AltName: Full=Protein EMBRYO DEFECTIVE 1444

 Score =  249 bits (637), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 143/359 (39%), Positives = 190/359 (52%), Gaps = 86/359 (23%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV 93
           +K+CS+ K LE   A ++KT+ N DC L  QFI+ CTS F  +D  +    QMQEPNVFV
Sbjct: 35  IKQCSTPKLLESALAAMIKTSLNQDCRLMNQFITACTS-FKRLDLAVSTMTQMQEPNVFV 93

Query: 94  YHA----FSSLRHPLQAIAFYLYMLRAEVLLTT-------------------VHGQVWKN 130
           Y+A    F +  HP++++  Y+ MLR  V  ++                   +   +WK 
Sbjct: 94  YNALFKGFVTCSHPIRSLELYVRMLRDSVSPSSYTYSSLVKASSFASRFGESLQAHIWKF 153

Query: 131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL------ 184
           GF   V +QT ++D YS + +  E+R+V    FDEMPER    W TM+ AY R+      
Sbjct: 154 GFGFHVKIQTTLIDFYSATGRIREARKV----FDEMPERDDIAWTTMVSAYRRVLDMDSA 209

Query: 185 ------------------------------AELLFNKMPAWDIRSWTTMITSYSQNKQFR 214
                                         AE LFN+MP  DI SWTTMI  YSQNK++R
Sbjct: 210 NSLANQMSEKNEATSNCLINGYMGLGNLEQAESLFNQMPVKDIISWTTMIKGYSQNKRYR 269

Query: 215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------- 257
           EA+  F K  + G   D+VTM+TV+SACAHLG L++G+ + +Y                 
Sbjct: 270 EAIAVFYKMMEEGIIPDEVTMSTVISACAHLGVLEIGKEVHMYTLQNGFVLDVYIGSALV 329

Query: 258 -----CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
                C SL R+LLVFF L +KNL CWNSI E LA HGFA EAL MF +M  E+V+PN 
Sbjct: 330 DMYSKCGSLERALLVFFNLPKKNLFCWNSIIEGLAAHGFAQEALKMFAKMEMESVKPNA 388

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62321090|dbj|BAD94184.1| hypothetical protein [Arabidopsis thaliana]

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 143/359 (39%), Positives = 189/359 (52%), Gaps = 86/359 (23%)

Query: 34  LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV 93
           +K+CS+ K LE   A ++KT+ N DC L  QFI+ CTS F  +D  +    QMQEPNVFV
Sbjct: 35  IKQCSTPKLLESALAAMIKTSLNQDCRLMNQFITACTS-FKCLDLAVSTMTQMQEPNVFV 93

Query: 94  YHA----FSSLRHPLQAIAFYLYMLRAEVLLTT-------------------VHGQVWKN 130
           Y+A    F +  HP++++  Y+ MLR  V  ++                   +   +WK 
Sbjct: 94  YNALFKGFVTCSHPIRSLELYVRMLRDSVSPSSYTYSSLVKASSFASRFGESLQAHIWKF 153

Query: 131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL------ 184
           GF   V +QT ++D YS +    E+R+V    FDEMPER    W TM+ AY R+      
Sbjct: 154 GFGFHVKIQTTLIDFYSATGGIREARKV----FDEMPERDDIAWTTMVSAYRRVLDMDSA 209

Query: 185 ------------------------------AELLFNKMPAWDIRSWTTMITSYSQNKQFR 214
                                         AE LFN+MP  DI SWTTMI  YSQNK++R
Sbjct: 210 NSLANQMSEKNEATSNCLINGYMGLGNLEQAESLFNQMPVKDIISWTTMIKGYSQNKRYR 269

Query: 215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------- 257
           EA+  F K  + G   D+VTM+TV+SACAHLG L++G+ + +Y                 
Sbjct: 270 EAIAVFYKMMEEGIIPDEVTMSTVISACAHLGVLEIGKEVHMYTLQNGFVLDVYIGSALV 329

Query: 258 -----CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
                C SL R+LLVFF L +KNL CWNSI E LA HGFA EAL MF +M  E+V+PN 
Sbjct: 330 DMYSKCGSLERALLVFFNLPKKNLFCWNSIIEGLAAHGFAQEALKMFAKMEMESVKPNA 388

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297848882|ref|XP_002892322.1| hypothetical protein ARALYDRAFT_311694 [Arabidopsis lyrata subsp. lyrata] gi|297338164|gb|EFH68581.1| hypothetical protein ARALYDRAFT_311694 [Arabidopsis lyrata subsp. lyrata]

 Score =  247 bits (630), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 140/359 (38%), Positives = 196/359 (54%), Gaps = 78/359 (21%)

Query: 29   IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE 88
            I+   +K+CS+ K LE   A ++KT+   +C+L  QFI+ C+S F+ +D  +    QMQ+
Sbjct: 782  ILKQIIKQCSTPKLLESALAAMIKTSQTQNCYLMNQFITACSS-FNRLDLAVSFMTQMQK 840

Query: 89   PNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTT-------------------VHG 125
            PNVFVY+A    F +  HP++++ FY+ MLR  V  ++                   +  
Sbjct: 841  PNVFVYNALIKGFVTCSHPIRSLEFYVRMLRDSVSPSSYTYSSLVQASAFASGFGESLQA 900

Query: 126  QVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV--------------------------- 158
             +WK GF   V +QT ++  YS S +  E+R+V                           
Sbjct: 901  HIWKFGFGFHVQIQTTLIGFYSASGRIREARKVFDEMPERDDVTWTTMVSAYRQVLDMDS 960

Query: 159  SRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQF 213
            +  L ++MPE+  ATWN +ID Y RL     AE LFN+MP  DI SWTTMI  YS+NK++
Sbjct: 961  ANSLANQMPEKNEATWNCLIDGYTRLGNLELAESLFNQMPVKDIISWTTMINGYSRNKRY 1020

Query: 214  REALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY---------------- 257
            REA+  F K  + G   D+VTM+TV+SACAHLG L++G+ + +Y                
Sbjct: 1021 REAIAVFYKMMEEGIIPDEVTMSTVISACAHLGVLEIGKEVHMYTVQNGFVLDVYIGSAL 1080

Query: 258  ------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
                  C SL R+LLVFF L +KNL CWNSI E LA HGFA EAL MF +M  E+V+PN
Sbjct: 1081 VDMYSKCGSLERALLVFFNLPKKNLFCWNSIIEGLAAHGFAQEALKMFAKMEMESVKPN 1139

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493640|ref|XP_002282675.2| PREDICTED: pentatricopeptide repeat-containing protein At1g06145-like [Vitis vinifera]

 Score =  240 bits (613), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 124/244 (50%), Positives = 149/244 (61%), Gaps = 54/244 (22%)

Query: 122 TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV----------------------- 158
            VHG +WK GF S VFVQTA+VD Y  + K  E+RRV                       
Sbjct: 31  AVHGHIWKYGFDSHVFVQTALVDFYGNAGKIVEARRVFDEMSERDVFAWTTMISVHARTG 90

Query: 159 ----SRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQ 209
               +R+LFDEMP R  A+WN MID Y+RL     AELLF++MP  DI SWTTMI  YSQ
Sbjct: 91  DMSSARQLFDEMPVRNTASWNAMIDGYSRLRNVESAELLFSQMPNRDIISWTTMIACYSQ 150

Query: 210 NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY------------ 257
           NKQFREAL  FN+ + +G   D+VTMAT++SACAHLGALDLG+ I +Y            
Sbjct: 151 NKQFREALAVFNEMQTNGIDPDEVTMATIISACAHLGALDLGKEIHLYAMEMGFDLDVYI 210

Query: 258 ----------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENV 307
                     C SL +SL+VFFKLR+KNL CWNSI E LA+HG+A EAL MF RM  E +
Sbjct: 211 GSALIDMYAKCGSLDKSLVVFFKLRKKNLFCWNSIIEGLAVHGYAEEALAMFSRMQREKI 270

Query: 308 RPNG 311
           +PNG
Sbjct: 271 KPNG 274

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356524477|ref|XP_003530855.1| PREDICTED: pentatricopeptide repeat-containing protein At1g06145-like [Glycine max]

 Score =  231 bits (589), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 134/341 (39%), Positives = 174/341 (51%), Gaps = 80/341 (23%)

Query: 50  IVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAF----SSLRHPLQ 105
           ++KTN   DCFL  QFIS C S    I+     F  +Q PNV V++A         +  Q
Sbjct: 1   MIKTNTTQDCFLVNQFISAC-SNLSCINLAASAFANVQNPNVLVFNALIRGCVHCCYSEQ 59

Query: 106 AIAFYLYMLRAEVLLTT---------------------VHGQVWKNGFSSPVFVQTAMVD 144
           A+  Y++MLR  V+ T+                     VHG VWK+GF S VFVQT +++
Sbjct: 60  ALVHYMHMLRNNVMPTSYSFSSLIKACTLLVDSAFGEAVHGHVWKHGFDSHVFVQTTLIE 119

Query: 145 NYSYSNKFFESRRV---------------------------SRRLFDEMPERKFATWNTM 177
            YS       SRRV                           + RLFDEMPE+  ATWN M
Sbjct: 120 FYSTFGDVGGSRRVFDDMPERDVFAWTTMISAHVRDGDMASAGRLFDEMPEKNVATWNAM 179

Query: 178 IDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ 232
           ID Y +L     AE LFN+MPA DI SWTTM+  YS+NK+++E +  F+     G   D+
Sbjct: 180 IDGYGKLGNAESAEFLFNQMPARDIISWTTMMNCYSRNKRYKEVIALFHDVIDKGMIPDE 239

Query: 233 VTMATVLSACAHLGALDLGRGIQIY----------------------CRSLGRSLLVFFK 270
           VTM TV+SACAHLGAL LG+ + +Y                      C S+  +LLVF+K
Sbjct: 240 VTMTTVISACAHLGALALGKEVHLYLVLQGFDLDVYIGSSLIDMYAKCGSIDMALLVFYK 299

Query: 271 LREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG 311
           L+ KNL CWN I + LA HG+  EAL MF  M  + +RPN 
Sbjct: 300 LQTKNLFCWNCIIDGLATHGYVEEALRMFGEMERKRIRPNA 340

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	311
TAIR|locus:2159602	511	AT5G08510 "AT5G08510" [Arabido	0.604	0.367	0.315	6.7e-26
TAIR|locus:2045580	559	AT2G42920 [Arabidopsis thalian	0.421	0.234	0.328	4.3e-25
TAIR|locus:2167593	657	AT5G44230 [Arabidopsis thalian	0.549	0.260	0.345	1.7e-22
TAIR|locus:2198678	500	PDE247 "pigment defective 247"	0.453	0.282	0.364	1.3e-21
TAIR|locus:2117084	545	AT4G18840 "AT4G18840" [Arabido	0.318	0.181	0.409	1.7e-21
TAIR|locus:2154389	646	LPA66 "LOW PSII ACCUMULATION 6	0.562	0.270	0.303	4.3e-21
TAIR|locus:2084963	661	AT3G04750 "AT3G04750" [Arabido	0.411	0.193	0.312	2e-19
TAIR|locus:2010012	474	AT1G13410 "AT1G13410" [Arabido	0.395	0.259	0.330	3.5e-19
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.553	0.232	0.289	7.1e-19
TAIR|locus:2054789	534	MEF21 "mitochondrial editing f	0.829	0.483	0.270	7.6e-19

TAIR|locus:2159602 AT5G08510 "AT5G08510" [Arabidopsis thaliana (taxid:3702)]

 Score = 238 (88.8 bits), Expect = 6.7e-26, Sum P(2) = 6.7e-26
 Identities = 65/206 (31%), Positives = 104/206 (50%)

Query:    69 CTSRFHFIDYTILVFPQMQEPNVFVYH--AFSSLRHPLQAIAFYLYMLRAEVL----LTT 122
             CT  ++ +     V  Q  E ++ +Y+  +F  LR P      +++   A       L  
Sbjct:    46 CTFLYNKLIQAYYVHHQPHE-SIVLYNLLSFDGLR-PSHHTFNFIFAASASFSSARPLRL 103

Query:   123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA 182
             +H Q +++GF S  F  T ++  Y+       +RRV    FDEM +R    WN MI  Y 
Sbjct:   104 LHSQFFRSGFESDSFCCTTLITAYAKLGALCCARRV----FDEMSKRDVPVWNAMITGYQ 159

Query:   183 RLAEL-----LFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKS-GTGSDQVTMA 236
             R  ++     LF+ MP  ++ SWTT+I+ +SQN  + EAL  F   +K      + +T+ 
Sbjct:   160 RRGDMKAAMELFDSMPRKNVTSWTTVISGFSQNGNYSEALKMFLCMEKDKSVKPNHITVV 219

Query:   237 TVLSACAHLGALDLGRGIQIYCRSLG 262
             +VL ACA+LG L++GR ++ Y R  G
Sbjct:   220 SVLPACANLGELEIGRRLEGYARENG 245

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2045580 AT2G42920 [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 4.3e-25, Sum P(3) = 4.3e-25
 Identities = 46/140 (32%), Positives = 74/140 (52%)

Query:   123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA 182
             +HG V K G     F++  M+  Y       E+ R+    F  M       WN+MI  +A
Sbjct:   148 LHGMVIKEGLEDDSFIRNTMLHMYVTCGCLIEAWRI----FLGMIGFDVVAWNSMIMGFA 203

Query:   183 RL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMAT 237
             +      A+ LF++MP  +  SW +MI+ + +N +F++ALD F + ++     D  TM +
Sbjct:   204 KCGLIDQAQNLFDEMPQRNGVSWNSMISGFVRNGRFKDALDMFREMQEKDVKPDGFTMVS 263

Query:   238 VLSACAHLGALDLGRGIQIY 257
             +L+ACA+LGA + GR I  Y
Sbjct:   264 LLNACAYLGASEQGRWIHEY 283

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2167593 AT5G44230 [Arabidopsis thaliana (taxid:3702)]

 Score = 245 (91.3 bits), Expect = 1.7e-22, Sum P(2) = 1.7e-22
 Identities = 66/191 (34%), Positives = 106/191 (55%)

Query:   124 HGQVWK-NGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA 182
             H Q ++  GF   V+V   M+D Y       ES   +R++FDEMPER   +W  +I AYA
Sbjct:   172 HAQTFRLRGFCF-VYVGNTMIDMYVKC----ESIDCARKVFDEMPERDVISWTELIAAYA 226

Query:   183 RLAEL-----LFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMAT 237
             R+  +     LF  +P  D+ +WT M+T ++QN + +EAL+ F++ +KSG  +D+VT+A 
Sbjct:   227 RVGNMECAAELFESLPTKDMVAWTAMVTGFAQNAKPQEALEYFDRMEKSGIRADEVTVAG 286

Query:   238 VLSACAHLGALDLG-RGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEAL 296
              +SACA LGA     R +QI  +S G S          +++  +++ +  +  G   EA+
Sbjct:   287 YISACAQLGASKYADRAVQIAQKS-GYS-------PSDHVVIGSALIDMYSKCGNVEEAV 338

Query:   297 GMFDRMTYENV 307
              +F  M  +NV
Sbjct:   339 NVFMSMNNKNV 349

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2198678 PDE247 "pigment defective 247" [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 1.3e-21, Sum P(2) = 1.3e-21
 Identities = 55/151 (36%), Positives = 78/151 (51%)

Query:   116 AEVLLTTVHGQVWKNGFS-SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATW 174
             +E L   +HG   K G   + V V TA++  YS   +F ++R V    FD M ++   TW
Sbjct:    88 SEALGDLLHGYACKLGLDRNHVMVGTAIIGMYSKRGRFKKARLV----FDYMEDKNSVTW 143

Query:   175 NTMIDAYARLAEL-----LFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG 229
             NTMID Y R  ++     +F+KMP  D+ SWT MI  + +     EAL  F + + SG  
Sbjct:   144 NTMIDGYMRSGQVDNAAKMFDKMPERDLISWTAMINGFVKKGYQEEALLWFREMQISGVK 203

Query:   230 SDQVTMATVLSACAHLGALDLGRGIQIYCRS 260
              D V +   L+AC +LGAL  G  +  Y  S
Sbjct:   204 PDYVAIIAALNACTNLGALSFGLWVHRYVLS 234

GO:0005739 "mitochondrion" evidence=ISM

GO:0009451 "RNA modification" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2117084 AT4G18840 "AT4G18840" [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 1.7e-21, Sum P(2) = 1.7e-21
 Identities = 43/105 (40%), Positives = 60/105 (57%)

Query:   159 SRRLFDEMPERKFATWNTMIDAYA-----RLAELLFNKMPAWDIRSWTTMITSYSQNKQF 213
             +R LFDEM ER   +WN MI  YA     + A+ +F+ MP  D+ SW  M+T+Y+    +
Sbjct:   225 ARALFDEMEERNVESWNFMISGYAAAGLVKEAKEVFDSMPVRDVVSWNAMVTAYAHVGCY 284

Query:   214 REALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIY 257
              E L+ FNK     T   D  T+ +VLSACA LG+L  G  + +Y
Sbjct:   285 NEVLEVFNKMLDDSTEKPDGFTLVSVLSACASLGSLSQGEWVHVY 329

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2154389 LPA66 "LOW PSII ACCUMULATION 66" [Arabidopsis thaliana (taxid:3702)]

 Score = 212 (79.7 bits), Expect = 4.3e-21, Sum P(2) = 4.3e-21
 Identities = 61/201 (30%), Positives = 101/201 (50%)

Query:   123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVS--RRLFDE----MPERK-----F 171
             +HG   K GF    FV + +V  Y     F +  RV   + + ++    M +R+      
Sbjct:   150 IHGLALKYGFGGDEFVMSNLVRMYVMCG-FMKDARVLFYKNIIEKDMVVMTDRRKRDGEI 208

Query:   172 ATWNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKS 226
               WN MID Y RL     A +LF+KM    + SW TMI+ YS N  F++A++ F + KK 
Sbjct:   209 VLWNVMIDGYMRLGDCKAARMLFDKMRQRSVVSWNTMISGYSLNGFFKDAVEVFREMKKG 268

Query:   227 GTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEAL 286
                 + VT+ +VL A + LG+L+LG  + +Y    G        +R  ++L  +++ +  
Sbjct:   269 DIRPNYVTLVSVLPAISRLGSLELGEWLHLYAEDSG--------IRIDDVL-GSALIDMY 319

Query:   287 AIHGFAHEALGMFDRMTYENV 307
             +  G   +A+ +F+R+  ENV
Sbjct:   320 SKCGIIEKAIHVFERLPRENV 340

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0007020 "microtubule nucleation" evidence=RCA

TAIR|locus:2084963 AT3G04750 "AT3G04750" [Arabidopsis thaliana (taxid:3702)]

 Score = 158 (60.7 bits), Expect = 2.0e-19, Sum P(3) = 2.0e-19
 Identities = 44/141 (31%), Positives = 76/141 (53%)

Query:   123 VHGQVWKNG--FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA 180
             VHG + + G  +SS + +  A++D Y    K  ES  +++R FD M ++   +WNTM+  
Sbjct:   254 VHGWIERRGPVYSSNLILSNALLDMYF---KCKESG-LAKRAFDAMKKKDMRSWNTMVVG 309

Query:   181 YARL-----AELLFNKMPAWDIRSWTTMITSYSQNK-QFREALDAFNK-TKKSGTGSDQV 233
             + RL     A+ +F++MP  D+ SW +++  YS+     R   + F + T       D+V
Sbjct:   310 FVRLGDMEAAQAVFDQMPKRDLVSWNSLLFGYSKKGCDQRTVRELFYEMTIVEKVKPDRV 369

Query:   234 TMATVLSACAHLGALDLGRGI 254
             TM +++S  A+ G L  GR +
Sbjct:   370 TMVSLISGAANNGELSHGRWV 390

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2010012 AT1G13410 "AT1G13410" [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 3.5e-19, Sum P(2) = 3.5e-19
 Identities = 44/133 (33%), Positives = 70/133 (52%)

Query:   136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAEL-----LFN 190
             + +   M+  Y       E+R     LFD+MP R   +WNT+++ YA + ++     +F+
Sbjct:    90 IVLWNTMISGYIEMGNMLEARS----LFDQMPCRDVMSWNTVLEGYANIGDMEACERVFD 145

Query:   191 KMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG-SDQVTMATVLSACAHLGALD 249
              MP  ++ SW  +I  Y+QN +  E L +F +    G+   +  TM  VLSACA LGA D
Sbjct:   146 DMPERNVFSWNGLIKGYAQNGRVSEVLGSFKRMVDEGSVVPNDATMTLVLSACAKLGAFD 205

Query:   250 LGRGIQIYCRSLG 262
              G+ +  Y  +LG
Sbjct:   206 FGKWVHKYGETLG 218

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2205200 OTP82 "AT1G08070" [Arabidopsis thaliana (taxid:3702)]

 Score = 237 (88.5 bits), Expect = 7.1e-19, P = 7.1e-19
 Identities = 55/190 (28%), Positives = 99/190 (52%)

Query:   123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA 182
             +HG V K G    ++V T+++  Y  + +  ++ +V    FD+ P R   ++  +I  YA
Sbjct:   156 IHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKV----FDKSPHRDVVSYTALIKGYA 211

Query:   183 RL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMAT 237
                    A+ LF+++P  D+ SW  MI+ Y++   ++EAL+ F    K+    D+ TM T
Sbjct:   212 SRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVT 271

Query:   238 VLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALG 297
             V+SACA  G+++LGR + ++    G            NL   N++ +  +  G    A G
Sbjct:   272 VVSACAQSGSIELGRQVHLWIDDHGFG---------SNLKIVNALIDLYSKCGELETACG 322

Query:   298 MFDRMTYENV 307
             +F+R+ Y++V
Sbjct:   323 LFERLPYKDV 332

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2054789 MEF21 "mitochondrial editing factor 21" [Arabidopsis thaliana (taxid:3702)]

 Score = 234 (87.4 bits), Expect = 7.6e-19, P = 7.6e-19
 Identities = 77/285 (27%), Positives = 140/285 (49%)

Query:    29 IIANQLKKCSSIKELECVYAT-IVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ 87
             ++   +  C  I++++  YAT +    +N + FL    I   T    + D  I ++ Q+ 
Sbjct:    44 MVTKMVDFCDKIEDMD--YATRLFNQVSNPNVFLYNSIIRAYTHNSLYCD-VIRIYKQLL 100

Query:    88 EPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYS 147
               +  +   F+      ++ A     L +  L   VHG + K G    V  + A++D Y 
Sbjct:   101 RKSFELPDRFT-FPFMFKSCA----SLGSCYLGKQVHGHLCKFGPRFHVVTENALIDMYM 155

Query:   148 YSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAEL-----LFNKMPAWDIRSWTT 202
               +   ++ +V    FDEM ER   +WN+++  YARL ++     LF+ M    I SWT 
Sbjct:   156 KFDDLVDAHKV----FDEMYERDVISWNSLLSGYARLGQMKKAKGLFHLMLDKTIVSWTA 211

Query:   203 MITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLG 262
             MI+ Y+    + EA+D F + + +G   D++++ +VL +CA LG+L+LG+ I +Y    G
Sbjct:   212 MISGYTGIGCYVEAMDFFREMQLAGIEPDEISLISVLPSCAQLGSLELGKWIHLYAERRG 271

Query:   263 RSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENV 307
                  F K   +  +C N++ E  +  G   +A+ +F +M  ++V
Sbjct:   272 -----FLK---QTGVC-NALIEMYSKCGVISQAIQLFGQMEGKDV 307

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00027739001 SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (581 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	311
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	5e-19
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	8e-19
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-12
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-11
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-11
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-09
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	6e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-05
pfam01535	31	pfam01535, PPR, PPR repeat	0.003

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 87.2 bits (216), Expect = 5e-19
 Identities = 62/227 (27%), Positives = 91/227 (40%), Gaps = 60/227 (26%)

Query: 113 MLRAEVLLTTV------HGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEM 166
           MLRA   L +       H  V K G     FV  A++D YS      ++R V    FD M
Sbjct: 230 MLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV----FDGM 285

Query: 167 PERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKS 226
           PE+    WN+M+  YA                     +  YS+     EAL  + + + S
Sbjct: 286 PEKTTVAWNSMLAGYA---------------------LHGYSE-----EALCLYYEMRDS 319

Query: 227 GTGSDQVTMATVLSACAHLGALDL-----------GRGIQI---------YCRSLGR--- 263
           G   DQ T + ++   + L  L+            G  + I         Y +  GR   
Sbjct: 320 GVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSK-WGRMED 378

Query: 264 SLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
           +  VF ++  KNL+ WN++      HG   +A+ MF+RM  E V PN
Sbjct: 379 ARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPN 425

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 86.8 bits (215), Expect = 8e-19
 Identities = 55/186 (29%), Positives = 91/186 (48%), Gaps = 32/186 (17%)

Query: 156 RRVSRRLFDEMPERKFAT----WNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITS 206
            R+ R +   + +  FA      N++I  Y  L     AE +F++M   D  SWT MI+ 
Sbjct: 304 ERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

Query: 207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLG---------RGIQIY 257
           Y +N    +AL+ +   ++     D++T+A+VLSACA LG LD+G         +G+  Y
Sbjct: 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISY 423

Query: 258 -------------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY 304
                        C+ + ++L VF  + EK+++ W SI   L ++    EAL  F +M  
Sbjct: 424 VVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL 483

Query: 305 ENVRPN 310
             ++PN
Sbjct: 484 -TLKPN 488

Length = 857

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 68.0 bits (166), Expect = 1e-12
 Identities = 45/163 (27%), Positives = 73/163 (44%), Gaps = 27/163 (16%)

Query: 175 NTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG 229
           N +I  Y +      A L+F++MP  D  SW  MI+ Y +N +  E L+ F   ++    
Sbjct: 226 NALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVD 285

Query: 230 SDQVTMATVLSACAHLGALDLGRGIQIY------------CRSL----------GRSLLV 267
            D +T+ +V+SAC  LG   LGR +  Y            C SL          G +  V
Sbjct: 286 PDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKV 345

Query: 268 FFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
           F ++  K+ + W ++      +G   +AL  +  M  +NV P+
Sbjct: 346 FSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPD 388

Length = 857

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 64.9 bits (158), Expect = 1e-11
 Identities = 42/162 (25%), Positives = 69/162 (42%), Gaps = 27/162 (16%)

Query: 175 NTMIDAYARLAEL-----LFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG 229
           N +I+ Y++   +     +F+ +P  D+ SWT++I     N +  EAL  F +   +   
Sbjct: 428 NALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LK 486

Query: 230 SDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVF--------------------- 268
            + VT+   LSACA +GAL  G+ I  +    G     F                     
Sbjct: 487 PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQ 546

Query: 269 FKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN 310
           F   EK+++ WN +      HG    A+ +F+RM    V P+
Sbjct: 547 FNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPD 588

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 62.2 bits (151), Expect = 8e-11
 Identities = 43/166 (25%), Positives = 66/166 (39%), Gaps = 48/166 (28%)

Query: 159 SRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALD 218
           +RRLFDEMPER  A+W T+I                                  +REA  
Sbjct: 177 ARRLFDEMPERNLASWGTIIGGLVDAG--------------------------NYREAFA 210

Query: 219 AFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRG--------------------IQIY- 257
            F +  + G+ ++  T   +L A A LG+   G+                     I +Y 
Sbjct: 211 LFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYS 270

Query: 258 -CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRM 302
            C  +  +  VF  + EK  + WNS+    A+HG++ EAL ++  M
Sbjct: 271 KCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEM 316

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 59.1 bits (143), Expect = 1e-09
 Identities = 48/186 (25%), Positives = 74/186 (39%), Gaps = 31/186 (16%)

Query: 154 ESRRVSRRLFDEMPERKFATWNTMIDAYARLAEL-----LFNKMPAWDIRSWTTMITSYS 208
           E  RV  R     P       N M+  + R  EL     +F KMP  D+ SW  ++  Y+
Sbjct: 104 EGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYA 163

Query: 209 QNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRG--------------- 253
           +   F EAL  +++   +G   D  T   VL  C   G  DL RG               
Sbjct: 164 KAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCG--GIPDLARGREVHAHVVRFGFELD 221

Query: 254 -------IQIY--CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY 304
                  I +Y  C  +  + LVF ++  ++ + WN++      +G   E L +F  M  
Sbjct: 222 VDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRE 281

Query: 305 ENVRPN 310
            +V P+
Sbjct: 282 LSVDPD 287

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 50.6 bits (121), Expect = 6e-07
 Identities = 44/179 (24%), Positives = 66/179 (36%), Gaps = 40/179 (22%)

Query: 124 HGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR 183
           H  + + GF   +   TA+VD YS                          W  M DA   
Sbjct: 348 HAGLIRTGFPLDIVANTALVDLYS-------------------------KWGRMEDA--- 379

Query: 184 LAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACA 243
               +F++MP  ++ SW  +I  Y  + +  +A++ F +    G   + VT   VLSAC 
Sbjct: 380 --RNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACR 437

Query: 244 HLGALDLGRGI-QIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDR 301
           + G  + G  I Q    +         K R  +  C   + E L   G   EA  M  R
Sbjct: 438 YSGLSEQGWEIFQSMSENHR------IKPRAMHYAC---MIELLGREGLLDEAYAMIRR 487

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 12/80 (15%)

Query: 175 NTMIDAYARLAELLFNKMPAW--------DIRSWTTMITSYSQNKQFREALDAFNKTKKS 226
           N ++D Y R   +      AW        D+ SW  ++T Y  + +   A++ FN+  +S
Sbjct: 528 NALLDLYVRCGRM----NYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVES 583

Query: 227 GTGSDQVTMATVLSACAHLG 246
           G   D+VT  ++L AC+  G
Sbjct: 584 GVNPDEVTFISLLCACSRSG 603

Length = 857

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 40.1 bits (95), Expect = 4e-05
 Identities = 13/49 (26%), Positives = 24/49 (48%)

Query: 196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH 244
           D+ ++ T+I  Y +  +  EAL  FN+ KK G   +  T + ++     
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 34.4 bits (80), Expect = 0.003
 Identities = 8/29 (27%), Positives = 18/29 (62%)

Query: 199 SWTTMITSYSQNKQFREALDAFNKTKKSG 227
           ++ ++I+ Y +  +  EAL+ F + K+ G
Sbjct: 2   TYNSLISGYCKAGKLEEALELFKEMKEKG 30

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	311
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.68
PF13041	50	PPR_2: PPR repeat family	99.63
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.55
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.53
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.47
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.39
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.24
PF13041	50	PPR_2: PPR repeat family	99.12
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.11
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.08
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.01
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.92
PF12854	34	PPR_1: PPR repeat	98.91
PF12854	34	PPR_1: PPR repeat	98.88
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.87
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.85
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.81
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.78
PRK14574	822	hmsH outer membrane protein; Provisional	98.78
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.77
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.75
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.74
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.72
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.71
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.7
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.68
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.67
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.66
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.66
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.62
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.61
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.6
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.59
PRK14574	822	hmsH outer membrane protein; Provisional	98.55
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.54
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.5
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.48
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.48
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.45
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.43
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.42
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.32
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.28
KOG1126	638	consensus DNA-binding cell division cycle control	98.26
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.26
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.2
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.2
KOG1126	638	consensus DNA-binding cell division cycle control	98.15
KOG1129	478	consensus TPR repeat-containing protein [General f	98.06
PRK12370	553	invasion protein regulator; Provisional	98.04
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.99
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.92
PRK11189	296	lipoprotein NlpI; Provisional	97.9
KOG2003	840	consensus TPR repeat-containing protein [General f	97.88
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.86
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	97.83
KOG2076	895	consensus RNA polymerase III transcription factor	97.79
PRK12370	553	invasion protein regulator; Provisional	97.72
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.7
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.7
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.67
KOG2076	895	consensus RNA polymerase III transcription factor	97.64
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.61
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.6
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.54
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.44
PRK15359	144	type III secretion system chaperone protein SscB;	97.43
KOG2003	840	consensus TPR repeat-containing protein [General f	97.36
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.35
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.34
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.31
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.3
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.3
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.27
KOG1129	478	consensus TPR repeat-containing protein [General f	97.25
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.23
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.2
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.15
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.13
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.09
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.09
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.07
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.04
PRK11189	296	lipoprotein NlpI; Provisional	97.02
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.0
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	96.99
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.98
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.98
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.96
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.95
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.95
PRK15359	144	type III secretion system chaperone protein SscB;	96.94
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	96.94
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.82
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	96.74
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	96.73
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.71
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.68
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.65
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.63
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.63
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.62
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.61
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.6
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.59
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.58
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.53
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.53
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.49
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.46
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.41
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	96.38
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.36
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.31
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.26
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.22
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.22
KOG0495	913	consensus HAT repeat protein [RNA processing and m	96.15
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.15
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.11
KOG3941	406	consensus Intermediate in Toll signal transduction	96.11
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.07
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.04
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	95.99
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	95.95
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	95.89
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	95.87
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.86
KOG0547	606	consensus Translocase of outer mitochondrial membr	95.73
PRK14720	906	transcript cleavage factor/unknown domain fusion p	95.71
KOG3060	289	consensus Uncharacterized conserved protein [Funct	95.68
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.63
KOG4340	459	consensus Uncharacterized conserved protein [Funct	95.57
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	95.53
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.53
PLN02789	320	farnesyltranstransferase	95.52
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	95.52
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.46
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	95.44
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	95.43
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	95.42
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.39
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.36
PLN02789	320	farnesyltranstransferase	95.24
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.22
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.17
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.08
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.08
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	94.99
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	94.89
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	94.87
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.86
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.85
COG4783	484	Putative Zn-dependent protease, contains TPR repea	94.76
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	94.57
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.56
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	94.43
PF03704	146	BTAD: Bacterial transcriptional activator domain;	93.99
PF12688	120	TPR_5: Tetratrico peptide repeat	93.77
KOG3941	406	consensus Intermediate in Toll signal transduction	93.77
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.51
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	93.44
KOG0553	304	consensus TPR repeat-containing protein [General f	93.38
KOG2376	652	consensus Signal recognition particle, subunit Srp	93.36
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.3
KOG1125	579	consensus TPR repeat-containing protein [General f	93.25
KOG2041	1189	consensus WD40 repeat protein [General function pr	92.97
PF12688	120	TPR_5: Tetratrico peptide repeat	92.88
PRK10803	263	tol-pal system protein YbgF; Provisional	92.74
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	92.22
PRK04841	903	transcriptional regulator MalT; Provisional	92.15
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	91.82
PRK14720	906	transcript cleavage factor/unknown domain fusion p	91.78
KOG0553	304	consensus TPR repeat-containing protein [General f	91.77
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	91.74
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	91.67
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	91.56
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	91.54
KOG3785	557	consensus Uncharacterized conserved protein [Funct	91.4
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	91.23
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	91.22
PRK04841	903	transcriptional regulator MalT; Provisional	91.2
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	91.06
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	90.61
smart00299	140	CLH Clathrin heavy chain repeat homology.	90.45
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	90.29
KOG2796	366	consensus Uncharacterized conserved protein [Funct	90.26
smart00299	140	CLH Clathrin heavy chain repeat homology.	90.22
KOG4340	459	consensus Uncharacterized conserved protein [Funct	90.21
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	90.14
PF13762	145	MNE1: Mitochondrial splicing apparatus component	90.07
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	89.78
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	89.72
KOG2796	366	consensus Uncharacterized conserved protein [Funct	89.4
COG3629	280	DnrI DNA-binding transcriptional activator of the	89.4
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	89.35
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	88.54
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	88.52
KOG3060	289	consensus Uncharacterized conserved protein [Funct	88.51
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	87.75
PF13371	73	TPR_9: Tetratricopeptide repeat	87.5
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	87.49
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	87.39
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	87.29
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	86.97
PF13428	44	TPR_14: Tetratricopeptide repeat	86.93
KOG1125	579	consensus TPR repeat-containing protein [General f	86.06
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	86.05
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	86.04
PF13371	73	TPR_9: Tetratricopeptide repeat	85.98
PRK10803	263	tol-pal system protein YbgF; Provisional	85.84
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	85.8
PRK15331	165	chaperone protein SicA; Provisional	85.68
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	85.68
COG4700	251	Uncharacterized protein conserved in bacteria cont	85.62
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	85.12
KOG4570	418	consensus Uncharacterized conserved protein [Funct	84.22
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	84.16
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	84.16
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	83.53
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	82.99
KOG2376	652	consensus Signal recognition particle, subunit Srp	82.43
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	82.34
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	82.29
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	82.0
PF13428	44	TPR_14: Tetratricopeptide repeat	81.8
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	81.16
PHA02875	413	ankyrin repeat protein; Provisional	81.1

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=4.3e-46  Score=353.50  Aligned_cols=278  Identities=20%  Similarity=0.317  Sum_probs=237.1

Q ss_pred             HHHHHHHhhc---cChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccC
Q 044412           28 HIIANQLKKC---SSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~---~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~  100 (311)
                      .+|..++.+|   +..+.+++++..|++.|+.||..+||.||++| ++.|+++.|.++|++|++||.++||+    |++.
T Consensus       124 ~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y-~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~  202 (697)
T PLN03081        124 STYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMH-VKCGMLIDARRLFDEMPERNLASWGTIIGGLVDA  202 (697)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHH-hcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHC
Confidence            3455555555   45556699999999999999999999999999 99999999999999999999999999    9999


Q ss_pred             CChhHHHHHHHHHHHCCCCch---------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLT---------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVS  159 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~---------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a  159 (311)
                      |++++|+++|++|.+.|+.|+                     ++|..+.+.|+.||..+||+||++|+++|++++    |
T Consensus       203 g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~----A  278 (697)
T PLN03081        203 GNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIED----A  278 (697)
T ss_pred             cCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHH----H
Confidence            999999999999999999887                     777888899999999999999999999999999    9


Q ss_pred             HHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC----CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC
Q 044412          160 RRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP----AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS  230 (311)
Q Consensus       160 ~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~----~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  230 (311)
                      .++|+.|+++|+++||++|.+|++.     |.++|++|.    .||..||+++|.+|++.|++++|.+++.+|.+.|+.|
T Consensus       279 ~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~  358 (697)
T PLN03081        279 RCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPL  358 (697)
T ss_pred             HHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCC
Confidence            9999999999999999999999987     899998884    5899999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHhccCChhhHHHHHHh------------------hCChHHHHHHHhhcC----CCCchhHHHHHHHHHh
Q 044412          231 DQVTMATVLSACAHLGALDLGRGIQIY------------------CRSLGRSLLVFFKLR----EKNLLCWNSITEALAI  288 (311)
Q Consensus       231 ~~~t~~~li~a~~~~~~~~~a~~~~~~------------------~~~~~~a~~~~~~~~----~p~~~~~~~li~~~~~  288 (311)
                      |..+|++||.+|++.|+++.|.++|+.                  .|+.++|.++|++|.    +||..||+++|.+|++
T Consensus       359 d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~  438 (697)
T PLN03081        359 DIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRY  438 (697)
T ss_pred             CeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhc
Confidence            999999999999999988877776665                  566666666666665    5666666666666666


Q ss_pred             cCChHHHHHHHHHHHH-cCCCCC
Q 044412          289 HGFAHEALGMFDRMTY-ENVRPN  310 (311)
Q Consensus       289 ~g~~~~a~~~~~~M~~-~g~~P~  310 (311)
                      .|..++|.++|+.|.+ .|+.||
T Consensus       439 ~g~~~~a~~~f~~m~~~~g~~p~  461 (697)
T PLN03081        439 SGLSEQGWEIFQSMSENHRIKPR  461 (697)
T ss_pred             CCcHHHHHHHHHHHHHhcCCCCC
Confidence            6666666666666654 466665

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.9e-46  Score=360.70  Aligned_cols=277  Identities=26%  Similarity=0.429  Sum_probs=250.4

Q ss_pred             HHHHHHHhhccChhh---HHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKE---LECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~---~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~  100 (311)
                      .+|..++.+|+..++   +++++..|.+.|+.||..++|+||.+| +++|+++.|.++|++|++||.++||+    |++.
T Consensus       188 ~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y-~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~  266 (857)
T PLN03077        188 YTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMY-VKCGDVVSARLVFDRMPRRDCISWNAMISGYFEN  266 (857)
T ss_pred             hHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHH-hcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhC
Confidence            345555555554333   367777777777777888889999999 99999999999999999999999999    9999


Q ss_pred             CChhHHHHHHHHHHHCCCCch---------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLT---------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVS  159 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~---------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a  159 (311)
                      |+.++|+++|++|.+.|+.||                     +++..+.+.|+.||..+||+||++|+++|++++    |
T Consensus       267 g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~----A  342 (857)
T PLN03077        267 GECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGE----A  342 (857)
T ss_pred             CCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHH----H
Confidence            999999999999999999999                     899999999999999999999999999999999    9


Q ss_pred             HHHhccCCCCCHhHHHHHHHHHHH--------------------------------------------------------
Q 044412          160 RRLFDEMPERKFATWNTMIDAYAR--------------------------------------------------------  183 (311)
Q Consensus       160 ~~~~~~~~~~~~~~~~~li~~~~~--------------------------------------------------------  183 (311)
                      .++|++|.+||.++||++|.+|++                                                        
T Consensus       343 ~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~  422 (857)
T PLN03077        343 EKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLIS  422 (857)
T ss_pred             HHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCc
Confidence            999999998888888888888877                                                        


Q ss_pred             --------------H-----HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc
Q 044412          184 --------------L-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       184 --------------~-----a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~  244 (311)
                                    +     |.++|++|.++|+.+||+||.+|++.|+.++|+++|++|.. +++||..||+++|.+|++
T Consensus       423 ~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~  501 (857)
T PLN03077        423 YVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACAR  501 (857)
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhh
Confidence                          1     77888888888999999999999999999999999999975 699999999999999999


Q ss_pred             cCChhhHHHHHHh----------------------hCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          245 LGALDLGRGIQIY----------------------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       245 ~~~~~~a~~~~~~----------------------~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                      .|+++.+.+++..                      +|++++|.++|+++ +||+.+||+||.+|+++|+.++|.++|++|
T Consensus       502 ~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M  580 (857)
T PLN03077        502 IGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRM  580 (857)
T ss_pred             hchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999999998876                      89999999999999 999999999999999999999999999999


Q ss_pred             HHcCCCCCC
Q 044412          303 TYENVRPNG  311 (311)
Q Consensus       303 ~~~g~~P~~  311 (311)
                      ++.|+.||+
T Consensus       581 ~~~g~~Pd~  589 (857)
T PLN03077        581 VESGVNPDE  589 (857)
T ss_pred             HHcCCCCCc
Confidence            999999985

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=9.1e-45  Score=349.37  Aligned_cols=283  Identities=14%  Similarity=0.214  Sum_probs=249.5

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC----CCCeeeeec----cc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ----EPNVFVYHA----FS   98 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~----~~~~~~~~~----~~   98 (311)
                      +..++..+...++.+.+.++|+.|.+.|+.||..+|+.||.+| ++.|+++.|.++|++|.    .||..+|+.    |+
T Consensus       440 yn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y-~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~  518 (1060)
T PLN03218        440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTC-AKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCA  518 (1060)
T ss_pred             HHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            4666777777788888899999999999999999999999999 99999999999999998    589999999    99


Q ss_pred             cCCChhHHHHHHHHHHHCCCCch---------------------HHHHHHHH--hcCCCchhHHHHHHHHHHhCCCCccc
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLT---------------------TVHGQVWK--NGFSSPVFVQTAMVDNYSYSNKFFES  155 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~---------------------~~~~~~~~--~g~~~~~~~~~~ll~~~~~~g~~~~a  155 (311)
                      +.|++++|+++|++|.+.|+.||                     +++++|..  .|+.||..+|+++|++|++.|++++|
T Consensus       519 k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA  598 (1060)
T PLN03218        519 RAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRA  598 (1060)
T ss_pred             HCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHH
Confidence            99999999999999999999998                     77888876  57899999999999999999999994


Q ss_pred             hHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC----CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc
Q 044412          156 RRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP----AWDIRSWTTMITSYSQNKQFREALDAFNKTKKS  226 (311)
Q Consensus       156 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~----~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  226 (311)
                      .++...+.+....|+..+||++|.+|++.     |.++|++|.    .||..+|+++|++|++.|++++|.++|++|.+.
T Consensus       599 ~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~  678 (1060)
T PLN03218        599 KEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQ  678 (1060)
T ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence            44444444444457778999999999987     899999887    488999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHhccCChhhHHHHHHh----------------------hCChHHHHHHHhhcC----CCCchhHH
Q 044412          227 GTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------------CRSLGRSLLVFFKLR----EKNLLCWN  280 (311)
Q Consensus       227 g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~----------------------~~~~~~a~~~~~~~~----~p~~~~~~  280 (311)
                      |+.||..||++||.+|++.|++++|.++|+.                      .|+.++|.++|++|.    .||..||+
T Consensus       679 G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~  758 (1060)
T PLN03218        679 GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYS  758 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            9999999999999999999999999988886                      788888888888886    68888888


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          281 SITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       281 ~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      ++|.+|++.|++++|.+++++|.+.|+.||
T Consensus       759 sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd  788 (1060)
T PLN03218        759 ILLVASERKDDADVGLDLLSQAKEDGIKPN  788 (1060)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            888888888888888888888888888887

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=1.7e-44  Score=342.60  Aligned_cols=261  Identities=19%  Similarity=0.288  Sum_probs=240.9

Q ss_pred             HHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccCCChhHHHHHHHHHHHCCCC
Q 044412           44 ECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVL  119 (311)
Q Consensus        44 ~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~  119 (311)
                      ++++..+.+.|+.||..++|+||++| +++|++++|.++|++|+++|.++||+    |++.|+.++|+++|++|.+.|+.
T Consensus       244 ~~l~~~~~~~g~~~d~~~~n~Li~~y-~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~  322 (697)
T PLN03081        244 QQLHCCVLKTGVVGDTFVSCALIDMY-SKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVS  322 (697)
T ss_pred             HHHHHHHHHhCCCccceeHHHHHHHH-HHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCC
Confidence            45555555666667777889999999 99999999999999999999999999    99999999999999999999999


Q ss_pred             ch---------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412          120 LT---------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus       120 p~---------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                      ||                     ++++.+.+.|+.||..+||+||++|+++|++++    |.++|++|.++|+++||+||
T Consensus       323 pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~----A~~vf~~m~~~d~~t~n~lI  398 (697)
T PLN03081        323 IDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMED----ARNVFDRMPRKNLISWNALI  398 (697)
T ss_pred             CCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHH----HHHHHHhCCCCCeeeHHHHH
Confidence            99                     889999999999999999999999999999999    99999999999999999999


Q ss_pred             HHHHHH-----HHHHHhhCC----CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh-cCCCCCHHHHHHHHHHHhccCCh
Q 044412          179 DAYARL-----AELLFNKMP----AWDIRSWTTMITSYSQNKQFREALDAFNKTKK-SGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       179 ~~~~~~-----a~~~~~~m~----~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      .+|++.     |.++|++|.    .||..||+++|.+|++.|.+++|.++|++|.+ .|+.|+..+|+.++++|++.|++
T Consensus       399 ~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~  478 (697)
T PLN03081        399 AGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLL  478 (697)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCH
Confidence            999997     999999986    59999999999999999999999999999986 69999999999999999999999


Q ss_pred             hhHHHHHHh-------------------hCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 044412          249 DLGRGIQIY-------------------CRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       249 ~~a~~~~~~-------------------~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g  306 (311)
                      ++|.++++.                   .|+.+.|..+++++.  +| +..+|+.|+.+|++.|++++|.+++++|++.|
T Consensus       479 ~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g  558 (697)
T PLN03081        479 DEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKG  558 (697)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence            999999987                   678888888888876  45 47799999999999999999999999999999


Q ss_pred             CCC
Q 044412          307 VRP  309 (311)
Q Consensus       307 ~~P  309 (311)
                      +++
T Consensus       559 ~~k  561 (697)
T PLN03081        559 LSM  561 (697)
T ss_pred             Ccc
Confidence            864

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=6.1e-44  Score=343.69  Aligned_cols=250  Identities=18%  Similarity=0.219  Sum_probs=218.3

Q ss_pred             cchhHHHHHHHHHhhccCChhHHHHhcccCC----CCCeeeeec----cccCCChhHHHHHHHHHHHCCCCch-------
Q 044412           57 LDCFLAKQFISFCTSRFHFIDYTILVFPQMQ----EPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLT-------  121 (311)
Q Consensus        57 p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~----~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~-------  121 (311)
                      ||..+|+.+|.+| ++.|+++.|.++|++|.    .||..+|++    |++.|++++|.++|++|.+.|+.||       
T Consensus       435 pd~~Tyn~LL~a~-~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaL  513 (1060)
T PLN03218        435 PTLSTFNMLMSVC-ASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGAL  513 (1060)
T ss_pred             CCHHHHHHHHHHH-HhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            7778888888888 88888888888888886    477788877    8888888888888888888888888       


Q ss_pred             --------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccC------CCCCHhHHHHHHHHH
Q 044412          122 --------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEM------PERKFATWNTMIDAY  181 (311)
Q Consensus       122 --------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~------~~~~~~~~~~li~~~  181 (311)
                                    .+++.|.+.|+.||..+||.||.+|++.|++++    |.++|++|      ..||.++|+++|.+|
T Consensus       514 I~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~de----A~~lf~eM~~~~~gi~PD~vTynaLI~ay  589 (1060)
T PLN03218        514 IDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDR----AFDVLAEMKAETHPIDPDHITVGALMKAC  589 (1060)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHhcCCCCCcHHHHHHHHHHH
Confidence                          777888888888888888888888888888888    55555555      357888999999998


Q ss_pred             HHH-----HHHHHhhCC----CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHH
Q 044412          182 ARL-----AELLFNKMP----AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGR  252 (311)
Q Consensus       182 ~~~-----a~~~~~~m~----~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~  252 (311)
                      +++     |.++|++|.    .|+..+||++|.+|++.|++++|+++|++|.+.|+.||..||++||.+|++.|++++|.
T Consensus       590 ~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~  669 (1060)
T PLN03218        590 ANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAF  669 (1060)
T ss_pred             HHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHH
Confidence            887     888888886    36778999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHh----------------------hCChHHHHHHHhhcC----CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 044412          253 GIQIY----------------------CRSLGRSLLVFFKLR----EKNLLCWNSITEALAIHGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       253 ~~~~~----------------------~~~~~~a~~~~~~~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g  306 (311)
                      ++|+.                      +|+.++|.++|++|.    .||+.+||+||.+|++.|++++|.++|++|.+.|
T Consensus       670 ~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~G  749 (1060)
T PLN03218        670 EILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLG  749 (1060)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            98888                      789999999999995    7999999999999999999999999999999999


Q ss_pred             CCCCC
Q 044412          307 VRPNG  311 (311)
Q Consensus       307 ~~P~~  311 (311)
                      +.||.
T Consensus       750 i~Pd~  754 (1060)
T PLN03218        750 LCPNT  754 (1060)
T ss_pred             CCCCH
Confidence            99983

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=5.9e-44  Score=346.20  Aligned_cols=301  Identities=16%  Similarity=0.209  Sum_probs=273.7

Q ss_pred             hHHHHHhhhhhcCCCCCch--------------hhhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHh
Q 044412            5 YVRAIITSFKKNSFPTSVS--------------FIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCT   70 (311)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~   70 (311)
                      .++.+|++|.+.+.+....              ..++.+++..+...++.+.+++++..|.+.|+.||..+||+||.+| 
T Consensus       255 s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y-  333 (857)
T PLN03077        255 SWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMY-  333 (857)
T ss_pred             hhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHH-
Confidence            3567777777766443222              1123445555555566667799999999999999999999999999 


Q ss_pred             hccCChhHHHHhcccCCCCCeeeeec----cccCCChhHHHHHHHHHHHCCCCch---------------------HHHH
Q 044412           71 SRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLT---------------------TVHG  125 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~---------------------~~~~  125 (311)
                      ++.|++++|.++|++|.+||..+||+    |++.|++++|+++|++|.+.|+.||                     ++++
T Consensus       334 ~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~  413 (857)
T PLN03077        334 LSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHE  413 (857)
T ss_pred             HhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHH
Confidence            99999999999999999999999999    9999999999999999999999999                     8999


Q ss_pred             HHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcH
Q 044412          126 QVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP---AWDI  197 (311)
Q Consensus       126 ~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~  197 (311)
                      .+.+.|+.|+..+||+||++|+++|++++    |.++|++|.++|+++||++|.+|++.     |.++|++|.   .||.
T Consensus       414 ~~~~~g~~~~~~~~n~Li~~y~k~g~~~~----A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~  489 (857)
T PLN03077        414 LAERKGLISYVVVANALIEMYSKCKCIDK----ALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNS  489 (857)
T ss_pred             HHHHhCCCcchHHHHHHHHHHHHcCCHHH----HHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCH
Confidence            99999999999999999999999999999    99999999999999999999999987     999999986   5999


Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh-----------------hCC
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY-----------------CRS  260 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~-----------------~~~  260 (311)
                      .||+++|.+|++.|.++.+.+++..|.+.|+.||..++++||.+|++.|+++.|..+|+.                 .|+
T Consensus       490 ~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~  569 (857)
T PLN03077        490 VTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGK  569 (857)
T ss_pred             hHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999999999999999999998876                 789


Q ss_pred             hHHHHHHHhhcC----CCCchhHHHHHHHHHhcCChHHHHHHHHHHH-HcCCCCC
Q 044412          261 LGRSLLVFFKLR----EKNLLCWNSITEALAIHGFAHEALGMFDRMT-YENVRPN  310 (311)
Q Consensus       261 ~~~a~~~~~~~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~-~~g~~P~  310 (311)
                      .++|.++|++|.    +||..||+.+|.+|++.|++++|.++|++|+ +.|+.||
T Consensus       570 ~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~  624 (857)
T PLN03077        570 GSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPN  624 (857)
T ss_pred             HHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCc
Confidence            999999999997    7999999999999999999999999999999 6899997

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.68  E-value=1.4e-14  Score=129.12  Aligned_cols=261  Identities=10%  Similarity=0.068  Sum_probs=170.7

Q ss_pred             HhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCC-Cee------eeec----cccCCC
Q 044412           34 LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEP-NVF------VYHA----FSSLRH  102 (311)
Q Consensus        34 l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~-~~~------~~~~----~~~~~~  102 (311)
                      ....++.+.+...+..+.+.+ +.+..++..+...+ .+.|++++|..+++.+... +..      .+..    +.+.|+
T Consensus        45 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~-~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         45 FLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLF-RRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHH-HHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            345677777888888887763 23455777777777 8888888888888776542 111      1111    677788


Q ss_pred             hhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCH----hHHHHHH
Q 044412          103 PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF----ATWNTMI  178 (311)
Q Consensus       103 ~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~----~~~~~li  178 (311)
                      +++|+++|+++.+..               +.+..+++.+...|.+.|++++|.+....+.+..+.+..    ..|..+.
T Consensus       123 ~~~A~~~~~~~l~~~---------------~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la  187 (389)
T PRK11788        123 LDRAEELFLQLVDEG---------------DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELA  187 (389)
T ss_pred             HHHHHHHHHHHHcCC---------------cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHH
Confidence            888888888876532               345566777777777777777744443333332222211    1223333


Q ss_pred             HHHHHH-----HHHHHhhCCC--C-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          179 DAYARL-----AELLFNKMPA--W-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       179 ~~~~~~-----a~~~~~~m~~--~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                      ..+.+.     |...|+++.+  | +...+..+...+.+.|++++|.++|+++.+.+-.....+++.+..+|...|+.++
T Consensus       188 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~  267 (389)
T PRK11788        188 QQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAE  267 (389)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHH
Confidence            333332     6666665532  2 3445666667777777777777777777654322224556677777777777777


Q ss_pred             HHHHHHh--------------------hCChHHHHHHHhhcC--CCCchhHHHHHHHHHh---cCChHHHHHHHHHHHHc
Q 044412          251 GRGIQIY--------------------CRSLGRSLLVFFKLR--EKNLLCWNSITEALAI---HGFAHEALGMFDRMTYE  305 (311)
Q Consensus       251 a~~~~~~--------------------~~~~~~a~~~~~~~~--~p~~~~~~~li~~~~~---~g~~~~a~~~~~~M~~~  305 (311)
                      |...++.                    .|+.++|..+|+++.  .|+..+++.++..+..   .|+.+++..++++|.+.
T Consensus       268 A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~  347 (389)
T PRK11788        268 GLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGE  347 (389)
T ss_pred             HHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHH
Confidence            7766665                    566777888887665  6899999999988875   56899999999999999


Q ss_pred             CCCCCC
Q 044412          306 NVRPNG  311 (311)
Q Consensus       306 g~~P~~  311 (311)
                      +++|+.
T Consensus       348 ~~~~~p  353 (389)
T PRK11788        348 QLKRKP  353 (389)
T ss_pred             HHhCCC
Confidence            988874

>PF13041 PPR_2: PPR repeat family

Probab=99.63  E-value=9.6e-16  Score=94.30  Aligned_cols=50  Identities=28%  Similarity=0.501  Sum_probs=48.9

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~  244 (311)
                      ||+.+||++|++|++.|++++|+++|++|.+.|++||..||++||++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            79999999999999999999999999999999999999999999999986

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.55  E-value=3e-12  Score=125.37  Aligned_cols=267  Identities=11%  Similarity=0.036  Sum_probs=178.4

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~  100 (311)
                      ..+...+...|+...+..+++.+.+.. +.++.+|..+...+ .+.|++++|...|+++.+  |+ ...+..    +.+.
T Consensus       571 ~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~  648 (899)
T TIGR02917       571 LALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLMLGRAQ-LAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVM  648 (899)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence            456666777778888877777776543 45667777778888 888888888888877643  22 222222    6667


Q ss_pred             CChhHHHHHHHHHHHCCCCch----------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLT----------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV  158 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~----------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~  158 (311)
                      |++++|.+.|+++.+..  |+                      .+.+.+.+.+ +.+...+..+...|.+.|++++|...
T Consensus       649 ~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~  725 (899)
T TIGR02917       649 KNYAKAITSLKRALELK--PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQA  725 (899)
T ss_pred             CCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHH
Confidence            77888888877776532  22                      2222232222 34556666677777777777773333


Q ss_pred             HHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC
Q 044412          159 SRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS  230 (311)
Q Consensus       159 a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  230 (311)
                      ....+..-  |+..++..+...+.+.     |.+.++.+.   ..+...++.+...|...|+.++|...|+++.+.. +.
T Consensus       726 ~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~  802 (899)
T TIGR02917       726 YRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PD  802 (899)
T ss_pred             HHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CC
Confidence            33333322  3334455555555543     555555543   2356778888888888888888888888887753 45


Q ss_pred             CHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC---CCCchhHHHHHHHH
Q 044412          231 DQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR---EKNLLCWNSITEAL  286 (311)
Q Consensus       231 ~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~---~p~~~~~~~li~~~  286 (311)
                      +..+++.+...+...|+ .+|...++.                     .|+.++|...|+++.   ..+..++..+..++
T Consensus       803 ~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~  881 (899)
T TIGR02917       803 NAVVLNNLAWLYLELKD-PRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALAL  881 (899)
T ss_pred             CHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHH
Confidence            67778888888888888 667766665                     677888888888777   23677888888888


Q ss_pred             HhcCChHHHHHHHHHHH
Q 044412          287 AIHGFAHEALGMFDRMT  303 (311)
Q Consensus       287 ~~~g~~~~a~~~~~~M~  303 (311)
                      .+.|++++|..++++|.
T Consensus       882 ~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       882 LATGRKAEARKELDKLL  898 (899)
T ss_pred             HHcCCHHHHHHHHHHHh
Confidence            88999999988888876

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.53  E-value=3.2e-12  Score=125.17  Aligned_cols=167  Identities=7%  Similarity=-0.046  Sum_probs=94.1

Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCC---CCCHhHHHHHHHHHHHH-----HHHHHhhCCC---CcHhHHH
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP---ERKFATWNTMIDAYARL-----AELLFNKMPA---WDIRSWT  201 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~---~~~~~~~~~li~~~~~~-----a~~~~~~m~~---~~~~~y~  201 (311)
                      +.+..+|..+..+|.+.|++++    |...++.+.   ..+...+..+...+.+.     |...|+++.+   .+..+|.
T Consensus       598 ~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  673 (899)
T TIGR02917       598 PDSPEAWLMLGRAQLAAGDLNK----AVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQI  673 (899)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHH
Confidence            4455667777777777777777    444444332   12334555555555443     5555554431   2455666


Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh--------------------hCCh
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY--------------------CRSL  261 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~--------------------~~~~  261 (311)
                      .+...+...|++++|.++++.+.+.+ +++...+..+...+...|++++|...++.                    .|+.
T Consensus       674 ~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  752 (899)
T TIGR02917       674 GLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNT  752 (899)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCH
Confidence            66666666666666666666665543 33445555555666666666666655554                    4455


Q ss_pred             HHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          262 GRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       262 ~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ++|.+.++++.   ..+...++.+...|...|++++|..+|+++.+
T Consensus       753 ~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  798 (899)
T TIGR02917       753 AEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTVVK  798 (899)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            55555555543   22345555566666666666666666666554

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.47  E-value=9.5e-12  Score=110.94  Aligned_cols=219  Identities=10%  Similarity=0.004  Sum_probs=168.8

Q ss_pred             hccCChhHHHHhcccCCCCCee---eeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQEPNVF---VYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMV  143 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~~~~---~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll  143 (311)
                      ...|+++.|...|+++.+.+..   ++..    +.+.|++++|.++++.+...+..+.           ......+..+.
T Consensus        46 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~-----------~~~~~~~~~La  114 (389)
T PRK11788         46 LLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTR-----------EQRLLALQELG  114 (389)
T ss_pred             HhcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCH-----------HHHHHHHHHHH
Confidence            5679999999999999753322   2222    7889999999999999876421000           01135688899


Q ss_pred             HHHHhCCCCccchHHHHHHhccCCC---CCHhHHHHHHHHHHHH-----HHHHHhhCCC--Cc------HhHHHHHHHHH
Q 044412          144 DNYSYSNKFFESRRVSRRLFDEMPE---RKFATWNTMIDAYARL-----AELLFNKMPA--WD------IRSWTTMITSY  207 (311)
Q Consensus       144 ~~~~~~g~~~~a~~~a~~~~~~~~~---~~~~~~~~li~~~~~~-----a~~~~~~m~~--~~------~~~y~~li~~~  207 (311)
                      ..|.+.|++++    |..+|+.+.+   .+..+++.+...+.+.     |.+.++.+..  |+      ...|..+...+
T Consensus       115 ~~~~~~g~~~~----A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~  190 (389)
T PRK11788        115 QDYLKAGLLDR----AEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQA  190 (389)
T ss_pred             HHHHHCCCHHH----HHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHH
Confidence            99999999999    7677766654   4567888888888876     7788877753  21      22456777888


Q ss_pred             HhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh----------------------hCChHHHH
Q 044412          208 SQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------------CRSLGRSL  265 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~----------------------~~~~~~a~  265 (311)
                      ...|++++|..+|+++.+.. +.+...+..+...+.+.|++++|..+++.                      .|+.++|.
T Consensus       191 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  269 (389)
T PRK11788        191 LARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGL  269 (389)
T ss_pred             HhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHH
Confidence            89999999999999998753 33456788888999999999999988877                      57778888


Q ss_pred             HHHhhcC--CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          266 LVFFKLR--EKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       266 ~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..++++.  .|+...+..+...+.+.|++++|..+++++.+.
T Consensus       270 ~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~  311 (389)
T PRK11788        270 EFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRR  311 (389)
T ss_pred             HHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            8888766  677777888899999999999999999988764

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.39  E-value=7e-11  Score=100.77  Aligned_cols=251  Identities=13%  Similarity=0.156  Sum_probs=170.6

Q ss_pred             hhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHh-hccCChhHH-HHhcccCC---CCCeeeeec-------------
Q 044412           35 KKCSSIKELECVYATIVKTNANLDCFLAKQFISFCT-SRFHFIDYT-ILVFPQMQ---EPNVFVYHA-------------   96 (311)
Q Consensus        35 ~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~-~~~g~~~~a-~~~~~~m~---~~~~~~~~~-------------   96 (311)
                      .+.+.+++.--+|+.|.+.|+..++..--.|+..-+ ....++-.| ++.|-.|.   +....+|..             
T Consensus       126 IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~~PK  205 (625)
T KOG4422|consen  126 ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFETLPK  205 (625)
T ss_pred             HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhhcCC
Confidence            456788899999999999999888877766665431 344444433 44555554   233344433             


Q ss_pred             -----------cccCCChhHHHHHHHHHHHCCCCch-----------------HHHHHHHHhcCCCchhHHHHHHHHHHh
Q 044412           97 -----------FSSLRHPLQAIAFYLYMLRAEVLLT-----------------TVHGQVWKNGFSSPVFVQTAMVDNYSY  148 (311)
Q Consensus        97 -----------~~~~~~~~~a~~~~~~m~~~~~~p~-----------------~~~~~~~~~g~~~~~~~~~~ll~~~~~  148 (311)
                                 +|+-...+.|.++|++-.....+.+                 ++..+|+...+.||..|+|+++++..+
T Consensus       206 T~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl~TfNalL~c~ak  285 (625)
T KOG4422|consen  206 TDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNLFTFNALLSCAAK  285 (625)
T ss_pred             CchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCchHhHHHHHHHHHH
Confidence                       6677788999999998877655444                 777788888888888888888888888


Q ss_pred             CCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH-HHHHHHHHHh--
Q 044412          149 SNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE-ALDAFNKTKK--  225 (311)
Q Consensus       149 ~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~-a~~~~~~m~~--  225 (311)
                      .|+++.|+..|.+++.+|++-++                      +|...+|.-+|..+++.+++.+ |..++.++..  
T Consensus       286 fg~F~~ar~aalqil~EmKeiGV----------------------ePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~l  343 (625)
T KOG4422|consen  286 FGKFEDARKAALQILGEMKEIGV----------------------EPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSL  343 (625)
T ss_pred             hcchHHHHHHHHHHHHHHHHhCC----------------------CcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhh
Confidence            88888877777777777665433                      5566666666666666655543 3333333322  


Q ss_pred             --cCCC---C-CHHHHHHHHHHHhccCChhhHHHHHHh-----------------------------hCChHHHHHHHhh
Q 044412          226 --SGTG---S-DQVTMATVLSACAHLGALDLGRGIQIY-----------------------------CRSLGRSLLVFFK  270 (311)
Q Consensus       226 --~g~~---p-~~~t~~~li~a~~~~~~~~~a~~~~~~-----------------------------~~~~~~a~~~~~~  270 (311)
                        +.++   | |..-|...++.|.+..+.+.|.++...                             +...+.-...++.
T Consensus       344 tGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~  423 (625)
T KOG4422|consen  344 TGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYED  423 (625)
T ss_pred             ccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              1122   2 223455556666666666666665554                             4444566677777


Q ss_pred             cC----CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 044412          271 LR----EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       271 ~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      |.    -|+..+...++++....|+++-.-+++.+|+..|-
T Consensus       424 lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~gh  464 (625)
T KOG4422|consen  424 LVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGH  464 (625)
T ss_pred             hccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhh
Confidence            76    58888999999999999999999999999988773

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.24  E-value=6.8e-10  Score=94.88  Aligned_cols=120  Identities=12%  Similarity=0.159  Sum_probs=99.1

Q ss_pred             HHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCC----CCCHhHHHHHHHHHHHH-HHHHHhhCC----CCcH
Q 044412          127 VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP----ERKFATWNTMIDAYARL-AELLFNKMP----AWDI  197 (311)
Q Consensus       127 ~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~----~~~~~~~~~li~~~~~~-a~~~~~~m~----~~~~  197 (311)
                      +.-.-.+.+..+|.++|.+.|+....+.    |.+++++-.    +-+..+||.+|.+-.-. .++++.+|.    .||.
T Consensus       198 L~~E~~PKT~et~s~mI~Gl~K~~~~ER----A~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl  273 (625)
T KOG4422|consen  198 LLFETLPKTDETVSIMIAGLCKFSSLER----ARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNL  273 (625)
T ss_pred             HHHhhcCCCchhHHHHHHHHHHHHhHHH----HHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCch
Confidence            4444467778999999999999999999    666665543    35667899998877655 677777775    5999


Q ss_pred             hHHHHHHHHHHhCCChhH----HHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          198 RSWTTMITSYSQNKQFRE----ALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~----a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                      .|+|+++++.++.|+++.    |.+++.+|++-|++|...+|..+|.-+++-++..+
T Consensus       274 ~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  274 FTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             HhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh
Confidence            999999999999998765    45789999999999999999999999999888754

>PF13041 PPR_2: PPR repeat family

Probab=99.12  E-value=7.5e-11  Score=72.30  Aligned_cols=45  Identities=27%  Similarity=0.465  Sum_probs=32.8

Q ss_pred             CchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC----CCHhHHHHHHHHHH
Q 044412          134 SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE----RKFATWNTMIDAYA  182 (311)
Q Consensus       134 ~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~----~~~~~~~~li~~~~  182 (311)
                      ||..+||++|++|++.|++++    |.++|++|.+    ||..||+++|++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~----a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEE----ALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHH----HHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            899999999999999999999    6666665554    44444444444443

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.11  E-value=5.4e-08  Score=92.32  Aligned_cols=107  Identities=15%  Similarity=0.065  Sum_probs=68.5

Q ss_pred             cHhHHHHHHHHHHhCCChhH----HHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHh-------------
Q 044412          196 DIRSWTTMITSYSQNKQFRE----ALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIY-------------  257 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~----a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~-------------  257 (311)
                      +...+..+-..+...|++++    |...|++..+.  .| +...+..+-..+...|++++|...++.             
T Consensus       245 ~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~  322 (656)
T PRK15174        245 GAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRA  322 (656)
T ss_pred             CHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            34455556666666666664    56666666553  23 344566666666666666666666655             


Q ss_pred             --------hCChHHHHHHHhhcC--CCCchh-HHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          258 --------CRSLGRSLLVFFKLR--EKNLLC-WNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       258 --------~~~~~~a~~~~~~~~--~p~~~~-~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                              .|+.++|...|+++.  .|+... +..+..++...|+.++|...|++..+
T Consensus       323 ~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~  380 (656)
T PRK15174        323 MYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQ  380 (656)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                    566667777777666  455433 33345678888899998888888765

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.08  E-value=8.3e-08  Score=91.03  Aligned_cols=259  Identities=12%  Similarity=-0.019  Sum_probs=186.9

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeee-eec----ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFV-YHA----FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~-~~~----~~~   99 (311)
                      ...++..+...|+..++..++.........+....+... .+. ...|+++.|...|+++.+  |+... +..    +..
T Consensus        45 ~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~-~~~-l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~  122 (656)
T PRK15174         45 IILFAIACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWV-ISP-LASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLK  122 (656)
T ss_pred             HHHHHHHHHhcCCcchhHHHhHHHHHhCCCchhHHHHHh-hhH-hhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH
Confidence            346677777889999999999888887665544455444 555 679999999999999863  44322 222    788


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMID  179 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~  179 (311)
                      .|+.++|+..|++....               -+.+...+..+...+...|++++|......+...-+.+.. .+..+..
T Consensus       123 ~g~~~~Ai~~l~~Al~l---------------~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~~~-a~~~~~~  186 (656)
T PRK15174        123 SKQYATVADLAEQAWLA---------------FSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPRGD-MIATCLS  186 (656)
T ss_pred             cCCHHHHHHHHHHHHHh---------------CCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCCHH-HHHHHHH
Confidence            99999999999998763               1334678888999999999999955544444443333322 2322222


Q ss_pred             HHHHH-----HHHHHhhCCC----CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          180 AYARL-----AELLFNKMPA----WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       180 ~~~~~-----a~~~~~~m~~----~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                       +...     |...++.+..    ++...+..+...+...|++++|+..|++..+.. +-+...+..+-..+...|+.++
T Consensus       187 -l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~e  264 (656)
T PRK15174        187 -FLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSRE  264 (656)
T ss_pred             -HHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchh
Confidence             3332     7777766543    234455566778889999999999999998753 3356677888889999999986


Q ss_pred             ----HHHHHHh---------------------hCChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          251 ----GRGIQIY---------------------CRSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       251 ----a~~~~~~---------------------~~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                          |...++.                     .|+.++|...+++..  .|+ ...+..+...+.+.|++++|...|+++
T Consensus       265 A~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~a  344 (656)
T PRK15174        265 AKLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQL  344 (656)
T ss_pred             hHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence                6777766                     688888888888766  444 456777888899999999999999888


Q ss_pred             HHc
Q 044412          303 TYE  305 (311)
Q Consensus       303 ~~~  305 (311)
                      ...
T Consensus       345 l~~  347 (656)
T PRK15174        345 ARE  347 (656)
T ss_pred             HHh
Confidence            753

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.01  E-value=3.7e-08  Score=93.13  Aligned_cols=234  Identities=12%  Similarity=0.043  Sum_probs=155.7

Q ss_pred             cChhhHHHHHHHHHHhc-cCc-chhHHHHHHHHHhhccCChhHHHHhcccCCC--CCee-eeec----cccCCChhHHHH
Q 044412           38 SSIKELECVYATIVKTN-ANL-DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVF-VYHA----FSSLRHPLQAIA  108 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g-~~p-~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~-~~~~----~~~~~~~~~a~~  108 (311)
                      ++..++...++..++.+ ..| +...++.+-.++ ...|++++|...|++..+  |+.. .|..    +...|++++|+.
T Consensus       308 ~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~-~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~  386 (615)
T TIGR00990       308 ESYEEAARAFEKALDLGKLGEKEAIALNLRGTFK-CLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEE  386 (615)
T ss_pred             hhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            45666777888887765 234 345667777777 889999999999998754  4322 2222    778899999999


Q ss_pred             HHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--C-CHhHHHHHHHHHHHH-
Q 044412          109 FYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--R-KFATWNTMIDAYARL-  184 (311)
Q Consensus       109 ~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~-  184 (311)
                      .|++..+..               +-+..+|..+-..|...|++++    |...|+...+  | +...+..+-..+.+. 
T Consensus       387 ~~~~al~~~---------------p~~~~~~~~lg~~~~~~g~~~~----A~~~~~kal~l~P~~~~~~~~la~~~~~~g  447 (615)
T TIGR00990       387 DFDKALKLN---------------SEDPDIYYHRAQLHFIKGEFAQ----AGKDYQKSIDLDPDFIFSHIQLGVTQYKEG  447 (615)
T ss_pred             HHHHHHHhC---------------CCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHcCccCHHHHHHHHHHHHHCC
Confidence            999886532               3457788899999999999999    5555554432  2 344455454444433 


Q ss_pred             ----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH------HHHHHHHHHhccCChhhH
Q 044412          185 ----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV------TMATVLSACAHLGALDLG  251 (311)
Q Consensus       185 ----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------t~~~li~a~~~~~~~~~a  251 (311)
                          |...|++..  .| +...|+.+-..+...|++++|++.|++-.+..-..+..      .++.....+...|+++  
T Consensus       448 ~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~--  525 (615)
T TIGR00990       448 SIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFI--  525 (615)
T ss_pred             CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHH--
Confidence                666666543  23 46678888888888999999999998877632111111      1111111222235555  


Q ss_pred             HHHHHhhCChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          252 RGIQIYCRSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       252 ~~~~~~~~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                                 +|.+.+++..  .|+ ...+..+...+...|++++|..+|++..+
T Consensus       526 -----------eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~  570 (615)
T TIGR00990       526 -----------EAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAE  570 (615)
T ss_pred             -----------HHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence                       4555554432  343 45788999999999999999999998754

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=98.92  E-value=1.2e-08  Score=94.34  Aligned_cols=185  Identities=8%  Similarity=0.038  Sum_probs=117.7

Q ss_pred             CCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCH----hHHHHHHHHHHHHHHHHHhh
Q 044412          116 AEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF----ATWNTMIDAYARLAELLFNK  191 (311)
Q Consensus       116 ~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~----~~~~~li~~~~~~a~~~~~~  191 (311)
                      .+..|+.++..+...|+.|+..||.++|.-||..|+++.    |- +|.-|...+.    ..++.++.+..... + .+.
T Consensus         5 ~kf~ptnfla~~e~~gi~PnRvtyqsLiarYc~~gdiea----at-if~fm~~ksLpv~e~vf~~lv~sh~~An-d-~En   77 (1088)
T KOG4318|consen    5 VKFFPTNFLALHEISGILPNRVTYQSLIARYCTKGDIEA----AT-IFPFMEIKSLPVREGVFRGLVASHKEAN-D-AEN   77 (1088)
T ss_pred             cccCcchHHHHHHHhcCCCchhhHHHHHHHHcccCCCcc----cc-chhhhhcccccccchhHHHHHhcccccc-c-ccC
Confidence            345677788888889999999999999999999999999    77 7877765433    45666666654430 0 001


Q ss_pred             CCCCcHhHHHHHHHHHHhCCChhH---HHHHHHHHH----hcCC-----------------CCCHHHHHHHHHHHhccCC
Q 044412          192 MPAWDIRSWTTMITSYSQNKQFRE---ALDAFNKTK----KSGT-----------------GSDQVTMATVLSACAHLGA  247 (311)
Q Consensus       192 m~~~~~~~y~~li~~~~~~g~~~~---a~~~~~~m~----~~g~-----------------~p~~~t~~~li~a~~~~~~  247 (311)
                      -.+|...||+.|..+|...|++..   +.+.+....    ..|+                 -||..+   ++.-....|.
T Consensus        78 pkep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n---~illlv~egl  154 (1088)
T KOG4318|consen   78 PKEPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAEN---AILLLVLEGL  154 (1088)
T ss_pred             CCCCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHH---HHHHHHHHHH
Confidence            115678899999999999999754   333222221    1232                 222222   1111222333


Q ss_pred             hhhHHHHHHh--------------------hCChHHHHHHHhhcC-CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 044412          248 LDLGRGIQIY--------------------CRSLGRSLLVFFKLR-EKNLLCWNSITEALAIHGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       248 ~~~a~~~~~~--------------------~~~~~~a~~~~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g  306 (311)
                      ++.+.++...                    ...+++-...-.... .|++.+|.+++++-..+|+.+.|..++.+|+++|
T Consensus       155 waqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~g  234 (1088)
T KOG4318|consen  155 WAQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKG  234 (1088)
T ss_pred             HHHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcC
Confidence            3433333322                    111111111111111 3899999999999999999999999999999999


Q ss_pred             CCCC
Q 044412          307 VRPN  310 (311)
Q Consensus       307 ~~P~  310 (311)
                      +..+
T Consensus       235 fpir  238 (1088)
T KOG4318|consen  235 FPIR  238 (1088)
T ss_pred             CCcc
Confidence            8654

>PF12854 PPR_1: PPR repeat

Probab=98.91  E-value=1.9e-09  Score=59.84  Aligned_cols=31  Identities=26%  Similarity=0.521  Sum_probs=29.4

Q ss_pred             CCcHhHHHHHHHHHHhCCChhHHHHHHHHHH
Q 044412          194 AWDIRSWTTMITSYSQNKQFREALDAFNKTK  224 (311)
Q Consensus       194 ~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~  224 (311)
                      .||..|||+||++||+.|++++|+++|++|+
T Consensus         4 ~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    4 EPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            6899999999999999999999999999984

>PF12854 PPR_1: PPR repeat

Probab=98.88  E-value=1.4e-09  Score=60.38  Aligned_cols=34  Identities=29%  Similarity=0.495  Sum_probs=31.4

Q ss_pred             hcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCC
Q 044412          130 NGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP  167 (311)
Q Consensus       130 ~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~  167 (311)
                      .|+.||..|||+||++||+.|++++    |.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~----A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDE----AFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHH----HHHHHHhCc
Confidence            3789999999999999999999999    999998874

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.87  E-value=2.1e-06  Score=86.95  Aligned_cols=262  Identities=11%  Similarity=0.081  Sum_probs=166.5

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCee------------eee
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVF------------VYH   95 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~------------~~~   95 (311)
                      ..+..++...|+.+++.+.++...+.. +.+...+..+...+ . .++.++|..+++.+......            .+.
T Consensus       389 ~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~-~-~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~  465 (1157)
T PRK11447        389 LGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLY-R-QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLA  465 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-H-hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHH
Confidence            356667777788888888887777653 22344555555555 4 35677887777766532100            011


Q ss_pred             c----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC
Q 044412           96 A----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK  170 (311)
Q Consensus        96 ~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~  170 (311)
                      .    +...|++++|++.|++..+.                .| +...+..+...|.+.|++++|+...+++.+.-+...
T Consensus       466 ~~a~~~~~~g~~~eA~~~~~~Al~~----------------~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~~~  529 (1157)
T PRK11447        466 QQAEALENQGKWAQAAELQRQRLAL----------------DPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPNDP  529 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh----------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCH
Confidence            1    55678888888888887653                33 355666777778888888884444444433222111


Q ss_pred             HhHHHHH-------------------------------------------HHHHHHH-----HHHHHhhCCCCcHhHHHH
Q 044412          171 FATWNTM-------------------------------------------IDAYARL-----AELLFNKMPAWDIRSWTT  202 (311)
Q Consensus       171 ~~~~~~l-------------------------------------------i~~~~~~-----a~~~~~~m~~~~~~~y~~  202 (311)
                      ...|..-                                           ...+...     |..+++.- ..+...+..
T Consensus       530 ~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~-p~~~~~~~~  608 (1157)
T PRK11447        530 EQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQ-PPSTRIDLT  608 (1157)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhC-CCCchHHHH
Confidence            1111100                                           0001110     44444422 224445666


Q ss_pred             HHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCCh
Q 044412          203 MITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSL  261 (311)
Q Consensus       203 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~  261 (311)
                      +-..+.+.|+.++|++.|++..+.. +-+...+..+...+...|+.++|...++.                     .|+.
T Consensus       609 La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~  687 (1157)
T PRK11447        609 LADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDT  687 (1157)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCH
Confidence            7788888899999999999988752 33567888888999999999999988877                     7888


Q ss_pred             HHHHHHHhhcCC--CC-------chhHHHHHHHHHhcCChHHHHHHHHHHH-HcCCCCC
Q 044412          262 GRSLLVFFKLRE--KN-------LLCWNSITEALAIHGFAHEALGMFDRMT-YENVRPN  310 (311)
Q Consensus       262 ~~a~~~~~~~~~--p~-------~~~~~~li~~~~~~g~~~~a~~~~~~M~-~~g~~P~  310 (311)
                      ++|.++|++..+  |+       ...+..+...+...|++++|...|++.. ..|+.|+
T Consensus       688 ~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~~~~~~~~  746 (1157)
T PRK11447        688 AAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMVASGITPT  746 (1157)
T ss_pred             HHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcCCCCC
Confidence            888888888752  21       1345555677888999999999988864 4567654

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.85  E-value=9e-07  Score=79.14  Aligned_cols=240  Identities=9%  Similarity=-0.033  Sum_probs=169.7

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHHHHH-HHHHhhccCChhHHHHhcccCCC--CCeeeee----c--cccCCChhHHHH
Q 044412           38 SSIKELECVYATIVKTNANLDCFLAKQF-ISFCTSRFHFIDYTILVFPQMQE--PNVFVYH----A--FSSLRHPLQAIA  108 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~~~l-l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~----~--~~~~~~~~~a~~  108 (311)
                      |++..+++......+.  .+++..+-.+ ..+. .+.|+.+.|...+.++.+  |+.....    .  +...|++++|++
T Consensus        98 Gd~~~A~k~l~~~~~~--~~~p~l~~llaA~aA-~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~  174 (398)
T PRK10747         98 GDYQQVEKLMTRNADH--AEQPVVNYLLAAEAA-QQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARH  174 (398)
T ss_pred             CCHHHHHHHHHHHHhc--ccchHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHH
Confidence            6777777555543332  2223333333 2333 789999999999999864  3332221    1  788999999999


Q ss_pred             HHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC---H--------hHHHHH
Q 044412          109 FYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK---F--------ATWNTM  177 (311)
Q Consensus       109 ~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~---~--------~~~~~l  177 (311)
                      .++++.+..               +-++.....+...|.+.|++++    +..++..+.+..   .        .+|..+
T Consensus       175 ~l~~~~~~~---------------P~~~~al~ll~~~~~~~gdw~~----a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l  235 (398)
T PRK10747        175 GVDKLLEVA---------------PRHPEVLRLAEQAYIRTGAWSS----LLDILPSMAKAHVGDEEHRAMLEQQAWIGL  235 (398)
T ss_pred             HHHHHHhcC---------------CCCHHHHHHHHHHHHHHHhHHH----HHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            999997752               4457888999999999999999    555555544321   1        123233


Q ss_pred             HHHHHHH-----HHHHHhhCCC---CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChh
Q 044412          178 IDAYARL-----AELLFNKMPA---WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALD  249 (311)
Q Consensus       178 i~~~~~~-----a~~~~~~m~~---~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~  249 (311)
                      +......     ..++++.++.   .+......+...+...|+.++|.+++++..+.  +||...  .++.+....++.+
T Consensus       236 ~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l--~~l~~~l~~~~~~  311 (398)
T PRK10747        236 MDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERL--VLLIPRLKTNNPE  311 (398)
T ss_pred             HHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHH--HHHHhhccCCChH
Confidence            3222222     4455555542   36778888999999999999999999998873  555532  2345555668888


Q ss_pred             hHHHHHHh---------------------hCChHHHHHHHhhcC--CCCchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          250 LGRGIQIY---------------------CRSLGRSLLVFFKLR--EKNLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       250 ~a~~~~~~---------------------~~~~~~a~~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      .+.+..+.                     .++.+.|.+.|+...  .|+..+|-.|-..+.+.|+.++|..++++-.
T Consensus       312 ~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        312 QLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            88777765                     888999999999887  7999999999999999999999999998754

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=98.81  E-value=2.6e-08  Score=84.75  Aligned_cols=105  Identities=19%  Similarity=0.165  Sum_probs=49.5

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHh-----------------
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIY-----------------  257 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~-----------------  257 (311)
                      +...|..+...+.+.|+.++|++.+++..+.  .|+ ....+.++..+...|+.+++..++..                 
T Consensus       145 ~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~  222 (280)
T PF13429_consen  145 SARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAA  222 (280)
T ss_dssp             -HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            4455555556666666666666666665553  343 44555566666666666655444433                 


Q ss_pred             ----hCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          258 ----CRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       258 ----~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                          .|+.++|...|++..   ..|+.+...+.+++...|+.++|..+..+.
T Consensus       223 ~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  223 AYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             HHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT---------------
T ss_pred             Hhcccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence                444445555555544   236666677777777777777777766554

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=98.78  E-value=1.1e-06  Score=72.98  Aligned_cols=248  Identities=12%  Similarity=0.114  Sum_probs=174.9

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHH---HHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-----------cccCCCh
Q 044412           38 SSIKELECVYATIVKTNANLDCFLA---KQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-----------FSSLRHP  103 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~---~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-----------~~~~~~~  103 (311)
                      .+++.+..+|-.|.+.    |+.|+   -+|=+.| .+.|.+|.|..+.+.+.+....|++-           |...|-+
T Consensus        49 ~Q~dKAvdlF~e~l~~----d~~t~e~~ltLGnLf-RsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~  123 (389)
T COG2956          49 NQPDKAVDLFLEMLQE----DPETFEAHLTLGNLF-RSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLL  123 (389)
T ss_pred             cCcchHHHHHHHHHhc----CchhhHHHHHHHHHH-HhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhh
Confidence            3556667788888873    44444   3455777 88999999999999876544445544           8999999


Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~  183 (311)
                      +.|.++|..+.+.|               .--......|+.-|-...++++|.++|+++.....++..+-   +-..||.
T Consensus       124 DRAE~~f~~L~de~---------------efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~e---IAqfyCE  185 (389)
T COG2956         124 DRAEDIFNQLVDEG---------------EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVE---IAQFYCE  185 (389)
T ss_pred             hHHHHHHHHHhcch---------------hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhH---HHHHHHH
Confidence            99999999997754               22344567899999999999999999999888777654321   1222332


Q ss_pred             H------------HHHHHhhCCC--CcHhHHHH-HHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          184 L------------AELLFNKMPA--WDIRSWTT-MITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       184 ~------------a~~~~~~m~~--~~~~~y~~-li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      .            |..++.+-.+  |+.+=-++ +-+.....|+++.|.+.++...+.+...-+.+...|..+|...|+.
T Consensus       186 LAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~  265 (389)
T COG2956         186 LAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKP  265 (389)
T ss_pred             HHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCH
Confidence            2            5555554432  32222222 3355667799999999999999987777778899999999999999


Q ss_pred             hhHHHHHHh--------------------hCChHHHHHHHh-hcC-CCCchhHHHHHHHHHhc---CChHHHHHHHHHHH
Q 044412          249 DLGRGIQIY--------------------CRSLGRSLLVFF-KLR-EKNLLCWNSITEALAIH---GFAHEALGMFDRMT  303 (311)
Q Consensus       249 ~~a~~~~~~--------------------~~~~~~a~~~~~-~~~-~p~~~~~~~li~~~~~~---g~~~~a~~~~~~M~  303 (311)
                      ++....+..                    ..-.+.|...+. .+. +|+...+..+|+.....   |...+-+.++++|.
T Consensus       266 ~~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mv  345 (389)
T COG2956         266 AEGLNFLRRAMETNTGADAELMLADLIELQEGIDAAQAYLTRQLRRKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMV  345 (389)
T ss_pred             HHHHHHHHHHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHHHhhCCcHHHHHHHHHhhhccccccchhhhHHHHHHHH
Confidence            998887777                    222223333322 333 89999999999987754   45677788888887


Q ss_pred             HcCCC
Q 044412          304 YENVR  308 (311)
Q Consensus       304 ~~g~~  308 (311)
                      ...++
T Consensus       346 ge~l~  350 (389)
T COG2956         346 GEQLR  350 (389)
T ss_pred             HHHHh
Confidence            65443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.78  E-value=1.1e-05  Score=77.83  Aligned_cols=80  Identities=10%  Similarity=0.036  Sum_probs=57.2

Q ss_pred             hhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------cccCCChhHHH
Q 044412           35 KKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------FSSLRHPLQAI  107 (311)
Q Consensus        35 ~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~~~~~~~~a~  107 (311)
                      -..|+...+...+.+..+..-.-.+.++ .++..+ ...|+.++|...+++...|+...+..       +...|++++|+
T Consensus        45 ~r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~-~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Ai  122 (822)
T PRK14574         45 ARAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIA-GWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQAL  122 (822)
T ss_pred             HhCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHH-HHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            3557777777777777665422222344 777888 88899999999998887665555544       56778999999


Q ss_pred             HHHHHHHHC
Q 044412          108 AFYLYMLRA  116 (311)
Q Consensus       108 ~~~~~m~~~  116 (311)
                      ++|+++.+.
T Consensus       123 ely~kaL~~  131 (822)
T PRK14574        123 ALWQSSLKK  131 (822)
T ss_pred             HHHHHHHhh
Confidence            999998765

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.77  E-value=1.5e-08  Score=56.77  Aligned_cols=35  Identities=26%  Similarity=0.502  Sum_probs=33.4

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCC
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTYENVRPNG  311 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~~  311 (311)
                      .+||+||.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999984

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.75  E-value=1.8e-08  Score=56.47  Aligned_cols=35  Identities=23%  Similarity=0.416  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ  232 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  232 (311)
                      .+||+||.+|++.|++++|.++|.+|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999984

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=98.74  E-value=5.4e-07  Score=83.75  Aligned_cols=84  Identities=11%  Similarity=0.058  Sum_probs=64.4

Q ss_pred             HHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeee----eec----cccCCChhHHHHHHHHHHH
Q 044412           44 ECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV----YHA----FSSLRHPLQAIAFYLYMLR  115 (311)
Q Consensus        44 ~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~----~~~----~~~~~~~~~a~~~~~~m~~  115 (311)
                      ..++..+...|+.|+..||.++|.-| +..|+++.|- +|.-|+-.+..+    ++.    ...+++.+.+         
T Consensus        10 tnfla~~e~~gi~PnRvtyqsLiarY-c~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enp---------   78 (1088)
T KOG4318|consen   10 TNFLALHEISGILPNRVTYQSLIARY-CTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENP---------   78 (1088)
T ss_pred             chHHHHHHHhcCCCchhhHHHHHHHH-cccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCC---------
Confidence            35677888999999999999999999 9999999998 998887544332    222    3334443332         


Q ss_pred             CCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCcc
Q 044412          116 AEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFE  154 (311)
Q Consensus       116 ~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~  154 (311)
                                      -.|..-+|+.|+.+|.+.||+..
T Consensus        79 ----------------kep~aDtyt~Ll~ayr~hGDli~  101 (1088)
T KOG4318|consen   79 ----------------KEPLADTYTNLLKAYRIHGDLIL  101 (1088)
T ss_pred             ----------------CCCchhHHHHHHHHHHhccchHH
Confidence                            25677899999999999999776

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.72  E-value=1.1e-06  Score=71.90  Aligned_cols=195  Identities=10%  Similarity=-0.020  Sum_probs=135.2

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHh
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKN  130 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~  130 (311)
                      ....+..+...+ .+.|+++.|.+.+++..+  |+ ...+..    +...|++++|.+.|++..+..             
T Consensus        30 ~~~~~~~la~~~-~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-------------   95 (234)
T TIGR02521        30 AAKIRVQLALGY-LEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-------------   95 (234)
T ss_pred             HHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-------------
Confidence            345666777777 888888888888877643  22 122222    777888888888888876532             


Q ss_pred             cCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhC
Q 044412          131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQN  210 (311)
Q Consensus       131 g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~  210 (311)
                        +.+...+..+...|...|++++    |...++.......                     .......+..+...+...
T Consensus        96 --~~~~~~~~~~~~~~~~~g~~~~----A~~~~~~~~~~~~---------------------~~~~~~~~~~l~~~~~~~  148 (234)
T TIGR02521        96 --PNNGDVLNNYGTFLCQQGKYEQ----AMQQFEQAIEDPL---------------------YPQPARSLENAGLCALKA  148 (234)
T ss_pred             --CCCHHHHHHHHHHHHHcccHHH----HHHHHHHHHhccc---------------------cccchHHHHHHHHHHHHc
Confidence              3445677778888889999999    5555554322100                     011344566677888899


Q ss_pred             CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcC
Q 044412          211 KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHG  290 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g  290 (311)
                      |++++|...+.+..+.. +.+...+..+...+...|++++|...++.....          ...+...+..+...+...|
T Consensus       149 g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~  217 (234)
T TIGR02521       149 GDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQT----------YNQTAESLWLGIRIARALG  217 (234)
T ss_pred             CCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----------CCCCHHHHHHHHHHHHHHh
Confidence            99999999999987742 234567888888888999998777665432211          1345667778888888999


Q ss_pred             ChHHHHHHHHHHHH
Q 044412          291 FAHEALGMFDRMTY  304 (311)
Q Consensus       291 ~~~~a~~~~~~M~~  304 (311)
                      +.++|..+.+.+..
T Consensus       218 ~~~~a~~~~~~~~~  231 (234)
T TIGR02521       218 DVAAAQRYGAQLQK  231 (234)
T ss_pred             hHHHHHHHHHHHHh
Confidence            99999999888765

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=98.71  E-value=6.1e-08  Score=82.52  Aligned_cols=196  Identities=14%  Similarity=0.106  Sum_probs=79.8

Q ss_pred             HHHHHHhhccCChhHHHHhccc-CCC---CCeeee-ec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC
Q 044412           64 QFISFCTSRFHFIDYTILVFPQ-MQE---PNVFVY-HA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS  134 (311)
Q Consensus        64 ~ll~~~~~~~g~~~~a~~~~~~-m~~---~~~~~~-~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~  134 (311)
                      .+-..+ .+.|++++|+++++. ...   |+...| ..    ....++.++|.+.|+++...+               .-
T Consensus        13 ~~A~~~-~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~---------------~~   76 (280)
T PF13429_consen   13 RLARLL-YQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD---------------KA   76 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccc-cccccccccccccccccccccccccccccccccccccccccccccccccccccccc---------------cc
Confidence            445667 888999999999954 322   333333 22    556788999999999987653               22


Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..++.. ...+++++|.++++..++.                            .++...+..++..+...++++
T Consensus        77 ~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~----------------------------~~~~~~l~~~l~~~~~~~~~~  127 (280)
T PF13429_consen   77 NPQDYERLIQL-LQDGDPEEALKLAEKAYER----------------------------DGDPRYLLSALQLYYRLGDYD  127 (280)
T ss_dssp             ----------------------------------------------------------------------H-HHHTT-HH
T ss_pred             ccccccccccc-ccccccccccccccccccc----------------------------ccccchhhHHHHHHHHHhHHH
Confidence            56677777777 7889999955555444443                            234556777888899999999


Q ss_pred             HHHHHHHHHHhcC-CCCCHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC
Q 044412          215 EALDAFNKTKKSG-TGSDQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR  272 (311)
Q Consensus       215 ~a~~~~~~m~~~g-~~p~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~  272 (311)
                      ++.++++...... .+++...|..+-..+.+.|+.++|..+++.                     .|+.+++.++++...
T Consensus       128 ~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~  207 (280)
T PF13429_consen  128 EAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLL  207 (280)
T ss_dssp             HHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            9999999987533 456778888899999999999999999988                     677777666666655


Q ss_pred             ---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          273 ---EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       273 ---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                         ..|...|..+-.+|...|+.++|..+|++..+
T Consensus       208 ~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~  242 (280)
T PF13429_consen  208 KAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALK  242 (280)
T ss_dssp             HH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHH
T ss_pred             HHCcCHHHHHHHHHHHhcccccccccccccccccc
Confidence               45677889999999999999999999999765

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.70  E-value=3.2e-08  Score=55.08  Aligned_cols=34  Identities=32%  Similarity=0.504  Sum_probs=32.6

Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYENVRP  309 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P  309 (311)
                      +.+||++|.+|++.|+++.|..+|++|++.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            3689999999999999999999999999999998

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.68  E-value=1.2e-05  Score=81.53  Aligned_cols=176  Identities=10%  Similarity=-0.007  Sum_probs=112.4

Q ss_pred             HHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeee---e---------ec-
Q 044412           32 NQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFV---Y---------HA-   96 (311)
Q Consensus        32 ~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~---~---------~~-   96 (311)
                      ..+...|+..++...++..++.. +-+...+..+-..+ .+.|+.++|...|++..+  |+...   |         .. 
T Consensus       277 ~~~~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~-~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        277 LAAVDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAY-SQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            34455688888888888888753 23677888888899 999999999999988653  33211   1         01 


Q ss_pred             ------cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC
Q 044412           97 ------FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK  170 (311)
Q Consensus        97 ------~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~  170 (311)
                            +.+.|++++|++.|++..+..               +.+...+..+-..|...|++++|++...++++.-+. +
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~---------------P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~  418 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVD---------------NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-N  418 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-C
Confidence                  568899999999999987642               334556667777888888888844433333332121 2


Q ss_pred             HhHHHHHHHHHH------------------------------------------HH-----HHHHHhhCC--CC-cHhHH
Q 044412          171 FATWNTMIDAYA------------------------------------------RL-----AELLFNKMP--AW-DIRSW  200 (311)
Q Consensus       171 ~~~~~~li~~~~------------------------------------------~~-----a~~~~~~m~--~~-~~~~y  200 (311)
                      ...+..+...|.                                          ..     |.+.|++..  .| +...+
T Consensus       419 ~~a~~~L~~l~~~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~  498 (1157)
T PRK11447        419 TNAVRGLANLYRQQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPGSVWLT  498 (1157)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHH
Confidence            222222222211                                          10     444454443  23 34556


Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          201 TTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       201 ~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      ..+...|.+.|++++|...+++..+
T Consensus       499 ~~LA~~~~~~G~~~~A~~~l~~al~  523 (1157)
T PRK11447        499 YRLAQDLRQAGQRSQADALMRRLAQ  523 (1157)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6677778888888888888888765

>TIGR00540 hemY_coli hemY protein

Probab=98.67  E-value=1.2e-05  Score=72.25  Aligned_cols=247  Identities=9%  Similarity=-0.098  Sum_probs=162.0

Q ss_pred             hccChhhHHHHHHHHHHhccCcchhHHHHH-HHHHhhccCChhHHHHhcccCCC--CCeee-----eec-cccCCChhHH
Q 044412           36 KCSSIKELECVYATIVKTNANLDCFLAKQF-ISFCTSRFHFIDYTILVFPQMQE--PNVFV-----YHA-FSSLRHPLQA  106 (311)
Q Consensus        36 ~~~~~~~~~~l~~~m~~~g~~p~~~~~~~l-l~~~~~~~g~~~~a~~~~~~m~~--~~~~~-----~~~-~~~~~~~~~a  106 (311)
                      ..|+++.+++......+.  .|++..+-.+ -.+. .+.|+.+.|.+.+++..+  |+...     +.. +...|++++|
T Consensus        96 ~~g~~~~A~~~l~~~~~~--~~~~~~~~llaA~aa-~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADH--AAEPVLNLIKAAEAA-QQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             hCCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHH
Confidence            346777777777655444  4665544444 3555 788999999999988642  33221     111 6778999999


Q ss_pred             HHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCC-CHh------HHHHHHH
Q 044412          107 IAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPER-KFA------TWNTMID  179 (311)
Q Consensus       107 ~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~-~~~------~~~~li~  179 (311)
                      .+.++.+.+..               +-+..+...+...|...|++++|.+....+.+..... ...      .+..++.
T Consensus       173 l~~l~~l~~~~---------------P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~  237 (409)
T TIGR00540       173 RHGVDKLLEMA---------------PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLD  237 (409)
T ss_pred             HHHHHHHHHhC---------------CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999998753               3457788899999999999999555444444442221 111      1211121


Q ss_pred             HHHH-----HHHHHHhhCCC---CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHH---HHHHHHHHhccCCh
Q 044412          180 AYAR-----LAELLFNKMPA---WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVT---MATVLSACAHLGAL  248 (311)
Q Consensus       180 ~~~~-----~a~~~~~~m~~---~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t---~~~li~a~~~~~~~  248 (311)
                      .-..     .....++..+.   .+...+-.+...+...|+.++|.+++++..+.  .||...   ...........++.
T Consensus       238 ~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~  315 (409)
T TIGR00540       238 EAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDN  315 (409)
T ss_pred             HHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCCh
Confidence            1111     13334444443   37888999999999999999999999999875  344432   11111122233555


Q ss_pred             hhHHHHHHh-----------------------hCChHHHHHHHhh--c-C-CCCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          249 DLGRGIQIY-----------------------CRSLGRSLLVFFK--L-R-EKNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       249 ~~a~~~~~~-----------------------~~~~~~a~~~~~~--~-~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      +.+.+.++.                       .|+.++|.+.|+.  . . .|+...+..+...+.+.|+.++|.+++++
T Consensus       316 ~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~  395 (409)
T TIGR00540       316 EKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQD  395 (409)
T ss_pred             HHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            555554433                       7888888888883  3 2 68888888899999999999999988887


Q ss_pred             H
Q 044412          302 M  302 (311)
Q Consensus       302 M  302 (311)
                      -
T Consensus       396 ~  396 (409)
T TIGR00540       396 S  396 (409)
T ss_pred             H
Confidence            4

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.66  E-value=1.5e-05  Score=72.19  Aligned_cols=232  Identities=10%  Similarity=0.120  Sum_probs=145.2

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCCC-------Ceeee----e-c---cccCCChhHHHHHHHHHHHCCCCchHHH
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQEP-------NVFVY----H-A---FSSLRHPLQAIAFYLYMLRAEVLLTTVH  124 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~-------~~~~~----~-~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~  124 (311)
                      .+...+...| ...|+++.|..++.+-.+.       +....    + .   |...+.+.+|..+|+++..-       .
T Consensus       200 ~~~~~La~~y-~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i-------~  271 (508)
T KOG1840|consen  200 RTLRNLAEMY-AVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTI-------R  271 (508)
T ss_pred             HHHHHHHHHH-HHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH-------H
Confidence            4555566777 7777777777777554321       11000    0 0   66777888888888877541       0


Q ss_pred             HHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC------CCHhH-HHHHHHHHHHH------------H
Q 044412          125 GQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE------RKFAT-WNTMIDAYARL------------A  185 (311)
Q Consensus       125 ~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~------~~~~~-~~~li~~~~~~------------a  185 (311)
                      +.....-.+.-..+++.|-.+|++.|++++|...+.+..+-...      +.+.+ ++.+...++..            +
T Consensus       272 e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~a  351 (508)
T KOG1840|consen  272 EEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKA  351 (508)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHH
Confidence            00000011112456777777899999999966654333332211      23332 23333333332            4


Q ss_pred             HHHHhhCCCC-c---HhHHHHHHHHHHhCCChhHHHHHHHHHHhc----C--CCC-CHHHHHHHHHHHhccCChhhHHHH
Q 044412          186 ELLFNKMPAW-D---IRSWTTMITSYSQNKQFREALDAFNKTKKS----G--TGS-DQVTMATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       186 ~~~~~~m~~~-~---~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g--~~p-~~~t~~~li~a~~~~~~~~~a~~~  254 (311)
                      .+++.....+ +   ..+|+.|-..|-..|++++|.+++++..+.    +  ..+ ....++-|-.+|.+.+..+.|.++
T Consensus       352 l~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l  431 (508)
T KOG1840|consen  352 LKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQL  431 (508)
T ss_pred             HHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHH
Confidence            4444433333 2   257999999999999999999999997652    1  223 356788889999999999999998


Q ss_pred             HHhhCChHHHHHHHhhcCCCCc-hhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          255 QIYCRSLGRSLLVFFKLREKNL-LCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       255 ~~~~~~~~~a~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      |.+++.+-.+.    ....|++ .+|..|...|-+.|+++.|.++.+...
T Consensus       432 ~~~~~~i~~~~----g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  432 FEEAKDIMKLC----GPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHHHHHh----CCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            86544433111    1113443 689999999999999999999987765

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.66  E-value=4.4e-08  Score=54.51  Aligned_cols=33  Identities=15%  Similarity=0.382  Sum_probs=32.1

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGS  230 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  230 (311)
                      .+||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            689999999999999999999999999999998

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.62  E-value=3.1e-05  Score=75.18  Aligned_cols=87  Identities=8%  Similarity=0.021  Sum_probs=53.6

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec----cccCC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA----FSSLR  101 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~----~~~~~  101 (311)
                      ..+..++...++...+..+++..++.. +.++..+..+...+ .+.|+.++|...+++..+  |+...+..    +...|
T Consensus        53 ~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l-~~~g~~~eA~~~l~~~l~~~P~~~~~~~la~~l~~~g  130 (765)
T PRK10049         53 AAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTL-ADAGQYDEALVKAKQLVSGAPDKANLLALAYVYKRAG  130 (765)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHCC
Confidence            455556666777777777777666542 22344555666666 777777777777776542  32222322    66677


Q ss_pred             ChhHHHHHHHHHHHC
Q 044412          102 HPLQAIAFYLYMLRA  116 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~  116 (311)
                      +.++|+..+++..+.
T Consensus       131 ~~~~Al~~l~~al~~  145 (765)
T PRK10049        131 RHWDELRAMTQALPR  145 (765)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            777777777776653

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=98.61  E-value=1.3e-05  Score=75.90  Aligned_cols=268  Identities=12%  Similarity=-0.020  Sum_probs=157.1

Q ss_pred             HHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhH
Q 044412           33 QLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQ  105 (311)
Q Consensus        33 ~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~  105 (311)
                      .+-..+++..+...|...++  +.|++..|..+-.+| .+.|+++.|.+.++...+  |+ ...|..    +...|++++
T Consensus       136 ~~~~~~~~~~Ai~~y~~al~--~~p~~~~~~n~a~~~-~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~a~a~~~lg~~~e  212 (615)
T TIGR00990       136 KAYRNKDFNKAIKLYSKAIE--CKPDPVYYSNRAACH-NALGDWEKVVEDTTAALELDPDYSKALNRRANAYDGLGKYAD  212 (615)
T ss_pred             HHHHcCCHHHHHHHHHHHHh--cCCchHHHHHHHHHH-HHhCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHH
Confidence            34455677778888877665  457788888888888 999999999998887654  32 222222    778888888


Q ss_pred             HHHHHHHHHHCC-CCch---HHHHHHHH-----------hcCCCchhHHHH-----------------------------
Q 044412          106 AIAFYLYMLRAE-VLLT---TVHGQVWK-----------NGFSSPVFVQTA-----------------------------  141 (311)
Q Consensus       106 a~~~~~~m~~~~-~~p~---~~~~~~~~-----------~g~~~~~~~~~~-----------------------------  141 (311)
                      |+.-|......+ ..+.   ........           ....++...+..                             
T Consensus       213 A~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (615)
T TIGR00990       213 ALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEETGN  292 (615)
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccccccccccc
Confidence            887665443211 1110   00000000           000000000000                             


Q ss_pred             -HHHHH------HhCCCCccchHHHHHHhccCC-CC-CHhHHHHHHHHHHHH-----HHHHHhhCC--CCc-HhHHHHHH
Q 044412          142 -MVDNY------SYSNKFFESRRVSRRLFDEMP-ER-KFATWNTMIDAYARL-----AELLFNKMP--AWD-IRSWTTMI  204 (311)
Q Consensus       142 -ll~~~------~~~g~~~~a~~~a~~~~~~~~-~~-~~~~~~~li~~~~~~-----a~~~~~~m~--~~~-~~~y~~li  204 (311)
                       ++..+      ...+++++|.+.....++... .| ....|+.+-..+...     |...|++..  .|+ ...|..+.
T Consensus       293 ~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la  372 (615)
T TIGR00990       293 GQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRA  372 (615)
T ss_pred             chHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHH
Confidence             00000      112455663333333332211 12 223344443333332     555555443  233 44666677


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGR  263 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~  263 (311)
                      ..+...|++++|+..|++..+.. +-+...|..+-..+...|++++|...|+.                     .|+.++
T Consensus       373 ~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~e  451 (615)
T TIGR00990       373 SMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIAS  451 (615)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHH
Confidence            77777778888888777776542 22456677777777777777777777766                     567777


Q ss_pred             HHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          264 SLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       264 a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      |...|++..  .| +...|+.+-..+...|++++|...|++...
T Consensus       452 A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~  495 (615)
T TIGR00990       452 SMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIE  495 (615)
T ss_pred             HHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            877777655  34 467889999999999999999999998765

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.60  E-value=1.2e-05  Score=79.14  Aligned_cols=215  Identities=9%  Similarity=-0.059  Sum_probs=142.9

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCC--CCCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQ--EPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~--~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      +...|..+-.++ .. ++.++|...+.+..  .|+......    +...|++++|...|+.+...               
T Consensus       476 ~~~a~~~LG~~l-~~-~~~~eAi~a~~~Al~~~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~---------------  538 (987)
T PRK09782        476 DAAAWNRLAKCY-RD-TLPGVALYAWLQAEQRQPDAWQHRAVAYQAYQVEDYATALAAWQKISLH---------------  538 (987)
T ss_pred             CHHHHHHHHHHH-Hh-CCcHHHHHHHHHHHHhCCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc---------------
Confidence            456677777666 65 78888888666543  344222111    45789999999999987542               


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHH---HHH--HHHHHhhCC--CCcHhHHHHHH
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAY---ARL--AELLFNKMP--AWDIRSWTTMI  204 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~---~~~--a~~~~~~m~--~~~~~~y~~li  204 (311)
                       .|+...+..+..++.+.|++++|.....+..+.-+ .....+..+....   .+.  |...+++..  .|+...|..+-
T Consensus       539 -~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P-~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA  616 (987)
T PRK09782        539 -DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRGL-GDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARA  616 (987)
T ss_pred             -CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence             44445566667788899999995544444443221 1222222222222   111  666666554  46777888888


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSI  282 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~l  282 (311)
                      ..+.+.|++++|+..|++..+.  .|+ ...++.+-.++...|+.++|...++.      |.+.     .| +...+..+
T Consensus       617 ~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~------AL~l-----~P~~~~a~~nL  683 (987)
T PRK09782        617 TIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREMLER------AHKG-----LPDDPALIRQL  683 (987)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHH------HHHh-----CCCCHHHHHHH
Confidence            8999999999999999998774  455 44566666688888888866655422      2211     34 45678889


Q ss_pred             HHHHHhcCChHHHHHHHHHHHH
Q 044412          283 TEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       283 i~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      -.++...|++++|...+++..+
T Consensus       684 A~al~~lGd~~eA~~~l~~Al~  705 (987)
T PRK09782        684 AYVNQRLDDMAATQHYARLVID  705 (987)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHh
Confidence            9999999999999999998875

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.59  E-value=3.3e-05  Score=75.02  Aligned_cols=278  Identities=9%  Similarity=-0.040  Sum_probs=173.5

Q ss_pred             CCCchhhhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec
Q 044412           19 PTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA   96 (311)
Q Consensus        19 ~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~   96 (311)
                      |..+..  ...+..++...++..++...++..++. .+.+.. +..+-.++ ...|+.++|...+++..+  |+......
T Consensus        80 P~~~~a--~~~la~~l~~~g~~~eA~~~l~~~l~~-~P~~~~-~~~la~~l-~~~g~~~~Al~~l~~al~~~P~~~~~~~  154 (765)
T PRK10049         80 PQNDDY--QRGLILTLADAGQYDEALVKAKQLVSG-APDKAN-LLALAYVY-KRAGRHWDELRAMTQALPRAPQTQQYPT  154 (765)
T ss_pred             CCCHHH--HHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHH-HHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            555443  346666777788888888888887776 233444 77777777 888888888888888753  43222111


Q ss_pred             -----cccCCChhHHHHHHHHHHHC-----CCC--c----------------------h---HHHHHHHHh-cCCCchh-
Q 044412           97 -----FSSLRHPLQAIAFYLYMLRA-----EVL--L----------------------T---TVHGQVWKN-GFSSPVF-  137 (311)
Q Consensus        97 -----~~~~~~~~~a~~~~~~m~~~-----~~~--p----------------------~---~~~~~~~~~-g~~~~~~-  137 (311)
                           +...+..++|++.++.....     +..  |                      +   ...+.+.+. .-.|+.. 
T Consensus       155 ~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~  234 (765)
T PRK10049        155 EYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATA  234 (765)
T ss_pred             HHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccch
Confidence                 55667777777766643320     000  0                      0   111122211 1223221 


Q ss_pred             HHH----HHHHHHHhCCCCccchHHHHHHhccCCCCC--HhHH--HHHHHHHHHH-----HHHHHhhCCC--Cc-----H
Q 044412          138 VQT----AMVDNYSYSNKFFESRRVSRRLFDEMPERK--FATW--NTMIDAYARL-----AELLFNKMPA--WD-----I  197 (311)
Q Consensus       138 ~~~----~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~--~~~~--~~li~~~~~~-----a~~~~~~m~~--~~-----~  197 (311)
                      .+.    ..+.++...|+.++    |...|+.+.+.+  ...+  ..+-..|...     |...|++...  |.     .
T Consensus       235 ~~~~a~~d~l~~Ll~~g~~~e----A~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~  310 (765)
T PRK10049        235 DYQRARIDRLGALLARDRYKD----VISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSD  310 (765)
T ss_pred             HHHHHHHHHHHHHHHhhhHHH----HHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCCh
Confidence            111    11334567788999    555555554421  1111  1123334333     7777776542  21     2


Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcC-----------CCCCH---HHHHHHHHHHhccCChhhHHHHHHh------
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSG-----------TGSDQ---VTMATVLSACAHLGALDLGRGIQIY------  257 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-----------~~p~~---~t~~~li~a~~~~~~~~~a~~~~~~------  257 (311)
                      ..+..+..++...|++++|..+++++.+..           -.|+.   ..+..+...+...|+.++|..+++.      
T Consensus       311 ~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P  390 (765)
T PRK10049        311 EELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAP  390 (765)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            345666677888999999999999988642           12332   2455677788889999999999887      


Q ss_pred             ---------------hCChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          258 ---------------CRSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       258 ---------------~~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                                     .|+.+.|.+.+++..  .|+ ...+-.....+.+.|++++|..+++++.+.
T Consensus       391 ~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        391 GNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence                           788889999888877  565 556677777888999999999999999863

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.55  E-value=0.00013  Score=70.64  Aligned_cols=288  Identities=10%  Similarity=0.042  Sum_probs=189.8

Q ss_pred             HHhhhhhcCCCCCchhhhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC
Q 044412            9 IITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE   88 (311)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~   88 (311)
                      .+..+.+...|....+........++...++.+.+.++++.+.+..-. ++..+..++..+ .+.++.++|.+.++.+.+
T Consensus        87 A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~dP~-n~~~l~gLa~~y-~~~~q~~eAl~~l~~l~~  164 (822)
T PRK14574         87 VIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSSLKKDPT-NPDLISGMIMTQ-ADAGRGGVVLKQATELAE  164 (822)
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHHH-hhcCCHHHHHHHHHHhcc
Confidence            344444444454444422233355667779999999999999887533 356667778888 999999999999999875


Q ss_pred             --CCeeeeec----cccCCChhHHHHHHHHHHHCCCCch-----------------------------------------
Q 044412           89 --PNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLT-----------------------------------------  121 (311)
Q Consensus        89 --~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~-----------------------------------------  121 (311)
                        |+...+..    +...++..+|++.++++.+..  |+                                         
T Consensus       165 ~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~--P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~  242 (822)
T PRK14574        165 RDPTVQNYMTLSYLNRATDRNYDALQASSEAVRLA--PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLE  242 (822)
T ss_pred             cCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHH
Confidence              44333322    333556656999999887753  44                                         


Q ss_pred             -H---------------------HHH-------HHH-HhcCCCch-hH----HHHHHHHHHhCCCCccchHHHHHHhccC
Q 044412          122 -T---------------------VHG-------QVW-KNGFSSPV-FV----QTAMVDNYSYSNKFFESRRVSRRLFDEM  166 (311)
Q Consensus       122 -~---------------------~~~-------~~~-~~g~~~~~-~~----~~~ll~~~~~~g~~~~a~~~a~~~~~~~  166 (311)
                       .                     +.+       .+. ..+-.|.. ..    .--.+-++...|+.++    +.+.++.+
T Consensus       243 ~~~~a~~vr~a~~~~~~~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~----vi~~y~~l  318 (822)
T PRK14574        243 RDAAAEQVRMAVLPTRSETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTAD----LIKEYEAM  318 (822)
T ss_pred             HHHHHHHHhhcccccccchhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHH----HHHHHHHh
Confidence             0                     000       111 11111321 11    1234457788899999    77777777


Q ss_pred             CCCC--Hh--HHHHHHHHHHHH-----HHHHHhhCCC---------CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC-
Q 044412          167 PERK--FA--TWNTMIDAYARL-----AELLFNKMPA---------WDIRSWTTMITSYSQNKQFREALDAFNKTKKSG-  227 (311)
Q Consensus       167 ~~~~--~~--~~~~li~~~~~~-----a~~~~~~m~~---------~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-  227 (311)
                      +.+.  +.  +--.+-++|...     |..+|.....         ++......|.-+|...+++++|..+++.+.+.- 
T Consensus       319 ~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p  398 (822)
T PRK14574        319 EAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTP  398 (822)
T ss_pred             hhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCC
Confidence            7433  23  334566666654     8888887632         133445788899999999999999999998731 


Q ss_pred             ------------CCCCHH-HHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC-
Q 044412          228 ------------TGSDQV-TMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR-  272 (311)
Q Consensus       228 ------------~~p~~~-t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~-  272 (311)
                                  --||-. -+..++..+.-.|++.+|++.++.                     -|.+..|++.++... 
T Consensus       399 ~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~  478 (822)
T PRK14574        399 YQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVES  478 (822)
T ss_pred             cEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence                        112222 344567778889999999999888                     777888888886655 


Q ss_pred             -CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          273 -EK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       273 -~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                       .| +..+......++...|++.+|..+.+...+
T Consensus       479 l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~  512 (822)
T PRK14574        479 LAPRSLILERAQAETAMALQEWHQMELLTDDVIS  512 (822)
T ss_pred             hCCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence             34 456777778888888888888888777654

>TIGR00540 hemY_coli hemY protein

Probab=98.54  E-value=3.3e-05  Score=69.42  Aligned_cols=225  Identities=10%  Similarity=0.001  Sum_probs=152.2

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchh--HHHHHHHHHhhccCChhHHHHhcccCCC--CCee-eeec----ccc
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCF--LAKQFISFCTSRFHFIDYTILVFPQMQE--PNVF-VYHA----FSS   99 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~--~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~-~~~~----~~~   99 (311)
                      ....+....|+.+.+...+....+.-  |+..  .--.....+ ...|+.+.|...++.+.+  |+.. ....    +..
T Consensus       123 laA~aa~~~g~~~~A~~~l~~a~~~~--p~~~l~~~~~~a~l~-l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~  199 (409)
T TIGR00540       123 KAAEAAQQRGDEARANQHLEEAAELA--GNDNILVEIARTRIL-LAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIR  199 (409)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC--CcCchHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            44555667788888888888876653  4443  333346677 889999999999999874  4332 2222    899


Q ss_pred             CCChhHHHHHHHHHHHCCCCch--------HHHHHHH-----Hh---------cCCC-----chhHHHHHHHHHHhCCCC
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLT--------TVHGQVW-----KN---------GFSS-----PVFVQTAMVDNYSYSNKF  152 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~--------~~~~~~~-----~~---------g~~~-----~~~~~~~ll~~~~~~g~~  152 (311)
                      .|++++|.+++..+.+.++.+.        .......     +.         .-.|     +...+..+...+...|+.
T Consensus       200 ~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~  279 (409)
T TIGR00540       200 SGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDH  279 (409)
T ss_pred             HhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCCh
Confidence            9999999999999999876543        1111101     00         1133     778899999999999999


Q ss_pred             ccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-------HHHHHhhCC--CCc-H--hHHHHHHHHHHhCCChhHHHHHH
Q 044412          153 FESRRVSRRLFDEMPERKFATWNTMIDAYARL-------AELLFNKMP--AWD-I--RSWTTMITSYSQNKQFREALDAF  220 (311)
Q Consensus       153 ~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-------a~~~~~~m~--~~~-~--~~y~~li~~~~~~g~~~~a~~~~  220 (311)
                      ++|..+..+.++.-+......+. ++..+...       +.+.++.-.  .|+ .  ....++-..+.+.|++++|.+.|
T Consensus       280 ~~A~~~l~~~l~~~pd~~~~~~~-~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~l  358 (409)
T TIGR00540       280 DSAQEIIFDGLKKLGDDRAISLP-LCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAF  358 (409)
T ss_pred             HHHHHHHHHHHhhCCCcccchhH-HHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHH
Confidence            99666666666554443211111 23333321       333333222  233 3  45557778888999999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          221 NKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       221 ~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +.-......||..++..+-..+.+.|+.++|.+++++
T Consensus       359 e~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~  395 (409)
T TIGR00540       359 KNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQD  395 (409)
T ss_pred             HHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            9655545689999999999999999999988888754

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.50  E-value=7.4e-06  Score=66.84  Aligned_cols=185  Identities=9%  Similarity=0.052  Sum_probs=134.1

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~  100 (311)
                      ..+...+...++...+...++...+.. +.+...+..+...+ ...|+++.|.+.+++..+  |+ ...+..    +...
T Consensus        35 ~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~-~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~  112 (234)
T TIGR02521        35 VQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYY-QQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQ  112 (234)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH-HHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHc
Confidence            345566667788888888888887654 33466778888888 999999999999987653  22 111211    7888


Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA  180 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~  180 (311)
                      |++++|.+.|++..+...             .......+..+-..+...|++++    |...+......+          
T Consensus       113 g~~~~A~~~~~~~~~~~~-------------~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~~----------  165 (234)
T TIGR02521       113 GKYEQAMQQFEQAIEDPL-------------YPQPARSLENAGLCALKAGDFDK----AEKYLTRALQID----------  165 (234)
T ss_pred             ccHHHHHHHHHHHHhccc-------------cccchHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhC----------
Confidence            999999999999865321             12234567778888999999999    555555422211          


Q ss_pred             HHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          181 YARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       181 ~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                                   ..+...+..+...+...|++++|.+.+++..+. .+.+...+..+...+...|+.+.|..+.
T Consensus       166 -------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~  226 (234)
T TIGR02521       166 -------------PQRPESLLELAELYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYG  226 (234)
T ss_pred             -------------cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHH
Confidence                         124557778888899999999999999998876 3456677777888888888888776654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=98.48  E-value=5.8e-06  Score=74.46  Aligned_cols=269  Identities=10%  Similarity=0.111  Sum_probs=161.3

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCc-chhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec-----cc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANL-DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA-----FS   98 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p-~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~-----~~   98 (311)
                      +..+..++...|+++++..+++.+++..  | ....|-.+-.++ ...|+.+.|...|.+..+  |+.....+     +-
T Consensus       119 ysn~aN~~kerg~~~~al~~y~~aiel~--p~fida~inla~al-~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnLlk  195 (966)
T KOG4626|consen  119 YSNLANILKERGQLQDALALYRAAIELK--PKFIDAYINLAAAL-VTQGDLELAVQCFFEALQLNPDLYCARSDLGNLLK  195 (966)
T ss_pred             HHHHHHHHHHhchHHHHHHHHHHHHhcC--chhhHHHhhHHHHH-HhcCCCcccHHHHHHHHhcCcchhhhhcchhHHHH
Confidence            4568889999999999999999888763  3 345677777778 888999988888877654  44444333     34


Q ss_pred             cCCChhHHHHHHHHHHHCCCCch--------------------HHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLT--------------------TVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRR  157 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~--------------------~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~  157 (311)
                      ..|+.++|..-|.+-.+.  .|.                    .++..-..-.+.|+ ...|-.|-+.|...+.+|+|..
T Consensus       196 a~Grl~ea~~cYlkAi~~--qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~ke~~~~d~Avs  273 (966)
T KOG4626|consen  196 AEGRLEEAKACYLKAIET--QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVYKEARIFDRAVS  273 (966)
T ss_pred             hhcccchhHHHHHHHHhh--CCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHHHHHhcchHHHH
Confidence            456666666666554331  122                    11111111224555 3456666666777777777333


Q ss_pred             HHHHHhccCCCCCH-hHHHHHHHHHHHH-----HHHHHhhCC--CCc-HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC
Q 044412          158 VSRRLFDEMPERKF-ATWNTMIDAYARL-----AELLFNKMP--AWD-IRSWTTMITSYSQNKQFREALDAFNKTKKSGT  228 (311)
Q Consensus       158 ~a~~~~~~~~~~~~-~~~~~li~~~~~~-----a~~~~~~m~--~~~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  228 (311)
                      ...+.+..  .|+. +.+..|-..|-..     |...+++-.  +|+ ...||.|-.++-..|++.+|.+.+..-..  +
T Consensus       274 ~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~--l  349 (966)
T KOG4626|consen  274 CYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALR--L  349 (966)
T ss_pred             HHHHHHhc--CCcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHH--h
Confidence            22222221  1221 2222221111111     555555443  344 34688888888888888888888887665  3


Q ss_pred             CCC-HHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC--CCCc-hhHHHHH
Q 044412          229 GSD-QVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR--EKNL-LCWNSIT  283 (311)
Q Consensus       229 ~p~-~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~--~p~~-~~~~~li  283 (311)
                      -|+ ....+.|-..+...|.++.|..++..                     .|++++|...+++..  +|+. ..|+.|-
T Consensus       350 ~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmG  429 (966)
T KOG4626|consen  350 CPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMG  429 (966)
T ss_pred             CCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcc
Confidence            444 35677777888888888888777765                     566666666655544  4543 3566666


Q ss_pred             HHHHhcCChHHHHHHHHHHHH
Q 044412          284 EALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       284 ~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..|-..|+...|...+.+.+.
T Consensus       430 nt~ke~g~v~~A~q~y~rAI~  450 (966)
T KOG4626|consen  430 NTYKEMGDVSAAIQCYTRAIQ  450 (966)
T ss_pred             hHHHHhhhHHHHHHHHHHHHh
Confidence            666666666666666655443

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.48  E-value=1.7e-05  Score=70.93  Aligned_cols=212  Identities=11%  Similarity=0.002  Sum_probs=148.4

Q ss_pred             hhccChhhHHHHHHHHHHhccCcchhHHH--HHHHHHhhccCChhHHHHhcccCCC--CCeee-eec----cccCCChhH
Q 044412           35 KKCSSIKELECVYATIVKTNANLDCFLAK--QFISFCTSRFHFIDYTILVFPQMQE--PNVFV-YHA----FSSLRHPLQ  105 (311)
Q Consensus        35 ~~~~~~~~~~~l~~~m~~~g~~p~~~~~~--~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~-~~~----~~~~~~~~~  105 (311)
                      ...|+.+.+...+..+.+.  .|+.....  .....+ ...|+.+.|...+++..+  |+... ...    +.+.|++++
T Consensus       129 ~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~-l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~  205 (398)
T PRK10747        129 QQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQ-LARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSS  205 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHH
Confidence            6778888888888888764  55654433  334577 889999999999999875  33221 111    889999999


Q ss_pred             HHHHHHHHHHCCCCchH--------HHHHHHH-------------------hcCCCchhHHHHHHHHHHhCCCCccchHH
Q 044412          106 AIAFYLYMLRAEVLLTT--------VHGQVWK-------------------NGFSSPVFVQTAMVDNYSYSNKFFESRRV  158 (311)
Q Consensus       106 a~~~~~~m~~~~~~p~~--------~~~~~~~-------------------~g~~~~~~~~~~ll~~~~~~g~~~~a~~~  158 (311)
                      |.+++..+.+.+..++.        .+..+..                   ...+.++.....+...+...|+.++|..+
T Consensus       206 a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~  285 (398)
T PRK10747        206 LLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQI  285 (398)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            99999999988775441        1101010                   01234677788889999999999996666


Q ss_pred             HHHHhccCCCCCHhHHHHHHHHHHHH-------HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC
Q 044412          159 SRRLFDEMPERKFATWNTMIDAYARL-------AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGT  228 (311)
Q Consensus       159 a~~~~~~~~~~~~~~~~~li~~~~~~-------a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  228 (311)
                      ..+.++.  .++.    .++..|...       +.+..+...  .| |...+..+-..+.+.+++++|.+.|+...+  .
T Consensus       286 L~~~l~~--~~~~----~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~--~  357 (398)
T PRK10747        286 ILDGLKR--QYDE----RLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALK--Q  357 (398)
T ss_pred             HHHHHhc--CCCH----HHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh--c
Confidence            6666653  2222    222222221       333333332  23 555677888889999999999999999987  4


Q ss_pred             CCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          229 GSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       229 ~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      .|+..+|..+-.++.+.|+.++|.+++++
T Consensus       358 ~P~~~~~~~La~~~~~~g~~~~A~~~~~~  386 (398)
T PRK10747        358 RPDAYDYAWLADALDRLHKPEEAAAMRRD  386 (398)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            79999999999999999999988777643

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.45  E-value=2.3e-07  Score=50.31  Aligned_cols=31  Identities=29%  Similarity=0.676  Sum_probs=29.2

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCC
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGT  228 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  228 (311)
                      ++||+||++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4899999999999999999999999999885

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=98.43  E-value=2.4e-05  Score=70.65  Aligned_cols=212  Identities=10%  Similarity=0.115  Sum_probs=137.5

Q ss_pred             HHHHHHHHHhhccCChhHHHHhcccCC--CCC-eee-eec---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCC
Q 044412           61 LAKQFISFCTSRFHFIDYTILVFPQMQ--EPN-VFV-YHA---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFS  133 (311)
Q Consensus        61 ~~~~ll~~~~~~~g~~~~a~~~~~~m~--~~~-~~~-~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~  133 (311)
                      .|-.|=..| ...+.++.|...+....  .|+ .+. .|.   |...|+.+-|++.|++-.+                ++
T Consensus       254 AYiNLGnV~-ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~----------------~~  316 (966)
T KOG4626|consen  254 AYINLGNVY-KEARIFDRAVSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALE----------------LQ  316 (966)
T ss_pred             HHhhHHHHH-HHHhcchHHHHHHHHHHhcCCcchhhccceEEEEeccccHHHHHHHHHHHHh----------------cC
Confidence            455555666 66777777777765542  333 222 333   8889999999999988765                46


Q ss_pred             Cc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CC-HhHHHHHHHHHHHH-----HHHHHhhCCC--Cc-HhHHH
Q 044412          134 SP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RK-FATWNTMIDAYARL-----AELLFNKMPA--WD-IRSWT  201 (311)
Q Consensus       134 ~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~-----a~~~~~~m~~--~~-~~~y~  201 (311)
                      |+ ...|+.|-+++-..|++++    |...++....  |+ ..+.+.|-..|...     |.++|..-.+  |. ...+|
T Consensus       317 P~F~~Ay~NlanALkd~G~V~e----a~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~n  392 (966)
T KOG4626|consen  317 PNFPDAYNNLANALKDKGSVTE----AVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHN  392 (966)
T ss_pred             CCchHHHhHHHHHHHhccchHH----HHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhh
Confidence            66 6789999999999999999    7777665443  22 23455555555554     5555543332  32 34578


Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCH-HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCCc-h
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQ-VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKNL-L  277 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~~-~  277 (311)
                      .|-..|-..|++++|+..+++-.+  +.|+- ..|+.+=..|-..|+++.|.+.+             .+-.  .|.. .
T Consensus       393 NLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y-------------~rAI~~nPt~Ae  457 (966)
T KOG4626|consen  393 NLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCY-------------TRAIQINPTFAE  457 (966)
T ss_pred             hHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHH-------------HHHHhcCcHHHH
Confidence            888888888888888888888765  67763 35555555555555555554444             3332  2332 3


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          278 CWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       278 ~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      .++.|-..|-..|++.+|..-|++-.+  ++||
T Consensus       458 AhsNLasi~kDsGni~~AI~sY~~aLk--lkPD  488 (966)
T KOG4626|consen  458 AHSNLASIYKDSGNIPEAIQSYRTALK--LKPD  488 (966)
T ss_pred             HHhhHHHHhhccCCcHHHHHHHHHHHc--cCCC
Confidence            567777777777777777777776553  4555

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.42  E-value=3.5e-07  Score=49.59  Aligned_cols=31  Identities=29%  Similarity=0.449  Sum_probs=29.5

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      .|||+||++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4899999999999999999999999999986

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=0.00012  Score=64.03  Aligned_cols=201  Identities=15%  Similarity=0.219  Sum_probs=143.3

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCC------eeeee----------------
Q 044412           38 SSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPN------VFVYH----------------   95 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~------~~~~~----------------   95 (311)
                      ....+..+=.......|++-+...-+..-.+. -...+++.|..+|+++.+.|      ..+|+                
T Consensus       241 ~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~-y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA  319 (559)
T KOG1155|consen  241 HQHEEALQKKERLSSVGFPNSMYIKTQIAAAS-YNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLA  319 (559)
T ss_pred             HHHHHHHHHHHHHHhccCCccHHHHHHHHHHH-hhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHH
Confidence            34444445555666778877777666666666 77889999999999886422      11111                


Q ss_pred             ---------------c----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccc
Q 044412           96 ---------------A----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFES  155 (311)
Q Consensus        96 ---------------~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a  155 (311)
                                     +    |+-.++.++|...|+.-.+                +.|. ...|+.+-+-|....+...|
T Consensus       320 ~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALk----------------LNp~~~~aWTLmGHEyvEmKNt~AA  383 (559)
T KOG1155|consen  320 QNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALK----------------LNPKYLSAWTLMGHEYVEMKNTHAA  383 (559)
T ss_pred             HHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHh----------------cCcchhHHHHHhhHHHHHhcccHHH
Confidence                           1    5555677778887777654                4454 55677777779999998884


Q ss_pred             hHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC
Q 044412          156 RRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSG  227 (311)
Q Consensus       156 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g  227 (311)
                      .+-.+...+ +.+.|-..|-.|=.+|.-.     |.-.|++-.   .-|...|.+|-++|-+.+++++|++.|..-...|
T Consensus       384 i~sYRrAvd-i~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~  462 (559)
T KOG1155|consen  384 IESYRRAVD-INPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG  462 (559)
T ss_pred             HHHHHHHHh-cCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc
Confidence            443333322 3446777787777777765     666666543   3489999999999999999999999999988765


Q ss_pred             CCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          228 TGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       228 ~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      =. +...+..|-+.|-+.++.++|.+.+..
T Consensus       463 dt-e~~~l~~LakLye~l~d~~eAa~~yek  491 (559)
T KOG1155|consen  463 DT-EGSALVRLAKLYEELKDLNEAAQYYEK  491 (559)
T ss_pred             cc-chHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            33 667899999999999999999888866

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.28  E-value=5e-05  Score=74.81  Aligned_cols=207  Identities=4%  Similarity=-0.086  Sum_probs=134.5

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeee-c---cccCC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYH-A---FSSLR  101 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~-~---~~~~~  101 (311)
                      ..+..++.. ++..++...+......-  |+......+...+ .+.|++++|...|+++..  |+...+. .   +.+.|
T Consensus       481 ~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L~lA~al-~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~G  556 (987)
T PRK09782        481 NRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHRAVAYQA-YQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAG  556 (987)
T ss_pred             HHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHHHHHHHH-HHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCC
Confidence            444555554 67777766555555443  5544433334444 688999999999987643  2222221 1   67889


Q ss_pred             ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHH
Q 044412          102 HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAY  181 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~  181 (311)
                      +.++|.+.|++..+..               +.+...+..+.....+.|++++|.....+..+.-  |+...|..+-..+
T Consensus       557 d~~eA~~~l~qAL~l~---------------P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~~l  619 (987)
T PRK09782        557 NGAARDRWLQQAEQRG---------------LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--PSANAYVARATIY  619 (987)
T ss_pred             CHHHHHHHHHHHHhcC---------------CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CCHHHHHHHHHHH
Confidence            9999999998886532               2223333333344455688888443333333322  4555666665555


Q ss_pred             HHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHH
Q 044412          182 ARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGR  252 (311)
Q Consensus       182 ~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~  252 (311)
                      .+.     |...|++..  .| +...++.+-..+...|+.++|+..|++..+.  .| +...+..+-.++...|+++.|+
T Consensus       620 ~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l--~P~~~~a~~nLA~al~~lGd~~eA~  697 (987)
T PRK09782        620 RQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKG--LPDDPALIRQLAYVNQRLDDMAATQ  697 (987)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            554     667676554  34 5667888888999999999999999998874  45 4567888889999999999777


Q ss_pred             HHHHh
Q 044412          253 GIQIY  257 (311)
Q Consensus       253 ~~~~~  257 (311)
                      ..++.
T Consensus       698 ~~l~~  702 (987)
T PRK09782        698 HYARL  702 (987)
T ss_pred             HHHHH
Confidence            66654

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=98.26  E-value=1.8e-05  Score=71.76  Aligned_cols=222  Identities=13%  Similarity=0.065  Sum_probs=153.0

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCC------CCeeeeec-cccCCChhHHHHHH-HHHHHCCCCchHHHHHHHHhc
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQE------PNVFVYHA-FSSLRHPLQAIAFY-LYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~------~~~~~~~~-~~~~~~~~~a~~~~-~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      -+...+=.+| ...++.++|.++|+..++      .+...|.+ +-+..+ +-++..+ +++.+.               
T Consensus       354 wvl~q~Gray-FEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~-~v~Ls~Laq~Li~~---------------  416 (638)
T KOG1126|consen  354 WVLSQLGRAY-FELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQD-EVALSYLAQDLIDT---------------  416 (638)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHh-hHHHHHHHHHHHhh---------------
Confidence            4555666777 778888888888877753      22223333 111111 1111111 111111               


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCH-hHHHHHHHHHHHH-------HHHHHhhCCCCcHhHHHHH
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF-ATWNTMIDAYARL-------AELLFNKMPAWDIRSWTTM  203 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~-~~~~~li~~~~~~-------a~~~~~~m~~~~~~~y~~l  203 (311)
                      -+-.+.+|-++-++|+-.++.+.    |.+.|++..+.|. ++|..-+-++-..       |..-|..-...|...||++
T Consensus       417 ~~~sPesWca~GNcfSLQkdh~~----Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAw  492 (638)
T KOG1126|consen  417 DPNSPESWCALGNCFSLQKDHDT----AIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAW  492 (638)
T ss_pred             CCCCcHHHHHhcchhhhhhHHHH----HHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHH
Confidence            24457899999999999999999    9999998877655 4554444444333       6666666666677766664


Q ss_pred             ---HHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHh---------------------h
Q 044412          204 ---ITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIY---------------------C  258 (311)
Q Consensus       204 ---i~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~  258 (311)
                         -..|.+.++++.|+-.|+.-.+  +-|. .+....+-..+-+.|+.++|.++++.                     .
T Consensus       493 YGlG~vy~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~  570 (638)
T KOG1126|consen  493 YGLGTVYLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSL  570 (638)
T ss_pred             HhhhhheeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhh
Confidence               4668889999999999998776  4453 44455555666788999999999998                     8


Q ss_pred             CChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          259 RSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       259 ~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ++.++|.+.+++++  -|+ ...|-.+-..|-+.|+.+.|+.-|.-+.+
T Consensus       571 ~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  571 GRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             cchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            88999999999888  454 56788888899999999999887777654

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=98.26  E-value=0.00047  Score=59.25  Aligned_cols=248  Identities=10%  Similarity=-0.015  Sum_probs=160.4

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCC-Ceeeeec-------cccCCChhHHHHH
Q 044412           38 SSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEP-NVFVYHA-------FSSLRHPLQAIAF  109 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-------~~~~~~~~~a~~~  109 (311)
                      |+++.++.+...-.++|-.|- ..|-.-..+. .+.|+.+.+..++.+.-++ +..+...       ....|+...|..-
T Consensus        98 G~~~qAEkl~~rnae~~e~p~-l~~l~aA~AA-~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          98 GDFQQAEKLLRRNAEHGEQPV-LAYLLAAEAA-QQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             CcHHHHHHHHHHhhhcCcchH-HHHHHHHHHH-HhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            555555555555444443321 1222233444 6677888888877776543 2222111       6667777777777


Q ss_pred             HHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC-----------HhHHHHHH
Q 044412          110 YLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK-----------FATWNTMI  178 (311)
Q Consensus       110 ~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~-----------~~~~~~li  178 (311)
                      ..++.+.+               +-++.+......+|.+.|++..    ...+...+.+.+           .-+|+.++
T Consensus       176 v~~ll~~~---------------pr~~~vlrLa~r~y~~~g~~~~----ll~~l~~L~ka~~l~~~e~~~le~~a~~glL  236 (400)
T COG3071         176 VDQLLEMT---------------PRHPEVLRLALRAYIRLGAWQA----LLAILPKLRKAGLLSDEEAARLEQQAWEGLL  236 (400)
T ss_pred             HHHHHHhC---------------cCChHHHHHHHHHHHHhccHHH----HHHHHHHHHHccCCChHHHHHHHHHHHHHHH
Confidence            77776543               4567788999999999999999    555555544322           13666666


Q ss_pred             HHHHHH--HHH---HHhhCCC---CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          179 DAYARL--AEL---LFNKMPA---WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       179 ~~~~~~--a~~---~~~~m~~---~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                      .-....  +..   -+++.+.   .++..-.+++.-+...|+.++|.++..+-.+++..|...+    +-.+.+.++.+.
T Consensus       237 ~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~----~~~~l~~~d~~~  312 (400)
T COG3071         237 QQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCR----LIPRLRPGDPEP  312 (400)
T ss_pred             HHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHH----HHhhcCCCCchH
Confidence            655544  333   4444442   2455666788889999999999999999888877665222    223445555544


Q ss_pred             HHHHHHh---------------------hCChHHHHHHHhhcC--CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 044412          251 GRGIQIY---------------------CRSLGRSLLVFFKLR--EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       251 a~~~~~~---------------------~~~~~~a~~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      -.+..+.                     .+...+|...|+.-.  +|+..+|+.+-+++.+.|+..+|...+++-...-.
T Consensus       313 l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~  392 (400)
T COG3071         313 LIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALLLTR  392 (400)
T ss_pred             HHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhc
Confidence            4444443                     455556666666443  79999999999999999999999999998765555


Q ss_pred             CCC
Q 044412          308 RPN  310 (311)
Q Consensus       308 ~P~  310 (311)
                      +|+
T Consensus       393 ~~~  395 (400)
T COG3071         393 QPN  395 (400)
T ss_pred             CCC
Confidence            554

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.20  E-value=9.8e-05  Score=72.29  Aligned_cols=176  Identities=12%  Similarity=0.102  Sum_probs=145.3

Q ss_pred             CCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCC------CH-hHHHHHHHHHHHH--HHHHHhhCCC--CcHhHH
Q 044412          133 SSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPER------KF-ATWNTMIDAYARL--AELLFNKMPA--WDIRSW  200 (311)
Q Consensus       133 ~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~------~~-~~~~~li~~~~~~--a~~~~~~m~~--~~~~~y  200 (311)
                      .|| ...|-..|......++.++|+.+|++.+..+-.+      ++ .+|-.+-.+|...  ..++|++..+  .-...|
T Consensus      1454 sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~V~ 1533 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCDAYTVH 1533 (1710)
T ss_pred             CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHHHH
Confidence            454 6789999999999999999999999988887322      22 3555566677633  8888888764  235679


Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh-----------------------
Q 044412          201 TTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY-----------------------  257 (311)
Q Consensus       201 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~-----------------------  257 (311)
                      ..|..-|.+.+..++|-++|+.|.+. +.-....|...+..+.+..+-+.|+.++..                       
T Consensus      1534 ~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk 1612 (1710)
T KOG1070|consen 1534 LKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFK 1612 (1710)
T ss_pred             HHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhh
Confidence            99999999999999999999999875 335667899999999999998999888887                       


Q ss_pred             hCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 044412          258 CRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYENVRP  309 (311)
Q Consensus       258 ~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P  309 (311)
                      +|+.+++..+|+...  .| -...|+..|+.=.++|+.+.+.++|++....++.|
T Consensus      1613 ~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1613 YGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             cCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            899999999999887  22 45689999999999999999999999999988876

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=98.20  E-value=0.00016  Score=60.49  Aligned_cols=189  Identities=14%  Similarity=0.166  Sum_probs=115.8

Q ss_pred             cCChhHHHHhcccCCCCCeeeeec-------cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCch------hHH
Q 044412           73 FHFIDYTILVFPQMQEPNVFVYHA-------FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPV------FVQ  139 (311)
Q Consensus        73 ~g~~~~a~~~~~~m~~~~~~~~~~-------~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~------~~~  139 (311)
                      ..+.++|.++|-+|.+-|..|+..       |-+.|..+.|+++-+.+.++                 ||.      ...
T Consensus        48 s~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s-----------------pdlT~~qr~lAl  110 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES-----------------PDLTFEQRLLAL  110 (389)
T ss_pred             hcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC-----------------CCCchHHHHHHH
Confidence            457788888888888777777765       77778888888888776542                 332      122


Q ss_pred             HHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHH
Q 044412          140 TAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDA  219 (311)
Q Consensus       140 ~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~  219 (311)
                      .-|-.-|-..|-+|.    |+.+|....+.+.+.                       ...-.-|+.-|-...++++|+++
T Consensus       111 ~qL~~Dym~aGl~DR----AE~~f~~L~de~efa-----------------------~~AlqqLl~IYQ~treW~KAId~  163 (389)
T COG2956         111 QQLGRDYMAAGLLDR----AEDIFNQLVDEGEFA-----------------------EGALQQLLNIYQATREWEKAIDV  163 (389)
T ss_pred             HHHHHHHHHhhhhhH----HHHHHHHHhcchhhh-----------------------HHHHHHHHHHHHHhhHHHHHHHH
Confidence            334455777788888    777776655532211                       12233445555555555555555


Q ss_pred             HHHHHhcCCCCCH----HHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcCCC
Q 044412          220 FNKTKKSGTGSDQ----VTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLREK  274 (311)
Q Consensus       220 ~~~m~~~g~~p~~----~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~~p  274 (311)
                      -+++.+.|-.+..    .-|.-|-..+.-..+++.|..++..                     .|+...|.+.++...+-
T Consensus       164 A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQ  243 (389)
T COG2956         164 AERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQ  243 (389)
T ss_pred             HHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHh
Confidence            5555554433322    1233344444444555555555544                     45555666666666633


Q ss_pred             Cc----hhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          275 NL----LCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       275 ~~----~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      |+    .+-..|..+|...|+.++....+.++.+.
T Consensus       244 n~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         244 NPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             ChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            32    46788999999999999999888887654

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=98.15  E-value=4.9e-05  Score=69.03  Aligned_cols=167  Identities=17%  Similarity=0.221  Sum_probs=111.4

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCC------CCHhHHHHHHHHHHHH------HHHHHhhCCCCcHhHHHHHH
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE------RKFATWNTMIDAYARL------AELLFNKMPAWDIRSWTTMI  204 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~------~~~~~~~~li~~~~~~------a~~~~~~m~~~~~~~y~~li  204 (311)
                      .+..-+-.+|...++.++    ++++|+...+      .++..|.+.+=.+-+.      |.++.+..+. ...+|.++-
T Consensus       354 wvl~q~GrayFEl~~Y~~----a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~~-sPesWca~G  428 (638)
T KOG1126|consen  354 WVLSQLGRAYFELIEYDQ----AERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDPN-SPESWCALG  428 (638)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCCC-CcHHHHHhc
Confidence            555566778999999999    8888876644      3566777776655543      5555555542 456788888


Q ss_pred             HHHHhCCChhHHHHHHHHHHhc------------------------------CCCCCHHHHHHHH---HHHhccCChhhH
Q 044412          205 TSYSQNKQFREALDAFNKTKKS------------------------------GTGSDQVTMATVL---SACAHLGALDLG  251 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~------------------------------g~~p~~~t~~~li---~a~~~~~~~~~a  251 (311)
                      .+|.-.++.+.|++.|++-.+-                              .+.+|+..||+..   -.|.+.++++.|
T Consensus       429 NcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqek~e~A  508 (638)
T KOG1126|consen  429 NCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQEKLEFA  508 (638)
T ss_pred             chhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheeccchhhHH
Confidence            8888888888888887776542                              1344555555432   335566666666


Q ss_pred             HHHHHh---------------------hCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 044412          252 RGIQIY---------------------CRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       252 ~~~~~~---------------------~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      +..|+.                     +|+.+.|.++|++-.   ..|+..---....+...++.++|+..++++++  +
T Consensus       509 e~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~--~  586 (638)
T KOG1126|consen  509 EFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEELKE--L  586 (638)
T ss_pred             HHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHH--h
Confidence            666666                     777778888877654   33454444455666677888888888888875  4


Q ss_pred             CCC
Q 044412          308 RPN  310 (311)
Q Consensus       308 ~P~  310 (311)
                      .|+
T Consensus       587 vP~  589 (638)
T KOG1126|consen  587 VPQ  589 (638)
T ss_pred             Ccc
Confidence            554

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.06  E-value=0.00013  Score=61.14  Aligned_cols=187  Identities=12%  Similarity=0.012  Sum_probs=143.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CCHhHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKFATW  174 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~~~~  174 (311)
                      |.+-|.+.+|.+.|+.-.+.                .|-+.||-.|-..|.+......    |..++.++.+  |.-+||
T Consensus       233 ylrLgm~r~AekqlqssL~q----------------~~~~dTfllLskvY~ridQP~~----AL~~~~~gld~fP~~VT~  292 (478)
T KOG1129|consen  233 YLRLGMPRRAEKQLQSSLTQ----------------FPHPDTFLLLSKVYQRIDQPER----ALLVIGEGLDSFPFDVTY  292 (478)
T ss_pred             HHHhcChhhhHHHHHHHhhc----------------CCchhHHHHHHHHHHHhccHHH----HHHHHhhhhhcCCchhhh
Confidence            78889999999999887653                5777788889999999999999    8888887765  555554


Q ss_pred             HHHHH----HHHHH--HHHHHhhCCC---CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc
Q 044412          175 NTMID----AYARL--AELLFNKMPA---WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL  245 (311)
Q Consensus       175 ~~li~----~~~~~--a~~~~~~m~~---~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~  245 (311)
                      -+=+.    +....  +.++++...+   -|+.....+-.+|...++++-|+++++++.+.|+. ++..|+.+--+|.-.
T Consensus       293 l~g~ARi~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~ya  371 (478)
T KOG1129|consen  293 LLGQARIHEAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYA  371 (478)
T ss_pred             hhhhHHHHHHHHhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhh
Confidence            32111    11111  7777766543   36667777778888999999999999999999976 556666666667777


Q ss_pred             CChhhHHHHHHh------------------------hCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHH
Q 044412          246 GALDLGRGIQIY------------------------CRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGM  298 (311)
Q Consensus       246 ~~~~~a~~~~~~------------------------~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~  298 (311)
                      ++++.+..-|..                        .|+...|.+.|+--.  .| +...+|.|----.+.|++++|..+
T Consensus       372 qQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsl  451 (478)
T KOG1129|consen  372 QQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSL  451 (478)
T ss_pred             cchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHH
Confidence            888877777766                        788888888888665  23 357899998888999999999999


Q ss_pred             HHHHHH
Q 044412          299 FDRMTY  304 (311)
Q Consensus       299 ~~~M~~  304 (311)
                      +.....
T Consensus       452 l~~A~s  457 (478)
T KOG1129|consen  452 LNAAKS  457 (478)
T ss_pred             HHHhhh
Confidence            987664

>PRK12370 invasion protein regulator; Provisional

Probab=98.04  E-value=0.00022  Score=66.70  Aligned_cols=185  Identities=8%  Similarity=-0.108  Sum_probs=101.1

Q ss_pred             hhHHHHHHHHHHhccCcch-hHHHHHHHHHh--h------ccCChhHHHHhcccCCC--CC-eeeeec----cccCCChh
Q 044412           41 KELECVYATIVKTNANLDC-FLAKQFISFCT--S------RFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPL  104 (311)
Q Consensus        41 ~~~~~l~~~m~~~g~~p~~-~~~~~ll~~~~--~------~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~  104 (311)
                      ..+..+++..++.  .|+- ..|..+-.++.  .      ..++.++|...+++..+  |+ ...+..    +...|+++
T Consensus       278 ~~A~~~~~~Al~l--dP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~  355 (553)
T PRK12370        278 QQALKLLTQCVNM--SPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSEYI  355 (553)
T ss_pred             HHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHH
Confidence            3445666665544  4543 33433333330  1      23447888888887653  33 223322    67788999


Q ss_pred             HHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH
Q 044412          105 QAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       105 ~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~  183 (311)
                      +|+..|++..+.                .|+ ...+..+-..|...|++++|....++..+.-+... ..+..+...+..
T Consensus       356 ~A~~~~~~Al~l----------------~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~-~~~~~~~~~~~~  418 (553)
T PRK12370        356 VGSLLFKQANLL----------------SPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRA-AAGITKLWITYY  418 (553)
T ss_pred             HHHHHHHHHHHh----------------CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCh-hhHHHHHHHHHh
Confidence            999999988663                454 56777788889999999994444444333322211 111111111111


Q ss_pred             H-----HHHHHhhCC---CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHH-HHHHHHHHhccC
Q 044412          184 L-----AELLFNKMP---AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVT-MATVLSACAHLG  246 (311)
Q Consensus       184 ~-----a~~~~~~m~---~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t-~~~li~a~~~~~  246 (311)
                      .     |...+++..   .| +...+..+-..+...|+.++|...+.++...  .|+..+ .+.+...++..|
T Consensus       419 ~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g  489 (553)
T PRK12370        419 HTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYCQNS  489 (553)
T ss_pred             ccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHhccH
Confidence            1     555554432   23 3334555666667777777777777776443  444333 333444455555

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=97.99  E-value=0.00017  Score=61.38  Aligned_cols=189  Identities=7%  Similarity=-0.001  Sum_probs=107.6

Q ss_pred             CcchhHHHHHHHHHhhccCChhHHHHhccc-CCCCCe---eeeec-----cccCCChhHHHHHHHHHHHCCCCchHHHHH
Q 044412           56 NLDCFLAKQFISFCTSRFHFIDYTILVFPQ-MQEPNV---FVYHA-----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQ  126 (311)
Q Consensus        56 ~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~-m~~~~~---~~~~~-----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~  126 (311)
                      .|.......+...+ ....+-+.+..-+++ +.++..   .++..     +...|++++|++++..-             
T Consensus        63 ~~~l~av~~la~y~-~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~-------------  128 (290)
T PF04733_consen   63 SPELQAVRLLAEYL-SSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG-------------  128 (290)
T ss_dssp             SCCCHHHHHHHHHH-CTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT-------------
T ss_pred             ChhHHHHHHHHHHH-hCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc-------------
Confidence            66666666665555 443444444443332 222211   11111     66677777777766432             


Q ss_pred             HHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHh---HHHHH
Q 044412          127 VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIR---SWTTM  203 (311)
Q Consensus       127 ~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~---~y~~l  203 (311)
                             .+.......+..|.+.+++|.    |.+.++.|.+-+                        .|..   ...+.
T Consensus       129 -------~~lE~~al~Vqi~L~~~R~dl----A~k~l~~~~~~~------------------------eD~~l~qLa~aw  173 (290)
T PF04733_consen  129 -------GSLELLALAVQILLKMNRPDL----AEKELKNMQQID------------------------EDSILTQLAEAW  173 (290)
T ss_dssp             -------TCHHHHHHHHHHHHHTT-HHH----HHHHHHHHHCCS------------------------CCHHHHHHHHHH
T ss_pred             -------CcccHHHHHHHHHHHcCCHHH----HHHHHHHHHhcC------------------------CcHHHHHHHHHH
Confidence                   233444556777778888887    666666654422                        1222   23333


Q ss_pred             HHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHH
Q 044412          204 ITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSIT  283 (311)
Q Consensus       204 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li  283 (311)
                      +..+.....+++|+.+|+++.+. ..++..+.+.+.-++...|++++|+.++...-..+          ..|..+.-.+|
T Consensus       174 v~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~----------~~~~d~LaNli  242 (290)
T PF04733_consen  174 VNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD----------PNDPDTLANLI  242 (290)
T ss_dssp             HHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-----------CCHHHHHHHHH
T ss_pred             HHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc----------cCCHHHHHHHH
Confidence            44443345789999999997654 67888888888888889888887776654321111          23445666677


Q ss_pred             HHHHhcCCh-HHHHHHHHHHHH
Q 044412          284 EALAIHGFA-HEALGMFDRMTY  304 (311)
Q Consensus       284 ~~~~~~g~~-~~a~~~~~~M~~  304 (311)
                      -.....|+. +.+.+++.+++.
T Consensus       243 v~~~~~gk~~~~~~~~l~qL~~  264 (290)
T PF04733_consen  243 VCSLHLGKPTEAAERYLSQLKQ  264 (290)
T ss_dssp             HHHHHTT-TCHHHHHHHHHCHH
T ss_pred             HHHHHhCCChhHHHHHHHHHHH
Confidence            777777776 667778887775

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=97.92  E-value=0.0039  Score=57.28  Aligned_cols=97  Identities=18%  Similarity=0.106  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCch
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLL  277 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~  277 (311)
                      ++..+-..|-..|++++|++++++-.++  .|+ +..|..--..+-+.|++++|....+....++.+          |..
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~----------DRy  263 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLA----------DRY  263 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChh----------hHH
Confidence            3455677788899999999999998875  576 567888888899999999998888777777765          445


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 044412          278 CWNSITEALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       278 ~~~~li~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      .=+--...+.++|++++|.+++......+.
T Consensus       264 iNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~  293 (517)
T PF12569_consen  264 INSKCAKYLLRAGRIEEAEKTASLFTREDV  293 (517)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhhcCCCC
Confidence            556667888899999999999888766554

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.90  E-value=0.00074  Score=57.93  Aligned_cols=182  Identities=11%  Similarity=-0.037  Sum_probs=98.3

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--C-CHhH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--R-KFAT  173 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~-~~~~  173 (311)
                      +.+.|+.++|...|++..+..               +.+...|+.+-..|...|++++    |...|+...+  | +...
T Consensus        74 ~~~~g~~~~A~~~~~~Al~l~---------------P~~~~a~~~lg~~~~~~g~~~~----A~~~~~~Al~l~P~~~~a  134 (296)
T PRK11189         74 YDSLGLRALARNDFSQALALR---------------PDMADAYNYLGIYLTQAGNFDA----AYEAFDSVLELDPTYNYA  134 (296)
T ss_pred             HHHCCCHHHHHHHHHHHHHcC---------------CCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHhCCCCHHH
Confidence            567788888888888876531               3347888999999999999999    6655555432  2 2334


Q ss_pred             HHHHHHHHHHH-----HHHHHhhCC--CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccC
Q 044412          174 WNTMIDAYARL-----AELLFNKMP--AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLG  246 (311)
Q Consensus       174 ~~~li~~~~~~-----a~~~~~~m~--~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~  246 (311)
                      |..+-..+...     |.+.|+...  .|+..............+++++|...|.+.... ..|+...+ .+..  ...|
T Consensus       135 ~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~-~~~~~~~~-~~~~--~~lg  210 (296)
T PRK11189        135 YLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQAKENLKQRYEK-LDKEQWGW-NIVE--FYLG  210 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhh-CCccccHH-HHHH--HHcc
Confidence            44443333322     544444432  232221111111223346677777777654432 22332221 2222  1233


Q ss_pred             ChhhHHHHHHh-hCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 044412          247 ALDLGRGIQIY-CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       247 ~~~~a~~~~~~-~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g  306 (311)
                      +...+. .+.. ....+.+.++    .......|..+-..+...|++++|...|++..+.+
T Consensus       211 ~~~~~~-~~~~~~~~~~~~~~l----~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~  266 (296)
T PRK11189        211 KISEET-LMERLKAGATDNTEL----AERLCETYFYLAKYYLSLGDLDEAAALFKLALANN  266 (296)
T ss_pred             CCCHHH-HHHHHHhcCCCcHHH----HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            333221 1111 0000000000    01234579999999999999999999999987644

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.88  E-value=0.0021  Score=56.43  Aligned_cols=175  Identities=13%  Similarity=0.065  Sum_probs=108.9

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCC---CCCHhH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP---ERKFAT  173 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~---~~~~~~  173 (311)
                      ..-+|++++|.+.|++-.....              .-....||.= -.+-+.|++++    |..+|-...   ..+...
T Consensus       500 ~f~ngd~dka~~~ykeal~nda--------------sc~ealfnig-lt~e~~~~lde----ald~f~klh~il~nn~ev  560 (840)
T KOG2003|consen  500 AFANGDLDKAAEFYKEALNNDA--------------SCTEALFNIG-LTAEALGNLDE----ALDCFLKLHAILLNNAEV  560 (840)
T ss_pred             eeecCcHHHHHHHHHHHHcCch--------------HHHHHHHHhc-ccHHHhcCHHH----HHHHHHHHHHHHHhhHHH
Confidence            4567899999999998754321              1112223321 24677889999    666554322   122222


Q ss_pred             HHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc
Q 044412          174 WNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL  245 (311)
Q Consensus       174 ~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~  245 (311)
                      ..-+-+-|-..     |.+++-+..   ..|....+-|-+.|-+.|+-..|+..+-+--+ -++-+..|...|-..|...
T Consensus       561 l~qianiye~led~aqaie~~~q~~slip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ayyidt  639 (840)
T KOG2003|consen  561 LVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAYYIDT  639 (840)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHHHHhh
Confidence            22222222221     444444332   23566677777778888888888776555322 2455677777777777776


Q ss_pred             CChhhHHHHHHhhCChHHHHHHHhhcC--CCCchhHHHHHHHHH-hcCChHHHHHHHHHHHH
Q 044412          246 GALDLGRGIQIYCRSLGRSLLVFFKLR--EKNLLCWNSITEALA-IHGFAHEALGMFDRMTY  304 (311)
Q Consensus       246 ~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~~~~~~~li~~~~-~~g~~~~a~~~~~~M~~  304 (311)
                      .-++             .+...|++-.  .|+..-|..||.+|. +.|++.+|+++|++.-.
T Consensus       640 qf~e-------------kai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hr  688 (840)
T KOG2003|consen  640 QFSE-------------KAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHR  688 (840)
T ss_pred             HHHH-------------HHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            6666             4555665544  899999999998887 67999999999998754

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=97.86  E-value=0.00027  Score=60.16  Aligned_cols=143  Identities=12%  Similarity=0.129  Sum_probs=93.8

Q ss_pred             HHHhhccCChhHHHHhcccCCCCCeeeeec--cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchh---HHHH
Q 044412           67 SFCTSRFHFIDYTILVFPQMQEPNVFVYHA--FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVF---VQTA  141 (311)
Q Consensus        67 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~---~~~~  141 (311)
                      ..+ ...|++++|+++++.-.........+  +.+.++++.|.+.++.|.+                +..|..   ...+
T Consensus       110 ~i~-~~~~~~~~AL~~l~~~~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~----------------~~eD~~l~qLa~a  172 (290)
T PF04733_consen  110 TIL-FHEGDYEEALKLLHKGGSLELLALAVQILLKMNRPDLAEKELKNMQQ----------------IDEDSILTQLAEA  172 (290)
T ss_dssp             HHH-CCCCHHHHHHCCCTTTTCHHHHHHHHHHHHHTT-HHHHHHHHHHHHC----------------CSCCHHHHHHHHH
T ss_pred             HHH-HHcCCHHHHHHHHHccCcccHHHHHHHHHHHcCCHHHHHHHHHHHHh----------------cCCcHHHHHHHHH
Confidence            445 77899999999998763322222222  8899999999999999975                334433   2333


Q ss_pred             HHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHH
Q 044412          142 MVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFN  221 (311)
Q Consensus       142 ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~  221 (311)
                      .++.+.-...+.+    |..+|+++.+..                       .+++.+.|.+..+....|++++|.+++.
T Consensus       173 wv~l~~g~e~~~~----A~y~f~El~~~~-----------------------~~t~~~lng~A~~~l~~~~~~eAe~~L~  225 (290)
T PF04733_consen  173 WVNLATGGEKYQD----AFYIFEELSDKF-----------------------GSTPKLLNGLAVCHLQLGHYEEAEELLE  225 (290)
T ss_dssp             HHHHHHTTTCCCH----HHHHHHHHHCCS-------------------------SHHHHHHHHHHHHHCT-HHHHHHHHH
T ss_pred             HHHHHhCchhHHH----HHHHHHHHHhcc-----------------------CCCHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            3433333446888    777777654321                       2467788889999999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHhccCCh-hhHHHH
Q 044412          222 KTKKSGTGSDQVTMATVLSACAHLGAL-DLGRGI  254 (311)
Q Consensus       222 ~m~~~g~~p~~~t~~~li~a~~~~~~~-~~a~~~  254 (311)
                      +-.... +-|..|...++-+....|+. +.+.+.
T Consensus       226 ~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~  258 (290)
T PF04733_consen  226 EALEKD-PNDPDTLANLIVCSLHLGKPTEAAERY  258 (290)
T ss_dssp             HHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHH
T ss_pred             HHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHH
Confidence            976543 33566777777777777766 433333

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=97.83  E-value=0.0035  Score=54.04  Aligned_cols=215  Identities=12%  Similarity=0.031  Sum_probs=137.8

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC---CCeeeeec----cccCCChhHHHHHH
Q 044412           38 SSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE---PNVFVYHA----FSSLRHPLQAIAFY  110 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~----~~~~~~~~~a~~~~  110 (311)
                      |+...+........+.--.++....-+..... ...|+.+.|..-+++..+   .+......    |.+.|++.+...++
T Consensus       132 gd~~~an~yL~eaae~~~~~~l~v~ltrarll-l~~~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l  210 (400)
T COG3071         132 GDEDRANRYLAEAAELAGDDTLAVELTRARLL-LNRRDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAIL  210 (400)
T ss_pred             ccHHHHHHHHHHHhccCCCchHHHHHHHHHHH-HhCCCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHH
Confidence            34444445555554443334445555555666 777888888777766543   22222333    88888889999999


Q ss_pred             HHHHHCCCCch------------HHHHHHHHh---------------cCCCchhHHHHHHHHHHhCCCCccchHHHHHHh
Q 044412          111 LYMLRAEVLLT------------TVHGQVWKN---------------GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLF  163 (311)
Q Consensus       111 ~~m~~~~~~p~------------~~~~~~~~~---------------g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~  163 (311)
                      ..|.+.|+--+            .+.++....               ..+-++..-.+++.-+.++|+.++|.++.++.+
T Consensus       211 ~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~L  290 (400)
T COG3071         211 PKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDAL  290 (400)
T ss_pred             HHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            88888887544            111111111               124456667788889999999999766666666


Q ss_pred             ccCCCCCHhHHHHHHHHHH-----HHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          164 DEMPERKFATWNTMIDAYA-----RLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       164 ~~~~~~~~~~~~~li~~~~-----~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                      +..-++....+-.-+..-.     +.++.-....++ +.-.+.+|=..|.+.+.+.+|...|+.-.+  ..|+..+|+-+
T Consensus       291 k~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~-~p~L~~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~l  367 (400)
T COG3071         291 KRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPE-DPLLLSTLGRLALKNKLWGKASEALEAALK--LRPSASDYAEL  367 (400)
T ss_pred             HhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHH
Confidence            6655554221111000000     003333333332 346677888889999999999999996554  68999999999


Q ss_pred             HHHHhccCChhhHHHHHH
Q 044412          239 LSACAHLGALDLGRGIQI  256 (311)
Q Consensus       239 i~a~~~~~~~~~a~~~~~  256 (311)
                      -.++...|+.++|.++.+
T Consensus       368 a~~~~~~g~~~~A~~~r~  385 (400)
T COG3071         368 ADALDQLGEPEEAEQVRR  385 (400)
T ss_pred             HHHHHHcCChHHHHHHHH
Confidence            999999999998887764

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=97.79  E-value=0.0099  Score=56.38  Aligned_cols=228  Identities=10%  Similarity=0.095  Sum_probs=138.7

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~~   99 (311)
                      +.++..++...|+.......+ .+..+--+-|...|-.+-+.. .+.|+++.|.-.|.+..+-+..-|..       |-+
T Consensus       176 y~tL~~IyEqrGd~eK~l~~~-llAAHL~p~d~e~W~~ladls-~~~~~i~qA~~cy~rAI~~~p~n~~~~~ers~L~~~  253 (895)
T KOG2076|consen  176 YYTLGEIYEQRGDIEKALNFW-LLAAHLNPKDYELWKRLADLS-EQLGNINQARYCYSRAIQANPSNWELIYERSSLYQK  253 (895)
T ss_pred             HHHHHHHHHHcccHHHHHHHH-HHHHhcCCCChHHHHHHHHHH-HhcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHH
Confidence            567777777777655554433 223334445667777777777 77888888888887765433222333       777


Q ss_pred             CCChhHHHHHHHHHHHCCCCch---------------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCC
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLT---------------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKF  152 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~---------------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~  152 (311)
                      .|+...|++-|.++.+..- |.                           .+.+.+...+-..+...++.+...|.+...+
T Consensus       254 ~G~~~~Am~~f~~l~~~~p-~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~  332 (895)
T KOG2076|consen  254 TGDLKRAMETFLQLLQLDP-PVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQS  332 (895)
T ss_pred             hChHHHHHHHHHHHHhhCC-chhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHH
Confidence            8999999999999876532 22                           1112222223344556677777777777777


Q ss_pred             ccchHHHHHHhccCCCC----------------------CHhHHHHHH-HH---HHHH-----HHHHHhhCC------CC
Q 044412          153 FESRRVSRRLFDEMPER----------------------KFATWNTMI-DA---YARL-----AELLFNKMP------AW  195 (311)
Q Consensus       153 ~~a~~~a~~~~~~~~~~----------------------~~~~~~~li-~~---~~~~-----a~~~~~~m~------~~  195 (311)
                      +.|.......-+.-.++                      +..+|..=+ +-   +.+.     ..-+.....      +.
T Consensus       333 d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d  412 (895)
T KOG2076|consen  333 DKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVEDNVWVSD  412 (895)
T ss_pred             HHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHhcCChhh
Confidence            77554433333311111                      111222211 11   1111     222222221      23


Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      ++..|.-+.++|...|++.+|+++|..+...-.--+...|-.+-.+|-..|..++|...++.
T Consensus       413 ~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~k  474 (895)
T KOG2076|consen  413 DVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEK  474 (895)
T ss_pred             hHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHH
Confidence            56678899999999999999999999998764444567888888888888888877766655

>PRK12370 invasion protein regulator; Provisional

Probab=97.72  E-value=0.002  Score=60.31  Aligned_cols=211  Identities=9%  Similarity=-0.023  Sum_probs=117.5

Q ss_pred             chhHHHHHHHHHhhc-----cCChhHHHHhcccCCC--CCeee-eec-------------cccCCChhHHHHHHHHHHHC
Q 044412           58 DCFLAKQFISFCTSR-----FHFIDYTILVFPQMQE--PNVFV-YHA-------------FSSLRHPLQAIAFYLYMLRA  116 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~-----~g~~~~a~~~~~~m~~--~~~~~-~~~-------------~~~~~~~~~a~~~~~~m~~~  116 (311)
                      +...|...+.+- ..     .++.+.|..+|++..+  |+... |..             +...++.++|...+++..+.
T Consensus       255 ~~da~~~~lrg~-~~~~~~~~~~~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l  333 (553)
T PRK12370        255 SIDSTMVYLRGK-HELNQYTPYSLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL  333 (553)
T ss_pred             ChHHHHHHHHhH-HHHHccCHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc
Confidence            445555555553 21     2346788888888754  43321 111             11345678999999887663


Q ss_pred             CCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CC-HhHHHHHHHHHHHH-----HHHH
Q 044412          117 EVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RK-FATWNTMIDAYARL-----AELL  188 (311)
Q Consensus       117 ~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~-----a~~~  188 (311)
                      .               +-+...+..+-..+...|++++    |...+++..+  |+ ...|..+-..+...     |...
T Consensus       334 d---------------P~~~~a~~~lg~~~~~~g~~~~----A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~  394 (553)
T PRK12370        334 D---------------HNNPQALGLLGLINTIHSEYIV----GSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQT  394 (553)
T ss_pred             C---------------CCCHHHHHHHHHHHHHccCHHH----HHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            2               3356777777778899999999    6666655432  32 23444444444433     6666


Q ss_pred             HhhCC--CCcH-hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhCChHHH
Q 044412          189 FNKMP--AWDI-RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIYCRSLGRS  264 (311)
Q Consensus       189 ~~~m~--~~~~-~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a  264 (311)
                      +++..  .|+. ..+..+...+...|++++|+..+++..+.. .|+ ...+..+-.++...|+.+             +|
T Consensus       395 ~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~-------------eA  460 (553)
T PRK12370        395 INECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHE-------------LA  460 (553)
T ss_pred             HHHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHH-------------HH
Confidence            65543  2332 223333444555677777877777766542 343 333455555566666666             44


Q ss_pred             HHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          265 LLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       265 ~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ...+.++.  .|+ ....+.+-..|+..|  ++|...++++.+
T Consensus       461 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~  501 (553)
T PRK12370        461 RKLTKEISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLE  501 (553)
T ss_pred             HHHHHHhhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHH
Confidence            44444433  233 233445555566666  366666666543

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=97.70  E-value=0.025  Score=54.31  Aligned_cols=178  Identities=13%  Similarity=0.082  Sum_probs=101.1

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCc--chhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec------cc
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANL--DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA------FS   98 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p--~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~------~~   98 (311)
                      .+..-+-..++.+.+..+...+...-..-  -...|-.+-++| ...|+++.|...|.+-.+  ++.+.+..      +.
T Consensus       275 ~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~-Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~GlgQm~i  353 (1018)
T KOG2002|consen  275 HLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSY-HAQGDFEKAFKYYMESLKADNDNFVLPLVGLGQMYI  353 (1018)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHH-HhhccHHHHHHHHHHHHccCCCCccccccchhHHHH
Confidence            44555556677777777777776654211  123466778888 999999999999977653  44444444      89


Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC---Hh--
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK---FA--  172 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~---~~--  172 (311)
                      +.|+.+.+...|+.....                .|| ..+...|-..|...+.-......|..+.....++.   .-  
T Consensus       354 ~~~dle~s~~~fEkv~k~----------------~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~  417 (1018)
T KOG2002|consen  354 KRGDLEESKFCFEKVLKQ----------------LPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAW  417 (1018)
T ss_pred             HhchHHHHHHHHHHHHHh----------------CcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHH
Confidence            999999999999988764                344 44444443445544422122222555554444322   11  


Q ss_pred             -----------HHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHH
Q 044412          173 -----------TWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTK  224 (311)
Q Consensus       173 -----------~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~  224 (311)
                                 +|.+ +.+|.++...+...+.......-|.+-......|.+++|...|..-.
T Consensus       418 l~laql~e~~d~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~  479 (1018)
T KOG2002|consen  418 LELAQLLEQTDPWAS-LDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSAL  479 (1018)
T ss_pred             HHHHHHHHhcChHHH-HHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHh
Confidence                       3333 44444432233333333444555555555555566666666555544

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.70  E-value=0.0017  Score=59.15  Aligned_cols=196  Identities=13%  Similarity=0.140  Sum_probs=133.1

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHh-----c-cCcc-hhHHHHHHHHHhhccCChhHHHHhcccCCC----------CCe
Q 044412           29 IIANQLKKCSSIKELECVYATIVKT-----N-ANLD-CFLAKQFISFCTSRFHFIDYTILVFPQMQE----------PNV   91 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~-----g-~~p~-~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~----------~~~   91 (311)
                      .+..++...+++.++..+|..+.+-     | -.|. ..+++.|-.+| .+.|++++|...++...+          +.+
T Consensus       246 ~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly-~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v  324 (508)
T KOG1840|consen  246 ILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLY-YKQGKFAEAEEYCERALEIYEKLLGASHPEV  324 (508)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH-hccCChHHHHHHHHHHHHHHHHhhccChHHH
Confidence            4777788889999998888877743     2 1222 25667777789 999999998888766532          222


Q ss_pred             eeeec-----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcC-C-CchhHHHHHHHHHHhCCCCccchHHHHHHhc
Q 044412           92 FVYHA-----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGF-S-SPVFVQTAMVDNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus        92 ~~~~~-----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~-~-~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~  164 (311)
                      .+...     +...+.+++|..+++.-.+.       +.  ...|. . --..+++.|-..|-+.|++++    |+++++
T Consensus       325 ~~~l~~~~~~~~~~~~~Eea~~l~q~al~i-------~~--~~~g~~~~~~a~~~~nl~~l~~~~gk~~e----a~~~~k  391 (508)
T KOG1840|consen  325 AAQLSELAAILQSMNEYEEAKKLLQKALKI-------YL--DAPGEDNVNLAKIYANLAELYLKMGKYKE----AEELYK  391 (508)
T ss_pred             HHHHHHHHHHHHHhcchhHHHHHHHHHHHH-------HH--hhccccchHHHHHHHHHHHHHHHhcchhH----HHHHHH
Confidence            22111     88889999999999865431       11  11111 1 124689999999999999999    555554


Q ss_pred             cCCCCCHhHHHHHHHHHHHHHHHHHhhCCC---C-cHhHHHHHHHHHHhCCChhHHHHHHHH----HHhcCC-CCC-HHH
Q 044412          165 EMPERKFATWNTMIDAYARLAELLFNKMPA---W-DIRSWTTMITSYSQNKQFREALDAFNK----TKKSGT-GSD-QVT  234 (311)
Q Consensus       165 ~~~~~~~~~~~~li~~~~~~a~~~~~~m~~---~-~~~~y~~li~~~~~~g~~~~a~~~~~~----m~~~g~-~p~-~~t  234 (311)
                      .                   |..+..+...   + .-..+|-|-..|-+.++.++|..+|.+    |+..|. .|| ..+
T Consensus       392 ~-------------------ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~  452 (508)
T KOG1840|consen  392 K-------------------AIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYT  452 (508)
T ss_pred             H-------------------HHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHH
Confidence            4                   2222222221   1 234677888889889999999999988    433342 333 367


Q ss_pred             HHHHHHHHhccCChhhHHHHHHh
Q 044412          235 MATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       235 ~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |..|...|.+.|+++.|.++.+.
T Consensus       453 ~~nL~~~Y~~~g~~e~a~~~~~~  475 (508)
T KOG1840|consen  453 YLNLAALYRAQGNYEAAEELEEK  475 (508)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHH
Confidence            99999999999999999888654

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.67  E-value=0.022  Score=52.39  Aligned_cols=268  Identities=13%  Similarity=0.193  Sum_probs=160.3

Q ss_pred             HHHHhhccChhhHHHHHHHHH-HhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccCCChhH
Q 044412           31 ANQLKKCSSIKELECVYATIV-KTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQ  105 (311)
Q Consensus        31 ~~~l~~~~~~~~~~~l~~~m~-~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~  105 (311)
                      ..++...+++...+..|+... +.-++....+|...+... ...|-.+.+..++....+-+...-+.    +++.+++++
T Consensus       109 lq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv-~~~~lPets~rvyrRYLk~~P~~~eeyie~L~~~d~~~e  187 (835)
T KOG2047|consen  109 LQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFV-ESHGLPETSIRVYRRYLKVAPEAREEYIEYLAKSDRLDE  187 (835)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHH-HhCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhccchHH
Confidence            334444445555555554333 345566667777777777 77777777777776654322222111    677777777


Q ss_pred             HHHHHHHHHHCCCCch-------HHHH-------------------HHHHhcC--CCc--hhHHHHHHHHHHhCCCCccc
Q 044412          106 AIAFYLYMLRAEVLLT-------TVHG-------------------QVWKNGF--SSP--VFVQTAMVDNYSYSNKFFES  155 (311)
Q Consensus       106 a~~~~~~m~~~~~~p~-------~~~~-------------------~~~~~g~--~~~--~~~~~~ll~~~~~~g~~~~a  155 (311)
                      |-+.+........-.+       +++.                   .+.+.|+  -+|  ...|++|-+-|.+.|++++ 
T Consensus       188 aa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ek-  266 (835)
T KOG2047|consen  188 AAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEK-  266 (835)
T ss_pred             HHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHH-
Confidence            7777777654322111       1111                   1222232  233  3579999999999999999 


Q ss_pred             hHHHHHHhccCCC--CCHhHHHHHHHHHHHH---------------------------HHHHHhhCC-------------
Q 044412          156 RRVSRRLFDEMPE--RKFATWNTMIDAYARL---------------------------AELLFNKMP-------------  193 (311)
Q Consensus       156 ~~~a~~~~~~~~~--~~~~~~~~li~~~~~~---------------------------a~~~~~~m~-------------  193 (311)
                         |+.++++...  ..+.-|+.+.++|+.-                           ...-|+.+.             
T Consensus       267 ---arDvyeeai~~v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLR  343 (835)
T KOG2047|consen  267 ---ARDVYEEAIQTVMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLLR  343 (835)
T ss_pred             ---HHHHHHHHHHhheehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHHh
Confidence               7777776544  3444567777777663                           011111110             


Q ss_pred             --CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC------HHHHHHHHHHHhccCChhhHHHHHHh--------
Q 044412          194 --AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD------QVTMATVLSACAHLGALDLGRGIQIY--------  257 (311)
Q Consensus       194 --~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~------~~t~~~li~a~~~~~~~~~a~~~~~~--------  257 (311)
                        ..++..|..-+.  +..|+..+-+..|.+..+. +.|-      ...|..+-+-|-..|+++.|+.+|+.        
T Consensus       344 Qn~~nV~eW~kRV~--l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~  420 (835)
T KOG2047|consen  344 QNPHNVEEWHKRVK--LYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKT  420 (835)
T ss_pred             cCCccHHHHHhhhh--hhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccc
Confidence              013445544433  3356778888888887653 3332      34577778888889999999999988        


Q ss_pred             -----------------hCChHHHHHHHhhcC---C------------------CCchhHHHHHHHHHhcCChHHHHHHH
Q 044412          258 -----------------CRSLGRSLLVFFKLR---E------------------KNLLCWNSITEALAIHGFAHEALGMF  299 (311)
Q Consensus       258 -----------------~~~~~~a~~~~~~~~---~------------------p~~~~~~~li~~~~~~g~~~~a~~~~  299 (311)
                                       ..+.+.|.++.++-.   +                  .....|...++---..|-++....+|
T Consensus       421 v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vY  500 (835)
T KOG2047|consen  421 VEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVY  500 (835)
T ss_pred             hHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHH
Confidence                             333444444444322   1                  13356777777777788888888888


Q ss_pred             HHHHHcC
Q 044412          300 DRMTYEN  306 (311)
Q Consensus       300 ~~M~~~g  306 (311)
                      +++.+-.
T Consensus       501 driidLr  507 (835)
T KOG2047|consen  501 DRIIDLR  507 (835)
T ss_pred             HHHHHHh
Confidence            8887643

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=97.64  E-value=0.03  Score=53.26  Aligned_cols=122  Identities=13%  Similarity=0.073  Sum_probs=85.3

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhc---ccCCCCCeeeeec----cccCC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVF---PQMQEPNVFVYHA----FSSLR  101 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~---~~m~~~~~~~~~~----~~~~~  101 (311)
                      .....+-+.|+..+++.++...++..- -....|..|-..| -..|+.+++...+   .++...|..-|..    ....|
T Consensus       144 ~eAN~lfarg~~eeA~~i~~EvIkqdp-~~~~ay~tL~~Iy-EqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~  221 (895)
T KOG2076|consen  144 GEANNLFARGDLEEAEEILMEVIKQDP-RNPIAYYTLGEIY-EQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLG  221 (895)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhCc-cchhhHHHHHHHH-HHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcc
Confidence            344555667999999999999998753 4677899999999 9999999998876   3344445444444    56678


Q ss_pred             ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCC
Q 044412          102 HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP  167 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~  167 (311)
                      .+.+|.-.|.+..+..               +++...+---...|-+.|+...|.+.-.+++..++
T Consensus       222 ~i~qA~~cy~rAI~~~---------------p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p  272 (895)
T KOG2076|consen  222 NINQARYCYSRAIQAN---------------PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDP  272 (895)
T ss_pred             cHHHHHHHHHHHHhcC---------------CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC
Confidence            8999999998876652               34444444455667777777775555555555555

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.61  E-value=0.0013  Score=46.63  Aligned_cols=86  Identities=16%  Similarity=0.093  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCC-CCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC----C
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGT-GSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR----E  273 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~----~  273 (311)
                      |-...|..+...+++.....+|+.+++.|+ -|+..+|+.++.+.++...-..+.     -.++-....++.+|.    +
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~i-----e~kl~~LLtvYqDiL~~~lK  101 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDI-----ENKLTNLLTVYQDILSNKLK  101 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhH-----HHHHHHHHHHHHHHHHhccC
Confidence            445667777777999999999999999999 999999999999998755322111     112335677777776    8


Q ss_pred             CCchhHHHHHHHHHhc
Q 044412          274 KNLLCWNSITEALAIH  289 (311)
Q Consensus       274 p~~~~~~~li~~~~~~  289 (311)
                      |+..|||+++.++.+.
T Consensus       102 P~~etYnivl~~Llkg  117 (120)
T PF08579_consen  102 PNDETYNIVLGSLLKG  117 (120)
T ss_pred             CcHHHHHHHHHHHHHh
Confidence            9999999999988753

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.60  E-value=0.00023  Score=56.51  Aligned_cols=90  Identities=13%  Similarity=0.149  Sum_probs=62.0

Q ss_pred             CCchhHHHHHHHHHHhC-----CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHH
Q 044412          133 SSPVFVQTAMVDNYSYS-----NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSY  207 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~-----g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~  207 (311)
                      ..+..+|..+|+.|.+.     |.++-    ....+..|.+-++                      +.|..+|+.||+.+
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeF----I~aAL~~M~efgv----------------------~kDL~~Y~~LLDvF   97 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEF----IYAALKKMDEFGV----------------------EKDLEVYKALLDVF   97 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHH----HHHHHHHHHHcCC----------------------cccHHHHHHHHHhC
Confidence            56788888888888766     33444    4445555544222                      23444444444444


Q ss_pred             HhC----------------CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          208 SQN----------------KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       208 ~~~----------------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      =+.                .+-+-|++++++|...|+-||..|+..|++.+++.+..
T Consensus        98 PKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen   98 PKGKFVPRNFFQAEFMHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             CCCCcccccHHHHHhccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence            331                23578999999999999999999999999999997754

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=97.54  E-value=0.073  Score=49.28  Aligned_cols=167  Identities=15%  Similarity=0.107  Sum_probs=112.6

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC--CCcHhHHHHHHHHH
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP--AWDIRSWTTMITSY  207 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~--~~~~~~y~~li~~~  207 (311)
                      ....|--...-+...|++..|+.+....|+.-+- +...|-.-++--...     |+.+|.+-.  .|+...|.--+.--
T Consensus       583 ae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~e  661 (913)
T KOG0495|consen  583 AEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLE  661 (913)
T ss_pred             chhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHH
Confidence            3445555555677778888855555555544332 223444444433333     777776554  46666666555555


Q ss_pred             HhCCChhHHHHHHHHHHhcCCCCCHH-HHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHH
Q 044412          208 SQNKQFREALDAFNKTKKSGTGSDQV-TMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSL  265 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~  265 (311)
                      -..+..++|++++++-.+.  -|+.. .|..+=+.+-..++++.|+..+..                     .|.+-.|.
T Consensus       662 r~ld~~eeA~rllEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR  739 (913)
T KOG0495|consen  662 RYLDNVEEALRLLEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRAR  739 (913)
T ss_pred             HHhhhHHHHHHHHHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHH
Confidence            5568889999998887763  45544 455555667778888888887776                     66777888


Q ss_pred             HHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          266 LVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       266 ~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+|++-.   ..|...|-..|+.=.+.|+.+.|..+..+..+
T Consensus       740 ~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQ  781 (913)
T KOG0495|consen  740 SILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQ  781 (913)
T ss_pred             HHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            8888766   34678899999999999999999887766543

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.44  E-value=0.052  Score=47.46  Aligned_cols=86  Identities=12%  Similarity=-0.068  Sum_probs=58.0

Q ss_pred             HHHHHHHhhccChhhH--HHHHHHHH-HhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------c
Q 044412           28 HIIANQLKKCSSIKEL--ECVYATIV-KTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------F   97 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~--~~l~~~m~-~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~   97 (311)
                      ..++.++..|...++.  -+.+-.+. ..-++-|......+-+.+ ...|+.+.|...|++...-|..+...       +
T Consensus       198 s~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~-~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL  276 (564)
T KOG1174|consen  198 SKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCL-YYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLL  276 (564)
T ss_pred             HHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhh-hhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHH
Confidence            4555555555444444  33333333 344667788889999999 99999999999999876555444333       6


Q ss_pred             ccCCChhHHHHHHHHHH
Q 044412           98 SSLRHPLQAIAFYLYML  114 (311)
Q Consensus        98 ~~~~~~~~a~~~~~~m~  114 (311)
                      .+.|+.++...+-..+.
T Consensus       277 ~~eg~~e~~~~L~~~Lf  293 (564)
T KOG1174|consen  277 GQEGGCEQDSALMDYLF  293 (564)
T ss_pred             HhccCHhhHHHHHHHHH
Confidence            77788777777766664

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.43  E-value=0.0034  Score=47.60  Aligned_cols=97  Identities=9%  Similarity=-0.109  Sum_probs=74.2

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCc
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNL  276 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~  276 (311)
                      ...+...-..+...|++++|...|....... +.+...|..+-.++...|++++|...|+..-..+          ..+.
T Consensus        24 p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~----------p~~~   92 (144)
T PRK15359         24 PETVYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD----------ASHP   92 (144)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC----------CCCc
Confidence            3345556777888999999999999987642 3467788888889999999996666553322111          2467


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..+..+-.++...|+.++|...|++..+
T Consensus        93 ~a~~~lg~~l~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359         93 EPVYQTGVCLKMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            8889999999999999999999998775

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.36  E-value=0.0035  Score=55.02  Aligned_cols=207  Identities=14%  Similarity=0.187  Sum_probs=131.2

Q ss_pred             HhhccChhhHHHHHHHHHHhccCcchhHHHHHHH---HHhhccCChhHHHHhcccCCCCCeee----eec---cccCCCh
Q 044412           34 LKKCSSIKELECVYATIVKTNANLDCFLAKQFIS---FCTSRFHFIDYTILVFPQMQEPNVFV----YHA---FSSLRHP  103 (311)
Q Consensus        34 l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~---~~~~~~g~~~~a~~~~~~m~~~~~~~----~~~---~~~~~~~  103 (311)
                      ++...++.++.+.-+..+..    |.+--.++..   .. .-.|++++|.+.+.+....|..+    ||+   +-..|++
T Consensus       466 lqggk~~~~aqqyad~aln~----dryn~~a~~nkgn~~-f~ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~l  540 (840)
T KOG2003|consen  466 LQGGKDFADAQQYADIALNI----DRYNAAALTNKGNIA-FANGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNL  540 (840)
T ss_pred             HhcccchhHHHHHHHHHhcc----cccCHHHhhcCCcee-eecCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCH
Confidence            34444566665555544432    3333333332   22 45688888888888877666544    344   6667888


Q ss_pred             hHHHHHHHHHHHCCCCch-------------------HHHHHHHH-hcC-CCchhHHHHHHHHHHhCCCCccchHHHHHH
Q 044412          104 LQAIAFYLYMLRAEVLLT-------------------TVHGQVWK-NGF-SSPVFVQTAMVDNYSYSNKFFESRRVSRRL  162 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~-------------------~~~~~~~~-~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~  162 (311)
                      ++|++.|-.+.  ++..+                   +..+++.+ ..+ +-|+.+..-|-+.|-+.|+-..|.+..-.-
T Consensus       541 deald~f~klh--~il~nn~evl~qianiye~led~aqaie~~~q~~slip~dp~ilskl~dlydqegdksqafq~~yds  618 (840)
T KOG2003|consen  541 DEALDCFLKLH--AILLNNAEVLVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDS  618 (840)
T ss_pred             HHHHHHHHHHH--HHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhc
Confidence            88888776543  22222                   33333322 234 446889999999999999999944443333


Q ss_pred             hccCCCCCHhHHHHHHHHHHHH-----HHHHHhh--CCCCcHhHHHHHHHHHHh-CCChhHHHHHHHHHHhcCCCCCHHH
Q 044412          163 FDEMPERKFATWNTMIDAYARL-----AELLFNK--MPAWDIRSWTTMITSYSQ-NKQFREALDAFNKTKKSGTGSDQVT  234 (311)
Q Consensus       163 ~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~--m~~~~~~~y~~li~~~~~-~g~~~~a~~~~~~m~~~g~~p~~~t  234 (311)
                      +...+. ++.+..=|-..|...     +...|++  +.+|+..-|..||..|.+ .|++++|+++|++..+. ++-|...
T Consensus       619 yryfp~-nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldc  696 (840)
T KOG2003|consen  619 YRYFPC-NIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDC  696 (840)
T ss_pred             ccccCc-chHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHH
Confidence            333322 333322233333332     7777764  458999999999976655 69999999999998765 7888999


Q ss_pred             HHHHHHHHhccCChh
Q 044412          235 MATVLSACAHLGALD  249 (311)
Q Consensus       235 ~~~li~a~~~~~~~~  249 (311)
                      ...|+..|...|..+
T Consensus       697 lkflvri~~dlgl~d  711 (840)
T KOG2003|consen  697 LKFLVRIAGDLGLKD  711 (840)
T ss_pred             HHHHHHHhccccchh
Confidence            999999998887543

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.35  E-value=0.0093  Score=55.59  Aligned_cols=64  Identities=11%  Similarity=0.189  Sum_probs=37.9

Q ss_pred             HHHHHhhCCCCcHhH--HHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          185 AELLFNKMPAWDIRS--WTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       185 a~~~~~~m~~~~~~~--y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |..+++.+++.++.+  |.-+-+.|+..|+++.|.++|.+--         .++-.|..|.+.|.++.|.++-.+
T Consensus       751 ai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw~da~kla~e  816 (1636)
T KOG3616|consen  751 AISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKWEDAFKLAEE  816 (1636)
T ss_pred             hHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccHHHHHHHHHH
Confidence            677788777655443  5555566777777777777665421         234445555566666555555444

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.34  E-value=0.0014  Score=46.46  Aligned_cols=79  Identities=8%  Similarity=0.171  Sum_probs=57.1

Q ss_pred             HHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCC--------C
Q 044412          141 AMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNK--------Q  212 (311)
Q Consensus       141 ~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g--------~  212 (311)
                      .-|..+...+++..    ...+++..++.+                     +.-|++.+||.++.+.++..        +
T Consensus        30 ~~I~~~~~~~d~N~----I~~lYqslkRN~---------------------i~lPsv~~Yn~VL~Si~~R~lD~~~ie~k   84 (120)
T PF08579_consen   30 DNINSCFENEDYNI----INPLYQSLKRNG---------------------ITLPSVELYNKVLKSIAKRELDSEDIENK   84 (120)
T ss_pred             HHHHHHHhhcchHH----HHHHHHHHHhcC---------------------CCCCcHHHHHHHHHHHHHccccchhHHHH
Confidence            34555555577877    555555544333                     23467778888888877752        3


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~  244 (311)
                      +-..+.+|++|...+++|+..||+.++..+.+
T Consensus        85 l~~LLtvYqDiL~~~lKP~~etYnivl~~Llk  116 (120)
T PF08579_consen   85 LTNLLTVYQDILSNKLKPNDETYNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHHHHHhccCCcHHHHHHHHHHHHH
Confidence            45678899999999999999999999998875

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.31  E-value=0.011  Score=48.52  Aligned_cols=125  Identities=15%  Similarity=0.113  Sum_probs=72.7

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCH-hHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF-ATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~-~~~~  175 (311)
                      |++.+++++|++..+...                  .....  ..=+..+.+..++|-    |+..++.|.+-|- .|.+
T Consensus       118 ~~~~~~~deAl~~~~~~~------------------~lE~~--Al~VqI~lk~~r~d~----A~~~lk~mq~ided~tLt  173 (299)
T KOG3081|consen  118 YMHDGDFDEALKALHLGE------------------NLEAA--ALNVQILLKMHRFDL----AEKELKKMQQIDEDATLT  173 (299)
T ss_pred             hhcCCChHHHHHHHhccc------------------hHHHH--HHHHHHHHHHHHHHH----HHHHHHHHHccchHHHHH
Confidence            677777777777665421                  12222  222334556667777    7777777766432 3444


Q ss_pred             HHHHHHHHH---------HHHHHhhCCC---CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Q 044412          176 TMIDAYARL---------AELLFNKMPA---WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACA  243 (311)
Q Consensus       176 ~li~~~~~~---------a~~~~~~m~~---~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~  243 (311)
                      -|-.+|.+.         |.-+|++|-+   |+..+-|.+.-++...|++++|..++++...+. .-|+.|...+|-+-.
T Consensus       174 QLA~awv~la~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd-~~dpetL~Nliv~a~  252 (299)
T KOG3081|consen  174 QLAQAWVKLATGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKD-AKDPETLANLIVLAL  252 (299)
T ss_pred             HHHHHHHHHhccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhcc-CCCHHHHHHHHHHHH
Confidence            455555543         5666666653   566666666777777788888888888877653 224555444444333


Q ss_pred             ccC
Q 044412          244 HLG  246 (311)
Q Consensus       244 ~~~  246 (311)
                      ..|
T Consensus       253 ~~G  255 (299)
T KOG3081|consen  253 HLG  255 (299)
T ss_pred             HhC
Confidence            333

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.30  E-value=0.005  Score=49.09  Aligned_cols=104  Identities=12%  Similarity=0.085  Sum_probs=82.7

Q ss_pred             HHHhhC--CCCcHhHHHHHHHHHHhC-----CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh--
Q 044412          187 LLFNKM--PAWDIRSWTTMITSYSQN-----KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY--  257 (311)
Q Consensus       187 ~~~~~m--~~~~~~~y~~li~~~~~~-----g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~--  257 (311)
                      ..|++.  ..+|-.+|..+|+.|.+.     |.++=...-+..|.+-|++-|..+|+.||+.+=+..-.  ...+|+.  
T Consensus        35 ~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fv--p~n~fQ~~F  112 (228)
T PF06239_consen   35 ELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFV--PRNFFQAEF  112 (228)
T ss_pred             HHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcc--cccHHHHHh
Confidence            445544  467889999999999875     66777788899999999999999999999999864322  2333332  


Q ss_pred             ---hCChHHHHHHHhhcC----CCCchhHHHHHHHHHhcCCh
Q 044412          258 ---CRSLGRSLLVFFKLR----EKNLLCWNSITEALAIHGFA  292 (311)
Q Consensus       258 ---~~~~~~a~~~~~~~~----~p~~~~~~~li~~~~~~g~~  292 (311)
                         ..+.+-|.+++++|+    -||..|+..++..+.+.+..
T Consensus       113 ~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  113 MHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             ccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence               556667899999999    69999999999999988864

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=97.30  E-value=0.11  Score=45.72  Aligned_cols=222  Identities=11%  Similarity=0.044  Sum_probs=122.2

Q ss_pred             HhhccChhhHHHHHHHHHHhccCcchhHHH---HHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------cccCCCh
Q 044412           34 LKKCSSIKELECVYATIVKTNANLDCFLAK---QFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------FSSLRHP  103 (311)
Q Consensus        34 l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~---~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~~~~~~  103 (311)
                      +...++.+.+..+++...+.. +.|...+.   .+.... ...+..+.+.+.++.....+...+..       +...|++
T Consensus        53 ~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~~  130 (355)
T cd05804          53 AWIAGDLPKALALLEQLLDDY-PRDLLALKLHLGAFGLG-DFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQY  130 (355)
T ss_pred             HHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHhHHHHHhc-ccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCCH
Confidence            445577777777777776652 22333333   122222 23455566666665422211111111       6778888


Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~  183 (311)
                      ++|.+.+++..+..               +.+...+..+-..|...|++++    +...++...+...            
T Consensus       131 ~~A~~~~~~al~~~---------------p~~~~~~~~la~i~~~~g~~~e----A~~~l~~~l~~~~------------  179 (355)
T cd05804         131 DRAEEAARRALELN---------------PDDAWAVHAVAHVLEMQGRFKE----GIAFMESWRDTWD------------  179 (355)
T ss_pred             HHHHHHHHHHHhhC---------------CCCcHHHHHHHHHHHHcCCHHH----HHHHHHhhhhccC------------
Confidence            88888888876642               3345667777778888888888    5555554332110            


Q ss_pred             HHHHHHhhCCCCc--HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC-CCCHHHH-H--HHHHHHhccCChhhHHHHHHh
Q 044412          184 LAELLFNKMPAWD--IRSWTTMITSYSQNKQFREALDAFNKTKKSGT-GSDQVTM-A--TVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       184 ~a~~~~~~m~~~~--~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~t~-~--~li~a~~~~~~~~~a~~~~~~  257 (311)
                               ..++  ...|..+...+...|++++|++++++...... .+..... +  .++.-+...|....+...   
T Consensus       180 ---------~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w---  247 (355)
T cd05804         180 ---------CSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRW---  247 (355)
T ss_pred             ---------CCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHH---
Confidence                     0122  23466777888999999999999999864322 2222211 1  233333344443333222   


Q ss_pred             hCChHHHHHHHhhcCCCCchhHH--HHHHHHHhcCChHHHHHHHHHHHH
Q 044412          258 CRSLGRSLLVFFKLREKNLLCWN--SITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       258 ~~~~~~a~~~~~~~~~p~~~~~~--~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                          +................++  ....++...|+.++|..+++.+..
T Consensus       248 ----~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~  292 (355)
T cd05804         248 ----EDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKG  292 (355)
T ss_pred             ----HHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence                0010110000000122233  567788899999999999998875

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.27  E-value=0.12  Score=47.77  Aligned_cols=225  Identities=13%  Similarity=0.148  Sum_probs=114.2

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-----------cccCCChhHHHHHHHHHHHCCCCchH-HHHH-
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-----------FSSLRHPLQAIAFYLYMLRAEVLLTT-VHGQ-  126 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-----------~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~-  126 (311)
                      ..|-.+-+.| -+.|+++.|..+|++..+.+-.+.+.           =.+..+++.|+++.   ++.-..|.. .... 
T Consensus       388 ~Lw~~faklY-e~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm---~~A~~vP~~~~~~~y  463 (835)
T KOG2047|consen  388 TLWVEFAKLY-ENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLM---RRATHVPTNPELEYY  463 (835)
T ss_pred             hHHHHHHHHH-HhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHH---HhhhcCCCchhhhhh
Confidence            3555666666 66677777777776655433222211           12233444444433   333333331 0000 


Q ss_pred             ----HHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh------HHHHHHH--HHHHHHHHHHhhCCC
Q 044412          127 ----VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA------TWNTMID--AYARLAELLFNKMPA  194 (311)
Q Consensus       127 ----~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~------~~~~li~--~~~~~a~~~~~~m~~  194 (311)
                          -.+..+.-+..+|.-.++.--..|-++.    .+.+++.+.+.-+.      -|..++.  .|...+.+++++-..
T Consensus       464 d~~~pvQ~rlhrSlkiWs~y~DleEs~gtfes----tk~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~  539 (835)
T KOG2047|consen  464 DNSEPVQARLHRSLKIWSMYADLEESLGTFES----TKAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGIS  539 (835)
T ss_pred             cCCCcHHHHHHHhHHHHHHHHHHHHHhccHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCc
Confidence                0011112233445555555555666666    56666655443222      2222222  122225555555542


Q ss_pred             ----CcHh-HHHHHHHHHHhC---CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHh--ccCChhhHHHHHHh-------
Q 044412          195 ----WDIR-SWTTMITSYSQN---KQFREALDAFNKTKKSGTGSDQVTMATVLSACA--HLGALDLGRGIQIY-------  257 (311)
Q Consensus       195 ----~~~~-~y~~li~~~~~~---g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~--~~~~~~~a~~~~~~-------  257 (311)
                          |++. .||.-+.-+.+.   ..++.|.++|++-.+ |++|...-+--|+.|-.  +.|....|..+++.       
T Consensus       540 LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~~v~~  618 (835)
T KOG2047|consen  540 LFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATSAVKE  618 (835)
T ss_pred             cCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCH
Confidence                4432 455555555542   346677777777666 66665544443333322  23555555555555       


Q ss_pred             ----------------------------------------------------hCChHHHHHHHhhcC---CC--CchhHH
Q 044412          258 ----------------------------------------------------CRSLGRSLLVFFKLR---EK--NLLCWN  280 (311)
Q Consensus       258 ----------------------------------------------------~~~~~~a~~~~~~~~---~p--~~~~~~  280 (311)
                                                                          .|+.+.|..++.--.   .|  +...|+
T Consensus       619 a~~l~myni~I~kaae~yGv~~TR~iYekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~  698 (835)
T KOG2047|consen  619 AQRLDMYNIYIKKAAEIYGVPRTREIYEKAIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWD  698 (835)
T ss_pred             HHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHH
Confidence                                                                888888888877554   34  556788


Q ss_pred             HHHHHHHhcCChH
Q 044412          281 SITEALAIHGFAH  293 (311)
Q Consensus       281 ~li~~~~~~g~~~  293 (311)
                      +.=.-=.++|+-+
T Consensus       699 twk~FEvrHGned  711 (835)
T KOG2047|consen  699 TWKEFEVRHGNED  711 (835)
T ss_pred             HHHHHHHhcCCHH
Confidence            8877788888843

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.25  E-value=0.0034  Score=52.94  Aligned_cols=201  Identities=12%  Similarity=0.062  Sum_probs=112.0

Q ss_pred             hccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec-----cccCCChhHHHH
Q 044412           36 KCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA-----FSSLRHPLQAIA  108 (311)
Q Consensus        36 ~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~-----~~~~~~~~~a~~  108 (311)
                      +.|-+++++.-+..-.+.  .|-+.||-.|-+.| .+..+...|+.+|.+-.+  |.-+||-.     +-.-++.++|.+
T Consensus       235 rLgm~r~AekqlqssL~q--~~~~dTfllLskvY-~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~  311 (478)
T KOG1129|consen  235 RLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVY-QRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQ  311 (478)
T ss_pred             HhcChhhhHHHHHHHhhc--CCchhHHHHHHHHH-HHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHH
Confidence            335666665444443333  46677788888888 888888888888877543  55555544     444566777777


Q ss_pred             HHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHH--HH--
Q 044412          109 FYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA--RL--  184 (311)
Q Consensus       109 ~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~--~~--  184 (311)
                      +|++..+.               ...++....++-..|.-.++.+-|.+..++++..+..... .|+.+--+|.  ..  
T Consensus       312 lYk~vlk~---------------~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~spe-Lf~NigLCC~yaqQ~D  375 (478)
T KOG1129|consen  312 LYKLVLKL---------------HPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPE-LFCNIGLCCLYAQQID  375 (478)
T ss_pred             HHHHHHhc---------------CCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChH-HHhhHHHHHHhhcchh
Confidence            77776553               2334444455555566666666644444444443332111 1111111111  00  


Q ss_pred             -----HHHHHhhCCCCcHh--HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          185 -----AELLFNKMPAWDIR--SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       185 -----a~~~~~~m~~~~~~--~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                           -.+-+..+..|+..  +|-.+-......|++..|.+.|+--..+. .-....+|.|--.-.+.|++++|+.+++
T Consensus       376 ~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~  453 (478)
T KOG1129|consen  376 LVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLN  453 (478)
T ss_pred             hhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHH
Confidence                 22223333344432  45555555566678888887777766542 2234566666666667777777776653

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.23  E-value=0.087  Score=51.18  Aligned_cols=183  Identities=11%  Similarity=0.064  Sum_probs=113.3

Q ss_pred             HHHHHHHHHhccC--cchhHHHHHHHHHhhccCChhHHHHhcccCC-CCCeeeeec------------------------
Q 044412           44 ECVYATIVKTNAN--LDCFLAKQFISFCTSRFHFIDYTILVFPQMQ-EPNVFVYHA------------------------   96 (311)
Q Consensus        44 ~~l~~~m~~~g~~--p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~-~~~~~~~~~------------------------   96 (311)
                      +++.++.++.+++  .|+.-.+..++++ ...+-..+-.++++.+. ++..++-|.                        
T Consensus       967 RqLiDqVv~tal~E~~dPe~vS~tVkAf-MtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAikad~trVm~YI~r 1045 (1666)
T KOG0985|consen  967 RQLIDQVVQTALPETQDPEEVSVTVKAF-MTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIKADRTRVMEYINR 1045 (1666)
T ss_pred             HHHHHHHHHhcCCccCChHHHHHHHHHH-HhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhhcChHHHHHHHHH
Confidence            4556666665542  4555555566666 66666666666666654 333333222                        


Q ss_pred             ------------cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhc
Q 044412           97 ------------FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus        97 ------------~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~  164 (311)
                                  +..++.+++|..+|+.                   +..+....+.||+   ..+++|.    |.++-+
T Consensus      1046 LdnyDa~~ia~iai~~~LyEEAF~ifkk-------------------f~~n~~A~~VLie---~i~~ldR----A~efAe 1099 (1666)
T KOG0985|consen 1046 LDNYDAPDIAEIAIENQLYEEAFAIFKK-------------------FDMNVSAIQVLIE---NIGSLDR----AYEFAE 1099 (1666)
T ss_pred             hccCCchhHHHHHhhhhHHHHHHHHHHH-------------------hcccHHHHHHHHH---HhhhHHH----HHHHHH
Confidence                        3344444555555543                   3455555566655   3466777    444444


Q ss_pred             cCCCCCHhHHHHHHHHHHHH--HHHHHh-hCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 044412          165 EMPERKFATWNTMIDAYARL--AELLFN-KMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSA  241 (311)
Q Consensus       165 ~~~~~~~~~~~~li~~~~~~--a~~~~~-~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a  241 (311)
                      +..+|.  .|..+-++-.+.  ..+-.+ -++..|...|--+|+...+.|.+++-.+++..-++..-+|...+  .||-|
T Consensus      1100 ~~n~p~--vWsqlakAQL~~~~v~dAieSyikadDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~A 1175 (1666)
T KOG0985|consen 1100 RCNEPA--VWSQLAKAQLQGGLVKDAIESYIKADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFA 1175 (1666)
T ss_pred             hhCChH--HHHHHHHHHHhcCchHHHHHHHHhcCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHH
Confidence            444444  355554444433  111111 12345777899999999999999999999998888888888775  78899


Q ss_pred             HhccCChhhHHHHHHh
Q 044412          242 CAHLGALDLGRGIQIY  257 (311)
Q Consensus       242 ~~~~~~~~~a~~~~~~  257 (311)
                      |++.+++.+.+.+..-
T Consensus      1176 yAkt~rl~elE~fi~g 1191 (1666)
T KOG0985|consen 1176 YAKTNRLTELEEFIAG 1191 (1666)
T ss_pred             HHHhchHHHHHHHhcC
Confidence            9999999888877654

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=97.20  E-value=0.041  Score=48.31  Aligned_cols=93  Identities=15%  Similarity=0.126  Sum_probs=49.5

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCc--hhH
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNL--LCW  279 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~--~~~  279 (311)
                      .+-..+...|++++|...+++..+.. +.+...+..+-..+...|++++|...++..-....      .  .|+.  ..|
T Consensus       119 ~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~------~--~~~~~~~~~  189 (355)
T cd05804         119 MLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWD------C--SSMLRGHNW  189 (355)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccC------C--CcchhHHHH
Confidence            33445556677777777777766542 22344555566666666666655544322111100      0  1222  234


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHH
Q 044412          280 NSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       280 ~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      ..+...+...|++++|..++++..
T Consensus       190 ~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         190 WHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHh
Confidence            456666667777777777776654

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=97.15  E-value=0.029  Score=53.85  Aligned_cols=263  Identities=12%  Similarity=0.117  Sum_probs=159.0

Q ss_pred             HHHHHHHhhccChhh---HHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC-------CCe------
Q 044412           28 HIIANQLKKCSSIKE---LECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE-------PNV------   91 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~---~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-------~~~------   91 (311)
                      -.+..++........   .....+.+...|-.+.+...|.+-... ...|++..|...|.+...       ++.      
T Consensus       418 l~laql~e~~d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslh-f~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~l  496 (1018)
T KOG2002|consen  418 LELAQLLEQTDPWASLDAYGNALDILESKGKQIPPEVLNNVASLH-FRLGNIEKALEHFKSALGKLLEVANKDEGKSTNL  496 (1018)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHH-HHhcChHHHHHHHHHHhhhhhhhcCccccccchh
Confidence            344555544332222   255666677777778888899988888 889999999888876541       233      


Q ss_pred             -eeeec---cccCCChhHHHHHHHHHHHCCCCch-------------------HHHHHHHHhc---CCCchhHHHHHHHH
Q 044412           92 -FVYHA---FSSLRHPLQAIAFYLYMLRAEVLLT-------------------TVHGQVWKNG---FSSPVFVQTAMVDN  145 (311)
Q Consensus        92 -~~~~~---~~~~~~~~~a~~~~~~m~~~~~~p~-------------------~~~~~~~~~g---~~~~~~~~~~ll~~  145 (311)
                       .-||.   .-..++.+.|.+.|.++.+.-  |.                   +...+ .+.+   ..-++..++.+-+.
T Consensus       497 t~~YNlarl~E~l~~~~~A~e~Yk~Ilkeh--p~YId~ylRl~~ma~~k~~~~ea~~~-lk~~l~~d~~np~arsl~G~~  573 (1018)
T KOG2002|consen  497 TLKYNLARLLEELHDTEVAEEMYKSILKEH--PGYIDAYLRLGCMARDKNNLYEASLL-LKDALNIDSSNPNARSLLGNL  573 (1018)
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHHHHHHHC--chhHHHHHHhhHHHHhccCcHHHHHH-HHHHHhcccCCcHHHHHHHHH
Confidence             13555   444567888888888876532  22                   00111 1111   12233344444445


Q ss_pred             HHhCCCCccchHHHHHHhccCCC-CCHhHHHHHHHHHHHH-----------------HHHHHhhCCC---CcHhHHHHHH
Q 044412          146 YSYSNKFFESRRVSRRLFDEMPE-RKFATWNTMIDAYARL-----------------AELLFNKMPA---WDIRSWTTMI  204 (311)
Q Consensus       146 ~~~~g~~~~a~~~a~~~~~~~~~-~~~~~~~~li~~~~~~-----------------a~~~~~~m~~---~~~~~y~~li  204 (311)
                      |.+...+..|..--..+++.-.. +|.++.-.|=+.|.+.                 |..+|.....   .|...=|-+-
T Consensus       574 ~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIg  653 (1018)
T KOG2002|consen  574 HLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIG  653 (1018)
T ss_pred             HHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchh
Confidence            55665666622222223333222 3444444444433332                 6667665542   3556666666


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITE  284 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~  284 (311)
                      -.++..|++.+|.++|...++... -+..+|-.|-.+|...|++..|.++|+.|      .+-|.  ++.++.+.+.|-+
T Consensus       654 iVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~------lkkf~--~~~~~~vl~~Lar  724 (1018)
T KOG2002|consen  654 IVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENC------LKKFY--KKNRSEVLHYLAR  724 (1018)
T ss_pred             hhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHH------HHHhc--ccCCHHHHHHHHH
Confidence            677788889999999988887643 34456777788888888888666665332      11111  2457788899999


Q ss_pred             HHHhcCChHHHHHHHHHHH
Q 044412          285 ALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       285 ~~~~~g~~~~a~~~~~~M~  303 (311)
                      ++.++|.+.+|.+.+-...
T Consensus       725 a~y~~~~~~eak~~ll~a~  743 (1018)
T KOG2002|consen  725 AWYEAGKLQEAKEALLKAR  743 (1018)
T ss_pred             HHHHhhhHHHHHHHHHHHH
Confidence            9999999999988876554

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.13  E-value=0.047  Score=43.97  Aligned_cols=118  Identities=8%  Similarity=-0.012  Sum_probs=81.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      |...|+...|..-++.-.+.                .|+ .-+|..+-..|-+.|..+.    |.+.|+.-..       
T Consensus        45 YL~~gd~~~A~~nlekAL~~----------------DPs~~~a~~~~A~~Yq~~Ge~~~----A~e~YrkAls-------   97 (250)
T COG3063          45 YLQQGDYAQAKKNLEKALEH----------------DPSYYLAHLVRAHYYQKLGENDL----ADESYRKALS-------   97 (250)
T ss_pred             HHHCCCHHHHHHHHHHHHHh----------------CcccHHHHHHHHHHHHHcCChhh----HHHHHHHHHh-------
Confidence            66888899999888887664                444 6678888888999999999    6666654322       


Q ss_pred             HHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHH
Q 044412          176 TMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~  254 (311)
                                      +...+..+-|.-=.-+|..|++++|...|++-...---| -..||..+--+..+.|+.+.|+..
T Consensus        98 ----------------l~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~  161 (250)
T COG3063          98 ----------------LAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEY  161 (250)
T ss_pred             ----------------cCCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHH
Confidence                            112234455555566777888888888888876642222 235677776667778888877777


Q ss_pred             HHh
Q 044412          255 QIY  257 (311)
Q Consensus       255 ~~~  257 (311)
                      +..
T Consensus       162 l~r  164 (250)
T COG3063         162 LKR  164 (250)
T ss_pred             HHH
Confidence            655

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.09  E-value=0.033  Score=45.80  Aligned_cols=126  Identities=13%  Similarity=0.085  Sum_probs=87.3

Q ss_pred             HHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHH--HHHHHHHHHH-HHHHHhhCCCC-cHhHHHH
Q 044412          127 VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATW--NTMIDAYARL-AELLFNKMPAW-DIRSWTT  202 (311)
Q Consensus       127 ~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~--~~li~~~~~~-a~~~~~~m~~~-~~~~y~~  202 (311)
                      +......-+...-..-...|+..|++++    |.+..+.+..-+....  .++++..... |++.++.|.+- +..|.+-
T Consensus        99 ~a~~~~~sn~i~~l~aa~i~~~~~~~de----Al~~~~~~~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQ  174 (299)
T KOG3081|consen   99 VADSTDGSNLIDLLLAAIIYMHDGDFDE----ALKALHLGENLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQ  174 (299)
T ss_pred             HHhhccchhHHHHHHhhHHhhcCCChHH----HHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHH
Confidence            3333344443333333446899999999    7777777544444332  3344444333 99999999874 4456665


Q ss_pred             HHHHHHh----CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          203 MITSYSQ----NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       203 li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |-.++.+    .+.+.+|+-+|++|-++ ..|+.-+.+-...++...|++++|+.+++.
T Consensus       175 LA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~e  232 (299)
T KOG3081|consen  175 LAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEE  232 (299)
T ss_pred             HHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHH
Confidence            5555544    46799999999999764 789999999999999999999988877654

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.09  E-value=0.031  Score=49.46  Aligned_cols=192  Identities=15%  Similarity=0.104  Sum_probs=136.9

Q ss_pred             cccCCChhHHHHHHHHHHHCC-CCch------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAE-VLLT------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRR  157 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~-~~p~------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~  157 (311)
                      .....++++|+.+|+++++.. ...+                  ..+.+.+-.--+--+.|+-.+-+-|+-.++.++   
T Consensus       272 ~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEK---  348 (559)
T KOG1155|consen  272 SYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEK---  348 (559)
T ss_pred             HhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHH---
Confidence            566789999999999998763 1112                  111111111112234566677777888888999   


Q ss_pred             HHHHHhccCCCCC---HhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc
Q 044412          158 VSRRLFDEMPERK---FATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKS  226 (311)
Q Consensus       158 ~a~~~~~~~~~~~---~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  226 (311)
                       |...|++..+.|   ...|+.|=+-|...     |.+-+.+-.   ..|-..|-.|-.+|.-.+.+.-|+-+|++-.+.
T Consensus       349 -Av~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~  427 (559)
T KOG1155|consen  349 -AVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALEL  427 (559)
T ss_pred             -HHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhc
Confidence             888888876633   35788888888775     555555433   458899999999999999999999999998764


Q ss_pred             CCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          227 GTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       227 g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                       -+-|...|.+|=.+|.+.++.++|.+.|...-...          ..+...+..|-+.|-+-++.++|...|.+-.
T Consensus       428 -kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~----------dte~~~l~~LakLye~l~d~~eAa~~yek~v  493 (559)
T KOG1155|consen  428 -KPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG----------DTEGSALVRLAKLYEELKDLNEAAQYYEKYV  493 (559)
T ss_pred             -CCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc----------ccchHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence             24478899999999999999997776664411111          1233578888888889999988877776644

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.07  E-value=0.0037  Score=55.69  Aligned_cols=82  Identities=7%  Similarity=-0.036  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchh
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLC  278 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~  278 (311)
                      |.+++|+.|...|..+++++++..=..-|+=||.+|||.||+.+.+.|++..|.++..++-.-+.         -.+..|
T Consensus       105 t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~---------~~~~~t  175 (429)
T PF10037_consen  105 THHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEE---------FDNPST  175 (429)
T ss_pred             cHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhc---------cCCchH
Confidence            44578888888888888888888877788888888888888888888888766554322111111         245566


Q ss_pred             HHHHHHHHHhc
Q 044412          279 WNSITEALAIH  289 (311)
Q Consensus       279 ~~~li~~~~~~  289 (311)
                      +..-+.+|.+.
T Consensus       176 ~~L~l~~~~~~  186 (429)
T PF10037_consen  176 QALALYSCYKY  186 (429)
T ss_pred             HHHHHHHHHHh
Confidence            66666666654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.04  E-value=0.011  Score=43.95  Aligned_cols=99  Identities=14%  Similarity=0.110  Sum_probs=74.8

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +......+...+...|++++|.+.|+.....+ +.+...+..+-..+...|+++.|..+++..-..+          ..+
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~----------p~~   84 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD----------PDD   84 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----------CCC
Confidence            34456667777888999999999999987753 4466778888888889899987766553322211          345


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..+|..+-..+...|++++|...|++..+.
T Consensus        85 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        85 PRPYFHAAECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            677888888999999999999999887763

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.02  E-value=0.059  Score=46.22  Aligned_cols=78  Identities=9%  Similarity=-0.061  Sum_probs=35.1

Q ss_pred             hhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCe-eeeec----cccCCChhHHH
Q 044412           35 KKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNV-FVYHA----FSSLRHPLQAI  107 (311)
Q Consensus        35 ~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~----~~~~~~~~~a~  107 (311)
                      ...|+...+...+...++.. +.++..|+.+-..+ ...|+++.|...|++..+  |+. ..|..    +...|++++|+
T Consensus        75 ~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~-~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~  152 (296)
T PRK11189         75 DSLGLRALARNDFSQALALR-PDMADAYNYLGIYL-TQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQ  152 (296)
T ss_pred             HHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            33344444444444444432 12334555555555 555555555555555432  221 11111    44445555555


Q ss_pred             HHHHHHH
Q 044412          108 AFYLYML  114 (311)
Q Consensus       108 ~~~~~m~  114 (311)
                      +.|+...
T Consensus       153 ~~~~~al  159 (296)
T PRK11189        153 DDLLAFY  159 (296)
T ss_pred             HHHHHHH
Confidence            5555543

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.00  E-value=0.0057  Score=54.53  Aligned_cols=117  Identities=10%  Similarity=0.061  Sum_probs=87.9

Q ss_pred             hccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC-CCee---eee--c----cccCCChhHHHHHHHHHHHCCCCchH
Q 044412           53 TNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE-PNVF---VYH--A----FSSLRHPLQAIAFYLYMLRAEVLLTT  122 (311)
Q Consensus        53 ~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-~~~~---~~~--~----~~~~~~~~~a~~~~~~m~~~~~~p~~  122 (311)
                      .+.+.+......+++.+ ....+++.+..++-.... |+..   .|+  +    |...|..++++++++.=...|     
T Consensus        60 ~~~~vS~~dld~fvn~~-~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yG-----  133 (429)
T PF10037_consen   60 RKKPVSSLDLDIFVNNV-ESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYG-----  133 (429)
T ss_pred             cCCCCcHHHHHHHHhhc-CCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcc-----
Confidence            45566778888899999 888888989888766653 2211   122  2    888889999999988765555     


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH
Q 044412          123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL  184 (311)
Q Consensus       123 ~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~  184 (311)
                               +-||..++|.||+.+.+.|++..|.+++..+..+-...+..|+...+.+|.+.
T Consensus       134 ---------iF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  134 ---------IFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             ---------cCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence                     89999999999999999999999777777666555555556666666666553

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=96.99  E-value=0.016  Score=51.38  Aligned_cols=105  Identities=16%  Similarity=0.105  Sum_probs=72.2

Q ss_pred             HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHH
Q 044412          185 AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRS  264 (311)
Q Consensus       185 a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a  264 (311)
                      |.++|+++.+.+....-.+...+...++-.+|.+++.+..+. .+-|......-..-|...++.+.|..           
T Consensus       188 ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~~~~lAL~-----------  255 (395)
T PF09295_consen  188 AIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKKKYELALE-----------  255 (395)
T ss_pred             HHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHH-----------
Confidence            555666665544445556777777777888888888887753 23355555555666777777775544           


Q ss_pred             HHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          265 LLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       265 ~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                        +.++..  .|+ ..+|..|..+|...|++++|+-.++-+.
T Consensus       256 --iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  256 --IAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             --HHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence              444433  354 5699999999999999999998888764

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=96.98  E-value=0.0097  Score=40.16  Aligned_cols=95  Identities=16%  Similarity=0.130  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchh
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLC  278 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~  278 (311)
                      +|..+...+...|++++|..++.+..+.. +.+...+..+...+...++++.|...+...-..          ...+..+
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~----------~~~~~~~   70 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALEL----------DPDNAKA   70 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC----------CCcchhH
Confidence            35566777888999999999999987752 233466777778888888888666554332111          1234468


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          279 WNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       279 ~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +..+...+...|++++|...+.+..+
T Consensus        71 ~~~~~~~~~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          71 YYNLGLAYYKLGKYEEALEAYEKALE   96 (100)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence            88888999999999999999988765

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=96.98  E-value=0.25  Score=44.19  Aligned_cols=82  Identities=13%  Similarity=0.080  Sum_probs=58.3

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC--CCCeeeeec----cccCCC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ--EPNVFVYHA----FSSLRH  102 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~--~~~~~~~~~----~~~~~~  102 (311)
                      -|+-+=...|++.-++++|+.=.+  ..||...|++.|++= .+-..++.|..+++...  .|++.+|--    =.+.|.
T Consensus       146 KY~ymEE~LgNi~gaRqiferW~~--w~P~eqaW~sfI~fE-lRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~  222 (677)
T KOG1915|consen  146 KYIYMEEMLGNIAGARQIFERWME--WEPDEQAWLSFIKFE-LRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGN  222 (677)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHc--CCCcHHHHHHHHHHH-HHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCc
Confidence            344444556677777777765443  579999999999999 99999999999998854  577666644    345566


Q ss_pred             hhHHHHHHHHH
Q 044412          103 PLQAIAFYLYM  113 (311)
Q Consensus       103 ~~~a~~~~~~m  113 (311)
                      ...|.++|+.-
T Consensus       223 ~~~aR~VyerA  233 (677)
T KOG1915|consen  223 VALARSVYERA  233 (677)
T ss_pred             HHHHHHHHHHH
Confidence            66666666543

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=96.96  E-value=0.0017  Score=55.20  Aligned_cols=139  Identities=16%  Similarity=0.212  Sum_probs=96.0

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec--------cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA--------FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--------~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      .+|-.++++. .|.+.++.|..+|.+..+....+|..        +...++.+.|.++|+...+.               
T Consensus         2 ~v~i~~m~~~-~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~---------------   65 (280)
T PF05843_consen    2 LVWIQYMRFM-RRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK---------------   65 (280)
T ss_dssp             HHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH---------------
T ss_pred             HHHHHHHHHH-HHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH---------------
Confidence            4677777777 77777778888877776555555554        44567777799999987654               


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCC-CC-cHhHHHHHHHHHHh
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMP-AW-DIRSWTTMITSYSQ  209 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~-~~-~~~~y~~li~~~~~  209 (311)
                      +..+...|...|+.+.+.|+.+.    ++.+|++....                      +. +. -...|...|+-=.+
T Consensus        66 f~~~~~~~~~Y~~~l~~~~d~~~----aR~lfer~i~~----------------------l~~~~~~~~iw~~~i~fE~~  119 (280)
T PF05843_consen   66 FPSDPDFWLEYLDFLIKLNDINN----ARALFERAISS----------------------LPKEKQSKKIWKKFIEFESK  119 (280)
T ss_dssp             HTT-HHHHHHHHHHHHHTT-HHH----HHHHHHHHCCT----------------------SSCHHHCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCcHHH----HHHHHHHHHHh----------------------cCchhHHHHHHHHHHHHHHH
Confidence            57788899999999999999999    77777654331                      11 11 24578888988888


Q ss_pred             CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 044412          210 NKQFREALDAFNKTKKSGTGSDQVTMATVLSAC  242 (311)
Q Consensus       210 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~  242 (311)
                      .|+++.+.++..++.+.  -|+..+...+++-|
T Consensus       120 ~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen  120 YGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             cCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            89999999999998874  45544545555433

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.95  E-value=0.041  Score=45.29  Aligned_cols=166  Identities=13%  Similarity=0.052  Sum_probs=96.3

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc----hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP----VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA  172 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~----~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~  172 (311)
                      +...|++++|...|++....                .|+    ...+..+-.+|.+.|++++|......+.+.-+.....
T Consensus        43 ~~~~~~~~~A~~~~~~~~~~----------------~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~  106 (235)
T TIGR03302        43 ALDSGDYTEAIKYFEALESR----------------YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDA  106 (235)
T ss_pred             HHHcCCHHHHHHHHHHHHHh----------------CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCch
Confidence            66788999999999988653                333    2466777889999999999555544444433321111


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHh--------CCChhHHHHHHHHHHhcCCCCCHH-HHHHHHHH--
Q 044412          173 TWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQ--------NKQFREALDAFNKTKKSGTGSDQV-TMATVLSA--  241 (311)
Q Consensus       173 ~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~--------~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~a--  241 (311)
                      .+                        ++..+-.++..        .|+.++|.+.|+...+.  .|+.. .+..+...  
T Consensus       107 ~~------------------------a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~~  160 (235)
T TIGR03302       107 DY------------------------AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMDY  160 (235)
T ss_pred             HH------------------------HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHHH
Confidence            11                        12122222222        26678888888888764  34432 22111110  


Q ss_pred             -Hhcc--CChhhHHHHHHhhCChHHHHHHHhhcC--CCC----chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          242 -CAHL--GALDLGRGIQIYCRSLGRSLLVFFKLR--EKN----LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       242 -~~~~--~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~----~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                       ....  .....| .++-..|+...|...|++..  .|+    ...+..+..++...|++++|..+++.+...
T Consensus       161 ~~~~~~~~~~~~a-~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       161 LRNRLAGKELYVA-RFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHHHH-HHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             0000  000111 12223455556666665554  232    468899999999999999999999988764

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=96.95  E-value=0.11  Score=45.56  Aligned_cols=210  Identities=7%  Similarity=-0.012  Sum_probs=129.9

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhc-cCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeee---eec----cc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTN-ANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV---YHA----FS   98 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g-~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~---~~~----~~   98 (311)
                      +..|.-+|+.-|+.++...+...+.... .+..+.....  ... ....+++.|+.+-+.-.+.+..+   +-.    +.
T Consensus       269 MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~--~~l-~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~  345 (564)
T KOG1174|consen  269 MDLYAVLLGQEGGCEQDSALMDYLFAKVKYTASHWFVHA--QLL-YDEKKFERALNFVEKCIDSEPRNHEALILKGRLLI  345 (564)
T ss_pred             HHHHHHHHHhccCHhhHHHHHHHHHhhhhcchhhhhhhh--hhh-hhhhhHHHHHHHHHHHhccCcccchHHHhccHHHH
Confidence            4455555555555555555544444321 1111111111  111 23445555555554433222221   111    55


Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCC-CchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC--HhHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFS-SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK--FATWN  175 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~-~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~--~~~~~  175 (311)
                      ..+++++|.=.|++-..                +. -+..+|.-|+++|...|++.+|.-+|....+.|+..-  .-.+.
T Consensus       346 ~~~R~~~A~IaFR~Aq~----------------Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~~sA~~LtL~g  409 (564)
T KOG1174|consen  346 ALERHTQAVIAFRTAQM----------------LAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQNSARSLTLFG  409 (564)
T ss_pred             hccchHHHHHHHHHHHh----------------cchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhhcchhhhhhhc
Confidence            66677777777766543                34 4578999999999999999999988988888877531  11111


Q ss_pred             HHHHHH---HHH-HHHHHhhCC--CCc-HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          176 TMIDAY---ARL-AELLFNKMP--AWD-IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       176 ~li~~~---~~~-a~~~~~~m~--~~~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      +.+...   .+. |+.+++.-.  .|+ ...-+.+-..+...|+.++++.+++.-..  ..||...-+.|-+-+.-.+.+
T Consensus       410 ~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~  487 (564)
T KOG1174|consen  410 TLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEP  487 (564)
T ss_pred             ceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhH
Confidence            122111   111 777777654  455 34567777888889999999999999776  479999989998888888888


Q ss_pred             hhHHHHHHh
Q 044412          249 DLGRGIQIY  257 (311)
Q Consensus       249 ~~a~~~~~~  257 (311)
                      +++...|..
T Consensus       488 Q~am~~y~~  496 (564)
T KOG1174|consen  488 QKAMEYYYK  496 (564)
T ss_pred             HHHHHHHHH
Confidence            888777665

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=96.94  E-value=0.0085  Score=45.40  Aligned_cols=94  Identities=11%  Similarity=0.057  Sum_probs=70.8

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      ++..+..+-..+...|++++    |...|+.....+                       ..+...|..+-..+...|+++
T Consensus        23 ~p~~~~~~g~~~~~~g~~~~----A~~~~~~al~~~-----------------------P~~~~a~~~lg~~~~~~g~~~   75 (144)
T PRK15359         23 DPETVYASGYASWQEGDYSR----AVIDFSWLVMAQ-----------------------PWSWRAHIALAGTWMMLKEYT   75 (144)
T ss_pred             CHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHcC-----------------------CCcHHHHHHHHHHHHHHhhHH
Confidence            33345567778899999999    666666543321                       236778888889999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +|+..|++..+.. +.+..++..+-.++...|+.++|...++
T Consensus        76 ~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~  116 (144)
T PRK15359         76 TAINFYGHALMLD-ASHPEPVYQTGVCLKMMGEPGLAREAFQ  116 (144)
T ss_pred             HHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999998742 4467788888888889899887766553

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=96.94  E-value=0.024  Score=54.17  Aligned_cols=115  Identities=11%  Similarity=0.038  Sum_probs=90.0

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      ..+.|..++|+.+++...+                +.|+ ......+...+.+.+++++|...+++.+..          
T Consensus        96 ~~~~g~~~ea~~~l~~~~~----------------~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~----------  149 (694)
T PRK15179         96 LEAAHRSDEGLAVWRGIHQ----------------RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG----------  149 (694)
T ss_pred             HHHcCCcHHHHHHHHHHHh----------------hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc----------
Confidence            4467888999999988876                4565 566677788899999999977777777665          


Q ss_pred             HHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHH
Q 044412          176 TMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRG  253 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~  253 (311)
                                        .| +....+.+-.++.+.|++++|+++|++....  .|+ ..++..+-.++-..|+.+.|..
T Consensus       150 ------------------~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G~~~~A~~  209 (694)
T PRK15179        150 ------------------GSSSAREILLEAKSWDEIGQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRGALWRARD  209 (694)
T ss_pred             ------------------CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHH
Confidence                              33 3456667778888899999999999999872  344 6788888888889999999988


Q ss_pred             HHHh
Q 044412          254 IQIY  257 (311)
Q Consensus       254 ~~~~  257 (311)
                      .|+.
T Consensus       210 ~~~~  213 (694)
T PRK15179        210 VLQA  213 (694)
T ss_pred             HHHH
Confidence            8877

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=96.82  E-value=0.016  Score=42.64  Aligned_cols=103  Identities=10%  Similarity=-0.022  Sum_probs=73.5

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      |..++.++|-++++.|+++....+..+++.--....... ..    +      --..-..|+..+-.+++.+|+..|++.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~-~~----~------~~~spl~Pt~~lL~AIv~sf~~n~~i~   69 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKE-GD----Y------PPSSPLYPTSRLLIAIVHSFGYNGDIF   69 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCcccc-Cc----c------CCCCCCCCCHHHHHHHHHHHHhcccHH
Confidence            456788999999999999995555555554322111000 00    0      000011489999999999999999999


Q ss_pred             HHHHHHHHHHh-cCCCCCHHHHHHHHHHHhccCCh
Q 044412          215 EALDAFNKTKK-SGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       215 ~a~~~~~~m~~-~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      .|+++.+...+ -+++.+..+|..|++-+....+.
T Consensus        70 ~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~~  104 (126)
T PF12921_consen   70 SALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSSK  104 (126)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCC
Confidence            99999999876 57888999999999877665543

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.74  E-value=0.098  Score=42.22  Aligned_cols=177  Identities=7%  Similarity=0.006  Sum_probs=126.4

Q ss_pred             HhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC---CCeeeeec----cccCCChhHH
Q 044412           34 LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE---PNVFVYHA----FSSLRHPLQA  106 (311)
Q Consensus        34 l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~----~~~~~~~~~a  106 (311)
                      +-..|+...++.-++..+++. +.+..+|..+-..| .+.|..+.|.+-|++...   .+-...|-    +|..|++++|
T Consensus        45 YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Y-q~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA  122 (250)
T COG3063          45 YLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYY-QKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEA  122 (250)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH-HHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHH
Confidence            345577777777777777763 23446778888888 999999999999987542   23333333    8888999999


Q ss_pred             HHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHH
Q 044412          107 IAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAE  186 (311)
Q Consensus       107 ~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~  186 (311)
                      ...|++-...-.             ..-...+|..+--|..+.|+++.    |+..|++-.+.|.               
T Consensus       123 ~q~F~~Al~~P~-------------Y~~~s~t~eN~G~Cal~~gq~~~----A~~~l~raL~~dp---------------  170 (250)
T COG3063         123 MQQFERALADPA-------------YGEPSDTLENLGLCALKAGQFDQ----AEEYLKRALELDP---------------  170 (250)
T ss_pred             HHHHHHHHhCCC-------------CCCcchhhhhhHHHHhhcCCchh----HHHHHHHHHHhCc---------------
Confidence            999988654311             23335688888889999999999    7777665433211               


Q ss_pred             HHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHH
Q 044412          187 LLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRG  253 (311)
Q Consensus       187 ~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~  253 (311)
                              ....+.-.+-...-+.|++-.|..+++.....|. ++..+.-..|.--.+.|+.+.+-.
T Consensus       171 --------~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~  228 (250)
T COG3063         171 --------QFPPALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQR  228 (250)
T ss_pred             --------CCChHHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHH
Confidence                    1233445666777788999999999999887765 888888888887777777775543

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=96.73  E-value=0.12  Score=47.01  Aligned_cols=114  Identities=18%  Similarity=0.125  Sum_probs=70.3

Q ss_pred             HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc--CC----CCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          185 AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKS--GT----GSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       185 a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~--g~----~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      |.+.|.+-.  .| |....+-+--..-..+.+.+|..+|+.-...  .+    .....|++.|=.+|.+.+..++|...+
T Consensus       399 Ae~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~  478 (611)
T KOG1173|consen  399 AEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYY  478 (611)
T ss_pred             HHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHH
Confidence            666665443  23 4445554444444467888999888876521  11    124456777777788877777555444


Q ss_pred             HhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          256 IYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       256 ~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      +..-          .+...|..+|.++--.|...|+++.|.+.|.+-..  +.||
T Consensus       479 q~aL----------~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~  521 (611)
T KOG1173|consen  479 QKAL----------LLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPD  521 (611)
T ss_pred             HHHH----------HcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCc
Confidence            3210          11245778888888888888888888888887653  4454

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=96.71  E-value=0.0071  Score=41.05  Aligned_cols=81  Identities=11%  Similarity=0.122  Sum_probs=55.5

Q ss_pred             CCChhHHHHHHHHHHhcCC-CCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHh
Q 044412          210 NKQFREALDAFNKTKKSGT-GSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAI  288 (311)
Q Consensus       210 ~g~~~~a~~~~~~m~~~g~-~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~  288 (311)
                      .|++++|+.+++++.+..- .|+...+-.+-.++.+.|++++|..+++. ...+          ..+....-.+-.+|..
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~----------~~~~~~~~l~a~~~~~   70 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD----------PSNPDIHYLLARCLLK   70 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH----------HCHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC----------CCCHHHHHHHHHHHHH
Confidence            5789999999999987533 22455555688899999999977666544 1111          1233444556788889


Q ss_pred             cCChHHHHHHHHH
Q 044412          289 HGFAHEALGMFDR  301 (311)
Q Consensus       289 ~g~~~~a~~~~~~  301 (311)
                      .|++++|.+.|++
T Consensus        71 l~~y~eAi~~l~~   83 (84)
T PF12895_consen   71 LGKYEEAIKALEK   83 (84)
T ss_dssp             TT-HHHHHHHHHH
T ss_pred             hCCHHHHHHHHhc
Confidence            9999999998875

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.68  E-value=0.054  Score=38.90  Aligned_cols=96  Identities=9%  Similarity=-0.043  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCC--CCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC-
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGT--GSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN-  275 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~--~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~-  275 (311)
                      ++......+.+.|++++|.+.|..+.+..-  ......+..+..++.+.|+++.|...++..-.      .     .|+ 
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------~-----~p~~   72 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVK------K-----YPKS   72 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHH------H-----CCCC
Confidence            455667778889999999999999987421  11234666788889999998866655432111      0     233 


Q ss_pred             ---chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 ---LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ---~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                         ...+..+...+...|+.++|...+++..+.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        73 PKAPDALLKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             CcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence               456788888899999999999999999875

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.65  E-value=0.21  Score=44.84  Aligned_cols=159  Identities=11%  Similarity=0.090  Sum_probs=98.4

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCC-----CCHhHHHHHHHHHHHH---HHHHHhhCCCC---cHhHHHHHHHHH
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPE-----RKFATWNTMIDAYARL---AELLFNKMPAW---DIRSWTTMITSY  207 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~---a~~~~~~m~~~---~~~~y~~li~~~  207 (311)
                      |--+-.+|....+.++    ....|+....     ||++....-+.-....   |..=|++-.+-   ++..|--+--+.
T Consensus       363 yI~~a~~y~d~~~~~~----~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~pe~~~~~iQl~~a~  438 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEK----MWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAISLDPENAYAYIQLCCAL  438 (606)
T ss_pred             HHHHHHHHhhhhccHH----HHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcChhhhHHHHHHHHHH
Confidence            5555557777777777    7777765543     3333222222222222   44445544432   233333332233


Q ss_pred             HhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh----------------------------hC
Q 044412          208 SQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------------------CR  259 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~----------------------------~~  259 (311)
                      -+.++++++...|++-+++ ++-.+..|+..-..+...++++.|.+-++.                            -+
T Consensus       439 Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~qwk~  517 (606)
T KOG0547|consen  439 YRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQWKE  517 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhchhh
Confidence            3456777777777776654 455556666666777777777777776666                            56


Q ss_pred             ChHHHHHHHhhcCCCCc---hhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          260 SLGRSLLVFFKLREKNL---LCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       260 ~~~~a~~~~~~~~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                      ++..|.+++++-.+-|+   ..|..|-.--...|+.++|.++|++-
T Consensus       518 d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEks  563 (606)
T KOG0547|consen  518 DINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKS  563 (606)
T ss_pred             hHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            66777777777665554   46888888889999999999999874

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=96.63  E-value=0.48  Score=42.47  Aligned_cols=128  Identities=12%  Similarity=-0.005  Sum_probs=93.0

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      ....|+.++|+..++++...               .+-|+.-+....+.+.+.|+.++    |.+.++.+...       
T Consensus       316 ~~~~~~~d~A~~~l~~L~~~---------------~P~N~~~~~~~~~i~~~~nk~~~----A~e~~~kal~l-------  369 (484)
T COG4783         316 TYLAGQYDEALKLLQPLIAA---------------QPDNPYYLELAGDILLEANKAKE----AIERLKKALAL-------  369 (484)
T ss_pred             HHHhcccchHHHHHHHHHHh---------------CCCCHHHHHHHHHHHHHcCChHH----HHHHHHHHHhc-------
Confidence            44788999999999998764               23445556666778999999999    66666554321       


Q ss_pred             HHHHHHHHHHHHHhhCCCCc-HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWD-IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                                       .|+ ...+-.+-.+|.+.|++.+|+.++.+-... .+-|+..|..|-.+|...|+..++....
T Consensus       370 -----------------~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~  431 (484)
T COG4783         370 -----------------DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLAR  431 (484)
T ss_pred             -----------------CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHH
Confidence                             233 344555678888999999999999998764 5678999999999999999998776544


Q ss_pred             Hh----hCChHHHHHHH
Q 044412          256 IY----CRSLGRSLLVF  268 (311)
Q Consensus       256 ~~----~~~~~~a~~~~  268 (311)
                      .+    .|+.+.|....
T Consensus       432 AE~~~~~G~~~~A~~~l  448 (484)
T COG4783         432 AEGYALAGRLEQAIIFL  448 (484)
T ss_pred             HHHHHhCCCHHHHHHHH
Confidence            33    44444444433

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=96.63  E-value=0.1  Score=52.25  Aligned_cols=179  Identities=10%  Similarity=0.059  Sum_probs=88.2

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCC--------CCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHH
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQE--------PNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQV  127 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--------~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  127 (311)
                      ..|-..|... ...+.++.|.+++++...        .-.-.|-+    -...|.-+...++|++..+.           
T Consensus      1459 i~WI~YMaf~-LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy----------- 1526 (1710)
T KOG1070|consen 1459 ILWIRYMAFH-LELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY----------- 1526 (1710)
T ss_pred             hHHHHHHHHH-hhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh-----------
Confidence            4555555555 566666666666555431        11112222    12223444555555555432           


Q ss_pred             HHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCCC--C---cH
Q 044412          128 WKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPA--W---DI  197 (311)
Q Consensus       128 ~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~~--~---~~  197 (311)
                           .-...+|..|..-|.+.+.+++|.++.+.+++... .....|...+..+.+.     |.+++.+-.+  |   .+
T Consensus      1527 -----cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv 1600 (1710)
T KOG1070|consen 1527 -----CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHV 1600 (1710)
T ss_pred             -----cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhH
Confidence                 23344555666666666666663333333333222 2233444444444443     4444433221  1   22


Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      ....-.+..-.+.|+.+.+..+|+..... .+--...|+..|+.=.+.|+.+.++.+|++
T Consensus      1601 ~~IskfAqLEFk~GDaeRGRtlfEgll~a-yPKRtDlW~VYid~eik~~~~~~vR~lfeR 1659 (1710)
T KOG1070|consen 1601 EFISKFAQLEFKYGDAERGRTLFEGLLSA-YPKRTDLWSVYIDMEIKHGDIKYVRDLFER 1659 (1710)
T ss_pred             HHHHHHHHHHhhcCCchhhHHHHHHHHhh-CccchhHHHHHHHHHHccCCHHHHHHHHHH
Confidence            22223333334567777777777776654 122345677777777777777777766665

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.62  E-value=0.041  Score=45.31  Aligned_cols=170  Identities=13%  Similarity=0.006  Sum_probs=102.1

Q ss_pred             cchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCee----e-eec---cccCCChhHHHHHHHHHHHCCCCchHHHHH
Q 044412           57 LDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVF----V-YHA---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQ  126 (311)
Q Consensus        57 p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~----~-~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~  126 (311)
                      .....+-.+...+ .+.|+++.|...|+++..  |+..    . +..   +...|++++|+..|+++.+.          
T Consensus        31 ~~~~~~~~~g~~~-~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~----------   99 (235)
T TIGR03302        31 WPAEELYEEAKEA-LDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL----------   99 (235)
T ss_pred             CCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH----------
Confidence            3445666666777 889999999999987653  3321    1 112   78889999999999998763          


Q ss_pred             HHHhcCCCc-hh---HHHHHHHHHHhC--------CCCccchHHHHHHhccCCC--CCH-hHHHHHHHHHHHHHHHHHhh
Q 044412          127 VWKNGFSSP-VF---VQTAMVDNYSYS--------NKFFESRRVSRRLFDEMPE--RKF-ATWNTMIDAYARLAELLFNK  191 (311)
Q Consensus       127 ~~~~g~~~~-~~---~~~~ll~~~~~~--------g~~~~a~~~a~~~~~~~~~--~~~-~~~~~li~~~~~~a~~~~~~  191 (311)
                            .|+ ..   .+..+-.++...        |+.++    |.+.++....  |+. ..+..+... ..    ....
T Consensus       100 ------~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~~p~~~~~~~a~~~~-~~----~~~~  164 (235)
T TIGR03302       100 ------HPNHPDADYAYYLRGLSNYNQIDRVDRDQTAARE----AFEAFQELIRRYPNSEYAPDAKKRM-DY----LRNR  164 (235)
T ss_pred             ------CcCCCchHHHHHHHHHHHHHhcccccCCHHHHHH----HHHHHHHHHHHCCCChhHHHHHHHH-HH----HHHH
Confidence                  232 11   333333444433        66777    4444444322  221 111111000 00    0000


Q ss_pred             CCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC--CCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          192 MPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSG--TGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       192 m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      .    ....-.+-..+.+.|++++|+..+++..+..  -+.....+..+..++...|+.++|..+++
T Consensus       165 ~----~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~  227 (235)
T TIGR03302       165 L----AGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAA  227 (235)
T ss_pred             H----HHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            0    0011244566888999999999999988752  22345788899999999999997776654

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=96.61  E-value=0.096  Score=48.36  Aligned_cols=199  Identities=11%  Similarity=0.078  Sum_probs=113.3

Q ss_pred             hccCChhHHHHhcccCCC--CCeeeeec-----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhH-HHHH
Q 044412           71 SRFHFIDYTILVFPQMQE--PNVFVYHA-----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFV-QTAM  142 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~--~~~~~~~~-----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~-~~~l  142 (311)
                      ...|++++|++.++.-..  .|..++..     +.+.|+.++|..+|+.+.+++                |+-.. |..+
T Consensus        15 ~e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN----------------Pdn~~Yy~~L   78 (517)
T PF12569_consen   15 EEAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN----------------PDNYDYYRGL   78 (517)
T ss_pred             HHCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC----------------CCcHHHHHHH
Confidence            677888888888866543  34334333     788888899999998887763                55444 4444


Q ss_pred             HHHHHhCCCCcc-chHHHHHHhccCCC--C--C-----------HhHHHHHHHHHHHHHHHHHhhCCCCcH-hHHHHHHH
Q 044412          143 VDNYSYSNKFFE-SRRVSRRLFDEMPE--R--K-----------FATWNTMIDAYARLAELLFNKMPAWDI-RSWTTMIT  205 (311)
Q Consensus       143 l~~~~~~g~~~~-a~~~a~~~~~~~~~--~--~-----------~~~~~~li~~~~~~a~~~~~~m~~~~~-~~y~~li~  205 (311)
                      ..+.+-...+.+ ..+...+++++...  |  +           ...|...+..|       +..+...++ .+|+.+-.
T Consensus        79 ~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~y-------l~~~l~KgvPslF~~lk~  151 (517)
T PF12569_consen   79 EEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEY-------LRPQLRKGVPSLFSNLKP  151 (517)
T ss_pred             HHHHhhhcccccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHH-------HHHHHhcCCchHHHHHHH
Confidence            444433321111 11114444443321  1  1           11222222222       222333333 35666666


Q ss_pred             HHHhCCChhHHHHHHHHHHhc----C----------CCCCH--HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHh
Q 044412          206 SYSQNKQFREALDAFNKTKKS----G----------TGSDQ--VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFF  269 (311)
Q Consensus       206 ~~~~~g~~~~a~~~~~~m~~~----g----------~~p~~--~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~  269 (311)
                      -|......+-..+++......    |          -.|+.  .++.-+-.-|...|+.+.|...             ++
T Consensus       152 Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~-------------Id  218 (517)
T PF12569_consen  152 LYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEY-------------ID  218 (517)
T ss_pred             HHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHH-------------HH
Confidence            666555555555666555432    1          13444  2455666777788888855544             33


Q ss_pred             hcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          270 KLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       270 ~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      +-.  .|+ +..|-+--+.+-..|++++|.+.++..+..
T Consensus       219 ~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~L  257 (517)
T PF12569_consen  219 KAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEAREL  257 (517)
T ss_pred             HHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence            322  466 567888888999999999999999887653

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=96.60  E-value=0.21  Score=41.02  Aligned_cols=162  Identities=11%  Similarity=0.000  Sum_probs=112.1

Q ss_pred             HhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCChhHHHHHHHHHHHCCCCchHHH
Q 044412           52 KTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVH  124 (311)
Q Consensus        52 ~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~  124 (311)
                      .....|+......+-..+ --.|+-+....+..+...  + |....+.    ..+.|++.+|...|++..+-        
T Consensus        59 ~~~~~p~d~~i~~~a~a~-~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l--------  129 (257)
T COG5010          59 AVLRNPEDLSIAKLATAL-YLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL--------  129 (257)
T ss_pred             HHhcCcchHHHHHHHHHH-HhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc--------
Confidence            344455333225555666 667777777777766432  1 1111111    78899999999999988664        


Q ss_pred             HHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHH
Q 044412          125 GQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMI  204 (311)
Q Consensus       125 ~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li  204 (311)
                             -++|...|+.+--+|-+.|++++    |+.-+.+..+                       +...+...+|.|-
T Consensus       130 -------~p~d~~~~~~lgaaldq~Gr~~~----Ar~ay~qAl~-----------------------L~~~~p~~~nNlg  175 (257)
T COG5010         130 -------APTDWEAWNLLGAALDQLGRFDE----ARRAYRQALE-----------------------LAPNEPSIANNLG  175 (257)
T ss_pred             -------CCCChhhhhHHHHHHHHccChhH----HHHHHHHHHH-----------------------hccCCchhhhhHH
Confidence                   37789999999999999999999    5555554221                       1112455677777


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      -.|.-.|+.+.|..++..-...+- -|...-..|.-.....|+++.|+++...
T Consensus       176 ms~~L~gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~i~~~  227 (257)
T COG5010         176 MSLLLRGDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAEDIAVQ  227 (257)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHhhccc
Confidence            778888999999999999877542 2566667777788899999988776543

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.59  E-value=0.021  Score=53.38  Aligned_cols=72  Identities=10%  Similarity=0.143  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      .++--|..|++.|+++.|+++-.+.  .|-+.+...|.+-..-.-..|.+.+|++++--.|.++.|.+.+++..
T Consensus       793 ~~~dai~my~k~~kw~da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~  864 (1636)
T KOG3616|consen  793 LFKDAIDMYGKAGKWEDAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHG  864 (1636)
T ss_pred             hhHHHHHHHhccccHHHHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhC
Confidence            4566799999999999999986654  45666677788877888888999999998888888888888887765

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=96.58  E-value=0.076  Score=43.55  Aligned_cols=150  Identities=12%  Similarity=0.067  Sum_probs=105.3

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.-.|+-+.+..+.......               ..-|....+.+.....+.|++..    |...+.+...++      
T Consensus        76 ~~~~G~a~~~l~~~~~~~~~---------------~~~d~~ll~~~gk~~~~~g~~~~----A~~~~rkA~~l~------  130 (257)
T COG5010          76 LYLRGDADSSLAVLQKSAIA---------------YPKDRELLAAQGKNQIRNGNFGE----AVSVLRKAARLA------  130 (257)
T ss_pred             HHhcccccchHHHHhhhhcc---------------CcccHHHHHHHHHHHHHhcchHH----HHHHHHHHhccC------
Confidence            44556666666665554322               34455666678888899999999    777766654432      


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                                       .+|-.+||.+--+|-+.|+.++|..-|.+-.+-  .| +...+|.|-..+.-.|+.+.|+.++
T Consensus       131 -----------------p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlgms~~L~gd~~~A~~ll  191 (257)
T COG5010         131 -----------------PTDWEAWNLLGAALDQLGRFDEARRAYRQALEL--APNEPSIANNLGMSLLLRGDLEDAETLL  191 (257)
T ss_pred             -----------------CCChhhhhHHHHHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHHHHHHHcCCHHHHHHHH
Confidence                             468899999999999999999999999988773  34 3455777777788889999887766


Q ss_pred             HhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHH
Q 044412          256 IYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFD  300 (311)
Q Consensus       256 ~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  300 (311)
                      .......          ..|...-+.+.......|++++|.++..
T Consensus       192 l~a~l~~----------~ad~~v~~NLAl~~~~~g~~~~A~~i~~  226 (257)
T COG5010         192 LPAYLSP----------AADSRVRQNLALVVGLQGDFREAEDIAV  226 (257)
T ss_pred             HHHHhCC----------CCchHHHHHHHHHHhhcCChHHHHhhcc
Confidence            4311111          2366666777777788888888877643

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=96.53  E-value=0.2  Score=44.79  Aligned_cols=105  Identities=10%  Similarity=0.163  Sum_probs=71.4

Q ss_pred             ChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCe--eeeec-c--ccCCChhHHHHHHH
Q 044412           39 SIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNV--FVYHA-F--SSLRHPLQAIAFYL  111 (311)
Q Consensus        39 ~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~--~~~~~-~--~~~~~~~~a~~~~~  111 (311)
                      ....++++|+...... ..+...|-..+.+= .++..+..|..+|+....  |.+  .=|.- +  -.-|++..|.++|+
T Consensus        88 e~~RARSv~ERALdvd-~r~itLWlkYae~E-mknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqife  165 (677)
T KOG1915|consen   88 EIQRARSVFERALDVD-YRNITLWLKYAEFE-MKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFE  165 (677)
T ss_pred             HHHHHHHHHHHHHhcc-cccchHHHHHHHHH-HhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHH
Confidence            3444467777766654 45667788888887 888888888888876531  211  11111 1  23467788888888


Q ss_pred             HHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhcc
Q 044412          112 YMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDE  165 (311)
Q Consensus       112 ~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~  165 (311)
                      ...+                +.|+...|++.|+.=.+...++.    |+++++.
T Consensus       166 rW~~----------------w~P~eqaW~sfI~fElRykeier----aR~IYer  199 (677)
T KOG1915|consen  166 RWME----------------WEPDEQAWLSFIKFELRYKEIER----ARSIYER  199 (677)
T ss_pred             HHHc----------------CCCcHHHHHHHHHHHHHhhHHHH----HHHHHHH
Confidence            7654                68888888888888888888888    5555554

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=96.53  E-value=0.074  Score=50.54  Aligned_cols=171  Identities=12%  Similarity=0.081  Sum_probs=100.0

Q ss_pred             cchhHHHHHHHHHhhccCChhHHHHhcccCCC-----------CCeeeeec-----cccCCChhHHHHHHHHHHHCCCCc
Q 044412           57 LDCFLAKQFISFCTSRFHFIDYTILVFPQMQE-----------PNVFVYHA-----FSSLRHPLQAIAFYLYMLRAEVLL  120 (311)
Q Consensus        57 p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----------~~~~~~~~-----~~~~~~~~~a~~~~~~m~~~~~~p  120 (311)
                      -+..+|..+.+.| .+..++|-|.-.+-.|..           .|..--.+     ....|..++|+.+|++-++..   
T Consensus       755 kS~~vW~nmA~Mc-VkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~e~eakvAvLAieLgMlEeA~~lYr~ckR~D---  830 (1416)
T KOG3617|consen  755 KSDSVWDNMASMC-VKTRRLDVAKVCLGHMKNARGARALRRAQQNGEEDEAKVAVLAIELGMLEEALILYRQCKRYD---  830 (1416)
T ss_pred             hhhHHHHHHHHHh-hhhccccHHHHhhhhhhhhhhHHHHHHHHhCCcchhhHHHHHHHHHhhHHHHHHHHHHHHHHH---
Confidence            3567899999999 999999999998888863           11111111     566788999999998876542   


Q ss_pred             hHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH----------HHHHHHHH------
Q 044412          121 TTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT----------MIDAYARL------  184 (311)
Q Consensus       121 ~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~----------li~~~~~~------  184 (311)
                                          .|=..|-..|++++|.++|+.--.--.+....-|.-          -|..|-+.      
T Consensus       831 --------------------LlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafe  890 (1416)
T KOG3617|consen  831 --------------------LLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFE  890 (1416)
T ss_pred             --------------------HHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHH
Confidence                                233346666778885555443211111111111111          11222221      


Q ss_pred             -----------HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHH
Q 044412          185 -----------AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRG  253 (311)
Q Consensus       185 -----------a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~  253 (311)
                                 .+...+++.+|  ..|.-.-.-+-..|+.+.|+.+|..-+.         |-++++..|-.|+.++|.+
T Consensus       891 v~rmL~e~p~~~e~Yv~~~~d~--~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~  959 (1416)
T KOG3617|consen  891 VFRMLKEYPKQIEQYVRRKRDE--SLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAAR  959 (1416)
T ss_pred             HHHHHHhChHHHHHHHHhccch--HHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeEeeccCchHHHH
Confidence                       22222333333  3333333333346888888888887653         5567777888899998888


Q ss_pred             HHHhhCChH
Q 044412          254 IQIYCRSLG  262 (311)
Q Consensus       254 ~~~~~~~~~  262 (311)
                      +-++.|+..
T Consensus       960 iA~esgd~A  968 (1416)
T KOG3617|consen  960 IAEESGDKA  968 (1416)
T ss_pred             HHHhcccHH
Confidence            876644443

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=96.49  E-value=0.034  Score=51.81  Aligned_cols=66  Identities=9%  Similarity=-0.048  Sum_probs=43.2

Q ss_pred             HhhhhhcCCCCCchh-hhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhccc
Q 044412           10 ITSFKKNSFPTSVSF-IRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQ   85 (311)
Q Consensus        10 ~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~   85 (311)
                      .+.++-...|+.++. ...+.+..++.++|-.+.+..+++.         +..|.-+|.+| ...|+..+|..+..+
T Consensus       383 ~nRlsy~ya~~lpp~Wq~q~~laell~slGitksAl~I~Er---------lemw~~vi~CY-~~lg~~~kaeei~~q  449 (777)
T KOG1128|consen  383 LNRLSYIYAPHLPPIWQLQRLLAELLLSLGITKSALVIFER---------LEMWDPVILCY-LLLGQHGKAEEINRQ  449 (777)
T ss_pred             HhcccccccCCCCCcchHHHHHHHHHHHcchHHHHHHHHHh---------HHHHHHHHHHH-HHhcccchHHHHHHH
Confidence            344454455555554 3467889999999999999777763         34566666666 666666666655533

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=96.46  E-value=0.021  Score=42.44  Aligned_cols=30  Identities=17%  Similarity=0.119  Sum_probs=17.5

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      +..+|..+-..|...|+.++|...|++..+
T Consensus        84 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        84 DPRPYFHAAECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444455556666666666666666555

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=96.41  E-value=0.063  Score=50.13  Aligned_cols=156  Identities=13%  Similarity=0.116  Sum_probs=90.2

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHh-hCC-CCcHhHHHHHHHHHHh
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFN-KMP-AWDIRSWTTMITSYSQ  209 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~-~m~-~~~~~~y~~li~~~~~  209 (311)
                      ..-..+-..+.+.|-...    |..++++..     .|...|..|+..     |..+.. +.. +||...|..+.+....
T Consensus       399 q~q~~laell~slGitks----Al~I~Erle-----mw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d  469 (777)
T KOG1128|consen  399 QLQRLLAELLLSLGITKS----ALVIFERLE-----MWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHD  469 (777)
T ss_pred             hHHHHHHHHHHHcchHHH----HHHHHHhHH-----HHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccC
Confidence            333444555666666666    555554422     233333333332     333322 222 4677778777777766


Q ss_pred             CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHH
Q 044412          210 NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVF  268 (311)
Q Consensus       210 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~  268 (311)
                      ..-+++|.++++.....    -...++.+   ..+.++++++.+.|+.                     +++...|-+.|
T Consensus       470 ~s~yEkawElsn~~sar----A~r~~~~~---~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF  542 (777)
T KOG1128|consen  470 PSLYEKAWELSNYISAR----AQRSLALL---ILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAF  542 (777)
T ss_pred             hHHHHHHHHHhhhhhHH----HHHhhccc---cccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHH
Confidence            67778888888775432    00011111   1124555555555554                     56666666666


Q ss_pred             hhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 044412          269 FKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMTYENVR  308 (311)
Q Consensus       269 ~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  308 (311)
                      ..-.  +|| ...||.+-.+|.+.|+-.+|...+.+-.+-+..
T Consensus       543 ~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~  585 (777)
T KOG1128|consen  543 HRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQ  585 (777)
T ss_pred             HHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCC
Confidence            5554  565 567999999999999999999888887765543

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=96.38  E-value=0.026  Score=50.12  Aligned_cols=117  Identities=9%  Similarity=0.004  Sum_probs=89.7

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~~   99 (311)
                      ..++...+..-++.+.+..+++.+.+..  |+  ....+.+.+ ...++-.+|.+++++..+.+...+..       +.+
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~-l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVY-LLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHH-HhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence            3467777788888888899999988875  44  445577777 77788888888887765422222222       788


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCC
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE  168 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~  168 (311)
                      .++.+.|+++.++..+.                .|+ ..+|..|..+|.+.|+++.    |...++.++.
T Consensus       247 k~~~~lAL~iAk~av~l----------------sP~~f~~W~~La~~Yi~~~d~e~----ALlaLNs~Pm  296 (395)
T PF09295_consen  247 KKKYELALEIAKKAVEL----------------SPSEFETWYQLAECYIQLGDFEN----ALLALNSCPM  296 (395)
T ss_pred             cCCHHHHHHHHHHHHHh----------------CchhHHHHHHHHHHHHhcCCHHH----HHHHHhcCcC
Confidence            89999999999998763                555 5699999999999999999    8888887763

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=96.36  E-value=0.093  Score=42.09  Aligned_cols=96  Identities=9%  Similarity=0.103  Sum_probs=74.1

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHH-hccCC--hhhHHHHHHhhCChHHHHHHHhh
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSAC-AHLGA--LDLGRGIQIYCRSLGRSLLVFFK  270 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~-~~~~~--~~~a~~~~~~~~~~~~a~~~~~~  270 (311)
                      .|...|..+-..|...|++++|...|++..+.  .| +...+..+-.++ ...|+  .++|             .+++++
T Consensus        71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l--~P~~~~~~~~lA~aL~~~~g~~~~~~A-------------~~~l~~  135 (198)
T PRK10370         71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQL--RGENAELYAALATVLYYQAGQHMTPQT-------------REMIDK  135 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCCCCcHHH-------------HHHHHH
Confidence            47788999999999999999999999998874  45 566666666654 56666  3644             444444


Q ss_pred             cC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          271 LR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       271 ~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..  .| ++..+..+-..+...|++++|...|+++.+.
T Consensus       136 al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        136 ALALDANEVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            43  23 5678899999999999999999999999764

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=96.31  E-value=0.23  Score=39.78  Aligned_cols=142  Identities=10%  Similarity=0.082  Sum_probs=89.8

Q ss_pred             HHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHH
Q 044412           65 FISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVD  144 (311)
Q Consensus        65 ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~  144 (311)
                      -+..| ...|+++.+....+.+..|.    +.+...++.++++..++...+..               +.|...|..+-.
T Consensus        22 ~~~~Y-~~~g~~~~v~~~~~~~~~~~----~~~~~~~~~~~~i~~l~~~L~~~---------------P~~~~~w~~Lg~   81 (198)
T PRK10370         22 CVGSY-LLSPKWQAVRAEYQRLADPL----HQFASQQTPEAQLQALQDKIRAN---------------PQNSEQWALLGE   81 (198)
T ss_pred             HHHHH-HHcchHHHHHHHHHHHhCcc----ccccCchhHHHHHHHHHHHHHHC---------------CCCHHHHHHHHH
Confidence            34566 77888887766654433321    11334566677777777765542               566888999999


Q ss_pred             HHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHH-HhCCC--hhHHHHHHH
Q 044412          145 NYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSY-SQNKQ--FREALDAFN  221 (311)
Q Consensus       145 ~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~-~~~g~--~~~a~~~~~  221 (311)
                      .|...|++++    |...++.....+                       ..+...+..+-.++ ...|+  .++|.++++
T Consensus        82 ~~~~~g~~~~----A~~a~~~Al~l~-----------------------P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~  134 (198)
T PRK10370         82 YYLWRNDYDN----ALLAYRQALQLR-----------------------GENAELYAALATVLYYQAGQHMTPQTREMID  134 (198)
T ss_pred             HHHHCCCHHH----HHHHHHHHHHhC-----------------------CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHH
Confidence            9999999999    666665433211                       12455666666653 45565  478888888


Q ss_pred             HHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHH
Q 044412          222 KTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       222 ~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      +..+.  .| +...+..+-.++...|++++|...+
T Consensus       135 ~al~~--dP~~~~al~~LA~~~~~~g~~~~Ai~~~  167 (198)
T PRK10370        135 KALAL--DANEVTALMLLASDAFMQADYAQAIELW  167 (198)
T ss_pred             HHHHh--CCCChhHHHHHHHHHHHcCCHHHHHHHH
Confidence            87764  33 4456666666777777777555444

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=96.26  E-value=0.16  Score=38.44  Aligned_cols=116  Identities=11%  Similarity=0.109  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHH----HHHHHhhCCC--CcH----hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH--HHHHHHHH
Q 044412          173 TWNTMIDAYARL----AELLFNKMPA--WDI----RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ--VTMATVLS  240 (311)
Q Consensus       173 ~~~~li~~~~~~----a~~~~~~m~~--~~~----~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~li~  240 (311)
                      .|..++..+...    +...++.+..  |+.    ...-.+-..+...|++++|...|+......-.|+.  ...-.|-.
T Consensus        14 ~y~~~~~~~~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~   93 (145)
T PF09976_consen   14 LYEQALQALQAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLAR   93 (145)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHH
Confidence            344555555332    4444555542  222    12222446677889999999999999987623322  23334566


Q ss_pred             HHhccCChhhHHHHHHhhCChHHHHHHHhhcCC--CCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          241 ACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE--KNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       241 a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      .+...|+++.|..             .++....  .....+...-+.|.+.|++++|...|+.
T Consensus        94 ~~~~~~~~d~Al~-------------~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   94 ILLQQGQYDEALA-------------TLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHcCCHHHHHH-------------HHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            6677777775544             4444332  2334667778889999999999999875

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.22  E-value=0.13  Score=44.42  Aligned_cols=119  Identities=10%  Similarity=0.008  Sum_probs=70.5

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH----HHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL----AELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~----a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      .+.-|.-+...|+...    |..+..+..-|+-.-|-..|.+++..    -.+-|..- ..++.-|-..+..|.+.|...
T Consensus       180 l~~Ti~~li~~~~~k~----A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s-kKsPIGyepFv~~~~~~~~~~  254 (319)
T PF04840_consen  180 LNDTIRKLIEMGQEKQ----AEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS-KKSPIGYEPFVEACLKYGNKK  254 (319)
T ss_pred             HHHHHHHHHHCCCHHH----HHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC-CCCCCChHHHHHHHHHCCCHH
Confidence            3334455555565555    55555554545555555555555544    11111111 234567888888888888888


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      +|..+...+          ++..-+..|.+.|++.+|.+.-...++.+.-..+.+..+
T Consensus       255 eA~~yI~k~----------~~~~rv~~y~~~~~~~~A~~~A~~~kd~~~L~~i~~~~~  302 (319)
T PF04840_consen  255 EASKYIPKI----------PDEERVEMYLKCGDYKEAAQEAFKEKDIDLLKQILKRCP  302 (319)
T ss_pred             HHHHHHHhC----------ChHHHHHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHCC
Confidence            888888772          224556778888888888776555555555555544444

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=96.22  E-value=0.022  Score=43.12  Aligned_cols=71  Identities=14%  Similarity=0.211  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHH
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREA  216 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a  216 (311)
                      +...++..+...|++++|.+++...+..                            +| |...|..+|.+|...|+..+|
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~----------------------------dP~~E~~~~~lm~~~~~~g~~~~A  115 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALAL----------------------------DPYDEEAYRLLMRALAAQGRRAEA  115 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH----------------------------STT-HHHHHHHHHHHHHTT-HHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhc----------------------------CCCCHHHHHHHHHHHHHCcCHHHH
Confidence            5566788888999999966666666554                            33 678999999999999999999


Q ss_pred             HHHHHHHHh-----cCCCCCHHHHH
Q 044412          217 LDAFNKTKK-----SGTGSDQVTMA  236 (311)
Q Consensus       217 ~~~~~~m~~-----~g~~p~~~t~~  236 (311)
                      .++|+++.+     -|+.|+..|-.
T Consensus       116 ~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen  116 LRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            999999753     59999987743

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=96.15  E-value=1.2  Score=41.79  Aligned_cols=119  Identities=9%  Similarity=0.011  Sum_probs=68.3

Q ss_pred             HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh-----------
Q 044412          185 AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL-----------  250 (311)
Q Consensus       185 a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~-----------  250 (311)
                      |+.+|++-.  .| |...|-..|..=.+.|..+.|..+..+-.+. ++-+...|.--|-...+.+.--.           
T Consensus       738 AR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~rkTks~DALkkce~d  816 (913)
T KOG0495|consen  738 ARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHD  816 (913)
T ss_pred             HHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcccchHHHHHHHhccCC
Confidence            666666443  33 5667888888888888888887766665542 22222233322222222211111           


Q ss_pred             ------HHHHHHhhCChHHHHHHHhhcC--CCCc-hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          251 ------GRGIQIYCRSLGRSLLVFFKLR--EKNL-LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       251 ------a~~~~~~~~~~~~a~~~~~~~~--~p~~-~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                            +-.+|-.-.+.+.|...|.+-.  .||. .+|--+..-+.++|.-++-.+++..-..
T Consensus       817 phVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~~~c~~  879 (913)
T KOG0495|consen  817 PHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVLKKCET  879 (913)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence                  1122323556667777777766  3433 5788888888888877777777766543

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=96.15  E-value=1  Score=41.11  Aligned_cols=106  Identities=10%  Similarity=0.085  Sum_probs=84.6

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHh-------------------
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIY-------------------  257 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~-------------------  257 (311)
                      .+|...|..--+..-+..|..+|.+.++.+..+ ..+.+++++.-+|. ++.+-|-++|+.                   
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~d~p~yv~~YldfL  445 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFGDSPEYVLKYLDFL  445 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            367777777777777889999999999988888 77788888886664 677788888887                   


Q ss_pred             --hCChHHHHHHHhhcCCC------CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          258 --CRSLGRSLLVFFKLREK------NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       258 --~~~~~~a~~~~~~~~~p------~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                        .++-..+..+|++..+.      ....|+.+|+-=..-|+...+.++-+++..
T Consensus       446 ~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  446 SHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence              66777788888877632      347899999999999999999888777653

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.11  E-value=0.8  Score=39.59  Aligned_cols=96  Identities=9%  Similarity=0.035  Sum_probs=54.5

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHH-HHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMA-TVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK  274 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~-~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p  274 (311)
                      |.+-|| +-.+++..|.+.+|+++|-......++ |..+|. .|.++|.+++..+.|+.++-......++          
T Consensus       393 D~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~~e~----------  460 (557)
T KOG3785|consen  393 DDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNTPSER----------  460 (557)
T ss_pred             chhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCCchhH----------
Confidence            444443 567778888888888888776544344 344544 5557777877777555544332222221          


Q ss_pred             CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          275 NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       275 ~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                       ......+-.-|.+.+.+--|.+.|+.+..
T Consensus       461 -fsLLqlIAn~CYk~~eFyyaaKAFd~lE~  489 (557)
T KOG3785|consen  461 -FSLLQLIANDCYKANEFYYAAKAFDELEI  489 (557)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHhhhHHHc
Confidence             12233344455566666666666655544

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.11  E-value=0.051  Score=45.18  Aligned_cols=90  Identities=10%  Similarity=0.182  Sum_probs=61.8

Q ss_pred             HHHHhccCC--CCCHhHHHHHHHHHHHH-------------HHHHHhhC-CCCcHhHHHHHHHHHHhCCC----------
Q 044412          159 SRRLFDEMP--ERKFATWNTMIDAYARL-------------AELLFNKM-PAWDIRSWTTMITSYSQNKQ----------  212 (311)
Q Consensus       159 a~~~~~~~~--~~~~~~~~~li~~~~~~-------------a~~~~~~m-~~~~~~~y~~li~~~~~~g~----------  212 (311)
                      .+..|...+  ++|-.+|-+.+..+...             |.+...+. .++|..+|+.||..+-+...          
T Consensus        53 ~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F  132 (406)
T KOG3941|consen   53 VEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVF  132 (406)
T ss_pred             hhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHH
Confidence            444555444  45556666666665543             22222222 25788888888887766432          


Q ss_pred             ------hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          213 ------FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       213 ------~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                            -+-+++++++|..+|+.||..+=-.|++++++.+-.
T Consensus       133 ~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  133 LHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence                  256789999999999999999999999999997754

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=96.07  E-value=0.03  Score=41.27  Aligned_cols=32  Identities=16%  Similarity=0.105  Sum_probs=29.9

Q ss_pred             CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          273 EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       273 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .|+..+-.+++.+|+..|++..|+++++...+
T Consensus        49 ~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen   49 YPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            58999999999999999999999999999765

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=96.04  E-value=0.044  Score=36.74  Aligned_cols=90  Identities=12%  Similarity=0.145  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHH
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALD  218 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~  218 (311)
                      +..+...+...|++++    |...++......                       ..+...+..+...+...|++++|.+
T Consensus         3 ~~~~a~~~~~~~~~~~----A~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~a~~   55 (100)
T cd00189           3 LLNLGNLYYKLGDYDE----ALEYYEKALELD-----------------------PDNADAYYNLAAAYYKLGKYEEALE   55 (100)
T ss_pred             HHHHHHHHHHHhcHHH----HHHHHHHHHhcC-----------------------CccHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556677788888999    555554432211                       1234567777788888899999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          219 AFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       219 ~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      .|....+.+ +.+..++..+...+...|+.+.|...+.
T Consensus        56 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~   92 (100)
T cd00189          56 DYEKALELD-PDNAKAYYNLGLAYYKLGKYEEALEAYE   92 (100)
T ss_pred             HHHHHHhCC-CcchhHHHHHHHHHHHHHhHHHHHHHHH
Confidence            999887753 3344677788888888888887766553

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=95.99  E-value=0.066  Score=51.28  Aligned_cols=131  Identities=10%  Similarity=-0.011  Sum_probs=98.7

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcch-hHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------cc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDC-FLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------FS   98 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~-~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~   98 (311)
                      +..+..+....|+.++++.+++...+.  .||. .....+...+ .+.+++++|+...++..+.+..+...       +.
T Consensus        89 ~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L-~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~  165 (694)
T PRK15179         89 QVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGV-KRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWD  165 (694)
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHH-HHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Confidence            568888999999999999999988876  4544 5566677778 99999999999999987543333333       88


Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC---CCHhHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE---RKFATWN  175 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~---~~~~~~~  175 (311)
                      ..|++++|..+|++....+               .-+..++.++-.++-+.|+.++    |...|+...+   ++.--|+
T Consensus       166 ~~g~~~~A~~~y~~~~~~~---------------p~~~~~~~~~a~~l~~~G~~~~----A~~~~~~a~~~~~~~~~~~~  226 (694)
T PRK15179        166 EIGQSEQADACFERLSRQH---------------PEFENGYVGWAQSLTRRGALWR----ARDVLQAGLDAIGDGARKLT  226 (694)
T ss_pred             HhcchHHHHHHHHHHHhcC---------------CCcHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhhCcchHHHH
Confidence            9999999999999997642               3347788889999999999999    6665654432   3444444


Q ss_pred             HHHH
Q 044412          176 TMID  179 (311)
Q Consensus       176 ~li~  179 (311)
                      ..+.
T Consensus       227 ~~~~  230 (694)
T PRK15179        227 RRLV  230 (694)
T ss_pred             HHHH
Confidence            4433

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=95.95  E-value=0.2  Score=46.48  Aligned_cols=193  Identities=11%  Similarity=0.099  Sum_probs=114.4

Q ss_pred             HHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHH
Q 044412           47 YATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQ  126 (311)
Q Consensus        47 ~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~  126 (311)
                      .+.+.+.|-.|+......   .| +-.|.+.+|-++|.              ++|.-..|+++|.+|+--..     .++
T Consensus       623 L~~~k~rge~P~~iLlA~---~~-Ay~gKF~EAAklFk--------------~~G~enRAlEmyTDlRMFD~-----aQE  679 (1081)
T KOG1538|consen  623 LEERKKRGETPNDLLLAD---VF-AYQGKFHEAAKLFK--------------RSGHENRALEMYTDLRMFDY-----AQE  679 (1081)
T ss_pred             HHHHHhcCCCchHHHHHH---HH-HhhhhHHHHHHHHH--------------HcCchhhHHHHHHHHHHHHH-----HHH
Confidence            346677888888765443   34 55688888888885              45666677777766643210     011


Q ss_pred             HHHhc--------------CCCchhHHHHHHHHHHhCCCCccchHHH------HHHhc---cCCCCCHhHHHHHHHHHHH
Q 044412          127 VWKNG--------------FSSPVFVQTAMVDNYSYSNKFFESRRVS------RRLFD---EMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       127 ~~~~g--------------~~~~~~~~~~ll~~~~~~g~~~~a~~~a------~~~~~---~~~~~~~~~~~~li~~~~~  183 (311)
                      ....|              +.-+..-=.+.-.++...|+.++|..+.      .-+++   .....+..+.- .+..|.+
T Consensus       680 ~~~~g~~~eKKmL~RKRA~WAr~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~-~~a~ylk  758 (1081)
T KOG1538|consen  680 FLGSGDPKEKKMLIRKRADWARNIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLL-LCATYLK  758 (1081)
T ss_pred             HhhcCChHHHHHHHHHHHHHhhhcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHH-HHHHHHh
Confidence            11111              1001000022345566778887754441      11111   11111222222 2223333


Q ss_pred             H------HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          184 L------AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       184 ~------a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      .      |-++|..|.+-     -.+++.....+++.+|+.+-+...+  +.||..  ..--+-++...++++|.+.|..
T Consensus       759 ~l~~~gLAaeIF~k~gD~-----ksiVqlHve~~~W~eAFalAe~hPe--~~~dVy--~pyaqwLAE~DrFeEAqkAfhk  829 (1081)
T KOG1538|consen  759 KLDSPGLAAEIFLKMGDL-----KSLVQLHVETQRWDEAFALAEKHPE--FKDDVY--MPYAQWLAENDRFEEAQKAFHK  829 (1081)
T ss_pred             hccccchHHHHHHHhccH-----HHHhhheeecccchHhHhhhhhCcc--cccccc--chHHHHhhhhhhHHHHHHHHHH
Confidence            2      88888888742     2456677788999999999888765  355543  2333556788899999999999


Q ss_pred             hCChHHHHHHHhhcC
Q 044412          258 CRSLGRSLLVFFKLR  272 (311)
Q Consensus       258 ~~~~~~a~~~~~~~~  272 (311)
                      .|+-.+|.++++++.
T Consensus       830 AGr~~EA~~vLeQLt  844 (1081)
T KOG1538|consen  830 AGRQREAVQVLEQLT  844 (1081)
T ss_pred             hcchHHHHHHHHHhh
Confidence            999999999998876

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=95.89  E-value=0.54  Score=35.88  Aligned_cols=106  Identities=7%  Similarity=-0.108  Sum_probs=67.9

Q ss_pred             HHHhhCC-CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH-HHHHHHHHHHhccCChhhHHHHHHhhCChHHH
Q 044412          187 LLFNKMP-AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ-VTMATVLSACAHLGALDLGRGIQIYCRSLGRS  264 (311)
Q Consensus       187 ~~~~~m~-~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a  264 (311)
                      .++..+. ..+....-.+-.-+...|++++|..+|+-...  +-|.. .-|-.|=-+|-..|++++|...+.....++  
T Consensus        24 ~~l~~~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~--~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~--   99 (157)
T PRK15363         24 RMLLDDDVTQPLNTLYRYAMQLMEVKEFAGAARLFQLLTI--YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK--   99 (157)
T ss_pred             HHHHCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--
Confidence            3344444 33333333444555677899999999888765  34444 344555555666788887766664433333  


Q ss_pred             HHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          265 LLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       265 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                              ..|+..+-.+-.++...|+.+.|.+-|+.-+.
T Consensus       100 --------~ddp~~~~~ag~c~L~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363        100 --------IDAPQAPWAAAECYLACDNVCYAIKALKAVVR  131 (157)
T ss_pred             --------CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                    24677788888888888888888888876543

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=95.87  E-value=0.058  Score=45.87  Aligned_cols=133  Identities=17%  Similarity=0.121  Sum_probs=85.0

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHH
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREA  216 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a  216 (311)
                      .+|..++...-+.+.++.    |+.+|.+..+.+..                     ..++....++|.-+ ..++.+.|
T Consensus         2 ~v~i~~m~~~~r~~g~~~----aR~vF~~a~~~~~~---------------------~~~vy~~~A~~E~~-~~~d~~~A   55 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEA----ARKVFKRARKDKRC---------------------TYHVYVAYALMEYY-CNKDPKRA   55 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHH----HHHHHHHHHCCCCS----------------------THHHHHHHHHHHH-TCS-HHHH
T ss_pred             HHHHHHHHHHHHhCChHH----HHHHHHHHHcCCCC---------------------CHHHHHHHHHHHHH-hCCCHHHH
Confidence            467777777777777777    77777664322111                     12344555555543 34677889


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHHHHHhcCChHHH
Q 044412          217 LDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITEALAIHGFAHEA  295 (311)
Q Consensus       217 ~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a  295 (311)
                      .++|+...+. +.-+..-|..-+.-+.+.++.+.|+.+|+.+-..-..        +. -...|...++-=.+.|+.+.+
T Consensus        56 ~~Ife~glk~-f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~~--------~~~~~~iw~~~i~fE~~~Gdl~~v  126 (280)
T PF05843_consen   56 RKIFERGLKK-FPSDPDFWLEYLDFLIKLNDINNARALFERAISSLPK--------EKQSKKIWKKFIEFESKYGDLESV  126 (280)
T ss_dssp             HHHHHHHHHH-HTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSSC--------HHHCHHHHHHHHHHHHHHS-HHHH
T ss_pred             HHHHHHHHHH-CCCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcCc--------hhHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999998775 5666777777788888888888777666552111000        11 234788889888899999999


Q ss_pred             HHHHHHHHH
Q 044412          296 LGMFDRMTY  304 (311)
Q Consensus       296 ~~~~~~M~~  304 (311)
                      ..+.+++.+
T Consensus       127 ~~v~~R~~~  135 (280)
T PF05843_consen  127 RKVEKRAEE  135 (280)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988888865

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.86  E-value=0.35  Score=37.53  Aligned_cols=123  Identities=9%  Similarity=-0.010  Sum_probs=78.9

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCC
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~  212 (311)
                      ....|..+...+...|++++    |...++.....                      .+.+  ...+|..+-..+...|+
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~----A~~~~~~al~l----------------------~~~~~~~~~~~~~lg~~~~~~g~   87 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAE----ALQNYYEAMRL----------------------EIDPYDRSYILYNIGLIHTSNGE   87 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhc----------------------cccchhhHHHHHHHHHHHHHcCC
Confidence            35566777778888999999    55555543210                      0111  23478888899999999


Q ss_pred             hhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHh-------ccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHH
Q 044412          213 FREALDAFNKTKKSGTGSD-QVTMATVLSACA-------HLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITE  284 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~-------~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~  284 (311)
                      +++|+..+++..+.  .|+ ..++..+...+.       ..|+++.|...+      ++|..+|++....++..+.....
T Consensus        88 ~~eA~~~~~~Al~~--~~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~------~~a~~~~~~a~~~~p~~~~~~~~  159 (168)
T CHL00033         88 HTKALEYYFQALER--NPFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWF------DQAAEYWKQAIALAPGNYIEAQN  159 (168)
T ss_pred             HHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHH------HHHHHHHHHHHHhCcccHHHHHH
Confidence            99999999998764  333 455666666666       666777665443      45666666665555554454444


Q ss_pred             HHHhcCC
Q 044412          285 ALAIHGF  291 (311)
Q Consensus       285 ~~~~~g~  291 (311)
                      -+...|+
T Consensus       160 ~~~~~~~  166 (168)
T CHL00033        160 WLKITGR  166 (168)
T ss_pred             HHHHhcC
Confidence            4444444

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.73  E-value=0.093  Score=46.92  Aligned_cols=48  Identities=6%  Similarity=-0.012  Sum_probs=22.3

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC
Q 044412           38 SSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ   87 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~   87 (311)
                      |+...++.-++..++....++. .|-.+-..| ....+.++..+.|+...
T Consensus       340 g~~~~a~~d~~~~I~l~~~~~~-lyI~~a~~y-~d~~~~~~~~~~F~~A~  387 (606)
T KOG0547|consen  340 GDSLGAQEDFDAAIKLDPAFNS-LYIKRAAAY-ADENQSEKMWKDFNKAE  387 (606)
T ss_pred             CCchhhhhhHHHHHhcCcccch-HHHHHHHHH-hhhhccHHHHHHHHHHH
Confidence            3444444555555544333222 133333445 55556666666665544

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=95.71  E-value=0.38  Score=47.17  Aligned_cols=28  Identities=7%  Similarity=-0.037  Sum_probs=17.8

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .++--+-..|-...+|+++..+++...+
T Consensus       224 ~~~~~l~~~y~~~~~~~~~i~iLK~iL~  251 (906)
T PRK14720        224 GLLEDLYEPYKALEDWDEVIYILKKILE  251 (906)
T ss_pred             HHHHHHHHHHhhhhhhhHHHHHHHHHHh
Confidence            3444555566666677777777777654

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.68  E-value=0.97  Score=37.25  Aligned_cols=172  Identities=12%  Similarity=0.105  Sum_probs=110.9

Q ss_pred             ChhhHHHHHHHHHH---hc-cCcch-hHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec-------cccCCChhHH
Q 044412           39 SIKELECVYATIVK---TN-ANLDC-FLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA-------FSSLRHPLQA  106 (311)
Q Consensus        39 ~~~~~~~l~~~m~~---~g-~~p~~-~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~~~~~~~~a  106 (311)
                      +.+++.+++..+..   +| ..++. ..|..++-+. ...|+.+.|...++++...=.-++..       +--.|++++|
T Consensus        27 nseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAA-ld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~~~~A  105 (289)
T KOG3060|consen   27 NSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAA-LDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGNYKEA  105 (289)
T ss_pred             CHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHH-HHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhchhhH
Confidence            55556667766663   34 55555 4566777777 88999999999998876432333333       6677899999


Q ss_pred             HHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHH
Q 044412          107 IAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAE  186 (311)
Q Consensus       107 ~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~  186 (311)
                      +++|+.+.+..               +.|..+|-.=+...-..|+--+|++-....++...                   
T Consensus       106 ~e~y~~lL~dd---------------pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~-------------------  151 (289)
T KOG3060|consen  106 IEYYESLLEDD---------------PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFM-------------------  151 (289)
T ss_pred             HHHHHHHhccC---------------cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhc-------------------
Confidence            99999987763               55666666666666666665563333333322211                   


Q ss_pred             HHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH-HHHHHHHHHHhc---cCChhhHHHHH
Q 044412          187 LLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ-VTMATVLSACAH---LGALDLGRGIQ  255 (311)
Q Consensus       187 ~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~a~~~---~~~~~~a~~~~  255 (311)
                              .|...|.-+-+-|...|++++|.-.++++.-.  .|.. .-|..+-..+-.   ..+.+.+++.+
T Consensus       152 --------~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~--~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy  214 (289)
T KOG3060|consen  152 --------NDQEAWHELAEIYLSEGDFEKAAFCLEELLLI--QPFNPLYFQRLAEVLYTQGGAENLELARKYY  214 (289)
T ss_pred             --------CcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence                    26788999999999999999999999998863  4543 333444443333   33444444443

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=95.63  E-value=0.097  Score=46.18  Aligned_cols=101  Identities=9%  Similarity=0.085  Sum_probs=74.5

Q ss_pred             ccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHH
Q 044412           98 SSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTM  177 (311)
Q Consensus        98 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~l  177 (311)
                      ...|++++|++.|++..+..               +-+...|..+-.+|.+.|++++|...+.+.++.            
T Consensus        13 ~~~~~~~~Ai~~~~~Al~~~---------------P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l------------   65 (356)
T PLN03088         13 FVDDDFALAVDLYTQAIDLD---------------PNNAELYADRAQANIKLGNFTEAVADANKAIEL------------   65 (356)
T ss_pred             HHcCCHHHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh------------
Confidence            36789999999999987642               345677888888999999999944444444332            


Q ss_pred             HHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 044412          178 IDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSAC  242 (311)
Q Consensus       178 i~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~  242 (311)
                                     ...+...|..+-.+|...|++++|+..|++..+  +.|+.......+..|
T Consensus        66 ---------------~P~~~~a~~~lg~~~~~lg~~~eA~~~~~~al~--l~P~~~~~~~~l~~~  113 (356)
T PLN03088         66 ---------------DPSLAKAYLRKGTACMKLEEYQTAKAALEKGAS--LAPGDSRFTKLIKEC  113 (356)
T ss_pred             ---------------CcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHH
Confidence                           112566788888889999999999999999887  457666655555444

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.57  E-value=0.72  Score=38.92  Aligned_cols=165  Identities=11%  Similarity=0.112  Sum_probs=100.9

Q ss_pred             ccChhhHHHHHHHHHHhccCc-chhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec-----cccCCChhHHHH
Q 044412           37 CSSIKELECVYATIVKTNANL-DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA-----FSSLRHPLQAIA  108 (311)
Q Consensus        37 ~~~~~~~~~l~~~m~~~g~~p-~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~-----~~~~~~~~~a~~  108 (311)
                      -.+..++.++...-.+.  .| +....+.|-.+| -...++..|-..++++.+  |...-|..     +.+++.+..|++
T Consensus        23 d~ry~DaI~~l~s~~Er--~p~~rAgLSlLgyCY-Y~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A~i~ADALr   99 (459)
T KOG4340|consen   23 DARYADAIQLLGSELER--SPRSRAGLSLLGYCY-YRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKACIYADALR   99 (459)
T ss_pred             HhhHHHHHHHHHHHHhc--CccchHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcccHHHHH
Confidence            34455554444333332  34 556666666777 888889999999988864  44444444     777888888988


Q ss_pred             HHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHH--HHhCCCCccchHHHHHHhccCCC-CCHhHHHHHHHHHH--H
Q 044412          109 FYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDN--YSYSNKFFESRRVSRRLFDEMPE-RKFATWNTMIDAYA--R  183 (311)
Q Consensus       109 ~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~--~~~~g~~~~a~~~a~~~~~~~~~-~~~~~~~~li~~~~--~  183 (311)
                      +...|..                 .|+...-..-+.+  .-..+++..    ++.+.++.+. .+..+.+.  .+|.  +
T Consensus       100 V~~~~~D-----------------~~~L~~~~lqLqaAIkYse~Dl~g----~rsLveQlp~en~Ad~~in--~gCllyk  156 (459)
T KOG4340|consen  100 VAFLLLD-----------------NPALHSRVLQLQAAIKYSEGDLPG----SRSLVEQLPSENEADGQIN--LGCLLYK  156 (459)
T ss_pred             HHHHhcC-----------------CHHHHHHHHHHHHHHhcccccCcc----hHHHHHhccCCCccchhcc--chheeec
Confidence            8888743                 2333222222333  234588888    8888888774 32222111  1111  1


Q ss_pred             -----HHHHHHhhCCC----CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC
Q 044412          184 -----LAELLFNKMPA----WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGT  228 (311)
Q Consensus       184 -----~a~~~~~~m~~----~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  228 (311)
                           .|.+-|+.-.+    .....||.-+-.|. .|+...|+++..++.+.|+
T Consensus       157 egqyEaAvqkFqaAlqvsGyqpllAYniALaHy~-~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  157 EGQYEAAVQKFQAALQVSGYQPLLAYNLALAHYS-SRQYASALKHISEIIERGI  209 (459)
T ss_pred             cccHHHHHHHHHHHHhhcCCCchhHHHHHHHHHh-hhhHHHHHHHHHHHHHhhh
Confidence                 14444544332    34668888777664 5899999999999998875

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=95.53  E-value=0.4  Score=45.88  Aligned_cols=21  Identities=10%  Similarity=0.018  Sum_probs=15.4

Q ss_pred             ChhhHHHHHHhhCChHHHHHH
Q 044412          247 ALDLGRGIQIYCRSLGRSLLV  267 (311)
Q Consensus       247 ~~~~a~~~~~~~~~~~~a~~~  267 (311)
                      ..+.|..++...|.+..|.++
T Consensus      1037 ~~~~AVmLYHkAGm~~kALel 1057 (1416)
T KOG3617|consen 1037 YAHKAVMLYHKAGMIGKALEL 1057 (1416)
T ss_pred             hhhHHHHHHHhhcchHHHHHH
Confidence            777777777777777777665

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=95.53  E-value=0.029  Score=36.06  Aligned_cols=52  Identities=12%  Similarity=0.086  Sum_probs=42.3

Q ss_pred             ccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC
Q 044412           98 SSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE  168 (311)
Q Consensus        98 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~  168 (311)
                      ...|++++|+++|++....               .+-+..++-.+..+|.+.|++++    |..+++....
T Consensus         2 l~~~~~~~A~~~~~~~l~~---------------~p~~~~~~~~la~~~~~~g~~~~----A~~~l~~~~~   53 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR---------------NPDNPEARLLLAQCYLKQGQYDE----AEELLERLLK   53 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH---------------TTTSHHHHHHHHHHHHHTT-HHH----HHHHHHCCHG
T ss_pred             hhccCHHHHHHHHHHHHHH---------------CCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHH
Confidence            3578999999999998765               24477888889999999999999    8888887765

...

>PLN02789 farnesyltranstransferase

Probab=95.52  E-value=0.52  Score=40.89  Aligned_cols=182  Identities=7%  Similarity=-0.057  Sum_probs=95.4

Q ss_pred             hccCChhHHHHhcccCCCCCeeeeec-------cccCC-ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQEPNVFVYHA-------FSSLR-HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAM  142 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~~~~~~~~-------~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~l  142 (311)
                      ...+..++|+.+.+++.+.+...|++       +...+ .++++++.++++.+..               +-+..+|+..
T Consensus        48 ~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n---------------pknyqaW~~R  112 (320)
T PLN02789         48 ASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN---------------PKNYQIWHHR  112 (320)
T ss_pred             HcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC---------------CcchHHhHHH
Confidence            44445555555555544322222222       22223 4677888877776542               3445566655


Q ss_pred             HHHHHhCCCC--ccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHH
Q 044412          143 VDNYSYSNKF--FESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAF  220 (311)
Q Consensus       143 l~~~~~~g~~--~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~  220 (311)
                      --.+.+.|+.  ++    +..+.+.+.+.                       ...|..+|+.---.+...|+++++++.+
T Consensus       113 ~~~l~~l~~~~~~~----el~~~~kal~~-----------------------dpkNy~AW~~R~w~l~~l~~~~eeL~~~  165 (320)
T PLN02789        113 RWLAEKLGPDAANK----ELEFTRKILSL-----------------------DAKNYHAWSHRQWVLRTLGGWEDELEYC  165 (320)
T ss_pred             HHHHHHcCchhhHH----HHHHHHHHHHh-----------------------CcccHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            5455555542  33    23333222211                       1347788888888888889999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHhccC---ChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhc----C
Q 044412          221 NKTKKSGTGSDQVTMATVLSACAHLG---ALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIH----G  290 (311)
Q Consensus       221 ~~m~~~g~~p~~~t~~~li~a~~~~~---~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~----g  290 (311)
                      +++.+.+.. |...|+.....+.+.+   ..+.         ..+.......+..  .| |...|+.+-..+...    +
T Consensus       166 ~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~---------~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~  235 (320)
T PLN02789        166 HQLLEEDVR-NNSAWNQRYFVITRSPLLGGLEA---------MRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALV  235 (320)
T ss_pred             HHHHHHCCC-chhHHHHHHHHHHhccccccccc---------cHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccc
Confidence            999886543 3445554444444332   2210         0112222221211  23 556777776666663    2


Q ss_pred             ChHHHHHHHHHHHH
Q 044412          291 FAHEALGMFDRMTY  304 (311)
Q Consensus       291 ~~~~a~~~~~~M~~  304 (311)
                      +..+|.+.+.+...
T Consensus       236 ~~~~~~~~~~~~~~  249 (320)
T PLN02789        236 SDPEVSSVCLEVLS  249 (320)
T ss_pred             cchhHHHHHHHhhc
Confidence            33456666555443

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=95.52  E-value=1.2  Score=38.51  Aligned_cols=52  Identities=17%  Similarity=-0.033  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~  254 (311)
                      +.+..|.-+...|+...|.++-.+.+    -||-.-|-.-|.+++..++|++-+.+
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~f  230 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKF  230 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHH
Confidence            34445566666677777766666653    36777777777777777777755443

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.46  E-value=1.8  Score=38.75  Aligned_cols=106  Identities=14%  Similarity=0.145  Sum_probs=77.6

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcC-CCCCHHHHHHHHHHHhccCChhhHHHHHHh------------------
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSG-TGSDQVTMATVLSACAHLGALDLGRGIQIY------------------  257 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~a~~~~~~~~~a~~~~~~------------------  257 (311)
                      ..+|...|...-+..-++.|..+|.+.++.| +.++...++++|.-++. |+...|-.+|+.                  
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~f~d~~~y~~kyl~f  475 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLKFPDSTLYKEKYLLF  475 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            3467777877777777888888888888888 77888888888886554 666777777776                  


Q ss_pred             ---hCChHHHHHHHhhcC---CCC--chhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          258 ---CRSLGRSLLVFFKLR---EKN--LLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       258 ---~~~~~~a~~~~~~~~---~p~--~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                         .++-..|..+|+.-.   +.+  ...|..||+-=..-|+...+..+=++|.
T Consensus       476 Li~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~  529 (660)
T COG5107         476 LIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFR  529 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHH
Confidence               666667777777443   223  4578888888888888877766666654

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=95.44  E-value=0.55  Score=35.41  Aligned_cols=116  Identities=12%  Similarity=0.119  Sum_probs=69.2

Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchh---HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVF---VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~---~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      .++...+...++.+....               +.+..   ..-.+-..+...|++++|......+.+.-+.++.     
T Consensus        24 ~~~~~~~~~~~~~l~~~~---------------~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l-----   83 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDY---------------PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPEL-----   83 (145)
T ss_pred             CCCHHHHHHHHHHHHHHC---------------CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHH-----
Confidence            456666666666665532               22212   2222446788899999944444444333211111     


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                                         -....-.+-..+...|++++|+..++......  +....+...=..+.+.|+.++|+..|+
T Consensus        84 -------------------~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~--~~~~~~~~~Gdi~~~~g~~~~A~~~y~  142 (145)
T PF09976_consen   84 -------------------KPLARLRLARILLQQGQYDEALATLQQIPDEA--FKALAAELLGDIYLAQGDYDEARAAYQ  142 (145)
T ss_pred             -------------------HHHHHHHHHHHHHHcCCHHHHHHHHHhccCcc--hHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence                               01233345677788899999999997754333  334455666677888999998877664

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=95.43  E-value=0.033  Score=37.67  Aligned_cols=82  Identities=15%  Similarity=0.145  Sum_probs=55.2

Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMID  179 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~  179 (311)
                      .|++++|+.+|+.+.+..-             -.++...+-.+-.+|.+.|++++    |..+++. .+.+         
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~-------------~~~~~~~~~~la~~~~~~~~y~~----A~~~~~~-~~~~---------   54 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDP-------------TNPNSAYLYNLAQCYFQQGKYEE----AIELLQK-LKLD---------   54 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHC-------------GTHHHHHHHHHHHHHHHTTHHHH----HHHHHHC-HTHH---------
T ss_pred             CccHHHHHHHHHHHHHHCC-------------CChhHHHHHHHHHHHHHCCCHHH----HHHHHHH-hCCC---------
Confidence            5789999999999876420             01244455558899999999999    7777766 2211         


Q ss_pred             HHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHH
Q 044412          180 AYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNK  222 (311)
Q Consensus       180 ~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~  222 (311)
                                    ..+....-.+-.+|.+.|++++|+++|++
T Consensus        55 --------------~~~~~~~~l~a~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   55 --------------PSNPDIHYLLARCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             --------------HCHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             --------------CCCHHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence                          11223333446788899999999999875

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.42  E-value=1.1  Score=43.98  Aligned_cols=235  Identities=9%  Similarity=0.047  Sum_probs=133.0

Q ss_pred             HhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec------cccCCChhHHH
Q 044412           34 LKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA------FSSLRHPLQAI  107 (311)
Q Consensus        34 l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~------~~~~~~~~~a~  107 (311)
                      ....+..+..+++.-...+.|.+||...   +|... .+ -..+.+.++...|.+.+...-+.      +...+..+.+.
T Consensus       488 i~cfAE~Gqf~KiilY~kKvGyTPdymf---lLq~l-~r-~sPD~~~qFa~~l~Q~~~~~~die~I~DlFme~N~iQq~T  562 (1666)
T KOG0985|consen  488 IQCFAETGQFKKIILYAKKVGYTPDYMF---LLQQL-KR-SSPDQALQFAMMLVQDEEPLADIEQIVDLFMELNLIQQCT  562 (1666)
T ss_pred             HHHHHHhcchhHHHHHHHHcCCCccHHH---HHHHH-Hc-cChhHHHHHHHHhhccCCCcccHHHHHHHHHHHHhhhhhH
Confidence            3444455555677778889999998654   44444 44 57778887777776533221111      44444555555


Q ss_pred             HHHHHHHHCCCCch-----------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--
Q 044412          108 AFYLYMLRAEVLLT-----------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--  168 (311)
Q Consensus       108 ~~~~~m~~~~~~p~-----------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--  168 (311)
                      .++-+..+ +-.|+                 ++.+.+..++.--. .-+..+-+.|.+.|-...    |.+.+.....  
T Consensus       563 SFLLdaLK-~~~Pd~g~LQTrLLE~NL~~aPqVADAILgN~mFtH-yDra~IAqLCEKAGL~qr----aLehytDl~DIK  636 (1666)
T KOG0985|consen  563 SFLLDALK-LNSPDEGHLQTRLLEMNLVHAPQVADAILGNDMFTH-YDRAEIAQLCEKAGLLQR----ALEHYTDLYDIK  636 (1666)
T ss_pred             HHHHHHhc-CCChhhhhHHHHHHHHHhccchHHHHHHHhcccccc-ccHHHHHHHHHhcchHHH----HHHhcccHHHHH
Confidence            55444432 22333                 22222222221111 113444455555555555    4444443221  


Q ss_pred             CCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          169 RKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       169 ~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      +.++.                ..+..|+      .+-.|...-.++.+.+.++.|...+++-|..+.--+-.-|...=-.
T Consensus       637 R~vVh----------------th~L~pE------wLv~yFg~lsve~s~eclkaml~~NirqNlQi~VQvatky~eqlg~  694 (1666)
T KOG0985|consen  637 RVVVH----------------THLLNPE------WLVNYFGSLSVEDSLECLKAMLSANIRQNLQIVVQVATKYHEQLGA  694 (1666)
T ss_pred             HHHHH----------------hccCCHH------HHHHHHHhcCHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCH
Confidence            00000                0011111      1333444457899999999999999999998888887777776666


Q ss_pred             hhHHHHHHhhCChHHHHHHHhhcC--CCCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          249 DLGRGIQIYCRSLGRSLLVFFKLR--EKNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       249 ~~a~~~~~~~~~~~~a~~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      +...++|+..+..+--.-++..+.  ..|+...--.|.+.|+.|++.+..++.++
T Consensus       695 ~~li~lFE~fks~eGL~yfLgSivn~seDpevh~KYIqAA~kt~QikEvERicre  749 (1666)
T KOG0985|consen  695 QALIELFESFKSYEGLYYFLGSIVNFSEDPEVHFKYIQAACKTGQIKEVERICRE  749 (1666)
T ss_pred             HHHHHHHHhhccchhHHHHHHHHhccccCchHHHHHHHHHHhhccHHHHHHHHhc
Confidence            666666666555444433333333  34555566789999999999998887664

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=95.39  E-value=0.82  Score=44.05  Aligned_cols=88  Identities=11%  Similarity=0.200  Sum_probs=50.5

Q ss_pred             hccCChhHHHHhcccCCCC---Ceeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQEP---NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMV  143 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~---~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll  143 (311)
                      .|.|+.++|..+++....+   |..|..+    |-..++.++|..+|+...+                .-|+......+.
T Consensus        54 ~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~----------------~~P~eell~~lF  117 (932)
T KOG2053|consen   54 FRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQ----------------KYPSEELLYHLF  117 (932)
T ss_pred             HHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHh----------------hCCcHHHHHHHH
Confidence            5667777777666665421   2222222    5666666666666666543                345566666666


Q ss_pred             HHHHhCCCCccchHHHHHHhccCCCCCHhHH
Q 044412          144 DNYSYSNKFFESRRVSRRLFDEMPERKFATW  174 (311)
Q Consensus       144 ~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~  174 (311)
                      .+|.|.+++.+-..+|.++++..++.--.-|
T Consensus       118 mayvR~~~yk~qQkaa~~LyK~~pk~~yyfW  148 (932)
T KOG2053|consen  118 MAYVREKSYKKQQKAALQLYKNFPKRAYYFW  148 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCcccchHH
Confidence            6677766666655556666665554433333

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=95.36  E-value=0.68  Score=39.39  Aligned_cols=73  Identities=11%  Similarity=0.109  Sum_probs=46.1

Q ss_pred             HHHHHhhCCCCc--HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC-----CCCHH-HHHHHHHHHhccCChhhHHHHHH
Q 044412          185 AELLFNKMPAWD--IRSWTTMITSYSQNKQFREALDAFNKTKKSGT-----GSDQV-TMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       185 a~~~~~~m~~~~--~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~-----~p~~~-t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      |.++|+.-..+.  ...+..+...+.+.|++++|.++|++....-.     +++.. .|-..+-++...||.-.|...++
T Consensus       141 A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~  220 (282)
T PF14938_consen  141 AAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALE  220 (282)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            556666555432  34677888889999999999999999876432     22222 23333335666788887777776


Q ss_pred             h
Q 044412          257 Y  257 (311)
Q Consensus       257 ~  257 (311)
                      .
T Consensus       221 ~  221 (282)
T PF14938_consen  221 R  221 (282)
T ss_dssp             H
T ss_pred             H
Confidence            6

>PLN02789 farnesyltranstransferase

Probab=95.24  E-value=1.8  Score=37.54  Aligned_cols=119  Identities=8%  Similarity=-0.040  Sum_probs=80.0

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcch-hHHHHHHHHHhhccC-ChhHHHHhcccCCCCCeee---eec----cc
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDC-FLAKQFISFCTSRFH-FIDYTILVFPQMQEPNVFV---YHA----FS   98 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~-~~~~~ll~~~~~~~g-~~~~a~~~~~~m~~~~~~~---~~~----~~   98 (311)
                      ..|..++...++...+..+...+++..  |+- .+|+.--.++ .+.| .+++++..++++.+.+...   |+.    +.
T Consensus        41 ~~~ra~l~~~e~serAL~lt~~aI~ln--P~~ytaW~~R~~iL-~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~  117 (320)
T PLN02789         41 DYFRAVYASDERSPRALDLTADVIRLN--PGNYTVWHFRRLCL-EALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHH-HHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHH
Confidence            366777777888888888888887653  433 3555444455 5666 6789999998876544444   433    33


Q ss_pred             cCCC--hhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC
Q 044412           99 SLRH--PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE  168 (311)
Q Consensus        99 ~~~~--~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~  168 (311)
                      +.+.  .++++.+++.+.+..               +-|..+|+..--.+.+.|++++    +.+.++++.+
T Consensus       118 ~l~~~~~~~el~~~~kal~~d---------------pkNy~AW~~R~w~l~~l~~~~e----eL~~~~~~I~  170 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLD---------------AKNYHAWSHRQWVLRTLGGWED----ELEYCHQLLE  170 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhC---------------cccHHHHHHHHHHHHHhhhHHH----HHHHHHHHHH
Confidence            3343  366788888876642               5568889988889999999999    5555555443

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.22  E-value=0.52  Score=36.72  Aligned_cols=128  Identities=11%  Similarity=0.009  Sum_probs=78.0

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCCh
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQF  213 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~~  213 (311)
                      ...+..+-..|...|++++    |...|++....                      -+.+  ....|..+...+.+.|++
T Consensus        35 a~~~~~lg~~~~~~g~~~~----A~~~~~~al~~----------------------~~~~~~~~~~~~~la~~~~~~g~~   88 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAE----ALENYEEALKL----------------------EEDPNDRSYILYNMGIIYASNGEH   88 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHHHHHH----------------------hhccchHHHHHHHHHHHHHHcCCH
Confidence            4456777778889999999    65555543210                      0111  135788888999999999


Q ss_pred             hHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHh-hCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCC
Q 044412          214 REALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIY-CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGF  291 (311)
Q Consensus       214 ~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~-~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~  291 (311)
                      ++|...+.+..+.  .|+ ...+..+-..+...|+...+..-+.. ....+.|.+++++..+.++..|..++.-+...|+
T Consensus        89 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~  166 (172)
T PRK02603         89 DKALEYYHQALEL--NPKQPSALNNIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRLAPNNYIEAQNWLKTTGR  166 (172)
T ss_pred             HHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhhCchhHHHHHHHHHhcCc
Confidence            9999999998874  453 45566666667676664433211111 2223456666665554454445555555544443

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=95.17  E-value=1  Score=34.84  Aligned_cols=111  Identities=13%  Similarity=0.098  Sum_probs=78.8

Q ss_pred             HHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-------HHHHHhhCCCCcHhH
Q 044412          127 VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-------AELLFNKMPAWDIRS  199 (311)
Q Consensus       127 ~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-------a~~~~~~m~~~~~~~  199 (311)
                      +.+.|+.|+...|..+|+.+.+.|++..    ...++..-.-+|.......+-.+...       +.+++.++..    .
T Consensus        20 l~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~----~   91 (167)
T PF07035_consen   20 LNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGT----A   91 (167)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhh----h
Confidence            4456689999999999999999999999    88888777666665544444444332       7788877752    4


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChh
Q 044412          200 WTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALD  249 (311)
Q Consensus       200 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~  249 (311)
                      +..+++.+-..|++-+|+++.+.....    +......++.|-...+|..
T Consensus        92 ~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~  137 (167)
T PF07035_consen   92 YEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQ  137 (167)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHH
Confidence            556778888899999999999885332    1122245666666666554

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.08  E-value=0.41  Score=37.09  Aligned_cols=96  Identities=10%  Similarity=-0.008  Sum_probs=65.8

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC--CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS--DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK  274 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p  274 (311)
                      ...|..+...+...|++++|+..|++.....-.|  ...++..+-..+...|+.++|...++..-      .+    ...
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al------~~----~~~  104 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQAL------ER----NPF  104 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH------Hh----CcC
Confidence            4567777788888999999999999987653222  23578888888999999997777653321      11    122


Q ss_pred             CchhHHHHHHHHH-------hcCChHHHHHHHHHH
Q 044412          275 NLLCWNSITEALA-------IHGFAHEALGMFDRM  302 (311)
Q Consensus       275 ~~~~~~~li~~~~-------~~g~~~~a~~~~~~M  302 (311)
                      ...+++.+...+.       ..|++++|...+++-
T Consensus       105 ~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        105 LPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             cHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            3345666666666       788888776666654

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.08  E-value=0.51  Score=36.77  Aligned_cols=85  Identities=14%  Similarity=0.076  Sum_probs=59.8

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC--HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD--QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE  273 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~  273 (311)
                      ....|..+-..+...|++++|...|++..+.+-.+.  ...+..+-..+.+.|+++.|...+..      +.+.     .
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~------al~~-----~  102 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQ------ALEL-----N  102 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHh-----C
Confidence            345677788888889999999999999887543332  45788888889999999987776533      2221     2


Q ss_pred             C-CchhHHHHHHHHHhcCC
Q 044412          274 K-NLLCWNSITEALAIHGF  291 (311)
Q Consensus       274 p-~~~~~~~li~~~~~~g~  291 (311)
                      | +...+..+...+...|+
T Consensus       103 p~~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603        103 PKQPSALNNIAVIYHKRGE  121 (172)
T ss_pred             cccHHHHHHHHHHHHHcCC
Confidence            3 34556666667777665

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=94.99  E-value=0.3  Score=43.09  Aligned_cols=87  Identities=10%  Similarity=-0.009  Sum_probs=44.5

Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEAL  286 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~  286 (311)
                      +...|++++|+++|++..+.. +-+...|..+-.+|...|+++.|...++.      |.++    ...+...|..+-.+|
T Consensus        12 a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~------Al~l----~P~~~~a~~~lg~~~   80 (356)
T PLN03088         12 AFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANK------AIEL----DPSLAKAYLRKGTAC   80 (356)
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHh----CcCCHHHHHHHHHHH
Confidence            334566666666666665531 12344455555556666666644443321      1111    012344555555666


Q ss_pred             HhcCChHHHHHHHHHHHH
Q 044412          287 AIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       287 ~~~g~~~~a~~~~~~M~~  304 (311)
                      ...|++++|...|++..+
T Consensus        81 ~~lg~~~eA~~~~~~al~   98 (356)
T PLN03088         81 MKLEEYQTAKAALEKGAS   98 (356)
T ss_pred             HHhCCHHHHHHHHHHHHH
Confidence            666666666666666553

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=94.89  E-value=0.14  Score=46.53  Aligned_cols=61  Identities=20%  Similarity=0.155  Sum_probs=48.5

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      -..+++.|-..|-+.+..++|+..++.-... .+-|..|+.++--.|...|+++.|...|+.
T Consensus       454 w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-~~k~~~~~asig~iy~llgnld~Aid~fhK  514 (611)
T KOG1173|consen  454 WEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-SPKDASTHASIGYIYHLLGNLDKAIDHFHK  514 (611)
T ss_pred             hhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-CCCchhHHHHHHHHHHHhcChHHHHHHHHH
Confidence            4456888888888999999999999997764 355788888888888998888866665543

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=94.87  E-value=0.12  Score=33.09  Aligned_cols=46  Identities=11%  Similarity=0.193  Sum_probs=34.7

Q ss_pred             HhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHH
Q 044412          208 SQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      ...|++++|+++|++..+.  .| +...+..+..+|.+.|++++|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l   48 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELL   48 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4578999999999998775  34 6667778889999988888555544

...

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=94.86  E-value=0.14  Score=33.90  Aligned_cols=66  Identities=14%  Similarity=0.196  Sum_probs=50.9

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCC--Cc-HhHHHHHHHHHHhCCC
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPA--WD-IRSWTTMITSYSQNKQ  212 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~--~~-~~~y~~li~~~~~~g~  212 (311)
                      ..+|+.+-..|...|++++    |...+++                   |.++.+....  |+ ..+++.+-..|...|+
T Consensus         5 a~~~~~la~~~~~~~~~~~----A~~~~~~-------------------al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~   61 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDE----ALDYYEK-------------------ALDIEEQLGDDHPDTANTLNNLGECYYRLGD   61 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHH----HHHHHHH-------------------HHHHHHHTTTHHHHHHHHHHHHHHHHHHTTH
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHH-------------------HHHHHHHHCCCCHHHHHHHHHHHHHHHHcCC
Confidence            3578888899999999999    7777766                   4555545543  23 5678999999999999


Q ss_pred             hhHHHHHHHHHH
Q 044412          213 FREALDAFNKTK  224 (311)
Q Consensus       213 ~~~a~~~~~~m~  224 (311)
                      +++|++++++-.
T Consensus        62 ~~~A~~~~~~al   73 (78)
T PF13424_consen   62 YEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999998754

...

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=94.85  E-value=0.13  Score=34.08  Aligned_cols=65  Identities=17%  Similarity=0.123  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          233 VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       233 ~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      .+|+.+-..|...|++++|...++      .|.++.+...  .|+ ..+++.+-..|...|++++|.+++++-.
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~------~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYE------KALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHH------HHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHH------HHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            467888888999999999988774      4555544443  233 5689999999999999999999998754

...

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=94.76  E-value=1.2  Score=40.04  Aligned_cols=103  Identities=14%  Similarity=0.051  Sum_probs=75.4

Q ss_pred             HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhCC
Q 044412          185 AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIYCRS  260 (311)
Q Consensus       185 a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~  260 (311)
                      |+..++.+.  .| |...+....+-+...++..+|.+.++.+..  ..|+ ....-.+-.++.+.|+..+|.        
T Consensus       325 A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~--l~P~~~~l~~~~a~all~~g~~~eai--------  394 (484)
T COG4783         325 ALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALA--LDPNSPLLQLNLAQALLKGGKPQEAI--------  394 (484)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHh--cCCCccHHHHHHHHHHHhcCChHHHH--------
Confidence            666676664  35 455566667889999999999999999987  4677 445556778888888888544        


Q ss_pred             hHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          261 LGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       261 ~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                           +.++...   .-|+..|+.|-.+|...|+..++..-..++
T Consensus       395 -----~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         395 -----RILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             -----HHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence                 4444433   347789999999999988888776665554

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=94.57  E-value=2.2  Score=40.66  Aligned_cols=196  Identities=10%  Similarity=-0.010  Sum_probs=128.9

Q ss_pred             HHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCC---Ceeeeec----cccCCChhHHHHHHHHHHHCC
Q 044412           45 CVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEP---NVFVYHA----FSSLRHPLQAIAFYLYMLRAE  117 (311)
Q Consensus        45 ~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~----~~~~~~~~~a~~~~~~m~~~~  117 (311)
                      .++.++....+..|..+|..+.-+. .++|+++.+-+.|++...-   ....|+.    +.-.|....|..++++-....
T Consensus       309 ~~~~k~r~~~~qnd~ai~d~Lt~al-~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~  387 (799)
T KOG4162|consen  309 LLLRKLRLKKFQNDAAIFDHLTFAL-SRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKS  387 (799)
T ss_pred             HHHHHHHHhhhcchHHHHHHHHHHH-HHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccc
Confidence            3445555666788999999999999 9999999999999887531   1222222    777888889999987753321


Q ss_pred             CCchHHHHHHHHhcCCCchhHHHHHHH--HHHhCCCCccchHHHHHHhccC--CCCC--HhHHHHHHHHHHHH-------
Q 044412          118 VLLTTVHGQVWKNGFSSPVFVQTAMVD--NYSYSNKFFESRRVSRRLFDEM--PERK--FATWNTMIDAYARL-------  184 (311)
Q Consensus       118 ~~p~~~~~~~~~~g~~~~~~~~~~ll~--~~~~~g~~~~a~~~a~~~~~~~--~~~~--~~~~~~li~~~~~~-------  184 (311)
                                    -.|+..+---+..  ++-+.+..+++...|.+..+..  ....  ...|-.+=-+|...       
T Consensus       388 --------------~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~  453 (799)
T KOG4162|consen  388 --------------EQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLK  453 (799)
T ss_pred             --------------cCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCCh
Confidence                          1233222222222  2344577888888888887733  2111  12333333333321       


Q ss_pred             ---------HHHHHhhCC-----CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          185 ---------AELLFNKMP-----AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       185 ---------a~~~~~~m~-----~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                               +.+.+++-.     +|++..|-++=  |+-.++++.|.+..++..+.+-.-+...|..|.-.+.-.+++..
T Consensus       454 seR~~~h~kslqale~av~~d~~dp~~if~lalq--~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~  531 (799)
T KOG4162|consen  454 SERDALHKKSLQALEEAVQFDPTDPLVIFYLALQ--YAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKE  531 (799)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHH--HHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHH
Confidence                     444444432     45555555443  45667899999999999998778888899988888999999999


Q ss_pred             HHHHHHh
Q 044412          251 GRGIQIY  257 (311)
Q Consensus       251 a~~~~~~  257 (311)
                      |+.+.+.
T Consensus       532 Al~vvd~  538 (799)
T KOG4162|consen  532 ALDVVDA  538 (799)
T ss_pred             HHHHHHH
Confidence            9887643

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.56  E-value=0.5  Score=34.81  Aligned_cols=110  Identities=15%  Similarity=0.167  Sum_probs=65.2

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH---HHHHHHHHHhccCC----hhhHHHHHHhhCChHHHHHHH
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV---TMATVLSACAHLGA----LDLGRGIQIYCRSLGRSLLVF  268 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~---t~~~li~a~~~~~~----~~~a~~~~~~~~~~~~a~~~~  268 (311)
                      +..-||-+|=.....-+.+-..++++..-+   -.|..   -...++.+|++.|.    ++.|...+-..|+.+.-.++.
T Consensus        33 ni~E~NWvICNiiDaa~C~yvv~~LdsIGk---iFDis~C~NlKrVi~C~~~~n~~se~vD~ALd~lv~~~kkDqLdki~  109 (161)
T PF09205_consen   33 NIKEYNWVICNIIDAADCDYVVETLDSIGK---IFDISKCGNLKRVIECYAKRNKLSEYVDLALDILVKQGKKDQLDKIY  109 (161)
T ss_dssp             -HHHHTHHHHHHHHH--HHHHHHHHHHHGG---GS-GGG-S-THHHHHHHHHTT---HHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             CccccceeeeecchhhchhHHHHHHHHHhh---hcCchhhcchHHHHHHHHHhcchHHHHHHHHHHHHHhccHHHHHHHH
Confidence            444555555555454555555555555432   22222   23345566665553    345555555566666777777


Q ss_pred             hhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 044412          269 FKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVR  308 (311)
Q Consensus       269 ~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  308 (311)
                      .++.   ++++...-.+-.||.+-|+..++.+++.+.-+.|++
T Consensus       110 ~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen  110 NELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            7654   688888889999999999999999999999998874

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=94.43  E-value=0.73  Score=32.83  Aligned_cols=92  Identities=10%  Similarity=0.069  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCC--CCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ++-.+...+.+.|++++    |...+.....  |+.                      ......+..+...+.+.|++++
T Consensus         4 ~~~~~~~~~~~~~~~~~----A~~~~~~~~~~~~~~----------------------~~~~~~~~~l~~~~~~~~~~~~   57 (119)
T TIGR02795         4 AYYDAALLVLKAGDYAD----AIQAFQAFLKKYPKS----------------------TYAPNAHYWLGEAYYAQGKYAD   57 (119)
T ss_pred             HHHHHHHHHHHcCCHHH----HHHHHHHHHHHCCCc----------------------cccHHHHHHHHHHHHhhccHHH
Confidence            45667778888999999    5555554322  110                      0013455667888999999999


Q ss_pred             HHHHHHHHHhcC--CCCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          216 ALDAFNKTKKSG--TGSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       216 a~~~~~~m~~~g--~~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      |...|++.....  -......+..+-.++...|+.+.|...+
T Consensus        58 A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~   99 (119)
T TIGR02795        58 AAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATL   99 (119)
T ss_pred             HHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHH
Confidence            999999988642  1112456677777788888888665554

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=93.99  E-value=0.17  Score=38.18  Aligned_cols=48  Identities=21%  Similarity=0.340  Sum_probs=31.3

Q ss_pred             HHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHH-----HcCCCCC
Q 044412          263 RSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMT-----YENVRPN  310 (311)
Q Consensus       263 ~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~-----~~g~~P~  310 (311)
                      .|.+......  .| |-..|-.+|.+|...|+..+|.+.|+++.     +-|+.|+
T Consensus        80 ~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps  135 (146)
T PF03704_consen   80 EALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPS  135 (146)
T ss_dssp             HHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcC
Confidence            4444444433  34 56689999999999999999999999885     3488886

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=93.77  E-value=0.64  Score=33.90  Aligned_cols=87  Identities=15%  Similarity=0.050  Sum_probs=58.8

Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCC--HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC---c-hh
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSD--QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN---L-LC  278 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~---~-~~  278 (311)
                      .++-..|+.++|+.+|++-...|....  ...+-.+-+++...|++++|..+++..-         .+  .|+   . ..
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~---------~~--~p~~~~~~~l   77 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEAL---------EE--FPDDELNAAL   77 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------HH--CCCccccHHH
Confidence            455667999999999999999887765  3356667778888888887766653310         11  243   1 12


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHH
Q 044412          279 WNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       279 ~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                      ...+-.++...|+.++|..++-..
T Consensus        78 ~~f~Al~L~~~gr~~eAl~~~l~~  101 (120)
T PF12688_consen   78 RVFLALALYNLGRPKEALEWLLEA  101 (120)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHH
Confidence            222334777889999998876543

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=93.77  E-value=1.5  Score=36.89  Aligned_cols=108  Identities=11%  Similarity=0.101  Sum_probs=81.8

Q ss_pred             HHHHHhhCC--CCcHhHHHHHHHHHHhC-----CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh--HHHHH
Q 044412          185 AELLFNKMP--AWDIRSWTTMITSYSQN-----KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL--GRGIQ  255 (311)
Q Consensus       185 a~~~~~~m~--~~~~~~y~~li~~~~~~-----g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~--a~~~~  255 (311)
                      .++.|...+  ++|-.+|-+++.-|...     +.++=...-++.|.+-|++-|..+|+.||+.+=+..-.-.  -.++|
T Consensus        53 ~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F  132 (406)
T KOG3941|consen   53 VEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVF  132 (406)
T ss_pred             hhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHH
Confidence            345566555  56888888888888764     5567777788899999999999999999999887654321  11222


Q ss_pred             Hh-hCChHHHHHHHhhcC----CCCchhHHHHHHHHHhcCCh
Q 044412          256 IY-CRSLGRSLLVFFKLR----EKNLLCWNSITEALAIHGFA  292 (311)
Q Consensus       256 ~~-~~~~~~a~~~~~~~~----~p~~~~~~~li~~~~~~g~~  292 (311)
                      -+ -..-.-+..++++|+    -||-.+-.+|+.++.+.+..
T Consensus       133 ~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  133 LHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence            22 445556889999998    79999999999999998865

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.51  E-value=5.5  Score=35.84  Aligned_cols=259  Identities=10%  Similarity=0.051  Sum_probs=148.3

Q ss_pred             HHhhccChhhHHHHHHHHHHhccCc----c-hhHHHHHHHHHhhccCChhHHHHhcccCCCCCeee-e----ec--cccC
Q 044412           33 QLKKCSSIKELECVYATIVKTNANL----D-CFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV-Y----HA--FSSL  100 (311)
Q Consensus        33 ~l~~~~~~~~~~~l~~~m~~~g~~p----~-~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~-~----~~--~~~~  100 (311)
                      +|+..++..+++.+|..+.+.--..    . ...-+.+|++| . ..+++.....+.+..+....+ |    ..  +.+.
T Consensus        15 ~Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAf-f-l~nld~Me~~l~~l~~~~~~s~~l~LF~~L~~Y~~   92 (549)
T PF07079_consen   15 ILQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAF-F-LNNLDLMEKQLMELRQQFGKSAYLPLFKALVAYKQ   92 (549)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHH-H-HhhHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHh
Confidence            4667788888888888877653211    1 23456788887 3 345666655555554322211 1    11  7788


Q ss_pred             CChhHHHHHHHHHHHC--CCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC----CCHhHH
Q 044412          101 RHPLQAIAFYLYMLRA--EVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE----RKFATW  174 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~--~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~----~~~~~~  174 (311)
                      +.+.+|++.+....++  +.+|.= .+.-. ....+|...=+...+++...|++++++.+..+++..+.+    -++.+|
T Consensus        93 k~~~kal~~ls~w~~~~~~~~~~~-Ld~ni-~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~y  170 (549)
T PF07079_consen   93 KEYRKALQALSVWKEQIKGTESPW-LDTNI-QQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMY  170 (549)
T ss_pred             hhHHHHHHHHHHHHhhhcccccch-hhhhH-HHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHH
Confidence            9999999999888765  433320 00000 002344445567788999999999977776666666655    577899


Q ss_pred             HHHHHHHHHH-HHHHHhhCCCCcHhHHHHHHHHHHhCC-------------------------------ChhHHHHHHHH
Q 044412          175 NTMIDAYARL-AELLFNKMPAWDIRSWTTMITSYSQNK-------------------------------QFREALDAFNK  222 (311)
Q Consensus       175 ~~li~~~~~~-a~~~~~~m~~~~~~~y~~li~~~~~~g-------------------------------~~~~a~~~~~~  222 (311)
                      |.++-.+++. -.++-+.+...=..-|--||..|-+.-                               +..--..++..
T Consensus       171 d~~vlmlsrSYfLEl~e~~s~dl~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~~mq~l~~  250 (549)
T PF07079_consen  171 DRAVLMLSRSYFLELKESMSSDLYPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVPKERLPPLMQILEN  250 (549)
T ss_pred             HHHHHHHhHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCCHhhccHHHHHHHH
Confidence            9988888886 333333332211112223333332211                               11111122222


Q ss_pred             HHhcCCCCCHHH-HHHHHHHHhccCChhhHHHHHHhhCChHHHHHHH--hhcCCCCchhHHHHHHHHHhcCChHHHHHHH
Q 044412          223 TKKSGTGSDQVT-MATVLSACAHLGALDLGRGIQIYCRSLGRSLLVF--FKLREKNLLCWNSITEALAIHGFAHEALGMF  299 (311)
Q Consensus       223 m~~~g~~p~~~t-~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~--~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  299 (311)
                      -...-+.|+-.. ...|+..+..  +.+++.++.       ++...+  +.+.+.=+.+|..++....+.++..+|..++
T Consensus       251 We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~c-------e~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l  321 (549)
T PF07079_consen  251 WENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFC-------EAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYL  321 (549)
T ss_pred             HHhhccCCchhHHHHHHHHHHhc--ChHHHHHHH-------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            233345665443 3455555555  555555554       333222  1222445678999999999999999998888


Q ss_pred             HHHHH
Q 044412          300 DRMTY  304 (311)
Q Consensus       300 ~~M~~  304 (311)
                      .-+.-
T Consensus       322 ~lL~~  326 (549)
T PF07079_consen  322 ALLKI  326 (549)
T ss_pred             HHHHh
Confidence            76653

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=93.44  E-value=0.35  Score=30.60  Aligned_cols=51  Identities=16%  Similarity=0.126  Sum_probs=39.8

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          204 ITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       204 i~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      -..+...|++++|.+.|++..+..  | +...+..+-.++...|++++|...++
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~   55 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYE   55 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            456778899999999999998865  5 56677788888889999997776654

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=93.38  E-value=0.88  Score=38.32  Aligned_cols=100  Identities=11%  Similarity=0.149  Sum_probs=77.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      +.+++++++|++.|.+-..                +.| |.+-|..--.+|++.|..+.|..=++..+..          
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~----------------l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i----------  144 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE----------------LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI----------  144 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh----------------cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc----------
Confidence            6788999999999998765                444 5666777778899999999944444443332          


Q ss_pred             HHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 044412          176 TMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSAC  242 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~  242 (311)
                                        +| -..+|..|=.+|...|++++|++.|++-+.  +.|+-.+|-.=|+.-
T Consensus       145 ------------------Dp~yskay~RLG~A~~~~gk~~~A~~aykKaLe--ldP~Ne~~K~nL~~A  192 (304)
T KOG0553|consen  145 ------------------DPHYSKAYGRLGLAYLALGKYEEAIEAYKKALE--LDPDNESYKSNLKIA  192 (304)
T ss_pred             ------------------ChHHHHHHHHHHHHHHccCcHHHHHHHHHhhhc--cCCCcHHHHHHHHHH
Confidence                              22 367899999999999999999999998775  789988887655544

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.36  E-value=1  Score=41.52  Aligned_cols=102  Identities=16%  Similarity=0.105  Sum_probs=58.9

Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh--------------------hCChHHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY--------------------CRSLGRS  264 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~--------------------~~~~~~a  264 (311)
                      +-+.+.|++++|......+...+ +-|...+..=+=+....+.+++|..+.+.                    .+++++|
T Consensus        20 n~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~~~~~~~fEKAYc~Yrlnk~Dea   98 (652)
T KOG2376|consen   20 NRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGALLVINSFFFEKAYCEYRLNKLDEA   98 (652)
T ss_pred             HHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhhhcchhhHHHHHHHHHcccHHHH
Confidence            33444555555555555555433 22233344444445555555555544443                    4455566


Q ss_pred             HHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 044412          265 LLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       265 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      ...++...+-|..+-..=-.-+.+.|++++|+++|..+.+.+.
T Consensus        99 lk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~  141 (652)
T KOG2376|consen   99 LKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNS  141 (652)
T ss_pred             HHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC
Confidence            6666644444544555555667889999999999999976543

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.30  E-value=1.4  Score=39.66  Aligned_cols=92  Identities=11%  Similarity=0.004  Sum_probs=69.1

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH----HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhc
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ----VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKL  271 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~  271 (311)
                      +...|+.+-.+|...|++++|+..|++-.+  +.|+.    .+|..+-.+|...|+.++|...++..-...  ...|..+
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALe--L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALels--n~~f~~i  149 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALE--LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDY--NLKFSTI  149 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc--chhHHHH
Confidence            567899999999999999999999999776  46774    468999999999999999988876632221  1223222


Q ss_pred             C-CCCc------hhHHHHHHHHHhcCC
Q 044412          272 R-EKNL------LCWNSITEALAIHGF  291 (311)
Q Consensus       272 ~-~p~~------~~~~~li~~~~~~g~  291 (311)
                      . .|+.      ..|..++..+.+.|.
T Consensus       150 ~~DpdL~plR~~pef~eLlee~rk~G~  176 (453)
T PLN03098        150 LNDPDLAPFRASPEFKELQEEARKGGE  176 (453)
T ss_pred             HhCcchhhhcccHHHHHHHHHHHHhCC
Confidence            2 4443      367888888888775

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=93.25  E-value=0.95  Score=41.46  Aligned_cols=136  Identities=17%  Similarity=0.167  Sum_probs=90.9

Q ss_pred             HHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHH
Q 044412          126 QVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMI  204 (311)
Q Consensus       126 ~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li  204 (311)
                      .....+..+|+.++..|=-.|--.|.+++    |...|+....                        .+| |...||-|=
T Consensus       420 aa~~~~~~~DpdvQ~~LGVLy~ls~efdr----aiDcf~~AL~------------------------v~Pnd~~lWNRLG  471 (579)
T KOG1125|consen  420 AARQLPTKIDPDVQSGLGVLYNLSGEFDR----AVDCFEAALQ------------------------VKPNDYLLWNRLG  471 (579)
T ss_pred             HHHhCCCCCChhHHhhhHHHHhcchHHHH----HHHHHHHHHh------------------------cCCchHHHHHHhh
Confidence            33444544566666666667777788888    6666665332                        133 678899999


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHH--HHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC------CCCc
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQV--TMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR------EKNL  276 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~------~p~~  276 (311)
                      -.++...+.++|+.-|.+-++  ++|+-+  -||.-| +|...|.+++|...|-      .|..+-.+-.      .++-
T Consensus       472 AtLAN~~~s~EAIsAY~rALq--LqP~yVR~RyNlgI-S~mNlG~ykEA~~hlL------~AL~mq~ks~~~~~~~~~se  542 (579)
T KOG1125|consen  472 ATLANGNRSEEAISAYNRALQ--LQPGYVRVRYNLGI-SCMNLGAYKEAVKHLL------EALSMQRKSRNHNKAPMASE  542 (579)
T ss_pred             HHhcCCcccHHHHHHHHHHHh--cCCCeeeeehhhhh-hhhhhhhHHHHHHHHH------HHHHhhhcccccccCCcchH
Confidence            999999999999999999887  577643  355544 5889999998866542      3333333311      1233


Q ss_pred             hhHHHHHHHHHhcCChHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGM  298 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~  298 (311)
                      ..|.+|=.++.-.++.+.+...
T Consensus       543 ~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  543 NIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             HHHHHHHHHHHHcCCchHHHHh
Confidence            5788887777777777755443

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=92.97  E-value=4.8  Score=38.22  Aligned_cols=61  Identities=15%  Similarity=0.056  Sum_probs=39.3

Q ss_pred             CcchhHHHHHHHHHhhccCChhHHHHhcccCCC-CCe------eeeec--------cccCCChhHHHHHHHHHHHCC
Q 044412           56 NLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE-PNV------FVYHA--------FSSLRHPLQAIAFYLYMLRAE  117 (311)
Q Consensus        56 ~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-~~~------~~~~~--------~~~~~~~~~a~~~~~~m~~~~  117 (311)
                      .|.+..|..+.... .+.-.++-|...|-.... +.+      .+..+        -+--|.+++|.++|-+|-++.
T Consensus       689 nPHprLWrllAe~A-l~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~drrD  764 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYA-LFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDADRRD  764 (1189)
T ss_pred             CCchHHHHHHHHHH-HHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhccchhh
Confidence            58888998888776 777777878777755432 111      11111        334577888888888776553

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=92.88  E-value=0.51  Score=34.39  Aligned_cols=101  Identities=15%  Similarity=0.087  Sum_probs=73.6

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcch--hHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec--------
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDC--FLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA--------   96 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~--~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~--------   96 (311)
                      ....++...|+..++..+|+.....|+..+.  ..+-.+-+.+ ...|+.++|..+|++...  |+......        
T Consensus         6 ~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastl-r~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen    6 ELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTL-RNLGRYDEALALLEEALEEFPDDELNAALRVFLALA   84 (120)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHH
Confidence            4566788899999999999999999987653  3555566778 899999999999987653  44221111        


Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSY  148 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~  148 (311)
                      +...|+.++|++.+-...                  .++..-|.--|..|..
T Consensus        85 L~~~gr~~eAl~~~l~~l------------------a~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   85 LYNLGRPKEALEWLLEAL------------------AETLPRYRRAIRFYAD  118 (120)
T ss_pred             HHHCCCHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHh
Confidence            778899999998886653                  3444467777766653

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.74  E-value=1.9  Score=36.24  Aligned_cols=93  Identities=12%  Similarity=0.040  Sum_probs=65.9

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH----HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC-
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ----VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR-  272 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~-  272 (311)
                      ..|+.-+.-+.+.|++++|+..|+.+.+.  .|+.    ..+-.+-.+|...|+++.|...             |+.+. 
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~-------------f~~vv~  208 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYY-------------FASVVK  208 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHH-------------HHHHHH
Confidence            45777666667779999999999999874  3543    4666777888888888855544             44443 


Q ss_pred             -CCC----chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          273 -EKN----LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       273 -~p~----~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                       -|+    ...+-.+...+...|+.++|..+|++..+.
T Consensus       209 ~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        209 NYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             132    233444556677899999999999988764

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=92.22  E-value=0.73  Score=29.42  Aligned_cols=60  Identities=17%  Similarity=0.211  Sum_probs=47.3

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccC-ChhhHHHHHH
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLG-ALDLGRGIQI  256 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~-~~~~a~~~~~  256 (311)
                      +..+|..+-..+...|++++|+..|++..+.. +-+...|..+-.++...| ++++|...++
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~   62 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFE   62 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHH
Confidence            45678888889999999999999999998853 224567788888888888 6887766553

...

>PRK04841 transcriptional regulator MalT; Provisional

Probab=92.15  E-value=14  Score=37.05  Aligned_cols=257  Identities=9%  Similarity=-0.039  Sum_probs=136.1

Q ss_pred             HHHHhhccChhhHHHHHHHHHH----hccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC-------CCee--eeec-
Q 044412           31 ANQLKKCSSIKELECVYATIVK----TNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE-------PNVF--VYHA-   96 (311)
Q Consensus        31 ~~~l~~~~~~~~~~~l~~~m~~----~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-------~~~~--~~~~-   96 (311)
                      ..+....|++..+...++...+    .....-....+.+-..+ ...|+++.|...+++...       +...  +... 
T Consensus       459 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~-~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~l  537 (903)
T PRK04841        459 AQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVH-HCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQ  537 (903)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHH
Confidence            3444566777777555554432    22222233455666667 788999999888877642       1111  1111 


Q ss_pred             ---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCC--C-chhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--
Q 044412           97 ---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFS--S-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--  168 (311)
Q Consensus        97 ---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~--~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--  168 (311)
                         +...|++++|...+++....          ....|..  + ....+..+-..+...|++++|...+.+.......  
T Consensus       538 a~~~~~~G~~~~A~~~~~~al~~----------~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~  607 (903)
T PRK04841        538 SEILFAQGFLQAAYETQEKAFQL----------IEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQ  607 (903)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHH----------HHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccC
Confidence               67789999999998876542          1122221  1 2233445555677779999955554444332221  


Q ss_pred             CCHh--HHHHHHHHHHHH-----HHHHHhhCC----CC-cHhHH-----HHHHHHHHhCCChhHHHHHHHHHHhcCCCCC
Q 044412          169 RKFA--TWNTMIDAYARL-----AELLFNKMP----AW-DIRSW-----TTMITSYSQNKQFREALDAFNKTKKSGTGSD  231 (311)
Q Consensus       169 ~~~~--~~~~li~~~~~~-----a~~~~~~m~----~~-~~~~y-----~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  231 (311)
                      +...  .+..+-..+...     |.+.++...    .. ....+     ...+..+...|+.+.|.+.+...........
T Consensus       608 ~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~  687 (903)
T PRK04841        608 PQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANN  687 (903)
T ss_pred             chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccc
Confidence            1111  111111111111     444333331    11 11111     1122444557888888888777554221111


Q ss_pred             H---HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          232 Q---VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       232 ~---~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .   ..+..+..++...|+.++|...+..      +....+....+  ...+...+-.++.+.|+.++|...+.+..+
T Consensus       688 ~~~~~~~~~~a~~~~~~g~~~~A~~~l~~------al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~  759 (903)
T PRK04841        688 HFLQGQWRNIARAQILLGQFDEAEIILEE------LNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALK  759 (903)
T ss_pred             hhHHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1   1134566667778888887776543      22222222211  124566677788899999999999888764

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=91.82  E-value=7.3  Score=33.09  Aligned_cols=86  Identities=12%  Similarity=0.200  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc-CChhhHHHHHHhhCChHHHHHHHhhcCCCC--
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL-GALDLGRGIQIYCRSLGRSLLVFFKLREKN--  275 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~-~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~--  275 (311)
                      .|.-.+..|...|++..|-+++.++               -..|-.. |+++.|...+.      .|..+|+.-..+.  
T Consensus        96 ~~~~A~~~y~~~G~~~~aA~~~~~l---------------A~~ye~~~~d~e~Ai~~Y~------~A~~~y~~e~~~~~a  154 (282)
T PF14938_consen   96 CYEKAIEIYREAGRFSQAAKCLKEL---------------AEIYEEQLGDYEKAIEYYQ------KAAELYEQEGSPHSA  154 (282)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHH---------------HHHHCCTT--HHHHHHHHH------HHHHHHHHTT-HHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHH---------------HHHHHHHcCCHHHHHHHHH------HHHHHHHHCCChhhH
Confidence            3555555555555555555555444               3446565 77777766653      4555554444222  


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..++.-+...+.+.|++++|.++|++....
T Consensus       155 ~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~  184 (282)
T PF14938_consen  155 AECLLKAADLYARLGRYEEAIEIYEEVAKK  184 (282)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            346777888899999999999999988654

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=91.78  E-value=15  Score=36.64  Aligned_cols=143  Identities=12%  Similarity=0.075  Sum_probs=63.1

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+-.+-.+|-+.|+.++|..+..++++.- ..|....|.+-..|...      .+ +.-...+.-.+..|...+++.
T Consensus       115 ~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~------dL-~KA~~m~~KAV~~~i~~kq~~  186 (906)
T PRK14720        115 NKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE------DK-EKAITYLKKAIYRFIKKKQYV  186 (906)
T ss_pred             hhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh------hH-HHHHHHHHHHHHHHHhhhcch
Confidence            33455666677777777777333333333322 12333333333333321      00 001122333344466666777


Q ss_pred             HHHHHHHHHHhcCCCCC-HHHHHHHHHHHhc----cCChhhHHHHHHh---hCChHHHHHHHhhcC---CCCchhHHHHH
Q 044412          215 EALDAFNKTKKSGTGSD-QVTMATVLSACAH----LGALDLGRGIQIY---CRSLGRSLLVFFKLR---EKNLLCWNSIT  283 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~----~~~~~~a~~~~~~---~~~~~~a~~~~~~~~---~p~~~~~~~li  283 (311)
                      +++++|.++...  .|+ ...|-.+++...+    ..-.+....+++.   ..+.+++..+++.+.   ..|.....-++
T Consensus       187 ~~~e~W~k~~~~--~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~  264 (906)
T PRK14720        187 GIEEIWSKLVHY--NSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELI  264 (906)
T ss_pred             HHHHHHHHHHhc--CcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHH
Confidence            777777776653  222 2222222222222    1122222233332   334446666666554   23445555566


Q ss_pred             HHHH
Q 044412          284 EALA  287 (311)
Q Consensus       284 ~~~~  287 (311)
                      .+|.
T Consensus       265 ~~y~  268 (906)
T PRK14720        265 RFYK  268 (906)
T ss_pred             HHHH
Confidence            6655

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.77  E-value=1.1  Score=37.75  Aligned_cols=85  Identities=16%  Similarity=0.210  Sum_probs=61.7

Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITE  284 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~  284 (311)
                      ..+.+++++|+..|.+-++  +.| |.+-|..=-.+|++.|..+.|.+-.+      .|..+     .| -..+|..|=.
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce------~Al~i-----Dp~yskay~RLG~  157 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCE------SALSI-----DPHYSKAYGRLGL  157 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHH------HHHhc-----ChHHHHHHHHHHH
Confidence            4456889999999999887  455 45566677788999998887765322      22221     22 2468899999


Q ss_pred             HHHhcCChHHHHHHHHHHHH
Q 044412          285 ALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       285 ~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +|...|++++|.+-|++-.+
T Consensus       158 A~~~~gk~~~A~~aykKaLe  177 (304)
T KOG0553|consen  158 AYLALGKYEEAIEAYKKALE  177 (304)
T ss_pred             HHHccCcHHHHHHHHHhhhc
Confidence            99999999999988887654

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=91.74  E-value=4.6  Score=31.27  Aligned_cols=115  Identities=13%  Similarity=0.011  Sum_probs=73.7

Q ss_pred             HHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHH---------------HHHHHHHHhccC-Chhh
Q 044412          187 LLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVT---------------MATVLSACAHLG-ALDL  250 (311)
Q Consensus       187 ~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t---------------~~~li~a~~~~~-~~~~  250 (311)
                      .+...-..|+...|..+|+.+.+.|++..    +..+.+.++-||...               +-.-++.+.+.+ ..+.
T Consensus        19 Sl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~~~~~   94 (167)
T PF07035_consen   19 SLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGTAYEE   94 (167)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhhhHHH
Confidence            34444456777789999999999987554    455555565555443               333444555555 5555


Q ss_pred             HHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          251 GRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       251 a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..+++-..|++-+|.++.+...+-+......++++..+.++...-..+++-..++
T Consensus        95 iievLL~~g~vl~ALr~ar~~~~~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~  149 (167)
T PF07035_consen   95 IIEVLLSKGQVLEALRYARQYHKVDSVPARKFLEAAANSNDDQLFYAVFRFFEER  149 (167)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCCcccCCHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5566666777788888877765555555567778887777776655555555443

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=91.67  E-value=7.2  Score=37.35  Aligned_cols=201  Identities=14%  Similarity=0.089  Sum_probs=113.8

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCch-----------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhcc
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLT-----------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDE  165 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~-----------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~  165 (311)
                      |...++.+++  .|-.+...-..|.           -...++....+..+..+|..|--+..++|+++.    +.+.|++
T Consensus       275 f~~~~~~Ee~--~Lllli~es~i~Re~~~d~ilslm~~~~k~r~~~~qnd~ai~d~Lt~al~~~g~f~~----lae~fE~  348 (799)
T KOG4162|consen  275 FLPKSGQEEV--ILLLLIEESLIPRENIEDAILSLMLLLRKLRLKKFQNDAAIFDHLTFALSRCGQFEV----LAEQFEQ  348 (799)
T ss_pred             cCCCCcHHHH--HHHHHHHhhccccccHHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHH----HHHHHHH
Confidence            6677777776  3333333333333           223334445577899999999999999999999    8888877


Q ss_pred             CCCC---CHhHHHHHHHHHHHH-----HHHHHhhCC--C--CcHhHHHHHHHHHHh--CCChhHHHHHHHHHHhc--C--
Q 044412          166 MPER---KFATWNTMIDAYARL-----AELLFNKMP--A--WDIRSWTTMITSYSQ--NKQFREALDAFNKTKKS--G--  227 (311)
Q Consensus       166 ~~~~---~~~~~~~li~~~~~~-----a~~~~~~m~--~--~~~~~y~~li~~~~~--~g~~~~a~~~~~~m~~~--g--  227 (311)
                      -..-   ....|+.+-..|..+     |..+++.-.  .  |+..+---|+...|-  .|..++++++-.+....  |  
T Consensus       349 ~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~  428 (799)
T KOG4162|consen  349 ALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQR  428 (799)
T ss_pred             HhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhh
Confidence            5542   223455555555444     777776543  2  443443334433332  37788888887776651  1  


Q ss_pred             --CCCCHHHHHHHHHHHh-ccCCh--------hhHHHHHHh---------------------hCChHHHHHHHhhcC---
Q 044412          228 --TGSDQVTMATVLSACA-HLGAL--------DLGRGIQIY---------------------CRSLGRSLLVFFKLR---  272 (311)
Q Consensus       228 --~~p~~~t~~~li~a~~-~~~~~--------~~a~~~~~~---------------------~~~~~~a~~~~~~~~---  272 (311)
                        +.|-..-+--+-.++. +.-..        .++.+.++.                     .+++..|.+..++..   
T Consensus       429 ~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~  508 (799)
T KOG4162|consen  429 SHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDPLVIFYLALQYAEQRQLTSALDYAREALALN  508 (799)
T ss_pred             hhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHhHHHHHHHHHHHHHhc
Confidence              2332222222211111 11111        111111111                     556666655544432   


Q ss_pred             -CCCchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          273 -EKNLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       273 -~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                       +-+...|..|.-.+...+++.+|+.+.+.-.
T Consensus       509 ~~~~~~~whLLALvlSa~kr~~~Al~vvd~al  540 (799)
T KOG4162|consen  509 RGDSAKAWHLLALVLSAQKRLKEALDVVDAAL  540 (799)
T ss_pred             CCccHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence             4567788888888888888888888877643

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=91.56  E-value=15  Score=36.02  Aligned_cols=20  Identities=15%  Similarity=0.056  Sum_probs=10.7

Q ss_pred             chhHHHHHHHHHHhCCCCcc
Q 044412          135 PVFVQTAMVDNYSYSNKFFE  154 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~  154 (311)
                      |..|...+-.+|-..|..|+
T Consensus        76 D~~tLq~l~~~y~d~~~~d~   95 (932)
T KOG2053|consen   76 DDLTLQFLQNVYRDLGKLDE   95 (932)
T ss_pred             chHHHHHHHHHHHHHhhhhH
Confidence            44555555555555555555

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=91.54  E-value=13  Score=35.25  Aligned_cols=73  Identities=12%  Similarity=0.160  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHhccCChhhHHHHHHh-------------hCChHHHHHHHhhcC--CCCch-----------hHHHHHHHH
Q 044412          233 VTMATVLSACAHLGALDLGRGIQIY-------------CRSLGRSLLVFFKLR--EKNLL-----------CWNSITEAL  286 (311)
Q Consensus       233 ~t~~~li~a~~~~~~~~~a~~~~~~-------------~~~~~~a~~~~~~~~--~p~~~-----------~~~~li~~~  286 (311)
                      .+...+-.-+.+...+-.|-++|..             .++..+|.++-++.+  .||+.           -|.--=.+|
T Consensus       748 e~l~~~a~ylk~l~~~gLAaeIF~k~gD~ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAf  827 (1081)
T KOG1538|consen  748 EPLLLCATYLKKLDSPGLAAEIFLKMGDLKSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAF  827 (1081)
T ss_pred             hHHHHHHHHHhhccccchHHHHHHHhccHHHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHH
Confidence            3444443334444445555555554             666677777777777  46653           245556789


Q ss_pred             HhcCChHHHHHHHHHHHHc
Q 044412          287 AIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       287 ~~~g~~~~a~~~~~~M~~~  305 (311)
                      .++|+-.||..+++++..-
T Consensus       828 hkAGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  828 HKAGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             HHhcchHHHHHHHHHhhhh
Confidence            9999999999999988643

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.40  E-value=9.2  Score=33.39  Aligned_cols=145  Identities=15%  Similarity=0.158  Sum_probs=94.6

Q ss_pred             HHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH--------------HHHHHhhCCCC-----cHhHHH
Q 044412          141 AMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL--------------AELLFNKMPAW-----DIRSWT  201 (311)
Q Consensus       141 ~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~--------------a~~~~~~m~~~-----~~~~y~  201 (311)
                      .|+--|.+.|++.+    |..+.++....  ..|-.++++....              |...|+-..+.     ++.--.
T Consensus       290 NL~iYyL~q~dVqe----A~~L~Kdl~Pt--tP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQ  363 (557)
T KOG3785|consen  290 NLIIYYLNQNDVQE----AISLCKDLDPT--TPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQ  363 (557)
T ss_pred             hheeeecccccHHH----HHHHHhhcCCC--ChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchH
Confidence            34556788888999    77766665432  2344555554432              77777665532     233345


Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHH
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNS  281 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~  281 (311)
                      +|-+.+.-..++++++-++..+++-=..-|.+-|| +.+|.+-.|+..+|+++|-....++.          .|..+|-.
T Consensus       364 smAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~i----------kn~~~Y~s  432 (557)
T KOG3785|consen  364 SMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEI----------KNKILYKS  432 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhh----------hhhHHHHH
Confidence            66666667778999999998887754444555555 57888888988877666644443333          45566654


Q ss_pred             -HHHHHHhcCChHHHHHHHHHH
Q 044412          282 -ITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       282 -li~~~~~~g~~~~a~~~~~~M  302 (311)
                       |-++|.++|.++.|.+++-+|
T Consensus       433 ~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  433 MLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             HHHHHHHhcCCchHHHHHHHhc
Confidence             556888999999988877655

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=91.23  E-value=13  Score=34.95  Aligned_cols=95  Identities=13%  Similarity=0.080  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH-HHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchh
Q 044412          200 WTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV-TMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLC  278 (311)
Q Consensus       200 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~  278 (311)
                      +-.++..|-+.|+++.|..+++.-..+  .|+.. -|..=-+.+...|+++.|-.++++...++.+.+.++         
T Consensus       374 ~y~laqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~IN---------  442 (700)
T KOG1156|consen  374 LYFLAQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAIN---------  442 (700)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHH---------
Confidence            344666677778888888887776643  55543 344444666777777777666666555555433322         


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 044412          279 WNSITEALAIHGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       279 ~~~li~~~~~~g~~~~a~~~~~~M~~~g  306 (311)
                       .-=..-..++.+.++|.++.....+.|
T Consensus       443 -sKcAKYmLrAn~i~eA~~~~skFTr~~  469 (700)
T KOG1156|consen  443 -SKCAKYMLRANEIEEAEEVLSKFTREG  469 (700)
T ss_pred             -HHHHHHHHHccccHHHHHHHHHhhhcc
Confidence             122223334566666666655554444

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=91.22  E-value=0.16  Score=38.15  Aligned_cols=91  Identities=12%  Similarity=0.161  Sum_probs=65.6

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--  272 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--  272 (311)
                      .+....|.++..|++.++.++..++++.       .+..-...++..|.+.|.++.+.-++...|+.++|.++...+.  
T Consensus        40 ~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~~~~l~~~a~~Ly~~~~~~~~al~i~~~~~~~  112 (143)
T PF00637_consen   40 NNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCEKHGLYEEAVYLYSKLGNHDEALEILHKLKDY  112 (143)
T ss_dssp             -SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHHTTTSHHHHHHHHHCCTTHTTCSSTSSSTHCS
T ss_pred             cCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHHhcchHHHHHHHHHHcccHHHHHHHHHHHccH
Confidence            3577888999999999888888888872       2223335667778888888888888888888887766533322  


Q ss_pred             ---------CCCchhHHHHHHHHHhcCCh
Q 044412          273 ---------EKNLLCWNSITEALAIHGFA  292 (311)
Q Consensus       273 ---------~p~~~~~~~li~~~~~~g~~  292 (311)
                               .++...|..+++.|...+..
T Consensus       113 ~~a~e~~~~~~~~~l~~~l~~~~l~~~~~  141 (143)
T PF00637_consen  113 EEAIEYAKKVDDPELWEQLLKYCLDSKPF  141 (143)
T ss_dssp             CCCTTTGGGCSSSHHHHHHHHHHCTSTCT
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHhcCcc
Confidence                     25678888888888776653

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=91.20  E-value=18  Score=36.34  Aligned_cols=214  Identities=9%  Similarity=-0.013  Sum_probs=112.3

Q ss_pred             HHHhhccCChhHHHHhcccCCC--CCeeee------ec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCC-
Q 044412           67 SFCTSRFHFIDYTILVFPQMQE--PNVFVY------HA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFS-  133 (311)
Q Consensus        67 ~~~~~~~g~~~~a~~~~~~m~~--~~~~~~------~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~-  133 (311)
                      ..+ ...|+++.|...+++..+  +....+      +.    +...|++++|...+++.....          ...|-. 
T Consensus       460 ~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~----------~~~g~~~  528 (903)
T PRK04841        460 QVA-INDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMA----------RQHDVYH  528 (903)
T ss_pred             HHH-HhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH----------hhhcchH
Confidence            444 678899999888876432  111111      11    667899999999998875421          111111 


Q ss_pred             CchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC---CC----HhHHHHHHHHHHHH-----HHHHHhhC-------CC
Q 044412          134 SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE---RK----FATWNTMIDAYARL-----AELLFNKM-------PA  194 (311)
Q Consensus       134 ~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~---~~----~~~~~~li~~~~~~-----a~~~~~~m-------~~  194 (311)
                      +....+..+-..+...|++++|.+.+.+.......   ++    ...+..+-..+...     |...+.+.       ..
T Consensus       529 ~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~  608 (903)
T PRK04841        529 YALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQP  608 (903)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCc
Confidence            11234555666788899999966554444332221   11    11121111111111     33333332       11


Q ss_pred             C-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCC-CCHHHH-----HHHHHHHhccCChhhHHHHHHhhCChHHHHHH
Q 044412          195 W-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG-SDQVTM-----ATVLSACAHLGALDLGRGIQIYCRSLGRSLLV  267 (311)
Q Consensus       195 ~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~t~-----~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~  267 (311)
                      + ....+..+-..+...|+.++|.+.+.+.....-. .....+     ...+..+...|+.+.|...+            
T Consensus       609 ~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l------------  676 (903)
T PRK04841        609 QQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWL------------  676 (903)
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHH------------
Confidence            1 1233444555667789999999888887542110 111111     11123334456666555443            


Q ss_pred             HhhcCCCC---c----hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          268 FFKLREKN---L----LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       268 ~~~~~~p~---~----~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                       .....+.   .    ..+..+..++...|+.++|..++++...
T Consensus       677 -~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~  719 (903)
T PRK04841        677 -RQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNE  719 (903)
T ss_pred             -HhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             2222111   1    1245667788899999999999888654

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=91.06  E-value=0.39  Score=30.37  Aligned_cols=44  Identities=20%  Similarity=0.273  Sum_probs=33.0

Q ss_pred             HHHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          262 GRSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       262 ~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      +.|.+.|+...  .| +...+..+-..+...|++++|..+|++..+.
T Consensus        14 ~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen   14 DEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            35555555555  23 4668888899999999999999999999763

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=90.61  E-value=8.8  Score=31.84  Aligned_cols=178  Identities=10%  Similarity=0.037  Sum_probs=101.7

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCch-hHH---HHHHHHHHhCCCCccchHHHHHHhccCCCCCHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPV-FVQ---TAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA  172 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~-~~~---~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~  172 (311)
                      +...|++++|.+.|+++...                -|+. ..-   -.+..+|-+.++.++|....+++.+.-+...-.
T Consensus        42 ~~~~g~y~~Ai~~f~~l~~~----------------yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~  105 (243)
T PRK10866         42 KLQDGNWKQAITQLEALDNR----------------YPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNI  105 (243)
T ss_pred             HHHCCCHHHHHHHHHHHHHh----------------CCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCch
Confidence            66789999999999999764                3332 222   345678899999999666666666665654445


Q ss_pred             HHHHHHHHHHHH--HHHHHhhCC-----CCc-------HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          173 TWNTMIDAYARL--AELLFNKMP-----AWD-------IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       173 ~~~~li~~~~~~--a~~~~~~m~-----~~~-------~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                      .|.....+.+..  ....|....     ..|       ...+..+|+-|-.+.-..+|...+..+...   .-..-+ .+
T Consensus       106 ~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~---la~~e~-~i  181 (243)
T PRK10866        106 DYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDR---LAKYEL-SV  181 (243)
T ss_pred             HHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHH---HHHHHH-HH
Confidence            555555555432  222222211     111       134566666666666666666555544321   000111 22


Q ss_pred             HHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCCchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          239 LSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKNLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       239 i~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      -.-|.+.|.+..|..         ....+.+.-+  .........++.+|...|..++|..+.....
T Consensus       182 a~~Y~~~~~y~AA~~---------r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        182 AEYYTKRGAYVAVVN---------RVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHcCchHHHHH---------HHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            333555555553322         2233333333  2233566788899999999999988776554

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=90.45  E-value=5.2  Score=29.74  Aligned_cols=47  Identities=6%  Similarity=0.172  Sum_probs=35.6

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCC
Q 044412          200 WTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGA  247 (311)
Q Consensus       200 y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~  247 (311)
                      ...+|..+-..+.+.....+++.+...|. .+....+.++..|++.+.
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~~   56 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYDP   56 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHCH
Confidence            44667777777888888888888887763 677788888888887543

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=90.29  E-value=9.1  Score=35.29  Aligned_cols=126  Identities=17%  Similarity=0.200  Sum_probs=70.6

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCCCC-----eeeeec---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQEPN-----VFVYHA---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~-----~~~~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      -+|-.+|+.. .|...++.|..+|.+..+-.     +...++   |...++.+-|.++|+.=.+.               
T Consensus       367 Lv~~~~mn~i-rR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD~~~AfrIFeLGLkk---------------  430 (656)
T KOG1914|consen  367 LVYCQYMNFI-RRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKDKETAFRIFELGLKK---------------  430 (656)
T ss_pred             eehhHHHHHH-HHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCChhHHHHHHHHHHHh---------------
Confidence            4566667776 77777777777776665321     222222   55566777777777653322               


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCC
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNK  211 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g  211 (311)
                      +.-++.--...++-+...|+=..    ++.+|++......                    -.+.....|..+|+-=..-|
T Consensus       431 f~d~p~yv~~YldfL~~lNdd~N----~R~LFEr~l~s~l--------------------~~~ks~~Iw~r~l~yES~vG  486 (656)
T KOG1914|consen  431 FGDSPEYVLKYLDFLSHLNDDNN----ARALFERVLTSVL--------------------SADKSKEIWDRMLEYESNVG  486 (656)
T ss_pred             cCCChHHHHHHHHHHHHhCcchh----HHHHHHHHHhccC--------------------ChhhhHHHHHHHHHHHHhcc
Confidence            22233334556667777777777    5555555332210                    00123456666666666667


Q ss_pred             ChhHHHHHHHHHHh
Q 044412          212 QFREALDAFNKTKK  225 (311)
Q Consensus       212 ~~~~a~~~~~~m~~  225 (311)
                      ++..+.++=+++..
T Consensus       487 dL~si~~lekR~~~  500 (656)
T KOG1914|consen  487 DLNSILKLEKRRFT  500 (656)
T ss_pred             cHHHHHHHHHHHHH
Confidence            77766666665543

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.26  E-value=9.9  Score=31.82  Aligned_cols=205  Identities=6%  Similarity=0.015  Sum_probs=102.0

Q ss_pred             HHHHHHhhccChhhH-HHHHHHHHHhccCc--chhHHHHHHHHHhhccCChhHHHHhcccCC---CCCeeeeec----cc
Q 044412           29 IIANQLKKCSSIKEL-ECVYATIVKTNANL--DCFLAKQFISFCTSRFHFIDYTILVFPQMQ---EPNVFVYHA----FS   98 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~-~~l~~~m~~~g~~p--~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~---~~~~~~~~~----~~   98 (311)
                      .+...+..||++..+ .+++....-....|  ....|+.-+.++ .+....+.|..=++...   .||..--.-    -.
T Consensus        36 ~~~~~~~~~g~~~~~~~~~~~~~~~l~~~t~~~lq~wT~r~~~l-~kLR~~~~a~~EL~~f~~lD~pdl~Yey~p~iyp~  114 (366)
T KOG2796|consen   36 NWRAAVDLCGRLLTAHGQGYGKSGLLTSHTTDSLQLWTVRLALL-VKLRLFQNAEMELEPFGNLDQPDLYYEYYPHVYPG  114 (366)
T ss_pred             hhHHHHhhhHHHHHHHhhhhhhhheeeccchhHHHHHHHHHHHH-HHHhhhHHHHhhhhhhccCCCcceeeeeccccCCC
Confidence            344455566665554 23322111111222  335667667777 88888888866655554   344321111    12


Q ss_pred             cCC-ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC--HhHH-
Q 044412           99 SLR-HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK--FATW-  174 (311)
Q Consensus        99 ~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~--~~~~-  174 (311)
                      +.| .+--+++++......               .-|+  -+++|++.+.-...+++    ....++....|.  +..| 
T Consensus       115 rrGSmVPFsmR~lhAe~~~---------------~lgn--pqesLdRl~~L~~~V~~----ii~~~e~~~~~ESsv~lW~  173 (366)
T KOG2796|consen  115 RRGSMVPFSMRILHAELQQ---------------YLGN--PQESLDRLHKLKTVVSK----ILANLEQGLAEESSIRLWR  173 (366)
T ss_pred             CcCccccHHHHHHHHHHHH---------------hcCC--cHHHHHHHHHHHHHHHH----HHHHHHhccchhhHHHHHH
Confidence            333 445566655433221               2233  24667666665555555    444444443322  1112 


Q ss_pred             ---HHHHHHHHHH---------HHHHHhhCCCC----cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          175 ---NTMIDAYARL---------AELLFNKMPAW----DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       175 ---~~li~~~~~~---------a~~~~~~m~~~----~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                         ..+...+..+         +..++++..+.    +...-..+.+.--+.|+.+.|..+|++..+..-..|..+++.+
T Consensus       174 KRl~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~  253 (366)
T KOG2796|consen  174 KRLGRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIM  253 (366)
T ss_pred             HHHHHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHH
Confidence               1122222221         44555544433    3444445555555579999999999988776556666666655


Q ss_pred             HH-----HHhccCChhhHHHHH
Q 044412          239 LS-----ACAHLGALDLGRGIQ  255 (311)
Q Consensus       239 i~-----a~~~~~~~~~a~~~~  255 (311)
                      +.     .|...+++-.|...+
T Consensus       254 V~~n~a~i~lg~nn~a~a~r~~  275 (366)
T KOG2796|consen  254 VLMNSAFLHLGQNNFAEAHRFF  275 (366)
T ss_pred             HHhhhhhheecccchHHHHHHH
Confidence            42     233344444444444

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=90.22  E-value=6.1  Score=29.36  Aligned_cols=15  Identities=20%  Similarity=0.282  Sum_probs=8.4

Q ss_pred             HHHHHHHHhCCCCcc
Q 044412          140 TAMVDNYSYSNKFFE  154 (311)
Q Consensus       140 ~~ll~~~~~~g~~~~  154 (311)
                      ..+|..+...+....
T Consensus        11 ~~vv~~~~~~~~~~~   25 (140)
T smart00299       11 SEVVELFEKRNLLEE   25 (140)
T ss_pred             HHHHHHHHhCCcHHH
Confidence            345555555555556

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.21  E-value=11  Score=32.18  Aligned_cols=170  Identities=11%  Similarity=0.068  Sum_probs=107.6

Q ss_pred             hccCChhHHHHhcccCCC-CCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQE-PNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDN  145 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~-~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~  145 (311)
                      -..+++..+..++++.+. .+..+.+-    ..+.|+++.|.+-|+.-.+-             +|++|- ..||.-+-.
T Consensus       123 Yse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqv-------------sGyqpl-lAYniALaH  188 (459)
T KOG4340|consen  123 YSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQV-------------SGYQPL-LAYNLALAH  188 (459)
T ss_pred             cccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhh-------------cCCCch-hHHHHHHHH
Confidence            346777778888888873 44433333    67899999999999886543             345554 467766655


Q ss_pred             HHhCCCCccchHHHHHHhccCCC-------------CCHh--------HHHHHHHHHHHH------------HHHHHhhC
Q 044412          146 YSYSNKFFESRRVSRRLFDEMPE-------------RKFA--------TWNTMIDAYARL------------AELLFNKM  192 (311)
Q Consensus       146 ~~~~g~~~~a~~~a~~~~~~~~~-------------~~~~--------~~~~li~~~~~~------------a~~~~~~m  192 (311)
                      |. .|+.+.|.....++.+++.+             +|+.        .-+.++.++--.            |.+-+..|
T Consensus       189 y~-~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDm  267 (459)
T KOG4340|consen  189 YS-SRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDM  267 (459)
T ss_pred             Hh-hhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcC
Confidence            54 56788866666666665432             2221        223344444321            88888888


Q ss_pred             CCC-----cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          193 PAW-----DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       193 ~~~-----~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +.+     |.+|...+--.- ..+++.+..+-+.-+...+ +.-..||..++-.||++.-++.|-+++.+
T Consensus       268 PPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~n-PfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  268 PPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQN-PFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             CCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcC-CCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            743     666655543322 2356666666666666542 23467999999999999999988877633

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=90.14  E-value=0.74  Score=29.39  Aligned_cols=64  Identities=11%  Similarity=0.023  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcC-ChHHHHHHHHHHHH
Q 044412          231 DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHG-FAHEALGMFDRMTY  304 (311)
Q Consensus       231 ~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~M~~  304 (311)
                      ++.+|..+=..+...|++++|...|..      |.++    ...+...|..+-.+|...| ++++|...+++-.+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~------ai~~----~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEK------AIEL----DPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHH------HHHH----STTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHc----CCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            356677777788888888866665533      2211    0235678899999999999 79999999988664

...

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=90.07  E-value=6.7  Score=29.58  Aligned_cols=101  Identities=13%  Similarity=0.071  Sum_probs=71.8

Q ss_pred             HHHhcCCCch--hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHH
Q 044412          127 VWKNGFSSPV--FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMI  204 (311)
Q Consensus       127 ~~~~g~~~~~--~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li  204 (311)
                      +.+.+..++.  ...|++|......+++..    ..++++.+..-+.    ..+.             ...+-.+|++++
T Consensus        28 ~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~----~v~~L~~l~~l~~----~~~~-------------~~~~~ssf~~if   86 (145)
T PF13762_consen   28 MQEENASQSTKTIFINCILNHLASYQNFSG----VVSILEHLHFLNT----DNII-------------GWLDNSSFHIIF   86 (145)
T ss_pred             hhhcccChhHHHHHHHHHHHHHHHccchHH----HHHHHHHHHHhhH----HHHh-------------hhcccchHHHHH
Confidence            3444566664  457889999898899999    6666665522111    0000             123566899999


Q ss_pred             HHHHhCCC-hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          205 TSYSQNKQ-FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       205 ~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                      .+.++..- ---+..+|.-|++.+.+++..-|..+|+++.+.-..
T Consensus        87 ~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g~~~  131 (145)
T PF13762_consen   87 KSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRGYFH  131 (145)
T ss_pred             HHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCC
Confidence            99977665 456778999999989999999999999999886433

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=89.78  E-value=1.7  Score=33.22  Aligned_cols=89  Identities=10%  Similarity=0.041  Sum_probs=63.9

Q ss_pred             HHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHHH
Q 044412          140 TAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREALD  218 (311)
Q Consensus       140 ~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~~  218 (311)
                      -.+-..+...|++++    |.++|+-...-                        +| +..-|-.|--++-..|++++|+.
T Consensus        39 Y~~A~~ly~~G~l~~----A~~~f~~L~~~------------------------Dp~~~~y~~gLG~~~Q~~g~~~~AI~   90 (157)
T PRK15363         39 YRYAMQLMEVKEFAG----AARLFQLLTIY------------------------DAWSFDYWFRLGECCQAQKHWGEAIY   90 (157)
T ss_pred             HHHHHHHHHCCCHHH----HHHHHHHHHHh------------------------CcccHHHHHHHHHHHHHHhhHHHHHH
Confidence            334455778899999    77777753321                        33 34456666666777799999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          219 AFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       219 ~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      .|....... +-|+..+-.+=.++...|+.+.|++.|+.
T Consensus        91 aY~~A~~L~-~ddp~~~~~ag~c~L~lG~~~~A~~aF~~  128 (157)
T PRK15363         91 AYGRAAQIK-IDAPQAPWAAAECYLACDNVCYAIKALKA  128 (157)
T ss_pred             HHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999988765 24567777778889999999988776644

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=89.72  E-value=14  Score=34.44  Aligned_cols=126  Identities=13%  Similarity=0.005  Sum_probs=81.4

Q ss_pred             HhcCCCchhHHHHHHHHHHhCCCCcc-chHHHHHHhccCCC--CCH-hHHHHHHHHHHHH-------------HHHHHhh
Q 044412          129 KNGFSSPVFVQTAMVDNYSYSNKFFE-SRRVSRRLFDEMPE--RKF-ATWNTMIDAYARL-------------AELLFNK  191 (311)
Q Consensus       129 ~~g~~~~~~~~~~ll~~~~~~g~~~~-a~~~a~~~~~~~~~--~~~-~~~~~li~~~~~~-------------a~~~~~~  191 (311)
                      ..+...+...|...+.+.......+. ...-|..+|++..+  |+- ..|..+..++...             +.+....
T Consensus       330 ~~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        330 QQGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             hccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            34566788999999998665543221 22237778777654  442 2333332222111             2222222


Q ss_pred             -----CCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          192 -----MPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       192 -----m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                           ....+...|.++--.....|++++|...+++....+  |+...|..+-..+...|+.++|...+.
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~  477 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYS  477 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                 112345677777666666799999999999998854  788999999999999999997766553

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.40  E-value=5.8  Score=33.13  Aligned_cols=86  Identities=14%  Similarity=0.065  Sum_probs=51.0

Q ss_pred             HHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC----CCeeeeec---------
Q 044412           30 IANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE----PNVFVYHA---------   96 (311)
Q Consensus        30 ~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~---------   96 (311)
                      +...+...+..+-...++..+++..-+.++.....|.+.- .+.|+.+.|...|+..++    -|-.+.+.         
T Consensus       183 ~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~-MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i  261 (366)
T KOG2796|consen  183 MANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRIS-MQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFL  261 (366)
T ss_pred             HHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHH-HhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhh
Confidence            3333444444444466666677766666777777777777 778888888877775432    12222211         


Q ss_pred             cccCCChhHHHHHHHHHHHC
Q 044412           97 FSSLRHPLQAIAFYLYMLRA  116 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~  116 (311)
                      +.-++++..|...|.+....
T Consensus       262 ~lg~nn~a~a~r~~~~i~~~  281 (366)
T KOG2796|consen  262 HLGQNNFAEAHRFFTEILRM  281 (366)
T ss_pred             eecccchHHHHHHHhhcccc
Confidence            55556666666666665443

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=89.40  E-value=2.3  Score=35.96  Aligned_cols=81  Identities=14%  Similarity=0.143  Sum_probs=62.9

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ..++..++..+..+|+++.    +.+.+++....+                       .-|...|..+|.+|.+.|+...
T Consensus       153 ~~~l~~lae~~~~~~~~~~----~~~~l~~Li~~d-----------------------p~~E~~~~~lm~~y~~~g~~~~  205 (280)
T COG3629         153 IKALTKLAEALIACGRADA----VIEHLERLIELD-----------------------PYDEPAYLRLMEAYLVNGRQSA  205 (280)
T ss_pred             HHHHHHHHHHHHhcccHHH----HHHHHHHHHhcC-----------------------ccchHHHHHHHHHHHHcCCchH
Confidence            3467778888888888888    555555433221                       2277899999999999999999


Q ss_pred             HHHHHHHHHh-----cCCCCCHHHHHHHHHHHh
Q 044412          216 ALDAFNKTKK-----SGTGSDQVTMATVLSACA  243 (311)
Q Consensus       216 a~~~~~~m~~-----~g~~p~~~t~~~li~a~~  243 (311)
                      |++.|+.+.+     .|+.|-..+.........
T Consensus       206 ai~~y~~l~~~~~edlgi~P~~~~~~~y~~~~~  238 (280)
T COG3629         206 AIRAYRQLKKTLAEELGIDPAPELRALYEEILR  238 (280)
T ss_pred             HHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhc
Confidence            9999999876     599999998888777743

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=89.35  E-value=14  Score=32.21  Aligned_cols=38  Identities=8%  Similarity=0.001  Sum_probs=20.7

Q ss_pred             CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH
Q 044412          194 AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV  233 (311)
Q Consensus       194 ~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  233 (311)
                      ..|..+.--+-..+-..|+.+.++...++-.+  +-||.-
T Consensus       220 ~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ldpdHK  257 (504)
T KOG0624|consen  220 QDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LDPDHK  257 (504)
T ss_pred             ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cCcchh
Confidence            33444444444555556666666666666554  345543

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=88.54  E-value=1.3  Score=24.28  Aligned_cols=26  Identities=12%  Similarity=0.346  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTK  224 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~  224 (311)
                      +|+.|-..|.+.|++++|+++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46778888999999999999998854

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=88.52  E-value=3.8  Score=32.19  Aligned_cols=97  Identities=13%  Similarity=0.110  Sum_probs=67.2

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH--HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ--VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      ..+..+.+-|++.|+.++|++.|.++......|..  ..+-.+|......+++..+......      |....+....++
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~k------a~~~~~~~~d~~  110 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEK------AESLIEKGGDWE  110 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH------HHHHHhccchHH
Confidence            46889999999999999999999999987666654  4577888999999999988766433      333333322111


Q ss_pred             ----chhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          276 ----LLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       276 ----~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                          ...|..+.  +...|++.+|-+.|-+.
T Consensus       111 ~~nrlk~~~gL~--~l~~r~f~~AA~~fl~~  139 (177)
T PF10602_consen  111 RRNRLKVYEGLA--NLAQRDFKEAAELFLDS  139 (177)
T ss_pred             HHHHHHHHHHHH--HHHhchHHHHHHHHHcc
Confidence                23333332  23467888888777554

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.51  E-value=13  Score=30.87  Aligned_cols=140  Identities=9%  Similarity=0.032  Sum_probs=90.1

Q ss_pred             hhhHHHHHhhhhhcCCCCCchhhhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchh---HHHHHHHHHhhccCChhHH
Q 044412            3 VKYVRAIITSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCF---LAKQFISFCTSRFHFIDYT   79 (311)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~---~~~~ll~~~~~~~g~~~~a   79 (311)
                      |..-++++...+.+-.-+..-.+....++.+ -.|++...++..+..+.+.= +-+..   ....++    --.|+.++|
T Consensus        32 v~l~~~~~~~~k~~~~g~e~w~l~EqV~IAA-ld~~~~~lAq~C~~~L~~~f-p~S~RV~~lkam~l----Ea~~~~~~A  105 (289)
T KOG3060|consen   32 VQLGSEVLNYSKSGALGDEIWTLYEQVFIAA-LDTGRDDLAQKCINQLRDRF-PGSKRVGKLKAMLL----EATGNYKEA  105 (289)
T ss_pred             HHHHHHHHHHhhhcccCchHHHHHHHHHHHH-HHhcchHHHHHHHHHHHHhC-CCChhHHHHHHHHH----HHhhchhhH
Confidence            3445566655555512222222333344444 45788888988888877653 22222   233333    445899999


Q ss_pred             HHhcccCCCCCe---eeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCC
Q 044412           80 ILVFPQMQEPNV---FVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKF  152 (311)
Q Consensus        80 ~~~~~~m~~~~~---~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~  152 (311)
                      .++++.+.+.|.   +++.-    .-..|...+|++-+.+..+.               +..|...|.-+-+.|...|++
T Consensus       106 ~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~---------------F~~D~EAW~eLaeiY~~~~~f  170 (289)
T KOG3060|consen  106 IEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK---------------FMNDQEAWHELAEIYLSEGDF  170 (289)
T ss_pred             HHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH---------------hcCcHHHHHHHHHHHHhHhHH
Confidence            999999876542   22211    34446666888777776654               678999999999999999999


Q ss_pred             ccchHHHHHHhccCC
Q 044412          153 FESRRVSRRLFDEMP  167 (311)
Q Consensus       153 ~~a~~~a~~~~~~~~  167 (311)
                      ++    |.-.++++.
T Consensus       171 ~k----A~fClEE~l  181 (289)
T KOG3060|consen  171 EK----AAFCLEELL  181 (289)
T ss_pred             HH----HHHHHHHHH
Confidence            99    777777653

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=87.75  E-value=6.4  Score=35.87  Aligned_cols=141  Identities=9%  Similarity=0.048  Sum_probs=99.5

Q ss_pred             hhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhH
Q 044412           59 CFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFV  138 (311)
Q Consensus        59 ~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~  138 (311)
                      ..-.+.+++.+ -+.|..+.|+++...-   + .-+....+.|+++.|.++-++                    ..+...
T Consensus       295 ~~~~~~i~~fL-~~~G~~e~AL~~~~D~---~-~rFeLAl~lg~L~~A~~~a~~--------------------~~~~~~  349 (443)
T PF04053_consen  295 KDQGQSIARFL-EKKGYPELALQFVTDP---D-HRFELALQLGNLDIALEIAKE--------------------LDDPEK  349 (443)
T ss_dssp             HHHHHHHHHHH-HHTT-HHHHHHHSS-H---H-HHHHHHHHCT-HHHHHHHCCC--------------------CSTHHH
T ss_pred             hhHHHHHHHHH-HHCCCHHHHHhhcCCh---H-HHhHHHHhcCCHHHHHHHHHh--------------------cCcHHH
Confidence            45578888888 9999999999887542   1 111114567777777666543                    346779


Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHH
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALD  218 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~  218 (311)
                      |..|-+...+.|+++-    |++.+....                               -|..|+--|...|+.++-.+
T Consensus       350 W~~Lg~~AL~~g~~~l----Ae~c~~k~~-------------------------------d~~~L~lLy~~~g~~~~L~k  394 (443)
T PF04053_consen  350 WKQLGDEALRQGNIEL----AEECYQKAK-------------------------------DFSGLLLLYSSTGDREKLSK  394 (443)
T ss_dssp             HHHHHHHHHHTTBHHH----HHHHHHHCT--------------------------------HHHHHHHHHHCT-HHHHHH
T ss_pred             HHHHHHHHHHcCCHHH----HHHHHHhhc-------------------------------CccccHHHHHHhCCHHHHHH
Confidence            9999999999999999    888888743                               35566777788888888777


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHH
Q 044412          219 AFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSL  265 (311)
Q Consensus       219 ~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~  265 (311)
                      +-+.-...|      -++..+.++.-.|+.++..+++...|+..+|.
T Consensus       395 l~~~a~~~~------~~n~af~~~~~lgd~~~cv~lL~~~~~~~~A~  435 (443)
T PF04053_consen  395 LAKIAEERG------DINIAFQAALLLGDVEECVDLLIETGRLPEAA  435 (443)
T ss_dssp             HHHHHHHTT-------HHHHHHHHHHHT-HHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHcc------CHHHHHHHHHHcCCHHHHHHHHHHcCCchHHH
Confidence            777766655      26777777888899998888888888887774

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=87.50  E-value=2.3  Score=27.36  Aligned_cols=52  Identities=15%  Similarity=0.137  Sum_probs=38.2

Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      ..|.+.+++++|.++++.+...+ +-+...+...-.++...|+++.|...++.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~   54 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLER   54 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHH
Confidence            46778899999999999998752 22455566677778888888877665543

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=87.49  E-value=20  Score=36.32  Aligned_cols=103  Identities=15%  Similarity=0.107  Sum_probs=53.4

Q ss_pred             HHHHHHHHHhCC--ChhHHHHHHHHH--HhcC---CCCCHHHHHHHHHHH-----------------hccCChhhHHHHH
Q 044412          200 WTTMITSYSQNK--QFREALDAFNKT--KKSG---TGSDQVTMATVLSAC-----------------AHLGALDLGRGIQ  255 (311)
Q Consensus       200 y~~li~~~~~~g--~~~~a~~~~~~m--~~~g---~~p~~~t~~~li~a~-----------------~~~~~~~~a~~~~  255 (311)
                      |..-+..+...|  .+++++++.++=  ...+   ..||...+..+..+|                 .+.|+.++|...+
T Consensus       896 y~~AL~hLs~~~~~~~~e~~n~I~kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~GklekAl~a~  975 (1265)
T KOG1920|consen  896 YEDALSHLSECGETYFPECKNYIKKHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKLEKALKAY  975 (1265)
T ss_pred             HHHHHHHHHHcCccccHHHHHHHHhcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccHHHHHHHH
Confidence            444555555554  455555544331  0111   367777666666444                 3444555555555


Q ss_pred             HhhCChHHHHHHHhhcCCCCch---hHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          256 IYCRSLGRSLLVFFKLREKNLL---CWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       256 ~~~~~~~~a~~~~~~~~~p~~~---~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                      ..+|+..++..+-.++..+-..   +-..|+.-+...|+.-+|-++..+-
T Consensus       976 ~~~~dWr~~l~~a~ql~~~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~ 1025 (1265)
T KOG1920|consen  976 KECGDWREALSLAAQLSEGKDELVILAEELVSRLVEQRKHYEAAKILLEY 1025 (1265)
T ss_pred             HHhccHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHcccchhHHHHHHHH
Confidence            5555555555554444432222   2256677777777777777666553

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=87.39  E-value=1.3  Score=39.52  Aligned_cols=122  Identities=11%  Similarity=0.178  Sum_probs=87.4

Q ss_pred             HHHhhccChhhHHHHHHHHHHhc-cCcchhHHHHHHHHHhhccCChhHHHHhccc-CC-CCCeeeeec-----cccCCCh
Q 044412           32 NQLKKCSSIKELECVYATIVKTN-ANLDCFLAKQFISFCTSRFHFIDYTILVFPQ-MQ-EPNVFVYHA-----FSSLRHP  103 (311)
Q Consensus        32 ~~l~~~~~~~~~~~l~~~m~~~g-~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~-m~-~~~~~~~~~-----~~~~~~~  103 (311)
                      ..+.....++.++.+|-...+.| +.|++.+++++|..+ + .|+...|.++|+- |. -||...|.-     +.+-++-
T Consensus       405 N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~-~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~fLi~inde  482 (660)
T COG5107         405 NYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYY-A-TGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDE  482 (660)
T ss_pred             HHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHH-h-cCCcchHHHHHHHHHHhCCCchHHHHHHHHHHHHhCcH
Confidence            33344455666788999999988 788999999999887 4 5777888888865 22 366555544     6777888


Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc--hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP--VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK  170 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~--~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~  170 (311)
                      ..|..+|+.-..+               +..+  ..+|..+|+-=...|++..+..+-..++...++.+
T Consensus       483 ~naraLFetsv~r---------------~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQen  536 (660)
T COG5107         483 ENARALFETSVER---------------LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQEN  536 (660)
T ss_pred             HHHHHHHHHhHHH---------------HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCcHh
Confidence            8888888865443               2233  56888999988889999887776666666666544

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=87.29  E-value=1.7  Score=23.84  Aligned_cols=26  Identities=12%  Similarity=0.226  Sum_probs=22.2

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          278 CWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       278 ~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      +|+.|-..|.+.|++++|.++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            47888999999999999999999854

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=86.97  E-value=19  Score=30.95  Aligned_cols=155  Identities=14%  Similarity=0.117  Sum_probs=86.8

Q ss_pred             HHHHHHHhhccC-hhhH----HHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCC
Q 044412           28 HIIANQLKKCSS-IKEL----ECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRH  102 (311)
Q Consensus        28 ~~~~~~l~~~~~-~~~~----~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~  102 (311)
                      .++...+...+. ++..    ..+++.|++.|++-+..+|-+..-.. .. .+-+..                    ...
T Consensus        61 ~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~-~~-~~~~~~--------------------~~~  118 (297)
T PF13170_consen   61 FILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIIL-EE-EEKEDY--------------------DEI  118 (297)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHH-Hh-cccccH--------------------HHH
Confidence            366677776666 4444    78899999999998887776644444 22 111111                    113


Q ss_pred             hhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHH
Q 044412          103 PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA  182 (311)
Q Consensus       103 ~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~  182 (311)
                      ..+|..+|+.|++.-.-.           -.++-.++..+|..  ..++++.-.+-++.+++.+.+.             
T Consensus       119 ~~ra~~iy~~mKk~H~fL-----------Ts~~D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~-------------  172 (297)
T PF13170_consen  119 IQRAKEIYKEMKKKHPFL-----------TSPEDYPFAALLAM--TSEDVEELAERMEQCYQKLADA-------------  172 (297)
T ss_pred             HHHHHHHHHHHHHhCccc-----------cCccchhHHHHHhc--ccccHHHHHHHHHHHHHHHHHh-------------
Confidence            577888888887643100           13445566666554  3344444222233333332211             


Q ss_pred             HHHHHHHhhCCCCcHhHHHHHHHHHHhCCC---hhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          183 RLAELLFNKMPAWDIRSWTTMITSYSQNKQ---FREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       183 ~~a~~~~~~m~~~~~~~y~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                              .+.+-|..-+-+-|-+++....   +.++.++++.+.+.|+++....|..+
T Consensus       173 --------~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  173 --------GFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             --------CCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence                    1222233333333444443322   55788999999999999988876643

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=86.93  E-value=1.9  Score=24.86  Aligned_cols=29  Identities=21%  Similarity=0.255  Sum_probs=25.4

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      .+|..+-..|.+.|++++|.++|++..+.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            35778889999999999999999999874

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=86.06  E-value=3.2  Score=38.23  Aligned_cols=100  Identities=10%  Similarity=0.071  Sum_probs=70.1

Q ss_pred             HHHHHHHH-HhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC---CCCeeeeec----cccCCChhHHHHHHHHHHH
Q 044412           44 ECVYATIV-KTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ---EPNVFVYHA----FSSLRHPLQAIAFYLYMLR  115 (311)
Q Consensus        44 ~~l~~~m~-~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~---~~~~~~~~~----~~~~~~~~~a~~~~~~m~~  115 (311)
                      .++|-.+. ..+-++|+.+...|=-.| --.|.+++|...|+...   ..|...||-    ++...+.++|+..|.+-.+
T Consensus       414 ~~~fLeaa~~~~~~~DpdvQ~~LGVLy-~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq  492 (579)
T KOG1125|consen  414 QELFLEAARQLPTKIDPDVQSGLGVLY-NLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQ  492 (579)
T ss_pred             HHHHHHHHHhCCCCCChhHHhhhHHHH-hcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHh
Confidence            44444443 455446666666666666 77889999999998865   345667777    8888889999999988766


Q ss_pred             CCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhc
Q 044412          116 AEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus       116 ~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~  164 (311)
                                      ++|+ +.+...|--+|...|.+++    |...|-
T Consensus       493 ----------------LqP~yVR~RyNlgIS~mNlG~ykE----A~~hlL  522 (579)
T KOG1125|consen  493 ----------------LQPGYVRVRYNLGISCMNLGAYKE----AVKHLL  522 (579)
T ss_pred             ----------------cCCCeeeeehhhhhhhhhhhhHHH----HHHHHH
Confidence                            5777 4455556667888899988    555443

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=86.05  E-value=0.5  Score=35.48  Aligned_cols=55  Identities=9%  Similarity=0.096  Sum_probs=44.2

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      .+|+.+-+.+.++....+++.+...+-.-+....+.++..|++.+..+....+++
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            3577777889999999999999988777788999999999999988776655554

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=86.04  E-value=15  Score=33.23  Aligned_cols=66  Identities=6%  Similarity=-0.020  Sum_probs=51.4

Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcH----hHHHHHHHHHH
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDI----RSWTTMITSYS  208 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~----~~y~~li~~~~  208 (311)
                      +.+...++.+-.+|.+.|++++    |...|++..+.                        .|+.    .+|..+-.+|.
T Consensus        72 P~~a~a~~NLG~AL~~lGryeE----AIa~f~rALeL------------------------~Pd~aeA~~A~yNLAcaya  123 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKD----ALAQFETALEL------------------------NPNPDEAQAAYYNKACCHA  123 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhh------------------------CCCchHHHHHHHHHHHHHH
Confidence            3457788999999999999999    66666553321                        2332    45889999999


Q ss_pred             hCCChhHHHHHHHHHHhc
Q 044412          209 QNKQFREALDAFNKTKKS  226 (311)
Q Consensus       209 ~~g~~~~a~~~~~~m~~~  226 (311)
                      ..|+.++|++.+++..+.
T Consensus       124 ~LGr~dEAla~LrrALel  141 (453)
T PLN03098        124 YREEGKKAADCLRTALRD  141 (453)
T ss_pred             HcCCHHHHHHHHHHHHHh
Confidence            999999999999998775

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=85.98  E-value=2.3  Score=27.31  Aligned_cols=53  Identities=17%  Similarity=0.080  Sum_probs=38.9

Q ss_pred             HHHhccCChhhHHHHHHhhCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          240 SACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       240 ~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..|.+.++++.|             .++++.+.   ..++..|...-..+...|++.+|...|++..+.
T Consensus         3 ~~~~~~~~~~~A-------------~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEA-------------LEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHH-------------HHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            346666777654             44444443   235677888889999999999999999998864

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=85.84  E-value=15  Score=30.95  Aligned_cols=94  Identities=11%  Similarity=-0.039  Sum_probs=58.1

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCCh
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQF  213 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~~  213 (311)
                      ...|+..+..+.+.|++++    |...|+....                      .-+..  ....+--+-..|-..|++
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~----Ai~af~~fl~----------------------~yP~s~~a~~A~y~LG~~y~~~g~~  196 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDD----AIVAFQNFVK----------------------KYPDSTYQPNANYWLGQLNYNKGKK  196 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHH----HHHHHHHHHH----------------------HCcCCcchHHHHHHHHHHHHHcCCH
Confidence            4557777766677789999    5555554322                      11111  023455677888899999


Q ss_pred             hHHHHHHHHHHhcC--CCCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          214 REALDAFNKTKKSG--TGSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       214 ~~a~~~~~~m~~~g--~~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      ++|...|..+.+.-  -......+-.+...+...|+.+.|..++
T Consensus       197 ~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~  240 (263)
T PRK10803        197 DDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVY  240 (263)
T ss_pred             HHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999998631  1112334444555566777777665544

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=85.80  E-value=12  Score=31.81  Aligned_cols=97  Identities=14%  Similarity=0.136  Sum_probs=70.8

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHh-cCCCCCHHHHHHHHHHHhcc-CChhhHHHHHHhhCChHHHHHHHhhcC-
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKK-SGTGSDQVTMATVLSACAHL-GALDLGRGIQIYCRSLGRSLLVFFKLR-  272 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~li~a~~~~-~~~~~a~~~~~~~~~~~~a~~~~~~~~-  272 (311)
                      |...|--|-..|...|+.+.|..-|..-.+ .|-.  ...+..+-.++... |....+           ++.++|++.. 
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n--~~~~~g~aeaL~~~a~~~~ta-----------~a~~ll~~al~  221 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDN--PEILLGLAEALYYQAGQQMTA-----------KARALLRQALA  221 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCC--HHHHHHHHHHHHHhcCCcccH-----------HHHHHHHHHHh
Confidence            788999999999999999999999999776 3433  44444444444332 222211           5666666665 


Q ss_pred             -C-CCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          273 -E-KNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       273 -~-p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                       + -|+..-..|-.++...|++.+|...++.|.+.
T Consensus       222 ~D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         222 LDPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             cCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc
Confidence             3 35677788888999999999999999999875

>PRK15331 chaperone protein SicA; Provisional

Probab=85.68  E-value=7.8  Score=29.88  Aligned_cols=87  Identities=9%  Similarity=-0.033  Sum_probs=55.4

Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEAL  286 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~  286 (311)
                      +-..|++++|..+|.-+..-+ .-+..-|..|-.+|-..++++.|...+..+..++.          -|+..+-..-.++
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~----------~dp~p~f~agqC~  115 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK----------NDYRPVFFTGQCQ  115 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc----------CCCCccchHHHHH
Confidence            345699999999998876532 22334455555666677888888877755333322          3444455556677


Q ss_pred             HhcCChHHHHHHHHHHHH
Q 044412          287 AIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       287 ~~~g~~~~a~~~~~~M~~  304 (311)
                      ...|+.+.|...|....+
T Consensus       116 l~l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        116 LLMRKAAKARQCFELVNE  133 (165)
T ss_pred             HHhCCHHHHHHHHHHHHh
Confidence            777777777777766544

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=85.68  E-value=31  Score=32.25  Aligned_cols=127  Identities=10%  Similarity=-0.016  Sum_probs=76.0

Q ss_pred             CCCCHhHHHHHHHHHHHH----------HHHHHhhCC--CCcH-hHHHHHHHHHHhC---C-----ChhHHHHHHHHHHh
Q 044412          167 PERKFATWNTMIDAYARL----------AELLFNKMP--AWDI-RSWTTMITSYSQN---K-----QFREALDAFNKTKK  225 (311)
Q Consensus       167 ~~~~~~~~~~li~~~~~~----------a~~~~~~m~--~~~~-~~y~~li~~~~~~---g-----~~~~a~~~~~~m~~  225 (311)
                      ...+...|...+.+....          |..+|++-.  +||- ..|..+..++...   +     ++..+.+...+...
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            345667788888776542          778887775  4643 3344333333221   1     12233333333222


Q ss_pred             c-CCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          226 S-GTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       226 ~-g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      . ....+...|.++--.....|++++|...++.      |..+     .|+...|..+-..+...|+.++|.+.+++-..
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~r------Al~L-----~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINK------AIDL-----EMSWLNYVLLGKVYELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHH------HHHc-----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            2 2344556677665555566788766554422      2221     47778899999999999999999999988654

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=85.62  E-value=12  Score=29.70  Aligned_cols=57  Identities=11%  Similarity=-0.002  Sum_probs=29.9

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQM   86 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m   86 (311)
                      .+...+...|+..+++..|.+....-+..|....-.+-.+- ...+++..|...++.+
T Consensus        94 rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aq-fa~~~~A~a~~tLe~l  150 (251)
T COG4700          94 RLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQ-FAIQEFAAAQQTLEDL  150 (251)
T ss_pred             HHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHH-HhhccHHHHHHHHHHH
Confidence            34444555555555555555555544455555555555555 5555555555555443

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.12  E-value=8.9  Score=37.19  Aligned_cols=90  Identities=14%  Similarity=0.166  Sum_probs=48.8

Q ss_pred             HHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh-HHHHHHHHHHHH-----HHHHHhhCCCCcHhHH
Q 044412          127 VWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA-TWNTMIDAYARL-----AELLFNKMPAWDIRSW  200 (311)
Q Consensus       127 ~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~-~~~~li~~~~~~-----a~~~~~~m~~~~~~~y  200 (311)
                      +.+.|+. +...-+.||++|.+.++.++    ..++.+...+...+ -.-..+.-+-+.     |..+=.+-. .+....
T Consensus       423 L~~~gla-~~dhttlLLncYiKlkd~~k----L~efI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~-~he~vl  496 (933)
T KOG2114|consen  423 LHKKGLA-NSDHTTLLLNCYIKLKDVEK----LTEFISKCDKGEWFFDVETALEILRKSNYLDEAELLATKFK-KHEWVL  496 (933)
T ss_pred             HHHcccc-cchhHHHHHHHHHHhcchHH----HHHHHhcCCCcceeeeHHHHHHHHHHhChHHHHHHHHHHhc-cCHHHH
Confidence            3344443 33444889999999999999    88888776632111 112222222221     222211111 133333


Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          201 TTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       201 ~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      ..+++   ..|++++|++++..|.=
T Consensus       497 ~ille---~~~ny~eAl~yi~slp~  518 (933)
T KOG2114|consen  497 DILLE---DLHNYEEALRYISSLPI  518 (933)
T ss_pred             HHHHH---HhcCHHHHHHHHhcCCH
Confidence            44443   45788889888877643

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.22  E-value=0.67  Score=39.35  Aligned_cols=104  Identities=11%  Similarity=0.123  Sum_probs=74.8

Q ss_pred             HHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC-------CCeeeeec--cccCCChhHHHHHHHHHHHC
Q 044412           46 VYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE-------PNVFVYHA--FSSLRHPLQAIAFYLYMLRA  116 (311)
Q Consensus        46 l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-------~~~~~~~~--~~~~~~~~~a~~~~~~m~~~  116 (311)
                      +...-...|.+.+..+...++..- .....++++...+=.+..       ++...+..  ++-.-++++++.++..=.  
T Consensus        51 ~~~kkF~~g~~~s~~~Vd~~V~v~-~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllky~pq~~i~~l~npI--  127 (418)
T KOG4570|consen   51 LMDKKFERGLPVSSLTVDRLVDVI-SSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLKYDPQKAIYTLVNPI--  127 (418)
T ss_pred             cchhhhhcCCCcceeehhhhhhcc-ccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHccChHHHHHHHhCcc--
Confidence            444445567777888888888877 777888888877655542       33333333  566667788887776554  


Q ss_pred             CCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhc
Q 044412          117 EVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus       117 ~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~  164 (311)
                                  +.|+-||..+++.+|+.+.+.++..+|-+++..+..
T Consensus       128 ------------qYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  128 ------------QYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             ------------hhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence                        455899999999999999999999996666555543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=84.16  E-value=15  Score=31.53  Aligned_cols=103  Identities=10%  Similarity=0.146  Sum_probs=63.5

Q ss_pred             HhHHHHHHHHHHh--CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc--cCChhhHHHHHHhhCChHHHHHHHhhcC
Q 044412          197 IRSWTTMITSYSQ--NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH--LGALDLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       197 ~~~y~~li~~~~~--~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~--~~~~~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      ..++.+++..-..  ...+++.+++++.|.+.|+.-+..+|-+..-....  ..+++.         ....|..+|+.|+
T Consensus        60 ~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~---------~~~ra~~iy~~mK  130 (297)
T PF13170_consen   60 RFILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDE---------IIQRAKEIYKEMK  130 (297)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHH---------HHHHHHHHHHHHH
Confidence            4444444443322  01245667899999999999999888764433333  333332         2337888888888


Q ss_pred             -------CCCchhHHHHHHHHHhcCCh----HHHHHHHHHHHHcCCCCC
Q 044412          273 -------EKNLLCWNSITEALAIHGFA----HEALGMFDRMTYENVRPN  310 (311)
Q Consensus       273 -------~p~~~~~~~li~~~~~~g~~----~~a~~~~~~M~~~g~~P~  310 (311)
                             .++-.++..|+..  ...+.    +++..+|+.+.+.|+..+
T Consensus       131 k~H~fLTs~~D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~~f~kg  177 (297)
T PF13170_consen  131 KKHPFLTSPEDYPFAALLAM--TSEDVEELAERMEQCYQKLADAGFKKG  177 (297)
T ss_pred             HhCccccCccchhHHHHHhc--ccccHHHHHHHHHHHHHHHHHhCCCCC
Confidence                   3445566666555  33333    446777888888787654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=84.16  E-value=2  Score=29.78  Aligned_cols=48  Identities=8%  Similarity=0.081  Sum_probs=40.7

Q ss_pred             ChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC
Q 044412           39 SIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ   87 (311)
Q Consensus        39 ~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~   87 (311)
                      +.=++++-++.+....+.|++.+..+.+++| .|..++..|.++|+.++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAc-RRvND~alAVR~lE~vK   69 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRAC-RRVNDFALAVRILEAIK   69 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHH-HHhhhHHHHHHHHHHHH
Confidence            3335577777788888999999999999999 99999999999998664

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=83.53  E-value=24  Score=29.24  Aligned_cols=54  Identities=7%  Similarity=0.153  Sum_probs=41.4

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhc--CCCCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKS--GTGSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~--g~~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      .+..-|-+.|.+.-|..=|+.+.+.  +.+........++.+|...|..++|....
T Consensus       180 ~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~  235 (243)
T PRK10866        180 SVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVA  235 (243)
T ss_pred             HHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHH
Confidence            3445578889999999988888873  45556677788889999999888776543

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=82.99  E-value=5.3  Score=30.62  Aligned_cols=93  Identities=10%  Similarity=0.012  Sum_probs=52.8

Q ss_pred             HHHHHHHHH--hhccCChhHHHHhcccCC--CCCeeeeec-----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           61 LAKQFISFC--TSRFHFIDYTILVFPQMQ--EPNVFVYHA-----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        61 ~~~~ll~~~--~~~~g~~~~a~~~~~~m~--~~~~~~~~~-----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      +.+.||...  +.+.++.+++..+++.+.  +|.......     +.+.|++.+|+++|+++...               
T Consensus         9 iv~gLie~~~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~---------------   73 (160)
T PF09613_consen    9 IVGGLIEVLSVALRLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEER---------------   73 (160)
T ss_pred             HHHHHHHHHHHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc---------------
Confidence            344444433  155677788888877765  455444433     77888888888888887654               


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCC
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPER  169 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~  169 (311)
                       .|......+|+..|.....=..=+..|.++.+....|
T Consensus        74 -~~~~p~~kALlA~CL~~~~D~~Wr~~A~evle~~~d~  110 (160)
T PF09613_consen   74 -APGFPYAKALLALCLYALGDPSWRRYADEVLESGADP  110 (160)
T ss_pred             -CCCChHHHHHHHHHHHHcCChHHHHHHHHHHhcCCCh
Confidence             3444444555555444433233223355555544433

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.43  E-value=44  Score=31.38  Aligned_cols=59  Identities=7%  Similarity=-0.076  Sum_probs=41.9

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHH--------HHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFN--------KTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~--------~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      ..+--+++..-...|+++.|++++.        .+.+.+-.|  .+...++..+.+.++-+.|..++..
T Consensus       376 ~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P--~~V~aiv~l~~~~~~~~~a~~vl~~  442 (652)
T KOG2376|consen  376 KVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLP--GTVGAIVALYYKIKDNDSASAVLDS  442 (652)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccCh--hHHHHHHHHHHhccCCccHHHHHHH
Confidence            3455566777888999999999999        555555555  4555666667777777777777655

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=82.34  E-value=2.1  Score=29.96  Aligned_cols=47  Identities=9%  Similarity=0.080  Sum_probs=36.0

Q ss_pred             hhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC
Q 044412           40 IKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ   87 (311)
Q Consensus        40 ~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~   87 (311)
                      .=++++-+..+....+.|++.+..+.+++| .|..++..|.++|+.++
T Consensus        26 ~we~rrglN~l~~~DlVP~P~ii~aALrAc-RRvND~a~AVR~lE~iK   72 (108)
T PF02284_consen   26 GWELRRGLNNLFGYDLVPEPKIIEAALRAC-RRVNDFALAVRILEGIK   72 (108)
T ss_dssp             HHHHHHHHHHHTTSSB---HHHHHHHHHHH-HHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCChHHHHHHHHHH-HHhhhHHHHHHHHHHHH
Confidence            334566777777888999999999999999 99999999999998764

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=82.29  E-value=3.3  Score=23.00  Aligned_cols=28  Identities=21%  Similarity=0.274  Sum_probs=24.0

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+++.|-..|...|++++|..++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4788999999999999999999998764

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=82.00  E-value=3.7  Score=22.77  Aligned_cols=28  Identities=14%  Similarity=0.407  Sum_probs=23.5

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      .+++.|-..|...|++++|..++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4788889999999999999999998764

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=81.80  E-value=3.8  Score=23.51  Aligned_cols=33  Identities=18%  Similarity=0.285  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV  233 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  233 (311)
                      +|..+-..|...|++++|+++|++..+.  .|+..
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~--~P~~~   35 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL--DPDDP   35 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCCH
Confidence            5677888999999999999999999885  55543

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=81.16  E-value=17  Score=33.24  Aligned_cols=144  Identities=10%  Similarity=0.008  Sum_probs=65.4

Q ss_pred             cccCCChhHHHHHHH--HHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHH
Q 044412           97 FSSLRHPLQAIAFYL--YMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATW  174 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~--~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~  174 (311)
                      ..-.++++++.++.+  ++..                 ..+..-.+.++.-+-+.|..+.    |..+...         
T Consensus       271 av~~~d~~~v~~~i~~~~ll~-----------------~i~~~~~~~i~~fL~~~G~~e~----AL~~~~D---------  320 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLP-----------------NIPKDQGQSIARFLEKKGYPEL----ALQFVTD---------  320 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGG-----------------G--HHHHHHHHHHHHHTT-HHH----HHHHSS----------
T ss_pred             HHHcCChhhhhhhhhhhhhcc-----------------cCChhHHHHHHHHHHHCCCHHH----HHhhcCC---------
Confidence            566778888777765  2211                 1124456778888888888888    5555432         


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHH
Q 044412          175 NTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       175 ~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~  254 (311)
                                          |+     .=.+-..+.|+++.|.++.++.      .+...|..|-....+.|+++.|+..
T Consensus       321 --------------------~~-----~rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c  369 (443)
T PF04053_consen  321 --------------------PD-----HRFELALQLGNLDIALEIAKEL------DDPEKWKQLGDEALRQGNIELAEEC  369 (443)
T ss_dssp             --------------------HH-----HHHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHH
T ss_pred             --------------------hH-----HHhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHH
Confidence                                10     0112223345555555443332      2444555555555555555555555


Q ss_pred             HHhhCChHHHHHHHhhcC-----------CCCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          255 QIYCRSLGRSLLVFFKLR-----------EKNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       255 ~~~~~~~~~a~~~~~~~~-----------~p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      +...++.+...-++.-..           .....-+|....++.-.|+.+++.+++.+
T Consensus       370 ~~k~~d~~~L~lLy~~~g~~~~L~kl~~~a~~~~~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  370 YQKAKDFSGLLLLYSSTGDREKLSKLAKIAEERGDINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHCT-HHHHHHHHHHCT-HHHHHHHHHHHHHTT-HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHhhcCccccHHHHHHhCCHHHHHHHHHHHHHccCHHHHHHHHHHcCCHHHHHHHHHH
Confidence            555443333222221111           01112356666667777777777776654

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PHA02875 ankyrin repeat protein; Provisional

Probab=81.10  E-value=39  Score=30.31  Aligned_cols=38  Identities=11%  Similarity=0.113  Sum_probs=16.9

Q ss_pred             HHHHHHhccCcchhH--HHHHHHHHhhccCChhHHHHhccc
Q 044412           47 YATIVKTNANLDCFL--AKQFISFCTSRFHFIDYTILVFPQ   85 (311)
Q Consensus        47 ~~~m~~~g~~p~~~~--~~~ll~~~~~~~g~~~~a~~~~~~   85 (311)
                      .+.+.+.|..|+...  ....+..+ ++.|+.+-+.-+++.
T Consensus        18 v~~Ll~~g~~~n~~~~~g~tpL~~A-~~~~~~~~v~~Ll~~   57 (413)
T PHA02875         18 ARRLLDIGINPNFEIYDGISPIKLA-MKFRDSEAIKLLMKH   57 (413)
T ss_pred             HHHHHHCCCCCCccCCCCCCHHHHH-HHcCCHHHHHHHHhC
Confidence            344445555544322  22233333 455555555444443

---

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	311
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-05

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 44.4 bits (103), Expect = 3e-05
 Identities = 13/133 (9%), Positives = 33/133 (24%), Gaps = 10/133 (7%)

Query: 182 ARLAELLFNKMPAWDIRSWTTMITS----YSQNKQFREALDAFNKTKKSGTGSDQVTMAT 237
            ++A  L +         W   +                     +  ++     Q  +  
Sbjct: 73  KQMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLA 132

Query: 238 VLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALG 297
               C     L L   + +      +   +        L  +N++    A  G   E + 
Sbjct: 133 FFKCCLLTDQLPLAHHLLVVHHGQRQKRKLL------TLDMYNAVMLGWARQGAFKELVY 186

Query: 298 MFDRMTYENVRPN 310
           +   +    + P+
Sbjct: 187 VLFMVKDAGLTPD 199

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	311
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.87
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.83
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.79
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.78
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.65
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.59
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.56
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.5
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.45
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.32
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.3
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.3
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.26
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.25
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.24
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.22
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.21
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.2
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.2
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.14
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.13
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.13
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.09
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.08
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.06
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.01
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.0
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.99
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.99
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.98
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.98
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.93
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.9
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.9
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.83
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.8
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.69
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.69
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.65
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.65
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.64
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.63
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.63
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.63
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.63
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.62
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.61
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.58
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.56
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.55
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.55
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.53
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.53
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.5
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.47
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.47
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.45
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.44
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.44
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.41
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.41
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.4
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.4
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.37
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.36
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.3
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.29
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.28
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.28
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.27
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.27
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.25
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.25
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.23
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.22
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.18
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.17
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.17
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.1
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.09
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.06
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.04
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.03
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.99
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.97
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.9
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.88
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.87
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.86
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.83
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.83
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.83
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.79
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.79
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.76
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.76
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.75
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.74
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	97.66
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.63
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.62
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.61
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.6
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.57
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.57
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.56
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.56
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.55
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.55
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.55
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.53
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.52
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.51
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.46
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.46
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.45
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.45
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.44
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.44
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.44
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.43
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.42
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.42
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.4
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.37
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.36
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.35
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.35
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.35
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.33
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.33
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.32
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.28
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.28
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.25
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.23
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.16
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.08
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.07
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.04
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.04
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.97
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	96.92
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.91
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	96.88
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.87
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.86
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.83
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.8
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.8
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.8
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	96.77
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.75
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.75
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.74
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	96.73
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	96.71
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	96.69
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.68
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.67
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	96.63
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	96.56
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.54
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.53
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.53
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.52
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	96.46
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.42
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.42
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.34
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.28
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	96.23
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.13
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.1
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.1
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.1
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.06
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.98
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	95.87
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	95.81
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	95.67
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	95.67
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	95.59
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.57
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	95.47
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.44
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	95.42
2l6j_A	111	TPR repeat-containing protein associated with HSP;	95.39
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.38
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	95.38
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.26
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	95.11
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.07
2l6j_A	111	TPR repeat-containing protein associated with HSP;	95.06
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.06
2kat_A	115	Uncharacterized protein; NESG, structure, structur	94.84
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	94.75
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.74
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	94.63
1klx_A	138	Cysteine rich protein B; structural genomics, heli	93.96
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	93.89
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	93.77
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	93.58
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	93.51
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	93.16
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	92.21
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	91.76
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	90.71
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	90.63
1klx_A	138	Cysteine rich protein B; structural genomics, heli	90.46
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	90.2
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	89.74
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	89.6
1pc2_A	152	Mitochondria fission protein; unknown function; NM	89.25
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	87.86
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	86.78
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	86.31
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	86.17
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	83.93
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	83.62
2p58_C	116	Putative type III secretion protein YSCG; type III	83.32
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	82.62
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	82.01
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	81.95
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	80.28
1pc2_A	152	Mitochondria fission protein; unknown function; NM	80.22

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.97  E-value=3.6e-31  Score=240.65  Aligned_cols=190  Identities=15%  Similarity=0.062  Sum_probs=132.2

Q ss_pred             HHHHHHHHHhccCcch-hHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchH
Q 044412           44 ECVYATIVKTNANLDC-FLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTT  122 (311)
Q Consensus        44 ~~l~~~m~~~g~~p~~-~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~  122 (311)
                      +.+...+.+.+..+.+ .+++.+|++| +|                           .|++++|+++|++|.+.|     
T Consensus        10 e~L~~~~~~k~~~~spe~~l~~~id~c-~k---------------------------~G~~~~A~~lf~~M~~~G-----   56 (501)
T 4g26_A           10 ENLSRKAKKKAIQQSPEALLKQKLDMC-SK---------------------------KGDVLEALRLYDEARRNG-----   56 (501)
T ss_dssp             --------------CHHHHHHHHHHHT-TT---------------------------SCCHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHHHHH-Hh---------------------------CCCHHHHHHHHHHHHHcC-----
Confidence            6777788888776655 4578888888 65                           555666677777886655     


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHhCCCCccc-----hHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcH
Q 044412          123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFES-----RRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDI  197 (311)
Q Consensus       123 ~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a-----~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~  197 (311)
                               +.||..+||+||++|++.+..+++     .+-|.++|++|...++                      .||.
T Consensus        57 ---------v~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~----------------------~Pd~  105 (501)
T 4g26_A           57 ---------VQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKV----------------------VPNE  105 (501)
T ss_dssp             ---------CCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTC----------------------CCCH
T ss_pred             ---------CCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCC----------------------CCCH
Confidence                     799999999999999998876442     1124555555443222                      5788


Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC----C
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR----E  273 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~----~  273 (311)
                      .|||+||.+|++.|++++|+++|++|.+.|+.||..||++||.+|++.|++++             |.++|++|.    +
T Consensus       106 ~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~-------------A~~l~~~M~~~G~~  172 (501)
T 4g26_A          106 ATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADK-------------AYEVDAHMVESEVV  172 (501)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHH-------------HHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHH-------------HHHHHHHHHhcCCC
Confidence            88888888888888888888888888888888888888888888888777774             444444443    6


Q ss_pred             CCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          274 KNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       274 p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      ||..||++||++|++.|++++|.++|++|++.|+.|+
T Consensus       173 Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps  209 (501)
T 4g26_A          173 PEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVS  209 (501)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBC
T ss_pred             CCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcC
Confidence            8888888888888888888888888888888888886

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.97  E-value=4.6e-31  Score=239.97  Aligned_cols=210  Identities=12%  Similarity=0.051  Sum_probs=166.3

Q ss_pred             hhhhhcCCCCCchhhhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCC
Q 044412           11 TSFKKNSFPTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPN   90 (311)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~   90 (311)
                      +...+.+....+.. ..+..+..+...|++.++.++|+.|.+.|++||..+||+||.+| ++.+..+.+           
T Consensus        14 ~~~~~k~~~~spe~-~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c-~~~~~~~~~-----------   80 (501)
T 4g26_A           14 RKAKKKAIQQSPEA-LLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVC-SLAEAATES-----------   80 (501)
T ss_dssp             ----------CHHH-HHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH-TTCCCCSSS-----------
T ss_pred             HHHHHhcccCCCHH-HHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHH-HhCCchhhh-----------
Confidence            33344444443332 13444556666678888899999999999999999999999999 888765443           


Q ss_pred             eeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC
Q 044412           91 VFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK  170 (311)
Q Consensus        91 ~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~  170 (311)
                             .+.+.+++|.++|++|...|              +.||..|||+||++|++.|++++    |.++|++|.+.+
T Consensus        81 -------~~~~~l~~A~~lf~~M~~~G--------------~~Pd~~tyn~lI~~~~~~g~~~~----A~~l~~~M~~~g  135 (501)
T 4g26_A           81 -------SPNPGLSRGFDIFKQMIVDK--------------VVPNEATFTNGARLAVAKDDPEM----AFDMVKQMKAFG  135 (501)
T ss_dssp             -------SCCHHHHHHHHHHHHHHHTT--------------CCCCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHTT
T ss_pred             -------hhcchHHHHHHHHHHHHHhC--------------CCCCHHHHHHHHHHHHhcCCHHH----HHHHHHHHHHcC
Confidence                   25667899999999998776              79999999999999999999999    777777766544


Q ss_pred             HhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          171 FATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       171 ~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                      .                      .||..|||+||.+|++.|++++|.++|++|.+.|+.||..||++||.+|++.|++++
T Consensus       136 ~----------------------~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~  193 (501)
T 4g26_A          136 I----------------------QPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADK  193 (501)
T ss_dssp             C----------------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHH
T ss_pred             C----------------------CCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHH
Confidence            3                      689999999999999999999999999999999999999999999999999999985


Q ss_pred             HHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhc
Q 044412          251 GRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIH  289 (311)
Q Consensus       251 a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~  289 (311)
                      |.++++++.+...         +|+..||++++..|+..
T Consensus       194 A~~ll~~Mr~~g~---------~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          194 VYKTLQRLRDLVR---------QVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHHHHHHTS---------SBCHHHHHHHHHHHHSH
T ss_pred             HHHHHHHHHHhCC---------CcCHHHHHHHHHHHhcC
Confidence            5444433322222         79999999999999874

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.87  E-value=1.1e-20  Score=175.64  Aligned_cols=276  Identities=9%  Similarity=0.002  Sum_probs=216.2

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCC-----------------
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPN-----------------   90 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~-----------------   90 (311)
                      ..+..++..+|+.+++..+++.+..  .++++.+++.++.+| .+.|++++|.++|+++...+                 
T Consensus       121 ~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~~~l~~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (597)
T 2xpi_A          121 FWLAQVYCCTGDYARAKCLLTKEDL--YNRSSACRYLAAFCL-VKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIK  197 (597)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHTCG--GGTCHHHHHHHHHHH-HHTTCHHHHHHHHCSSCTTC----------CCCSSCC
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHhc--cccchhHHHHHHHHH-HHHhhHHHHHHHHhccCCccccccccccccccccccc
Confidence            4567777788888888888887654  368899999999999 99999999999999654332                 


Q ss_pred             --eeeeec----cccCCChhHHHHHHHHHHHCCCC-ch------------------------------------------
Q 044412           91 --VFVYHA----FSSLRHPLQAIAFYLYMLRAEVL-LT------------------------------------------  121 (311)
Q Consensus        91 --~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~-p~------------------------------------------  121 (311)
                        ..+|+.    +.+.|++++|+++|++|.+.+.. ++                                          
T Consensus       198 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  277 (597)
T 2xpi_A          198 LEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYML  277 (597)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHH
Confidence              455555    89999999999999999875421 11                                          


Q ss_pred             ---------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH--
Q 044412          122 ---------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL--  184 (311)
Q Consensus       122 ---------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~--  184 (311)
                                     .+++.+.+  ..++..+|+.++.+|.+.|++++|.++..++.+.. ..+..+|+.++.+|.+.  
T Consensus       278 ~~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~  354 (597)
T 2xpi_A          278 KLNKTSHEDELRRAEDYLSSING--LEKSSDLLLCKADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGE  354 (597)
T ss_dssp             TSCTTTTHHHHHHHHHHHHTSTT--GGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTC
T ss_pred             HHHHHcCcchHHHHHHHHHHhhc--CCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCC
Confidence                           01111111  13788899999999999999999444433333322 23667888888888876  


Q ss_pred             ---HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh-
Q 044412          185 ---AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY-  257 (311)
Q Consensus       185 ---a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~-  257 (311)
                         |.++|+++.   ..+..+|+.++..|.+.|++++|.++|+++.+.. +.+..+|+.++.+|.+.|++++|..+|+. 
T Consensus       355 ~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  433 (597)
T 2xpi_A          355 KNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTA  433 (597)
T ss_dssp             HHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence               777887664   3468889999999999999999999999998742 33577999999999999999999999887 


Q ss_pred             --------------------hCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCC
Q 044412          258 --------------------CRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYE----NVRPN  310 (311)
Q Consensus       258 --------------------~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~----g~~P~  310 (311)
                                          .|+.++|.++|+++.   ..+..+|+.+...|.+.|++++|.++|++|.+.    +..|+
T Consensus       434 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~  513 (597)
T 2xpi_A          434 ARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEK  513 (597)
T ss_dssp             HHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSG
T ss_pred             HHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchh
Confidence                                889999999999886   356889999999999999999999999999875    66664

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.83  E-value=4.1e-19  Score=164.92  Aligned_cols=245  Identities=8%  Similarity=-0.001  Sum_probs=187.9

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC---CCeeeeec----ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE---PNVFVYHA----FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~----~~~   99 (311)
                      ...+..++..+|+.+++..+++.+.+.+. .+..+++.++.++ .+.|+.++|.++|+++.+   .+..+|+.    +.+
T Consensus       308 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  385 (597)
T 2xpi_A          308 LLCKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASL-HESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLC  385 (597)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHH-HHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHH
Confidence            45677777778888888888888877653 3677788888888 888888888888877642   33444444    778


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCC---CCCHhHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP---ERKFATWNT  176 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~---~~~~~~~~~  176 (311)
                      .|++++|.++|+++.+.               .+.+..+|+.++.+|.+.|++++    |..+|+++.   ..+..+|+.
T Consensus       386 ~g~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~~~~~~~~~~~  446 (597)
T 2xpi_A          386 VNKISEARRYFSKSSTM---------------DPQFGPAWIGFAHSFAIEGEHDQ----AISAYTTAARLFQGTHLPYLF  446 (597)
T ss_dssp             TTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHTTTTCSHHHHH
T ss_pred             hccHHHHHHHHHHHHHh---------------CCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhCccchHHHHH
Confidence            88888888888887653               23457788889999999999999    555554432   246678888


Q ss_pred             HHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCCC--HHHHHHHHHHH
Q 044412          177 MIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGSD--QVTMATVLSAC  242 (311)
Q Consensus       177 li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~t~~~li~a~  242 (311)
                      +..+|.+.     |.++|+++.   ..+..+|+.++..|.+.|++++|+++|+++.+.    +..|+  ..+|..+..+|
T Consensus       447 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~  526 (597)
T 2xpi_A          447 LGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAY  526 (597)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHH
Confidence            88888876     888888764   246788999999999999999999999988775    77887  77889999999


Q ss_pred             hccCChhhHHHHHHhhCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          243 AHLGALDLGRGIQIYCRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       243 ~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      .+.|++++|..++             +++.   ..+..+|..+..+|.+.|++++|.++|+++.+.
T Consensus       527 ~~~g~~~~A~~~~-------------~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  579 (597)
T 2xpi_A          527 RKLKMYDAAIDAL-------------NQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAI  579 (597)
T ss_dssp             HHTTCHHHHHHHH-------------HHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHH-------------HHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            9988888665554             3332   347889999999999999999999999998863

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.79  E-value=8.9e-20  Score=172.14  Aligned_cols=136  Identities=10%  Similarity=0.075  Sum_probs=100.9

Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~  212 (311)
                      .--..|||+||++||+.|++++    |.++|+.|.+..                   .....||+.|||+||+|||+.|+
T Consensus       124 ~~~~~TynaLIdglcK~G~lee----A~~Lf~eM~~m~-------------------~kG~~PdvvTYNtLI~Glck~G~  180 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPL----AHHLLVVHHGQR-------------------QKRKLLTLDMYNAVMLGWARQGA  180 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHSH-------------------HHHTTCCHHHHHHHHHHHHHHTC
T ss_pred             HhHHHHHHHHHHHHHhCCCHHH----HHHHHHHHHHHh-------------------hcCCCCCHhHHHHHHHHHHhCCC
Confidence            3346799999999999999999    888876643210                   01125788889999999999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh-hhHHHHHHhhCChHHHHHHHhhcC----CCCchhHHHHHHHHH
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL-DLGRGIQIYCRSLGRSLLVFFKLR----EKNLLCWNSITEALA  287 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~-~~a~~~~~~~~~~~~a~~~~~~~~----~p~~~~~~~li~~~~  287 (311)
                      +++|.++|++|.+.|+.||..|||+||.++|+.|+. +             .|.++|++|.    .||..||++++.++.
T Consensus       181 ~~eA~~Lf~eM~~~G~~PDvvTYntLI~glcK~G~~~e-------------~A~~Ll~EM~~kG~~PD~vtY~~ll~~~e  247 (1134)
T 3spa_A          181 FKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAG-------------TIERCLEQMSQEGLKLQALFTAVLLSEED  247 (1134)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCCHH-------------HHHHHHHHHHHHTCCSHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhCCCcHH-------------HHHHHHHHHHHcCCCCChhhcccccChhh
Confidence            999999999999999999999999999999888764 4             4555666665    688889998887766


Q ss_pred             hcCChHHHHHHHHHHHHcCCCC
Q 044412          288 IHGFAHEALGMFDRMTYENVRP  309 (311)
Q Consensus       288 ~~g~~~~a~~~~~~M~~~g~~P  309 (311)
                      +.+    +++..+++ ..++.|
T Consensus       248 R~~----vL~~Vrkv-~P~f~p  264 (1134)
T 3spa_A          248 RAT----VLKAVHKV-KPTFSL  264 (1134)
T ss_dssp             HHH----HHHHHGGG-CCCCCC
T ss_pred             HHH----HHHHHHHh-CcccCC
Confidence            643    33334444 335554

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.78  E-value=2.5e-19  Score=169.15  Aligned_cols=101  Identities=12%  Similarity=0.141  Sum_probs=91.7

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHH---hcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC-
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTK---KSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR-  272 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~---~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~-  272 (311)
                      ..|||+||++||+.|++++|.++|.+|.   +.|+.||..|||+||.+||+.|+++             +|.++|++|. 
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~-------------eA~~Lf~eM~~  193 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFK-------------ELVYVLFMVKD  193 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHH-------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHH-------------HHHHHHHHHHH
Confidence            4689999999999999999999998876   4689999999999999999999888             5566666665 


Q ss_pred             ---CCCchhHHHHHHHHHhcCCh-HHHHHHHHHHHHcCCCCC
Q 044412          273 ---EKNLLCWNSITEALAIHGFA-HEALGMFDRMTYENVRPN  310 (311)
Q Consensus       273 ---~p~~~~~~~li~~~~~~g~~-~~a~~~~~~M~~~g~~P~  310 (311)
                         +||+.|||+||+++|+.|+. ++|.++|++|.+.|+.||
T Consensus       194 ~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD  235 (1134)
T 3spa_A          194 AGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQ  235 (1134)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSH
T ss_pred             cCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCC
Confidence               79999999999999999985 789999999999999998

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.65  E-value=2e-14  Score=126.30  Aligned_cols=270  Identities=9%  Similarity=0.066  Sum_probs=164.9

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC--CCCee-eeec----cccCC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ--EPNVF-VYHA----FSSLR  101 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~--~~~~~-~~~~----~~~~~  101 (311)
                      .+..++..+++.+.+...+...++.. +.+..+|..+...+ .+.|++++|...|+++.  .|+.. +|..    +.+.|
T Consensus        38 ~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g  115 (388)
T 1w3b_A           38 LLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVY-KERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAG  115 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHH-HHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcC
Confidence            33444445555555555554444432 33445555555555 55555555555555543  22221 1222    44455


Q ss_pred             ChhHHHHHHHHHHHCCCCch----------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHH
Q 044412          102 HPLQAIAFYLYMLRAEVLLT----------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVS  159 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~~~~p~----------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a  159 (311)
                      ++++|++.|+++.+..  |+                      ..++.+++. .+-+..+|+.+...|.+.|++++    |
T Consensus       116 ~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~----A  188 (388)
T 1w3b_A          116 DMEGAVQAYVSALQYN--PDLYCVRSDLGNLLKALGRLEEAKACYLKAIET-QPNFAVAWSNLGCVFNAQGEIWL----A  188 (388)
T ss_dssp             CSSHHHHHHHHHHHHC--TTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHH----H
T ss_pred             CHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHH----H
Confidence            5555555555544321  22                      112222221 12235677777778888888888    4


Q ss_pred             HHHhccCCC--C-CHhHHHHHHHHHHHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC
Q 044412          160 RRLFDEMPE--R-KFATWNTMIDAYARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGT  228 (311)
Q Consensus       160 ~~~~~~~~~--~-~~~~~~~li~~~~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  228 (311)
                      ...|+++.+  | +...|..+-..+...     |...|++..  .| +..+|+.+...|...|++++|++.|+++.+.+ 
T Consensus       189 ~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-  267 (388)
T 1w3b_A          189 IHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-  267 (388)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-
Confidence            444443322  2 333454444444433     555554332  23 56778888888888888888888888887742 


Q ss_pred             CCCHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC--CC-CchhHHHHHH
Q 044412          229 GSDQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR--EK-NLLCWNSITE  284 (311)
Q Consensus       229 ~p~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~--~p-~~~~~~~li~  284 (311)
                      +-+..+|..+..++.+.|++++|...++.                     .|+.++|...|+++.  .| +..+|..+..
T Consensus       268 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~  347 (388)
T 1w3b_A          268 PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLAS  347 (388)
T ss_dssp             SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHH
Confidence            22466788888888888888888887776                     678888888888877  34 4678999999


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          285 ALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       285 ~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      .|.+.|++++|...|+++.+  +.|+
T Consensus       348 ~~~~~g~~~~A~~~~~~a~~--~~p~  371 (388)
T 1w3b_A          348 VLQQQGKLQEALMHYKEAIR--ISPT  371 (388)
T ss_dssp             HHHTTTCCHHHHHHHHHHHT--TCTT
T ss_pred             HHHHcCCHHHHHHHHHHHHh--hCCC
Confidence            99999999999999999986  4554

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.59  E-value=1.2e-13  Score=123.45  Aligned_cols=262  Identities=10%  Similarity=0.006  Sum_probs=158.6

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~   99 (311)
                      .......+...|+...+..+++.+.+.. +.+..++..+..++ .+.|++++|...|+++.+  |+ ...+..    +.+
T Consensus        29 ~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  106 (450)
T 2y4t_A           29 HLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVF-LAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLK  106 (450)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHH
Confidence            4566777888899999999999988763 44688899999999 999999999999998753  33 333333    889


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCch---hHHHHHH------------HHHHhCCCCccchHHHHHHhc
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPV---FVQTAMV------------DNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~---~~~~~ll------------~~~~~~g~~~~a~~~a~~~~~  164 (311)
                      .|++++|++.|+++.+..-               .+.   ..+..+.            ..|.+.|++++|.....++.+
T Consensus       107 ~g~~~~A~~~~~~~~~~~~---------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  171 (450)
T 2y4t_A          107 QGKLDEAEDDFKKVLKSNP---------------SENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILE  171 (450)
T ss_dssp             TTCHHHHHHHHHHHHTSCC---------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCC---------------CChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            9999999999999976431               111   2222222            224455555552222222221


Q ss_pred             cCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH-HH
Q 044412          165 EMPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV-TM  235 (311)
Q Consensus       165 ~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~  235 (311)
                      . ...+...+..+...|.+.     |.+.|+++.   ..+..+|+.+...|...|++++|+..|+++.+.  .|+.. .+
T Consensus       172 ~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~  248 (450)
T 2y4t_A          172 V-CVWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCF  248 (450)
T ss_dssp             H-CTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             h-CCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHH
Confidence            1 112333444444444443     444444332   123444555555555555555555555555432  22222 22


Q ss_pred             HHH------------HHHHhccCChhhHHHHHHh-------------------------hCChHHHHHHHhhcC--CC-C
Q 044412          236 ATV------------LSACAHLGALDLGRGIQIY-------------------------CRSLGRSLLVFFKLR--EK-N  275 (311)
Q Consensus       236 ~~l------------i~a~~~~~~~~~a~~~~~~-------------------------~~~~~~a~~~~~~~~--~p-~  275 (311)
                      ..+            ..+|.+.|++++|...++.                         .|+.++|...+++..  .| +
T Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~  328 (450)
T 2y4t_A          249 AHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEPDN  328 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc
Confidence            222            3444455555555444443                         344556666666544  34 5


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      ...|..+..+|...|++++|...+++..+  +.|+
T Consensus       329 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~--~~p~  361 (450)
T 2y4t_A          329 VNALKDRAEAYLIEEMYDEAIQDYETAQE--HNEN  361 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHT--TSSS
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHH--hCcc
Confidence            78999999999999999999999999876  4454

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.56  E-value=2.4e-13  Score=119.40  Aligned_cols=253  Identities=11%  Similarity=0.069  Sum_probs=148.3

Q ss_pred             HHHHhhccChhhHHHHHHHHHHhccCcc-hhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCC
Q 044412           31 ANQLKKCSSIKELECVYATIVKTNANLD-CFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRH  102 (311)
Q Consensus        31 ~~~l~~~~~~~~~~~l~~~m~~~g~~p~-~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~  102 (311)
                      ...+-..|+++++.+.+..+.+..  |+ ...+..+-..+ .+.|+++.|...++...+  | +..+|..    +.+.|+
T Consensus         6 a~~~~~~g~~~~A~~~~~~~~~~~--p~~~~~~~~l~~~~-~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~   82 (388)
T 1w3b_A            6 AHREYQAGDFEAAERHCMQLWRQE--PDNTGVLLLLSSIH-FQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCC
Confidence            344567789999988888877653  44 44555666677 899999999999977642  3 3344444    889999


Q ss_pred             hhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCH-hHHHHHHHH
Q 044412          103 PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF-ATWNTMIDA  180 (311)
Q Consensus       103 ~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~-~~~~~li~~  180 (311)
                      +++|++.|+++.+.                .|+ ...|..+..+|.+.|++++|.....+..+.  .|+. ..+..+-..
T Consensus        83 ~~~A~~~~~~al~~----------------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~  144 (388)
T 1w3b_A           83 LQEAIEHYRHALRL----------------KPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY--NPDLYCVRSDLGNL  144 (388)
T ss_dssp             HHHHHHHHHHHHHH----------------CTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH--CTTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc----------------CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHH
Confidence            99999999998763                233 445666666666666666633332222222  1222 222323223


Q ss_pred             HHHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC-------------------------
Q 044412          181 YARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSG-------------------------  227 (311)
Q Consensus       181 ~~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-------------------------  227 (311)
                      +...     |.+.|+++.  .| +..+|+.+...+...|++++|+..|+++.+.+                         
T Consensus       145 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~  224 (388)
T 1w3b_A          145 LKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVA  224 (388)
T ss_dssp             HHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            3221     444444432  12 33445555555555555555555555544321                         


Q ss_pred             -------CCC-CHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC---CCC
Q 044412          228 -------TGS-DQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR---EKN  275 (311)
Q Consensus       228 -------~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~---~p~  275 (311)
                             +.| +..++..+..++...|++++|...++.                     .|+.++|...|+++.   ..+
T Consensus       225 ~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  304 (388)
T 1w3b_A          225 AYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTH  304 (388)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCccc
Confidence                   123 245555666666666666666655554                     566666666666554   334


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..+|+.+...+...|++++|...++++.+
T Consensus       305 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~  333 (388)
T 1w3b_A          305 ADSLNNLANIKREQGNIEEAVRLYRKALE  333 (388)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            55666666666666666666666666654

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.50  E-value=5.9e-14  Score=123.29  Aligned_cols=219  Identities=11%  Similarity=0.116  Sum_probs=84.9

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccCCCh
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHP  103 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~  103 (311)
                      .....++..+|+++++.+.++.+      +++.+|..|..++ .+.|++++|.+.|...  +|...|..    +...|++
T Consensus         7 ~a~~~ll~~~~~ld~A~~fae~~------~~~~vWs~La~A~-l~~g~~~eAIdsfika--~D~~~y~~V~~~ae~~g~~   77 (449)
T 1b89_A            7 SAVQVLIEHIGNLDRAYEFAERC------NEPAVWSQLAKAQ-LQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNW   77 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHccCHHHHHHHHHhC------CChHHHHHHHHHH-HHcCCHHHHHHHHHcC--CCHHHHHHHHHHHHhCCCH
Confidence            34567788999999998888877      4456999999999 9999999999999775  44445554    8888999


Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~  183 (311)
                      ++|+++++..++.                .+++.+.+.|+.+|.+.|++++    +.++++.   |+..+|+.+-..|..
T Consensus        78 EeAi~yl~~ark~----------------~~~~~i~~~Li~~Y~Klg~l~e----~e~f~~~---pn~~a~~~IGd~~~~  134 (449)
T 1b89_A           78 EELVKYLQMARKK----------------ARESYVETELIFALAKTNRLAE----LEEFING---PNNAHIQQVGDRCYD  134 (449)
T ss_dssp             -----------------------------------------------CHHH----HTTTTTC---C--------------
T ss_pred             HHHHHHHHHHHHh----------------CccchhHHHHHHHHHHhCCHHH----HHHHHcC---CcHHHHHHHHHHHHH
Confidence            9999977655442                4557889999999999999999    8888764   777899999999988


Q ss_pred             H-----HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhh
Q 044412          184 L-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYC  258 (311)
Q Consensus       184 ~-----a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~  258 (311)
                      .     |...|+.+     ..|..+.+++.+.|++++|.+.+.+.      -++.||..++.+|...|+++.|...... 
T Consensus       135 ~g~yeeA~~~Y~~a-----~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~-  202 (449)
T 1b89_A          135 EKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLH-  202 (449)
T ss_dssp             --CTTTHHHHHHHT-----TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-
T ss_pred             cCCHHHHHHHHHHh-----hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHH-
Confidence            7     99999987     48999999999999999999999988      3789999999999999999988543211 


Q ss_pred             CChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          259 RSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       259 ~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                                  +. .++.-...++..|.+.|++++|..+++...
T Consensus       203 ------------L~-~~ad~l~~lv~~Yek~G~~eEai~lLe~aL  234 (449)
T 1b89_A          203 ------------IV-VHADELEELINYYQDRGYFEELITMLEAAL  234 (449)
T ss_dssp             ------------TT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             ------------HH-hCHhhHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence                        11 122223457888888888888888887754

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.45  E-value=2.1e-12  Score=115.30  Aligned_cols=228  Identities=11%  Similarity=0.063  Sum_probs=179.9

Q ss_pred             cchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHH
Q 044412           57 LDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWK  129 (311)
Q Consensus        57 p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~  129 (311)
                      .+...+..+...+ .+.|++++|..+|+++.+  | +...|..    +...|++++|++.|+++.+.+            
T Consensus        24 ~~~~~~~~~~~~~-~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~------------   90 (450)
T 2y4t_A           24 ADVEKHLELGKKL-LAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK------------   90 (450)
T ss_dssp             HHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC------------
Confidence            4567888889999 999999999999998753  3 3333433    888999999999999987642            


Q ss_pred             hcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--C-CH---hHHHHHHHH------------HHHH-----HH
Q 044412          130 NGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--R-KF---ATWNTMIDA------------YARL-----AE  186 (311)
Q Consensus       130 ~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~-~~---~~~~~li~~------------~~~~-----a~  186 (311)
                         +.+...+..+..+|.+.|++++    |...|+.+..  | +.   ..+..+...            +.+.     |.
T Consensus        91 ---p~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~  163 (450)
T 2y4t_A           91 ---MDFTAARLQRGHLLLKQGKLDE----AEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAI  163 (450)
T ss_dssp             ---TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             ---CCcHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence               4457889999999999999999    5555555433  2 23   555555444            3332     77


Q ss_pred             HHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh------
Q 044412          187 LLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY------  257 (311)
Q Consensus       187 ~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~------  257 (311)
                      ..|+++.   ..+..++..+...|...|++++|+++|+++.+.. +.+..++..+..++...|++++|...++.      
T Consensus       164 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p  242 (450)
T 2y4t_A          164 AFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQ  242 (450)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            7777664   3477889999999999999999999999998752 45688999999999999999999988876      


Q ss_pred             ---------------------------hCChHHHHHHHhhcC--CCC-----chhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          258 ---------------------------CRSLGRSLLVFFKLR--EKN-----LLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       258 ---------------------------~~~~~~a~~~~~~~~--~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                                                 .|+.++|...|+++.  .|+     ...|..+...+.+.|++++|...++++.
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~  322 (450)
T 2y4t_A          243 DHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVL  322 (450)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                                       477778888888776  455     3478888999999999999999999987


Q ss_pred             Hc
Q 044412          304 YE  305 (311)
Q Consensus       304 ~~  305 (311)
                      +.
T Consensus       323 ~~  324 (450)
T 2y4t_A          323 QM  324 (450)
T ss_dssp             HH
T ss_pred             Hh
Confidence            53

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.32  E-value=5.8e-11  Score=100.44  Aligned_cols=211  Identities=9%  Similarity=0.020  Sum_probs=142.1

Q ss_pred             HHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-
Q 044412           61 LAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-  135 (311)
Q Consensus        61 ~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-  135 (311)
                      ..-.+.++| ...|+++.|..-++....|+..++..    +...++.++|++.++++...+              ..|+ 
T Consensus        36 ~~~~l~r~y-i~~g~~~~al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~--------------~~P~~  100 (291)
T 3mkr_A           36 RDVFLYRAY-LAQRKYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRS--------------VDVTN  100 (291)
T ss_dssp             HHHHHHHHH-HHTTCHHHHHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSC--------------CCCSC
T ss_pred             HHHHHHHHH-HHCCCHHHHHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcc--------------cCCCC
Confidence            334456777 77788888877776643343333333    667777888888888776543              2344 


Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC--CCcHhH---HHHHHH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP--AWDIRS---WTTMIT  205 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~--~~~~~~---y~~li~  205 (311)
                      ...+..+-..|...|++++    |...++.  ..+...+..+...|.+.     |...|+++.  .|+...   ...++.
T Consensus       101 ~~~~~~la~~~~~~g~~~~----Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~  174 (291)
T 3mkr_A          101 TTFLLMAASIYFYDQNPDA----ALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVS  174 (291)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHH----HHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHH
Confidence            4444555567788888888    7777776  34555666666666664     666666664  344321   122334


Q ss_pred             HHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHH
Q 044412          206 SYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITE  284 (311)
Q Consensus       206 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~  284 (311)
                      .+...|++++|+.+|+++.+. .+.+...++.+-.++.+.|++++|+..++.      +.+.     .| +..++..++.
T Consensus       175 l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~------al~~-----~p~~~~~l~~l~~  242 (291)
T 3mkr_A          175 LAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQE------ALDK-----DSGHPETLINLVV  242 (291)
T ss_dssp             HHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTTCHHHHHHHHH
T ss_pred             HHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHh-----CCCCHHHHHHHHH
Confidence            444558999999999999886 466788899999999999999966665532      1111     34 5678999999


Q ss_pred             HHHhcCChHH-HHHHHHHHHH
Q 044412          285 ALAIHGFAHE-ALGMFDRMTY  304 (311)
Q Consensus       285 ~~~~~g~~~~-a~~~~~~M~~  304 (311)
                      .+...|+.++ +..+++++.+
T Consensus       243 ~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          243 LSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHHHHHH
Confidence            9999999876 5788888875

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.30  E-value=6.7e-11  Score=100.73  Aligned_cols=249  Identities=10%  Similarity=0.010  Sum_probs=185.2

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~  100 (311)
                      ......+...|+...+..+++.+.+.. +.+...+..+...+ .+.|++++|..+++++.+  | +...|..    +...
T Consensus        26 ~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~  103 (330)
T 3hym_B           26 VSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTL-VELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMV  103 (330)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHH-HHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHh
Confidence            456666777799999999999988765 33556677777888 899999999999988753  3 2333333    7778


Q ss_pred             C-ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHH
Q 044412          101 R-HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMID  179 (311)
Q Consensus       101 ~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~  179 (311)
                      | ++++|++.|++..+..               +.+...|..+...|...|++++|.....+..+..+. +...+..+..
T Consensus       104 ~~~~~~A~~~~~~a~~~~---------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~  167 (330)
T 3hym_B          104 GHKNEHARRYLSKATTLE---------------KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG-CHLPMLYIGL  167 (330)
T ss_dssp             CSCHHHHHHHHHHHHTTC---------------TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT-CSHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHhC---------------CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc-cHHHHHHHHH
Confidence            8 9999999999987642               345778999999999999999955554444444333 3345555666


Q ss_pred             HHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC--------CCCCHHHHHHHHHHHh
Q 044412          180 AYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSG--------TGSDQVTMATVLSACA  243 (311)
Q Consensus       180 ~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g--------~~p~~~t~~~li~a~~  243 (311)
                      .|...     |.+.+++..   ..+...|..+...+...|++++|...|++..+..        .+.+..++..+..++.
T Consensus       168 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~  247 (330)
T 3hym_B          168 EYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCR  247 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHH
Confidence            66554     777777654   2367789999999999999999999999987631        1444678899999999


Q ss_pred             ccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          244 HLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       244 ~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..|++++|...++..-      +.    ...+...|..+...+...|++++|...+++..+
T Consensus       248 ~~g~~~~A~~~~~~a~------~~----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  298 (330)
T 3hym_B          248 KLKKYAEALDYHRQAL------VL----IPQNASTYSAIGYIHSLMGNFENAVDYFHTALG  298 (330)
T ss_dssp             HTTCHHHHHHHHHHHH------HH----STTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTT
T ss_pred             HhcCHHHHHHHHHHHH------hh----CccchHHHHHHHHHHHHhccHHHHHHHHHHHHc
Confidence            9999997776654321      11    123677888999999999999999999988765

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.30  E-value=2e-10  Score=104.06  Aligned_cols=58  Identities=3%  Similarity=-0.075  Sum_probs=44.8

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccC
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQM   86 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m   86 (311)
                      ...+..++...|+.+.+...++.+++.. +.+..++..+..++ .+.|++++|...|+++
T Consensus        42 ~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~-~~~g~~~~A~~~~~~~   99 (514)
T 2gw1_A           42 YSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASAN-EGLGKFADAMFDLSVL   99 (514)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHH-HHTTCHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHH-HHHhhHHHHHHHHHHH
Confidence            4566677777788888888888888765 34556788888888 8889999998888665

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.26  E-value=3.1e-10  Score=98.50  Aligned_cols=261  Identities=11%  Similarity=-0.010  Sum_probs=181.7

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~   99 (311)
                      .......+...|+...+...++.+++.. +.+..++..+...+ .+.|++++|...|++..+  |+ ..++..    +..
T Consensus        68 ~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  145 (365)
T 4eqf_A           68 AFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQ-AENENEQAAIVALQRCLELQPNNLKALMALAVSYTN  145 (365)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHH-HHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHc
Confidence            4566777788899999999999998875 34678899999999 999999999999988753  33 333433    889


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCC-CHhHHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPER-KFATWNTMI  178 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~-~~~~~~~li  178 (311)
                      .|++++|++.|++..+..  |+....   .........++..+...|.+.|++++|.....+..+..+.. +..+|..+.
T Consensus       146 ~g~~~~A~~~~~~al~~~--p~~~~~---~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~  220 (365)
T 4eqf_A          146 TSHQQDACEALKNWIKQN--PKYKYL---VKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLG  220 (365)
T ss_dssp             TTCHHHHHHHHHHHHHHC--HHHHCC----------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhC--ccchHH---HhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHH
Confidence            999999999999987632  110000   00000113344556788999999999555555555543331 566788787


Q ss_pred             HHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          179 DAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       179 ~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                      ..|...     |.+.|++..   ..+..+|+.+...|...|++++|+..|++..+.. +-+..++..+-.+|...|++++
T Consensus       221 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~  299 (365)
T 4eqf_A          221 VLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYRE  299 (365)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHH
Confidence            777775     777777654   2467899999999999999999999999998752 3347889999999999999998


Q ss_pred             HHHHHHhhCChHHHHHHHhhcCC--------CCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          251 GRGIQIYCRSLGRSLLVFFKLRE--------KNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       251 a~~~~~~~~~~~~a~~~~~~~~~--------p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      |...++.      +.++..+...        .+...|..+-.++...|+.+.+..+..+
T Consensus       300 A~~~~~~------al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          300 AVSNFLT------ALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHH------HHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHH------HHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            8887754      3333222211        1467899999999999999998887664

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.25  E-value=3.3e-09  Score=95.95  Aligned_cols=81  Identities=11%  Similarity=0.010  Sum_probs=40.5

Q ss_pred             HHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCe-eeeec----cccCCCh
Q 044412           31 ANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNV-FVYHA----FSSLRHP  103 (311)
Q Consensus        31 ~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~----~~~~~~~  103 (311)
                      ...+...|+..++...+..+.+..  ||+.++..+..++ .+.|++++|...|+++.+  |+. ..|..    +.+.|++
T Consensus        13 g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~   89 (514)
T 2gw1_A           13 GNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACY-VSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEGLGKF   89 (514)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHH-HHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHhhH
Confidence            334444555555555555555544  4555555555555 555666666555555431  221 11211    4455555


Q ss_pred             hHHHHHHHHHH
Q 044412          104 LQAIAFYLYML  114 (311)
Q Consensus       104 ~~a~~~~~~m~  114 (311)
                      ++|+..|+++.
T Consensus        90 ~~A~~~~~~~~  100 (514)
T 2gw1_A           90 ADAMFDLSVLS  100 (514)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555555443

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.24  E-value=9.9e-10  Score=94.38  Aligned_cols=249  Identities=10%  Similarity=-0.032  Sum_probs=172.6

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCe------eeee-----
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNV------FVYH-----   95 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~------~~~~-----   95 (311)
                      ...+..++...|+...+...++...+.. +-+...+..+...+ .+.|++++|...|++..+.+.      ..+.     
T Consensus        40 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~  117 (359)
T 3ieg_A           40 YYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLL-LKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKA  117 (359)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHH-HHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHH
Confidence            4556666777788888888888877763 23557778888888 888889888888887654221      1110     


Q ss_pred             ---------c--cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhc
Q 044412           96 ---------A--FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus        96 ---------~--~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~  164 (311)
                               .  +...|++++|++.|++..+.               .+.+...+..+...|...|++++|.....+...
T Consensus       118 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  182 (359)
T 3ieg_A          118 DEMQRLRSQALDAFDGADYTAAITFLDKILEV---------------CVWDAELRELRAECFIKEGEPRKAISDLKAASK  182 (359)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh---------------CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                     1  66788888888888887654               245678888899999999999995554444444


Q ss_pred             cCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC--CC-cHhHHHH------------HHHHHHhCCChhHHHHHHHHHH
Q 044412          165 EMPERKFATWNTMIDAYARL-----AELLFNKMP--AW-DIRSWTT------------MITSYSQNKQFREALDAFNKTK  224 (311)
Q Consensus       165 ~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~--~~-~~~~y~~------------li~~~~~~g~~~~a~~~~~~m~  224 (311)
                      .. ..+..+|..+...+...     |...|++..  .| +...+..            +...+.+.|++++|...+++..
T Consensus       183 ~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~  261 (359)
T 3ieg_A          183 LK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVM  261 (359)
T ss_dssp             TC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            32 23456777777777665     666666553  23 3333332            2556888999999999999988


Q ss_pred             hcCCCCCHH-----HHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHH
Q 044412          225 KSGTGSDQV-----TMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMF  299 (311)
Q Consensus       225 ~~g~~p~~~-----t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  299 (311)
                      +..  |+..     .+..+-.++...|+++.|...++..      .+.    ...+..+|..+...+...|++++|...|
T Consensus       262 ~~~--~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~------~~~----~~~~~~~~~~~~~~~~~~g~~~~A~~~~  329 (359)
T 3ieg_A          262 KTE--PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEV------LQM----EPDNVNALKDRAEAYLIEEMYDEAIQDY  329 (359)
T ss_dssp             HHC--CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hcC--CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHH------HHh----CcccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            743  4422     2445667788888888666655321      111    1236788999999999999999999999


Q ss_pred             HHHHHc
Q 044412          300 DRMTYE  305 (311)
Q Consensus       300 ~~M~~~  305 (311)
                      ++..+.
T Consensus       330 ~~a~~~  335 (359)
T 3ieg_A          330 EAAQEH  335 (359)
T ss_dssp             HHHHTT
T ss_pred             HHHHhc
Confidence            998863

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.22  E-value=1.3e-11  Score=108.45  Aligned_cols=178  Identities=15%  Similarity=0.048  Sum_probs=56.6

Q ss_pred             hccCChhHHHHhcccCCCCCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNY  146 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~  146 (311)
                      -+.|++++|.++++++..|+  +|..    +.+.|++++|++.|..                    .+|...|..+++++
T Consensus        14 ~~~~~ld~A~~fae~~~~~~--vWs~La~A~l~~g~~~eAIdsfik--------------------a~D~~~y~~V~~~a   71 (449)
T 1b89_A           14 EHIGNLDRAYEFAERCNEPA--VWSQLAKAQLQKGMVKEAIDSYIK--------------------ADDPSSYMEVVQAA   71 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHccCHHHHHHHHHhCCChH--HHHHHHHHHHHcCCHHHHHHHHHc--------------------CCCHHHHHHHHHHH
Confidence            56688999999999997775  6666    8999999999999953                    35777999999999


Q ss_pred             HhCCCCccchHHHHHHhccCCC--CCHhHHHHHHHHHHHH--HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHH
Q 044412          147 SYSNKFFESRRVSRRLFDEMPE--RKFATWNTMIDAYARL--AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNK  222 (311)
Q Consensus       147 ~~~g~~~~a~~~a~~~~~~~~~--~~~~~~~~li~~~~~~--a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~  222 (311)
                      ...|++++    |...++...+  ++..+.+.++.+|.++  -.++.+-...|+..+|+.+...|...|.+++|..+|..
T Consensus        72 e~~g~~Ee----Ai~yl~~ark~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~  147 (449)
T 1b89_A           72 NTSGNWEE----LVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNN  147 (449)
T ss_dssp             -----------------------------------------CHHHHTTTTTCC----------------CTTTHHHHHHH
T ss_pred             HhCCCHHH----HHHHHHHHHHhCccchhHHHHHHHHHHhCCHHHHHHHHcCCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            99999999    6665554443  3456788888899887  33333444467888999999999999999999999997


Q ss_pred             HHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHH
Q 044412          223 TKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGM  298 (311)
Q Consensus       223 m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  298 (311)
                      +         ..|..|..++.+.|+++.|.+.             +++.  .++.+|..++.+|...|+++.|...
T Consensus       148 a---------~n~~~LA~~L~~Lg~yq~AVea-------------~~KA--~~~~~Wk~v~~aCv~~~ef~lA~~~  199 (449)
T 1b89_A          148 V---------SNFGRLASTLVHLGEYQAAVDG-------------ARKA--NSTRTWKEVCFACVDGKEFRLAQMC  199 (449)
T ss_dssp             T---------TCHHHHHHHHHTTTCHHHHHHH-------------HHHH--TCHHHHHHHHHHHHHTTCHHHHHHT
T ss_pred             h---------hhHHHHHHHHHHhccHHHHHHH-------------HHHc--CCchhHHHHHHHHHHcCcHHHHHHH
Confidence            7         3788999999998888865554             3433  3788999999999999999999654

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.21  E-value=1.7e-09  Score=98.65  Aligned_cols=273  Identities=10%  Similarity=0.007  Sum_probs=195.4

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC-CCCeeeee----------
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ-EPNVFVYH----------   95 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~-~~~~~~~~----------   95 (311)
                      ...+..++...|+...+...++...+.. +.+..++..+..++ .+.|++++|...|+.+. .|+.....          
T Consensus        62 ~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (537)
T 3fp2_A           62 YSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASAN-ESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLN  139 (537)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHC-----------CHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHH-HHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence            4566677778889999999999888875 34667888888888 99999999998885442 11111000          


Q ss_pred             -----------------------------------------------------------c----ccc--------CCChh
Q 044412           96 -----------------------------------------------------------A----FSS--------LRHPL  104 (311)
Q Consensus        96 -----------------------------------------------------------~----~~~--------~~~~~  104 (311)
                                                                                 .    +..        .++++
T Consensus       140 ~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~  219 (537)
T 3fp2_A          140 KQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLT  219 (537)
T ss_dssp             HHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence                                                                       0    000        02566


Q ss_pred             HHHHHHHHHHHCCCC-ch--------------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchH
Q 044412          105 QAIAFYLYMLRAEVL-LT--------------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRR  157 (311)
Q Consensus       105 ~a~~~~~~m~~~~~~-p~--------------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~  157 (311)
                      +|+++|+++.+..-. ++                          ..++...+  ..|+...|..+...|...|++++|..
T Consensus       220 ~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~  297 (537)
T 3fp2_A          220 KSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESIN--LHPTPNSYIFLALTLADKENSQEFFK  297 (537)
T ss_dssp             HHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCCCHHHHHHHHHHTCCSSCCHHHHH
T ss_pred             HHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHh--cCCCchHHHHHHHHHHHhcCHHHHHH
Confidence            777777766543211 00                          22233333  35667888889999999999999555


Q ss_pred             HHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCC
Q 044412          158 VSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG  229 (311)
Q Consensus       158 ~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~  229 (311)
                      ...+..+..+ .+..+|..+...+...     |...|++..  .| +...|..+...+...|++++|.+.|++..+.. +
T Consensus       298 ~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~  375 (537)
T 3fp2_A          298 FFQKAVDLNP-EYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-P  375 (537)
T ss_dssp             HHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHhccCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-C
Confidence            4444444322 3455677777777664     777776654  23 56789999999999999999999999998763 4


Q ss_pred             CCHHHHHHHHHHHhccCChhhHHHHHHh---------------------------h----------CChHHHHHHHhhcC
Q 044412          230 SDQVTMATVLSACAHLGALDLGRGIQIY---------------------------C----------RSLGRSLLVFFKLR  272 (311)
Q Consensus       230 p~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------------~----------~~~~~a~~~~~~~~  272 (311)
                      .+...+..+-..+...|+++.|...++.                           .          |+.++|...|++..
T Consensus       376 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~  455 (537)
T 3fp2_A          376 TLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKAC  455 (537)
T ss_dssp             TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHH
Confidence            4567888999999999999999999888                           1          88888999998876


Q ss_pred             --CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          273 --EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       273 --~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                        .| +...|..+...|...|++++|...|++..+.
T Consensus       456 ~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  491 (537)
T 3fp2_A          456 ELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAIL  491 (537)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence              34 5678999999999999999999999998763

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.20  E-value=4.1e-10  Score=97.61  Aligned_cols=251  Identities=14%  Similarity=0.050  Sum_probs=180.1

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~   99 (311)
                      .......+...|+...+...++.+.+.. +.+..++..+..++ .+.|++++|.+.|++..+  | +..++..    +..
T Consensus        67 ~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~  144 (368)
T 1fch_A           67 PFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQ-AENEQELLAISALRRCLELKPDNQTALMALAVSFTN  144 (368)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            3466777888899999999999998764 34677888899999 999999999999988652  3 3333333    888


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHH---------------HHHHHHhCCCCccchHHHHHHhc
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTA---------------MVDNYSYSNKFFESRRVSRRLFD  164 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~---------------ll~~~~~~g~~~~a~~~a~~~~~  164 (311)
                      .|++++|++.|+++....-               .+...+..               .+..+...|++++|.....+..+
T Consensus       145 ~g~~~~A~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~  209 (368)
T 1fch_A          145 ESLQRQACEILRDWLRYTP---------------AYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVR  209 (368)
T ss_dssp             TTCHHHHHHHHHHHHHTST---------------TTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCc---------------CcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHH
Confidence            9999999999999876431               11111111               23344477888885555444444


Q ss_pred             cCCCC-CHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHH
Q 044412          165 EMPER-KFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTM  235 (311)
Q Consensus       165 ~~~~~-~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  235 (311)
                      ..+.. +..++..+...|.+.     |...|++..   ..+..+|+.+...+...|++++|+..|++..+.. +.+..++
T Consensus       210 ~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~  288 (368)
T 1fch_A          210 LDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSR  288 (368)
T ss_dssp             HSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             hCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHH
Confidence            43332 456677777766664     666666553   2357789999999999999999999999988752 3457789


Q ss_pred             HHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC-------CCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          236 ATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE-------KNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       236 ~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-------p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      ..+..++.+.|++++|...++.      +.++......       ....+|..+..+|...|+.++|..++.+
T Consensus       289 ~~l~~~~~~~g~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          289 YNLGISCINLGAHREAVEHFLE------ALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHH------HHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHH------HHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHH
Confidence            9999999999999988877644      2222211111       1257899999999999999999988764

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.20  E-value=1.4e-09  Score=92.41  Aligned_cols=234  Identities=11%  Similarity=-0.009  Sum_probs=169.8

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccC-ChhHHHHhcccCCC--C-Ceeeeec----ccc
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFH-FIDYTILVFPQMQE--P-NVFVYHA----FSS   99 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g-~~~~a~~~~~~m~~--~-~~~~~~~----~~~   99 (311)
                      ..+...+...|+.+++..++..+.+.. +.+...+..+...+ ...| +++.|...|++..+  | +...|..    +..
T Consensus        60 ~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~-~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~  137 (330)
T 3hym_B           60 PVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYY-LMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAV  137 (330)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHH-HHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHH-HHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH
Confidence            456677788899999999999888864 33677888888888 9999 99999999988653  3 2333333    888


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMID  179 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~  179 (311)
                      .|++++|++.|++..+..               +.+...+..+...|...|++++|.....+.++.-+ .+...+..+..
T Consensus       138 ~~~~~~A~~~~~~a~~~~---------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~l~~  201 (330)
T 3hym_B          138 ESEHDQAMAAYFTAAQLM---------------KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAP-EDPFVMHEVGV  201 (330)
T ss_dssp             HTCHHHHHHHHHHHHHHT---------------TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCT-TCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhc---------------cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCC-CChHHHHHHHH
Confidence            899999999999987642               34467788899999999999995554444444322 34567777777


Q ss_pred             HHHHH-----HHHHHhhCC------------CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 044412          180 AYARL-----AELLFNKMP------------AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSAC  242 (311)
Q Consensus       180 ~~~~~-----a~~~~~~m~------------~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~  242 (311)
                      .+...     |...+++..            ..+..+|..+...+...|++++|+..|++..+.. +.+...+..+-..+
T Consensus       202 ~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~  280 (330)
T 3hym_B          202 VAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIH  280 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHH
Confidence            77664     555554332            1235689999999999999999999999998753 33677888888999


Q ss_pred             hccCChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHHHHH-HhcCChH
Q 044412          243 AHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSITEAL-AIHGFAH  293 (311)
Q Consensus       243 ~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~-~~~g~~~  293 (311)
                      ...|++++|             ...|++..  .| +...+..+..++ ...|+.+
T Consensus       281 ~~~g~~~~A-------------~~~~~~al~~~p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          281 SLMGNFENA-------------VDYFHTALGLRRDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHTCHHHH-------------HHHHHTTTTTCSCCHHHHHHHHHHHHTTTTC--
T ss_pred             HHhccHHHH-------------HHHHHHHHccCCCchHHHHHHHHHHHHHhCchh
Confidence            998888844             45555444  24 566777777777 3555543

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.14  E-value=7.9e-10  Score=95.77  Aligned_cols=218  Identities=11%  Similarity=0.023  Sum_probs=159.8

Q ss_pred             hhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           59 CFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        59 ~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      ...+..+-..+ .+.|++++|...|+++.+  |+ ...+..    +.+.|++++|++.|++..+..              
T Consensus        64 ~~~~~~~~~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--------------  128 (368)
T 1fch_A           64 HPQPFEEGLRR-LQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK--------------  128 (368)
T ss_dssp             CSSHHHHHHHH-HHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------------
T ss_pred             hHHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC--------------
Confidence            45677888888 999999999999988753  32 223322    888999999999999987642              


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhH------------------HHHHHHHHHHH--HHHHHhh
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFAT------------------WNTMIDAYARL--AELLFNK  191 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~------------------~~~li~~~~~~--a~~~~~~  191 (311)
                       +.+..++..+...|...|++++|.....+.+...+......                  ...+. ...+.  |...|++
T Consensus       129 -~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~A~~~~~~  206 (368)
T 1fch_A          129 -PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLL-SDSLFLEVKELFLA  206 (368)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHH-HHHHHHHHHHHHHH
T ss_pred             -CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHh-hcccHHHHHHHHHH
Confidence             44678899999999999999996555555554433321111                  11111 11111  6667766


Q ss_pred             CC--CC---cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHH
Q 044412          192 MP--AW---DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLL  266 (311)
Q Consensus       192 m~--~~---~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~  266 (311)
                      ..  .|   +..+|..+...|...|++++|+..|++..+.. +.+..+|..+...+...|++++|...++..      .+
T Consensus       207 a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a------l~  279 (368)
T 1fch_A          207 AVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRA------LE  279 (368)
T ss_dssp             HHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HH
T ss_pred             HHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHH------HH
Confidence            54  23   47889999999999999999999999988752 335778999999999999999776665332      11


Q ss_pred             HHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          267 VFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       267 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .    ...+...|..+...|.+.|++++|...|++..+
T Consensus       280 ~----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  313 (368)
T 1fch_A          280 L----QPGYIRSRYNLGISCINLGAHREAVEHFLEALN  313 (368)
T ss_dssp             H----CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             h----CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            1    123567899999999999999999999999865

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.13  E-value=7.8e-10  Score=93.92  Aligned_cols=250  Identities=12%  Similarity=0.090  Sum_probs=173.5

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~  100 (311)
                      ......+...|+..++..+++.+.+.. +.+...+..+...+ .+.|++++|...|++..+  | +...+..    +...
T Consensus        25 ~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~  102 (327)
T 3cv0_A           25 MEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQ-AENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNE  102 (327)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHc
Confidence            455667778899999999999988864 33677888888899 999999999999988753  3 2233322    8889


Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHH--------------HH-HHHhCCCCccchHHHHHHhcc
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAM--------------VD-NYSYSNKFFESRRVSRRLFDE  165 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~l--------------l~-~~~~~g~~~~a~~~a~~~~~~  165 (311)
                      |++++|++.|++..+..               +.+...+..+              .. .+...|++++|.....+..+.
T Consensus       103 ~~~~~A~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  167 (327)
T 3cv0_A          103 HNANAALASLRAWLLSQ---------------PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEM  167 (327)
T ss_dssp             TCHHHHHHHHHHHHHTS---------------TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC---------------CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhh
Confidence            99999999999987642               1111222221              11 266667777744444444333


Q ss_pred             CCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHH
Q 044412          166 MPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMAT  237 (311)
Q Consensus       166 ~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  237 (311)
                      .+ .+...+..+...|...     |.+.+++..   ..+..+|..+...+...|++++|...|++..+.. +.+..++..
T Consensus       168 ~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~  245 (327)
T 3cv0_A          168 NP-NDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYN  245 (327)
T ss_dssp             ST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             CC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHH
Confidence            22 2445666666666554     666665543   2357789999999999999999999999988753 345778889


Q ss_pred             HHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--------CchhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          238 VLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--------NLLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       238 li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--------~~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                      +...+...|++++|...++.      +.+.......+        +...|..+..++...|+.++|..++++.
T Consensus       246 l~~~~~~~g~~~~A~~~~~~------a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  312 (327)
T 3cv0_A          246 MAVSYSNMSQYDLAAKQLVR------AIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQN  312 (327)
T ss_dssp             HHHHHHHTTCHHHHHHHHHH------HHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCC
T ss_pred             HHHHHHHhccHHHHHHHHHH------HHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            99999999999988776643      22221110000        3678999999999999999999988754

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.13  E-value=2e-10  Score=99.75  Aligned_cols=218  Identities=13%  Similarity=0.013  Sum_probs=157.2

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHh
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKN  130 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~  130 (311)
                      +...+..+...+ .+.|++++|...|+++.+  | +..+|..    +.+.|++++|++.|++..+..             
T Consensus        64 ~~~~~~~~~~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------  129 (365)
T 4eqf_A           64 DWPGAFEEGLKR-LKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-------------  129 (365)
T ss_dssp             TCTTHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------
T ss_pred             chhHHHHHHHHH-HHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-------------
Confidence            345588888888 999999999999998753  3 3333333    888999999999999987642             


Q ss_pred             cCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHH----------HHHHHHHHHH-----HHHHHhhCC--
Q 044412          131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATW----------NTMIDAYARL-----AELLFNKMP--  193 (311)
Q Consensus       131 g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~----------~~li~~~~~~-----a~~~~~~m~--  193 (311)
                        +.+..+|..+..+|...|++++|.....+.++..+. +...+          ..+...+.+.     |...|++..  
T Consensus       130 --p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  206 (365)
T 4eqf_A          130 --PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPK-YKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQ  206 (365)
T ss_dssp             --TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHH-HHCC-------------------CCHHHHHHHHHHHHHHHH
T ss_pred             --CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCcc-chHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence              445788999999999999999944444444332211 11111          1122223221     666666554  


Q ss_pred             CC---cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhh
Q 044412          194 AW---DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFK  270 (311)
Q Consensus       194 ~~---~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~  270 (311)
                      .|   +..+|..+...|...|++++|++.|++..+.. +.+..+|..+..+|...|++++|...++.      +.+.   
T Consensus       207 ~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~------al~~---  276 (365)
T 4eqf_A          207 NGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTR------ALEI---  276 (365)
T ss_dssp             SCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH---
T ss_pred             CcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHH------HHhc---
Confidence            23   57889999999999999999999999988752 34678899999999999999977666533      2111   


Q ss_pred             cCCC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          271 LREK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       271 ~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                        .| +..+|..+...|...|++++|...|++..+
T Consensus       277 --~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  309 (365)
T 4eqf_A          277 --QPGFIRSRYNLGISCINLGAYREAVSNFLTALS  309 (365)
T ss_dssp             --CTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             --CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              34 477899999999999999999999999875

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.09  E-value=6.1e-09  Score=89.39  Aligned_cols=243  Identities=7%  Similarity=0.003  Sum_probs=169.7

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLR  101 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~  101 (311)
                      .....+...|+..++...+....+.. +.++.++..+...+ .+.|++++|...|++..+  |+ ...+..    +...|
T Consensus         8 ~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   85 (359)
T 3ieg_A            8 ELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVF-LAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQG   85 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHH-HHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcC
Confidence            45666778899999999999888864 34577888888999 999999999999988753  33 222322    88899


Q ss_pred             ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC----chhHHHHH------------HHHHHhCCCCccchHHHHHHhcc
Q 044412          102 HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS----PVFVQTAM------------VDNYSYSNKFFESRRVSRRLFDE  165 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~----~~~~~~~l------------l~~~~~~g~~~~a~~~a~~~~~~  165 (311)
                      ++++|++.|++..+.                .|    +...+..+            ...+...|++++|.....+..+.
T Consensus        86 ~~~~A~~~~~~~~~~----------------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  149 (359)
T 3ieg_A           86 KLDEAEDDFKKVLKS----------------NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEV  149 (359)
T ss_dssp             CHHHHHHHHHHHHTS----------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhc----------------CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            999999999998764                33    23333333            57899999999955554444443


Q ss_pred             CCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH-HHHH
Q 044412          166 MPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ-VTMA  236 (311)
Q Consensus       166 ~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~  236 (311)
                      -+ .+...+..+...+...     |...+++..   ..+..+|..+...+...|++++|...|++..+.  .|+. ..+.
T Consensus       150 ~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~  226 (359)
T 3ieg_A          150 CV-WDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFA  226 (359)
T ss_dssp             CT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHH
T ss_pred             CC-CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CccchHHHH
Confidence            22 3445666666666654     677766553   236778888888999999999999999988764  3332 2222


Q ss_pred             H------------HHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCCc-----hhHHHHHHHHHhcCChHHHHH
Q 044412          237 T------------VLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKNL-----LCWNSITEALAIHGFAHEALG  297 (311)
Q Consensus       237 ~------------li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~~-----~~~~~li~~~~~~g~~~~a~~  297 (311)
                      .            +...+.+.|++++|...             |++..  .|+.     ..|..+...+...|++++|..
T Consensus       227 ~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~-------------~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          227 HYKQVKKLNKLIESAEELIRDGRYTDATSK-------------YESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHH-------------HHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHH-------------HHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            2            24446666666655544             44333  3432     235567789999999999999


Q ss_pred             HHHHHHHc
Q 044412          298 MFDRMTYE  305 (311)
Q Consensus       298 ~~~~M~~~  305 (311)
                      .+++..+.
T Consensus       294 ~~~~~~~~  301 (359)
T 3ieg_A          294 ICSEVLQM  301 (359)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99998764

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.08  E-value=3.1e-09  Score=87.07  Aligned_cols=195  Identities=11%  Similarity=-0.079  Sum_probs=138.7

Q ss_pred             hhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           59 CFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        59 ~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      ...+..+...+ ...|++++|.+.|++..+  | +...+..    +...|++++|++.|++..+..              
T Consensus        37 ~~~~~~~a~~~-~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--------------  101 (252)
T 2ho1_A           37 RDAYIQLGLGY-LQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD--------------  101 (252)
T ss_dssp             HHHHHHHHHHH-HHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------------
T ss_pred             HHHHHHHHHHH-HHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--------------
Confidence            34566666677 777788888777776542  2 2222222    677888888888888876542              


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCC
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNK  211 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g  211 (311)
                       +.+...+..+...|...|++++    |...++.....+                     ....+...|..+...+...|
T Consensus       102 -~~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~~---------------------~~~~~~~~~~~la~~~~~~g  155 (252)
T 2ho1_A          102 -SRNARVLNNYGGFLYEQKRYEE----AYQRLLEASQDT---------------------LYPERSRVFENLGLVSLQMK  155 (252)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHTTCT---------------------TCTTHHHHHHHHHHHHHHTT
T ss_pred             -cCcHHHHHHHHHHHHHHhHHHH----HHHHHHHHHhCc---------------------cCcccHHHHHHHHHHHHHcC
Confidence             3467788888899999999999    555554433200                     00124667888889999999


Q ss_pred             ChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCC
Q 044412          212 QFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGF  291 (311)
Q Consensus       212 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~  291 (311)
                      ++++|.+.|++..+.. +.+...+..+...+...|++++|...++..-.          ....+...+..+...+...|+
T Consensus       156 ~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~g~  224 (252)
T 2ho1_A          156 KPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQYYDLFAQ----------GGGQNARSLLLGIRLAKVFED  224 (252)
T ss_dssp             CHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT----------TSCCCHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH----------hCcCcHHHHHHHHHHHHHccC
Confidence            9999999999988753 33577888899999999988866665533211          113456678888999999999


Q ss_pred             hHHHHHHHHHHHHc
Q 044412          292 AHEALGMFDRMTYE  305 (311)
Q Consensus       292 ~~~a~~~~~~M~~~  305 (311)
                      .++|..+++++.+.
T Consensus       225 ~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          225 RDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999998764

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.06  E-value=1e-09  Score=88.54  Aligned_cols=190  Identities=10%  Similarity=-0.064  Sum_probs=130.2

Q ss_pred             CcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHH
Q 044412           56 NLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVW  128 (311)
Q Consensus        56 ~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~  128 (311)
                      ++++..+..+-..+ .+.|++++|...|++..+  |+ ...+..    +.+.|++++|+..|++..+..           
T Consensus         2 p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-----------   69 (217)
T 2pl2_A            2 QTAEQNPLRLGVQL-YALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVART-----------   69 (217)
T ss_dssp             --CCHHHHHHHHHH-HHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----------
T ss_pred             CCcHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-----------
Confidence            46677777777888 888899999888887643  32 222222    778899999999999886632           


Q ss_pred             HhcCCCchhHHHHHHHHHHhC-----------CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-c
Q 044412          129 KNGFSSPVFVQTAMVDNYSYS-----------NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-D  196 (311)
Q Consensus       129 ~~g~~~~~~~~~~ll~~~~~~-----------g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~  196 (311)
                          +-+...+..+-..|.+.           |++++    |...++...+.                        .| +
T Consensus        70 ----P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~----A~~~~~~al~~------------------------~P~~  117 (217)
T 2pl2_A           70 ----PRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQ----ALSVLKDAERV------------------------NPRY  117 (217)
T ss_dssp             ----TTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHH----HHHHHHHHHHH------------------------CTTC
T ss_pred             ----CCcHHHHHHHHHHHHHhhhhhhhhcccccCHHH----HHHHHHHHHHh------------------------Cccc
Confidence                33467888888889888           99999    55554442210                        22 5


Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-C
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-N  275 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~  275 (311)
                      ...|..+-..+...|++++|+..|++..+..  .+...+..+-.++...|++++|...++..      .+.     .| +
T Consensus       118 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~a------l~~-----~P~~  184 (217)
T 2pl2_A          118 APLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKA------LEQ-----APKD  184 (217)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHH------HHH-----STTC
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHH------HHh-----CCCC
Confidence            6778888899999999999999999999877  78889999999999999999766655321      111     34 5


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                      ...+..+...+...|++++|...+++.
T Consensus       185 ~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          185 LDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHHHHHHTC--------------
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            678889999999999999999988764

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.01  E-value=1.2e-09  Score=88.87  Aligned_cols=194  Identities=16%  Similarity=0.090  Sum_probs=118.7

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHh
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKN  130 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~  130 (311)
                      ....+..+-..+ .+.|+++.|...|++..+  |+ ...+..    +...|++++|++.|++..+..             
T Consensus        22 ~~~~~~~~a~~~-~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-------------   87 (243)
T 2q7f_A           22 ASMTGGQQMGRG-SEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-------------   87 (243)
T ss_dssp             ---------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------
T ss_pred             HHHHHHHHHHHH-HHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------------
Confidence            344555555566 666777777666666532  21 222211    566777788888887765532             


Q ss_pred             cCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhC
Q 044412          131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQN  210 (311)
Q Consensus       131 g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~  210 (311)
                        +.+..++..+...|...|++++    |...++...+                       ....+...|..+...+...
T Consensus        88 --~~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~-----------------------~~~~~~~~~~~~a~~~~~~  138 (243)
T 2q7f_A           88 --SSAATAYYGAGNVYVVKEMYKE----AKDMFEKALR-----------------------AGMENGDLFYMLGTVLVKL  138 (243)
T ss_dssp             --TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH-----------------------HTCCSHHHHHHHHHHHHHT
T ss_pred             --CcchHHHHHHHHHHHHhccHHH----HHHHHHHHHH-----------------------hCCCCHHHHHHHHHHHHHh
Confidence              3456777888888888888888    4444443211                       0123566788888888899


Q ss_pred             CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcC
Q 044412          211 KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHG  290 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g  290 (311)
                      |++++|..++++..+.. +.+...+..+...+...|+++.|...++..      .+.    ...+..+|..+...|...|
T Consensus       139 ~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~------~~~----~~~~~~~~~~la~~~~~~~  207 (243)
T 2q7f_A          139 EQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEALSQFAAV------TEQ----DPGHADAFYNAGVTYAYKE  207 (243)
T ss_dssp             SCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHH------HHH----CTTCHHHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHH------HHh----CcccHHHHHHHHHHHHHcc
Confidence            99999999999987652 346778888888888888888776655332      111    1235678888899999999


Q ss_pred             ChHHHHHHHHHHHHc
Q 044412          291 FAHEALGMFDRMTYE  305 (311)
Q Consensus       291 ~~~~a~~~~~~M~~~  305 (311)
                      ++++|...+++..+.
T Consensus       208 ~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          208 NREKALEMLDKAIDI  222 (243)
T ss_dssp             CTTHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcc
Confidence            999999999988763

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.00  E-value=1.2e-08  Score=93.02  Aligned_cols=273  Identities=11%  Similarity=-0.038  Sum_probs=156.8

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~  100 (311)
                      ......+...|+...+...++.+++.. +.++..+..+..++ .+.|++++|.+.|++..+  |+ ...+..    +...
T Consensus        29 ~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~  106 (537)
T 3fp2_A           29 KNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACY-ISTGDLEKVIEFTTKALEIKPDHSKALLRRASANESL  106 (537)
T ss_dssp             HHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHH-HHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHc
Confidence            455666778899999999999998875 34778899999999 999999999999998753  43 222222    8888


Q ss_pred             CChhHHHHHHHHHHHCCCCch----------------HHHHHHHH------hcCCCchh---------------------
Q 044412          101 RHPLQAIAFYLYMLRAEVLLT----------------TVHGQVWK------NGFSSPVF---------------------  137 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~----------------~~~~~~~~------~g~~~~~~---------------------  137 (311)
                      |++++|++.|+.+....-.++                ..++....      ....|+..                     
T Consensus       107 g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (537)
T 3fp2_A          107 GNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTS  186 (537)
T ss_dssp             TCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCC
T ss_pred             CCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhc
Confidence            999999999964421111000                00111100      00011111                     


Q ss_pred             ---------HHHHHHHHHHhC--------CCCccchHHHHHHhccCCCCCHhH-------HHHHHHHHHHH-----HHHH
Q 044412          138 ---------VQTAMVDNYSYS--------NKFFESRRVSRRLFDEMPERKFAT-------WNTMIDAYARL-----AELL  188 (311)
Q Consensus       138 ---------~~~~ll~~~~~~--------g~~~~a~~~a~~~~~~~~~~~~~~-------~~~li~~~~~~-----a~~~  188 (311)
                               ....+...+...        |++++|..+..++++.-+. +...       |..+-..+...     |...
T Consensus       187 ~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~  265 (537)
T 3fp2_A          187 SNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTV-DDPLRENAALALCYTGIFHFLKNNLLDAQVL  265 (537)
T ss_dssp             CSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCC-cchhhHHHHHHHHHHHHHHHhcccHHHHHHH
Confidence                     111111111111        2455533333333322221 1111       22222222111     4444


Q ss_pred             HhhCC--CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh---------
Q 044412          189 FNKMP--AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY---------  257 (311)
Q Consensus       189 ~~~m~--~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~---------  257 (311)
                      |++..  .|+...|..+...+...|++++|++.|++..+.. +.+..+|..+...+...|+++.|...++.         
T Consensus       266 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~  344 (537)
T 3fp2_A          266 LQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENV  344 (537)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCS
T ss_pred             HHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCH
Confidence            44433  3445566666666666677777777776666532 22455666666666666777766666665         


Q ss_pred             ------------hCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          258 ------------CRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       258 ------------~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                                  .|+.++|...|++..   ..+...|..+...+...|++++|...|++..+
T Consensus       345 ~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  406 (537)
T 3fp2_A          345 YPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKR  406 (537)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence                        666667777776655   33466888888888899999999988888764

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.99  E-value=1.3e-08  Score=81.30  Aligned_cols=195  Identities=10%  Similarity=-0.103  Sum_probs=132.3

Q ss_pred             hhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           59 CFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        59 ~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      +..+..+...+ .+.|++++|.+.|++..+  | +...+..    +...|++++|++.|++..+.               
T Consensus         8 ~~~~~~~~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~---------------   71 (225)
T 2vq2_A            8 SNIKTQLAMEY-MRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSI---------------   71 (225)
T ss_dssp             HHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------
T ss_pred             HHHHHHHHHHH-HHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHh---------------
Confidence            34555555556 666666666666655432  2 1222222    55677778888888777653               


Q ss_pred             CCCchhHHHHHHHHHHhC-CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhC
Q 044412          132 FSSPVFVQTAMVDNYSYS-NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQN  210 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~-g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~  210 (311)
                      .+.+..++..+...|... |++++|.....+..+ .  +.                      ...+...|..+...+...
T Consensus        72 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~-~--~~----------------------~~~~~~~~~~l~~~~~~~  126 (225)
T 2vq2_A           72 KPDSAEINNNYGWFLCGRLNRPAESMAYFDKALA-D--PT----------------------YPTPYIANLNKGICSAKQ  126 (225)
T ss_dssp             CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHT-S--TT----------------------CSCHHHHHHHHHHHHHHT
T ss_pred             CCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHc-C--cC----------------------CcchHHHHHHHHHHHHHc
Confidence            234577888899999999 999994444444433 0  10                      012356788888999999


Q ss_pred             CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC-CCchhHHHHHHHHHhc
Q 044412          211 KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE-KNLLCWNSITEALAIH  289 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-p~~~~~~~li~~~~~~  289 (311)
                      |++++|++.|++..+.. +.+...+..+...+...|++++|...++..      .+..    . .+...+..+...+...
T Consensus       127 ~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~------~~~~----~~~~~~~~~~~~~~~~~~  195 (225)
T 2vq2_A          127 GQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKY------QSRV----EVLQADDLLLGWKIAKAL  195 (225)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH------HHHH----CSCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHH------HHhC----CCCCHHHHHHHHHHHHhc
Confidence            99999999999988753 334778888888999999988776665331      1110    2 4566788888888999


Q ss_pred             CChHHHHHHHHHHHHc
Q 044412          290 GFAHEALGMFDRMTYE  305 (311)
Q Consensus       290 g~~~~a~~~~~~M~~~  305 (311)
                      |+.++|..+++.+.+.
T Consensus       196 ~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          196 GNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHh
Confidence            9999999999988753

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=98.99  E-value=4.7e-09  Score=89.06  Aligned_cols=220  Identities=9%  Similarity=-0.033  Sum_probs=157.1

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHh
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKN  130 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~  130 (311)
                      +...+-.+...+ .+.|++++|..+|+++.+  |+ ...+..    +.+.|++++|++.|++..+.              
T Consensus        20 ~~~~~~~~a~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------------   84 (327)
T 3cv0_A           20 YHENPMEEGLSM-LKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARML--------------   84 (327)
T ss_dssp             GSSCHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------------
T ss_pred             hhHHHHHHHHHH-HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--------------
Confidence            444556667778 899999999999988753  33 223322    88899999999999998764              


Q ss_pred             cCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH-------------HH--HHH-----HHHHHHh
Q 044412          131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI-------------DA--YAR-----LAELLFN  190 (311)
Q Consensus       131 g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li-------------~~--~~~-----~a~~~~~  190 (311)
                       .+.+..++..+...|...|++++|.....+..+.-+. +...+..+.             ..  +..     .|.+.++
T Consensus        85 -~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~  162 (327)
T 3cv0_A           85 -DPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQ-YEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLH  162 (327)
T ss_dssp             -CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTT-TTTC--------------------CCTTSHHHHHHHHHHHH
T ss_pred             -CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHH
Confidence             2446788999999999999999955555555543322 111222220             11  111     1666665


Q ss_pred             hCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHH
Q 044412          191 KMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLV  267 (311)
Q Consensus       191 ~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~  267 (311)
                      +..   ..+...+..+...+...|++++|.+.+++..+.. +.+..++..+...+...|++++|...++..      .+.
T Consensus       163 ~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a------~~~  235 (327)
T 3cv0_A          163 AALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRA------LDI  235 (327)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH
T ss_pred             HHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH------HHc
Confidence            543   2367889999999999999999999999998753 345778999999999999999776665332      111


Q ss_pred             HhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          268 FFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       268 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                          ...+...|..+...+...|++++|...+++..+.
T Consensus       236 ----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  269 (327)
T 3cv0_A          236 ----NPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYM  269 (327)
T ss_dssp             ----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ----CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence                1235678999999999999999999999998753

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.98  E-value=1e-08  Score=86.60  Aligned_cols=191  Identities=9%  Similarity=0.076  Sum_probs=129.2

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC----CCCeeeeec-----ccc
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ----EPNVFVYHA-----FSS   99 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~----~~~~~~~~~-----~~~   99 (311)
                      .+...+-..|+.+.+..-++.    .-+|+..++..+...+ .+.++.+.|.+.++++.    .|+...+..     +..
T Consensus        39 ~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~-~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~  113 (291)
T 3mkr_A           39 FLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYL-ASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFY  113 (291)
T ss_dssp             HHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHH-HCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHH-cCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHH
Confidence            344556666666666443322    2456777778888888 88888888888888753    244333222     778


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CCHhHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKFATWNTM  177 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~~~~~~l  177 (311)
                      .|++++|++.|++                    +.+...+..+...|.+.|++++    |...++.+.+  |+.. ...+
T Consensus       114 ~g~~~~Al~~l~~--------------------~~~~~~~~~l~~~~~~~g~~~~----A~~~l~~~~~~~p~~~-~~~l  168 (291)
T 3mkr_A          114 DQNPDAALRTLHQ--------------------GDSLECMAMTVQILLKLDRLDL----ARKELKKMQDQDEDAT-LTQL  168 (291)
T ss_dssp             TTCHHHHHHHHTT--------------------CCSHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHCTTCH-HHHH
T ss_pred             CCCHHHHHHHHhC--------------------CCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHhhCcCcH-HHHH
Confidence            8888888888764                    2355677788888888888888    4444444332  3321 1222


Q ss_pred             HHHHH-------HH--HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc
Q 044412          178 IDAYA-------RL--AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL  245 (311)
Q Consensus       178 i~~~~-------~~--a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~  245 (311)
                      ..++.       +.  |..+|+++.   ..+...|+.+-.++.+.|++++|+..|++..+.. +-+..++..+...+...
T Consensus       169 ~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~~~l~~l~~~~~~~  247 (291)
T 3mkr_A          169 ATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHPETLINLVVLSQHL  247 (291)
T ss_dssp             HHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc
Confidence            22221       11  777776664   2477889999999999999999999999988752 33677899999999998


Q ss_pred             CChhh
Q 044412          246 GALDL  250 (311)
Q Consensus       246 ~~~~~  250 (311)
                      |+.++
T Consensus       248 g~~~e  252 (291)
T 3mkr_A          248 GKPPE  252 (291)
T ss_dssp             TCCHH
T ss_pred             CCCHH
Confidence            88864

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.98  E-value=3.1e-09  Score=87.00  Aligned_cols=218  Identities=10%  Similarity=-0.047  Sum_probs=137.5

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHHH
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAI  107 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~  107 (311)
                      ......+...|+...+...+....+..  .+...+..+..++ .+.|++++|.+.+++..+                   
T Consensus         9 ~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~-~~~~~~~~A~~~~~~a~~-------------------   66 (258)
T 3uq3_A            9 KAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAE-YEKGEYETAISTLNDAVE-------------------   66 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHH-HHTTCHHHHHHHHHHHHH-------------------
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHH-HHcccHHHHHHHHHHHHH-------------------
Confidence            344555666777788888888777777  6777777777777 777777777776654321                   


Q ss_pred             HHHHHHHHCCCCchHHHHHHHHhcCCCc----hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH
Q 044412          108 AFYLYMLRAEVLLTTVHGQVWKNGFSSP----VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       108 ~~~~~m~~~~~~p~~~~~~~~~~g~~~~----~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~  183 (311)
                       +...                   ..++    ..+|..+...|.+.|++++|.....+....-  |+...+    ....+
T Consensus        67 -~~~~-------------------~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~----~~~~~  120 (258)
T 3uq3_A           67 -QGRE-------------------MRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEH--RTADIL----TKLRN  120 (258)
T ss_dssp             -HHHH-------------------TTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHH----HHHHH
T ss_pred             -hCcc-------------------cccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC--chhHHH----HHHhH
Confidence             1100                   1111    3444555555555555555222222222211  111110    00011


Q ss_pred             H--HHHHHhhCC--C-CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhh
Q 044412          184 L--AELLFNKMP--A-WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYC  258 (311)
Q Consensus       184 ~--a~~~~~~m~--~-~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~  258 (311)
                      .  |...++...  . .+...|..+...+...|++++|+..|++..+.. +.+..+|..+..++...|++++|...++..
T Consensus       121 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  199 (258)
T 3uq3_A          121 AEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKA  199 (258)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            1  333333322  2 245678888999999999999999999998753 346788999999999999999776665432


Q ss_pred             CChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          259 RSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       259 ~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                            .+.    ...+...|..+-..+...|++++|...+++..+
T Consensus       200 ------l~~----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  235 (258)
T 3uq3_A          200 ------IEK----DPNFVRAYIRKATAQIAVKEYASALETLDAART  235 (258)
T ss_dssp             ------HHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ------HHh----CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                  111    123567899999999999999999999998765

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.93  E-value=1.9e-07  Score=77.10  Aligned_cols=225  Identities=11%  Similarity=0.013  Sum_probs=163.4

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeee----eec----cc
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFV----YHA----FS   98 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~----~~~----~~   98 (311)
                      .....+...|+.+.+...+....+... .+...+..+...+ .+.|++++|...+++..+  ++...    |..    +.
T Consensus         8 ~~a~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~   85 (272)
T 3u4t_A            8 RYADFLFKNNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCY-YELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILM   85 (272)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHH-HHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHH-HHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHH
Confidence            456667778899999999988887642 3455788888888 999999999999987643  22221    222    88


Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                      ..|++++|++.|+...+..               +.+..+|..+-..|...|++++    |...++...+.+        
T Consensus        86 ~~~~~~~A~~~~~~a~~~~---------------~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~al~~~--------  138 (272)
T 3u4t_A           86 KKGQDSLAIQQYQAAVDRD---------------TTRLDMYGQIGSYFYNKGNFPL----AIQYMEKQIRPT--------  138 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHS---------------TTCTHHHHHHHHHHHHTTCHHH----HHHHHGGGCCSS--------
T ss_pred             HcccHHHHHHHHHHHHhcC---------------cccHHHHHHHHHHHHHccCHHH----HHHHHHHHhhcC--------
Confidence            8899999999999887642               4456788999999999999999    777777765422        


Q ss_pred             HHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCC---hhhHHHH
Q 044412          179 DAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGA---LDLGRGI  254 (311)
Q Consensus       179 ~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~---~~~a~~~  254 (311)
                                     ..+...|..+-..+-..+++++|++.|++..+.  .|+ ...+..+-.++...|+   .+.|...
T Consensus       139 ---------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~  201 (272)
T 3u4t_A          139 ---------------TTDPKVFYELGQAYYYNKEYVKADSSFVKVLEL--KPNIYIGYLWRARANAAQDPDTKQGLAKPY  201 (272)
T ss_dssp             ---------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHSTTCSSCTTHHH
T ss_pred             ---------------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHcCcchhhHHHHHH
Confidence                           224566666662333456999999999999875  344 6677777777777777   7767665


Q ss_pred             HHhhCChHHHHHHHhhcCCCC----chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          255 QIYCRSLGRSLLVFFKLREKN----LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       255 ~~~~~~~~~a~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ++      .+.++....+.++    ...|..+-..|...|++++|...+++..+.
T Consensus       202 ~~------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  250 (272)
T 3u4t_A          202 YE------KLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILAL  250 (272)
T ss_dssp             HH------HHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HH------HHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            53      3333333222221    257888999999999999999999998763

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.90  E-value=3.8e-08  Score=82.76  Aligned_cols=232  Identities=7%  Similarity=-0.032  Sum_probs=142.5

Q ss_pred             hcCCCCCchhh-hHHHHHHHHhhccChhhHHHHHHHHHHh-------ccCcchhHHHHHHHHHhhccCChhHHHHhcccC
Q 044412           15 KNSFPTSVSFI-RIHIIANQLKKCSSIKELECVYATIVKT-------NANLDCFLAKQFISFCTSRFHFIDYTILVFPQM   86 (311)
Q Consensus        15 ~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~l~~~m~~~-------g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m   86 (311)
                      +...++.+... ....+...+...|+...+...+....+.       ..+....++..+...+ ...|++++|...+   
T Consensus        17 q~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~-~~~g~~~~A~~~~---   92 (311)
T 3nf1_A           17 QGGGYEIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVY-RDQNKYKDAANLL---   92 (311)
T ss_dssp             SSSCTTSCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHH-HHTTCHHHHHHHH---
T ss_pred             cCCCCcchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH-HHCCCHHHHHHHH---
Confidence            33444444432 2445556666777888887777766653       2233445666667777 7777777776665   


Q ss_pred             CCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccC
Q 044412           87 QEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEM  166 (311)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~  166 (311)
                                       +++++++++.....              ......++..+...|...|++++    |...++..
T Consensus        93 -----------------~~al~~~~~~~~~~--------------~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~a  137 (311)
T 3nf1_A           93 -----------------NDALAIREKTLGKD--------------HPAVAATLNNLAVLYGKRGKYKE----AEPLCKRA  137 (311)
T ss_dssp             -----------------HHHHHHHHHHHCTT--------------CHHHHHHHHHHHHHHHTTTCHHH----HHHHHHHH
T ss_pred             -----------------HHHHHHHHHHhCCC--------------ChHHHHHHHHHHHHHHHcCcHHH----HHHHHHHH
Confidence                             44555554442111              12235678889999999999999    55555542


Q ss_pred             CCCCHhHHHHHHHHHHHHHHHHHhhC--CC--CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc------CCCCC-HHHH
Q 044412          167 PERKFATWNTMIDAYARLAELLFNKM--PA--WDIRSWTTMITSYSQNKQFREALDAFNKTKKS------GTGSD-QVTM  235 (311)
Q Consensus       167 ~~~~~~~~~~li~~~~~~a~~~~~~m--~~--~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p~-~~t~  235 (311)
                                         .++....  ..  .....|..+...+...|++++|+++|++..+.      +-.|+ ..++
T Consensus       138 -------------------~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  198 (311)
T 3nf1_A          138 -------------------LEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTK  198 (311)
T ss_dssp             -------------------HHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHH
T ss_pred             -------------------HHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence                               1222211  11  13456777778888888888888888887653      22332 3467


Q ss_pred             HHHHHHHhccCChhhHHHHHHhhCChH------------------------------------HHHHHHhhcC--CC-Cc
Q 044412          236 ATVLSACAHLGALDLGRGIQIYCRSLG------------------------------------RSLLVFFKLR--EK-NL  276 (311)
Q Consensus       236 ~~li~a~~~~~~~~~a~~~~~~~~~~~------------------------------------~a~~~~~~~~--~p-~~  276 (311)
                      ..+...+...|++++|...++..-...                                    ++...++...  .| +.
T Consensus       199 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  278 (311)
T 3nf1_A          199 NNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVT  278 (311)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHH
Confidence            777788888888888887776522111                                    1111111111  11 34


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+|..+...|.+.|++++|..+|++..+
T Consensus       279 ~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          279 TTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6788999999999999999999998765

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.90  E-value=3.2e-08  Score=81.82  Aligned_cols=218  Identities=9%  Similarity=-0.074  Sum_probs=138.9

Q ss_pred             hccChhhHHHHHHHHHHhcc---CcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCCChhH
Q 044412           36 KCSSIKELECVYATIVKTNA---NLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLRHPLQ  105 (311)
Q Consensus        36 ~~~~~~~~~~l~~~m~~~g~---~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~~~~~  105 (311)
                      ..++.+.+...++.+.+.+.   +.+..++..+...+ ...|++++|...|++..+  | +...|..    +...|++++
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLY-DSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHH-HHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHH
Confidence            34667777888888887642   12467788888888 999999999999988653  3 2333333    888899999


Q ss_pred             HHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHH
Q 044412          106 AIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLA  185 (311)
Q Consensus       106 a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a  185 (311)
                      |++.|++..+..               +.+..++..+..+|.+.|++++    |...++...+.                
T Consensus        96 A~~~~~~al~~~---------------~~~~~~~~~la~~~~~~g~~~~----A~~~~~~a~~~----------------  140 (275)
T 1xnf_A           96 AYEAFDSVLELD---------------PTYNYAHLNRGIALYYGGRDKL----AQDDLLAFYQD----------------  140 (275)
T ss_dssp             HHHHHHHHHHHC---------------TTCTHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH----------------
T ss_pred             HHHHHHHHHhcC---------------ccccHHHHHHHHHHHHhccHHH----HHHHHHHHHHh----------------
Confidence            999999887642               3457888999999999999999    55554442210                


Q ss_pred             HHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHH
Q 044412          186 ELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSL  265 (311)
Q Consensus       186 ~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~  265 (311)
                              .|+...+...+..+...|++++|...+.+.... .+++...+. +...+...++.+.|...+...-......
T Consensus       141 --------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~  210 (275)
T 1xnf_A          141 --------DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK-SDKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSL  210 (275)
T ss_dssp             --------CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH-SCCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHH
T ss_pred             --------CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhc-CCcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccc
Confidence                    122222223333445557888888888766654 233433443 5555666666665544443322111100


Q ss_pred             HHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          266 LVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       266 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      .      ..+...|..+...|...|++++|...|++....
T Consensus       211 ~------~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  244 (275)
T 1xnf_A          211 A------EHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  244 (275)
T ss_dssp             H------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             c------ccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            0      012456777777888888888888888877653

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=98.83  E-value=4.9e-08  Score=79.79  Aligned_cols=187  Identities=6%  Similarity=-0.040  Sum_probs=141.8

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~  100 (311)
                      ..+...+...|+...+...++...+.. +.+...+..+...+ .+.|++++|.+.|++..+  | +...+..    +...
T Consensus        41 ~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~  118 (252)
T 2ho1_A           41 IQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVF-QTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQ  118 (252)
T ss_dssp             HHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHH
Confidence            455566778899999999999888764 34677888888999 999999999999988652  3 3333332    8889


Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA  180 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~  180 (311)
                      |++++|++.|++..+.+.             .+.+...+..+...|.+.|++++    |...++...+.           
T Consensus       119 g~~~~A~~~~~~~~~~~~-------------~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~-----------  170 (252)
T 2ho1_A          119 KRYEEAYQRLLEASQDTL-------------YPERSRVFENLGLVSLQMKKPAQ----AKEYFEKSLRL-----------  170 (252)
T ss_dssp             TCHHHHHHHHHHHTTCTT-------------CTTHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------
T ss_pred             hHHHHHHHHHHHHHhCcc-------------CcccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhc-----------
Confidence            999999999999866221             23356788889999999999999    55555442110           


Q ss_pred             HHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          181 YARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       181 ~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                                  ...+...|..+...+...|++++|...|++..+. .+.+...+..+...+...|+.+.|...++.
T Consensus       171 ------------~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~  234 (252)
T 2ho1_A          171 ------------NRNQPSVALEMADLLYKEREYVPARQYYDLFAQG-GGQNARSLLLGIRLAKVFEDRDTAASYGLQ  234 (252)
T ss_dssp             ------------CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             ------------CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CcCcHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence                        1125677888999999999999999999998764 235677788888889999999877666543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.80  E-value=9.5e-08  Score=76.24  Aligned_cols=157  Identities=11%  Similarity=0.023  Sum_probs=117.3

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|++.|++..+.               .+.+...+..+...|...|++++    |...++....        
T Consensus        18 ~~~~~~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~a~~--------   70 (225)
T 2vq2_A           18 YMRGQDYRQATASIEDALKS---------------DPKNELAWLVRAEIYQYLKVNDK----AQESFRQALS--------   70 (225)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH--------
T ss_pred             HHHHhhHHHHHHHHHHHHHh---------------CccchHHHHHHHHHHHHcCChHH----HHHHHHHHHH--------
Confidence            56778888888888887653               23456778888888888888888    5544443211        


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhC-CChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQN-KQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~  254 (311)
                                     ....+..+|..+...+... |++++|++.+++..+.+..|+ ...+..+..++...|++++|...
T Consensus        71 ---------------~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  135 (225)
T 2vq2_A           71 ---------------IKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAY  135 (225)
T ss_dssp             ---------------HCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ---------------hCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHH
Confidence                           0123567888899999999 999999999999988444454 56788888999999999977666


Q ss_pred             HHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          255 QIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       255 ~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ++..      .+.    ...+...+..+...+...|++++|..++++..+.
T Consensus       136 ~~~~------~~~----~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  176 (225)
T 2vq2_A          136 LKRS------LAA----QPQFPPAFKELARTKMLAGQLGDADYYFKKYQSR  176 (225)
T ss_dssp             HHHH------HHH----STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHH------HHh----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5432      111    1234778999999999999999999999998763

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.69  E-value=8.1e-08  Score=84.44  Aligned_cols=258  Identities=10%  Similarity=0.007  Sum_probs=169.5

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcch----hHHHHHHHHHhhccCChhHHHHhcccCCC-----CC----eeeee
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDC----FLAKQFISFCTSRFHFIDYTILVFPQMQE-----PN----VFVYH   95 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~----~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----~~----~~~~~   95 (311)
                      .....+...|+..++...++...+.+.. +.    .++..+-..+ ...|++++|...+++..+     .+    ...+.
T Consensus        53 ~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  130 (411)
T 4a1s_A           53 LEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAY-FYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSG  130 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHH
Confidence            4455667778999999999998887432 22    4778888888 999999999999877642     11    11111


Q ss_pred             c----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCC-----------------Cc
Q 044412           96 A----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNK-----------------FF  153 (311)
Q Consensus        96 ~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~-----------------~~  153 (311)
                      .    +...|++++|++.|++..+..          .+.+-.+ ...++..+-..|...|+                 ++
T Consensus       131 ~l~~~~~~~g~~~~A~~~~~~al~~~----------~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~  200 (411)
T 4a1s_A          131 NLGNTLKVMGRFDEAAICCERHLTLA----------RQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALT  200 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHH----------HHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHH----------HHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHH
Confidence            1    888999999999999875421          1112122 25578888889999999                 88


Q ss_pred             cchHHHHHHhccC---CCC--CHhHHHHHHHHHHHH-----HHHHHhhCC-------CC--cHhHHHHHHHHHHhCCChh
Q 044412          154 ESRRVSRRLFDEM---PER--KFATWNTMIDAYARL-----AELLFNKMP-------AW--DIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       154 ~a~~~a~~~~~~~---~~~--~~~~~~~li~~~~~~-----a~~~~~~m~-------~~--~~~~y~~li~~~~~~g~~~  214 (311)
                      +|.....+.++..   ..+  ...++..+-..|...     |.+.+++..       .+  ...+|..+...|...|+++
T Consensus       201 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  280 (411)
T 4a1s_A          201 RAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFE  280 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHH
Confidence            8444333322211   111  112444444444443     555554432       11  1237888888899999999


Q ss_pred             HHHHHHHHHHhcC--C--C-CCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC--CCchhHHHHHHHHH
Q 044412          215 EALDAFNKTKKSG--T--G-SDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE--KNLLCWNSITEALA  287 (311)
Q Consensus       215 ~a~~~~~~m~~~g--~--~-p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~--p~~~~~~~li~~~~  287 (311)
                      +|...|++..+..  .  . ....++..+-..+...|++++|...++.      +..+......  ....+|..+...|.
T Consensus       281 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~la~~~~  354 (411)
T 4a1s_A          281 DAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNR------HLAIAQELGDRIGEARACWSLGNAHS  354 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHHHHHCCChHHHHHHHHHHHHHHH
Confidence            9999998876521  1  1 1145777888888888999988877643      3333333321  12457888999999


Q ss_pred             hcCChHHHHHHHHHHHH
Q 044412          288 IHGFAHEALGMFDRMTY  304 (311)
Q Consensus       288 ~~g~~~~a~~~~~~M~~  304 (311)
                      ..|++++|..++++..+
T Consensus       355 ~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          355 AIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHH
Confidence            99999999999998754

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.69  E-value=6.7e-08  Score=78.27  Aligned_cols=184  Identities=9%  Similarity=0.004  Sum_probs=130.4

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----cccCC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSSLR  101 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~~~  101 (311)
                      .....+...|+...+...++...+.. +.+...+..+...+ .+.|++++|.+.|++..+  | +...+..    +...|
T Consensus        28 ~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~  105 (243)
T 2q7f_A           28 QQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLL-SSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKE  105 (243)
T ss_dssp             --------------CCTTHHHHHTTC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhc
Confidence            34445566788888888888887743 34677888888999 999999999999988652  3 3333332    88899


Q ss_pred             ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHH
Q 044412          102 HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAY  181 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~  181 (311)
                      ++++|++.|++..+..               +.+...+..+...|.+.|++++    |...++...+.            
T Consensus       106 ~~~~A~~~~~~~~~~~---------------~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~------------  154 (243)
T 2q7f_A          106 MYKEAKDMFEKALRAG---------------MENGDLFYMLGTVLVKLEQPKL----ALPYLQRAVEL------------  154 (243)
T ss_dssp             CHHHHHHHHHHHHHHT---------------CCSHHHHHHHHHHHHHTSCHHH----HHHHHHHHHHH------------
T ss_pred             cHHHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHhccHHH----HHHHHHHHHHh------------
Confidence            9999999999987642               4567788999999999999999    55555442210            


Q ss_pred             HHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          182 ARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       182 ~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                                 ...+...|..+...+...|++++|++.|++..+.. +.+..++..+..++...|+.++|...++.
T Consensus       155 -----------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~  218 (243)
T 2q7f_A          155 -----------NENDTEARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDK  218 (243)
T ss_dssp             -----------CTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHH
T ss_pred             -----------CCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence                       12256678888899999999999999999988753 34577888999999999999977766543

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.65  E-value=1.1e-07  Score=78.47  Aligned_cols=214  Identities=10%  Similarity=-0.009  Sum_probs=135.7

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--C-Ceeeeec----ccc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--P-NVFVYHA----FSS   99 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~----~~~   99 (311)
                      ...+..++...|+...+...+....+.. +.+..++..+...+ .+.|++++|.+.|++..+  | +...+..    +.+
T Consensus        46 ~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~-~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~  123 (275)
T 1xnf_A           46 LYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYL-TQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYY  123 (275)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHH-HHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHH
Confidence            4566777778899999999999888874 33678899999999 999999999999988753  3 2333333    889


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMID  179 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~  179 (311)
                      .|++++|++.|++..+.                .|+.......+..+...|++++|...........+            
T Consensus       124 ~g~~~~A~~~~~~a~~~----------------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~------------  175 (275)
T 1xnf_A          124 GGRDKLAQDDLLAFYQD----------------DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSD------------  175 (275)
T ss_dssp             TTCHHHHHHHHHHHHHH----------------CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSC------------
T ss_pred             hccHHHHHHHHHHHHHh----------------CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC------------
Confidence            99999999999998763                45555555566666777999994443333333211            


Q ss_pred             HHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCC--C-CHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          180 AYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG--S-DQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       180 ~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~--p-~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                                     ++...|. +...+...++.++|++.+.+..+....  | +..++..+-..+...|++++|...  
T Consensus       176 ---------------~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~--  237 (275)
T 1xnf_A          176 ---------------KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATAL--  237 (275)
T ss_dssp             ---------------CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHH--
T ss_pred             ---------------cchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHH--
Confidence                           1222332 555556666777777777776543211  1 145666667777776766644443  


Q ss_pred             hhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHH
Q 044412          257 YCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMF  299 (311)
Q Consensus       257 ~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  299 (311)
                                 |++..+-++..+.....++...|++++|..-+
T Consensus       238 -----------~~~al~~~p~~~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          238 -----------FKLAVANNVHNFVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             -----------HHHHHTTCCTTCHHHHHHHHHHHHHHHC----
T ss_pred             -----------HHHHHhCCchhHHHHHHHHHHHHHHHhhHHHH
Confidence                       33333222222334455666667777766554

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.65  E-value=1.9e-06  Score=66.15  Aligned_cols=154  Identities=14%  Similarity=0.070  Sum_probs=115.9

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCC---CCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE---RKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMI  204 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~---~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li  204 (311)
                      ...|..+...+...|++++    |...++....   .+...+..+...+...     |.+.+++..   ..+...|..+.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a   83 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQ----AVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLG   83 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHH----HHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHH----HHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence            4567778888999999999    8888887765   2455666666666554     666666543   23677888888


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITE  284 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~  284 (311)
                      ..+...|++++|.+.+++..+.. +.+...+..+...+...|++++|...++..      .+.    ...+...+..+..
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~------~~~----~~~~~~~~~~la~  152 (186)
T 3as5_A           84 LTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIA------LGL----RPNEGKVHRAIAF  152 (186)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH----CTTCHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHH------Hhc----CccchHHHHHHHH
Confidence            89999999999999999987752 446778888888888888888776655332      111    1235678999999


Q ss_pred             HHHhcCChHHHHHHHHHHHH
Q 044412          285 ALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       285 ~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+...|++++|...+++..+
T Consensus       153 ~~~~~~~~~~A~~~~~~~~~  172 (186)
T 3as5_A          153 SYEQMGRHEEALPHFKKANE  172 (186)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999998865

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.64  E-value=5.1e-07  Score=74.46  Aligned_cols=189  Identities=10%  Similarity=-0.027  Sum_probs=123.0

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchh
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVF  137 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~  137 (311)
                      ...++..+-..+ ...|++++|...+                    ++++++.++.....              ......
T Consensus        42 ~~~~~~~l~~~~-~~~g~~~~A~~~~--------------------~~al~~~~~~~~~~--------------~~~~~~   86 (283)
T 3edt_B           42 VATMLNILALVY-RDQNKYKEAAHLL--------------------NDALAIREKTLGKD--------------HPAVAA   86 (283)
T ss_dssp             HHHHHHHHHHHH-HHTTCHHHHHHHH--------------------HHHHHHHHHHTCTT--------------CHHHHH
T ss_pred             HHHHHHHHHHHH-HHcccHHHHHHHH--------------------HHHHHHHHHHcCCc--------------chHHHH
Confidence            456677777777 7777777777766                    44455554431110              122356


Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCC---C-cHhHHHHHHHHHHhCCCh
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPA---W-DIRSWTTMITSYSQNKQF  213 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~---~-~~~~y~~li~~~~~~g~~  213 (311)
                      ++..+-..|...|++++    |...+.+                   +.+++++...   | ...+|..+-..|...|++
T Consensus        87 ~~~~l~~~~~~~g~~~~----A~~~~~~-------------------al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~  143 (283)
T 3edt_B           87 TLNNLAVLYGKRGKYKE----AEPLCKR-------------------ALEIREKVLGKFHPDVAKQLNNLALLCQNQGKA  143 (283)
T ss_dssp             HHHHHHHHHHTTTCHHH----HHHHHHH-------------------HHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHHHHHhccHHH----HHHHHHH-------------------HHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCH
Confidence            88889999999999999    5555554                   2222222211   2 355678888888888999


Q ss_pred             hHHHHHHHHHHhc------CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCCh-------------------------
Q 044412          214 REALDAFNKTKKS------GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSL-------------------------  261 (311)
Q Consensus       214 ~~a~~~~~~m~~~------g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~-------------------------  261 (311)
                      ++|+++|++..+.      +-.| ...++..+-..+...|++++|...++..-..                         
T Consensus       144 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (283)
T 3edt_B          144 EEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREE  223 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHh
Confidence            9999988887764      1133 2456778888888889998888887662221                         


Q ss_pred             -----------HHHHHHHhhcCC--C-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          262 -----------GRSLLVFFKLRE--K-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       262 -----------~~a~~~~~~~~~--p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                                 ..+...++....  | ...++..+...|...|++++|..++++..+
T Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          224 SKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             TTCCCCC------------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             cCCchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                       111122222221  1 235788899999999999999999998765

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.63  E-value=3.1e-07  Score=73.77  Aligned_cols=182  Identities=12%  Similarity=0.005  Sum_probs=131.8

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC--CCCe-eeeec----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ--EPNV-FVYHA----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~--~~~~-~~~~~----~~~~  100 (311)
                      ..+...+...|+.+++...++..++.. +.++..+..+-..+ .+.|++++|...|++..  .|+. ..+..    +...
T Consensus         9 ~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~-~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~   86 (217)
T 2pl2_A            9 LRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQ-LKLGLVNPALENGKTLVARTPRYLGGYMVLSEAYVAL   86 (217)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHh
Confidence            456677788899999999999888764 23567788888888 99999999999998875  3442 23322    6667


Q ss_pred             -----------CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCCCccchHHHHHHhccCCC
Q 044412          101 -----------RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE  168 (311)
Q Consensus       101 -----------~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~  168 (311)
                                 |++++|+..|++..+.                .| +...+..+-..|...|++++    |...+++.. 
T Consensus        87 ~~~~~~~~~~~g~~~~A~~~~~~al~~----------------~P~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al-  145 (217)
T 2pl2_A           87 YRQAEDRERGKGYLEQALSVLKDAERV----------------NPRYAPLHLQRGLVYALLGERDK----AEASLKQAL-  145 (217)
T ss_dssp             HHTCSSHHHHHHHHHHHHHHHHHHHHH----------------CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHH-
T ss_pred             hhhhhhhcccccCHHHHHHHHHHHHHh----------------CcccHHHHHHHHHHHHHcCChHH----HHHHHHHHH-
Confidence                       9999999999988663                44 47788888899999999999    655555411 


Q ss_pred             CCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCCh
Q 044412          169 RKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGAL  248 (311)
Q Consensus       169 ~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~  248 (311)
                                        ++    . .+...|..+-..|...|++++|+..|++..+.. +-+...+..+-..+...|+.
T Consensus       146 ------------------~~----~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~  201 (217)
T 2pl2_A          146 ------------------AL----E-DTPEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKA  201 (217)
T ss_dssp             ------------------HH----C-CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC----
T ss_pred             ------------------hc----c-cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCH
Confidence                              11    1 467788889999999999999999999998752 33567888899999999999


Q ss_pred             hhHHHHHH
Q 044412          249 DLGRGIQI  256 (311)
Q Consensus       249 ~~a~~~~~  256 (311)
                      ++|...++
T Consensus       202 ~~A~~~~~  209 (217)
T 2pl2_A          202 EEAARAAA  209 (217)
T ss_dssp             --------
T ss_pred             HHHHHHHH
Confidence            97776654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.63  E-value=9.3e-07  Score=77.09  Aligned_cols=260  Identities=10%  Similarity=0.030  Sum_probs=172.0

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcc---hhHHHHHHHHHhhccCChhHHHHhcccCCC-----CC----eeeee
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLD---CFLAKQFISFCTSRFHFIDYTILVFPQMQE-----PN----VFVYH   95 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~---~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----~~----~~~~~   95 (311)
                      ......+...|+...+...++...+.+....   ..++..+-..+ ...|+++.|...+++..+     .+    ...+.
T Consensus        13 ~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~   91 (406)
T 3sf4_A           13 ALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAY-FYLHDYAKALEYHHHDLTLARTIGDQLGEAKASG   91 (406)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHH-HHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHH
Confidence            3456667788999999999999888742211   35777888888 999999999999877531     11    11121


Q ss_pred             c----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCC-------------------
Q 044412           96 A----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNK-------------------  151 (311)
Q Consensus        96 ~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~-------------------  151 (311)
                      .    +...|++++|+..+++..+..          .+.+-.+ ...++..+-..|...|+                   
T Consensus        92 ~la~~~~~~g~~~~A~~~~~~al~~~----------~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~  161 (406)
T 3sf4_A           92 NLGNTLKVLGNFDEAIVCCQRHLDIS----------RELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRD  161 (406)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHH----------HHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHH----------HhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHH
Confidence            1    788899999999998875421          1111111 14578888889999999                   


Q ss_pred             -CccchHHHHHHhc---cCCCC--CHhHHHHHHHHHHHH-----HHHHHhhC-------CCC--cHhHHHHHHHHHHhCC
Q 044412          152 -FFESRRVSRRLFD---EMPER--KFATWNTMIDAYARL-----AELLFNKM-------PAW--DIRSWTTMITSYSQNK  211 (311)
Q Consensus       152 -~~~a~~~a~~~~~---~~~~~--~~~~~~~li~~~~~~-----a~~~~~~m-------~~~--~~~~y~~li~~~~~~g  211 (311)
                       +++|.....+...   ....+  ...++..+-..|...     |...+++.       ..+  ...+|..+-..|...|
T Consensus       162 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  241 (406)
T 3sf4_A          162 ALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLG  241 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcC
Confidence             8884444333222   22111  112455555555543     44444433       222  1347888889999999


Q ss_pred             ChhHHHHHHHHHHhc----CCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHH
Q 044412          212 QFREALDAFNKTKKS----GTGSD-QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITE  284 (311)
Q Consensus       212 ~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~  284 (311)
                      ++++|...+++..+.    +-.+. ..++..+-..+...|++++|...++.      +..+......+  ...++..+-.
T Consensus       242 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~------a~~~~~~~~~~~~~~~~~~~la~  315 (406)
T 3sf4_A          242 EFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLK------HLAIAQELNDRIGEGRACWSLGN  315 (406)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHH------HHHHHHhcCCcHHHHHHHHHHHH
Confidence            999999999987642    21111 55778888889999999988877643      33333333211  1457888899


Q ss_pred             HHHhcCChHHHHHHHHHHHH
Q 044412          285 ALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       285 ~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .|...|++++|...+++..+
T Consensus       316 ~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          316 AYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999988653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.63  E-value=2.9e-07  Score=77.85  Aligned_cols=260  Identities=10%  Similarity=0.028  Sum_probs=170.4

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcc---hhHHHHHHHHHhhccCChhHHHHhcccCCC-----CC----eeeeec
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLD---CFLAKQFISFCTSRFHFIDYTILVFPQMQE-----PN----VFVYHA   96 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~---~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----~~----~~~~~~   96 (311)
                      .....+...|+.+++...++...+......   ...+..+...+ ...|+++.|.+.+++..+     ++    ...+..
T Consensus        10 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~   88 (338)
T 3ro2_A           10 LEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAY-FYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGN   88 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHH
Confidence            345566677899999999999888742211   36777888888 999999999999877542     11    111211


Q ss_pred             ----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCC--------------------
Q 044412           97 ----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNK--------------------  151 (311)
Q Consensus        97 ----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~--------------------  151 (311)
                          +...|++++|++.+++..+..          .+.+-.+ ...++..+-..|...|+                    
T Consensus        89 l~~~~~~~g~~~~A~~~~~~al~~~----------~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  158 (338)
T 3ro2_A           89 LGNTLKVLGNFDEAIVCCQRHLDIS----------RELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNA  158 (338)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHH----------HHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHH----------HHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHH
Confidence                788899999999998875421          1111111 14478888889999999                    


Q ss_pred             CccchHHHHHHhcc---CCCC--CHhHHHHHHHHHHHH-----HHHHHhhCC-------CC--cHhHHHHHHHHHHhCCC
Q 044412          152 FFESRRVSRRLFDE---MPER--KFATWNTMIDAYARL-----AELLFNKMP-------AW--DIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       152 ~~~a~~~a~~~~~~---~~~~--~~~~~~~li~~~~~~-----a~~~~~~m~-------~~--~~~~y~~li~~~~~~g~  212 (311)
                      +++|.....+....   ...+  ....+..+-..+...     |...+++..       .+  ...++..+...+...|+
T Consensus       159 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  238 (338)
T 3ro2_A          159 LQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGE  238 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCC
Confidence            88844333322221   1111  112445555555443     555554432       22  23378888888999999


Q ss_pred             hhHHHHHHHHHHhc----CCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHH
Q 044412          213 FREALDAFNKTKKS----GTGSD-QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEA  285 (311)
Q Consensus       213 ~~~a~~~~~~m~~~----g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~  285 (311)
                      +++|...+++..+.    +-.+. ..++..+-..+...|++++|...++.      +..++.....+  ...++..+...
T Consensus       239 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~------a~~~~~~~~~~~~~~~~~~~la~~  312 (338)
T 3ro2_A          239 FETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLK------HLAIAQELKDRIGEGRACWSLGNA  312 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHH------HHHHHHhcCCcHHHHHHHHHHHHH
Confidence            99999999887642    11111 45777888888899999988877643      33333332211  24578889999


Q ss_pred             HHhcCChHHHHHHHHHHHHc
Q 044412          286 LAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       286 ~~~~g~~~~a~~~~~~M~~~  305 (311)
                      |...|++++|..++++..+.
T Consensus       313 ~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          313 YTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             HHHHTCHHHHHHHHHHHHHC
T ss_pred             HHHcCChHHHHHHHHHHHHH
Confidence            99999999999999998753

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.63  E-value=2e-06  Score=71.18  Aligned_cols=213  Identities=10%  Similarity=-0.007  Sum_probs=152.9

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhc----cCChhHHHHhcccCCCCC-eeeeec----cc
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSR----FHFIDYTILVFPQMQEPN-VFVYHA----FS   98 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~----~g~~~~a~~~~~~m~~~~-~~~~~~----~~   98 (311)
                      ..+...+...++.+.+...+....+.   -+...+..+-..+ .+    .+++++|...|++..+.+ ...+..    +.
T Consensus        10 ~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~-~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~   85 (273)
T 1ouv_A           10 VGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLY-YQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYY   85 (273)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHH-HHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHH-HcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            34556666778888888888888873   3556777777888 88    899999999998765433 222221    55


Q ss_pred             c----CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHh----CCCCccchHHHHHHhccCCCCC
Q 044412           99 S----LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSY----SNKFFESRRVSRRLFDEMPERK  170 (311)
Q Consensus        99 ~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~a~~~~~~~~~~~  170 (311)
                      .    .+++++|++.|++..+.+                 +...+..+-..|..    .|++++    |...++...+. 
T Consensus        86 ~g~~~~~~~~~A~~~~~~a~~~~-----------------~~~a~~~lg~~~~~~~~~~~~~~~----A~~~~~~a~~~-  143 (273)
T 1ouv_A           86 SGQGVSQNTNKALQYYSKACDLK-----------------YAEGCASLGGIYHDGKVVTRDFKK----AVEYFTKACDL-  143 (273)
T ss_dssp             HTSSSCCCHHHHHHHHHHHHHTT-----------------CHHHHHHHHHHHHHCSSSCCCHHH----HHHHHHHHHHT-
T ss_pred             CCCCcccCHHHHHHHHHHHHHcC-----------------CccHHHHHHHHHHcCCCcccCHHH----HHHHHHHHHhc-
Confidence            5    889999999998875532                 56677778888888    888888    55555542211 


Q ss_pred             HhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHh----CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc--
Q 044412          171 FATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQ----NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH--  244 (311)
Q Consensus       171 ~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~--  244 (311)
                                              .+...+..+-..|..    .+++++|+..|++..+.+   +...+..+-..|..  
T Consensus       144 ------------------------~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~  196 (273)
T 1ouv_A          144 ------------------------NDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGE  196 (273)
T ss_dssp             ------------------------TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTC
T ss_pred             ------------------------CcHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCC
Confidence                                    145566667777777    899999999999988764   45677777777877  


Q ss_pred             --cCChhhHHHHHHhhCChHHHHHHHhhcC-CCCchhHHHHHHHHHh----cCChHHHHHHHHHHHHcC
Q 044412          245 --LGALDLGRGIQIYCRSLGRSLLVFFKLR-EKNLLCWNSITEALAI----HGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       245 --~~~~~~a~~~~~~~~~~~~a~~~~~~~~-~p~~~~~~~li~~~~~----~g~~~~a~~~~~~M~~~g  306 (311)
                        .++.++|...++.             .. ..+...+..+-..|..    .+++++|..+|++..+.|
T Consensus       197 ~~~~~~~~A~~~~~~-------------a~~~~~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          197 GATKNFKEALARYSK-------------ACELENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             SSCCCHHHHHHHHHH-------------HHHTTCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             CCCccHHHHHHHHHH-------------HHhCCCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence              7888866665533             22 1235667788888888    899999999999887654

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.62  E-value=4.9e-07  Score=69.56  Aligned_cols=154  Identities=11%  Similarity=0.033  Sum_probs=116.8

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCCCC---eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcC
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQEPN---VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGF  132 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~  132 (311)
                      ..+..+...+ ...|++++|...|+++.+.+   ...+..    +...|++++|.+.+++..+.               .
T Consensus         9 ~~~~~~~~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---------------~   72 (186)
T 3as5_A            9 VYYRDKGISH-AKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLAD---------------A   72 (186)
T ss_dssp             HHHHHHHHHH-HHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------C
T ss_pred             HHHHHHHHHH-HHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---------------C
Confidence            4556667777 88999999999999886532   222222    77889999999999988654               2


Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~  212 (311)
                      +.+...+..+...|...|++++    |...++.....                       ...+...+..+...+...|+
T Consensus        73 ~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~-----------------------~~~~~~~~~~~a~~~~~~~~  125 (186)
T 3as5_A           73 PDNVKVATVLGLTYVQVQKYDL----AVPLLIKVAEA-----------------------NPINFNVRFRLGVALDNLGR  125 (186)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHHHHhcCHHH----HHHHHHHHHhc-----------------------CcHhHHHHHHHHHHHHHcCc
Confidence            4467788888999999999999    55555442210                       12356778888899999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +++|.+.+++..+.. +.+...+..+...+...|++++|...++.
T Consensus       126 ~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~  169 (186)
T 3as5_A          126 FDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALPHFKK  169 (186)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999999988763 44678889999999999999988777644

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.61  E-value=1.6e-06  Score=85.54  Aligned_cols=98  Identities=11%  Similarity=0.049  Sum_probs=51.4

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChH------------
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLG------------  262 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~------------  262 (311)
                      ++...|..+-..|-..|++++|..+|...         ..|..+..++.+.|+++.|.+.++..++.+            
T Consensus      1193 ~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~ 1263 (1630)
T 1xi4_A         1193 PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDG 1263 (1630)
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhh
Confidence            34444444445555555555555555552         245555555555555555555554422221            


Q ss_pred             ----HHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          263 ----RSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       263 ----~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                          .|...... ...+...+..++.-|.+.|.+++|..+++.-
T Consensus      1264 ~Ef~LA~~cgl~-Iiv~~deLeeli~yYe~~G~feEAI~LlE~a 1306 (1630)
T 1xi4_A         1264 KEFRLAQMCGLH-IVVHADELEELINYYQDRGYFEELITMLEAA 1306 (1630)
T ss_pred             hHHHHHHHHHHh-hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                11111111 0234455667788888888888888888654

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.58  E-value=1.3e-06  Score=67.65  Aligned_cols=155  Identities=13%  Similarity=0.080  Sum_probs=107.0

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHH
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITS  206 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~  206 (311)
                      ++.+|..+-..|.+.|++++|.....+.++.- +.+..+|..+-..|.+.     |...+....   ..+...+..+-..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~   82 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSA   82 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHH
Confidence            56789999999999999999444444443321 23445666666666554     444444432   2345566667777


Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSIT  283 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li  283 (311)
                      +...++++.|...+.+..+.. +-+...+..+-..+.+.|++++|...+             ++..  .| +...|..+-
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~-------------~~~l~~~p~~~~~~~~lg  148 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAY-------------EKTISIKPGFIRAYQSIG  148 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH-------------HHHHHHCTTCHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHH-------------HHHHHhcchhhhHHHHHH
Confidence            777888888888888776642 334566777777777777777665554             3332  33 567899999


Q ss_pred             HHHHhcCChHHHHHHHHHHHH
Q 044412          284 EALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       284 ~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..|.+.|++++|...|++..+
T Consensus       149 ~~~~~~g~~~~A~~~~~~al~  169 (184)
T 3vtx_A          149 LAYEGKGLRDEAVKYFKKALE  169 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHh
Confidence            999999999999999999875

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.56  E-value=1.3e-06  Score=76.41  Aligned_cols=217  Identities=11%  Similarity=0.040  Sum_probs=151.9

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCC-hhHHHHhcccCCC--C-Ceeeeec----cc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHF-IDYTILVFPQMQE--P-NVFVYHA----FS   98 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~-~~~a~~~~~~m~~--~-~~~~~~~----~~   98 (311)
                      +..+..++...++..++...++..++..- -+...|+.+-.++ .+.|+ +++|...|++..+  | +...|+.    +.
T Consensus       100 ~~~lg~~~~~~g~~~~Al~~~~~al~l~P-~~~~a~~~~g~~l-~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~  177 (382)
T 2h6f_A          100 YDYFRAVLQRDERSERAFKLTRDAIELNA-ANYTVWHFRRVLL-KSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVE  177 (382)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHH-HHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHhCc-cCHHHHHHHHHHH-HHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            34556667777888888888888887642 2456777777788 88886 8888888888753  3 3333333    67


Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                      ..|++++|+..|+...+..               +-+...|..+-.++.+.|++++    |...+++..+.+        
T Consensus       178 ~~g~~~eAl~~~~kal~ld---------------P~~~~a~~~lg~~~~~~g~~~e----Al~~~~~al~l~--------  230 (382)
T 2h6f_A          178 WLRDPSQELEFIADILNQD---------------AKNYHAWQHRQWVIQEFKLWDN----ELQYVDQLLKED--------  230 (382)
T ss_dssp             HHTCCTTHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHTCCTT----HHHHHHHHHHHC--------
T ss_pred             HccCHHHHHHHHHHHHHhC---------------ccCHHHHHHHHHHHHHcCChHH----HHHHHHHHHHhC--------
Confidence            7788888888888876642               3457788888888888888888    555554432211        


Q ss_pred             HHHHHHHHHHHhhCCCCcHhHHHHHHHHHHh-CCChhHH-----HHHHHHHHhcCCCCC-HHHHHHHHHHHhccC--Chh
Q 044412          179 DAYARLAELLFNKMPAWDIRSWTTMITSYSQ-NKQFREA-----LDAFNKTKKSGTGSD-QVTMATVLSACAHLG--ALD  249 (311)
Q Consensus       179 ~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~-~g~~~~a-----~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~--~~~  249 (311)
                                     ..+...|+.+-..+.. .|..++|     ++.|++..+.  .|+ ...|..+-..+...|  +.+
T Consensus       231 ---------------P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~  293 (382)
T 2h6f_A          231 ---------------VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYP  293 (382)
T ss_dssp             ---------------TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCH
T ss_pred             ---------------CCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchH
Confidence                           1357788888888888 6666888     4788887763  454 567888888888877  466


Q ss_pred             hHHHHHHhhCChHHHHHHHhhc--CCCCchhHHHHHHHHHhcC---------ChHHHHHHHHHH
Q 044412          250 LGRGIQIYCRSLGRSLLVFFKL--REKNLLCWNSITEALAIHG---------FAHEALGMFDRM  302 (311)
Q Consensus       250 ~a~~~~~~~~~~~~a~~~~~~~--~~p~~~~~~~li~~~~~~g---------~~~~a~~~~~~M  302 (311)
                      +|...             +.++  ...+...+..+...|.+.|         ..++|..+|+++
T Consensus       294 ~a~~~-------------~~~~~~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l  344 (382)
T 2h6f_A          294 NLLNQ-------------LLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEIL  344 (382)
T ss_dssp             HHHHH-------------HHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHH-------------HHHhccCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHH
Confidence            55443             3332  2345677888999998874         258999999998

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.55  E-value=9.4e-07  Score=63.96  Aligned_cols=130  Identities=12%  Similarity=0.171  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHH
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREAL  217 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~  217 (311)
                      .|..+...|...|++++    |..+++.+...                       ...+...|..+...+...|++++|.
T Consensus         3 ~~~~l~~~~~~~~~~~~----A~~~~~~~~~~-----------------------~~~~~~~~~~~a~~~~~~~~~~~A~   55 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDE----AIEYYQKALEL-----------------------DPRSAEAWYNLGNAYYKQGDYDEAI   55 (136)
T ss_dssp             HHHHHHHHHHHHTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHcCcHHH----HHHHHHHHHHc-----------------------CCcchhHHHHHHHHHHHhcCHHHHH
Confidence            56778888999999999    55555542210                       1235667888889999999999999


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHH
Q 044412          218 DAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALG  297 (311)
Q Consensus       218 ~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  297 (311)
                      .+|+++.+.+ +.+...+..+...+...|++++|...++..-.      .    ...+...+..+...+...|++++|..
T Consensus        56 ~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------~----~~~~~~~~~~la~~~~~~~~~~~A~~  124 (136)
T 2fo7_A           56 EYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE------L----DPRSAEAWYNLGNAYYKQGDYDEAIE  124 (136)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH------H----CTTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHH------h----CCCChHHHHHHHHHHHHHccHHHHHH
Confidence            9999998754 44577888888999999999877666533211      1    12356788999999999999999999


Q ss_pred             HHHHHHHc
Q 044412          298 MFDRMTYE  305 (311)
Q Consensus       298 ~~~~M~~~  305 (311)
                      .++++...
T Consensus       125 ~~~~~~~~  132 (136)
T 2fo7_A          125 YYQKALEL  132 (136)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHcc
Confidence            99998864

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.55  E-value=1.9e-06  Score=70.15  Aligned_cols=157  Identities=10%  Similarity=0.033  Sum_probs=101.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|++.|++..+.               . .+...|..+..+|...|++++    |...++...+        
T Consensus        15 ~~~~~~~~~A~~~~~~a~~~---------------~-~~~~~~~~~~~~~~~~~~~~~----A~~~~~~a~~--------   66 (258)
T 3uq3_A           15 FYKARQFDEAIEHYNKAWEL---------------H-KDITYLNNRAAAEYEKGEYET----AISTLNDAVE--------   66 (258)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------S-CCTHHHHHHHHHHHHTTCHHH----HHHHHHHHHH--------
T ss_pred             HHHhccHHHHHHHHHHHHHh---------------h-ccHHHHHHHHHHHHHcccHHH----HHHHHHHHHH--------
Confidence            45678888888888887543               2 677889999999999999999    5555544221        


Q ss_pred             HHHHHHHHHHHHHhhCCCC---cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC------------------------CC
Q 044412          177 MIDAYARLAELLFNKMPAW---DIRSWTTMITSYSQNKQFREALDAFNKTKKSG------------------------TG  229 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~---~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g------------------------~~  229 (311)
                                 +.......   ...+|..+...+...|++++|++.|++..+..                        ..
T Consensus        67 -----------~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  135 (258)
T 3uq3_A           67 -----------QGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVN  135 (258)
T ss_dssp             -----------HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             -----------hCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcC
Confidence                       11000000   03445555555555566666666555555421                        12


Q ss_pred             C-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          230 S-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       230 p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      | +...+..+...+...|++++|...             |++..   ..+...|..+...|...|++++|...+++..+.
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~A~~~-------------~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  202 (258)
T 3uq3_A          136 PEKAEEARLEGKEYFTKSDWPNAVKA-------------YTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEK  202 (258)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHH-------------HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhcCHHHHHHH-------------HHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            2 234556666666666666655544             44333   345778999999999999999999999998764

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.53  E-value=1.8e-06  Score=72.34  Aligned_cols=141  Identities=11%  Similarity=0.118  Sum_probs=105.3

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhC--C--CCcHhHHHHHHHHHHhC
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKM--P--AWDIRSWTTMITSYSQN  210 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m--~--~~~~~~y~~li~~~~~~  210 (311)
                      ...++..+-..|...|++++    |...++.                   +.+++...  .  .....+|..+...|...
T Consensus        68 ~~~~~~~la~~~~~~g~~~~----A~~~~~~-------------------al~~~~~~~~~~~~~~~~~~~~l~~~~~~~  124 (311)
T 3nf1_A           68 VATMLNILALVYRDQNKYKD----AANLLND-------------------ALAIREKTLGKDHPAVAATLNNLAVLYGKR  124 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHHHCTTCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHCCCHHH----HHHHHHH-------------------HHHHHHHHhCCCChHHHHHHHHHHHHHHHc
Confidence            45678888999999999999    6555554                   22223222  1  12456788899999999


Q ss_pred             CChhHHHHHHHHHHhc------CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC----CchhH
Q 044412          211 KQFREALDAFNKTKKS------GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK----NLLCW  279 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~------g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p----~~~~~  279 (311)
                      |++++|.+.|++..+.      +-.| ....+..+-..+...|++++|..+++      .+.+++++...+    ...++
T Consensus       125 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~------~a~~~~~~~~~~~~~~~~~~~  198 (311)
T 3nf1_A          125 GKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQ------RALEIYQTKLGPDDPNVAKTK  198 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHH------HHHHHHHHTSCTTCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHH------HHHHHHHHHhCCCCHHHHHHH
Confidence            9999999999998764      3333 34568888899999999999988764      445555554322    24578


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          280 NSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       280 ~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..+...|...|++++|..++++..+
T Consensus       199 ~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          199 NNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            8999999999999999999999875

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.53  E-value=5.2e-06  Score=72.36  Aligned_cols=228  Identities=7%  Similarity=-0.101  Sum_probs=140.3

Q ss_pred             HHhhccChhhHHHHHHHHHHh----ccCc-chhHHHHHHHHHhhccCChhHHHHhcccCCC-----CC-----eeeeec-
Q 044412           33 QLKKCSSIKELECVYATIVKT----NANL-DCFLAKQFISFCTSRFHFIDYTILVFPQMQE-----PN-----VFVYHA-   96 (311)
Q Consensus        33 ~l~~~~~~~~~~~l~~~m~~~----g~~p-~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----~~-----~~~~~~-   96 (311)
                      .+...|+...+...+....+.    +-.+ ...++..+-..+ ...|+++.|...+++..+     ++     ..+++. 
T Consensus       112 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~-~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  190 (383)
T 3ulq_A          112 YELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESY-YYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLF  190 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHH
Confidence            344557777777777776654    1111 234666677777 778888877777655431     11     011111 


Q ss_pred             ---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh
Q 044412           97 ---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA  172 (311)
Q Consensus        97 ---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~  172 (311)
                         +...|++++|++.|++..+..          .+.+-.+. ..++..+-.+|...|++++    |...+++       
T Consensus       191 g~~~~~~g~~~~A~~~~~~al~~~----------~~~~~~~~~~~~~~~lg~~y~~~g~~~~----A~~~~~~-------  249 (383)
T 3ulq_A          191 ATNFLDLKQYEDAISHFQKAYSMA----------EAEKQPQLMGRTLYNIGLCKNSQSQYED----AIPYFKR-------  249 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH----------HHTTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHH-------
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHH----------HHcCChHHHHHHHHHHHHHHHHCCCHHH----HHHHHHH-------
Confidence               666677777777776654310          11111111 2366666666777777777    7776666       


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCC-Cc-HhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCCCHHHHHHHHHHHhccC
Q 044412          173 TWNTMIDAYARLAELLFNKMPA-WD-IRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGSDQVTMATVLSACAHLG  246 (311)
Q Consensus       173 ~~~~li~~~~~~a~~~~~~m~~-~~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~t~~~li~a~~~~~  246 (311)
                                  |.+++..... |+ ..++..+-..|...|++++|...+++..+.    +-+.....+..+-..+...|
T Consensus       250 ------------al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~  317 (383)
T 3ulq_A          250 ------------AIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGP  317 (383)
T ss_dssp             ------------HHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSC
T ss_pred             ------------HHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCC
Confidence                        7777777665 53 456888888888899999999988886542    11222233566667777777


Q ss_pred             ChhhHHHHHHhhCChHHHHHHHhhcCC-C-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          247 ALDLGRGIQIYCRSLGRSLLVFFKLRE-K-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       247 ~~~~a~~~~~~~~~~~~a~~~~~~~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +.+.          ...|..++++... | ....+..+-..|...|++++|...+++..+
T Consensus       318 ~~~~----------~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          318 DEEA----------IQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             CHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHH----------HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7211          2244445544431 1 234678889999999999999999998764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.50  E-value=1e-05  Score=68.44  Aligned_cols=186  Identities=9%  Similarity=0.012  Sum_probs=101.6

Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHH-------hCCCC-------ccchHHHHHHhccCCCC
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYS-------YSNKF-------FESRRVSRRLFDEMPER  169 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~-------~~g~~-------~~a~~~a~~~~~~~~~~  169 (311)
                      ++|..+|++....               .+-+...|..+...+.       +.|++       ++|..+..+........
T Consensus        33 ~~a~~~~~~al~~---------------~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~   97 (308)
T 2ond_A           33 KRVMFAYEQCLLV---------------LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKK   97 (308)
T ss_dssp             HHHHHHHHHHHHH---------------HTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTT
T ss_pred             HHHHHHHHHHHHH---------------cCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcc
Confidence            5666677666542               1334445555555543       24555       55333333333322222


Q ss_pred             CHhHHHHHHHHHHHH-----HHHHHhhCCC--Cc-Hh-HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 044412          170 KFATWNTMIDAYARL-----AELLFNKMPA--WD-IR-SWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLS  240 (311)
Q Consensus       170 ~~~~~~~li~~~~~~-----a~~~~~~m~~--~~-~~-~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  240 (311)
                      +...|..+...+.+.     |..+|++..+  |+ .. .|..+...+.+.|++++|..+|++..+.. +++...|.....
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~  176 (308)
T 2ond_A           98 NMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAAL  176 (308)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            334555555554433     5555554432  32 22 56666666666666666666666665532 122333332222


Q ss_pred             HH-hccCChhhHHHHHHh---------------------hCChHHHHHHHhhcCC-----C--CchhHHHHHHHHHhcCC
Q 044412          241 AC-AHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLRE-----K--NLLCWNSITEALAIHGF  291 (311)
Q Consensus       241 a~-~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~~-----p--~~~~~~~li~~~~~~g~  291 (311)
                      .. ...|+.+.|..+|+.                     .|+.++|..+|++..+     |  ....|..++..+.+.|+
T Consensus       177 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~  256 (308)
T 2ond_A          177 MEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGD  256 (308)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCC
Confidence            21 124666666666655                     4566666666665542     2  34578888888889999


Q ss_pred             hHHHHHHHHHHHHc
Q 044412          292 AHEALGMFDRMTYE  305 (311)
Q Consensus       292 ~~~a~~~~~~M~~~  305 (311)
                      .++|..+++++.+.
T Consensus       257 ~~~a~~~~~~a~~~  270 (308)
T 2ond_A          257 LASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999888753

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.47  E-value=8e-06  Score=80.73  Aligned_cols=226  Identities=9%  Similarity=0.000  Sum_probs=129.7

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC----CCeeeeec--cccCC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE----PNVFVYHA--FSSLR  101 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~--~~~~~  101 (311)
                      ..+...+...|+++++...|...      -|...|..++.+| .+.|++++|.+.+....+    +.+.++-.  |++.+
T Consensus      1109 sqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~-~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~ 1181 (1630)
T 1xi4_A         1109 SQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAA-NTSGNWEELVKYLQMARKKARESYVETELIFALAKTN 1181 (1630)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHH-HHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhc
Confidence            45566666666666665555331      4566666677777 777777777777644221    11222211  44444


Q ss_pred             Chh----------------------------HHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCc
Q 044412          102 HPL----------------------------QAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFF  153 (311)
Q Consensus       102 ~~~----------------------------~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~  153 (311)
                      +++                            +|..+|..                       ...|..+..+|++.|+++
T Consensus      1182 rleele~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y~k-----------------------A~ny~rLA~tLvkLge~q 1238 (1630)
T 1xi4_A         1182 RLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNN-----------------------VSNFGRLASTLVHLGEYQ 1238 (1630)
T ss_pred             CHHHHHHHHhCCCHHHHHHHHHHHHhcCCHHHHHHHHHh-----------------------hhHHHHHHHHHHHhCCHH
Confidence            444                            33333332                       237888888888888888


Q ss_pred             cchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCC
Q 044412          154 ESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGT  228 (311)
Q Consensus       154 ~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~  228 (311)
                      +|.+.+++.      .+..+|..+-.+|...     |......+ .-+...+..++.-|-+.|.+++|+++++.-..  +
T Consensus      1239 ~AIEaarKA------~n~~aWkev~~acve~~Ef~LA~~cgl~I-iv~~deLeeli~yYe~~G~feEAI~LlE~aL~--L 1309 (1630)
T 1xi4_A         1239 AAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI-VVHADELEELINYYQDRGYFEELITMLEAALG--L 1309 (1630)
T ss_pred             HHHHHHHHh------CCHHHHHHHHHHHhhhhHHHHHHHHHHhh-hcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhc--c
Confidence            844444333      3445666655555432     43333322 22445566888889999999999999966553  3


Q ss_pred             CCC-HHHHHHHHHHHh--ccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHH
Q 044412          229 GSD-QVTMATVLSACA--HLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALG  297 (311)
Q Consensus       229 ~p~-~~t~~~li~a~~--~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  297 (311)
                      .|. ...|+-|-.+++  +-+++.++.++|...++.....+.     .-+...|.-++--|.+.|+++.|..
T Consensus      1310 eraH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~-----~e~~~lW~elv~LY~~~~e~dnA~~ 1376 (1630)
T 1xi4_A         1310 ERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRA-----AEQAHLWAELVFLYDKYEEYDNAII 1376 (1630)
T ss_pred             ChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHH-----HHHHHHHHHHHHHHHhcccHHHHHH
Confidence            332 234443444444  444555444444332222211100     1356789999999999999999874

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.47  E-value=7e-06  Score=67.48  Aligned_cols=179  Identities=10%  Similarity=0.032  Sum_probs=111.7

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCH--hHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKF--ATW  174 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~--~~~  174 (311)
                      +...|++++|++.|++..+..               +.+...+..+..+|...|++++|.....+.++....++.  ..|
T Consensus        13 ~~~~~~~~~A~~~~~~~l~~~---------------p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~   77 (272)
T 3u4t_A           13 LFKNNNYAEAIEVFNKLEAKK---------------YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADF   77 (272)
T ss_dssp             HHTTTCHHHHHHHHHHHHHTT---------------CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhC---------------CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHH
Confidence            567889999999999987642               334558888889999999999966666666652222222  234


Q ss_pred             HHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccC
Q 044412          175 NTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLG  246 (311)
Q Consensus       175 ~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~  246 (311)
                      ..+-..+...     |.+.|++..   ..+..+|..+-..|...|++++|+..|++..+. -+-+...|..+-..+...+
T Consensus        78 ~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~l~~~~~~~~  156 (272)
T 3u4t_A           78 EYYGKILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP-TTTDPKVFYELGQAYYYNK  156 (272)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS-SCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc-CCCcHHHHHHHHHHHHHHH
Confidence            5555555443     555555443   224567777777777788888888877777654 1223444544441333334


Q ss_pred             ChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhcCC---hHHHHHHHHHHHH
Q 044412          247 ALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIHGF---AHEALGMFDRMTY  304 (311)
Q Consensus       247 ~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~---~~~a~~~~~~M~~  304 (311)
                      ++++|...+             ++..  .| +...+..+...+...|+   +++|...+++..+
T Consensus       157 ~~~~A~~~~-------------~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~  207 (272)
T 3u4t_A          157 EYVKADSSF-------------VKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIE  207 (272)
T ss_dssp             CHHHHHHHH-------------HHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHH
T ss_pred             HHHHHHHHH-------------HHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHH
Confidence            666554443             3322  23 35666777777777777   6667777776553

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.45  E-value=2.7e-07  Score=83.35  Aligned_cols=189  Identities=10%  Similarity=-0.031  Sum_probs=140.4

Q ss_pred             cchhHHHHHHHHHhhccCCh-hHHHHhcccCC--CCC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHH
Q 044412           57 LDCFLAKQFISFCTSRFHFI-DYTILVFPQMQ--EPN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVW  128 (311)
Q Consensus        57 p~~~~~~~ll~~~~~~~g~~-~~a~~~~~~m~--~~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~  128 (311)
                      .+...+..+-..+ ...|++ ++|.+.|++..  .|+ ...|..    +...|++++|++.|++..+             
T Consensus       100 ~~a~~~~~lg~~~-~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-------------  165 (474)
T 4abn_A          100 VEAQALMLKGKAL-NVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALT-------------  165 (474)
T ss_dssp             CCHHHHHHHHHHH-TSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT-------------
T ss_pred             hhHHHHHHHHHHH-HhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-------------
Confidence            3667788888888 999999 99999998875  233 333433    8889999999999999876             


Q ss_pred             HhcCCCchhHHHHHHHHHHhC---------CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhH
Q 044412          129 KNGFSSPVFVQTAMVDNYSYS---------NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRS  199 (311)
Q Consensus       129 ~~g~~~~~~~~~~ll~~~~~~---------g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~  199 (311)
                         ..|+...+..+-..|...         |++++|.....+.++.-                           ..+...
T Consensus       166 ---~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~---------------------------p~~~~~  215 (474)
T 4abn_A          166 ---HCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD---------------------------VLDGRS  215 (474)
T ss_dssp             ---TCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC---------------------------TTCHHH
T ss_pred             ---hCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC---------------------------CCCHHH
Confidence               467788899999999999         99999444333333321                           124667


Q ss_pred             HHHHHHHHHhC--------CChhHHHHHHHHHHhcCCCC----CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHH
Q 044412          200 WTTMITSYSQN--------KQFREALDAFNKTKKSGTGS----DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLV  267 (311)
Q Consensus       200 y~~li~~~~~~--------g~~~~a~~~~~~m~~~g~~p----~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~  267 (311)
                      |..+-..|...        |++++|++.|++..+.  .|    +...|..+-.+|...|++++|...++.      |.++
T Consensus       216 ~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~------al~l  287 (474)
T 4abn_A          216 WYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKV--DRKASSNPDLHLNRATLHKYEESYGEALEGFSQ------AAAL  287 (474)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH--CGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH
T ss_pred             HHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHh
Confidence            77788888877        8899999999998874  35    778888888999998988877665533      2221


Q ss_pred             HhhcCCC-CchhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          268 FFKLREK-NLLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       268 ~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                           .| +...+..+-..+...|++++|...+.++
T Consensus       288 -----~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          288 -----DPAWPEPQQREQQLLEFLSRLTSLLESKGKT  318 (474)
T ss_dssp             -----CTTCHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             -----CCCCHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence                 23 4557888888888888888888765443

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.44  E-value=4.9e-06  Score=68.82  Aligned_cols=187  Identities=10%  Similarity=-0.044  Sum_probs=136.7

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCCCCee-eeec----ccc----CCChhHHHHHHHHHHHCCCCchHHHHHHH
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVF-VYHA----FSS----LRHPLQAIAFYLYMLRAEVLLTTVHGQVW  128 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~-~~~~----~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~~  128 (311)
                      ++.++..+-..+ .+.|++++|...|++..+++.. .+..    +..    .+++++|++.|++..+.+           
T Consensus         5 ~~~a~~~lg~~~-~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~-----------   72 (273)
T 1ouv_A            5 DPKELVGLGAKS-YKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN-----------   72 (273)
T ss_dssp             CHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT-----------
T ss_pred             ChHHHHHHHHHH-HhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC-----------
Confidence            455666777778 8889999999999876654422 2211    556    889999999998876532           


Q ss_pred             HhcCCCchhHHHHHHHHHHh----CCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHH
Q 044412          129 KNGFSSPVFVQTAMVDNYSY----SNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMI  204 (311)
Q Consensus       129 ~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li  204 (311)
                            +...+..+-..|..    .|++++    |...++...+.                         .+...+..+-
T Consensus        73 ------~~~a~~~lg~~~~~g~~~~~~~~~----A~~~~~~a~~~-------------------------~~~~a~~~lg  117 (273)
T 1ouv_A           73 ------YSNGCHLLGNLYYSGQGVSQNTNK----ALQYYSKACDL-------------------------KYAEGCASLG  117 (273)
T ss_dssp             ------CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHHHT-------------------------TCHHHHHHHH
T ss_pred             ------CHHHHHHHHHHHhCCCCcccCHHH----HHHHHHHHHHc-------------------------CCccHHHHHH
Confidence                  56677778888888    899999    66555542211                         2566777888


Q ss_pred             HHHHh----CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc----cCChhhHHHHHHhhCChHHHHHHHhhcCCCCc
Q 044412          205 TSYSQ----NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH----LGALDLGRGIQIYCRSLGRSLLVFFKLREKNL  276 (311)
Q Consensus       205 ~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~----~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~  276 (311)
                      ..|..    .+++++|+..|++..+.+   +...+..+-..|..    .++.++|...++..      .+      ..+.
T Consensus       118 ~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a------~~------~~~~  182 (273)
T 1ouv_A          118 GIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKA------CD------LKDS  182 (273)
T ss_dssp             HHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHH------HH------TTCH
T ss_pred             HHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH------HH------CCCH
Confidence            88888    999999999999998876   56667777777776    77888666655331      11      2355


Q ss_pred             hhHHHHHHHHHh----cCChHHHHHHHHHHHHcC
Q 044412          277 LCWNSITEALAI----HGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       277 ~~~~~li~~~~~----~g~~~~a~~~~~~M~~~g  306 (311)
                      ..+..+-..|..    .+++++|..+|++..+.+
T Consensus       183 ~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~  216 (273)
T 1ouv_A          183 PGCFNAGNMYHHGEGATKNFKEALARYSKACELE  216 (273)
T ss_dssp             HHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC
Confidence            678888888989    999999999999887654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.44  E-value=3.1e-06  Score=71.65  Aligned_cols=173  Identities=10%  Similarity=0.001  Sum_probs=109.6

Q ss_pred             hhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCee--eeec----cccCCChhHHHHHHHH
Q 044412           41 KELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVF--VYHA----FSSLRHPLQAIAFYLY  112 (311)
Q Consensus        41 ~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~--~~~~----~~~~~~~~~a~~~~~~  112 (311)
                      +++..+++..++.--+-+...|..+...+ .+.|++++|.++|++..+  |+..  .|..    +.+.|+.++|.++|++
T Consensus        81 ~~A~~~~~rAl~~~~p~~~~~~~~~~~~~-~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  159 (308)
T 2ond_A           81 DEAANIYERAISTLLKKNMLLYFAYADYE-ESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  159 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHHHHHHH-HhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            56666666666532222445777777777 777777777777766543  2211  2333    4556677777777776


Q ss_pred             HHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHH-HhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhh
Q 044412          113 MLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNY-SYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNK  191 (311)
Q Consensus       113 m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~-~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~  191 (311)
                      ..+..               +.+...|....... ...|+.++    |..+|+...+                   .+  
T Consensus       160 a~~~~---------------p~~~~~~~~~a~~~~~~~~~~~~----A~~~~~~al~-------------------~~--  199 (308)
T 2ond_A          160 AREDA---------------RTRHHVYVTAALMEYYCSKDKSV----AFKIFELGLK-------------------KY--  199 (308)
T ss_dssp             HHTST---------------TCCTHHHHHHHHHHHHTSCCHHH----HHHHHHHHHH-------------------HH--
T ss_pred             HHhcC---------------CCCHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHH-------------------hC--
Confidence            65431               22333443332221 12567777    5555544221                   10  


Q ss_pred             CCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC-CCCC--HHHHHHHHHHHhccCChhhHHHHHH
Q 044412          192 MPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSG-TGSD--QVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       192 m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                        ..+...|..++..+.+.|++++|..+|++..+.. +.|+  ...|..++....+.|+.+.|..+++
T Consensus       200 --p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~  265 (308)
T 2ond_A          200 --GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEK  265 (308)
T ss_dssp             --TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             --CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence              1257788999999999999999999999999863 5663  5678888888888899987776653

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.41  E-value=6.5e-05  Score=67.00  Aligned_cols=196  Identities=5%  Similarity=-0.069  Sum_probs=125.1

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHh-----cc--Cc-chhHHHHHHHHHhhccCChhHHHHhcccCCC-------C--
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKT-----NA--NL-DCFLAKQFISFCTSRFHFIDYTILVFPQMQE-------P--   89 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~-----g~--~p-~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-------~--   89 (311)
                      ++.+..+....|+.+++.+.+....+.     +.  .| ...+|+.+-..| ...|++++|...+++..+       +  
T Consensus        54 yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y-~~~g~~~~A~~~~~ka~~i~~~~~~~~~  132 (472)
T 4g1t_A           54 CNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVY-YHMGRLSDVQIYVDKVKHVCEKFSSPYR  132 (472)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHSCCSSC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHH-HHcCChHHHHHHHHHHHHHhHhcccccc
Confidence            456777888889999997777665432     11  22 346788999999 999999999988876531       1  


Q ss_pred             -C-eeeeec------cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHH---HHhCCCCccchH
Q 044412           90 -N-VFVYHA------FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDN---YSYSNKFFESRR  157 (311)
Q Consensus        90 -~-~~~~~~------~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~---~~~~g~~~~a~~  157 (311)
                       + ..++..      ....+++++|++.|++..+.                .|+ +..+..+..+   +...|+.++|.+
T Consensus       133 ~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~----------------~p~~~~~~~~~~~~~~~l~~~~~~~~al~  196 (472)
T 4g1t_A          133 IESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK----------------KPKNPEFTSGLAIASYRLDNWPPSQNAID  196 (472)
T ss_dssp             CCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH----------------STTCHHHHHHHHHHHHHHHHSCCCCCTHH
T ss_pred             hhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh----------------CCCCHHHHHHHHHHHHHhcCchHHHHHHH
Confidence             1 111111      22346789999999987653                444 4444444444   455677788554


Q ss_pred             HHHHHhccCCCCCHhHHHHHHHHHHHH---------HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          158 VSRRLFDEMPERKFATWNTMIDAYARL---------AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       158 ~a~~~~~~~~~~~~~~~~~li~~~~~~---------a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      ...+.++. ...+...+..+-..+...         |.+.+++..   ..+..+++.+-..|...|++++|+..|.+..+
T Consensus       197 ~~~~al~l-~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  275 (472)
T 4g1t_A          197 PLRQAIRL-NPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALE  275 (472)
T ss_dssp             HHHHHHHH-CSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhc-CCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence            44444332 223444555444444331         666665443   34667888999999999999999999999887


Q ss_pred             cCCCCC-HHHHHHHHHHH
Q 044412          226 SGTGSD-QVTMATVLSAC  242 (311)
Q Consensus       226 ~g~~p~-~~t~~~li~a~  242 (311)
                      .  .|+ ..++..+-.+|
T Consensus       276 ~--~p~~~~~~~~lg~~y  291 (472)
T 4g1t_A          276 Y--IPNNAYLHCQIGCCY  291 (472)
T ss_dssp             H--STTCHHHHHHHHHHH
T ss_pred             h--CCChHHHHHHHHHHH
Confidence            4  454 44555554444

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.41  E-value=1e-06  Score=68.27  Aligned_cols=156  Identities=10%  Similarity=-0.020  Sum_probs=93.5

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHh
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKN  130 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~  130 (311)
                      ++.+|..+=..+ .+.|++++|.+.|++..+  |+ ...+..    +.+.|++++|+..++.....              
T Consensus         4 ~~~iy~~lG~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~--------------   68 (184)
T 3vtx_A            4 TTTIYMDIGDKK-RTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL--------------   68 (184)
T ss_dssp             CHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------------
T ss_pred             HHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------------
Confidence            345566666666 666666666666655431  22 112211    55566666666666665443              


Q ss_pred             cCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhC
Q 044412          131 GFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQN  210 (311)
Q Consensus       131 g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~  210 (311)
                       .+-+...+..+-..+...++++.    +...+.....                       ....+...+..+-..|...
T Consensus        69 -~~~~~~~~~~~~~~~~~~~~~~~----a~~~~~~a~~-----------------------~~~~~~~~~~~lg~~~~~~  120 (184)
T 3vtx_A           69 -DTTSAEAYYILGSANFMIDEKQA----AIDALQRAIA-----------------------LNTVYADAYYKLGLVYDSM  120 (184)
T ss_dssp             -CCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH-----------------------HCTTCHHHHHHHHHHHHHT
T ss_pred             -CchhHHHHHHHHHHHHHcCCHHH----HHHHHHHHHH-----------------------hCccchHHHHHHHHHHHHh
Confidence             13334555555666666777777    4433332111                       1122566777777888888


Q ss_pred             CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          211 KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |++++|++.|++..+.. +-+..+|..+-.++.+.|++++|...|+.
T Consensus       121 g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  166 (184)
T 3vtx_A          121 GEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKK  166 (184)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            88888888888877642 33566778888888888888877666644

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.40  E-value=4.5e-05  Score=69.57  Aligned_cols=108  Identities=7%  Similarity=0.012  Sum_probs=88.8

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH--HHHHHHHHHHhccCChhhHHHHHHh----------------
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ--VTMATVLSACAHLGALDLGRGIQIY----------------  257 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~li~a~~~~~~~~~a~~~~~~----------------  257 (311)
                      +...|..+...+.+.|++++|..+|++..+  +.|+.  ..|......+.+.|+++.|+.+|+.                
T Consensus       320 ~~~l~~~~~~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a  397 (530)
T 2ooe_A          320 NMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAA  397 (530)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhC--ccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHH
Confidence            567888899999999999999999999987  45653  4788888888888889998888876                


Q ss_pred             ------hCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          258 ------CRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       258 ------~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                            .|+.+.|..+|++..  .| +...|..++..+.+.|+.++|..+|++....
T Consensus       398 ~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~  454 (530)
T 2ooe_A          398 LMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTS  454 (530)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhc
Confidence                  467778888888665  34 5678899999999999999999999998775

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.40  E-value=5.7e-06  Score=68.06  Aligned_cols=164  Identities=8%  Similarity=0.025  Sum_probs=107.4

Q ss_pred             hhHHHHHhhhhhcCCCCCchh-hhHHHHHHHHhhccChhhHHHHHHHHHHh------ccCc-chhHHHHHHHHHhhccCC
Q 044412            4 KYVRAIITSFKKNSFPTSVSF-IRIHIIANQLKKCSSIKELECVYATIVKT------NANL-DCFLAKQFISFCTSRFHF   75 (311)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~l~~~m~~~------g~~p-~~~~~~~ll~~~~~~~g~   75 (311)
                      ..+...+..+.+...++.+.. .....+..++...|+...+...+....+.      +-.| ...++..+-..+ ...|+
T Consensus        22 ~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~  100 (283)
T 3edt_B           22 PLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLY-GKRGK  100 (283)
T ss_dssp             HHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHH-HTTTC
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHH-HHhcc
Confidence            345555555555444443332 23456777778889999998888877765      2223 346777788888 88888


Q ss_pred             hhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccc
Q 044412           76 IDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFES  155 (311)
Q Consensus        76 ~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a  155 (311)
                      +++|.+.|                    ++|++++++.....              .+....++..+-..|...|++++ 
T Consensus       101 ~~~A~~~~--------------------~~al~~~~~~~~~~--------------~~~~~~~~~~la~~~~~~g~~~~-  145 (283)
T 3edt_B          101 YKEAEPLC--------------------KRALEIREKVLGKF--------------HPDVAKQLNNLALLCQNQGKAEE-  145 (283)
T ss_dssp             HHHHHHHH--------------------HHHHHHHHHHHCTT--------------CHHHHHHHHHHHHHHHTTTCHHH-
T ss_pred             HHHHHHHH--------------------HHHHHHHHHHcCCC--------------ChHHHHHHHHHHHHHHHcCCHHH-
Confidence            88887776                    55555555542211              12236678889999999999999 


Q ss_pred             hHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCC---CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          156 RRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMP---AW-DIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       156 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~---~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                         |...+++                   +.+++....   .| ...++..+-..|...|++++|..+|++..+
T Consensus       146 ---A~~~~~~-------------------al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          146 ---VEYYYRR-------------------ALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             ---HHHHHHH-------------------HHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ---HHHHHHH-------------------HHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               5555554                   222222221   11 355788888888899999999999988765

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.37  E-value=1.8e-06  Score=75.62  Aligned_cols=191  Identities=12%  Similarity=0.075  Sum_probs=140.1

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCC-hhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRH-PLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~-~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      ..|+.+-..+ .+.|++++|.+.+++..+  |+ ...|+.    +...|+ +++|+..|++..+..              
T Consensus        98 ~a~~~lg~~~-~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--------------  162 (382)
T 2h6f_A           98 DVYDYFRAVL-QRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--------------  162 (382)
T ss_dssp             HHHHHHHHHH-HHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--------------
T ss_pred             HHHHHHHHHH-HHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--------------
Confidence            5667777778 889999999999988753  43 333433    777786 999999999987642              


Q ss_pred             CCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCC
Q 044412          132 FSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNK  211 (311)
Q Consensus       132 ~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g  211 (311)
                       +-+...|+.+-.+|.+.|++++    |...++.....                       ...+...|..+-..+...|
T Consensus       163 -P~~~~a~~~~g~~~~~~g~~~e----Al~~~~kal~l-----------------------dP~~~~a~~~lg~~~~~~g  214 (382)
T 2h6f_A          163 -PKNYQVWHHRRVLVEWLRDPSQ----ELEFIADILNQ-----------------------DAKNYHAWQHRQWVIQEFK  214 (382)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCCTT----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHHT
T ss_pred             -CCCHHHHHHHHHHHHHccCHHH----HHHHHHHHHHh-----------------------CccCHHHHHHHHHHHHHcC
Confidence             3457889999999999999999    55555543221                       1236788999999999999


Q ss_pred             ChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc-cCChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHHHHHH
Q 044412          212 QFREALDAFNKTKKSGTGSDQVTMATVLSACAH-LGALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSITEALA  287 (311)
Q Consensus       212 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~-~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~  287 (311)
                      ++++|+..|++..+.. +-+...|+.+-.++.+ .|..++|..        +.+...|++..  .| +...|+.+-..+.
T Consensus       215 ~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~eA~~--------~~el~~~~~Al~l~P~~~~a~~~l~~ll~  285 (382)
T 2h6f_A          215 LWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVL--------EREVQYTLEMIKLVPHNESAWNYLKGILQ  285 (382)
T ss_dssp             CCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHH--------HHHHHHHHHHHHHSTTCHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcchHHHH--------HHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            9999999999999853 2256788888888888 666566531        11223333322  34 4678888888888


Q ss_pred             hcC--ChHHHHHHHHHH
Q 044412          288 IHG--FAHEALGMFDRM  302 (311)
Q Consensus       288 ~~g--~~~~a~~~~~~M  302 (311)
                      ..|  ++++|.+.+.++
T Consensus       286 ~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          286 DRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             TTCGGGCHHHHHHHHHH
T ss_pred             ccCccchHHHHHHHHHh
Confidence            888  689999988887

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.36  E-value=4.9e-06  Score=75.02  Aligned_cols=172  Identities=10%  Similarity=0.003  Sum_probs=112.8

Q ss_pred             hhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCC-ccchHHHHHHhccCCCCCHhHHHHHHHHH
Q 044412          103 PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKF-FESRRVSRRLFDEMPERKFATWNTMIDAY  181 (311)
Q Consensus       103 ~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~-~~a~~~a~~~~~~~~~~~~~~~~~li~~~  181 (311)
                      .+++++.+++....               .+.+...+..+-.+|...|++ ++|+....+.++.- ..+...|..+-..|
T Consensus        84 ~~~al~~l~~~~~~---------------~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~  147 (474)
T 4abn_A           84 MEKTLQQMEEVLGS---------------AQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVY  147 (474)
T ss_dssp             HHHHHHHHHHHHTT---------------CCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc---------------CchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            56666666665443               234678888888999999999 99444444433321 12344566665555


Q ss_pred             HHH-----HHHHHhhCC--CCcHhHHHHHHHHHHhC---------CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc
Q 044412          182 ARL-----AELLFNKMP--AWDIRSWTTMITSYSQN---------KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL  245 (311)
Q Consensus       182 ~~~-----a~~~~~~m~--~~~~~~y~~li~~~~~~---------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~  245 (311)
                      .+.     |.+.|++..  .|+...|..+-..|...         |++++|++.|++..+.. +-+...|..+-.+|...
T Consensus       148 ~~~g~~~~A~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~  226 (474)
T 4abn_A          148 WKKGDVTSAHTCFSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSL  226 (474)
T ss_dssp             HHHTCHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHH
Confidence            554     555555443  35556666666777777         77777777777766542 22355666666666665


Q ss_pred             --------CChhhHHHHHHhhCChHHHHHHHhhcC--CC----CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          246 --------GALDLGRGIQIYCRSLGRSLLVFFKLR--EK----NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       246 --------~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p----~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                              |++++|.             ..|++..  .|    +...|..+-..|...|++++|...|++..+
T Consensus       227 ~~~~~~~~g~~~~A~-------------~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  286 (474)
T 4abn_A          227 YFNTGQNPKISQQAL-------------SAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAA  286 (474)
T ss_dssp             HHHTTCCHHHHHHHH-------------HHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhhccccchHHHHH-------------HHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                    5565554             4444433  34    678899999999999999999999999875

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.30  E-value=3.6e-05  Score=66.94  Aligned_cols=107  Identities=8%  Similarity=-0.049  Sum_probs=70.8

Q ss_pred             HHHHHhhCCCCc-HhHHHHHHHHHHhCCChhHHHHHHHHHHhcC----CCCCHHHHHHHHHHHhccCC---hhhHHHHHH
Q 044412          185 AELLFNKMPAWD-IRSWTTMITSYSQNKQFREALDAFNKTKKSG----TGSDQVTMATVLSACAHLGA---LDLGRGIQI  256 (311)
Q Consensus       185 a~~~~~~m~~~~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~t~~~li~a~~~~~~---~~~a~~~~~  256 (311)
                      +.++++....|+ ..++..+-..|.+.|++++|...+++..+..    -+.....+..+-..+...++   ++       
T Consensus       248 al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~-------  320 (378)
T 3q15_A          248 AAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIH-------  320 (378)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHH-------
T ss_pred             HHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHH-------
Confidence            555555544443 4567778888888899999999988876632    12223345555556666666   44       


Q ss_pred             hhCChHHHHHHHhhcCC-C-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          257 YCRSLGRSLLVFFKLRE-K-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       257 ~~~~~~~a~~~~~~~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                            +|...+++... | ....+..+-..|...|++++|...|++..+
T Consensus       321 ------~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          321 ------DLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             ------HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ------HHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  44444444331 1 224567888999999999999999988754

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.29  E-value=4.6e-06  Score=70.30  Aligned_cols=225  Identities=13%  Similarity=0.080  Sum_probs=144.3

Q ss_pred             HHHHHHHhhccCChhHHHHhcccCCC--CCe-----eeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           63 KQFISFCTSRFHFIDYTILVFPQMQE--PNV-----FVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        63 ~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~-----~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      ...-..+ .+.|++++|...|++..+  |+.     ..+..    +...|++++|++.+++..+.          ....+
T Consensus         9 ~~~g~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----------~~~~~   77 (338)
T 3ro2_A            9 ALEGERL-CKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTL----------ARTIG   77 (338)
T ss_dssp             HHHHHHH-HHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------HHHHT
T ss_pred             HHHHHHH-HHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH----------hhccc
Confidence            3344566 889999999999988753  332     12222    78899999999999887542          11122


Q ss_pred             CCC-chhHHHHHHHHHHhCCCCccchHHHHHHhccCCC-CC----HhHHHHHHHHHH---H-------------------
Q 044412          132 FSS-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE-RK----FATWNTMIDAYA---R-------------------  183 (311)
Q Consensus       132 ~~~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~-~~----~~~~~~li~~~~---~-------------------  183 (311)
                      ..| ...++..+-..|...|++++|.....+.++..+. ++    ..++..+-..|.   +                   
T Consensus        78 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~  157 (338)
T 3ro2_A           78 DQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRN  157 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHH
Confidence            222 2567888888999999999955554443332221 11    113333333322   1                   


Q ss_pred             -H--HH-------HHHhhCCCC--cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHhccC
Q 044412          184 -L--AE-------LLFNKMPAW--DIRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGS-DQVTMATVLSACAHLG  246 (311)
Q Consensus       184 -~--a~-------~~~~~m~~~--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~  246 (311)
                       .  |.       .+......+  ...++..+...+...|++++|.+.+++..+.    +-.+ ...++..+...+...|
T Consensus       158 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g  237 (338)
T 3ro2_A          158 ALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLG  237 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcC
Confidence             1  33       333333322  2346888888899999999999999987652    1111 1337788888889999


Q ss_pred             ChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          247 ALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       247 ~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ++++|...++.      +..+......+  ...++..+-..+...|++++|..++++..+
T Consensus       238 ~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  291 (338)
T 3ro2_A          238 EFETASEYYKK------TLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLA  291 (338)
T ss_dssp             CHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHH------HHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            99988877643      33333333211  145788889999999999999999988754

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.28  E-value=4.8e-06  Score=60.07  Aligned_cols=117  Identities=13%  Similarity=0.164  Sum_probs=89.1

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|+++|+++.+..               +.+...+..+...+...|++++    |...++.....       
T Consensus        11 ~~~~~~~~~A~~~~~~~~~~~---------------~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~-------   64 (136)
T 2fo7_A           11 YYKQGDYDEAIEYYQKALELD---------------PRSAEAWYNLGNAYYKQGDYDE----AIEYYQKALEL-------   64 (136)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHcCcHHHHHHHHHHHHHcC---------------CcchhHHHHHHHHHHHhcCHHH----HHHHHHHHHHH-------
Confidence            445678888888888876532               3467788889999999999999    65555542210       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                                      ...+...|..+...+...|++++|.++++++.+.. +.+..++..+...+...|+++.|...+.
T Consensus        65 ----------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~  127 (136)
T 2fo7_A           65 ----------------DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQ  127 (136)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             ----------------CCCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHH
Confidence                            12356678888899999999999999999998753 3457788889999999999997776654

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.28  E-value=0.00012  Score=65.99  Aligned_cols=76  Identities=8%  Similarity=-0.085  Sum_probs=38.6

Q ss_pred             ccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhc----cCChhHHHHhcccCCCCCe-eeeec----ccc----CCCh
Q 044412           37 CSSIKELECVYATIVKTNANLDCFLAKQFISFCTSR----FHFIDYTILVFPQMQEPNV-FVYHA----FSS----LRHP  103 (311)
Q Consensus        37 ~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~----~g~~~~a~~~~~~m~~~~~-~~~~~----~~~----~~~~  103 (311)
                      .++...+...+....+.|   ++..+..|-..| ..    .++.++|..+|++..+++. ..+..    |..    .++.
T Consensus        92 ~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y-~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~  167 (490)
T 2xm6_A           92 PQDYAQAVIWYKKAALKG---LPQAQQNLGVMY-HEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDY  167 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHH-HHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCH
T ss_pred             CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHH-HcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCH
Confidence            445555555555555544   444445555555 44    5566666666665443321 11111    222    4566


Q ss_pred             hHHHHHHHHHHHC
Q 044412          104 LQAIAFYLYMLRA  116 (311)
Q Consensus       104 ~~a~~~~~~m~~~  116 (311)
                      ++|++.|+...+.
T Consensus       168 ~~A~~~~~~a~~~  180 (490)
T 2xm6_A          168 VMAREWYSKAAEQ  180 (490)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHC
Confidence            6666666665443

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.27  E-value=3.4e-05  Score=68.83  Aligned_cols=249  Identities=8%  Similarity=-0.060  Sum_probs=143.4

Q ss_pred             cChhhHHHHHHHHHHhccCcc-hhHHHHHHHH---HhhccCChhHHHHhcccCC--CCC-eeeeec--------cccCCC
Q 044412           38 SSIKELECVYATIVKTNANLD-CFLAKQFISF---CTSRFHFIDYTILVFPQMQ--EPN-VFVYHA--------FSSLRH  102 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~-~~~~~~ll~~---~~~~~g~~~~a~~~~~~m~--~~~-~~~~~~--------~~~~~~  102 (311)
                      ++.+.+...|+...+..  |+ +..+..+..+   + ...++.++|.+.+++..  .|+ ...+..        ....++
T Consensus       152 ~~y~~A~~~~~kal~~~--p~~~~~~~~~~~~~~~l-~~~~~~~~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~  228 (472)
T 4g1t_A          152 NQNERAKVCFEKALEKK--PKNPEFTSGLAIASYRL-DNWPPSQNAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEE  228 (472)
T ss_dssp             THHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHH-HHSCCCCCTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC-----
T ss_pred             ccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHh-cCchHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhH
Confidence            35678888888877764  43 3344433333   3 55677788887776543  232 222221        345578


Q ss_pred             hhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHH
Q 044412          103 PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYA  182 (311)
Q Consensus       103 ~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~  182 (311)
                      .++|.+.+++....               .+.+..++..+-..|.+.|++++|.....+..+.-+ .+..++..+-..|.
T Consensus       229 ~~~a~~~~~~al~~---------------~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~y~  292 (472)
T 4g1t_A          229 EGEGEKLVEEALEK---------------APGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIP-NNAYLHCQIGCCYR  292 (472)
T ss_dssp             -CHHHHHHHHHHHH---------------CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh---------------CccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCC-ChHHHHHHHHHHHH
Confidence            88999999887653               245577889999999999999995554444444322 23344444433332


Q ss_pred             HH------------------------HHHHHhhCC---CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH--
Q 044412          183 RL------------------------AELLFNKMP---AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV--  233 (311)
Q Consensus       183 ~~------------------------a~~~~~~m~---~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--  233 (311)
                      ..                        |...|+...   ..+..+|..+-..|...|++++|++.|++..+....|...  
T Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~  372 (472)
T 4g1t_A          293 AKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQL  372 (472)
T ss_dssp             HHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHH
Confidence            21                        444444332   2355678889999999999999999999988754433321  


Q ss_pred             HHHHHHH-HHhccCChhhHHHHHHhh-----------CChHHHHHHHhhcC---CCCchhHHHHHHHHHhcCChHHHHHH
Q 044412          234 TMATVLS-ACAHLGALDLGRGIQIYC-----------RSLGRSLLVFFKLR---EKNLLCWNSITEALAIHGFAHEALGM  298 (311)
Q Consensus       234 t~~~li~-a~~~~~~~~~a~~~~~~~-----------~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~  298 (311)
                      .+..+-. .....|+.++|...+...           +....+.+++++..   ..+..+|+.+-..|...|++++|.+.
T Consensus       373 ~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~  452 (472)
T 4g1t_A          373 LHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADED  452 (472)
T ss_dssp             HHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC-----
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            1222211 234678899998887761           11122233333322   34678999999999999999999999


Q ss_pred             HHHHHHc
Q 044412          299 FDRMTYE  305 (311)
Q Consensus       299 ~~~M~~~  305 (311)
                      |++..+.
T Consensus       453 y~kALe~  459 (472)
T 4g1t_A          453 SERGLES  459 (472)
T ss_dssp             -------
T ss_pred             HHHHHhc
Confidence            9998764

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.27  E-value=0.00013  Score=65.78  Aligned_cols=250  Identities=12%  Similarity=0.047  Sum_probs=154.0

Q ss_pred             HHHHHHhh----ccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhc----cCChhHHHHhcccCCCCC-eeeeec---
Q 044412           29 IIANQLKK----CSSIKELECVYATIVKTNANLDCFLAKQFISFCTSR----FHFIDYTILVFPQMQEPN-VFVYHA---   96 (311)
Q Consensus        29 ~~~~~l~~----~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~----~g~~~~a~~~~~~m~~~~-~~~~~~---   96 (311)
                      .+..++..    .++...+...++...+.|   ++..+..|-..| ..    .++.++|.++|++..+.+ ...+..   
T Consensus       116 ~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y-~~g~g~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~  191 (490)
T 2xm6_A          116 NLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAY-FEGDGVTRDYVMAREWYSKAAEQGNVWSCNQLGY  191 (490)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHH-HHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHH-HcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            34444444    457777788888887776   556667777777 65    789999999998765433 222221   


Q ss_pred             -ccc----CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHh----CCCCccchHHHHHHhccCC
Q 044412           97 -FSS----LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSY----SNKFFESRRVSRRLFDEMP  167 (311)
Q Consensus        97 -~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~a~~~~~~~~  167 (311)
                       +..    .++.++|++.|+.-.+.|                 +...+..+-..|..    .++.++    |...++...
T Consensus       192 ~y~~g~g~~~~~~~A~~~~~~a~~~~-----------------~~~a~~~lg~~y~~g~g~~~~~~~----A~~~~~~a~  250 (490)
T 2xm6_A          192 MYSRGLGVERNDAISAQWYRKSATSG-----------------DELGQLHLADMYYFGIGVTQDYTQ----SRVLFSQSA  250 (490)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTT-----------------CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHH
T ss_pred             HHhcCCCCCcCHHHHHHHHHHHHHCC-----------------CHHHHHHHHHHHHcCCCCCCCHHH----HHHHHHHHH
Confidence             333    789999999998876543                 34455556666654    566777    444444432


Q ss_pred             C-CCHhHHHHHHHHHHH----H-----HHHHHhhCCC-CcHhHHHHHHHHHHhC-----CChhHHHHHHHHHHhcCCCCC
Q 044412          168 E-RKFATWNTMIDAYAR----L-----AELLFNKMPA-WDIRSWTTMITSYSQN-----KQFREALDAFNKTKKSGTGSD  231 (311)
Q Consensus       168 ~-~~~~~~~~li~~~~~----~-----a~~~~~~m~~-~~~~~y~~li~~~~~~-----g~~~~a~~~~~~m~~~g~~p~  231 (311)
                      + .+...+..+-..|..    .     |.+.|++..+ .+...+..+-..|...     +++++|+..|++..+.|   +
T Consensus       251 ~~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~  327 (490)
T 2xm6_A          251 EQGNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---D  327 (490)
T ss_dssp             TTTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---C
T ss_pred             HCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---C
Confidence            2 233333344334433    1     5555554432 2445566666666665     77788888887777654   3


Q ss_pred             HHHHHHHHHHHhccC---ChhhHHHHHHh-----------------------hCChHHHHHHHhhcC-CCCchhHHHHHH
Q 044412          232 QVTMATVLSACAHLG---ALDLGRGIQIY-----------------------CRSLGRSLLVFFKLR-EKNLLCWNSITE  284 (311)
Q Consensus       232 ~~t~~~li~a~~~~~---~~~~a~~~~~~-----------------------~~~~~~a~~~~~~~~-~p~~~~~~~li~  284 (311)
                      ...+..|-..|...|   +.++|...++.                       .++.++|...|++.. ..+...+..|-.
T Consensus       328 ~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~~~~a~~~Lg~  407 (490)
T 2xm6_A          328 ATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQGLSAAQVQLGE  407 (490)
T ss_dssp             HHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            344444545554434   56666666655                       255666666666654 335667777777


Q ss_pred             HHHh----cCChHHHHHHHHHHHHcC
Q 044412          285 ALAI----HGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       285 ~~~~----~g~~~~a~~~~~~M~~~g  306 (311)
                      .|..    .++.++|..+|++..+.|
T Consensus       408 ~y~~g~g~~~d~~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          408 IYYYGLGVERDYVQAWAWFDTASTND  433 (490)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCCCCCHHHHHHHHHHHHHCC
Confidence            7777    788888888888877654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.25  E-value=3.6e-05  Score=60.15  Aligned_cols=162  Identities=13%  Similarity=0.048  Sum_probs=112.8

Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                      ..|++++|.+.++.+...               ......++..+-..|...|++++    |...+++             
T Consensus         4 ~~g~~~~A~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~-------------   51 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAH---------------PATASGARFMLGYVYAFMDRFDE----ARASFQA-------------   51 (203)
T ss_dssp             ---CHHHHHHHHHHHHTS---------------TTTHHHHHHHHHHHHHHTTCHHH----HHHHHHH-------------
T ss_pred             ccccHHHHHHHHHHhcCC---------------hHHHHHHHHHHHHHHHHhCcHHH----HHHHHHH-------------
Confidence            568889999855554321               22456788888899999999999    6666655             


Q ss_pred             HHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCC--CHHHHHHHHHHHhccCChhh
Q 044412          179 DAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGS--DQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       179 ~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p--~~~t~~~li~a~~~~~~~~~  250 (311)
                            +.+++.....+  ...+++.+-..+...|++++|.+.+.+..+.    |-.|  ....+..+-..+...|++++
T Consensus        52 ------al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~  125 (203)
T 3gw4_A           52 ------LQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAG  125 (203)
T ss_dssp             ------HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             ------HHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHH
Confidence                  44444444432  3457888888999999999999999987652    2122  23457778888889999999


Q ss_pred             HHHHHHhhCChHHHHHHHhhcCCCC--chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          251 GRGIQIYCRSLGRSLLVFFKLREKN--LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       251 a~~~~~~~~~~~~a~~~~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      |...++.      +.++......+.  ..++..+-..+...|++++|...+++..+
T Consensus       126 A~~~~~~------al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          126 ARQEYEK------SLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHH------HHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            9887643      444444433322  24568888899999999999999887653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.25  E-value=3.7e-06  Score=73.26  Aligned_cols=230  Identities=13%  Similarity=0.073  Sum_probs=149.5

Q ss_pred             chhHHHHHHHHHhhccCChhHHHHhcccCCC--CCe-----eeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHH
Q 044412           58 DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNV-----FVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQ  126 (311)
Q Consensus        58 ~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~-----~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~  126 (311)
                      ....+...-..+ .+.|++++|...|++..+  |+.     ..+..    +...|++++|+..|++.....         
T Consensus         8 ~~~~l~~~g~~~-~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~---------   77 (406)
T 3sf4_A            8 SCLELALEGERL-CKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLA---------   77 (406)
T ss_dssp             CHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH---------
T ss_pred             HHHHHHHHHHHH-HHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH---------
Confidence            344555566677 899999999999988653  332     12222    788999999999999865421         


Q ss_pred             HHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCC-CC----HhHHHHHHHHHH---H--------------
Q 044412          127 VWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE-RK----FATWNTMIDAYA---R--------------  183 (311)
Q Consensus       127 ~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~-~~----~~~~~~li~~~~---~--------------  183 (311)
                       ...+..|. ..++..+-..|...|++++|.....+.++..+. ++    ..++..+-..|.   +              
T Consensus        78 -~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~  156 (406)
T 3sf4_A           78 -RTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFP  156 (406)
T ss_dssp             -HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCC
T ss_pred             -HhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhh
Confidence             11112222 557888888999999999955544333332221 11    113333322221   1              


Q ss_pred             ------H---------HHHHHhhCCCC--cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC-CCCC----HHHHHHHHHH
Q 044412          184 ------L---------AELLFNKMPAW--DIRSWTTMITSYSQNKQFREALDAFNKTKKSG-TGSD----QVTMATVLSA  241 (311)
Q Consensus       184 ------~---------a~~~~~~m~~~--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~t~~~li~a  241 (311)
                            .         +.+++.....+  ...+|..+-..|...|++++|+..+++..+.. -.++    ..++..+-..
T Consensus       157 ~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  236 (406)
T 3sf4_A          157 EEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNA  236 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence                  1         44444444432  23468888899999999999999999976521 1122    3378888888


Q ss_pred             HhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          242 CAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       242 ~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +...|++++|...++.      +.++......+  ...++..+-..|...|++++|...+++..+
T Consensus       237 ~~~~g~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  295 (406)
T 3sf4_A          237 YIFLGEFETASEYYKK------TLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLA  295 (406)
T ss_dssp             HHHTTCHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHH------HHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHH
Confidence            9999999988877643      34443333211  146788999999999999999999988754

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.23  E-value=8.9e-06  Score=77.00  Aligned_cols=152  Identities=9%  Similarity=0.044  Sum_probs=112.4

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      +.+.|++++|++.|++..+                +.|+ ...|+.+-.+|.+.|++++    |...+++..+.      
T Consensus        19 ~~~~G~~~eAi~~~~kAl~----------------l~P~~~~a~~nLg~~l~~~g~~~e----A~~~~~~Al~l------   72 (723)
T 4gyw_A           19 KREQGNIEEAVRLYRKALE----------------VFPEFAAAHSNLASVLQQQGKLQE----ALMHYKEAIRI------   72 (723)
T ss_dssp             HHHTTCHHHHHHHHHHHHH----------------HCSCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------
T ss_pred             HHHcCCHHHHHHHHHHHHH----------------hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------
Confidence            3455666777777766654                2444 6788888889999999999    55555542210      


Q ss_pred             HHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHH
Q 044412          176 TMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~  254 (311)
                                       ...+...|+.+-..|...|++++|++.|++..+.  .|+ ...|+.+-.++...|++++|...
T Consensus        73 -----------------~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~  133 (723)
T 4gyw_A           73 -----------------SPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIAS  133 (723)
T ss_dssp             -----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             -----------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence                             1125678999999999999999999999998874  454 67889999999999999877665


Q ss_pred             HHhhCChHHHHHHHhhcCCC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          255 QIYCRSLGRSLLVFFKLREK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       255 ~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ++.      |.++     .| +...|..+...+...|++++|.+.+++..+
T Consensus       134 ~~~------Al~l-----~P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          134 YRT------ALKL-----KPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HHH------HHHH-----CSCCHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             HHH------HHHh-----CCCChHHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence            532      2222     45 457899999999999999999988887653

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.22  E-value=0.00067  Score=58.48  Aligned_cols=159  Identities=8%  Similarity=-0.027  Sum_probs=91.2

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCC---C---CCH-hHHHHHHHHHHHH-----HHHHHhhC----C---CC-c
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMP---E---RKF-ATWNTMIDAYARL-----AELLFNKM----P---AW-D  196 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~---~---~~~-~~~~~li~~~~~~-----a~~~~~~m----~---~~-~  196 (311)
                      .++..+-..+...|++++|.+...+.+....   .   +.. ..+..+-..+...     |...+++.    +   .+ .
T Consensus        94 ~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  173 (373)
T 1hz4_A           94 WSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQ  173 (373)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGG
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHH
Confidence            3456677788999999996655544443321   1   111 2334344444332     44444432    2   12 2


Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHH-----HHHHHHhccCChhhHHHHHHhhCChHHHHHHHhh
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMA-----TVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFK  270 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~-----~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~  270 (311)
                      ..+|..+-..+...|++++|...+++.....-.++ ...+.     .....+...|+.+.|...++.......       
T Consensus       174 ~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~-------  246 (373)
T 1hz4_A          174 LQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEF-------  246 (373)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCC-------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCC-------
Confidence            34677788888889999999999998765321221 11121     222336677777755555443221110       


Q ss_pred             cCCCC---chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          271 LREKN---LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       271 ~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                        .++   ...+..+...+...|++++|...+++...
T Consensus       247 --~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~  281 (373)
T 1hz4_A          247 --ANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNE  281 (373)
T ss_dssp             --TTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --CcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              011   12456777888899999999998887643

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.18  E-value=7e-05  Score=63.23  Aligned_cols=184  Identities=8%  Similarity=-0.068  Sum_probs=110.6

Q ss_pred             cCChhHHHHhcccCCCCCeeeeeccccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCC
Q 044412           73 FHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNK  151 (311)
Q Consensus        73 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~  151 (311)
                      .++++.|...|++.       -+.+...|++++|.+.|.+..+..          .+.|-.+ -..+|+.+-..|.+.|+
T Consensus        29 ~~~~~~A~~~~~~a-------~~~~~~~g~~~~A~~~~~~al~~~----------~~~~~~~~~a~~~~~lg~~~~~~g~   91 (307)
T 2ifu_A           29 KPDYDSAASEYAKA-------AVAFKNAKQLEQAKDAYLQEAEAH----------ANNRSLFHAAKAFEQAGMMLKDLQR   91 (307)
T ss_dssp             SCCHHHHHHHHHHH-------HHHHHHTTCHHHHHHHHHHHHHHH----------HHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHH-------HHHHHHcCCHHHHHHHHHHHHHHH----------HHcCCHHHHHHHHHHHHHHHHhCCC
Confidence            45666666665543       011455677777777777654311          1111111 14578888889999999


Q ss_pred             CccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhCCChhHHHHHHHHHHhc---
Q 044412          152 FFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQNKQFREALDAFNKTKKS---  226 (311)
Q Consensus       152 ~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~g~~~~a~~~~~~m~~~---  226 (311)
                      +++    |...+++                   |.+++.+...+.  ..+|+.+-..|.. |++++|+..|++-.+.   
T Consensus        92 ~~~----A~~~~~~-------------------Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~  147 (307)
T 2ifu_A           92 MPE----AVQYIEK-------------------ASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFEN  147 (307)
T ss_dssp             GGG----GHHHHHH-------------------HHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHH
T ss_pred             HHH----HHHHHHH-------------------HHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHh
Confidence            999    5555554                   444444444433  3467777777777 8888888888876542   


Q ss_pred             -CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC-CC-chhHHHHHHHHHhcCChHHHHHHHHHH
Q 044412          227 -GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE-KN-LLCWNSITEALAIHGFAHEALGMFDRM  302 (311)
Q Consensus       227 -g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~M  302 (311)
                       |-.+ ...++..+-..+...|++++|...++.      +.+++.+... +. ...+..+...+...|++++|...|++.
T Consensus       148 ~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~a  221 (307)
T 2ifu_A          148 EERLRQAAELIGKASRLLVRQQKFDEAAASLQK------EKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRES  221 (307)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence             1111 135677777888888888877776643      2333222211 11 125556666667778888888887776


Q ss_pred             H
Q 044412          303 T  303 (311)
Q Consensus       303 ~  303 (311)
                      .
T Consensus       222 l  222 (307)
T 2ifu_A          222 Y  222 (307)
T ss_dssp             T
T ss_pred             h
Confidence            5

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.17  E-value=9.6e-06  Score=71.03  Aligned_cols=186  Identities=9%  Similarity=0.129  Sum_probs=113.1

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCch----hHHHHHHHHHHhCCCCccchHHHHHHhccC---CC-
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPV----FVQTAMVDNYSYSNKFFESRRVSRRLFDEM---PE-  168 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~----~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~---~~-  168 (311)
                      +...|++++|++.|++..+..               +.+.    .+|..+-..|...|++++|.....+.++..   .. 
T Consensus        58 ~~~~g~~~~A~~~~~~al~~~---------------~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~  122 (411)
T 4a1s_A           58 LCNAGDCRAGVAFFQAAIQAG---------------TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDR  122 (411)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC---------------CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHhCcHHHHHHHHHHHHHhc---------------ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCc
Confidence            346778888888888776532               1222    478888889999999999555443333321   11 


Q ss_pred             C-CHhHHHHHHHHHHHH-----HHHHHhhC-------CCC--cHhHHHHHHHHHHhCCC-----------------hhHH
Q 044412          169 R-KFATWNTMIDAYARL-----AELLFNKM-------PAW--DIRSWTTMITSYSQNKQ-----------------FREA  216 (311)
Q Consensus       169 ~-~~~~~~~li~~~~~~-----a~~~~~~m-------~~~--~~~~y~~li~~~~~~g~-----------------~~~a  216 (311)
                      + ...++..+-..|...     |...+++.       ..+  ...+|..+-..|...|+                 +++|
T Consensus       123 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A  202 (411)
T 4a1s_A          123 LGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRA  202 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHH
Confidence            1 123444454444443     44444332       221  34478888888888899                 8999


Q ss_pred             HHHHHHHHhc----CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHHHHhc
Q 044412          217 LDAFNKTKKS----GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEALAIH  289 (311)
Q Consensus       217 ~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~~~~~  289 (311)
                      ++.+.+..+.    +-.| ...++..+-..+...|++++|...++.      +.++......+  ....+..+...|...
T Consensus       203 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~la~~~~~~  276 (411)
T 4a1s_A          203 VEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQE------RLRIAREFGDRAAERRANSNLGNSHIFL  276 (411)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHHTCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHH------HHHHHHhcCCcHHHHHHHHHHHHHHHHC
Confidence            9888876442    2222 234677788888889999988877754      22222221111  123566677777777


Q ss_pred             CChHHHHHHHHHHH
Q 044412          290 GFAHEALGMFDRMT  303 (311)
Q Consensus       290 g~~~~a~~~~~~M~  303 (311)
                      |++++|..++++..
T Consensus       277 g~~~~A~~~~~~al  290 (411)
T 4a1s_A          277 GQFEDAAEHYKRTL  290 (411)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHH
Confidence            77777777776654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.17  E-value=0.00022  Score=59.71  Aligned_cols=140  Identities=11%  Similarity=0.016  Sum_probs=88.1

Q ss_pred             hhHHHHHHHHHHhC-CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhCCC
Q 044412          136 VFVQTAMVDNYSYS-NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQNKQ  212 (311)
Q Consensus       136 ~~~~~~ll~~~~~~-g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~g~  212 (311)
                      ..+++.+-..|... |++++    |...+++                   |.+++.....+.  ..+|+.+-..+...|+
T Consensus       117 a~~~~~lg~~~~~~lg~~~~----A~~~~~~-------------------Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~  173 (292)
T 1qqe_A          117 ANFKFELGEILENDLHDYAK----AIDCYEL-------------------AGEWYAQDQSVALSNKCFIKCADLKALDGQ  173 (292)
T ss_dssp             HHHHHHHHHHHHHTTCCHHH----HHHHHHH-------------------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhhcCHHH----HHHHHHH-------------------HHHHHHhCCChHHHHHHHHHHHHHHHHhCC
Confidence            45788888899996 99999    7666665                   334443332221  3468888899999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCH------HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHH
Q 044412          213 FREALDAFNKTKKSGTGSDQ------VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEAL  286 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~------~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~  286 (311)
                      +++|+..|++..+.......      .+|..+..++...|+++.|...++..-.+.....-     ......+..++.++
T Consensus       174 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~-----~~~~~~l~~l~~~~  248 (292)
T 1qqe_A          174 YIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFAD-----SRESNFLKSLIDAV  248 (292)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC--------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCC-----cHHHHHHHHHHHHH
Confidence            99999999998875432221      25667777788888888776666553332221000     00112344556666


Q ss_pred             H--hcCChHHHHHHHHHHH
Q 044412          287 A--IHGFAHEALGMFDRMT  303 (311)
Q Consensus       287 ~--~~g~~~~a~~~~~~M~  303 (311)
                      .  ..+++++|...|+++.
T Consensus       249 ~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          249 NEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             HTTCTTTHHHHHHHHTTSS
T ss_pred             HcCCHHHHHHHHHHhccCC
Confidence            4  4566888888776653

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.10  E-value=4.7e-05  Score=60.97  Aligned_cols=152  Identities=10%  Similarity=0.017  Sum_probs=104.3

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|++.|++..+..              ..++...+..+-.+|...|++++    |...++...+        
T Consensus        17 ~~~~~~~~~A~~~~~~al~~~--------------~~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~al~--------   70 (228)
T 4i17_A           17 ALNAKNYAVAFEKYSEYLKLT--------------NNQDSVTAYNCGVCADNIKKYKE----AADYFDIAIK--------   70 (228)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHT--------------TTCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH--------
T ss_pred             HHHccCHHHHHHHHHHHHhcc--------------CCCCcHHHHHHHHHHHHhhcHHH----HHHHHHHHHH--------
Confidence            456788888888888776532              12667777778888999999999    5555544221        


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-H-------HHHHHHHHHHhccCCh
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-Q-------VTMATVLSACAHLGAL  248 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~-------~t~~~li~a~~~~~~~  248 (311)
                                     ....+...|..+-..|...|++++|+..|++..+.  .|+ .       ..|..+=..+...|++
T Consensus        71 ---------------~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~  133 (228)
T 4i17_A           71 ---------------KNYNLANAYIGKSAAYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNI  133 (228)
T ss_dssp             ---------------TTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCH
T ss_pred             ---------------hCcchHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccH
Confidence                           11225677888999999999999999999998874  344 4       2344444555555555


Q ss_pred             hhHHHHHHhhCChHHHHHHHhhcC--CCC---chhHHHHHHHHHhcCCh---------------------------HHHH
Q 044412          249 DLGRGIQIYCRSLGRSLLVFFKLR--EKN---LLCWNSITEALAIHGFA---------------------------HEAL  296 (311)
Q Consensus       249 ~~a~~~~~~~~~~~~a~~~~~~~~--~p~---~~~~~~li~~~~~~g~~---------------------------~~a~  296 (311)
                      +             +|...|++..  .|+   ...|..+-..|...|+.                           ++|.
T Consensus       134 ~-------------~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~  200 (228)
T 4i17_A          134 E-------------KAEENYKHATDVTSKKWKTDALYSLGVLFYNNGADVLRKATPLASSNKEKYASEKAKADAAFKKAV  200 (228)
T ss_dssp             H-------------HHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             H-------------HHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHH
Confidence            5             5555555544  343   45667777777777776                           8888


Q ss_pred             HHHHHHHH
Q 044412          297 GMFDRMTY  304 (311)
Q Consensus       297 ~~~~~M~~  304 (311)
                      ..+++..+
T Consensus       201 ~~~~~a~~  208 (228)
T 4i17_A          201 DYLGEAVT  208 (228)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhh
Confidence            88888765

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.09  E-value=8.7e-06  Score=77.06  Aligned_cols=152  Identities=8%  Similarity=0.011  Sum_probs=99.4

Q ss_pred             hHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcC
Q 044412           60 FLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGF  132 (311)
Q Consensus        60 ~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~  132 (311)
                      ..++.|-..+ .+.|++++|.+.|++..+  |+ ...|+.    +.+.|++++|++.|++..+                +
T Consensus        10 ~al~nLG~~~-~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~----------------l   72 (723)
T 4gyw_A           10 DSLNNLANIK-REQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR----------------I   72 (723)
T ss_dssp             HHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH----------------H
T ss_pred             HHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH----------------h
Confidence            3445555555 555555555555554431  22 111211    5566677777777776654                2


Q ss_pred             CCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCC
Q 044412          133 SSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNK  211 (311)
Q Consensus       133 ~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g  211 (311)
                      .|+ ...|+.+-.+|.+.|++++    |.+.+++..+.                       ...+...|+.+-..|...|
T Consensus        73 ~P~~~~a~~nLg~~l~~~g~~~~----A~~~~~kAl~l-----------------------~P~~~~a~~~Lg~~~~~~g  125 (723)
T 4gyw_A           73 SPTFADAYSNMGNTLKEMQDVQG----ALQCYTRAIQI-----------------------NPAFADAHSNLASIHKDSG  125 (723)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-----------------------CCCCHHHHHHHHHHHHHcC
Confidence            343 6788888888999999999    55555442210                       1125677888888888889


Q ss_pred             ChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          212 QFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       212 ~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      ++++|++.|++..+.  .|+ ...|..+..++...|++++|.+.++.
T Consensus       126 ~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~~~~A~~~~~k  170 (723)
T 4gyw_A          126 NIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCDWTDYDERMKK  170 (723)
T ss_dssp             CHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCCTTHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhcccHHHHHHHHHH
Confidence            999999999888764  454 56788888888888888888877655

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.06  E-value=0.00041  Score=63.16  Aligned_cols=132  Identities=9%  Similarity=0.015  Sum_probs=75.6

Q ss_pred             HhHHHHHHHHHHHH-----HHHHHhhCC--CC-cH-hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHH
Q 044412          171 FATWNTMIDAYARL-----AELLFNKMP--AW-DI-RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLS  240 (311)
Q Consensus       171 ~~~~~~li~~~~~~-----a~~~~~~m~--~~-~~-~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~  240 (311)
                      ...|..+...+.+.     |..+|++..  .| +. ..|......+.+.|++++|.++|++-.+.  .|+ ...|.....
T Consensus       321 ~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~--~~~~~~~~~~~a~  398 (530)
T 2ooe_A          321 MLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED--ARTRHHVYVTAAL  398 (530)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--TTCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--cCCchHHHHHHHH
Confidence            44455544444432     555555432  22 22 35666666666666666666666665543  222 222221111


Q ss_pred             -HHhccCChhhHHHHHHh---------------------hCChHHHHHHHhhcC--CC-C----chhHHHHHHHHHhcCC
Q 044412          241 -ACAHLGALDLGRGIQIY---------------------CRSLGRSLLVFFKLR--EK-N----LLCWNSITEALAIHGF  291 (311)
Q Consensus       241 -a~~~~~~~~~a~~~~~~---------------------~~~~~~a~~~~~~~~--~p-~----~~~~~~li~~~~~~g~  291 (311)
                       .+...|+.+.|..+|+.                     .|+.+.|..+|++..  .| +    ...|...+.-....|+
T Consensus       399 ~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~  478 (530)
T 2ooe_A          399 MEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGD  478 (530)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSC
T ss_pred             HHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCC
Confidence             12235666666666665                     566667777776654  12 2    3378888998899999


Q ss_pred             hHHHHHHHHHHHH
Q 044412          292 AHEALGMFDRMTY  304 (311)
Q Consensus       292 ~~~a~~~~~~M~~  304 (311)
                      .+.+..+++++.+
T Consensus       479 ~~~~~~~~~r~~~  491 (530)
T 2ooe_A          479 LASILKVEKRRFT  491 (530)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998865

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.04  E-value=4.2e-05  Score=70.42  Aligned_cols=153  Identities=4%  Similarity=-0.149  Sum_probs=96.1

Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMID  179 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~  179 (311)
                      .|++++|++.|++..+.               -+-+...|..+-..|.+.|++++    |...+++..+.+         
T Consensus         2 ~g~~~~A~~~~~~al~~---------------~p~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~~---------   53 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH---------------RPQDFVAWLMLADAELGMGDTTA----GEMAVQRGLALH---------   53 (568)
T ss_dssp             ----------------------------------CCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHTTS---------
T ss_pred             CccHHHHHHHHHHHHHh---------------CCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhC---------
Confidence            46788999999887553               13347788889999999999999    555554432211         


Q ss_pred             HHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhC
Q 044412          180 AYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCR  259 (311)
Q Consensus       180 ~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~  259 (311)
                                    ..+...|..+-..|...|++++|.+.|++..+.. +-+...+..+-.++...|++++|...++.  
T Consensus        54 --------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~--  116 (568)
T 2vsy_A           54 --------------PGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTR--  116 (568)
T ss_dssp             --------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH--
T ss_pred             --------------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHH--
Confidence                          1256678888888888999999999999887752 23466788888888888888866665532  


Q ss_pred             ChHHHHHHHhhcCCCCchhHHHHHHHHHhc---CChHHHHHHHHHHHHc
Q 044412          260 SLGRSLLVFFKLREKNLLCWNSITEALAIH---GFAHEALGMFDRMTYE  305 (311)
Q Consensus       260 ~~~~a~~~~~~~~~p~~~~~~~li~~~~~~---g~~~~a~~~~~~M~~~  305 (311)
                          +.+.    ...+...+..+...+...   |+.++|...+++..+.
T Consensus       117 ----al~~----~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A          117 ----AHQL----LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             ----HHHH----CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             ----HHHh----CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence                1111    123456788888888888   8889998888887654

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.03  E-value=0.0001  Score=61.99  Aligned_cols=166  Identities=9%  Similarity=-0.015  Sum_probs=105.5

Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC-CCHhHHHHHHHHHHHH-----HHHHHhhCC--CC-----cHhH
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE-RKFATWNTMIDAYARL-----AELLFNKMP--AW-----DIRS  199 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~-~~~~~~~~li~~~~~~-----a~~~~~~m~--~~-----~~~~  199 (311)
                      .++..++..+-..+...|+.++|+++..+..+..+. .+...+..++..+.+.     |.+.+++|.  .|     +..+
T Consensus        97 ~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~~~d~~~~~d~~  176 (310)
T 3mv2_B           97 QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNAIEDTVSGDNEM  176 (310)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCccccccchHH
Confidence            455555667778899999999955555554444332 2445677777777775     999998886  35     2455


Q ss_pred             HHHHHHHHHh----CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhc---C
Q 044412          200 WTTMITSYSQ----NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKL---R  272 (311)
Q Consensus       200 y~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~---~  272 (311)
                      ...+..++..    .++.++|+.+|+++.+.  .|+..+-..++.++.+.|++++|+..++......-.   ++..   .
T Consensus       177 l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~---~~~k~~~~  251 (310)
T 3mv2_B          177 ILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYS---VEQKENAV  251 (310)
T ss_dssp             HHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHH---TTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhccc---ccccccCC
Confidence            5666666333    34899999999998764  466455556666888999999887776432111000   0000   0


Q ss_pred             CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          273 EKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       273 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ..|..+.-.+|......|+  +|.+++.++++.
T Consensus       252 p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          252 LYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             SSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence            1245566444444444576  788999998863

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=97.99  E-value=9.6e-05  Score=61.89  Aligned_cols=166  Identities=8%  Similarity=-0.070  Sum_probs=111.7

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      +...|++++|++.|++..+..          .+.|-.++ ..+|+.+-.+|.+.|++++    |...++.          
T Consensus        47 ~~~~g~~~~A~~~~~~al~~~----------~~~~~~~~~a~~~~~lg~~~~~~g~~~~----A~~~~~~----------  102 (292)
T 1qqe_A           47 YRLRKELNLAGDSFLKAADYQ----------KKAGNEDEAGNTYVEAYKCFKSGGNSVN----AVDSLEN----------  102 (292)
T ss_dssp             HHHTTCTHHHHHHHHHHHHHH----------HHTTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHH----------
T ss_pred             HHHcCCHHHHHHHHHHHHHHH----------HHhCCHHHHHHHHHHHHHHHHHCCCHHH----HHHHHHH----------
Confidence            445667777777776654310          11122222 5688999999999999999    7666665          


Q ss_pred             HHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhC-CChhHHHHHHHHHHhc----CCCCC-HHHHHHHHHHHhccCC
Q 044412          176 TMIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQN-KQFREALDAFNKTKKS----GTGSD-QVTMATVLSACAHLGA  247 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~-g~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~a~~~~~~  247 (311)
                               |.+++.....+.  ..+|+.+-..|... |++++|+..|++-.+.    |-.+. ..++..+-..+...|+
T Consensus       103 ---------Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~  173 (292)
T 1qqe_A          103 ---------AIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQ  173 (292)
T ss_dssp             ---------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             ---------HHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCC
Confidence                     445555554433  35788888999996 9999999999997653    11111 3568888888999999


Q ss_pred             hhhHHHHHHhhCChHHHHHHHhhcCC-CCc-----hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          248 LDLGRGIQIYCRSLGRSLLVFFKLRE-KNL-----LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       248 ~~~a~~~~~~~~~~~~a~~~~~~~~~-p~~-----~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +++|...++......         +. +..     ..|..+..++...|++++|...|++..+
T Consensus       174 ~~~A~~~~~~al~~~---------~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          174 YIEASDIYSKLIKSS---------MGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HHHHHHHHHHHHHTT---------SSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             HHHHHHHHHHHHHHH---------hcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            987766654311111         11 111     1567778889999999999999988754

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.97  E-value=0.00021  Score=61.69  Aligned_cols=94  Identities=13%  Similarity=-0.026  Sum_probs=63.7

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhcCCCC---CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-Cc-hh
Q 044412          204 ITSYSQNKQFREALDAFNKTKKSGTGS---DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NL-LC  278 (311)
Q Consensus       204 i~~~~~~g~~~~a~~~~~~m~~~g~~p---~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~-~~  278 (311)
                      +..+...|++++|...+++.......+   ....+..+...+...|+.++|...++..      .........+ +. ..
T Consensus       222 ~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a------~~~~~~~~~~~~~~~~  295 (373)
T 1hz4_A          222 VIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEEL------NENARSLRLMSDLNRN  295 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHHHHHTTCHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHH------HHHHHhCcchhhHHHH
Confidence            344778999999999999887643221   1335667778888889999888776542      2222222111 12 35


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          279 WNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       279 ~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      +..+-.++...|+.++|...+++..
T Consensus       296 ~~~la~~~~~~g~~~~A~~~l~~al  320 (373)
T 1hz4_A          296 LLLLNQLYWQAGRKSDAQRVLLDAL  320 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            6667788889999999999888765

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.90  E-value=4.4e-05  Score=60.53  Aligned_cols=152  Identities=7%  Similarity=-0.000  Sum_probs=101.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHH----------------HHHHHHhCCCCccchHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTA----------------MVDNYSYSNKFFESRRVS  159 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~----------------ll~~~~~~g~~~~a~~~a  159 (311)
                      +...|++++|+..|++..+.                .|+ ...|..                +-.+|.+.|++++    |
T Consensus        14 ~~~~g~~~~A~~~~~~al~~----------------~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~----A   73 (208)
T 3urz_A           14 AIEAGQNGQAVSYFRQTIAL----------------NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDK----A   73 (208)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH----------------CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHH----H
T ss_pred             HHHCCCHHHHHHHHHHHHHh----------------CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHH----H
Confidence            44678888999888887653                232 233333                7788999999999    5


Q ss_pred             HHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHH
Q 044412          160 RRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATV  238 (311)
Q Consensus       160 ~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~l  238 (311)
                      ...++...+.                       ...+...|..+-..+...|++++|+..|++..+.  .| +..++..+
T Consensus        74 ~~~~~~al~~-----------------------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~l  128 (208)
T 3urz_A           74 YLFYKELLQK-----------------------APNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFL  128 (208)
T ss_dssp             HHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHHHH-----------------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHH
Confidence            5555542211                       1125778889999999999999999999999874  45 45677777


Q ss_pred             HHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchh--HHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          239 LSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLC--WNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       239 i~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~--~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      -.++...|..+..           .+...++....|+...  +...-.++...|++++|...|++..+
T Consensus       129 g~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~  185 (208)
T 3urz_A          129 GNYYYLTAEQEKK-----------KLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL  185 (208)
T ss_dssp             HHHHHHHHHHHHH-----------HHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT
T ss_pred             HHHHHHHhHHHHH-----------HHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            6666554433221           4455555555565443  33344456678899999999998875

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.88  E-value=0.00023  Score=50.29  Aligned_cols=98  Identities=14%  Similarity=0.199  Sum_probs=78.7

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCc
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNL  276 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~  276 (311)
                      ...|..+...+...|++++|.++|++..+.. +.+..++..+...+...|++++|..+++..-      +.    ...+.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~------~~----~~~~~   77 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKAL------EL----DPNNA   77 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH------HH----CTTCH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH------Hh----CCccH
Confidence            5678888999999999999999999998753 3467788889999999999997766653321      11    13466


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      .++..+...+...|++++|..+++++.+.
T Consensus        78 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           78 EAWYNLGNAYYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            78899999999999999999999998764

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=97.87  E-value=0.00047  Score=54.23  Aligned_cols=130  Identities=12%  Similarity=-0.097  Sum_probs=96.4

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHH
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALD  218 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~  218 (311)
                      +..+-..+...|++++    |...++...                          +|+...|..+-..|...|++++|++
T Consensus         9 ~~~~g~~~~~~~~~~~----A~~~~~~a~--------------------------~~~~~~~~~lg~~~~~~g~~~~A~~   58 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKG----ALDAFSAVQ--------------------------DPHSRICFNIGCMYTILKNMTEAEK   58 (213)
T ss_dssp             HHHHHHHHHHTTCHHH----HHHHHHTSS--------------------------SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCHHH----HHHHHHHHc--------------------------CCChHHHHHHHHHHHHcCCHHHHHH
Confidence            4455667778888888    666666543                          4467788899999999999999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhc-----------CCC-CchhHHHHHHHH
Q 044412          219 AFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKL-----------REK-NLLCWNSITEAL  286 (311)
Q Consensus       219 ~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~-----------~~p-~~~~~~~li~~~  286 (311)
                      .|++..+.. +.+...|..+-.++...|++++|...++..      .+....-           ..| ....|..+-..|
T Consensus        59 ~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a------l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  131 (213)
T 1hh8_A           59 AFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEA------LIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMY  131 (213)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-ccchHHHHHHHHHHHHcccHHHHHHHHHHH------HHhCCCccHHHHHHhccccCccchHHHHHHHHHH
Confidence            999988753 346678888899999999999777665431      1110000           000 126788899999


Q ss_pred             HhcCChHHHHHHHHHHHHc
Q 044412          287 AIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       287 ~~~g~~~~a~~~~~~M~~~  305 (311)
                      ...|++++|...|++..+.
T Consensus       132 ~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A          132 AKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHTT
T ss_pred             HHccCHHHHHHHHHHHHHc
Confidence            9999999999999998753

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=97.86  E-value=0.0002  Score=54.94  Aligned_cols=140  Identities=15%  Similarity=0.096  Sum_probs=100.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CCHhHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKFATW  174 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~~~~  174 (311)
                      +...|++++|+..|++..+.               -+-+...+..+-..|.+.|++++    |...++....  |+.. +
T Consensus        16 ~~~~g~~~~A~~~~~~al~~---------------~P~~~~a~~~la~~~~~~g~~~~----A~~~~~~a~~~~p~~~-~   75 (176)
T 2r5s_A           16 LLQQGEHAQALNVIQTLSDE---------------LQSRGDVKLAKADCLLETKQFEL----AQELLATIPLEYQDNS-Y   75 (176)
T ss_dssp             HHHTTCHHHHHHHHHTSCHH---------------HHTSHHHHHHHHHHHHHTTCHHH----HHHHHTTCCGGGCCHH-H
T ss_pred             HHHcCCHHHHHHHHHHHHHH---------------CCCcHHHHHHHHHHHHHCCCHHH----HHHHHHHhhhccCChH-H
Confidence            55678888998888876542               13356788889999999999999    8888887754  3222 2


Q ss_pred             HHHHHHH--HHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHh
Q 044412          175 NTMIDAY--ARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACA  243 (311)
Q Consensus       175 ~~li~~~--~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~  243 (311)
                      ..+....  ...     +...|++..  .| +...+..+-..+...|++++|...|++..+..-.+ +...+..+...+.
T Consensus        76 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~  155 (176)
T 2r5s_A           76 KSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILS  155 (176)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHH
Confidence            2221111  111     455555443  34 57788899999999999999999999998754322 3568888999999


Q ss_pred             ccCChhhHHHHHH
Q 044412          244 HLGALDLGRGIQI  256 (311)
Q Consensus       244 ~~~~~~~a~~~~~  256 (311)
                      ..|+.++|...++
T Consensus       156 ~~g~~~~A~~~y~  168 (176)
T 2r5s_A          156 ALGQGNAIASKYR  168 (176)
T ss_dssp             HHCSSCHHHHHHH
T ss_pred             HhCCCCcHHHHHH
Confidence            9999997776653

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.83  E-value=0.0019  Score=57.57  Aligned_cols=268  Identities=8%  Similarity=-0.039  Sum_probs=137.3

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCCh---hHHHHhcccCCCCCeeeeec----cccC-
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFI---DYTILVFPQMQEPNVFVYHA----FSSL-  100 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~---~~a~~~~~~m~~~~~~~~~~----~~~~-  100 (311)
                      .+.......|+...+.+++....+.|-   +..+..|-..| ...|+.   ++|..+|++..+.+...+..    +... 
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g~---~~A~~~Lg~~y-~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~   83 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELGY---SEAQVGLADIQ-VGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKP   83 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTC---CTGGGTCC-----------------------------CHHHHHHHHHTC-
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCC---HHHHHHHHHHH-HccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCC
Confidence            345666677889999999999888873   33344444555 556766   89999998877653333222    2222 


Q ss_pred             ----CChhHHHHHHHHHHHCCCCch---------------------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccc
Q 044412          101 ----RHPLQAIAFYLYMLRAEVLLT---------------------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFES  155 (311)
Q Consensus       101 ----~~~~~a~~~~~~m~~~~~~p~---------------------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a  155 (311)
                          ++.++|++.|+.-.+.|...-                     ..+......|   +...+..|-..|...+.++++
T Consensus        84 ~~~~~~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~~~~~~~~  160 (452)
T 3e4b_A           84 GATEAEHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRTQGTYDQH  160 (452)
T ss_dssp             -CCHHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHHHTCGGGG
T ss_pred             CCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcccC
Confidence                377899999988877653222                     1111111112   233444555666666666665


Q ss_pred             hHHHHHHhccCCCCCHhHHHHHHHHHHHH--------HHHHHhhCC---CCcHhHHHHHHHHHHhC----CChhHHHHHH
Q 044412          156 RRVSRRLFDEMPERKFATWNTMIDAYARL--------AELLFNKMP---AWDIRSWTTMITSYSQN----KQFREALDAF  220 (311)
Q Consensus       156 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~--------a~~~~~~m~---~~~~~~y~~li~~~~~~----g~~~~a~~~~  220 (311)
                      ..-+..++......+...+..+-..|...        |.+.|..-.   .++...+..+-..|...    +++++|++.|
T Consensus       161 ~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~  240 (452)
T 3e4b_A          161 LDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALL  240 (452)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHH
Confidence            55566666655544444555444444332        444444332   23344334455555433    5777788777


Q ss_pred             HHHHhcCCCCCHHHHHHHHHH-H--hccCChhhHHHHHHh------------------hC-----ChHHHHHHHhhcCCC
Q 044412          221 NKTKKSGTGSDQVTMATVLSA-C--AHLGALDLGRGIQIY------------------CR-----SLGRSLLVFFKLREK  274 (311)
Q Consensus       221 ~~m~~~g~~p~~~t~~~li~a-~--~~~~~~~~a~~~~~~------------------~~-----~~~~a~~~~~~~~~p  274 (311)
                      ++.. .|   +...+..|-.. +  ...++.++|...++.                  .|     +.++|...|++-..-
T Consensus       241 ~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~g  316 (452)
T 3e4b_A          241 EKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYYEGKWVPADAKAAEAHFEKAVGR  316 (452)
T ss_dssp             HHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHTTTTT
T ss_pred             HHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHhCC
Confidence            7766 33   22333333332 2  346777777777776                  33     777788888777722


Q ss_pred             CchhHHHHHHHHHh----cCChHHHHHHHHHHHHcCC
Q 044412          275 NLLCWNSITEALAI----HGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       275 ~~~~~~~li~~~~~----~g~~~~a~~~~~~M~~~g~  307 (311)
                      +...+..|-..|..    ..+.++|..+|++-.+.|.
T Consensus       317 ~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  353 (452)
T 3e4b_A          317 EVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ  353 (452)
T ss_dssp             CHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC
T ss_pred             CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh
Confidence            34455555555544    3378888888888766553

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.83  E-value=0.00032  Score=58.62  Aligned_cols=171  Identities=10%  Similarity=0.019  Sum_probs=115.1

Q ss_pred             HHHHHHHHHhhccCChhHHHHhcccCCC--CCee--------eeec---cccCCChhHHHHHHHHHHHCCCCchHHHHHH
Q 044412           61 LAKQFISFCTSRFHFIDYTILVFPQMQE--PNVF--------VYHA---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQV  127 (311)
Q Consensus        61 ~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~--------~~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  127 (311)
                      .+...+..+ ...|++++|.+.+++..+  +...        .+..   +...|++++|++.|++..+....        
T Consensus        77 ~l~~~~~~~-~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~--------  147 (293)
T 2qfc_A           77 QFKDQVIML-CKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLT--------  147 (293)
T ss_dssp             HHHHHHHHH-HHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCC--------
T ss_pred             HHHHHHHHH-HHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc--------
Confidence            344566777 889999999988865431  1110        0111   67788999999999887643210        


Q ss_pred             HHhcCCCc--hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC---cHhHHHH
Q 044412          128 WKNGFSSP--VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW---DIRSWTT  202 (311)
Q Consensus       128 ~~~g~~~~--~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~---~~~~y~~  202 (311)
                         ...+.  ..+|+.+-..|...|++++    |...++.                   |.++++..+..   ...+|+.
T Consensus       148 ---~~~~~~~~~~~~~lg~~y~~~~~~~~----A~~~~~k-------------------al~~~~~~~~~~~~~~~~~~n  201 (293)
T 2qfc_A          148 ---GIDVYQNLYIENAIANIYAENGYLKK----GIDLFEQ-------------------ILKQLEALHDNEEFDVKVRYN  201 (293)
T ss_dssp             ---SSCTTHHHHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHSCCCHHHHHHHHHH
T ss_pred             ---CCchHHHHHHHHHHHHHHHHcCCHHH----HHHHHHH-------------------HHHHHHhcCccccchHHHHHh
Confidence               01111  4588889999999999999    6666665                   33444444322   2358889


Q ss_pred             HHHHHHhCCChhHHHHHHHHHHhc----CCCCC-HHHHHHHHHHHhccCChhhH-HHHHHhhCChHHHHHHHhhcC
Q 044412          203 MITSYSQNKQFREALDAFNKTKKS----GTGSD-QVTMATVLSACAHLGALDLG-RGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       203 li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~a~~~~~~~~~a-~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      +-..|...|++++|+..+++..+.    +..+. ..+|..+-.++.+.|+.++| ...++      .|..+++...
T Consensus       202 lg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~------~Al~~~~~~~  271 (293)
T 2qfc_A          202 HAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYK------KASFFFDILE  271 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHH------HHHHHHHHTT
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHH------HHHHHHHHhC
Confidence            999999999999999999987642    22222 56788888999999999988 65442      4555554444

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=97.83  E-value=0.00089  Score=55.84  Aligned_cols=165  Identities=8%  Similarity=-0.002  Sum_probs=111.7

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCch----hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPV----FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA  172 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~----~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~  172 (311)
                      +...|++++|.+++++..+...             ..|+.    ..+..+...+...|++++|.......++.....   
T Consensus        85 ~~~~~~y~~a~~~~~~~l~~~~-------------~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~---  148 (293)
T 3u3w_A           85 LCKQKRYKEIYNKVWNELKKEE-------------YHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTG---  148 (293)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTCC-------------CCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCC---
T ss_pred             HHHHhhHHHHHHHHHHHhcccc-------------CChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhccc---
Confidence            5678899999999988765321             12231    234456667777889999444433333321111   


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCChhHHHHHHHHHHh----c-CCCCCH-HHHHHHHHHHhc
Q 044412          173 TWNTMIDAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQFREALDAFNKTKK----S-GTGSDQ-VTMATVLSACAH  244 (311)
Q Consensus       173 ~~~~li~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~----~-g~~p~~-~t~~~li~a~~~  244 (311)
                                          ..+  -..+|+.+-..|...|++++|+..|++..+    . +..|.. .+|..+-..|.+
T Consensus       149 --------------------~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~  208 (293)
T 3u3w_A          149 --------------------IDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYL  208 (293)
T ss_dssp             --------------------SCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHH
T ss_pred             --------------------ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHH
Confidence                                011  134688999999999999999999999874    1 222332 378888999999


Q ss_pred             cCChhhHHHHHHhhCChHHHHHHHhhcCC-CC-chhHHHHHHHHHhcCC-hHHHHHHHHHHH
Q 044412          245 LGALDLGRGIQIYCRSLGRSLLVFFKLRE-KN-LLCWNSITEALAIHGF-AHEALGMFDRMT  303 (311)
Q Consensus       245 ~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-p~-~~~~~~li~~~~~~g~-~~~a~~~~~~M~  303 (311)
                      .|++++|...++      .|.++..+... +. ..+|..+-..|.+.|+ +++|...+++..
T Consensus       209 ~~~y~~A~~~~~------~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          209 DSRYEESLYQVN------KAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             TTCHHHHHHHHH------HHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHH------HHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            999999988764      34444444432 22 4678889999999995 699999888764

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.79  E-value=0.00051  Score=59.57  Aligned_cols=169  Identities=11%  Similarity=0.068  Sum_probs=117.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCC-CchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFS-SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~-~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      +...|++++|++.|++..+....          .+-. ....++..+-..|...|+++.    |...+..          
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~----------~~~~~~~a~~~~~lg~~y~~~~~~~~----A~~~~~~----------  166 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPF----------VSDDIEKAEFHFKVAEAYYHMKQTHV----SMYHILQ----------  166 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGG----------CCCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHH----------
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhh----------CCChHHHHHHHHHHHHHHHHcCCcHH----HHHHHHH----------
Confidence            67889999999999987653100          0001 124577888889999999999    6665555          


Q ss_pred             HHHHHHHHHHHHHHhhCCCC---cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHhccCC
Q 044412          176 TMIDAYARLAELLFNKMPAW---DIRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGS-DQVTMATVLSACAHLGA  247 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~~---~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~~  247 (311)
                               |.+++......   ...+++.+-..|...|++++|++.|.+..+.    |-.+ ...++..+-..|...|+
T Consensus       167 ---------al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~  237 (378)
T 3q15_A          167 ---------ALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGD  237 (378)
T ss_dssp             ---------HHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             ---------HHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCC
Confidence                     44455544431   2456788888889999999999988886652    2111 23467777788888899


Q ss_pred             hhhHHHHHHhhCChHHHHHHHhhcCCCC-chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          248 LDLGRGIQIYCRSLGRSLLVFFKLREKN-LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       248 ~~~a~~~~~~~~~~~~a~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +++|...+.      .|..+++....|+ ..++..+-..|.+.|++++|..++++..+
T Consensus       238 ~~~A~~~~~------~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  289 (378)
T 3q15_A          238 DQMAVEHFQ------KAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLD  289 (378)
T ss_dssp             HHHHHHHHH------HHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH------HHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            998887764      3444444444332 45778888888999999999999888765

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.79  E-value=0.00062  Score=59.03  Aligned_cols=169  Identities=15%  Similarity=0.056  Sum_probs=122.7

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWN  175 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~  175 (311)
                      +...|++++|++.|++..+.-.          ..+-.+ ...+|..+-..|...|++++    |...+.+          
T Consensus       113 ~~~~g~~~~A~~~~~~al~~~~----------~~~~~~~~a~~~~~lg~~~~~~~~~~~----A~~~~~~----------  168 (383)
T 3ulq_A          113 ELDQREYLSAIKFFKKAESKLI----------FVKDRIEKAEFFFKMSESYYYMKQTYF----SMDYARQ----------  168 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGG----------GCCCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHH----------
T ss_pred             HHHhcCHHHHHHHHHHHHHHHh----------hCCCHHHHHHHHHHHHHHHHHcCCHHH----HHHHHHH----------
Confidence            6788999999999998765310          000111 24678888889999999999    6666665          


Q ss_pred             HHHHHHHHHHHHHHhhCCC--C-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHhccCC
Q 044412          176 TMIDAYARLAELLFNKMPA--W-DIRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGS-DQVTMATVLSACAHLGA  247 (311)
Q Consensus       176 ~li~~~~~~a~~~~~~m~~--~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~~  247 (311)
                               |.+++.....  + ...+++.+-..|...|++++|++.|.+..+.    +-.+ ...++..+-..|...|+
T Consensus       169 ---------al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~  239 (383)
T 3ulq_A          169 ---------AYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQ  239 (383)
T ss_dssp             ---------HHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             ---------HHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCC
Confidence                     4555555543  1 2457888889999999999999999987652    2111 12478888889999999


Q ss_pred             hhhHHHHHHhhCChHHHHHHHhhcCC-CC-chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          248 LDLGRGIQIYCRSLGRSLLVFFKLRE-KN-LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       248 ~~~a~~~~~~~~~~~~a~~~~~~~~~-p~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +++|...++      .|.++++.... |+ ..++..+-..|.+.|++++|...+++..+
T Consensus       240 ~~~A~~~~~------~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          240 YEDAIPYFK------RAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             HHHHHHHHH------HHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH------HHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999988764      45555555543 43 45788899999999999999999988653

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.76  E-value=0.00036  Score=57.03  Aligned_cols=153  Identities=9%  Similarity=0.039  Sum_probs=102.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc----hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP----VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA  172 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~----~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~  172 (311)
                      +.+.|++++|+..|++..+.                .|+    ...+..+-.+|.+.|++++|......+.+.-+.    
T Consensus        25 ~~~~g~~~~A~~~~~~~l~~----------------~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~----   84 (261)
T 3qky_A           25 FYNQGKYDRAIEYFKAVFTY----------------GRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQI----   84 (261)
T ss_dssp             HHHTTCHHHHHHHHHHHGGG----------------CSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----
T ss_pred             HHHhCCHHHHHHHHHHHHHh----------------CCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCC----
Confidence            56788999999999998764                233    567778888999999999944443333333221    


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHh--------CCChhHHHHHHHHHHhcCCCCCH-HHH-------
Q 044412          173 TWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQ--------NKQFREALDAFNKTKKSGTGSDQ-VTM-------  235 (311)
Q Consensus       173 ~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~--------~g~~~~a~~~~~~m~~~g~~p~~-~t~-------  235 (311)
                                           .| ....+..+-.++..        .|++++|+..|++..+.  .|+. ...       
T Consensus        85 ---------------------~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~~~  141 (261)
T 3qky_A           85 ---------------------DPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR--YPNHELVDDATQKIR  141 (261)
T ss_dssp             ---------------------CTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH--CTTCTTHHHHHHHHH
T ss_pred             ---------------------CchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH--CcCchhHHHHHHHHH
Confidence                                 11 23456666677777        89999999999998874  2432 222       


Q ss_pred             ----------HHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCC----chhHHHHHHHHHhc----------
Q 044412          236 ----------ATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN----LLCWNSITEALAIH----------  289 (311)
Q Consensus       236 ----------~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~----~~~~~~li~~~~~~----------  289 (311)
                                ..+-..+.+.|+++             .|...|++..  .|+    ...+..+..+|...          
T Consensus       142 ~~~~~~~~~~~~la~~~~~~g~~~-------------~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~  208 (261)
T 3qky_A          142 ELRAKLARKQYEAARLYERRELYE-------------AAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQP  208 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHH-------------HHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHH
T ss_pred             HHHHHHHHHHHHHHHHHHHccCHH-------------HHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhccc
Confidence                      23344555666666             4555554443  343    34677777788766          


Q ss_pred             CChHHHHHHHHHHHHc
Q 044412          290 GFAHEALGMFDRMTYE  305 (311)
Q Consensus       290 g~~~~a~~~~~~M~~~  305 (311)
                      |++++|...|++..+.
T Consensus       209 ~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          209 ERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHH
Confidence            8899999999998763

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.76  E-value=0.00063  Score=50.97  Aligned_cols=98  Identities=6%  Similarity=-0.086  Sum_probs=77.4

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-  274 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-  274 (311)
                      +...+..+-..+.+.|++++|+..|++..+.. +-+...|..+-.++...|++++|...|+.      |.++     .| 
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~------al~l-----~P~  102 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAV------AFAL-----GKN  102 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----SSS
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHH------HHhh-----CCC
Confidence            45577788888999999999999999998752 33577888888899999999866655432      2221     34 


Q ss_pred             CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          275 NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       275 ~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      +...|..+-.+|...|++++|...|++..+.
T Consensus       103 ~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          103 DYTPVFHTGQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5778999999999999999999999998764

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.75  E-value=0.00055  Score=57.11  Aligned_cols=83  Identities=10%  Similarity=0.055  Sum_probs=57.0

Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCC---chhHHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN---LLCWNS  281 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~---~~~~~~  281 (311)
                      +...++.++|+..|++..+.. +.+...+..+-.++...|++++|...+             .+..  .|+   ...+..
T Consensus       195 l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l-------------~~~l~~~p~~~~~~a~~~  260 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELL-------------FGHLRXDLTAADGQTRXT  260 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH-------------HHHHHHCTTGGGGHHHHH
T ss_pred             HHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHH-------------HHHHhcccccccchHHHH
Confidence            555677777888887776642 334667777777788878777555444             3322  243   557888


Q ss_pred             HHHHHHhcCChHHHHHHHHHHH
Q 044412          282 ITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       282 li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      +...+...|+.++|...+++-.
T Consensus       261 l~~~~~~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          261 FQEILAALGTGDALASXYRRQL  282 (287)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHH
Confidence            8888888999888888777644

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=97.74  E-value=0.0015  Score=54.46  Aligned_cols=165  Identities=8%  Similarity=-0.028  Sum_probs=115.6

Q ss_pred             HHHHHhhccCChhHHHHhcccCCCCCe-----e----eee-c---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhc
Q 044412           65 FISFCTSRFHFIDYTILVFPQMQEPNV-----F----VYH-A---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNG  131 (311)
Q Consensus        65 ll~~~~~~~g~~~~a~~~~~~m~~~~~-----~----~~~-~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g  131 (311)
                      .+..+ .+.|++++|.+++++..+...     .    .+. .   +...+++++|++.|++..+...             
T Consensus        81 ~i~~~-~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~-------------  146 (293)
T 3u3w_A           81 QVIML-CKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQL-------------  146 (293)
T ss_dssp             HHHHH-HHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCC-------------
T ss_pred             HHHHH-HHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhc-------------
Confidence            35667 889999999999988643111     1    111 1   6677899999999999876321             


Q ss_pred             CCCc----hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCC--C-cHhHHHHHH
Q 044412          132 FSSP----VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPA--W-DIRSWTTMI  204 (311)
Q Consensus       132 ~~~~----~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~--~-~~~~y~~li  204 (311)
                      -.++    ..+|+.+-..|...|++++    |...++.                   |.++++..+.  + ...+|+.+-
T Consensus       147 ~~~~~~~~~~~~~~lg~~y~~~g~~~~----A~~~~~~-------------------al~~~~~~~~~~~~~~~~~~nlg  203 (293)
T 3u3w_A          147 TGIDVYQNLYIENAIANIYAENGYLKK----GIDLFEQ-------------------ILKQLEALHDNEEFDVKVRYNHA  203 (293)
T ss_dssp             CCSCTTHHHHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHSSCCHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHHHHcCCHHH----HHHHHHH-------------------HHHHHHhcccchhHHHHHHHHHH
Confidence            1222    3368999999999999999    6666665                   3344444421  1 234788999


Q ss_pred             HHHHhCCChhHHHHHHHHHHh----cCCCCC-HHHHHHHHHHHhccCC-hhhHHHHHHhhCChHHHHHHHhhcC
Q 044412          205 TSYSQNKQFREALDAFNKTKK----SGTGSD-QVTMATVLSACAHLGA-LDLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~----~g~~p~-~~t~~~li~a~~~~~~-~~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      ..|.+.|++++|+..+++..+    .+..+. ..+|..+-.++.+.|+ .++|...++      .|..+++...
T Consensus       204 ~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~------~Al~i~~~~~  271 (293)
T 3u3w_A          204 KALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYK------KASFFFDILE  271 (293)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHH------HHHHHHHHTT
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHH------HHHHHHHHhC
Confidence            999999999999999998654    333333 5678888888999995 588877653      4555555544

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=97.66  E-value=0.0011  Score=52.89  Aligned_cols=106  Identities=11%  Similarity=-0.030  Sum_probs=70.0

Q ss_pred             HHHHHhhCC---C-CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCChhhHHHHHHhhC
Q 044412          185 AELLFNKMP---A-WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGALDLGRGIQIYCR  259 (311)
Q Consensus       185 a~~~~~~m~---~-~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~  259 (311)
                      |.+.|++..   . ++...|..+-.++...|++++|++.|++..+.  .|+ ...|..+-..+...|++++|...+    
T Consensus        26 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~----   99 (228)
T 4i17_A           26 AFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKSAAYRDMKNNQEYIATL----   99 (228)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHHHHHHHTTCHHHHHHHH----
T ss_pred             HHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHcccHHHHHHHH----
Confidence            555555432   1 45556666667777777777777777777653  343 445666667777777777555544    


Q ss_pred             ChHHHHHHHhhcC--CCC-c-------hhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          260 SLGRSLLVFFKLR--EKN-L-------LCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       260 ~~~~a~~~~~~~~--~p~-~-------~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                               ++..  .|+ .       ..|..+-..+...|++++|...|++..+.
T Consensus       100 ---------~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~  146 (228)
T 4i17_A          100 ---------TEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV  146 (228)
T ss_dssp             ---------HHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS
T ss_pred             ---------HHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc
Confidence                     3332  233 3       45777788888999999999999998753

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.63  E-value=0.00033  Score=58.88  Aligned_cols=165  Identities=6%  Similarity=-0.055  Sum_probs=104.2

Q ss_pred             HHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCe-----eeeec----cccCCChhHHHHHHHHH
Q 044412           43 LECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNV-----FVYHA----FSSLRHPLQAIAFYLYM  113 (311)
Q Consensus        43 ~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~-----~~~~~----~~~~~~~~~a~~~~~~m  113 (311)
                      +...++..++.+ .++..+...+-.++ ...|++++|++++.+-..++.     ..+-.    +.+.|+.+.|.+.++.|
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~-~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~  162 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQ-AILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNY  162 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHH-HHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            444555555554 45666666777888 889999999999988633321     11111    89999999999999999


Q ss_pred             HHCCCCchHHHHHHHHhcCCC-----chhHHHHHHHHHHh----CCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH
Q 044412          114 LRAEVLLTTVHGQVWKNGFSS-----PVFVQTAMVDNYSY----SNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL  184 (311)
Q Consensus       114 ~~~~~~p~~~~~~~~~~g~~~-----~~~~~~~ll~~~~~----~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~  184 (311)
                      .+                ..|     +..+..-|..++..    .++..+    |..+|+++.+.               
T Consensus       163 ~~----------------~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~----A~~~f~El~~~---------------  207 (310)
T 3mv2_B          163 TN----------------AIEDTVSGDNEMILNLAESYIKFATNKETATS----NFYYYEELSQT---------------  207 (310)
T ss_dssp             HH----------------HSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTH----HHHHHHHHHTT---------------
T ss_pred             Hh----------------cCccccccchHHHHHHHHHHHHHHhCCccHHH----HHHHHHHHHHh---------------
Confidence            76                356     24555555555322    347888    66666664321               


Q ss_pred             HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc-----CC----CCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          185 AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKS-----GT----GSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       185 a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-----g~----~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                               .|+..+-..++.++.+.|++++|.+.++.+.+.     +-    +-|+.+...+|......|+  .|.+++
T Consensus       208 ---------~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~  276 (310)
T 3mv2_B          208 ---------FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLT  276 (310)
T ss_dssp             ---------SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHH
T ss_pred             ---------CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHH
Confidence                     233223334444788889999999999977653     11    3356666455555555565  444443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.62  E-value=0.00082  Score=49.65  Aligned_cols=140  Identities=10%  Similarity=0.064  Sum_probs=98.0

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhCCCh
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQNKQF  213 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~g~~  213 (311)
                      ..++..+-..|...|++++    |...+.+                   +.++......+.  ..++..+-..+...|++
T Consensus         9 ~~~~~~l~~~~~~~~~~~~----A~~~~~~-------------------al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~   65 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRD----AVIAHEQ-------------------RLLIAKEFGDKAAERIAYSNLGNAYIFLGEF   65 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHHTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhcCHHH----HHHHHHH-------------------HHHHHHHhCCchHHHHHHHHHHHHHHHcCCH
Confidence            3467778888999999999    5555554                   222332222221  24688888899999999


Q ss_pred             hHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHHH
Q 044412          214 REALDAFNKTKKS----GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEAL  286 (311)
Q Consensus       214 ~~a~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~~  286 (311)
                      ++|.+.+++..+.    +-.+ ....+..+-..+...|++++|...++.      +.++......+  ....+..+-..+
T Consensus        66 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~------a~~~~~~~~~~~~~~~~~~~la~~~  139 (164)
T 3ro3_A           66 ETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLK------HLAIAQELKDRIGEGRACWSLGNAY  139 (164)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHH------HHHHHHHccchHhHHHHHHHHHHHH
Confidence            9999999997652    1111 145677778888899999988887643      44444333322  235688888999


Q ss_pred             HhcCChHHHHHHHHHHHH
Q 044412          287 AIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       287 ~~~g~~~~a~~~~~~M~~  304 (311)
                      ...|++++|...+++..+
T Consensus       140 ~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          140 TALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHTCHHHHHHHHHHHHH
T ss_pred             HHccCHHHHHHHHHHHHH
Confidence            999999999999998764

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=97.61  E-value=0.00037  Score=54.81  Aligned_cols=138  Identities=7%  Similarity=0.029  Sum_probs=93.4

Q ss_pred             HHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchh
Q 044412           62 AKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVF  137 (311)
Q Consensus        62 ~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~  137 (311)
                      +..+-..+ .+.|++++|...|++..+++...|..    +.+.|++++|++.|++..+.               .+.+..
T Consensus         9 ~~~~g~~~-~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~---------------~~~~~~   72 (213)
T 1hh8_A            9 LWNEGVLA-ADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINR---------------DKHLAV   72 (213)
T ss_dssp             HHHHHHHH-HHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------CTTCHH
T ss_pred             HHHHHHHH-HHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------------CccchH
Confidence            34445566 78899999999998887665544433    77889999999999887653               244577


Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHH
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREA  216 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a  216 (311)
                      .|..+-.+|...|++++|.....+.++..+......|..            ...-..| +...|..+-..|...|++++|
T Consensus        73 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  140 (213)
T 1hh8_A           73 AYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKI------------LGLQFKLFACEVLYNIAFMYAKKEEWKKA  140 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGG------------GTBCCEEEHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHH------------hccccCccchHHHHHHHHHHHHccCHHHH
Confidence            888999999999999995444444444322211000000            0000011 346788889999999999999


Q ss_pred             HHHHHHHHhcC
Q 044412          217 LDAFNKTKKSG  227 (311)
Q Consensus       217 ~~~~~~m~~~g  227 (311)
                      .+.|++..+..
T Consensus       141 ~~~~~~al~~~  151 (213)
T 1hh8_A          141 EEQLALATSMK  151 (213)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHHcC
Confidence            99999988753

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.60  E-value=0.0009  Score=48.29  Aligned_cols=101  Identities=10%  Similarity=0.066  Sum_probs=79.0

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCc
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNL  276 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~  276 (311)
                      ...|...-..|.+.|++++|++.|++..+.. +-+...|..+-.++.+.|++++|...++.      |.++    ...+.
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~------al~~----~p~~~   81 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDT------CIRL----DSKFI   81 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH----CTTCH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHH------HHHh----hhhhh
Confidence            3467777888999999999999999988752 34677888899999999999977665533      2221    13456


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      ..|..+-.+|...|++++|...|++..+  +.|+
T Consensus        82 ~a~~~lg~~~~~~~~~~~A~~~~~~al~--l~P~  113 (126)
T 4gco_A           82 KGYIRKAACLVAMREWSKAQRAYEDALQ--VDPS  113 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTT
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH--HCcC
Confidence            7899999999999999999999999876  3454

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=97.57  E-value=0.00022  Score=65.56  Aligned_cols=145  Identities=3%  Similarity=-0.150  Sum_probs=73.0

Q ss_pred             cChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccCCChhHHHHHH
Q 044412           38 SSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLRHPLQAIAFY  110 (311)
Q Consensus        38 ~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~~~~~a~~~~  110 (311)
                      |+.+++...++...+.. +-+...+..+-..+ .+.|++++|.+.|++..+  |+ ...+..    +...|++++|++.|
T Consensus         3 g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~-~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            3 ADGPRELLQLRAAVRHR-PQDFVAWLMLADAE-LGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             -------------------CCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            34455555555554432 12345666666666 667777777777666532  22 222222    56666777777776


Q ss_pred             HHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHh
Q 044412          111 LYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFN  190 (311)
Q Consensus       111 ~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~  190 (311)
                      ++..+..               +-+...+..+-.+|.+.|++++    |...+++..+.                     
T Consensus        81 ~~al~~~---------------p~~~~~~~~la~~~~~~g~~~~----A~~~~~~al~~---------------------  120 (568)
T 2vsy_A           81 QQASDAA---------------PEHPGIALWLGHALEDAGQAEA----AAAAYTRAHQL---------------------  120 (568)
T ss_dssp             HHHHHHC---------------TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH---------------------
T ss_pred             HHHHhcC---------------CCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh---------------------
Confidence            6655421               2335566666666777777777    44443331110                     


Q ss_pred             hCCCCcHhHHHHHHHHHHhC---CChhHHHHHHHHHHhc
Q 044412          191 KMPAWDIRSWTTMITSYSQN---KQFREALDAFNKTKKS  226 (311)
Q Consensus       191 ~m~~~~~~~y~~li~~~~~~---g~~~~a~~~~~~m~~~  226 (311)
                        ...+...+..+...+...   |+.++|.+.+++..+.
T Consensus       121 --~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A          121 --LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             --CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             --CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence              112455666777777777   7777777777777664

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.57  E-value=0.00018  Score=56.05  Aligned_cols=98  Identities=10%  Similarity=-0.037  Sum_probs=70.0

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCC-CC--cHhHHHHHHHHHHhCCC
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMP-AW--DIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~-~~--~~~~y~~li~~~~~~g~  212 (311)
                      ..++..+-..|...|++++    |...+++                   +.++++... .+  ....++.+-..+...|+
T Consensus        66 ~~~~~~l~~~~~~~g~~~~----A~~~~~~-------------------al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~  122 (203)
T 3gw4_A           66 HRALHQVGMVERMAGNWDA----ARRCFLE-------------------ERELLASLPEDPLAASANAYEVATVALHFGD  122 (203)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHSCCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHH-------------------HHHHHHHcCccHHHHHHHHHHHHHHHHHhCC
Confidence            5677888889999999999    6666665                   444555444 22  24467888888999999


Q ss_pred             hhHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          213 FREALDAFNKTKKS----GTGS-DQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       213 ~~~a~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +++|.+.+++..+.    +-.+ -..++..+-..+...|++++|...++
T Consensus       123 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  171 (203)
T 3gw4_A          123 LAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWL  171 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            99999999987642    2111 12346777788888999998876653

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.56  E-value=0.0041  Score=51.73  Aligned_cols=169  Identities=8%  Similarity=-0.029  Sum_probs=110.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|++.+++..+..-.....         ......+..+...|...|++++|.....+.++.....       
T Consensus        85 ~~~~~~y~~A~~~~~~~l~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~-------  148 (293)
T 2qfc_A           85 LCKQKRYKEIYNKVWNELKKEEYHPEF---------QQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTG-------  148 (293)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTCCCCHHH---------HHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCS-------
T ss_pred             HHHhhhHHHHHHHHHHHhccccCChhH---------HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcC-------
Confidence            457889999999998876542100000         0011223445566788899999444433333322211       


Q ss_pred             HHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhCCChhHHHHHHHHHHhc-CCCCC-----HHHHHHHHHHHhccCCh
Q 044412          177 MIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQNKQFREALDAFNKTKKS-GTGSD-----QVTMATVLSACAHLGAL  248 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~-----~~t~~~li~a~~~~~~~  248 (311)
                                      ..+.  ..+|+.+-..|...|++++|+..|++..+. ...|+     ..+|..+-..|...|++
T Consensus       149 ----------------~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y  212 (293)
T 2qfc_A          149 ----------------IDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRY  212 (293)
T ss_dssp             ----------------SCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             ----------------CchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhH
Confidence                            1111  457889999999999999999999998631 11222     25888899999999999


Q ss_pred             hhHHHHHHhhCChHHHHHHHhhcCCCC--chhHHHHHHHHHhcCChHHH-HHHHHHHH
Q 044412          249 DLGRGIQIYCRSLGRSLLVFFKLREKN--LLCWNSITEALAIHGFAHEA-LGMFDRMT  303 (311)
Q Consensus       249 ~~a~~~~~~~~~~~~a~~~~~~~~~p~--~~~~~~li~~~~~~g~~~~a-~~~~~~M~  303 (311)
                      ++|...++.      |.++......+.  ..+|..+-..|.+.|+.++| ...+++..
T Consensus       213 ~~Al~~~~k------al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          213 EESLYQVNK------AIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHH------HHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH------HHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            999887743      333333322111  45788889999999999999 77777653

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.56  E-value=0.0006  Score=50.98  Aligned_cols=129  Identities=7%  Similarity=-0.019  Sum_probs=90.2

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ...+..+-..+...|++++    |...++.....                       ...+..+|..+...+...|++++
T Consensus        13 ~~~~~~~a~~~~~~~~~~~----A~~~~~~al~~-----------------------~~~~~~~~~~~a~~~~~~~~~~~   65 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYEN----AIKFYSQAIEL-----------------------NPSNAIYYGNRSLAYLRTECYGY   65 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------STTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHccCHHH----HHHHHHHHHHh-----------------------CCCChHHHHHHHHHHHHcCCHHH
Confidence            3456777788899999999    55555442110                       12256778888899999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHH--HHHHHhcCCh
Q 044412          216 ALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSI--TEALAIHGFA  292 (311)
Q Consensus       216 a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~l--i~~~~~~g~~  292 (311)
                      |+..+.+..+.. +.+...|..+-.++...|++++|...++..      .+.     .| +...+..+  ...+...|++
T Consensus        66 A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a------~~~-----~p~~~~~~~~~~~~~~~~~~~~~  133 (166)
T 1a17_A           66 ALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETV------VKV-----KPHDKDAKMKYQECNKIVKQKAF  133 (166)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH-----STTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHH------HHh-----CCCCHHHHHHHHHHHHHHHHHHH
Confidence            999999988753 345678888888899999998776665331      111     23 33444333  3447788999


Q ss_pred             HHHHHHHHHHH
Q 044412          293 HEALGMFDRMT  303 (311)
Q Consensus       293 ~~a~~~~~~M~  303 (311)
                      ++|...+.+..
T Consensus       134 ~~A~~~~~~~~  144 (166)
T 1a17_A          134 ERAIAGDEHKR  144 (166)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHcccchH
Confidence            99999888764

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.55  E-value=0.00048  Score=48.53  Aligned_cols=93  Identities=12%  Similarity=0.154  Sum_probs=71.3

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ...|..+...|...|++++    |...++.....                       ...+..+|..+...+...|++++
T Consensus         9 ~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~-----------------------~~~~~~~~~~la~~~~~~~~~~~   61 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDE----AIEYYQKALEL-----------------------DPNNAEAWYNLGNAYYKQGDYDE   61 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHHHHHH-----------------------CcCcHHHHHHHHHHHHHhCCHHH
Confidence            5678888899999999999    55555542210                       11256778888999999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          216 ALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       216 a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      |+.+|+++.+.. +.+..++..+...+...|+++.|...++
T Consensus        62 A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~  101 (125)
T 1na0_A           62 AIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQ  101 (125)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            999999998753 4467788889999999999887766553

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.55  E-value=0.00025  Score=66.91  Aligned_cols=168  Identities=10%  Similarity=-0.036  Sum_probs=81.1

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcC-CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--C-CHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGF-SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--R-KFA  172 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~-~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~-~~~  172 (311)
                      -...|++++|++.|++..+....        ..... +.+...+..+-.+|...|++++    |...+++..+  | +..
T Consensus       401 a~~~~~~~~A~~~~~~al~~~~~--------~~~~~~p~~~~~~~~~a~~~~~~g~~~~----A~~~~~~al~~~p~~~~  468 (681)
T 2pzi_A          401 ATVLSQPVQTLDSLRAARHGALD--------ADGVDFSESVELPLMEVRALLDLGDVAK----ATRKLDDLAERVGWRWR  468 (681)
T ss_dssp             HTTTCCHHHHHHHHHHHHTC---------------CCTTCSHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHHCCCHH
T ss_pred             cccccCHHHHHHHHHHhhhhccc--------ccccccccchhHHHHHHHHHHhcCCHHH----HHHHHHHHhccCcchHH
Confidence            46788999999999988621000        00002 3456778888889999999999    5555554332  1 222


Q ss_pred             HHHHHHHHHHHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc
Q 044412          173 TWNTMIDAYARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       173 ~~~~li~~~~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~  244 (311)
                      .|..+-..|...     |.+.|++..  .| +...|..+-..+...|++++ ++.|++..+.. +-+...|..+-.++.+
T Consensus       469 a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~  546 (681)
T 2pzi_A          469 LVWYRAVAELLTGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSA  546 (681)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHH
Confidence            333333333332     444443332  12 23344444444444455555 44444444321 1123344444444444


Q ss_pred             cCChhhHHHHHHhhCChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCC
Q 044412          245 LGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGF  291 (311)
Q Consensus       245 ~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~  291 (311)
                      .|+++             +|...|++..  .|+ ...|..+..++...|+
T Consensus       547 ~g~~~-------------~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          547 EGDRV-------------GAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             TTCHH-------------HHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             cCCHH-------------HHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            44444             4444444444  232 3345555555555444

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.55  E-value=0.0012  Score=47.10  Aligned_cols=99  Identities=9%  Similarity=0.014  Sum_probs=78.1

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +...|..+...+...|++++|++.|++..+.. +.+...+..+-..+...|++++|...++.      +.+.    ...+
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~------a~~~----~~~~   83 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEE------CIQL----EPTF   83 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHH------HHHH----CTTC
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHH------HHHh----CCCc
Confidence            56778889999999999999999999988642 33677888888999999999977666533      2111    1235


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ...|..+-..+...|++++|...|++..+.
T Consensus        84 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           84 IKGYTRKAAALEAMKDYTKAMDVYQKALDL  113 (133)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            678889999999999999999999987653

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.53  E-value=0.00094  Score=55.67  Aligned_cols=155  Identities=7%  Similarity=-0.105  Sum_probs=111.7

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeeeeec-----cccC
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFVYHA-----FSSL  100 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~-----~~~~  100 (311)
                      ......+...|+...+...++...+..- -+...+..+...+ .+.|++++|...+++...  |+......     +...
T Consensus       121 ~~~a~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~la~~~-~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~  198 (287)
T 3qou_A          121 AQQAMQLMQESNYTDALPLLXDAWQLSN-QNGEIGLLLAETL-IALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIELLXQ  198 (287)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHTT-SCHHHHHHHHHHH-HHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHhCC-cchhHHHHHHHHH-HHCCCHHHHHHHHHhCchhhcchHHHHHHHHHHHHhh
Confidence            3555666778899999888888877642 2556777888888 999999999999999864  43322211     5566


Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA  180 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~  180 (311)
                      ++.++|+..|++....               -+.+...+..+-..|...|++++|.....+++..-+.            
T Consensus       199 ~~~~~a~~~l~~al~~---------------~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~------------  251 (287)
T 3qou_A          199 AADTPEIQQLQQQVAE---------------NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLT------------  251 (287)
T ss_dssp             HTSCHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------------
T ss_pred             cccCccHHHHHHHHhc---------------CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccc------------
Confidence            7777788888777654               2445778888999999999999944444444333111            


Q ss_pred             HHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHH
Q 044412          181 YARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTK  224 (311)
Q Consensus       181 ~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~  224 (311)
                                   ..+...+..+...|...|+.++|...|++-.
T Consensus       252 -------------~~~~~a~~~l~~~~~~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          252 -------------AADGQTRXTFQEILAALGTGDALASXYRRQL  282 (287)
T ss_dssp             -------------GGGGHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             -------------cccchHHHHHHHHHHHcCCCCcHHHHHHHHH
Confidence                         1236678899999999999999998888754

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.52  E-value=0.00064  Score=64.07  Aligned_cols=167  Identities=7%  Similarity=-0.101  Sum_probs=122.5

Q ss_pred             hhccChhhHHHHHHHHHH-------hccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC--CC-eeeeec----cccC
Q 044412           35 KKCSSIKELECVYATIVK-------TNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSL  100 (311)
Q Consensus        35 ~~~~~~~~~~~l~~~m~~-------~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~  100 (311)
                      ...++.+++.+.++...+       ..-+.+...+..+-..+ .+.|++++|.+.|++..+  |+ ...|..    +...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~-~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRAL-LDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHH-HhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHc
Confidence            566778888888877761       11234556788888888 999999999999988763  33 333332    7888


Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA  180 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~  180 (311)
                      |++++|++.|++..+..               +-+...|..+-.+|.+.|++++ .....+.++.-+             
T Consensus       481 g~~~~A~~~~~~al~l~---------------P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P-------------  531 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTF---------------PGELAPKLALAATAELAGNTDE-HKFYQTVWSTND-------------  531 (681)
T ss_dssp             TCHHHHHHHHHHHHHHS---------------TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCT-------------
T ss_pred             CCHHHHHHHHHHHHHhC---------------CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCC-------------
Confidence            99999999999986631               3356788888889999999998 877777665421             


Q ss_pred             HHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHHHhccCC
Q 044412          181 YARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSACAHLGA  247 (311)
Q Consensus       181 ~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a~~~~~~  247 (311)
                                    .+...|..+-..+.+.|++++|++.|++..+  +.|+ ...+..+..++...++
T Consensus       532 --------------~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~--l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          532 --------------GVISAAFGLARARSAEGDRVGAVRTLDEVPP--TSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             --------------TCHHHHHHHHHHHHHTTCHHHHHHHHHTSCT--TSTTHHHHHHHHHHHTC----
T ss_pred             --------------chHHHHHHHHHHHHHcCCHHHHHHHHHhhcc--cCcccHHHHHHHHHHHHccCC
Confidence                          2567888999999999999999999998876  4576 4567777777766555

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.51  E-value=0.0015  Score=54.99  Aligned_cols=59  Identities=10%  Similarity=-0.014  Sum_probs=31.2

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCCC-HHHHHHHHHHHhccCChhhHHHHHH
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKS----GTGSD-QVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      .+|+.+-..|...|++++|+..|++..+.    +..+. ..++..+..++...|+++.|...++
T Consensus       156 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~  219 (307)
T 2ifu_A          156 ELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVR  219 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            35566666666666666666666665541    11111 1244444455555566665555443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.46  E-value=0.0015  Score=45.02  Aligned_cols=100  Identities=18%  Similarity=0.109  Sum_probs=77.8

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-  274 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-  274 (311)
                      +...|..+-..+...|++++|...|++..+.. +.+...+..+-.++...|++++|...++..      .+.    ... 
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a------~~~----~~~~   73 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYV------INV----IEDE   73 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHT----SCCT
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHH------HHh----Cccc
Confidence            45567778888999999999999999988753 345678888888899999998776655321      111    122 


Q ss_pred             -CchhHHHHHHHHHhc-CChHHHHHHHHHHHHcC
Q 044412          275 -NLLCWNSITEALAIH-GFAHEALGMFDRMTYEN  306 (311)
Q Consensus       275 -~~~~~~~li~~~~~~-g~~~~a~~~~~~M~~~g  306 (311)
                       +...|..+...+... |++++|.+.+++.....
T Consensus        74 ~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           74 YNKDVWAAKADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             TCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             chHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhcc
Confidence             567889999999999 99999999999988754

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.46  E-value=0.0051  Score=48.99  Aligned_cols=95  Identities=9%  Similarity=-0.055  Sum_probs=56.2

Q ss_pred             CCChhHHHHHHHHHHhcCCCCCHH-HHHHHH---HHHhccCChh-hHHHHHHhhCChHHHHHHHhhcC--CCCc----hh
Q 044412          210 NKQFREALDAFNKTKKSGTGSDQV-TMATVL---SACAHLGALD-LGRGIQIYCRSLGRSLLVFFKLR--EKNL----LC  278 (311)
Q Consensus       210 ~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li---~a~~~~~~~~-~a~~~~~~~~~~~~a~~~~~~~~--~p~~----~~  278 (311)
                      .|++++|+..|++..+.  -|+.. .+.+..   ......+..+ ..-.++...|+...|...|+++.  .|+.    ..
T Consensus       109 ~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  186 (225)
T 2yhc_A          109 PQQARAAFSDFSKLVRG--YPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDA  186 (225)
T ss_dssp             CHHHHHHHHHHHHHHTT--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHH
Confidence            46888999999988764  34432 111110   0000000000 00012222555566766666655  3543    46


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 044412          279 WNSITEALAIHGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       279 ~~~li~~~~~~g~~~~a~~~~~~M~~~g  306 (311)
                      +..+..+|.+.|+.++|...++.+...+
T Consensus       187 ~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          187 LPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            8889999999999999999999888753

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.45  E-value=0.0019  Score=44.83  Aligned_cols=99  Identities=11%  Similarity=0.028  Sum_probs=76.6

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +...|..+...+...|++++|...|++..+.. +.+...+..+-..+...|+++.|...++..      .+.    ...+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~------~~~----~~~~   71 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKT------VDL----KPDW   71 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH------HHH----CTTC
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHH------HHh----Cccc
Confidence            34567788888999999999999999988752 336778888888888989998776655331      111    1235


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ...|..+...+...|++++|...+++..+.
T Consensus        72 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           72 GKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence            678889999999999999999999988753

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.45  E-value=0.0018  Score=48.11  Aligned_cols=98  Identities=13%  Similarity=0.005  Sum_probs=74.6

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +...+..+-..+...|++++|+..|++..+.. +.+...|..+-.++...|++++|...++..      ..+    ...+
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a------l~l----~p~~   88 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYG------AVM----DIXE   88 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH----STTC
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHH------Hhc----CCCC
Confidence            45567777888889999999999999987742 336777888888888989888666655332      111    1235


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ...|..+-.+|...|++++|...|++..+
T Consensus        89 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           89 PRFPFHAAECLLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             THHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            67888889999999999999999988765

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.44  E-value=0.0019  Score=45.78  Aligned_cols=101  Identities=13%  Similarity=0.159  Sum_probs=78.3

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC-
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN-  275 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~-  275 (311)
                      ...|..+...+...|++++|...|.+..+.. +.+...+..+...+...|+++.|...++..-....      .- .++ 
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~------~~-~~~~   75 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR------EN-REDY   75 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH------HS-TTCH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc------cc-chhH
Confidence            3567788888999999999999999988753 44677888888999999999988777644222111      10 122 


Q ss_pred             ---chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 ---LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ---~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                         ..+|..+...+...|++++|...|++..+.
T Consensus        76 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           76 RQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence               667888999999999999999999998764

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=97.44  E-value=0.00087  Score=51.26  Aligned_cols=146  Identities=10%  Similarity=0.102  Sum_probs=92.2

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCC--C-CHhHHHHHHHHHHHH-----HHHHHhhCCC--CcHhHHHHHHHH--
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPE--R-KFATWNTMIDAYARL-----AELLFNKMPA--WDIRSWTTMITS--  206 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~-----a~~~~~~m~~--~~~~~y~~li~~--  206 (311)
                      +..+-..+.+.|++++    |...+++..+  | +...+..+-..+...     |...|++...  |+...+ .+...  
T Consensus         9 ~~~~a~~~~~~g~~~~----A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~~-~~~~~~~   83 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQ----ALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYK-SLIAKLE   83 (176)
T ss_dssp             HHHHHHHHHHTTCHHH----HHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHcCCHHH----HHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHHH-HHHHHHH
Confidence            4455667889999999    8888887765  2 344555555555544     7777777653  333222 22111  


Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCC---chhHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN---LLCWN  280 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~---~~~~~  280 (311)
                      +...+...+|+..|++..+.  .| +...+..+-.++...|++++|..             .|++..  .|+   ...+.
T Consensus        84 ~~~~~~~~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~-------------~~~~~l~~~p~~~~~~a~~  148 (176)
T 2r5s_A           84 LHQQAAESPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALE-------------LLWNILKVNLGAQDGEVKK  148 (176)
T ss_dssp             HHHHHTSCHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHH-------------HHHHHHTTCTTTTTTHHHH
T ss_pred             HHhhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHH-------------HHHHHHHhCcccChHHHHH
Confidence            11222334567777776653  34 35667777777777777775544             444333  333   45788


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHH
Q 044412          281 SITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       281 ~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+...+...|+.++|...|++...
T Consensus       149 ~l~~~~~~~g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          149 TFMDILSALGQGNAIASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcHHHHHHHHHH
Confidence            999999999999999998887654

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.44  E-value=0.0024  Score=46.08  Aligned_cols=99  Identities=7%  Similarity=-0.043  Sum_probs=77.8

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK  274 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p  274 (311)
                      .+...|..+-..+...|++++|+..|.+..+.. +.+...|..+-.++...|+++.|...++.      +.++    ...
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~------al~~----~p~   75 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRR------ALEL----DGQ   75 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH----CTT
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHH------HHHh----Cch
Confidence            467788888899999999999999999987753 33577888888889999999977665533      2111    123


Q ss_pred             CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          275 NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       275 ~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +...|..+-..+...|++++|...|++..+
T Consensus        76 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           76 SVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            567889999999999999999999998764

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.43  E-value=0.0014  Score=46.82  Aligned_cols=96  Identities=8%  Similarity=0.065  Sum_probs=73.0

Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~  212 (311)
                      ..+...+..+-..+.+.|++++    |...++.....                       ...+...|..+...+...|+
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~al~~-----------------------~~~~~~~~~~la~~~~~~~~   65 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQ----AMKHYTEAIKR-----------------------NPKDAKLYSNRAACYTKLLE   65 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHH----HHHHHHHHHTT-----------------------CTTCHHHHHHHHHHHTTTTC
T ss_pred             cccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHc-----------------------CCCcHHHHHHHHHHHHHhcc
Confidence            4456778888889999999999    55555542221                       12256778888889999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +++|+..+++..+.. +.+...+..+-.++...|++++|...++
T Consensus        66 ~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~  108 (133)
T 2lni_A           66 FQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQ  108 (133)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            999999999988752 3357788888889999999997776654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.42  E-value=0.011  Score=49.65  Aligned_cols=222  Identities=7%  Similarity=-0.025  Sum_probs=145.5

Q ss_pred             HHHHHhhccChhhHHHHHHHHHHhccCcch-hHHHHHHHHHhhccC--ChhHHHHhcccCCCCCeee---eec----c--
Q 044412           30 IANQLKKCSSIKELECVYATIVKTNANLDC-FLAKQFISFCTSRFH--FIDYTILVFPQMQEPNVFV---YHA----F--   97 (311)
Q Consensus        30 ~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~-~~~~~ll~~~~~~~g--~~~~a~~~~~~m~~~~~~~---~~~----~--   97 (311)
                      +..++......+++..+.+.++...  |+- ..|+.-=..+ ...|  ++++++++++.+...+...   |+.    +  
T Consensus        39 ~~a~~~~~e~s~~aL~~t~~~L~~n--P~~~taWn~R~~~L-~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~  115 (306)
T 3dra_A           39 LLALMKAEEYSERALHITELGINEL--ASHYTIWIYRFNIL-KNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQ  115 (306)
T ss_dssp             HHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHH-HTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHC--cHHHHHHHHHHHHH-HHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHH
Confidence            3333444445556778888777764  443 4556555556 6677  9999999999886533333   333    3  


Q ss_pred             --ccC---CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCc--cchHHHHHHhccCCCCC
Q 044412           98 --SSL---RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFF--ESRRVSRRLFDEMPERK  170 (311)
Q Consensus        98 --~~~---~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~--~a~~~a~~~~~~~~~~~  170 (311)
                        .+.   +++++++.+++.+.+.               -+-+...|+.---.+.+.|.++  +    +...++.+.+.|
T Consensus       116 ~~~~l~~~~~~~~EL~~~~~~l~~---------------~pkny~aW~~R~~vl~~l~~~~~~~----EL~~~~~~i~~d  176 (306)
T 3dra_A          116 IMELNNNDFDPYREFDILEAMLSS---------------DPKNHHVWSYRKWLVDTFDLHNDAK----ELSFVDKVIDTD  176 (306)
T ss_dssp             HHHHTTTCCCTHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCTTCHH----HHHHHHHHHHHC
T ss_pred             HHHhccccCCHHHHHHHHHHHHHh---------------CCCCHHHHHHHHHHHHHhcccChHH----HHHHHHHHHHhC
Confidence              333   7889999999998775               3667888988888888899888  7    444443332211


Q ss_pred             HhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC------hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc
Q 044412          171 FATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ------FREALDAFNKTKKSGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       171 ~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~------~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~  244 (311)
                                             ..|...|+.--..+.+.|+      ++++++.+++..... +-|...|+-+-..+.+
T Consensus       177 -----------------------~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~  232 (306)
T 3dra_A          177 -----------------------LKNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHER  232 (306)
T ss_dssp             -----------------------TTCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHH
T ss_pred             -----------------------CCCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHh
Confidence                                   2355566655555555555      889999999988753 3366677777777777


Q ss_pred             cCChhh-HHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          245 LGALDL-GRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       245 ~~~~~~-a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .|.... +..+....-..+.       ...++...+..+.+.|.+.|+.++|.++++.+.+
T Consensus       233 ~~~~~~~~~~~~~~~~~~~~-------~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          233 FDRSITQLEEFSLQFVDLEK-------DQVTSSFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             TTCCGGGGHHHHHTTEEGGG-------TEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCCChHHHHHHHHHHHhccC-------CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            666433 3233322211110       0124667889999999999999999999999875

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.42  E-value=0.0021  Score=47.14  Aligned_cols=98  Identities=12%  Similarity=-0.033  Sum_probs=73.4

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +...+..+-..+...|++++|+..|++..... +-+...|..+-.++...|+++.|...++..      ..+    ...+
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a------l~~----~p~~   85 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYG------ALM----DINE   85 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH----CTTC
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHH------Hhc----CCCC
Confidence            34456667778888999999999999988742 336677888888888989888766655331      111    1235


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ...|..+-.+|...|++++|...|++..+
T Consensus        86 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           86 PRFPFHAAECHLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             THHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            67788889999999999999999988764

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.40  E-value=0.0023  Score=45.28  Aligned_cols=99  Identities=12%  Similarity=0.072  Sum_probs=74.1

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +...|..+...+...|++++|+..|++..+.. +.+...+..+...+...|++++|...++..      .+.    ...+
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~------~~~----~~~~   79 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERA------ICI----DPAY   79 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH----CTTC
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHH------Hhc----CccC
Confidence            45677788888888999999999999987652 335777888888888888888776655331      111    1234


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ...|..+...+...|++++|...+++..+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  109 (131)
T 2vyi_A           80 SKAYGRMGLALSSLNKHVEAVAYYKKALEL  109 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            667888888999999999999999887653

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.37  E-value=0.0073  Score=53.79  Aligned_cols=210  Identities=7%  Similarity=-0.052  Sum_probs=108.0

Q ss_pred             hhHHHHHHHHHhhccCCh----hHHHHhcccCCCCCeeeeec----cccCC---ChhHHHHHHHHHHHCCCCchHHHHHH
Q 044412           59 CFLAKQFISFCTSRFHFI----DYTILVFPQMQEPNVFVYHA----FSSLR---HPLQAIAFYLYMLRAEVLLTTVHGQV  127 (311)
Q Consensus        59 ~~~~~~ll~~~~~~~g~~----~~a~~~~~~m~~~~~~~~~~----~~~~~---~~~~a~~~~~~m~~~~~~p~~~~~~~  127 (311)
                      +.....|-..| ...+.+    +.+..++......+...+..    +...|   +.++|++.|+.-.+.|          
T Consensus       141 ~~a~~~Lg~~y-~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g----------  209 (452)
T 3e4b_A          141 PEAGLAQVLLY-RTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG----------  209 (452)
T ss_dssp             TTHHHHHHHHH-HHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT----------
T ss_pred             HHHHHHHHHHH-HcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC----------
Confidence            33444444555 444533    33344444443322223222    55677   8888888888877765          


Q ss_pred             HHhcCCCchhHHHHHHHHHHhC----CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH---H-----HHHHHhhCCC-
Q 044412          128 WKNGFSSPVFVQTAMVDNYSYS----NKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR---L-----AELLFNKMPA-  194 (311)
Q Consensus       128 ~~~g~~~~~~~~~~ll~~~~~~----g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~---~-----a~~~~~~m~~-  194 (311)
                           .++...+..|-..|...    ++.++    |...|+.....+...+..+-..|..   .     |.+.|++-.+ 
T Consensus       210 -----~~~a~~~~~Lg~~y~~g~~~~~d~~~----A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~  280 (452)
T 3e4b_A          210 -----TVTAQRVDSVARVLGDATLGTPDEKT----AQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAA  280 (452)
T ss_dssp             -----CSCHHHHHHHHHHHTCGGGSSCCHHH----HHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHT
T ss_pred             -----CHHHHHHHHHHHHHhCCCCCCCCHHH----HHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHC
Confidence                 45555556666666554    57777    6666655442233344433333221   0     5555544332 


Q ss_pred             CcHhHHHHHHHHHHhCC-----ChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc----cCChhhHHHHHHhhCChHHHH
Q 044412          195 WDIRSWTTMITSYSQNK-----QFREALDAFNKTKKSGTGSDQVTMATVLSACAH----LGALDLGRGIQIYCRSLGRSL  265 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g-----~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~----~~~~~~a~~~~~~~~~~~~a~  265 (311)
                      .+...+..|-..|. .|     ++++|++.|++-.    .-+...+..|-..|..    ..+.++|.             
T Consensus       281 g~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~-------------  342 (452)
T 3e4b_A          281 DQPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV----GREVAADYYLGQIYRRGYLGKVYPQKAL-------------  342 (452)
T ss_dssp             TCHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT----TTCHHHHHHHHHHHHTTTTSSCCHHHHH-------------
T ss_pred             CCHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh----CCCHHHHHHHHHHHHCCCCCCcCHHHHH-------------
Confidence            24555555555555 34     7777777777665    2234444444444444    22455444             


Q ss_pred             HHHhhcCCC-CchhHHHHHHHHHh----cCChHHHHHHHHHHHHcC
Q 044412          266 LVFFKLREK-NLLCWNSITEALAI----HGFAHEALGMFDRMTYEN  306 (311)
Q Consensus       266 ~~~~~~~~p-~~~~~~~li~~~~~----~g~~~~a~~~~~~M~~~g  306 (311)
                      ..|++-.++ +......|-..|..    ..+.++|..+|+.-.+.|
T Consensus       343 ~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g  388 (452)
T 3e4b_A          343 DHLLTAARNGQNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQD  388 (452)
T ss_dssp             HHHHHHHTTTCTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhhChHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCC
Confidence            444443322 33344444444442    346677777776665554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.36  E-value=0.00075  Score=48.73  Aligned_cols=92  Identities=8%  Similarity=0.053  Sum_probs=58.8

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|++.|++..+.               -+.+...|..+-.+|.+.|++++    |...++...+        
T Consensus        23 ~~~~g~~~~A~~~~~~al~~---------------~p~~~~~~~~~~~~~~~~~~~~~----A~~~~~~al~--------   75 (126)
T 4gco_A           23 YFKKGDYPTAMRHYNEAVKR---------------DPENAILYSNRAACLTKLMEFQR----ALDDCDTCIR--------   75 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH--------
T ss_pred             HHHcCCHHHHHHHHHHHHHh---------------CCCCHHHHHHHhhHHHhhccHHH----HHHHHHHHHH--------
Confidence            45667777777777776543               13456677777777888888888    4444443211        


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ  232 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  232 (311)
                                     +...+...|..+-.+|...|++++|++.|++..+.  .|+.
T Consensus        76 ---------------~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~l--~P~~  114 (126)
T 4gco_A           76 ---------------LDSKFIKGYIRKAACLVAMREWSKAQRAYEDALQV--DPSN  114 (126)
T ss_dssp             ---------------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             ---------------hhhhhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcCC
Confidence                           01224666777777778888888888888877663  4543

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.35  E-value=0.0032  Score=45.85  Aligned_cols=98  Identities=11%  Similarity=0.032  Sum_probs=77.9

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC----HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhc
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD----QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKL  271 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~  271 (311)
                      +...+..+-..+...|++++|++.|++..+.  .|+    ...+..+-.++...|++++|...++.      +.+.    
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~------~~~~----   94 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASK------AIEK----   94 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH----
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHH------HHhh----
Confidence            5677888889999999999999999998874  566    57788888889999999977665533      1111    


Q ss_pred             CCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          272 REKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       272 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ...+...|..+-..+...|++++|...|++..+.
T Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           95 DGGDVKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             TSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            1235678888999999999999999999988753

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.35  E-value=0.0029  Score=45.05  Aligned_cols=97  Identities=12%  Similarity=-0.004  Sum_probs=75.2

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCc
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNL  276 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~  276 (311)
                      ...|..+-..+.+.|++++|+..|++..+.. +.+...|..+-.++.+.|++++|...++.      +.++    ...+.
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~------al~~----~p~~~   72 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNK------AIEK----DPNFV   72 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH----CTTCH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHH------HHHh----CCCcH
Confidence            3456677788889999999999999988752 33578888899999999999977665533      2221    12356


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..|..+-.++...|++++|...|++..+
T Consensus        73 ~~~~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           73 RAYIRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence            7888999999999999999999998765

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.35  E-value=0.00039  Score=51.90  Aligned_cols=139  Identities=8%  Similarity=-0.001  Sum_probs=94.8

Q ss_pred             ccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           98 SSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        98 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      ...|++++|+..++.....                .|+ ...+-.+-..|.+.|++++    |...|+...+.       
T Consensus         8 ~~~~~~e~ai~~~~~a~~~----------------~p~~~~~~~~la~~y~~~~~~~~----A~~~~~~al~~-------   60 (150)
T 4ga2_A            8 RSKADVERYIASVQGSTPS----------------PRQKSIKGFYFAKLYYEAKEYDL----AKKYICTYINV-------   60 (150)
T ss_dssp             CCHHHHHHHHHHHHHHSCS----------------HHHHHTTHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHcChHHHHHHHHHHhccc----------------CcccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-------
Confidence            3456788888888776432                222 4455567788999999999    66555542211       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                                      ...+..+|..+-..|...|++++|+..|++..+.  .| +...|..+-..+.+.|+.+++...+
T Consensus        61 ----------------~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~~~  122 (150)
T 4ga2_A           61 ----------------QERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAKYW  122 (150)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHHHH
T ss_pred             ----------------CCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHH
Confidence                            1236778999999999999999999999998874  45 4678888888999999887554332


Q ss_pred             HhhCChHHHHHHHhhcCCC-CchhHHHHHHHHHhcCC
Q 044412          256 IYCRSLGRSLLVFFKLREK-NLLCWNSITEALAIHGF  291 (311)
Q Consensus       256 ~~~~~~~~a~~~~~~~~~p-~~~~~~~li~~~~~~g~  291 (311)
                           .+.|.++     .| +...|+..-..+...|+
T Consensus       123 -----~~~al~l-----~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A          123 -----VERAAKL-----FPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             -----HHHHHHH-----STTCHHHHHHHHHHHHTCCC
T ss_pred             -----HHHHHHh-----CcCCHHHHHHHHHHHHHhCc
Confidence                 1123322     34 45566666666655553

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.33  E-value=0.0024  Score=57.56  Aligned_cols=103  Identities=10%  Similarity=0.052  Sum_probs=82.7

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhc---CC---CCC-HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHh
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKS---GT---GSD-QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFF  269 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~---g~---~p~-~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~  269 (311)
                      ..+++.|...|...|++++|+.++++..+-   -+   .|+ ..+++.|-..|...|++++|+.++      ..|.++++
T Consensus       351 a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~------~~Al~i~~  424 (490)
T 3n71_A          351 LRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMI------CKAYAILL  424 (490)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHH------HHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHH------HHHHHHHH
Confidence            457999999999999999999999987542   22   333 357999999999999999999886      46777777


Q ss_pred             hcCCCC----chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          270 KLREKN----LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       270 ~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ....||    ..+.+.+-.++...|.+++|..+|.+++++
T Consensus       425 ~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          425 VTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            766443    245677778888999999999999999763

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.33  E-value=0.0026  Score=48.36  Aligned_cols=98  Identities=9%  Similarity=0.166  Sum_probs=72.3

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHH-HhccCCh--hhHHHHHHhhCChHHHHHHHhhcC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSA-CAHLGAL--DLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a-~~~~~~~--~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      +...|..+-..|...|++++|+..|++..+.. +.+...+..+-.+ +...|++  +.|...++.      +.+.     
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~------al~~-----  110 (177)
T 2e2e_A           43 NSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQTRAMIDK------ALAL-----  110 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHH------HHHH-----
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHHHHHHHH------HHHh-----
Confidence            56778888889999999999999999987743 2356667777777 6677877  756554422      1111     


Q ss_pred             CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          273 EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       273 ~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      .| +...|..+...|...|++++|...|++..+.
T Consensus       111 ~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A          111 DSNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            23 4567888888999999999999999988764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.32  E-value=0.0026  Score=47.77  Aligned_cols=98  Identities=10%  Similarity=0.087  Sum_probs=74.1

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN  275 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~  275 (311)
                      +...|..+-..+...|++++|+..|++..+.. +-+...|..+-.+|...|++++|...++.      +.++    ...+
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~------al~~----~p~~   78 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAEL------ATVV----DPKY   78 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH----CTTC
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHH------HHHh----CCCC
Confidence            45677788888889999999999999987752 23677788888888888888877665532      2211    1234


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ...|..+-..|...|++++|...|++..+
T Consensus        79 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           79 SKAWSRLGLARFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            67888888899999999999999888765

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.28  E-value=0.0013  Score=46.56  Aligned_cols=120  Identities=9%  Similarity=-0.055  Sum_probs=83.6

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+...+...|++++    |...++.....                       ...+...|..+...+...|+++
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~-----------------------~~~~~~~~~~~a~~~~~~~~~~   63 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEA----AVHFYGKAIEL-----------------------NPANAVYFCNRAAAYSKLGNYA   63 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             hhHHHHHHHHHHHHccCHHH----HHHHHHHHHHc-----------------------CCCCHHHHHHHHHHHHHhhchH
Confidence            45677778888999999999    55555442110                       1125677888889999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCCh
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFA  292 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~  292 (311)
                      +|.+.+.+..+.. +.+...+..+-..+...|+++.|...++..      .+.    ...+...+..+...+...|++
T Consensus        64 ~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~------~~~----~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           64 GAVQDCERAICID-PAYSKAYGRMGLALSSLNKHVEAVAYYKKA------LEL----DPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH----STTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhcC-ccCHHHHHHHHHHHHHhCCHHHHHHHHHHH------Hhc----CccchHHHHHHHHHHHHHhcC
Confidence            9999999988752 334677888888899999988776655331      111    122456677777777776654

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.28  E-value=0.00098  Score=49.79  Aligned_cols=117  Identities=14%  Similarity=0.019  Sum_probs=82.6

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|...|++..+.               .+.+..++..+..+|...|++++    |...++.....       
T Consensus        23 ~~~~~~~~~A~~~~~~al~~---------------~~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~a~~~-------   76 (166)
T 1a17_A           23 YFKAKDYENAIKFYSQAIEL---------------NPSNAIYYGNRSLAYLRTECYGY----ALGDATRAIEL-------   76 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------STTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHccCHHHHHHHHHHHHHh---------------CCCChHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-------
Confidence            44677888888888887653               24467888889999999999999    55555442110       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHH--HHHHHHHhccCChhhHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTM--ATVLSACAHLGALDLGRGI  254 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~--~~li~a~~~~~~~~~a~~~  254 (311)
                                      ...+...|..+-..+...|++++|...|++..+.. +-+...+  ..+...+...|++++|...
T Consensus        77 ----------------~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~  139 (166)
T 1a17_A           77 ----------------DKKYIKGYYRRAASNMALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAG  139 (166)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence                            12256678888899999999999999999988752 2234444  3344446777888888776


Q ss_pred             HH
Q 044412          255 QI  256 (311)
Q Consensus       255 ~~  256 (311)
                      +.
T Consensus       140 ~~  141 (166)
T 1a17_A          140 DE  141 (166)
T ss_dssp             HH
T ss_pred             cc
Confidence            53

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.25  E-value=0.0071  Score=52.96  Aligned_cols=189  Identities=11%  Similarity=-0.031  Sum_probs=115.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCch----------HHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccC
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLT----------TVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEM  166 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~----------~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~  166 (311)
                      +.+.|++++|++.|.+..+..-...          ....        .....+..|...|.+.|++++    |.+.+...
T Consensus        14 l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--------~~~~al~~l~~~y~~~~~~~~----a~~~~~~~   81 (434)
T 4b4t_Q           14 LVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRN--------EQETSILELGQLYVTMGAKDK----LREFIPHS   81 (434)
T ss_dssp             HHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHH--------HHHHHHHHHHHHHHHHTCHHH----HHHHHHHT
T ss_pred             HHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhh--------hHHHHHHHHHHHHHHCCCHHH----HHHHHHHH
Confidence            3467788888888888765421100          0000        001246778899999999999    55555443


Q ss_pred             CC----C-CHh---HHHHHHHHHHH-------------HHHHHHhhCCC-C-cHhHHHHHHHHHHhCCChhHHHHHHHHH
Q 044412          167 PE----R-KFA---TWNTMIDAYAR-------------LAELLFNKMPA-W-DIRSWTTMITSYSQNKQFREALDAFNKT  223 (311)
Q Consensus       167 ~~----~-~~~---~~~~li~~~~~-------------~a~~~~~~m~~-~-~~~~y~~li~~~~~~g~~~~a~~~~~~m  223 (311)
                      .+    . +..   .....+..+..             .+..+...... + -..++..+...|...|++++|..++.+.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~  161 (434)
T 4b4t_Q           82 TEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDL  161 (434)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHH
Confidence            22    1 111   11111111110             02233333221 2 2357888899999999999999999987


Q ss_pred             Hhc--CC--CC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC---chhHHHHHHHHHhcCChHHH
Q 044412          224 KKS--GT--GS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN---LLCWNSITEALAIHGFAHEA  295 (311)
Q Consensus       224 ~~~--g~--~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~---~~~~~~li~~~~~~g~~~~a  295 (311)
                      ...  +.  .| ...+|..+...|...|++++|..+++.      +..+......|.   ...+..+...+...|++++|
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A  235 (434)
T 4b4t_Q          162 LREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTA------ARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTA  235 (434)
T ss_dssp             HHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHH
T ss_pred             HHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHH------HHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHH
Confidence            652  21  22 245788899999999999999887643      444444444332   24677777778889999999


Q ss_pred             HHHHHHHH
Q 044412          296 LGMFDRMT  303 (311)
Q Consensus       296 ~~~~~~M~  303 (311)
                      ...|.+..
T Consensus       236 ~~~~~~a~  243 (434)
T 4b4t_Q          236 FSYFFESF  243 (434)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88877654

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.23  E-value=0.0011  Score=50.63  Aligned_cols=116  Identities=12%  Similarity=0.111  Sum_probs=81.3

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|+..|++..+.               -+.+...|..+-..|...|++++    |...++.....       
T Consensus        20 ~~~~~~~~~A~~~~~~al~~---------------~p~~~~~~~~lg~~~~~~~~~~~----A~~~~~~al~~-------   73 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRA---------------NPQNSEQWALLGEYYLWQNDYSN----SLLAYRQALQL-------   73 (177)
T ss_dssp             CC-----CCCCHHHHHHHHH---------------CCSCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             hhhccCHHHHHHHHHHHHHh---------------CCCcHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHc-------
Confidence            56788999999999887654               24467888999999999999999    55555542210       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHH-HHhCCCh--hHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITS-YSQNKQF--REALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRG  253 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~-~~~~g~~--~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~  253 (311)
                                      ...+...|..+... +...|++  ++|...|++..+.. +-+...+..+-..+...|+++.|..
T Consensus        74 ----------------~p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~  136 (177)
T 2e2e_A           74 ----------------RGENAELYAALATVLYYQASQHMTAQTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIE  136 (177)
T ss_dssp             ----------------HCSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ----------------CCCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHH
Confidence                            01245667777777 7788998  99999999988753 2346677788888888888886665


Q ss_pred             HH
Q 044412          254 IQ  255 (311)
Q Consensus       254 ~~  255 (311)
                      .+
T Consensus       137 ~~  138 (177)
T 2e2e_A          137 LW  138 (177)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.16  E-value=0.0027  Score=54.23  Aligned_cols=145  Identities=11%  Similarity=0.039  Sum_probs=95.8

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+-..|.+.|++++|.....+.++..+........        .+.    ....-....|..+-.+|.+.|+++
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~--------~~~----~~~~~~~~~~~nla~~~~~~g~~~  213 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNE--------EAQ----KAQALRLASHLNLAMCHLKLQAFS  213 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSH--------HHH----HHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChH--------HHH----HHHHHHHHHHHHHHHHHHHcCCHH
Confidence            35577788888999999999444433333322211000000        000    000001468889999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHHHHHhcCChH
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITEALAIHGFAH  293 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~~~~~~g~~~  293 (311)
                      +|+..|++..+.. +-+...|..+-.+|...|++++|...|+.      |.++     .| +...+..+-..+...|+.+
T Consensus       214 ~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~------al~l-----~P~~~~a~~~l~~~~~~~~~~~  281 (336)
T 1p5q_A          214 AAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQK------VLQL-----YPNNKAAKTQLAVCQQRIRRQL  281 (336)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHH------HHHH-----CCCCHHHHHHHHHHHHHHHHHH
Confidence            9999999998753 33677888889999999999877665532      2222     34 4668888899999999999


Q ss_pred             HH-HHHHHHHH
Q 044412          294 EA-LGMFDRMT  303 (311)
Q Consensus       294 ~a-~~~~~~M~  303 (311)
                      +| ..++..|.
T Consensus       282 ~a~~~~~~~~~  292 (336)
T 1p5q_A          282 AREKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            88 44666664

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.08  E-value=0.002  Score=50.80  Aligned_cols=124  Identities=13%  Similarity=0.043  Sum_probs=81.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++..+..               +-+...+..+-.+|...|++++|.....++++.- +.+..+|..
T Consensus        64 ~~~~g~~~~A~~~~~~al~~~---------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~  127 (208)
T 3urz_A           64 YKKNRNYDKAYLFYKELLQKA---------------PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIF  127 (208)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC---------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHH
Confidence            667889999999998876632               3457888999999999999999444444444332 234556666


Q ss_pred             HHHHHHHH-------HHHHHhhCCCCcHhH--HHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          177 MIDAYARL-------AELLFNKMPAWDIRS--WTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       177 li~~~~~~-------a~~~~~~m~~~~~~~--y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                      +-..|...       +...++....|+...  +...-.++...|++++|+..|++..+  +.|+......+
T Consensus       128 lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~l  196 (208)
T 3urz_A          128 LGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHHH
Confidence            66555432       556666666665433  33334445567899999999999886  56886554443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.07  E-value=0.011  Score=48.00  Aligned_cols=130  Identities=8%  Similarity=-0.059  Sum_probs=89.1

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-c---HhHHHHHHHHHHhC
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-D---IRSWTTMITSYSQN  210 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~---~~~y~~li~~~~~~  210 (311)
                      +...+-.+-..+.+.|++++    |...|+.....                        .| +   ...+..+-.+|...
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~----A~~~~~~~l~~------------------------~p~~~~~~~a~~~lg~~~~~~   65 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDR----AIEYFKAVFTY------------------------GRTHEWAADAQFYLARAYYQN   65 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHH----HHHHHHHHGGG------------------------CSCSTTHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHh------------------------CCCCcchHHHHHHHHHHHHHh
Confidence            45566667778889999999    55555543221                        12 2   45677888889999


Q ss_pred             CChhHHHHHHHHHHhcCC-CCC-HHHHHHHHHHHhc--------cCChhhHHHHHHhhCChHHHHHHHhhcC--CCC-ch
Q 044412          211 KQFREALDAFNKTKKSGT-GSD-QVTMATVLSACAH--------LGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN-LL  277 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~-~p~-~~t~~~li~a~~~--------~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~-~~  277 (311)
                      |++++|+..|++..+..- .|. ...+..+-.++..        .|+++.|...|+             +..  .|+ ..
T Consensus        66 ~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~-------------~~l~~~p~~~~  132 (261)
T 3qky_A           66 KEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQ-------------LFIDRYPNHEL  132 (261)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHH-------------HHHHHCTTCTT
T ss_pred             CcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHH-------------HHHHHCcCchh
Confidence            999999999999987521 222 3456666666766        777776655543             332  233 22


Q ss_pred             hH-----------------HHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          278 CW-----------------NSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       278 ~~-----------------~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      .+                 ..+-..|...|++++|...|++..+.
T Consensus       133 ~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  177 (261)
T 3qky_A          133 VDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDA  177 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            33                 45577888999999999999998764

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.04  E-value=0.00034  Score=52.24  Aligned_cols=132  Identities=5%  Similarity=-0.093  Sum_probs=86.7

Q ss_pred             hccCChhHHHHhcccCCCCC----eeeeec---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQEPN----VFVYHA---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMV  143 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~~----~~~~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll  143 (311)
                      ...|+++.|.+.++...+.+    ...++.   |.+.|++++|++.|++..+..               +-+...|..+-
T Consensus         8 ~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~---------------p~~~~a~~~lg   72 (150)
T 4ga2_A            8 RSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ---------------ERDPKAHRFLG   72 (150)
T ss_dssp             CCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHH
T ss_pred             HHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC---------------CCCHHHHHHHH
Confidence            44566777777776654321    111222   778889999999998876631               33578889999


Q ss_pred             HHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHH-HHH
Q 044412          144 DNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDA-FNK  222 (311)
Q Consensus       144 ~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~-~~~  222 (311)
                      .+|.+.|++++    |...|+...+.                       ...+...|..+-..|.+.|+.++|.+. +++
T Consensus        73 ~~~~~~~~~~~----A~~~~~~al~~-----------------------~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~  125 (150)
T 4ga2_A           73 LLYELEENTDK----AVECYRRSVEL-----------------------NPTQKDLVLKIAELLCKNDVTDGRAKYWVER  125 (150)
T ss_dssp             HHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHH
T ss_pred             HHHHHcCchHH----HHHHHHHHHHh-----------------------CCCCHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            99999999999    55555542211                       112567888888899999998877665 466


Q ss_pred             HHhcCCCCC-HHHHHHHHHHHhccC
Q 044412          223 TKKSGTGSD-QVTMATVLSACAHLG  246 (311)
Q Consensus       223 m~~~g~~p~-~~t~~~li~a~~~~~  246 (311)
                      ..+  +.|+ ...|...-..+...|
T Consensus       126 al~--l~P~~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A          126 AAK--LFPGSPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             HHH--HSTTCHHHHHHHHHHHHTCC
T ss_pred             HHH--hCcCCHHHHHHHHHHHHHhC
Confidence            655  3454 455665555555544

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=97.04  E-value=0.045  Score=51.31  Aligned_cols=106  Identities=6%  Similarity=-0.013  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhc-C-CCCCHHHHHHHHHHHhccCChhhHHHHHHh-------------------
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKS-G-TGSDQVTMATVLSACAHLGALDLGRGIQIY-------------------  257 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~-g-~~p~~~t~~~li~a~~~~~~~~~a~~~~~~-------------------  257 (311)
                      .|-..+...-+.|.++.|..+|.+..+. + ..+......+.+.-. ..++.+.|+.+|+.                   
T Consensus       436 vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~-~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe  514 (679)
T 4e6h_A          436 VYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYH-ISKDTKTACKVLELGLKYFATDGEYINKYLDFL  514 (679)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHT-TTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHH
Confidence            5666666666677788888888887664 2 233333333333322 23457777777776                   


Q ss_pred             --hCChHHHHHHHhhcCC--C----CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          258 --CRSLGRSLLVFFKLRE--K----NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       258 --~~~~~~a~~~~~~~~~--p----~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                        .++.+.|..+|+....  |    ....|...++--.+.|+.+.+..+.+++.+.
T Consensus       515 ~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~  570 (679)
T 4e6h_A          515 IYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK  570 (679)
T ss_dssp             HHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence              6777788888887662  3    2357888888888999999999999999864

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=96.97  E-value=0.013  Score=41.51  Aligned_cols=91  Identities=8%  Similarity=-0.078  Sum_probs=67.3

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCH----HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC--
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQ----VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN--  275 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~--  275 (311)
                      .+-..+...|++++|...|++..+..  |+.    ..+..+-.++...|++++|...++..      .+.     .|+  
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~------~~~-----~p~~~   73 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDL------VSR-----YPTHD   73 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH-----CTTST
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHH------HHH-----CCCCc
Confidence            44566778899999999999988743  332    46777778888888888666655321      111     243  


Q ss_pred             --chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          276 --LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       276 --~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                        ...+..+-.++...|++++|...|++..+.
T Consensus        74 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           74 KAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence              456788888999999999999999998764

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=96.92  E-value=0.0038  Score=42.81  Aligned_cols=95  Identities=13%  Similarity=0.032  Sum_probs=70.7

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+-..+.+.|++++    |...++...+                       +...+...|..+-..+...|+++
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~----A~~~~~~a~~-----------------------~~~~~~~~~~~~a~~~~~~~~~~   57 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTE----SIDLFEKAIQ-----------------------LDPEESKYWLMKGKALYNLERYE   57 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHH----HHHHHHHHHH-----------------------HCCCCHHHHHHHHHHHHHTTCHH
T ss_pred             cHHHHHHHHHHHHHhhhHHH----HHHHHHHHHH-----------------------hCcCCHHHHHHHHHHHHHccCHH
Confidence            35567778888999999999    5555544211                       01235667888889999999999


Q ss_pred             HHHHHHHHHHhcCCCC--CHHHHHHHHHHHhcc-CChhhHHHHHHh
Q 044412          215 EALDAFNKTKKSGTGS--DQVTMATVLSACAHL-GALDLGRGIQIY  257 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p--~~~t~~~li~a~~~~-~~~~~a~~~~~~  257 (311)
                      +|+..|++..+.. +.  +...+..+-.++... |+.++|.+.+..
T Consensus        58 ~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~  102 (112)
T 2kck_A           58 EAVDCYNYVINVI-EDEYNKDVWAAKADALRYIEGKEVEAEIAEAR  102 (112)
T ss_dssp             HHHHHHHHHHHTS-CCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-cccchHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            9999999998753 22  477888999999999 999977666543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=96.91  E-value=0.0068  Score=48.23  Aligned_cols=158  Identities=8%  Similarity=0.036  Sum_probs=103.8

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCc--chhHHHHHHHHHhhccCChhHHHHhcccCCC--CCeee-----eec---
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANL--DCFLAKQFISFCTSRFHFIDYTILVFPQMQE--PNVFV-----YHA---   96 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p--~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~~~-----~~~---   96 (311)
                      .....+-..|+..++...++.+++.....  ....+..+..++ .+.|++++|...|++..+  |+...     |..   
T Consensus         9 ~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~-~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~   87 (225)
T 2yhc_A            9 ATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAY-YKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLT   87 (225)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHH-HhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHH
Confidence            34455667789999999999988764321  135677778888 999999999999988752  33221     111   


Q ss_pred             c------------------ccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHH-----------------HH
Q 044412           97 F------------------SSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQ-----------------TA  141 (311)
Q Consensus        97 ~------------------~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~-----------------~~  141 (311)
                      +                  ...|+.++|+..|++..+..  |+             +...+                 -.
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--P~-------------~~~a~~a~~~l~~~~~~~~~~~~~  152 (225)
T 2yhc_A           88 NMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY--PN-------------SQYTTDATKRLVFLKDRLAKYEYS  152 (225)
T ss_dssp             HHHHHC--------------CCHHHHHHHHHHHHHHTTC--TT-------------CTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC--cC-------------ChhHHHHHHHHHHHHHHHHHHHHH
Confidence            1                  13578999999999987642  21             11111                 23


Q ss_pred             HHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHHHHH
Q 044412          142 MVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREALDAF  220 (311)
Q Consensus       142 ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~~~~  220 (311)
                      +-..|.+.|++++|.....++++.-+.                         .| ....+..+..+|.+.|+.++|.+.+
T Consensus       153 ~a~~~~~~~~~~~A~~~~~~~l~~~p~-------------------------~~~~~~a~~~l~~~~~~~g~~~~A~~~~  207 (225)
T 2yhc_A          153 VAEYYTERGAWVAVVNRVEGMLRDYPD-------------------------TQATRDALPLMENAYRQMQMNAQAEKVA  207 (225)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHSTT-------------------------SHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHHCcC-------------------------CCccHHHHHHHHHHHHHcCCcHHHHHHH
Confidence            445677788888833333333332111                         01 1246778899999999999999999


Q ss_pred             HHHHhcC
Q 044412          221 NKTKKSG  227 (311)
Q Consensus       221 ~~m~~~g  227 (311)
                      +.+...+
T Consensus       208 ~~l~~~~  214 (225)
T 2yhc_A          208 KIIAANS  214 (225)
T ss_dssp             HHHHHCC
T ss_pred             HHHHhhC
Confidence            9988753

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=96.88  E-value=0.0037  Score=46.72  Aligned_cols=94  Identities=12%  Similarity=0.058  Sum_probs=71.1

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ...+..+-..+.+.|++++    |...|+.....                       ...+...|..+-.+|...|++++
T Consensus        36 ~~~~~~lg~~~~~~g~~~e----A~~~~~~al~~-----------------------~P~~~~~~~~lg~~~~~~g~~~~   88 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEE----AEVFFRFLCIY-----------------------DFYNVDYIMGLAAIYQIKEQFQQ   88 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-----------------------CCCCHHHHHHHHHHHHHHccHHH
Confidence            4466677778899999999    66665543221                       11267788999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          216 ALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       216 a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |+..|++..+.. +-+...|..+-.+|...|++++|...|+.
T Consensus        89 Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~~~eA~~~~~~  129 (151)
T 3gyz_A           89 AADLYAVAFALG-KNDYTPVFHTGQCQLRLKAPLKAKECFEL  129 (151)
T ss_dssp             HHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999998742 22467888888999999999977766643

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=96.87  E-value=0.0083  Score=42.30  Aligned_cols=105  Identities=13%  Similarity=0.121  Sum_probs=72.4

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|+..|++..+.               .+.+...+..+...|...|++++    |...++....        
T Consensus        14 ~~~~~~~~~A~~~~~~a~~~---------------~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~--------   66 (131)
T 1elr_A           14 AYKKKDFDTALKHYDKAKEL---------------DPTNMTYITNQAAVYFEKGDYNK----CRELCEKAIE--------   66 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHH--------
T ss_pred             HHHhcCHHHHHHHHHHHHhc---------------CCccHHHHHHHHHHHHHhccHHH----HHHHHHHHHh--------
Confidence            44677888888888887653               24467788888889999999999    5555544211        


Q ss_pred             HHHHHHHHHHHHHhhCCCCc----HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWD----IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSAC  242 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~----~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~  242 (311)
                                 +.... .++    ..+|..+...+...|++++|.+.|++..+.  .|+......+-...
T Consensus        67 -----------~~~~~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~  122 (131)
T 1elr_A           67 -----------VGREN-REDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQAE  122 (131)
T ss_dssp             -----------HHHHS-TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHH
T ss_pred             -----------hcccc-chhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHHHH
Confidence                       11111 111    567888889999999999999999999885  46665555544433

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.86  E-value=0.0049  Score=45.28  Aligned_cols=97  Identities=13%  Similarity=0.168  Sum_probs=69.5

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhCCChh
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~g~~~  214 (311)
                      .++..+-..|...|++++    |...++.                   +.++......+.  ...+..+-..+...|+++
T Consensus        50 ~~~~~l~~~~~~~g~~~~----A~~~~~~-------------------a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  106 (164)
T 3ro3_A           50 IAYSNLGNAYIFLGEFET----ASEYYKK-------------------TLLLARQLKDRAVEAQSCYSLGNTYTLLQDYE  106 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHcCCHHH----HHHHHHH-------------------HHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHH
Confidence            578888889999999999    6666555                   333444443322  446778888899999999


Q ss_pred             HHHHHHHHHHhc----CCCC-CHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          215 EALDAFNKTKKS----GTGS-DQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       215 ~a~~~~~~m~~~----g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +|.+.+++..+.    +-.+ ...++..+-..+...|++++|...++
T Consensus       107 ~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  153 (164)
T 3ro3_A          107 KAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAE  153 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            999999987642    2111 13467778888889999998877663

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=96.83  E-value=0.022  Score=44.81  Aligned_cols=166  Identities=5%  Similarity=-0.150  Sum_probs=106.7

Q ss_pred             HHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCC-eeeee-c---cccCC----ChhHHHHHHHHH
Q 044412           43 LECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPN-VFVYH-A---FSSLR----HPLQAIAFYLYM  113 (311)
Q Consensus        43 ~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~-~~~~~-~---~~~~~----~~~~a~~~~~~m  113 (311)
                      +.+.+....+.|   ++..+..+-..| ...+++++|.++|++..+++ ...+. .   +.. +    +.++|+++|+.-
T Consensus         5 A~~~~~~aa~~g---~~~a~~~lg~~~-~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A   79 (212)
T 3rjv_A            5 PGSQYQQQAEAG---DRRAQYYLADTW-VSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKA   79 (212)
T ss_dssp             TTHHHHHHHHTT---CHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHH-hcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHH
Confidence            445555556553   666777777777 77888888888887765433 22221 1   444 5    899999999887


Q ss_pred             HHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHh----CCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHH
Q 044412          114 LRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSY----SNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLF  189 (311)
Q Consensus       114 ~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~----~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~  189 (311)
                      .+.|                 +...+..|-..|..    .++.++    |...++...+.+..                 
T Consensus        80 ~~~g-----------------~~~a~~~Lg~~y~~g~g~~~d~~~----A~~~~~~A~~~~~~-----------------  121 (212)
T 3rjv_A           80 VEAG-----------------SKSGEIVLARVLVNRQAGATDVAH----AITLLQDAARDSES-----------------  121 (212)
T ss_dssp             HHTT-----------------CHHHHHHHHHHHTCGGGSSCCHHH----HHHHHHHHTSSTTS-----------------
T ss_pred             HHCC-----------------CHHHHHHHHHHHHcCCCCccCHHH----HHHHHHHHHHcCCC-----------------
Confidence            6543                 45566667777766    778888    66666654432200                 


Q ss_pred             hhCCCCcHhHHHHHHHHHHh----CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc-C-----ChhhHHHHHHh
Q 044412          190 NKMPAWDIRSWTTMITSYSQ----NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL-G-----ALDLGRGIQIY  257 (311)
Q Consensus       190 ~~m~~~~~~~y~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~-~-----~~~~a~~~~~~  257 (311)
                          ..+...+..|-..|..    .+++++|+..|++-.+.  ..+...+..|-..|... |     +.++|...++.
T Consensus       122 ----~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~  193 (212)
T 3rjv_A          122 ----DAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNV  193 (212)
T ss_dssp             ----HHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHH
T ss_pred             ----cchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHH
Confidence                0015667777777777    78999999999998876  23444555555555432 2     67766666544

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=96.80  E-value=0.0077  Score=42.86  Aligned_cols=93  Identities=11%  Similarity=-0.045  Sum_probs=72.6

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-Cc
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NL  276 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~  276 (311)
                      .+..+-..+.+.|++++|+..|++..+.  .| +...|..+-.++...|++++|...++.      |.++     .| +.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~------al~l-----~P~~~   85 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNH------ARML-----DPKDI   85 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTTCH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHh-----CCCCH
Confidence            3555667788999999999999999874  45 567788888888899998866655432      2211     34 46


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..|..+-..+...|++++|...+++..+
T Consensus        86 ~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           86 AVHAALAVSHTNEHNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            7888999999999999999999999875

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=96.80  E-value=0.017  Score=41.37  Aligned_cols=102  Identities=12%  Similarity=0.045  Sum_probs=70.6

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|++.|++..+.               -+-+...|+.+-.+|.+.|++++    |...++...         
T Consensus        18 ~~~~~~~~~A~~~y~~Al~~---------------~p~~~~~~~nlg~~~~~~~~~~~----A~~~~~~al---------   69 (127)
T 4gcn_A           18 AYKQKDFEKAHVHYDKAIEL---------------DPSNITFYNNKAAVYFEEKKFAE----CVQFCEKAV---------   69 (127)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHH---------
T ss_pred             HHHcCCHHHHHHHHHHHHHh---------------CCCCHHHHHhHHHHHHHhhhHHH----HHHHHHHHH---------
Confidence            55778899999999887653               13457788899999999999999    555554422         


Q ss_pred             HHHHHHHHHHHHHhhCCCC---cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAW---DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~---~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                                ++-......   -..+|..+-..+...|++++|++.|++-.+  ..||..+...|
T Consensus        70 ----------~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~--~~~~~~~~~~l  122 (127)
T 4gcn_A           70 ----------EVGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLS--EFRDPELVKKV  122 (127)
T ss_dssp             ----------HHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HSCCHHHHHHH
T ss_pred             ----------HhCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCcCHHHHHHH
Confidence                      111111110   123677777888899999999999999776  35776665443

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=96.80  E-value=0.012  Score=48.68  Aligned_cols=90  Identities=9%  Similarity=0.048  Sum_probs=49.8

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCCC--C-cHhHHHHHHHH
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMPA--W-DIRSWTTMITS  206 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~~--~-~~~~y~~li~~  206 (311)
                      +...+..+-..+.+.|++++|.....+....-+ .+...|..+-..|.+.     |...+++..+  | +...|..+-.+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            345666777788888999994433333333211 2333444444444432     4444444332  2 45566666666


Q ss_pred             HHhCCChhHHHHHHHHHHh
Q 044412          207 YSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~  225 (311)
                      |...|++++|+..|++..+
T Consensus        82 ~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            6677777777776666544

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=96.77  E-value=0.0055  Score=43.58  Aligned_cols=87  Identities=13%  Similarity=0.104  Sum_probs=56.9

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++..+.               .+.+...|..+-.+|.+.|++++    |...++...+.       
T Consensus        14 ~~~~~~~~~A~~~~~~al~~---------------~p~~~~~~~~~a~~~~~~~~~~~----A~~~~~~al~~-------   67 (126)
T 3upv_A           14 YFTKSDWPNAVKAYTEMIKR---------------APEDARGYSNRAAALAKLMSFPE----AIADCNKAIEK-------   67 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHhcCHHHHHHHHHHHHHh---------------CCCChHHHHHHHHHHHHhcCHHH----HHHHHHHHHHh-------
Confidence            44667777777777776553               13356777777778888888888    44444331110       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                                      ...+...|..+-.++...|++++|+..|++..+
T Consensus        68 ----------------~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           68 ----------------DPNFVRAYIRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ----------------CCCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence                            112456677777778888888888888887765

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=96.75  E-value=0.0092  Score=42.85  Aligned_cols=97  Identities=11%  Similarity=0.011  Sum_probs=74.6

Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~  212 (311)
                      ..+...|..+-..+...|++++    |...+......                       ...+...|..+-..+...|+
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~----A~~~~~~al~~-----------------------~~~~~~~~~~l~~~~~~~~~   58 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPE----AAACYGRAITR-----------------------NPLVAVYYTNRALCYLKMQQ   58 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTC
T ss_pred             cccHHHHHHHHHHHHHhCcHHH----HHHHHHHHHhh-----------------------CcCcHHHHHHHHHHHHHhcC
Confidence            3457788888899999999999    55555542211                       12256788889999999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +++|+..|++..+.. +-+...+..+-.++...|+++.|...+..
T Consensus        59 ~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~  102 (137)
T 3q49_B           59 PEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAIANLQR  102 (137)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            999999999988753 33567888889999999999988777644

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=96.75  E-value=0.016  Score=41.59  Aligned_cols=101  Identities=12%  Similarity=-0.031  Sum_probs=74.3

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC---
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK---  274 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p---  274 (311)
                      ..+..+=..+.+.|++++|++.|++..+.. +-+...|..+-.+|...|++++|...++.      |.++-......   
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~------al~~~~~~~~~~~~   81 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEK------AVEVGRETRADYKL   81 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHH------HHHhCcccchhhHH
Confidence            457777888999999999999999988742 23467788899999999999988776644      22221111110   


Q ss_pred             CchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          275 NLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       275 ~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      -..+|..+-..+...|++++|.+.|++-...
T Consensus        82 ~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~  112 (127)
T 4gcn_A           82 IAKAMSRAGNAFQKQNDLSLAVQWFHRSLSE  112 (127)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            0136777788889999999999999987653

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.74  E-value=0.0013  Score=46.56  Aligned_cols=28  Identities=7%  Similarity=-0.064  Sum_probs=14.5

Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      ...+..+-.++...|++++|...+++..
T Consensus        61 ~~~~~~l~~~~~~~g~~~~A~~~~~~al   88 (117)
T 3k9i_A           61 QALRVFYAMVLYNLGRYEQGVELLLKII   88 (117)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444555555555555555555555443

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=96.73  E-value=0.011  Score=55.49  Aligned_cols=200  Identities=8%  Similarity=-0.021  Sum_probs=117.0

Q ss_pred             CCCchhhhHHHHHHHHhhccChhhHH-HHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCC---------
Q 044412           19 PTSVSFIRIHIIANQLKKCSSIKELE-CVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQE---------   88 (311)
Q Consensus        19 ~~~~~~~~~~~~~~~l~~~~~~~~~~-~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~---------   88 (311)
                      |..+..  .-.+...+...+....+. .+++..+.. ++.+...|-..+... -+.|+++.|.++|+...+         
T Consensus       340 p~~~~l--W~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~e-e~~~~~e~aR~iyek~l~~l~~~~~~~  415 (679)
T 4e6h_A          340 CFAPEI--WFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQY-ELNTKIPEIETTILSCIDRIHLDLAAL  415 (679)
T ss_dssp             TTCHHH--HHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHH--HHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHH-HHhCCHHHHHHHHHHHHHHHHHHhhhh
Confidence            444443  445566666677777774 888777753 345666677777777 788888888888877642         


Q ss_pred             ----CC------------eeeeec----cccCCChhHHHHHHHHHHHC-CCCchHHHHHHHHhcCCCchhHHHHHHHHHH
Q 044412           89 ----PN------------VFVYHA----FSSLRHPLQAIAFYLYMLRA-EVLLTTVHGQVWKNGFSSPVFVQTAMVDNYS  147 (311)
Q Consensus        89 ----~~------------~~~~~~----~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~  147 (311)
                          |.            ...|-.    ..+.|..+.|..+|....+. +.             ..+...+..+.+.  .
T Consensus       416 ~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~-------------~~~~lyi~~A~lE--~  480 (679)
T 4e6h_A          416 MEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKL-------------VTPDIYLENAYIE--Y  480 (679)
T ss_dssp             HHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGG-------------SCTHHHHHHHHHH--H
T ss_pred             hhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCC-------------CChHHHHHHHHHH--H
Confidence                21            012222    34556778888888877543 10             1222333333333  2


Q ss_pred             hC-CCCccchHHHHHHhccCCC--C-CHhHHHHHHHHHHHH-----HHHHHhhCCC--C----cHhHHHHHHHHHHhCCC
Q 044412          148 YS-NKFFESRRVSRRLFDEMPE--R-KFATWNTMIDAYARL-----AELLFNKMPA--W----DIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       148 ~~-g~~~~a~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~-----a~~~~~~m~~--~----~~~~y~~li~~~~~~g~  212 (311)
                      +. ++.+.    |+.+|+.+.+  | +...|...+.-....     |+.+|++...  |    ....|...+.-=...|+
T Consensus       481 ~~~~d~e~----Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~  556 (679)
T 4e6h_A          481 HISKDTKT----ACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGS  556 (679)
T ss_dssp             TTTSCCHH----HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCC
T ss_pred             HhCCCHHH----HHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCC
Confidence            33 44777    5555554433  2 233333333333222     6777766442  2    34578888888888899


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACA  243 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~  243 (311)
                      .+.+.++.+++.+.  -|+......+++=|.
T Consensus       557 ~~~~~~v~~R~~~~--~P~~~~~~~f~~ry~  585 (679)
T 4e6h_A          557 LNSVRTLEKRFFEK--FPEVNKLEEFTNKYK  585 (679)
T ss_dssp             SHHHHHHHHHHHHH--STTCCHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHh--CCCCcHHHHHHHHhc
Confidence            99999999998875  455555555555443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.71  E-value=0.026  Score=40.76  Aligned_cols=94  Identities=12%  Similarity=-0.023  Sum_probs=70.0

Q ss_pred             CchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc----HhHHHHHHHHHHh
Q 044412          134 SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD----IRSWTTMITSYSQ  209 (311)
Q Consensus       134 ~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~----~~~y~~li~~~~~  209 (311)
                      .+...+..+-..+...|++++    |...++...+.                        .|+    ...|..+-..|..
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~----A~~~~~~a~~~------------------------~~~~~~~~~~~~~~a~~~~~   77 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGG----ALAAYTQALGL------------------------DATPQDQAVLHRNRAACHLK   77 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHH----HHHHHHHHHTS------------------------CCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHH------------------------cccchHHHHHHHHHHHHHHH
Confidence            356678888889999999999    55555442221                        233    5678888888999


Q ss_pred             CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          210 NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       210 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      .|++++|+..+++..+.. +.+...+..+-.++...|++++|...++
T Consensus        78 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~  123 (148)
T 2dba_A           78 LEDYDKAETEASKAIEKD-GGDVKALYRRSQALEKLGRLDQAVLDLQ  123 (148)
T ss_dssp             TTCHHHHHHHHHHHHHHT-SCCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HccHHHHHHHHHHHHhhC-ccCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999999999999987752 2356778888888889898887766653

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=96.69  E-value=0.0078  Score=41.54  Aligned_cols=94  Identities=9%  Similarity=0.008  Sum_probs=68.5

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+...+...|++++    |...++.....                       ...+...|..+...+...|+++
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~-----------------------~~~~~~~~~~~a~~~~~~~~~~   55 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDD----ALQCYSEAIKL-----------------------DPHNHVLYSNRSAAYAKKGDYQ   55 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHHTCHH
T ss_pred             hHHHHHHHHHHHHHcccHHH----HHHHHHHHHHH-----------------------CCCcHHHHHHHHHHHHhhccHH
Confidence            34567778888999999999    55555442110                       1125667888888889999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +|...+++..+.. +.+...+..+..++...|+++.|...++
T Consensus        56 ~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~   96 (118)
T 1elw_A           56 KAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYE   96 (118)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            9999999988753 3357778888888989888886666553

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=96.68  E-value=0.0052  Score=55.23  Aligned_cols=116  Identities=13%  Similarity=0.035  Sum_probs=82.4

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|++.|++..+.               .+-+...|..+-.+|.+.|++++    |...+++..+        
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~---------------~p~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~--------   68 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIEL---------------NPSNAIYYGNRSLAYLRTECYGY----ALGDATRAIE--------   68 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH--------
T ss_pred             HHHhCCHHHHHHHHHHHHHh---------------CCccHHHHHHHHHHHHHhcCHHH----HHHHHHHHHH--------
Confidence            67889999999999988663               23457889999999999999999    5555443221        


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC-HHHHHHHHHH--HhccCChhhHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD-QVTMATVLSA--CAHLGALDLGRG  253 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~a--~~~~~~~~~a~~  253 (311)
                                     +...+...|..+-.+|...|++++|++.|++..+.  .|+ ...+..+-.+  +.+.|++++|..
T Consensus        69 ---------------l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~g~~~~A~~  131 (477)
T 1wao_1           69 ---------------LDKKYIKGYYRRAASNMALGKFRAALRDYETVVKV--KPHDKDAKMKYQECNKIVKQKAFERAIA  131 (477)
T ss_dssp             ---------------SCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCTTHHHHHHHHHHHHHHHHHCCC--
T ss_pred             ---------------hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence                           11235678888999999999999999999998874  232 2334444334  778888998887


Q ss_pred             HHH
Q 044412          254 IQI  256 (311)
Q Consensus       254 ~~~  256 (311)
                      .++
T Consensus       132 ~~~  134 (477)
T 1wao_1          132 GDE  134 (477)
T ss_dssp             ---
T ss_pred             ccc
Confidence            776

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=96.67  E-value=0.03  Score=46.30  Aligned_cols=97  Identities=7%  Similarity=-0.017  Sum_probs=71.3

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK  274 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p  274 (311)
                      +...+..+-..+...|++++|+..|++..+.  .| +...|..+-.++.+.|++++|...++..-..+          ..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~----------p~   70 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALELD----------GQ   70 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC----------TT
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC----------CC
Confidence            3456677778888899999999999988774  34 66778888888888888886655443322211          23


Q ss_pred             CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          275 NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       275 ~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +...|..+-.+|...|++++|...|++..+
T Consensus        71 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           71 SVKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            566788888889999999999998887654

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=96.63  E-value=0.0079  Score=44.53  Aligned_cols=94  Identities=10%  Similarity=0.029  Sum_probs=70.4

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ...+..+-..+.+.|++++    |...|+.....                       ...+...|..+-.+|...|++++
T Consensus        21 ~~~~~~~g~~~~~~g~~~~----A~~~~~~al~~-----------------------~p~~~~~~~~lg~~~~~~g~~~~   73 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYED----AHXVFQALCVL-----------------------DHYDSRFFLGLGACRQAMGQYDL   73 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCChHH----HHHHHHHHHHc-----------------------CcccHHHHHHHHHHHHHHhhHHH
Confidence            4566677778999999999    55555542211                       12367788888889999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          216 ALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       216 a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |+..|++..+.. +-+...+..+-.++...|++++|...++.
T Consensus        74 A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  114 (148)
T 2vgx_A           74 AIHSYSYGAVMD-IXEPRFPFHAAECLLQXGELAEAESGLFL  114 (148)
T ss_dssp             HHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999988752 23567788888899999999977776643

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=96.56  E-value=0.0097  Score=43.47  Aligned_cols=94  Identities=13%  Similarity=0.066  Sum_probs=69.2

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ...+..+-..+.+.|++++    |...|+.....                       ...+...|..+-.+|...|++++
T Consensus        18 ~~~~~~~a~~~~~~g~~~~----A~~~~~~al~~-----------------------~p~~~~~~~~lg~~~~~~g~~~~   70 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDD----AQKIFQALCML-----------------------DHYDARYFLGLGACRQSLGLYEQ   70 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHccHHH----HHHHHHHHHHh-----------------------CCccHHHHHHHHHHHHHHhhHHH
Confidence            3445556678889999999    55555542211                       11256778888899999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          216 ALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       216 a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      |+..|++..+.. +-+...+..+-.++...|++++|...++.
T Consensus        71 A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  111 (142)
T 2xcb_A           71 ALQSYSYGALMD-INEPRFPFHAAECHLQLGDLDGAESGFYS  111 (142)
T ss_dssp             HHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999988753 33566778888889999999977776643

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=96.54  E-value=0.011  Score=44.31  Aligned_cols=95  Identities=6%  Similarity=-0.070  Sum_probs=72.2

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+-..|.+.|++++    |...|+...+.                       ...+...|..+-.+|...|+++
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~----A~~~~~~al~~-----------------------~p~~~~~~~~l~~~~~~~g~~~   62 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSK----AIDLYTQALSI-----------------------APANPIYLSNRAAAYSASGQHE   62 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------STTCHHHHHHHHHHHHHTTCHH
T ss_pred             hHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-----------------------CCcCHHHHHHHHHHHHHccCHH
Confidence            45677788889999999999    55555542211                       1125778888999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +|+..|++..+.. +-+...|..+-.++...|++++|...++.
T Consensus        63 ~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  104 (164)
T 3sz7_A           63 KAAEDAELATVVD-PKYSKAWSRLGLARFDMADYKGAKEAYEK  104 (164)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            9999999988753 23477888888999999999977766543

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=96.53  E-value=0.052  Score=42.61  Aligned_cols=28  Identities=11%  Similarity=0.086  Sum_probs=20.6

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccC
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEM  166 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~  166 (311)
                      +...+..|-..|...+++++    |...|+..
T Consensus        17 ~~~a~~~lg~~~~~~~~~~~----A~~~~~~a   44 (212)
T 3rjv_A           17 DRRAQYYLADTWVSSGDYQK----AEYWAQKA   44 (212)
T ss_dssp             CHHHHHHHHHHHHHHTCHHH----HHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCHHH----HHHHHHHH
Confidence            56677777778888899999    66666553

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=96.53  E-value=0.024  Score=40.03  Aligned_cols=95  Identities=13%  Similarity=0.024  Sum_probs=64.9

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-h---hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-V---FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFA  172 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~---~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~  172 (311)
                      +...|++++|++.|++..+.                .|+ .   ..+..+-.+|.+.|++++|......+.+.-+...  
T Consensus        12 ~~~~~~~~~A~~~~~~~~~~----------------~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~--   73 (129)
T 2xev_A           12 ALKNGKYDDASQLFLSFLEL----------------YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHD--   73 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH----------------CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTST--
T ss_pred             HHHhCCHHHHHHHHHHHHHH----------------CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCc--
Confidence            45678999999999988653                233 2   4777788889999999994443333333211100  


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH
Q 044412          173 TWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV  233 (311)
Q Consensus       173 ~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  233 (311)
                                            .....+..+-.++...|++++|...|++..+.  .|+..
T Consensus        74 ----------------------~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~--~p~~~  110 (129)
T 2xev_A           74 ----------------------KAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ--YPGSD  110 (129)
T ss_dssp             ----------------------THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTSH
T ss_pred             ----------------------ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCh
Confidence                                  01455777788889999999999999998875  35544

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.52  E-value=0.0067  Score=42.66  Aligned_cols=106  Identities=6%  Similarity=0.002  Sum_probs=66.9

Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                      ..|++++|+..|++..+.+..            -+-+...+..+-.+|.+.|++++    |...+++..+.         
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~------------~p~~~~~~~~lg~~~~~~~~~~~----A~~~~~~al~~---------   56 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQ------------GKDLAECYLGLGSTFRTLGEYRK----AEAVLANGVKQ---------   56 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCC------------HHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH---------
T ss_pred             CCCcHHHHHHHHHHHHHcCCC------------CccHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh---------
Confidence            457888999999888653210            02235678888889999999999    55555542211         


Q ss_pred             HHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc-CCCCCHHHHHHHHHHHh
Q 044412          179 DAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKS-GTGSDQVTMATVLSACA  243 (311)
Q Consensus       179 ~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~a~~  243 (311)
                                    ...+...|..+-.++...|++++|+..|++..+. .-.|+...|...+..+.
T Consensus        57 --------------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~ai~~~~  108 (117)
T 3k9i_A           57 --------------FPNHQALRVFYAMVLYNLGRYEQGVELLLKIIAETSDDETIQSYKQAILFYA  108 (117)
T ss_dssp             --------------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHTHHHHHHHT
T ss_pred             --------------CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHH
Confidence                          0124667888889999999999999999988764 22333344444444443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=96.46  E-value=0.022  Score=48.51  Aligned_cols=98  Identities=13%  Similarity=-0.031  Sum_probs=78.2

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC----------------HHHHHHHHHHHhccCChhhHHHHHHhhC
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD----------------QVTMATVLSACAHLGALDLGRGIQIYCR  259 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----------------~~t~~~li~a~~~~~~~~~a~~~~~~~~  259 (311)
                      +...|..+-..|.+.|++++|+..|++..+..  |+                ...|..+-.++.+.|++++|...++.  
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~--  221 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNK--  221 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH--
Confidence            35578888889999999999999999988753  43                47889999999999999977666533  


Q ss_pred             ChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          260 SLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       260 ~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                          |.++    ...+...|..+-.+|...|++++|...|++..+.
T Consensus       222 ----al~~----~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l  259 (336)
T 1p5q_A          222 ----ALEL----DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  259 (336)
T ss_dssp             ----HHHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ----HHHh----CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                2222    1236778999999999999999999999998763

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=96.42  E-value=0.043  Score=42.33  Aligned_cols=95  Identities=9%  Similarity=0.031  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcC-CCCC--------------HHHHHHHHHHHhccCChhhHHHHHHhhCChHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSG-TGSD--------------QVTMATVLSACAHLGALDLGRGIQIYCRSLGR  263 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--------------~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~  263 (311)
                      .+..+-..+...|++++|+..|.+..+.. -.|+              ...|..+-.++...|++++|...++.      
T Consensus        40 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~------  113 (198)
T 2fbn_A           40 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASK------  113 (198)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH------
Confidence            34444455555566666666666655421 0110              14455555555555555544444322      


Q ss_pred             HHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          264 SLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       264 a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      +.++    ...+...|..+-.+|...|++++|...|++..
T Consensus       114 al~~----~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al  149 (198)
T 2fbn_A          114 VLKI----DKNNVKALYKLGVANMYFGFLEEAKENLYKAA  149 (198)
T ss_dssp             HHHH----STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHh----CcccHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            1111    01233445555555555555555555555543

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=96.42  E-value=0.028  Score=43.49  Aligned_cols=97  Identities=19%  Similarity=0.111  Sum_probs=64.0

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-Cc
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NL  276 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~  276 (311)
                      ..|..+-.+|...|++++|+..+++..+.. +.+...+..+-.++...|+++.|...++.      +.++     .| +.
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~------al~~-----~p~~~  156 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYK------AASL-----NPNNL  156 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHH------HHHH-----STTCH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHH------HHHH-----CCCcH
Confidence            678888889999999999999999988752 34567888888889999999877665533      2111     23 45


Q ss_pred             hhHHHHHHHHHhcCChHHHH-HHHHHHHHcC
Q 044412          277 LCWNSITEALAIHGFAHEAL-GMFDRMTYEN  306 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~-~~~~~M~~~g  306 (311)
                      ..+..+-..+...++.+++. ..+..|...|
T Consensus       157 ~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          157 DIRNSYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHHHHHHHHHHHHHHHHC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            67777777777777777766 4566655443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.34  E-value=0.12  Score=45.09  Aligned_cols=193  Identities=7%  Similarity=-0.068  Sum_probs=128.3

Q ss_pred             HHHhhccChhhHHHHHHHHHHhccCcch----------------hHHHHHHHHHhhccCChhHHHHhcccCCC-----CC
Q 044412           32 NQLKKCSSIKELECVYATIVKTNANLDC----------------FLAKQFISFCTSRFHFIDYTILVFPQMQE-----PN   90 (311)
Q Consensus        32 ~~l~~~~~~~~~~~l~~~m~~~g~~p~~----------------~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----~~   90 (311)
                      .-+...|+..++.+.+....+..-....                ..+..+...| .+.|++++|.+.+.+..+     ++
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y-~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLY-VTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHH-HHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHccc
Confidence            3455668888888888888765322111                2467888999 999999999999987752     11


Q ss_pred             eee----eec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHH
Q 044412           91 VFV----YHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRR  161 (311)
Q Consensus        91 ~~~----~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~  161 (311)
                      ..+    .+.    +...|+.+++.+++++....          ..+.+..+. ..++..+...|...|++++|..+..+
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----------~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~  160 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEF----------AKREKRVFLKHSLSIKLATLHYQKKQYKDSLALIND  160 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHH----------HHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH----------HHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHH
Confidence            111    111    56678899999998876432          122223333 56788889999999999994444333


Q ss_pred             HhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc----CCCCC--HHH
Q 044412          162 LFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREALDAFNKTKKS----GTGSD--QVT  234 (311)
Q Consensus       162 ~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~t  234 (311)
                      +.......                      +..+ ...+|..++..|...|++++|..++++....    +..|.  ...
T Consensus       161 ~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  218 (434)
T 4b4t_Q          161 LLREFKKL----------------------DDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAEL  218 (434)
T ss_dssp             HHHHHTTS----------------------SCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHH
T ss_pred             HHHHHHhc----------------------ccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHH
Confidence            33322211                      1122 2457889999999999999999999887542    22222  345


Q ss_pred             HHHHHHHHhccCChhhHHHHHHh
Q 044412          235 MATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       235 ~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +..+...+...|+++.|...|..
T Consensus       219 ~~~~g~~~~~~~~y~~A~~~~~~  241 (434)
T 4b4t_Q          219 DLMSGILHCEDKDYKTAFSYFFE  241 (434)
T ss_dssp             HHHHHHHTTSSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHH
Confidence            66777778888999998877655

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.28  E-value=0.024  Score=51.01  Aligned_cols=133  Identities=8%  Similarity=-0.069  Sum_probs=92.4

Q ss_pred             HhhccChhhHHHHHHHHHHhc---c---Ccc-hhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeeccccCCChhHH
Q 044412           34 LKKCSSIKELECVYATIVKTN---A---NLD-CFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHAFSSLRHPLQA  106 (311)
Q Consensus        34 l~~~~~~~~~~~l~~~m~~~g---~---~p~-~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~a  106 (311)
                      +...|+..+++.+++...+..   +   .|+ ..+++.|...| ...|++++|..++                    +++
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y-~~~g~~~eA~~~~--------------------~~a  377 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVL-SYLQAYEEASHYA--------------------RRM  377 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHH-HHTTCHHHHHHHH--------------------HHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH-HHhcCHHHHHHHH--------------------HHH
Confidence            456678888877777666432   1   222 35778888888 8888888887776                    666


Q ss_pred             HHHHHHHHHCCCCchHHHHHHHHhcCCCc-hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHH
Q 044412          107 IAFYLYMLRAEVLLTTVHGQVWKNGFSSP-VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLA  185 (311)
Q Consensus       107 ~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a  185 (311)
                      +.+++...-.               -.|+ ..+++.|-..|...|++++    |..++++                   |
T Consensus       378 L~i~~~~lG~---------------~Hp~~a~~l~nLa~~~~~~G~~~e----A~~~~~~-------------------A  419 (490)
T 3n71_A          378 VDGYMKLYHH---------------NNAQLGMAVMRAGLTNWHAGHIEV----GHGMICK-------------------A  419 (490)
T ss_dssp             HHHHHHHSCT---------------TCHHHHHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------H
T ss_pred             HHHHHHHcCC---------------CCHHHHHHHHHHHHHHHHCCCHHH----HHHHHHH-------------------H
Confidence            7776665322               1333 5678999999999999999    6666665                   4


Q ss_pred             HHHHhhCC---CCcH-hHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          186 ELLFNKMP---AWDI-RSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       186 ~~~~~~m~---~~~~-~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      .++++...   .|++ .+.+.+-.++...+.+++|+.+|.++++
T Consensus       420 l~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          420 YAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444433   2333 3456666778888999999999999876

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=96.23  E-value=0.16  Score=43.42  Aligned_cols=231  Identities=10%  Similarity=0.059  Sum_probs=137.4

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccC-ChhHHHHhcccCCCCCeeeeec-------cccC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFH-FIDYTILVFPQMQEPNVFVYHA-------FSSL  100 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~-------~~~~  100 (311)
                      .+..++......+++..+.+.++...-. +..+|+.-=..+ ...| .+++++++++.+...+...|.+       +.+.
T Consensus        59 ~~r~~~~~~e~se~AL~lt~~~L~~nP~-~ytaWn~R~~iL-~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l  136 (349)
T 3q7a_A           59 YFRAIAAKEEKSERALELTEIIVRMNPA-HYTVWQYRFSLL-TSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRI  136 (349)
T ss_dssp             HHHHHHHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHH-HHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHhCch-hHHHHHHHHHHH-HHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHh
Confidence            4455556666667788888888876422 334566655555 6667 5999999999987655555555       2222


Q ss_pred             -C-ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCc--------cchHHHHHHhccCCCCC
Q 044412          101 -R-HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFF--------ESRRVSRRLFDEMPERK  170 (311)
Q Consensus       101 -~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~--------~a~~~a~~~~~~~~~~~  170 (311)
                       + ++++++++++.+.+..               +-|...|+.---.+.+.|.++        +    +.+..+.+.+. 
T Consensus       137 ~~~~~~~EL~~~~k~L~~d---------------pkNy~AW~~R~wvl~~l~~~~~~~~~~~~e----ELe~~~k~I~~-  196 (349)
T 3q7a_A          137 SPQDPVSEIEYIHGSLLPD---------------PKNYHTWAYLHWLYSHFSTLGRISEAQWGS----ELDWCNEMLRV-  196 (349)
T ss_dssp             CCSCCHHHHHHHHHHTSSC---------------TTCHHHHHHHHHHHHHHHHTTCCCHHHHHH----HHHHHHHHHHH-
T ss_pred             cCCChHHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHhccccccchhhHHH----HHHHHHHHHHh-
Confidence             4 7889999999987642               456777777666666666666        4    22222221111 


Q ss_pred             HhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC-------hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Q 044412          171 FATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ-------FREALDAFNKTKKSGTGSDQVTMATVLSACA  243 (311)
Q Consensus       171 ~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~-------~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~  243 (311)
                                            ...|...|+---..+.+.++       ++++++.+.+..... +-|...|+-+-..+.
T Consensus       197 ----------------------dp~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~  253 (349)
T 3q7a_A          197 ----------------------DGRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLK  253 (349)
T ss_dssp             ----------------------CTTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             ----------------------CCCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence                                  12366677776666666665       688999998887742 235556665555455


Q ss_pred             ccCChhh--HHHHHHhhC-----ChHHHHHHHhhcC---------CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          244 HLGALDL--GRGIQIYCR-----SLGRSLLVFFKLR---------EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       244 ~~~~~~~--a~~~~~~~~-----~~~~a~~~~~~~~---------~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +.|....  -..+.=..+     .......+..++.         -+.......|.+.|...|+.++|.++++.+.+
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          254 HFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             HTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            4443310  000000000     0001111111111         24566789999999999999999999999864

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=96.13  E-value=0.0059  Score=43.47  Aligned_cols=87  Identities=10%  Similarity=-0.051  Sum_probs=63.1

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++..+..               +-+...|..+-.++...|++++    |...+++..+.       
T Consensus        27 ~~~~g~~~~A~~~~~~al~~~---------------P~~~~a~~~lg~~~~~~g~~~~----A~~~~~~al~l-------   80 (121)
T 1hxi_A           27 MLKLANLAEAALAFEAVCQKE---------------PEREEAWRSLGLTQAENEKDGL----AIIALNHARML-------   80 (121)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---------------TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHcCCHHHHHHHHHHHHHHC---------------CCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-------
Confidence            667888888888888876631               3357777888888889999999    55555442211       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                                      ...+...|..+-..+...|++++|+..|++..+
T Consensus        81 ----------------~P~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           81 ----------------DPKDIAVHAALAVSHTNEHNANAALASLRAWLL  113 (121)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ----------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                            012466777888888888999999999988775

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.10  E-value=0.082  Score=39.21  Aligned_cols=98  Identities=14%  Similarity=0.066  Sum_probs=72.8

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhc-------CC---------CC-CHHHHHHHHHHHhccCChhhHHHHHHhhC
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKS-------GT---------GS-DQVTMATVLSACAHLGALDLGRGIQIYCR  259 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-------g~---------~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~  259 (311)
                      ...+...-..+.+.|++++|+..|.+..+.       .-         .| +...|..+-.+|.+.|+++.|...++.  
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~--   88 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSE--   88 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHH--
Confidence            445677778888999999999999997764       11         12 235788888888899998877665432  


Q ss_pred             ChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          260 SLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       260 ~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                          |.++    ...+...|..+-.+|...|++++|...|++..+
T Consensus        89 ----al~~----~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           89 ----VLKR----EETNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             ----HHHH----STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ----HHhc----CCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence                2221    123567899999999999999999999998765

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.10  E-value=0.063  Score=47.43  Aligned_cols=96  Identities=11%  Similarity=0.067  Sum_probs=75.8

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhc---CCCCC----HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC-
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKS---GTGSD----QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE-  273 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~----~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-  273 (311)
                      ..+..+.+.|++++|+.++++..+.   -+.|+    ..+++.|..+|...|++++|+.+++      .+..++++... 
T Consensus       292 ~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~------~~L~i~~~~lg~  365 (429)
T 3qwp_A          292 KKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT------RTMEPYRIFFPG  365 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHH------HHHHHHHHHSCS
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHH------HHHHhHHHHcCC
Confidence            3356677889999999999998753   24444    3589999999999999999988863      56666666553 


Q ss_pred             --CCc-hhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          274 --KNL-LCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       274 --p~~-~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                        |++ .+++.|-..|...|++++|..++++..
T Consensus       366 ~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          366 SHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence              333 579999999999999999999998865

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.10  E-value=0.05  Score=48.09  Aligned_cols=90  Identities=10%  Similarity=0.032  Sum_probs=71.3

Q ss_pred             hCCChhHHHHHHHHHHh---cCCCCC----HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC---CCc-h
Q 044412          209 QNKQFREALDAFNKTKK---SGTGSD----QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE---KNL-L  277 (311)
Q Consensus       209 ~~g~~~~a~~~~~~m~~---~g~~p~----~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~---p~~-~  277 (311)
                      ..|++++|+.++++..+   .-+.|+    ..|++.|..+|...|++++|+.+++      .+..++++...   |++ .
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~------~aL~i~~~~lG~~Hp~~a~  383 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQ------KIIKPYSKHYPVYSLNVAS  383 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHH------HHHHHHHHHSCSSCHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHH------HHHHHHHHHcCCCChHHHH
Confidence            35889999999998655   234444    3689999999999999999998873      56666666653   333 5


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          278 CWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       278 ~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +++.|-..|...|++++|..++++..+
T Consensus       384 ~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          384 MWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            799999999999999999999998653

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.06  E-value=0.28  Score=40.46  Aligned_cols=109  Identities=11%  Similarity=0.034  Sum_probs=72.8

Q ss_pred             HHHHHhhCC--CCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH----HHHHHHHHHHhccCChhhHHHHHHhh
Q 044412          185 AELLFNKMP--AWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ----VTMATVLSACAHLGALDLGRGIQIYC  258 (311)
Q Consensus       185 a~~~~~~m~--~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~a~~~~~~~~~a~~~~~~~  258 (311)
                      |.++|+...  .|+......+-..+.+.+++++|+..|+...+   .|+.    ..+..+=.++...|++++|...++..
T Consensus       121 A~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~---~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a  197 (282)
T 4f3v_A          121 AMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGK---WPDKFLAGAAGVAHGVAAANLALFTEAERRLTEA  197 (282)
T ss_dssp             HHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGG---CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhc---cCCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            788887775  35333555555678888999999999985543   2332    35666677788888888666555432


Q ss_pred             CChHHHHHHHhhcCCCC--chhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          259 RSLGRSLLVFFKLREKN--LLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       259 ~~~~~a~~~~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      ....         ..|.  .......-.++.+.|+.++|..+|+++...
T Consensus       198 ~~g~---------~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          198 NDSP---------AGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HTST---------TTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hcCC---------CCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            1000         0132  234566677888999999999999998864

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=95.98  E-value=0.13  Score=38.45  Aligned_cols=98  Identities=17%  Similarity=0.119  Sum_probs=76.1

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC--------H-----HHHHHHHHHHhccCChhhHHHHHHhhCChHHHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGSD--------Q-----VTMATVLSACAHLGALDLGRGIQIYCRSLGRSL  265 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--------~-----~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~  265 (311)
                      .+...-..+.+.|++++|++.|++-.+.  .|+        .     ..|..+-.++.+.|++++|...+      +.|.
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~------~kAL   84 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSA------DKAL   84 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHH------HHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHH------HHHH
Confidence            3455566677889999999999998763  333        2     38888899999999999998766      4566


Q ss_pred             HHHhhcC--CCC-chhH----HHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          266 LVFFKLR--EKN-LLCW----NSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       266 ~~~~~~~--~p~-~~~~----~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ++|++-.  .|+ ...|    ...-.++...|++++|...|++..+
T Consensus        85 ~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           85 HYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            6666554  343 4567    8888999999999999999998764

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=95.87  E-value=0.043  Score=47.45  Aligned_cols=125  Identities=4%  Similarity=-0.053  Sum_probs=86.8

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhh------------CCCCcHhHHHHHH
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNK------------MPAWDIRSWTTMI  204 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~------------m~~~~~~~y~~li  204 (311)
                      ..+..+-..|.+.|++++    |...+++..                   +++..            ....+...|+.+-
T Consensus       224 ~~~~~~g~~~~~~g~~~~----Ai~~y~kAl-------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~nla  280 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEM----AIKKYTKVL-------------------RYVEGSRAAAEDADGAKLQPVALSCVLNIG  280 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHH----HHHHHHHHH-------------------HHHHHHHHHSCHHHHGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHH----HHHHHHHHH-------------------HHhhcCccccChHHHHHHHHHHHHHHHHHH
Confidence            346677778889999999    555554411                   11111            1112456888999


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSI  282 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~l  282 (311)
                      .+|.+.|++++|++.+++..+.  .| +...|..+-.+|...|++++|...++.      |.++     .| +...+..+
T Consensus       281 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~------Al~l-----~P~~~~~~~~l  347 (370)
T 1ihg_A          281 ACKLKMSDWQGAVDSCLEALEI--DPSNTKALYRRAQGWQGLKEYDQALADLKK------AQEI-----APEDKAIQAEL  347 (370)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTTCHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHHccCHHHHHHHHHH------HHHh-----CCCCHHHHHHH
Confidence            9999999999999999999874  34 567888888999999999977665532      2222     24 45667777


Q ss_pred             HHHHHhcCChHHHHH
Q 044412          283 TEALAIHGFAHEALG  297 (311)
Q Consensus       283 i~~~~~~g~~~~a~~  297 (311)
                      -..+...++.+++.+
T Consensus       348 ~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          348 LKVKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            777777777777654

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=95.81  E-value=0.053  Score=48.26  Aligned_cols=134  Identities=8%  Similarity=0.088  Sum_probs=89.5

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCC-----------CCcHhHHHHHH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMP-----------AWDIRSWTTMI  204 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~-----------~~~~~~y~~li  204 (311)
                      ...|..+-..|.+.|++++    |...|++...                   +.....           .-....|+.+-
T Consensus       268 a~~~~~~G~~~~~~g~~~~----A~~~y~~Al~-------------------~~p~~~~~~~~~~~~~~~~~~~~~~nla  324 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQ----AVIQYGKIVS-------------------WLEMEYGLSEKESKASESFLLAAFLNLA  324 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHH-------------------HHTTCCSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHH----HHHHHHHHHH-------------------HhcccccCChHHHHHHHHHHHHHHHHHH
Confidence            4467777888999999999    5555544211                   110000           00146788889


Q ss_pred             HHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITE  284 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~  284 (311)
                      .+|.+.|++++|+..|++..+.. +-+...|..+-.+|...|++++|...|+..-.++          ..+...+..+-.
T Consensus       325 ~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~----------P~~~~a~~~l~~  393 (457)
T 1kt0_A          325 MCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN----------PQNKAARLQISM  393 (457)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--------------CHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC----------CCCHHHHHHHHH
Confidence            99999999999999999988753 3356778888888999898886666554322211          134567888888


Q ss_pred             HHHhcCChHHHHH-HHHHHH
Q 044412          285 ALAIHGFAHEALG-MFDRMT  303 (311)
Q Consensus       285 ~~~~~g~~~~a~~-~~~~M~  303 (311)
                      .+.+.|+.++|.. ++..|.
T Consensus       394 ~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          394 CQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            8888888887754 566554

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=95.67  E-value=0.067  Score=45.51  Aligned_cols=145  Identities=10%  Similarity=0.044  Sum_probs=69.1

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      ..+..+-..|.+.|++++    |...|+....  |+...+... .-+......+       ....|+.+-.+|.+.|+++
T Consensus       180 ~~~~~~g~~~~~~g~~~~----A~~~y~~Al~~~p~~~~~~~~-~~~~~~~~~l-------~~~~~~nla~~~~~~g~~~  247 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEE----AMQQYEMAIAYMGDDFMFQLY-GKYQDMALAV-------KNPCHLNIAACLIKLKRYD  247 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHH----HHHHHHHHHHHSCHHHHHTCC-HHHHHHHHHH-------HTHHHHHHHHHHHTTTCCH
T ss_pred             HHHHHHHHHHHhcCCHHH----HHHHHHHHHHHhccchhhhhc-ccHHHHHHHH-------HHHHHHHHHHHHHHcCCHH
Confidence            346667778889999999    5555544221  111100000 0000000000       1137888889999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHH-HHhcCChH
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEA-LAIHGFAH  293 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~-~~~~g~~~  293 (311)
                      +|+..+++..+.. +-+...|..+-.+|...|++++|...|+..-..+.          .+...+..+-.. ....+..+
T Consensus       248 ~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p----------~~~~a~~~L~~l~~~~~~~~~  316 (338)
T 2if4_A          248 EAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAP----------DDKAIRRELRALAEQEKALYQ  316 (338)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC----------------------------------
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC----------CCHHHHHHHHHHHHHHHHHHH
Confidence            9999999988742 23577888999999999999866665544332221          133445544444 23456677


Q ss_pred             HHHHHHHHHHH
Q 044412          294 EALGMFDRMTY  304 (311)
Q Consensus       294 ~a~~~~~~M~~  304 (311)
                      ++..+|.+|..
T Consensus       317 ~a~~~~~~~l~  327 (338)
T 2if4_A          317 KQKEMYKGIFK  327 (338)
T ss_dssp             -----------
T ss_pred             HHHHHHHHhhC
Confidence            78888888864

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=95.67  E-value=0.0083  Score=53.89  Aligned_cols=93  Identities=9%  Similarity=-0.045  Sum_probs=67.0

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-  274 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-  274 (311)
                      +...|..+-.+|.+.|++++|++.+++..+.. +-+...|..+-.+|...|++++|...++.      |.++     .| 
T Consensus        39 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~~~~------al~~-----~p~  106 (477)
T 1wao_1           39 NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYET------VVKV-----KPH  106 (477)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHH------HHHH-----STT
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHh-----CCC
Confidence            57789999999999999999999999998752 23567888889999999999977766533      2221     23 


Q ss_pred             CchhHHHHHHH--HHhcCChHHHHHHHH
Q 044412          275 NLLCWNSITEA--LAIHGFAHEALGMFD  300 (311)
Q Consensus       275 ~~~~~~~li~~--~~~~g~~~~a~~~~~  300 (311)
                      +...+..+-.+  +.+.|++++|...++
T Consensus       107 ~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1          107 DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            34455555555  888899999999887

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=95.59  E-value=0.68  Score=41.54  Aligned_cols=171  Identities=12%  Similarity=0.014  Sum_probs=104.6

Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH------HHHHHhhCC---
Q 044412          123 VHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL------AELLFNKMP---  193 (311)
Q Consensus       123 ~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~------a~~~~~~m~---  193 (311)
                      +++..+.. ++.+...|-..+.-+.+.|++++|..+..+.+.. +. +...|.    .|+..      ...+.+...   
T Consensus       201 ~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~-P~-~~~l~~----~y~~~~e~~~~~~~l~~~~~~~~  273 (493)
T 2uy1_A          201 IHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM-SD-GMFLSL----YYGLVMDEEAVYGDLKRKYSMGE  273 (493)
T ss_dssp             HHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CC-SSHHHH----HHHHHTTCTHHHHHHHHHTC---
T ss_pred             HHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-CC-cHHHHH----HHHhhcchhHHHHHHHHHHHhhc
Confidence            44444443 3455778888888888999999977776666666 32 222221    11111      111221110   


Q ss_pred             -------C--CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHH--HHHHHHhccCChhhHHHHHHh-----
Q 044412          194 -------A--WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMA--TVLSACAHLGALDLGRGIQIY-----  257 (311)
Q Consensus       194 -------~--~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~--~li~a~~~~~~~~~a~~~~~~-----  257 (311)
                             .  .....|-..+.-.-+.+.++.|..+|++....+  ++...|.  +.+.... .++.+.|+.+|+.     
T Consensus       274 ~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~  350 (493)
T 2uy1_A          274 AESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH  350 (493)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC
T ss_pred             cchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC
Confidence                   0  012346666666656677888888888882222  2334443  3333222 3368888888876     


Q ss_pred             ----------------hCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          258 ----------------CRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       258 ----------------~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                                      .|+.+.|..+|+...+ ....|...+.--...|+.+.+..+++++..
T Consensus       351 ~~~~~~~~~yid~e~~~~~~~~aR~l~er~~k-~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          351 PDSTLLKEEFFLFLLRIGDEENARALFKRLEK-TSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSCC-BHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                            4566778888888743 567788888887888999999998888764

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=95.57  E-value=0.16  Score=37.95  Aligned_cols=105  Identities=17%  Similarity=0.124  Sum_probs=73.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc-------------hhHHHHHHHHHHhCCCCccchHHHHHHh
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP-------------VFVQTAMVDNYSYSNKFFESRRVSRRLF  163 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~-------------~~~~~~ll~~~~~~g~~~~a~~~a~~~~  163 (311)
                      +.+.|++++|+..|+.-.+.                .|+             ...|+.+-.++.+.|++++    |...+
T Consensus        21 l~~~g~~eeAi~~Y~kAL~l----------------~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~e----Al~~~   80 (159)
T 2hr2_A           21 QLVAGEYDEAAANCRRAMEI----------------SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDE----ALHSA   80 (159)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH----------------HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHH----HHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhh----------------CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHH----HHHHH
Confidence            34567888888888776542                222             2389999999999999999    55555


Q ss_pred             ccCCCCCHhHHHHHHHHHHHHHHHHHhhCC--CC-cHhHH----HHHHHHHHhCCChhHHHHHHHHHHh-----cCCCCC
Q 044412          164 DEMPERKFATWNTMIDAYARLAELLFNKMP--AW-DIRSW----TTMITSYSQNKQFREALDAFNKTKK-----SGTGSD  231 (311)
Q Consensus       164 ~~~~~~~~~~~~~li~~~~~~a~~~~~~m~--~~-~~~~y----~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~  231 (311)
                      +.                   |.++|++-.  .| +...|    ...-.++...|++++|+..|++-.+     .|+.+.
T Consensus        81 ~k-------------------AL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~  141 (159)
T 2hr2_A           81 DK-------------------ALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPG  141 (159)
T ss_dssp             HH-------------------HHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTT
T ss_pred             HH-------------------HHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHH
Confidence            54                   334443322  23 45677    8888999999999999999999764     466666


Q ss_pred             HHHHHHHHH
Q 044412          232 QVTMATVLS  240 (311)
Q Consensus       232 ~~t~~~li~  240 (311)
                      .......+.
T Consensus       142 ~~~~~~~~~  150 (159)
T 2hr2_A          142 KERMMEVAI  150 (159)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555554443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=95.47  E-value=0.22  Score=41.09  Aligned_cols=115  Identities=9%  Similarity=-0.011  Sum_probs=77.2

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCC--CCHhHHHHHHHHHHHH-----HHHHHhhCCC-Cc----HhHHHHHHHH
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKFATWNTMIDAYARL-----AELLFNKMPA-WD----IRSWTTMITS  206 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~~~~~~li~~~~~~-----a~~~~~~m~~-~~----~~~y~~li~~  206 (311)
                      +-.+..++...|++++    |.++|+....  |+....-.+-..+.+.     +...|+.... |+    ...+..+=.+
T Consensus       105 ~LayA~~L~~~g~y~e----A~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~a  180 (282)
T 4f3v_A          105 TMGFAACEAAQGNYAD----AMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVA  180 (282)
T ss_dssp             HHHHHHHHHHHTCHHH----HHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHH----HHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHH
Confidence            3446677888999999    8889988865  3332221111122222     8888875543 22    2356677788


Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCC--HHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSD--QVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +...|++++|++.|++-......|.  .......-.++.+.|+.++|..+|+.
T Consensus       181 l~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~  233 (282)
T 4f3v_A          181 AANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEW  233 (282)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            9999999999999999875444365  23455556667888999988887766

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.44  E-value=0.043  Score=52.25  Aligned_cols=34  Identities=9%  Similarity=0.099  Sum_probs=18.8

Q ss_pred             HHHHHhccCChhhHHHHHHhhCChHHHHHHHhhc
Q 044412          238 VLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKL  271 (311)
Q Consensus       238 li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~  271 (311)
                      ...++.+.|++++|.+++..+++.++|..+-+..
T Consensus       742 A~~~~~~~g~~~~a~~~~~~~~~~~~A~~lA~~~  775 (814)
T 3mkq_A          742 AFNAYWIAGDIQGAKDLLIKSQRFSEAAFLGSTY  775 (814)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHcCChHHHHHHHHHh
Confidence            3344555566666666666666666665554443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=95.42  E-value=0.091  Score=46.75  Aligned_cols=96  Identities=13%  Similarity=-0.023  Sum_probs=76.2

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCC----------------HHHHHHHHHHHhccCChhhHHHHHHhhCC
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSD----------------QVTMATVLSACAHLGALDLGRGIQIYCRS  260 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----------------~~t~~~li~a~~~~~~~~~a~~~~~~~~~  260 (311)
                      ...|..+-..|.+.|++++|+..|++..+.  .|+                ...|..+-.+|.+.|+++.|...++.   
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~---  342 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSW--LEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDK---  342 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH---
Confidence            456778888899999999999999998773  233                57888888999999999977666533   


Q ss_pred             hHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          261 LGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       261 ~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                         |.++    ...+...|..+-.+|...|++++|...|++..+
T Consensus       343 ---al~~----~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~  379 (457)
T 1kt0_A          343 ---ALGL----DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLE  379 (457)
T ss_dssp             ---HHHH----STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             ---HHhc----CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence               2221    123677899999999999999999999999875

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=95.39  E-value=0.0098  Score=40.83  Aligned_cols=59  Identities=14%  Similarity=0.141  Sum_probs=47.2

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHH
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      +...|..+-..+...|++++|++.|++..+.. +.+...+..+-.++...|++++|...+
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~   61 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMC   61 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            45677788888999999999999999988752 336778888888899999988666554

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=95.38  E-value=0.093  Score=46.36  Aligned_cols=67  Identities=9%  Similarity=0.084  Sum_probs=51.5

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCC---CCcH-hHHHHHHHHHHhCC
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMP---AWDI-RSWTTMITSYSQNK  211 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~---~~~~-~~y~~li~~~~~~g  211 (311)
                      ..+++.|..+|...|++++    |..++++                   +.++++..-   .|++ .+|+.|-..|...|
T Consensus       340 a~~~~nLa~~y~~~g~~~e----A~~~~~~-------------------aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg  396 (433)
T 3qww_A          340 LHMMYQAMGVCLYMQDWEG----ALKYGQK-------------------IIKPYSKHYPVYSLNVASMWLKLGRLYMGLE  396 (433)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHHHSCSSCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhhcCHHH----HHHHHHH-------------------HHHHHHHHcCCCChHHHHHHHHHHHHHHhcc
Confidence            4789999999999999999    6666555                   333343332   3443 47999999999999


Q ss_pred             ChhHHHHHHHHHHh
Q 044412          212 QFREALDAFNKTKK  225 (311)
Q Consensus       212 ~~~~a~~~~~~m~~  225 (311)
                      ++++|+.++++-.+
T Consensus       397 ~~~eA~~~~~~Al~  410 (433)
T 3qww_A          397 NKAAGEKALKKAIA  410 (433)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999998654

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=95.38  E-value=0.093  Score=38.89  Aligned_cols=98  Identities=11%  Similarity=0.050  Sum_probs=69.5

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhC--------------CCCcHhHHH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKM--------------PAWDIRSWT  201 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m--------------~~~~~~~y~  201 (311)
                      ...+...-..+.+.|++++    |...|...                   .+++...              ...+...|.
T Consensus        11 a~~~~~~G~~~~~~~~~~~----A~~~y~~a-------------------l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKE----AIDAYRDA-------------------LTRLDTLILREKPGEPEWVELDRKNIPLYA   67 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHH-------------------HHHHHHHHHTSCTTSHHHHHHHHTHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHHH-------------------HHHHHHhcccCCCCHHHHHHHHHHHHHHHH
Confidence            3455666778899999999    55555441                   1111110              012346788


Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      .+-.+|.+.|++++|+..+++..+.. +-+...|..+-.++...|+++.|...+..
T Consensus        68 nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~  122 (162)
T 3rkv_A           68 NMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKL  122 (162)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHH
Confidence            88999999999999999999988753 33567888888999999999977766543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.26  E-value=0.16  Score=48.30  Aligned_cols=76  Identities=13%  Similarity=0.205  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcC-------CCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhh
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSG-------TGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFK  270 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g-------~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~  270 (311)
                      ..|..+-..+.+.|+++.|.+.|..+....       ..-+..-...+.......|+.+.|..++.++|++++|.+++.+
T Consensus       682 ~~W~~la~~al~~~~~~~A~~~y~~~~d~~~l~~l~~~~~~~~~~~~~~~~a~~~~~~~~A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          682 MKWRALGDASLQRFNFKLAIEAFTNAHDLESLFLLHSSFNNKEGLVTLAKDAETTGKFNLAFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCHHHHHHHHHHccChhhhHHHHHHcCCHHHHHHHHHHHHHcCchHHHHHHHHHcCCHHHHHHHHHH
Confidence            345555555555555555555555443210       0224444555666677788888888888888888888776655


Q ss_pred             cCC
Q 044412          271 LRE  273 (311)
Q Consensus       271 ~~~  273 (311)
                      +.+
T Consensus       762 ~~~  764 (814)
T 3mkq_A          762 SQR  764 (814)
T ss_dssp             TTC
T ss_pred             cCC
Confidence            553

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=95.11  E-value=0.096  Score=45.22  Aligned_cols=98  Identities=5%  Similarity=-0.007  Sum_probs=73.5

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhc--------------CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChH
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKS--------------GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLG  262 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~--------------g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~  262 (311)
                      ..|..+-..+.+.|++++|++.|++..+.              ...| +...|..+-.+|.+.|++++|...++..-.. 
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~-  302 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI-  302 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-
Confidence            35777788889999999999999988751              0223 3467888888888999998776654332111 


Q ss_pred             HHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          263 RSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       263 ~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                               ...+...|..+-.+|...|++++|...|++..+.
T Consensus       303 ---------~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          303 ---------DPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             ---------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ---------CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence                     1235678899999999999999999999998753

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.07  E-value=0.088  Score=36.42  Aligned_cols=61  Identities=15%  Similarity=0.038  Sum_probs=48.0

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      .+...|..+-..|...|++++|+..|++..+.. +.+...|..+-.++...|+.++|...++
T Consensus        17 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~   77 (115)
T 2kat_A           17 DNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWE   77 (115)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            366788888888999999999999999988753 2346678888888888888887776653

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=95.06  E-value=0.043  Score=37.44  Aligned_cols=88  Identities=8%  Similarity=0.067  Sum_probs=60.7

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+-..+.+.|++++    |...++.....                       ...+...|..+-.++...|+++
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~----A~~~~~~al~~-----------------------~p~~~~~~~~lg~~~~~~g~~~   55 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYRE----AVHCYDQLITA-----------------------QPQNPVGYSNKAMALIKLGEYT   55 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             hHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhc-----------------------CCCCHHHHHHHHHHHHHhcCHH
Confidence            45677778889999999999    55555442110                       1225677888899999999999


Q ss_pred             HHHHHHHHHHhcCCCCC-------HHHHHHHHHHHhccCChhhH
Q 044412          215 EALDAFNKTKKSGTGSD-------QVTMATVLSACAHLGALDLG  251 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~-------~~t~~~li~a~~~~~~~~~a  251 (311)
                      +|++.|++..+.  .|+       ...+..+-.++...|+.+.|
T Consensus        56 ~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~a   97 (111)
T 2l6j_A           56 QAIQMCQQGLRY--TSTAEHVAIRSKLQYRLELAQGAVGSVQIP   97 (111)
T ss_dssp             HHHHHHHHHHTS--CSSTTSHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             HHHHHHHHHHHh--CCCccHHHHHHHHHHHHHHHHHHHHhHhhh
Confidence            999999998864  455       34445555555555555433

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=95.06  E-value=0.17  Score=32.77  Aligned_cols=60  Identities=13%  Similarity=0.213  Sum_probs=47.8

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +...|..+-..+...|++++|+..|++..+.. +.+...+..+-.++...|++++|...++
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~   67 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQ   67 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            35577788888999999999999999988753 3356778888888999999987766653

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=94.84  E-value=0.064  Score=37.14  Aligned_cols=80  Identities=9%  Similarity=0.019  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHH
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYAR  183 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~  183 (311)
                      ++|++.|++..+.               -+.+...+..+-..|...|++++    |...++.....              
T Consensus         2 ~~a~~~~~~al~~---------------~p~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~--------------   48 (115)
T 2kat_A            2 QAITERLEAMLAQ---------------GTDNMLLRFTLGKTYAEHEQFDA----ALPHLRAALDF--------------   48 (115)
T ss_dssp             CCHHHHHHHHHTT---------------TCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH--------------
T ss_pred             hHHHHHHHHHHHh---------------CCCcHHHHHHHHHHHHHccCHHH----HHHHHHHHHHH--------------
Confidence            3566777776553               23457788889999999999999    55555442210              


Q ss_pred             HHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          184 LAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       184 ~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                               ...+...|..+-..|...|++++|...|++..+
T Consensus        49 ---------~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           49 ---------DPTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             ---------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ---------CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                     112466788889999999999999999999875

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=94.75  E-value=0.16  Score=34.23  Aligned_cols=61  Identities=11%  Similarity=-0.026  Sum_probs=50.7

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +...|..+-..|...|++++|+..|++..+.. +-+...|..+-.+|...|++++|...++.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~   66 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQ   66 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            56778888999999999999999999998753 22466888899999999999988776644

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.74  E-value=0.24  Score=35.83  Aligned_cols=113  Identities=10%  Similarity=0.039  Sum_probs=78.5

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhc-CCCCCHHHHHHHHHHHhccCC----hhhHHHHHHhhCChHHHHHHHh
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKS-GTGSDQVTMATVLSACAHLGA----LDLGRGIQIYCRSLGRSLLVFF  269 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~a~~~~~~----~~~a~~~~~~~~~~~~a~~~~~  269 (311)
                      .+..-||-+|=.....-+.+-.+++++..-+- .+.|. .-...++++|.+.+.    ++.|...+-..|+.+.-.++..
T Consensus        37 sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C-~NlKrVi~C~~~~n~~se~vd~ALd~lv~~~KkDqLdki~~  115 (172)
T 1wy6_A           37 STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKC-QNLKSVVECGVINNTLNEHVNKALDILVIQGKRDKLEEIGR  115 (172)
T ss_dssp             SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGC-SCTHHHHHHHHHTTCCCHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhh-hcHHHHHHHHHHhcchHHHHHHHHHHHHHhccHhHHHHHHH
Confidence            34556666666666666677666666665431 11111 123456666666553    4556666666777778888888


Q ss_pred             hc-C--CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 044412          270 KL-R--EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVR  308 (311)
Q Consensus       270 ~~-~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  308 (311)
                      ++ .  +|++...-.+-.||.+-|+..+|.+++.+.-+.|++
T Consensus       116 ~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A          116 EILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            84 3  677888888999999999999999999999999874

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=94.63  E-value=0.081  Score=44.97  Aligned_cols=96  Identities=17%  Similarity=0.058  Sum_probs=72.6

Q ss_pred             HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHH------------------HHHHHHHHHhccCChhhHHHHHHhh
Q 044412          197 IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQV------------------TMATVLSACAHLGALDLGRGIQIYC  258 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------------------t~~~li~a~~~~~~~~~a~~~~~~~  258 (311)
                      ...|..+-..+.+.|++++|+..|.+..+.  .|+..                  .|..+-.++.+.|+++.|...++. 
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~-  255 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNI-  255 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH-
Confidence            345666777778889999999999997763  35543                  677888888888988877665532 


Q ss_pred             CChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          259 RSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       259 ~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                           +.++    ...+...|..+-.+|...|++++|...|++..+
T Consensus       256 -----al~~----~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          256 -----VLTE----EEKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             -----HHHH----CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             -----HHHh----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                 2221    123677899999999999999999999998754

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=93.96  E-value=0.17  Score=36.63  Aligned_cols=89  Identities=4%  Similarity=-0.143  Sum_probs=60.4

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc----cCChhhHHHHHHhhCChHHHHHHHhhcC-CCCch
Q 044412          203 MITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH----LGALDLGRGIQIYCRSLGRSLLVFFKLR-EKNLL  277 (311)
Q Consensus       203 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~----~~~~~~a~~~~~~~~~~~~a~~~~~~~~-~p~~~  277 (311)
                      |-..|...+.+++|++.|++-.+.|   +...+..|=..|..    .++.++|...++.             -. .-+..
T Consensus        31 lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~-------------Aa~~g~~~   94 (138)
T 1klx_A           31 LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSK-------------ACGLNDQD   94 (138)
T ss_dssp             HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHH-------------HHHTTCHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHH-------------HHcCCCHH
Confidence            4445555567778888888877764   44555555555555    5666655555433             22 24566


Q ss_pred             hHHHHHHHHHh----cCChHHHHHHHHHHHHcCC
Q 044412          278 CWNSITEALAI----HGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       278 ~~~~li~~~~~----~g~~~~a~~~~~~M~~~g~  307 (311)
                      .+..|-..|..    .++.++|..+|++-.+.|.
T Consensus        95 a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           95 GCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            77778888888    8999999999999887764

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=93.89  E-value=0.14  Score=45.17  Aligned_cols=78  Identities=8%  Similarity=-0.091  Sum_probs=54.6

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCC---CCc-HhHHHHHHHHHHhCC
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMP---AWD-IRSWTTMITSYSQNK  211 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~---~~~-~~~y~~li~~~~~~g  211 (311)
                      ..+++.|...|...|++++    |..++++                   +..+++..-   .|+ ..+++.|-..|...|
T Consensus       329 ~~~~~~L~~~y~~~g~~~e----A~~~~~~-------------------~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g  385 (429)
T 3qwp_A          329 LKVLDCAMDACINLGLLEE----ALFYGTR-------------------TMEPYRIFFPGSHPVRGVQVMKVGKLQLHQG  385 (429)
T ss_dssp             HHHHHHHHHHHHHHTCHHH----HHHHHHH-------------------HHHHHHHHSCSSCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhhccHHH----HHHHHHH-------------------HHHhHHHHcCCCChHHHHHHHHHHHHHHhcC
Confidence            5689999999999999999    5555544                   233333322   244 357999999999999


Q ss_pred             ChhHHHHHHHHHHh---cCCCCCHHHHH
Q 044412          212 QFREALDAFNKTKK---SGTGSDQVTMA  236 (311)
Q Consensus       212 ~~~~a~~~~~~m~~---~g~~p~~~t~~  236 (311)
                      ++++|+.++++-.+   .-..||.....
T Consensus       386 ~~~eA~~~~~~Al~i~~~~lG~~Hp~~~  413 (429)
T 3qwp_A          386 MFPQAMKNLRLAFDIMRVTHGREHSLIE  413 (429)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCTTSHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhcCCCChHHH
Confidence            99999999998653   22445544333

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=93.77  E-value=0.22  Score=33.52  Aligned_cols=63  Identities=5%  Similarity=-0.044  Sum_probs=47.6

Q ss_pred             CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          231 DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       231 ~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +...+..+-.++...|++++|...|+..      .+.     .| +...|..+-.+|...|++++|...|++..+
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~a------l~~-----~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEEL------VET-----DPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHH------HHH-----STTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHH------HHh-----CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4567788888888989998666655321      111     24 567899999999999999999999988653

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=93.58  E-value=0.8  Score=41.08  Aligned_cols=172  Identities=10%  Similarity=0.014  Sum_probs=90.5

Q ss_pred             HHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCC-hhHHHHhcccCC------CCCe---eeeec-
Q 044412           28 HIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHF-IDYTILVFPQMQ------EPNV---FVYHA-   96 (311)
Q Consensus        28 ~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~-~~~a~~~~~~m~------~~~~---~~~~~-   96 (311)
                      ..++..+...|....++.+++..++.  +.+...+......  .+.+. ++...+.+....      .+..   ..|-. 
T Consensus       217 ~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~~--~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y  292 (493)
T 2uy1_A          217 FFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGLV--MDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINH  292 (493)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHH--TTCTHHHHHHHHHTC----------CHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHhh--cchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHH
Confidence            34556667778888889999999988  4444444332221  11111 111111110000      0000   11111 


Q ss_pred             ---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHH--HHHHHHHhCCCCccchHHHHHHhccCCC--C
Q 044412           97 ---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQT--AMVDNYSYSNKFFESRRVSRRLFDEMPE--R  169 (311)
Q Consensus        97 ---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~--~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~  169 (311)
                         ..+.+..+.|..+|+.. +.               ...+..+|-  +.+.... .++.+.    |+.+|+.+.+  |
T Consensus       293 ~~~~~r~~~~~~AR~i~~~A-~~---------------~~~~~~v~i~~A~lE~~~-~~d~~~----ar~ife~al~~~~  351 (493)
T 2uy1_A          293 LNYVLKKRGLELFRKLFIEL-GN---------------EGVGPHVFIYCAFIEYYA-TGSRAT----PYNIFSSGLLKHP  351 (493)
T ss_dssp             HHHHHHHHCHHHHHHHHHHH-TT---------------SCCCHHHHHHHHHHHHHH-HCCSHH----HHHHHHHHHHHCT
T ss_pred             HHHHHHcCCHHHHHHHHHHh-hC---------------CCCChHHHHHHHHHHHHH-CCChHH----HHHHHHHHHHHCC
Confidence               33466789999999887 21               112333443  3333333 236888    5555554322  2


Q ss_pred             C-HhHHHHHHHHHHHH-----HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          170 K-FATWNTMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       170 ~-~~~~~~li~~~~~~-----a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      + ...|...+.-..+.     |+.+|++.. .....|...++-=...|+.+.+.+++++..+
T Consensus       352 ~~~~~~~~yid~e~~~~~~~~aR~l~er~~-k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          352 DSTLLKEEFFLFLLRIGDEENARALFKRLE-KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHSC-CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2 22233333322222     788888874 3567788888766677888888888888764

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=93.51  E-value=0.26  Score=31.86  Aligned_cols=81  Identities=11%  Similarity=0.183  Sum_probs=55.6

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...+..+-..|...|++++    |...++.....                       ...+...|..+-..+...|+++
T Consensus         8 ~~~~~~~la~~~~~~~~~~~----A~~~~~~a~~~-----------------------~~~~~~~~~~l~~~~~~~~~~~   60 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDE----AIEYYQKALEL-----------------------DPNNAEAWYNLGNAYYKQGDYD   60 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-----------------------CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             cHHHHHHHHHHHHHccCHHH----HHHHHHHHHhc-----------------------CCCCHHHHHHHHHHHHHHhhHH
Confidence            35677778888999999999    55555442110                       1125667888889999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACA  243 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~  243 (311)
                      +|...|++..+.. +-+...+..+-.++.
T Consensus        61 ~A~~~~~~a~~~~-p~~~~~~~~l~~~~~   88 (91)
T 1na3_A           61 EAIEYYQKALELD-PNNAEAKQNLGNAKQ   88 (91)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            9999999988742 223445555444443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=93.16  E-value=0.7  Score=35.08  Aligned_cols=89  Identities=15%  Similarity=0.157  Sum_probs=63.5

Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC-----------CC
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE-----------KN  275 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-----------p~  275 (311)
                      -...|+++.|.++.+++      -+...|..|-......|+++.|+..|...++.+...-++.....           -.
T Consensus        15 AL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D~~~L~~Ly~~tg~~e~L~kla~iA~~   88 (177)
T 3mkq_B           15 ALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHSFDKLSFLYLVTGDVNKLSKMQNIAQT   88 (177)
T ss_dssp             HHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTCHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            34569999999998876      36788999999999999999999999998888876444322210           01


Q ss_pred             chhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          276 LLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       276 ~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      ..-+|.-...+.-.|+++++.++|.+
T Consensus        89 ~g~~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           89 REDFGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             TTCHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHcCCHHHHHHHHHH
Confidence            12355666666677777777777654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=92.21  E-value=1.5  Score=36.54  Aligned_cols=182  Identities=5%  Similarity=-0.027  Sum_probs=107.6

Q ss_pred             hccCChhHHHHhcccCCC--CCe-eeeec----cccCC--ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHH
Q 044412           71 SRFHFIDYTILVFPQMQE--PNV-FVYHA----FSSLR--HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTA  141 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~--~~~-~~~~~----~~~~~--~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~  141 (311)
                      .+....++|+++++.+..  |+. ..|+.    +...+  ++++++++++.+....               +-+..+|+.
T Consensus        44 ~~~e~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n---------------Pk~y~aW~~  108 (306)
T 3dra_A           44 KAEEYSERALHITELGINELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN---------------EKNYQIWNY  108 (306)
T ss_dssp             HTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC---------------TTCCHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC---------------cccHHHHHH
Confidence            333445677777777653  332 23444    44455  8999999999987642               345666666


Q ss_pred             HHHHH----HhC---CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          142 MVDNY----SYS---NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       142 ll~~~----~~~---g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      --..+    .+.   ++++++..+...+++.    +                       ..|...|+----.+.+.|.++
T Consensus       109 R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~----~-----------------------pkny~aW~~R~~vl~~l~~~~  161 (306)
T 3dra_A          109 RQLIIGQIMELNNNDFDPYREFDILEAMLSS----D-----------------------PKNHHVWSYRKWLVDTFDLHN  161 (306)
T ss_dssp             HHHHHHHHHHHTTTCCCTHHHHHHHHHHHHH----C-----------------------TTCHHHHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHHHhccccCCHHHHHHHHHHHHHh----C-----------------------CCCHHHHHHHHHHHHHhcccC
Confidence            55555    555   6777833333333332    1                       246777877777777788888


Q ss_pred             --HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC---CCCchhHHHHHHHHHhc
Q 044412          215 --EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR---EKNLLCWNSITEALAIH  289 (311)
Q Consensus       215 --~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~---~p~~~~~~~li~~~~~~  289 (311)
                        ++++.++++.+... -|...|+---..+.+.+.... ..      ..+++.+.+++..   ..|...|+.+-..+.+.
T Consensus       162 ~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~-~~------~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~  233 (306)
T 3dra_A          162 DAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLAT-DN------TIDEELNYVKDKIVKCPQNPSTWNYLLGIHERF  233 (306)
T ss_dssp             CHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCC-HH------HHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccch-hh------hHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhc
Confidence              99999999998643 355566544444444443100 00      0224444444333   34677888888888888


Q ss_pred             CChHH-HHHHHHHH
Q 044412          290 GFAHE-ALGMFDRM  302 (311)
Q Consensus       290 g~~~~-a~~~~~~M  302 (311)
                      |+..+ +.....+.
T Consensus       234 ~~~~~~~~~~~~~~  247 (306)
T 3dra_A          234 DRSITQLEEFSLQF  247 (306)
T ss_dssp             TCCGGGGHHHHHTT
T ss_pred             CCChHHHHHHHHHH
Confidence            87444 34444443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=91.76  E-value=2.1  Score=36.17  Aligned_cols=212  Identities=15%  Similarity=0.077  Sum_probs=110.7

Q ss_pred             ccCChh-HHHHhcccCCCCCeeeeec-------cccCCC----------hhHHHHHHHHHHHCCCCchHHHHHHHHhcCC
Q 044412           72 RFHFID-YTILVFPQMQEPNVFVYHA-------FSSLRH----------PLQAIAFYLYMLRAEVLLTTVHGQVWKNGFS  133 (311)
Q Consensus        72 ~~g~~~-~a~~~~~~m~~~~~~~~~~-------~~~~~~----------~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~  133 (311)
                      +.|.++ +|+++++.+..-|...|.+       +...+.          +++++.+++.+...               .+
T Consensus        41 ~~~e~s~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~---------------~P  105 (331)
T 3dss_A           41 QAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV---------------NP  105 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH---------------CT
T ss_pred             HcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHh---------------CC
Confidence            344444 6777777766544333333       111111          56777777777654               35


Q ss_pred             CchhHHHHHHHHHHhCCC--CccchHHHHHHhccCCCCCHhHHHHHHHHHHH------HHHHHHhhCC---CCcHhHHHH
Q 044412          134 SPVFVQTAMVDNYSYSNK--FFESRRVSRRLFDEMPERKFATWNTMIDAYAR------LAELLFNKMP---AWDIRSWTT  202 (311)
Q Consensus       134 ~~~~~~~~ll~~~~~~g~--~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~------~a~~~~~~m~---~~~~~~y~~  202 (311)
                      -+..+|+.---.+.+.|+  ++++..+...+++. ...|...|+.---.+..      .+.+.++.+.   ..|...|+.
T Consensus       106 Kny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~-dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~~  184 (331)
T 3dss_A          106 KSYGTWHHRCWLLSRLPEPNWARELELCARFLEA-DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHY  184 (331)
T ss_dssp             TCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHHH
T ss_pred             CCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHHH
Confidence            578888888888888885  67844444444432 12344444432222211      1333333332   236666776


Q ss_pred             HHHHHHhC--------------CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcc-CChhhHHHHHHhhCChHHHHHH
Q 044412          203 MITSYSQN--------------KQFREALDAFNKTKKSGTGSDQVTMATVLSACAHL-GALDLGRGIQIYCRSLGRSLLV  267 (311)
Q Consensus       203 li~~~~~~--------------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~-~~~~~a~~~~~~~~~~~~a~~~  267 (311)
                      .-..+.+.              +.++++++.+....... +-|...|+-+-..+.+. |.-+..   -+..+.++++.+.
T Consensus       185 R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~---~~~~~~l~~el~~  260 (331)
T 3dss_A          185 RSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELS---VEKSTVLQSELES  260 (331)
T ss_dssp             HHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCC---HHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccc---hHHHHHHHHHHHH
Confidence            65555554              34677888888777632 22444555333333332 111000   0012334566666


Q ss_pred             HhhcC--CCCchhHHHHHHHH-----HhcCChHHHHHHHHHHHH
Q 044412          268 FFKLR--EKNLLCWNSITEAL-----AIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       268 ~~~~~--~p~~~~~~~li~~~-----~~~g~~~~a~~~~~~M~~  304 (311)
                      ++++.  .||. .|+.+-.+.     -..|..+++..+++++++
T Consensus       261 ~~elle~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          261 CKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHHHHHCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             HHHHHhhCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            66665  6765 454332222     245777788888888764

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=90.71  E-value=4.3  Score=30.70  Aligned_cols=89  Identities=7%  Similarity=-0.017  Sum_probs=46.9

Q ss_pred             chhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh
Q 044412          135 PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       135 ~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~  214 (311)
                      +...|..|-+...+.|+++-    |++.|.....                               |..+.--|...|+.+
T Consensus        33 ~~~~Wk~Lg~~AL~~gn~~l----Ae~cy~~~~D-------------------------------~~~L~~Ly~~tg~~e   77 (177)
T 3mkq_B           33 DSITWERLIQEALAQGNASL----AEMIYQTQHS-------------------------------FDKLSFLYLVTGDVN   77 (177)
T ss_dssp             CHHHHHHHHHHHHHTTCHHH----HHHHHHHTTC-------------------------------HHHHHHHHHHHTCHH
T ss_pred             CHHHHHHHHHHHHHcCChHH----HHHHHHHhCC-------------------------------HHHHHHHHHHhCCHH
Confidence            34566666666666666666    6666555332                               222233333345554


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHH
Q 044412          215 EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRS  264 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a  264 (311)
                      +-.++-+.-...|      -++.-..++.-.|+++++.+++...|+..+|
T Consensus        78 ~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~~r~~eA  121 (177)
T 3mkq_B           78 KLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEGGSLPLA  121 (177)
T ss_dssp             HHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHCCChHHH
Confidence            4443333322222      2344455555666777776666666666665

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=90.63  E-value=0.6  Score=34.79  Aligned_cols=93  Identities=12%  Similarity=0.006  Sum_probs=65.9

Q ss_pred             HhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CCC-chhHHHHHH
Q 044412          208 SQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EKN-LLCWNSITE  284 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p~-~~~~~~li~  284 (311)
                      .+.+.+++|+..+++-.+.. +-+...|..+=.++...++++.+....   +..++|...|++-.  .|+ ...|+.+-.
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al---~~~~eAi~~le~AL~ldP~~~~A~~~LG~   88 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAK---QMIQEAITKFEEALLIDPKKDEAVWCIGN   88 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHH---HHHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhH---hHHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence            45567899999999887743 335667776777777777665444332   23556666666655  454 568999999


Q ss_pred             HHHhcC-----------ChHHHHHHHHHHHH
Q 044412          285 ALAIHG-----------FAHEALGMFDRMTY  304 (311)
Q Consensus       285 ~~~~~g-----------~~~~a~~~~~~M~~  304 (311)
                      +|...|           ++++|...|++..+
T Consensus        89 ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~  119 (158)
T 1zu2_A           89 AYTSFAFLTPDETEAKHNFDLATQFFQQAVD  119 (158)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcccCcchhhhhccHHHHHHHHHHHHH
Confidence            998774           89999999999876

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=90.46  E-value=2.3  Score=30.41  Aligned_cols=106  Identities=10%  Similarity=-0.065  Sum_probs=70.3

Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA  180 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~  180 (311)
                      ++.++|+++|+.-.+.|               .|+..    |-..|...+.+++    |...|+...+.           
T Consensus         9 ~d~~~A~~~~~~aa~~g---------------~~~a~----lg~~y~~g~~~~~----A~~~~~~Aa~~-----------   54 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN---------------EMFGC----LSLVSNSQINKQK----LFQYLSKACEL-----------   54 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT---------------CTTHH----HHHHTCTTSCHHH----HHHHHHHHHHT-----------
T ss_pred             cCHHHHHHHHHHHHcCC---------------CHhhh----HHHHHHcCCCHHH----HHHHHHHHHcC-----------
Confidence            36788888888876654               33333    4455556566666    55555542221           


Q ss_pred             HHHHHHHHHhhCCCCcHhHHHHHHHHHHh----CCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc----cCChhhHH
Q 044412          181 YARLAELLFNKMPAWDIRSWTTMITSYSQ----NKQFREALDAFNKTKKSGTGSDQVTMATVLSACAH----LGALDLGR  252 (311)
Q Consensus       181 ~~~~a~~~~~~m~~~~~~~y~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~----~~~~~~a~  252 (311)
                                    -+...++.|-..|..    .+++++|++.|++-.+.|   +...+..|-..|..    .++.++|.
T Consensus        55 --------------g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~  117 (138)
T 1klx_A           55 --------------NSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAV  117 (138)
T ss_dssp             --------------TCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             --------------CCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHH
Confidence                          245666667777777    789999999999988875   45566666666666    67888777


Q ss_pred             HHHHh
Q 044412          253 GIQIY  257 (311)
Q Consensus       253 ~~~~~  257 (311)
                      ..++.
T Consensus       118 ~~~~~  122 (138)
T 1klx_A          118 KTFEK  122 (138)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76655

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=90.20  E-value=3.5  Score=35.05  Aligned_cols=173  Identities=11%  Similarity=0.050  Sum_probs=102.3

Q ss_pred             hccCChhHHHHhcccCCC--CC-eeeeec----cccCC-ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQE--PN-VFVYHA----FSSLR-HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAM  142 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~--~~-~~~~~~----~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~l  142 (311)
                      .+....++|+++++.+..  |+ ...|+.    +...+ .+++++++++.+...               .+-+..+|+.-
T Consensus        65 ~~~e~se~AL~lt~~~L~~nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~---------------nPKny~aW~hR  129 (349)
T 3q7a_A           65 AKEEKSERALELTEIIVRMNPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQ---------------NLKSYQVWHHR  129 (349)
T ss_dssp             HTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHT---------------TCCCHHHHHHH
T ss_pred             HhCCCCHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh---------------CCCcHHHHHHH
Confidence            445556678888877754  22 233443    44445 589999999998765               25567788887


Q ss_pred             HHHHHhC-C-CCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChh------
Q 044412          143 VDNYSYS-N-KFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFR------  214 (311)
Q Consensus       143 l~~~~~~-g-~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~------  214 (311)
                      -..+.+. + +.++    +..+++.+.+.+                       ..|...|+----.+.+.|..+      
T Consensus       130 ~wlL~~l~~~~~~~----EL~~~~k~L~~d-----------------------pkNy~AW~~R~wvl~~l~~~~~~~~~~  182 (349)
T 3q7a_A          130 LLLLDRISPQDPVS----EIEYIHGSLLPD-----------------------PKNYHTWAYLHWLYSHFSTLGRISEAQ  182 (349)
T ss_dssp             HHHHHHHCCSCCHH----HHHHHHHHTSSC-----------------------TTCHHHHHHHHHHHHHHHHTTCCCHHH
T ss_pred             HHHHHHhcCCChHH----HHHHHHHHHHhC-----------------------CCCHHHHHHHHHHHHHhccccccchhh
Confidence            7777776 6 7777    455555444332                       235555554444444444444      


Q ss_pred             --HHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHHHHHHhc
Q 044412          215 --EALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSITEALAIH  289 (311)
Q Consensus       215 --~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li~~~~~~  289 (311)
                        ++++.++++.+.. .-|...|+-.-..+.+.+.......+      .+++.+.+++..  .| |...|+.+-..+.+.
T Consensus       183 ~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~------~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~  255 (349)
T 3q7a_A          183 WGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRS------LQDELIYILKSIHLIPHNVSAWNYLRGFLKHF  255 (349)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHH------HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHH------HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhc
Confidence              9999999998864 33666777766666666642111111      123444443332  34 567787776666666


Q ss_pred             CCh
Q 044412          290 GFA  292 (311)
Q Consensus       290 g~~  292 (311)
                      |+.
T Consensus       256 ~~~  258 (349)
T 3q7a_A          256 SLP  258 (349)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=89.74  E-value=1.1  Score=29.36  Aligned_cols=51  Identities=14%  Similarity=0.096  Sum_probs=38.7

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhcCCCC-CHH-HHHHHHHHHhccCChhhHHHHHH
Q 044412          204 ITSYSQNKQFREALDAFNKTKKSGTGS-DQV-TMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       204 i~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~-t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      ...+...|++++|++.|++..+.  .| +.. .+..+-.++...|++++|...++
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~   59 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQT--EPVGKDEAYYLMGNAYRKLGDWQKALNNYQ   59 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHH--CSSTHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            44567789999999999998875  34 456 77778888888888887766553

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=89.60  E-value=0.47  Score=35.36  Aligned_cols=105  Identities=11%  Similarity=-0.029  Sum_probs=69.6

Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHH------HHHHhccCCCCCHh
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRV------SRRLFDEMPERKFA  172 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~------a~~~~~~~~~~~~~  172 (311)
                      +.+.+++|++.++.-.+..               +-+...|+.+-.++...|+++.+.+.      |...|++..+    
T Consensus        14 r~~~feeA~~~~~~Ai~l~---------------P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~----   74 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSN---------------PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL----   74 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH----
T ss_pred             HHhHHHHHHHHHHHHHHHC---------------CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHH----
Confidence            4456788888887766532               44678888888888888887642210      3333332211    


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhC-----------CChhHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 044412          173 TWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQN-----------KQFREALDAFNKTKKSGTGSDQVTMATVLS  240 (311)
Q Consensus       173 ~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~-----------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  240 (311)
                                         + .| +...|+.+-.+|...           |++++|++.|++-.+  +.|+...|...+.
T Consensus        75 -------------------l-dP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~  132 (158)
T 1zu2_A           75 -------------------I-DPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLE  132 (158)
T ss_dssp             -------------------H-CTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHH
T ss_pred             -------------------h-CcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHH
Confidence                               0 23 456777777787766           489999999999887  5788888776666


Q ss_pred             HHhc
Q 044412          241 ACAH  244 (311)
Q Consensus       241 a~~~  244 (311)
                      ..-+
T Consensus       133 ~~~k  136 (158)
T 1zu2_A          133 MTAK  136 (158)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            5544

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=89.25  E-value=2.2  Score=31.45  Aligned_cols=81  Identities=11%  Similarity=-0.073  Sum_probs=43.5

Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccC---ChhhHHHHHHhhCChHHHHHHHhhcCCC--CchhHHHHHHHHH
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLG---ALDLGRGIQIYCRSLGRSLLVFFKLREK--NLLCWNSITEALA  287 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~---~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~~~~~~~li~~~~  287 (311)
                      +..+.+-|.+-.+.|- ++..+--.+--++++.+   +.+++..+++.         +++.- .|  +...+-.|--+|.
T Consensus        14 l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~---------ll~~~-~p~~~rd~lY~LAv~~~   82 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEE---------LLPKG-SKEEQRDYVFYLAVGNY   82 (152)
T ss_dssp             HHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHH---------HHHHS-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHH---------HHhcC-CccchHHHHHHHHHHHH
Confidence            3455555555555443 56666555555666666   33444433322         11110 12  1233444555668


Q ss_pred             hcCChHHHHHHHHHHHH
Q 044412          288 IHGFAHEALGMFDRMTY  304 (311)
Q Consensus       288 ~~g~~~~a~~~~~~M~~  304 (311)
                      +.|++++|.++++...+
T Consensus        83 kl~~Y~~A~~y~~~lL~   99 (152)
T 1pc2_A           83 RLKEYEKALKYVRGLLQ   99 (152)
T ss_dssp             HTSCHHHHHHHHHHHHH
T ss_pred             HccCHHHHHHHHHHHHh
Confidence            88888888888887765

>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=87.86  E-value=5.2  Score=36.49  Aligned_cols=164  Identities=13%  Similarity=0.026  Sum_probs=96.4

Q ss_pred             hhhHHHHHHHHHHhccCcc-hhHHHHHHHHHhhccCC----------hhHHHHhcccCCCCCeeeeec-------cccCC
Q 044412           40 IKELECVYATIVKTNANLD-CFLAKQFISFCTSRFHF----------IDYTILVFPQMQEPNVFVYHA-------FSSLR  101 (311)
Q Consensus        40 ~~~~~~l~~~m~~~g~~p~-~~~~~~ll~~~~~~~g~----------~~~a~~~~~~m~~~~~~~~~~-------~~~~~  101 (311)
                      .+++...++.++...  |+ ..+|+.-=.++ .+.|+          ++++.+.++.+.+.+...|.+       +.+.+
T Consensus        45 ~eeal~~~~~~l~~n--P~~~taW~~R~~~l-~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~  121 (567)
T 1dce_A           45 DESVLELTSQILGAN--PDFATLWNCRREVL-QHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLP  121 (567)
T ss_dssp             SHHHHHHHHHHHHHC--TTCHHHHHHHHHHH-HHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHHHHHHC--chhHHHHHHHHHHH-HhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcc
Confidence            344466666666653  33 34444433333 44444          777777777765433333333       44445


Q ss_pred             --ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCC-CCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412          102 --HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSN-KFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus       102 --~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g-~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                        +++++++.++.+.+..               +-+...|+.--..+.+.| ..++    +.+.++.+.+.+.       
T Consensus       122 ~~~~~~el~~~~k~l~~d---------------~~N~~aW~~R~~~l~~l~~~~~~----el~~~~~~I~~~p-------  175 (567)
T 1dce_A          122 EPNWARELELCARFLEAD---------------ERNFHCWDYRRFVAAQAAVAPAE----ELAFTDSLITRNF-------  175 (567)
T ss_dssp             SCCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTCCCHHH----HHHHHHTTTTTTC-------
T ss_pred             cccHHHHHHHHHHHHhhc---------------cccccHHHHHHHHHHHcCCChHH----HHHHHHHHHHHCC-------
Confidence              5688888888876642               456677777666677777 6666    6666565554321       


Q ss_pred             HHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhC--------------CChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhc
Q 044412          179 DAYARLAELLFNKMPAWDIRSWTTMITSYSQN--------------KQFREALDAFNKTKKSGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       179 ~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~--------------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~  244 (311)
                                      .|...|+..-..+.+.              +.++++++.+.+..... +-|...|.-+-..+.+
T Consensus       176 ----------------~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~  238 (567)
T 1dce_A          176 ----------------SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGR  238 (567)
T ss_dssp             ----------------CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSC
T ss_pred             ----------------CCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhc
Confidence                            2445555555444442              45789999998877642 2356667776666666


Q ss_pred             cCChh
Q 044412          245 LGALD  249 (311)
Q Consensus       245 ~~~~~  249 (311)
                      .+..+
T Consensus       239 ~~~~~  243 (567)
T 1dce_A          239 AEPHD  243 (567)
T ss_dssp             CCCCS
T ss_pred             CCCcc
Confidence            66543

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=86.78  E-value=1.6  Score=29.44  Aligned_cols=76  Identities=9%  Similarity=-0.136  Sum_probs=59.3

Q ss_pred             ChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec--cccCCChhHHHHHHHHHHHC
Q 044412           39 SIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA--FSSLRHPLQAIAFYLYMLRA  116 (311)
Q Consensus        39 ~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--~~~~~~~~~a~~~~~~m~~~  116 (311)
                      +.+++..|-+.+...|- -..++.- =+..+ .+.|++++|+.+.+.+.-||+.+|-+  -.+.|..+++...+.++...
T Consensus        21 ~HqEA~tIAdwL~~~~~-~E~v~lI-R~sSL-mNrG~Yq~Al~l~~~~c~pdlepw~ALce~rlGl~s~le~rL~~la~s   97 (115)
T 2uwj_G           21 CHEEALCIAEWLERLGQ-DEAARLI-RISSL-ANQGRYQEALAFAHGNPWPALEPWFALCEWHLGLGAALDRRLAGLGGS   97 (115)
T ss_dssp             CHHHHHHHHHHHHHTTC-HHHHHHH-HHHHH-HHTTCHHHHHGGGTTCCCGGGHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHhCCc-HHHHHHH-HHHHH-HcchhHHHHHHhcCCCCCchHHHHHHHHHHhcccHHHHHHHHHHHHhC
Confidence            66777888888887765 2222222 23344 78999999999999999999999998  57889999999888888877


Q ss_pred             C
Q 044412          117 E  117 (311)
Q Consensus       117 ~  117 (311)
                      |
T Consensus        98 g   98 (115)
T 2uwj_G           98 S   98 (115)
T ss_dssp             S
T ss_pred             C
Confidence            6

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=86.31  E-value=6.4  Score=39.29  Aligned_cols=212  Identities=7%  Similarity=0.011  Sum_probs=124.8

Q ss_pred             HHHHHHHhhccCChhHHHHhcccCCCCCeeeeec---cccCCChhHHHHHHHHHHHCCCCch-------HHHHHHHHhcC
Q 044412           63 KQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA---FSSLRHPLQAIAFYLYMLRAEVLLT-------TVHGQVWKNGF  132 (311)
Q Consensus        63 ~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~---~~~~~~~~~a~~~~~~m~~~~~~p~-------~~~~~~~~~g~  132 (311)
                      ..++..+ .+.+..+.+.++....++....+|-.   +...|++++|.+.|++-. .|+..+       .-...+.....
T Consensus       816 ~~l~~~l-~~~~~~~~~~~l~~~~~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa-~~~~~~~~l~~~~~~~~~~~~~~~  893 (1139)
T 4fhn_B          816 TELVEKL-FLFKQYNACMQLIGWLNSDPIAVYLKALIYLKSKEAVKAVRCFKTTS-LVLYSHTSQFAVLREFQEIAEKYH  893 (1139)
T ss_dssp             HHHHHHH-HHHSCTTHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHTCC-CSCTTCCCSCSSHHHHHHHHHTTT
T ss_pred             HHHHHHH-HHhhhHHHHHHHhhhccCCcHHHHHHHHHHHhcCCHHHHHHHHHHHh-hhhcccchhhhhhccccccccccc
Confidence            3455556 67777777777666555433333322   777888999988887642 222221       11111111111


Q ss_pred             --CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHH
Q 044412          133 --SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD--IRSWTTMITSYS  208 (311)
Q Consensus       133 --~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~  208 (311)
                        ..-..=|..++..|-+.|..+.+.++|....+.....+                        ++  ...|..+.+++.
T Consensus       894 ~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~------------------------~~~~~~l~~~iFk~~L  949 (1139)
T 4fhn_B          894 HQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDD------------------------EDLSIAITHETLKTAC  949 (1139)
T ss_dssp             SCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCC------------------------HHHHHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCC------------------------hhhHHHHHHHHHHHHH
Confidence              11123477888888888888887777666655433221                        12  235889999999


Q ss_pred             hCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC------CCCchhHHHH
Q 044412          209 QNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR------EKNLLCWNSI  282 (311)
Q Consensus       209 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~------~p~~~~~~~l  282 (311)
                      ..|++++|...+..+.....+  ......||...|..|.++.-.. |...|..++-.+++..--      ...+.=|..|
T Consensus       950 ~l~~ye~Ay~aL~~~pd~~~r--~~cLr~LV~~lce~~~~~~L~~-lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iL 1026 (1139)
T 4fhn_B          950 AAGKFDAAHVALMVLSTTPLK--KSCLLDFVNQLTKQGKINQLLN-YSMPTLRQDVDNLLERKAFQMINVESQPCWYNIL 1026 (1139)
T ss_dssp             HHCCSGGGGHHHHHHHHSSSC--HHHHHHHHHHHHHHCCHHHHHH-HTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHH
T ss_pred             hhCCHHHHHHHHHhCCCHHHH--HHHHHHHHHHHHhCCChhhhhC-CCCccHHHHHHHHHHHHHHhCCccccCCCHHHHh
Confidence            999999999999988765444  4567788888888887765443 222444444444443211      1111224444


Q ss_pred             HHHHHhcCChHHHHH-HHHHHH
Q 044412          283 TEALAIHGFAHEALG-MFDRMT  303 (311)
Q Consensus       283 i~~~~~~g~~~~a~~-~~~~M~  303 (311)
                      =.=+..+|++..|-. +|+...
T Consensus      1027 Ys~ri~r~dyR~AA~vmYe~~~ 1048 (1139)
T 4fhn_B         1027 FSWRYKHQNYRDAAAIIYEKLS 1048 (1139)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HhhhhccCChHHHHHHHHHHHH
Confidence            444557777766544 566654

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=86.17  E-value=2.4  Score=36.67  Aligned_cols=70  Identities=21%  Similarity=0.181  Sum_probs=51.5

Q ss_pred             HHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHH
Q 044412          139 QTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREAL  217 (311)
Q Consensus       139 ~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~  217 (311)
                      ...++.++...|+.+++...+..+...                            +| +...|-.+|.++.+.|+..+|+
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~----------------------------~P~~E~~~~~lm~al~~~Gr~~~Al  225 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFE----------------------------HPYREPLWTQLITAYYLSDRQSDAL  225 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH----------------------------STTCHHHHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh----------------------------CCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            344566677778877744444444332                            23 6778999999999999999999


Q ss_pred             HHHHHHHh-----cCCCCCHHHHH
Q 044412          218 DAFNKTKK-----SGTGSDQVTMA  236 (311)
Q Consensus       218 ~~~~~m~~-----~g~~p~~~t~~  236 (311)
                      +.|++..+     -|+.|...+-.
T Consensus       226 ~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          226 GAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHH
Confidence            99999754     49999987743

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=83.93  E-value=6.7  Score=26.26  Aligned_cols=76  Identities=7%  Similarity=-0.034  Sum_probs=54.3

Q ss_pred             CchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhC---CCCcHhHHHHHHHHHHhC
Q 044412          134 SPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKM---PAWDIRSWTTMITSYSQN  210 (311)
Q Consensus       134 ~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m---~~~~~~~y~~li~~~~~~  210 (311)
                      .+...+-.|-..+.+.|+++.    |...++.                   |.+.+..-   ..+....|..+-.++.+.
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~----A~~W~~~-------------------Al~~~~~~~~~~~~~~~i~~~L~~~~~~~   59 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYH----TELWMEQ-------------------ALRQLDEGEISTIDKVSVLDYLSYAVYQQ   59 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHTTCCCSSCHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHccchHH----HHHHHHH-------------------HHHhhhccCCCcccHHHHHHHHHHHHHHc
Confidence            455566778888889999999    6666554                   22333211   123566788999999999


Q ss_pred             CChhHHHHHHHHHHhcCCCCCHHH
Q 044412          211 KQFREALDAFNKTKKSGTGSDQVT  234 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~~p~~~t  234 (311)
                      |++++|+.++++..+  +.|+...
T Consensus        60 g~~~~A~~~~~~al~--l~P~~~~   81 (104)
T 2v5f_A           60 GDLDKALLLTKKLLE--LDPEHQR   81 (104)
T ss_dssp             TCHHHHHHHHHHHHH--HCTTCHH
T ss_pred             cCHHHHHHHHHHHHh--cCCCCHH
Confidence            999999999999987  4676543

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=83.62  E-value=1.4  Score=29.93  Aligned_cols=57  Identities=12%  Similarity=0.108  Sum_probs=44.1

Q ss_pred             HHHHHhhcc-ChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC
Q 044412           30 IANQLKKCS-SIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ   87 (311)
Q Consensus        30 ~~~~l~~~~-~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~   87 (311)
                      |..-+..-. +.=++++-.+.+....+.|++.+..+.+++| .|..++..|.++|+-++
T Consensus        15 y~~~F~~~~iD~~e~rrglN~l~~~DlVP~P~ii~aaLrAc-RRvND~alAVR~lE~iK   72 (109)
T 1v54_E           15 WVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRAC-RRLNDFASAVRILEVVK   72 (109)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHH-HHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHH-HHhhhHHHHHHHHHHHH
Confidence            344443333 3445577777778888999999999999999 99999999999987764

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=83.32  E-value=1.7  Score=29.35  Aligned_cols=76  Identities=9%  Similarity=-0.067  Sum_probs=58.8

Q ss_pred             ChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec--cccCCChhHHHHHHHHHHHC
Q 044412           39 SIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA--FSSLRHPLQAIAFYLYMLRA  116 (311)
Q Consensus        39 ~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--~~~~~~~~~a~~~~~~m~~~  116 (311)
                      +.+++..|-+.+...|- -..++.- =+..+ .+.|++++|+.+.+.+.-||+.+|-+  -.+.|..+++...+.++...
T Consensus        22 ~HqEA~tIAdwL~~~~~-~E~v~lI-R~sSL-mNrG~Yq~Al~l~~~~c~pdlepw~ALce~rlGl~s~le~rL~~la~s   98 (116)
T 2p58_C           22 YHEEANCIAEWLHLKGE-EEAVQLI-RLSSL-MNRGDYASALQQGNKLAYPDLEPWLALCEYRLGLGSALESRLNRLARS   98 (116)
T ss_dssp             CHHHHHHHHHHHHHTTC-HHHHHHH-HHHHH-HHTTCHHHHHHHHTTSCCGGGHHHHHHHHHHHTCHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhCCc-HHHHHHH-HHHHH-HcchhHHHHHHhcCCCCCchHHHHHHHHHHhcccHHHHHHHHHHHHhC
Confidence            66777888888888765 2222222 22344 78999999999999999999999988  56788888888888888777


Q ss_pred             C
Q 044412          117 E  117 (311)
Q Consensus       117 ~  117 (311)
                      |
T Consensus        99 g   99 (116)
T 2p58_C           99 Q   99 (116)
T ss_dssp             C
T ss_pred             C
Confidence            6

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=82.62  E-value=7  Score=25.78  Aligned_cols=51  Identities=4%  Similarity=-0.091  Sum_probs=21.9

Q ss_pred             HhHHHHHHHHHHhCCC---hhHHHHHHHHHHhcCCCCCH-HHHHHHHHHHhccCChh
Q 044412          197 IRSWTTMITSYSQNKQ---FREALDAFNKTKKSGTGSDQ-VTMATVLSACAHLGALD  249 (311)
Q Consensus       197 ~~~y~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~-~t~~~li~a~~~~~~~~  249 (311)
                      ...+..+-.++...++   .++|..+|++..+.  .|+. .....+-..+...|+++
T Consensus         6 ~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~   60 (93)
T 3bee_A            6 ATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQ   60 (93)
T ss_dssp             HHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHH
Confidence            3344444444433322   45555555555542  3332 23333333444444444

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=82.01  E-value=3.8  Score=27.11  Aligned_cols=67  Identities=15%  Similarity=0.136  Sum_probs=45.8

Q ss_pred             CCchhHHHHHHHHHHhCCC---CccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHh
Q 044412          133 SSPVFVQTAMVDNYSYSNK---FFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQ  209 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~---~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~  209 (311)
                      +.+...+..+-.++...++   .++    +..++++....|                       ..++.....+-..+..
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~----A~~~l~~AL~~d-----------------------p~~~rA~~~lg~~~~~   55 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDE----VSLLLEQALQLE-----------------------PYNEAALSLIANDHFI   55 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHH----HHHHHHHHHHHC-----------------------TTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHH----HHHHHHHHHHHC-----------------------cCCHHHHHHHHHHHHH
Confidence            3456666666666654444   577    555555433211                       1256777777788899


Q ss_pred             CCChhHHHHHHHHHHhc
Q 044412          210 NKQFREALDAFNKTKKS  226 (311)
Q Consensus       210 ~g~~~~a~~~~~~m~~~  226 (311)
                      .|++++|+..|+++.+.
T Consensus        56 ~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A           56 SFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             TTCHHHHHHHHHHHHTC
T ss_pred             cCCHHHHHHHHHHHHhh
Confidence            99999999999999875

>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=81.95  E-value=23  Score=32.24  Aligned_cols=95  Identities=12%  Similarity=0.077  Sum_probs=64.0

Q ss_pred             cHhHHHHHHHHHHhCC--ChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccC-ChhhHHHHHHhhCChHHHHHHHhhcC
Q 044412          196 DIRSWTTMITSYSQNK--QFREALDAFNKTKKSGTGSDQVTMATVLSACAHLG-ALDLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~-~~~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      +..+|+.=--.+.+.|  +++++++.++++.+.. +-+...|+----.+.+.| ..+             ++.+.++++.
T Consensus       106 ~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~-------------~el~~~~~~I  171 (567)
T 1dce_A          106 SYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPA-------------EELAFTDSLI  171 (567)
T ss_dssp             CHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHH-------------HHHHHHHTTT
T ss_pred             CHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChH-------------HHHHHHHHHH
Confidence            5667777666777778  6699999999999854 225566665555555555 444             5666666666


Q ss_pred             C---CCchhHHHHHHHHHhc--------------CChHHHHHHHHHHHH
Q 044412          273 E---KNLLCWNSITEALAIH--------------GFAHEALGMFDRMTY  304 (311)
Q Consensus       273 ~---p~~~~~~~li~~~~~~--------------g~~~~a~~~~~~M~~  304 (311)
                      +   .|...|+..-..+.+.              +.++++.+.+++...
T Consensus       172 ~~~p~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~  220 (567)
T 1dce_A          172 TRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFF  220 (567)
T ss_dssp             TTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHh
Confidence            3   3556777776666653              456888888887764

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=80.28  E-value=4.2  Score=26.40  Aligned_cols=43  Identities=14%  Similarity=0.049  Sum_probs=32.2

Q ss_pred             HHHHHHhhcC--CC-Cch-hHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          263 RSLLVFFKLR--EK-NLL-CWNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       263 ~a~~~~~~~~--~p-~~~-~~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      +|...|++..  .| +.. .|..+-..|...|++++|...|++..+.
T Consensus        18 ~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A           18 NALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            4444444433  34 456 8888889999999999999999998764

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=80.22  E-value=15  Score=26.92  Aligned_cols=77  Identities=10%  Similarity=-0.039  Sum_probs=49.8

Q ss_pred             CCchhHHHHHHHHHHhCC---CCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC--cHhHHHHHHHHH
Q 044412          133 SSPVFVQTAMVDNYSYSN---KFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW--DIRSWTTMITSY  207 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g---~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~--~~~~y~~li~~~  207 (311)
                      .++..+.-.+--++++.+   +++++..+.+.+++.-                           .|  +...+-.+--+|
T Consensus        29 ~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~---------------------------~p~~~rd~lY~LAv~~   81 (152)
T 1pc2_A           29 SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG---------------------------SKEEQRDYVFYLAVGN   81 (152)
T ss_dssp             CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS---------------------------CHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC---------------------------CccchHHHHHHHHHHH
Confidence            366666666777888888   5667555555554431                           12  122333455567


Q ss_pred             HhCCChhHHHHHHHHHHhcCCCCCHHHHHHH
Q 044412          208 SQNKQFREALDAFNKTKKSGTGSDQVTMATV  238 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  238 (311)
                      .+.|++++|.++++...+  +.|+..--..|
T Consensus        82 ~kl~~Y~~A~~y~~~lL~--ieP~n~QA~~L  110 (152)
T 1pc2_A           82 YRLKEYEKALKYVRGLLQ--TEPQNNQAKEL  110 (152)
T ss_dssp             HHTSCHHHHHHHHHHHHH--HCTTCHHHHHH
T ss_pred             HHccCHHHHHHHHHHHHh--cCCCCHHHHHH
Confidence            899999999999999987  47865433333

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	311
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.23
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.86
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.68
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.35
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.21
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.06
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.05
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.82
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.81
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.78
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.64
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.48
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.47
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.34
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.3
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.22
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.21
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.16
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.1
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.08
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	96.97
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	96.91
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.9
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.8
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	96.69
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.51
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.45
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.23
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.99
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.98
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.95
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.95
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.94
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.92
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	95.92
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.86
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	95.71
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	95.52
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	94.36
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	94.18
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	94.13
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	94.08
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	93.82
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	93.47
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.45
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	93.41
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	91.94
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	91.76
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	90.96
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	89.37
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	88.1
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	81.65

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.9e-09  Score=91.24  Aligned_cols=170  Identities=8%  Similarity=0.048  Sum_probs=116.0

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----HHHHHhhCC---CCcHhHHHHHHHHH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----AELLFNKMP---AWDIRSWTTMITSY  207 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----a~~~~~~m~---~~~~~~y~~li~~~  207 (311)
                      ...+..+...+...|+.++|.....+.... .+.+...|..+-..+...     |...++...   ..+...+..+-..+
T Consensus       169 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  247 (388)
T d1w3ba_         169 AVAWSNLGCVFNAQGEIWLAIHHFEKAVTL-DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVY  247 (388)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHhhcccccccCcHHHHHHHHHHHHHh-CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHH
Confidence            455666667777778888844333333322 112334555555544443     555555433   23556677777778


Q ss_pred             HhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHh---------------------hCChHHHH
Q 044412          208 SQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIY---------------------CRSLGRSL  265 (311)
Q Consensus       208 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~---------------------~~~~~~a~  265 (311)
                      .+.|++++|++.|++..+.  .| +..++..+-..+...|+.++|...++.                     .|+.++|.
T Consensus       248 ~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  325 (388)
T d1w3ba_         248 YEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAV  325 (388)
T ss_dssp             HHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHH
Confidence            8888888888888887663  34 356777777788888888888777765                     67888888


Q ss_pred             HHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          266 LVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       266 ~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      ..|++..  .| +..+|..+-..|...|++++|...|++..+  +.|+
T Consensus       326 ~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--l~P~  371 (388)
T d1w3ba_         326 RLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR--ISPT  371 (388)
T ss_dssp             HHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT--TCTT
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCC
Confidence            8888765  44 456788899999999999999999999875  4565

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=8.4e-08  Score=80.75  Aligned_cols=248  Identities=8%  Similarity=0.044  Sum_probs=158.8

Q ss_pred             CCCchhhhHHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeee-----
Q 044412           19 PTSVSFIRIHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFV-----   93 (311)
Q Consensus        19 ~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~-----   93 (311)
                      |+.+..  ...+..++...|+.+++...++..++.. +-+..++..+..++ .+.|++++|...+....+.+...     
T Consensus        30 p~~~~~--~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~  105 (388)
T d1w3ba_          30 PDNTGV--LLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVY-KERGQLQEAIEHYRHALRLKPDFIDGYI  105 (388)
T ss_dssp             TTCHHH--HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             CCCHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHh-hhhccccccccccccccccccccccccc
Confidence            554443  3456667777888889988888887764 23456788888888 88999999888876553100000     


Q ss_pred             ------------------------------------------------------------------eec----cccCCCh
Q 044412           94 ------------------------------------------------------------------YHA----FSSLRHP  103 (311)
Q Consensus        94 ------------------------------------------------------------------~~~----~~~~~~~  103 (311)
                                                                                        +..    +...|+.
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  185 (388)
T d1w3ba_         106 NLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEI  185 (388)
T ss_dssp             HHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccCcchhHHHHhhcccccccCcH
Confidence                                                                              000    2233344


Q ss_pred             hHHHHHHHHHHHCCCCchHHHHHHHHhcCCC-chhHHHHHHHHHHhCCCCccchHHHHHHhccCC---CCCHhHHHHHHH
Q 044412          104 LQAIAFYLYMLRAEVLLTTVHGQVWKNGFSS-PVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMP---ERKFATWNTMID  179 (311)
Q Consensus       104 ~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~-~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~---~~~~~~~~~li~  179 (311)
                      ++|...++...+                ..| +...|..+...|...|++++    |...+....   ......+..+-.
T Consensus       186 ~~A~~~~~~al~----------------~~p~~~~~~~~l~~~~~~~~~~~~----A~~~~~~~~~~~~~~~~~~~~l~~  245 (388)
T d1w3ba_         186 WLAIHHFEKAVT----------------LDPNFLDAYINLGNVLKEARIFDR----AVAAYLRALSLSPNHAVVHGNLAC  245 (388)
T ss_dssp             HHHHHHHHHHHH----------------HCTTCHHHHHHHHHHHHTTTCTTH----HHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH----------------hCcccHHHHHHHhhhhhccccHHH----HHHHHHHhHHHhhhHHHHHHHHHH
Confidence            444444433322                233 35667777788888888888    444444332   223344555555


Q ss_pred             HHHHH-----HHHHHhhCC--CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhH
Q 044412          180 AYARL-----AELLFNKMP--AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLG  251 (311)
Q Consensus       180 ~~~~~-----a~~~~~~m~--~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a  251 (311)
                      .+.+.     |...|++..  .| +..+|..+...+...|++++|++.++..... .+.+...+..+...+...|++++|
T Consensus       246 ~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A  324 (388)
T d1w3ba_         246 VYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIEEA  324 (388)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHHHCCCHHHH
Confidence            55443     666665432  23 4567777777888888888888888776654 345666777777778888888888


Q ss_pred             HHHHHh---------------------hCChHHHHHHHhhcC--CCC-chhHHHHHHHHHhcCC
Q 044412          252 RGIQIY---------------------CRSLGRSLLVFFKLR--EKN-LLCWNSITEALAIHGF  291 (311)
Q Consensus       252 ~~~~~~---------------------~~~~~~a~~~~~~~~--~p~-~~~~~~li~~~~~~g~  291 (311)
                      ...++.                     .|+.++|...|++..  .|+ ...|..+-..|.+.||
T Consensus       325 ~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         325 VRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            877776                     777778888887754  454 5678888888877765

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.68  E-value=1.5e-07  Score=77.96  Aligned_cols=97  Identities=11%  Similarity=0.043  Sum_probs=76.7

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-  274 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-  274 (311)
                      +...+..+-..+...|++++|+..|++..... +-+...|..+-.++...|++++|...++.      +.++     .| 
T Consensus       171 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~------al~~-----~p~  238 (323)
T d1fcha_         171 DPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRR------ALEL-----QPG  238 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTT
T ss_pred             ccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHH------HHHH-----hhc
Confidence            56678888889999999999999999987642 22467788888899999999977666533      2221     34 


Q ss_pred             CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          275 NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       275 ~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +...|..+-..|.+.|++++|...|++..+
T Consensus       239 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         239 YIRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            466789999999999999999999998764

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=8.5e-06  Score=67.00  Aligned_cols=226  Identities=14%  Similarity=0.076  Sum_probs=137.0

Q ss_pred             HHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC--CCC-eeeeec----cccCCChhH
Q 044412           33 QLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ--EPN-VFVYHA----FSSLRHPLQ  105 (311)
Q Consensus        33 ~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~--~~~-~~~~~~----~~~~~~~~~  105 (311)
                      .+-..|+.+++...++..++.. +-+..+|..+-.++ ...|+++.|...|++..  .|+ ...|..    +...|++++
T Consensus        28 ~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~-~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~  105 (323)
T d1fcha_          28 RRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQ-AENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQ  105 (323)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHH-HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHcCChHHHHHHHHhhhccccccccccccccccccccccccc
Confidence            4456677777777777766653 12455666666777 77777777777776643  232 122211    666777777


Q ss_pred             HHHHHHHHHHCCCCch-----------------------------------HHHHHHHHhc-CCCchhHHHHHHHHHHhC
Q 044412          106 AIAFYLYMLRAEVLLT-----------------------------------TVHGQVWKNG-FSSPVFVQTAMVDNYSYS  149 (311)
Q Consensus       106 a~~~~~~m~~~~~~p~-----------------------------------~~~~~~~~~g-~~~~~~~~~~ll~~~~~~  149 (311)
                      |.+.+++.....-...                                   ..+...++.. -.++..++..+-..+...
T Consensus       106 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~  185 (323)
T d1fcha_         106 ACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLS  185 (323)
T ss_dssp             HHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHT
T ss_pred             cccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHH
Confidence            7777776654221000                                   1111111111 123455666677777777


Q ss_pred             CCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCC
Q 044412          150 NKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTG  229 (311)
Q Consensus       150 g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~  229 (311)
                      |++++    |...++....                       ....+...|..+-..|...|++++|++.|++..+.  .
T Consensus       186 ~~~~~----A~~~~~~al~-----------------------~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~  236 (323)
T d1fcha_         186 GEYDK----AVDCFTAALS-----------------------VRPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--Q  236 (323)
T ss_dssp             TCHHH----HHHHHHHHHH-----------------------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C
T ss_pred             HHHhh----hhcccccccc-----------------------cccccccchhhhhhcccccccchhHHHHHHHHHHH--h
Confidence            77777    4444443111                       01125678888999999999999999999998874  4


Q ss_pred             C-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC-------CCchhHHHHHHHHHhcCChHHH
Q 044412          230 S-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE-------KNLLCWNSITEALAIHGFAHEA  295 (311)
Q Consensus       230 p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~-------p~~~~~~~li~~~~~~g~~~~a  295 (311)
                      | +...|..+-.+|.+.|++++|...|+.      |.++..+-..       -....|+.+=.++...|+.+.+
T Consensus       237 p~~~~a~~~lg~~~~~~g~~~~A~~~~~~------al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~  304 (323)
T d1fcha_         237 PGYIRSRYNLGISCINLGAHREAVEHFLE------ALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY  304 (323)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHH------HHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH
T ss_pred             hccHHHHHHHHHHHHHCCCHHHHHHHHHH------HHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            5 466788899999999999988887744      3333322221       1123566666677767776544

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.21  E-value=7.3e-06  Score=67.36  Aligned_cols=158  Identities=13%  Similarity=0.130  Sum_probs=90.6

Q ss_pred             HHHHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCCCCCeeeeec--------cc
Q 044412           27 IHIIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQEPNVFVYHA--------FS   98 (311)
Q Consensus        27 ~~~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--------~~   98 (311)
                      ...+..+....|+...++.+++.+++........+|...+..+ .+.|+++.|.++|+...+....++..        +.
T Consensus       102 ~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~-~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~~  180 (308)
T d2onda1         102 YFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFA-RRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYY  180 (308)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHH-HHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHH-HHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            3455666666777777777777766543333344667777777 77777777777776654322111111        33


Q ss_pred             cCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHH
Q 044412           99 SLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMI  178 (311)
Q Consensus        99 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li  178 (311)
                      ..|+.+.|.++|+.....               .+.+...|...++.+.+.|+++.    |+.+|++.....        
T Consensus       181 ~~~~~~~a~~i~e~~l~~---------------~p~~~~~w~~y~~~~~~~g~~~~----aR~~fe~ai~~~--------  233 (308)
T d2onda1         181 CSKDKSVAFKIFELGLKK---------------YGDIPEYVLAYIDYLSHLNEDNN----TRVLFERVLTSG--------  233 (308)
T ss_dssp             TSCCHHHHHHHHHHHHHH---------------HTTCHHHHHHHHHHHHTTCCHHH----HHHHHHHHHHSS--------
T ss_pred             hccCHHHHHHHHHHHHHh---------------hhhhHHHHHHHHHHHHHcCChHH----HHHHHHHHHHhC--------
Confidence            446667777777666543               23445667777777777777777    555555421100        


Q ss_pred             HHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          179 DAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       179 ~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                                   ...|  ....|...+.--...|+++.+.++++++.+
T Consensus       234 -------------~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         234 -------------SLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             -------------SSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             -------------CCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                         0011  234566666655556777777777776654

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.06  E-value=0.0002  Score=58.50  Aligned_cols=256  Identities=9%  Similarity=-0.094  Sum_probs=162.5

Q ss_pred             HHHHhhccChhhHHHHHHHHHHhccCcc----hhHHHHHHHHHhhccCChhHHHHhcccCCC-----CCeee----e-ec
Q 044412           31 ANQLKKCSSIKELECVYATIVKTNANLD----CFLAKQFISFCTSRFHFIDYTILVFPQMQE-----PNVFV----Y-HA   96 (311)
Q Consensus        31 ~~~l~~~~~~~~~~~l~~~m~~~g~~p~----~~~~~~ll~~~~~~~g~~~~a~~~~~~m~~-----~~~~~----~-~~   96 (311)
                      ..+....|+++.+..+++...+..-..+    ...++.+-..+ ...|++++|...|++..+     ++...    + +.
T Consensus        19 A~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~-~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   97 (366)
T d1hz4a_          19 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVL-HCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQ   97 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHH-HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            3445677899999999988876532211    23566667788 899999999999987642     22111    1 11


Q ss_pred             ---cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc---hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCC
Q 044412           97 ---FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP---VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERK  170 (311)
Q Consensus        97 ---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~---~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~  170 (311)
                         +...|++..+...+.+.....          ...+....   ...+..+-..+...|+++.+..............+
T Consensus        98 ~~~~~~~~~~~~a~~~~~~al~~~----------~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~  167 (366)
T d1hz4a_          98 SEILFAQGFLQTAWETQEKAFQLI----------NEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQ  167 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH----------HHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh----------HhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhh
Confidence               778889999999888764311          11111211   23555666788999999996555555544443322


Q ss_pred             H----hHHHHHHHHHHHH------------HHHHHhhCCCC---cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-
Q 044412          171 F----ATWNTMIDAYARL------------AELLFNKMPAW---DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-  230 (311)
Q Consensus       171 ~----~~~~~li~~~~~~------------a~~~~~~m~~~---~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-  230 (311)
                      .    .++......+...            +..++......   ....+..+...+...|++++|...+.+........ 
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  247 (366)
T d1hz4a_         168 PQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANN  247 (366)
T ss_dssp             GGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTC
T ss_pred             hhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccc
Confidence            1    2222222222221            44555554432   23356667777888999999999999876533222 


Q ss_pred             --CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC-CC-CchhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          231 --DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR-EK-NLLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       231 --~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                        ...++..+-.++...|+++.|...++.      +....+... .| ....+..+-..|.+.|++++|.+.+++..
T Consensus       248 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~------al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         248 HFLQGQWRNIARAQILLGEFEPAEIVLEE------LNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             GGGHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHH------HHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence              244566778889999999988877643      333333333 12 24577888899999999999999998754

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.05  E-value=0.00021  Score=58.26  Aligned_cols=179  Identities=14%  Similarity=0.060  Sum_probs=119.4

Q ss_pred             ChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHH
Q 044412          102 HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAY  181 (311)
Q Consensus       102 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~  181 (311)
                      ..++|..+|+.-.+..              .+.+...|...+..+-+.|+++.|+.+....+...+......|...+...
T Consensus        79 ~~~~a~~i~~ral~~~--------------~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~  144 (308)
T d2onda1          79 FSDEAANIYERAISTL--------------LKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFA  144 (308)
T ss_dssp             HHHHHHHHHHHHHTTT--------------TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHc--------------CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHH
Confidence            3567777777665431              34456788888999999999999444444443333333334677766666


Q ss_pred             HHH-----HHHHHhhCCC--C-cHhHHHHHHHH-HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHH
Q 044412          182 ARL-----AELLFNKMPA--W-DIRSWTTMITS-YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGR  252 (311)
Q Consensus       182 ~~~-----a~~~~~~m~~--~-~~~~y~~li~~-~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~  252 (311)
                      .+.     |.++|++...  | +...|-..... +...|+.+.|..+|+...+. .+-+...|...+..+.+.|+.+.|+
T Consensus       145 ~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR  223 (308)
T d2onda1         145 RRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTR  223 (308)
T ss_dssp             HHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHH
Confidence            554     8888887642  2 22333332222 33468999999999999875 3445778889999999999999777


Q ss_pred             HHHHhhCChHHHHHHHhhcC-CC--CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          253 GIQIYCRSLGRSLLVFFKLR-EK--NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       253 ~~~~~~~~~~~a~~~~~~~~-~p--~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+|+..      .   .... .|  ....|...+.--...|+.+.+.++++++.+
T Consensus       224 ~~fe~a------i---~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         224 VLFERV------L---TSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HHHHHH------H---HSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHH------H---HhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            776542      1   1111 12  234788888888899999999999998865

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.82  E-value=6.7e-05  Score=59.23  Aligned_cols=165  Identities=11%  Similarity=-0.092  Sum_probs=96.0

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|++.|++..+.               -+-+..+|+.+-.+|.+.|++++    |...|++..+-+      
T Consensus        47 y~~~g~~~~A~~~~~~al~l---------------~p~~~~a~~~lg~~~~~~g~~~~----A~~~~~~al~~~------  101 (259)
T d1xnfa_          47 YDSLGLRALARNDFSQALAI---------------RPDMPEVFNYLGIYLTQAGNFDA----AYEAFDSVLELD------  101 (259)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHC------
T ss_pred             HHHCCCHHHHHHHHHHhhcc---------------CCCCHHHHhhhchHHHHHHHHHH----hhhhhhHHHHHH------
Confidence            55677888888888877652               13347788899999999999999    555555432210      


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                                       ..+..+|..+-..|...|++++|++.|++..+.. +.+......+..++.+.+..+....+..
T Consensus       102 -----------------p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (259)
T d1xnfa_         102 -----------------PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQ  163 (259)
T ss_dssp             -----------------TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             -----------------hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence                             1134456666677777777777777777766542 2233333333333333333333222222


Q ss_pred             h-----------------hCCh------HHHHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          257 Y-----------------CRSL------GRSLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       257 ~-----------------~~~~------~~a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .                 .+..      ..+...+..-.  .| ...+|..+-..|...|++++|.+.|++...
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  237 (259)
T d1xnfa_         164 HFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  237 (259)
T ss_dssp             HHHHSCCCSTHHHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2                 1111      11111110000  12 224677788899999999999999999875

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.81  E-value=0.0001  Score=60.60  Aligned_cols=218  Identities=9%  Similarity=0.005  Sum_probs=127.2

Q ss_pred             HHHHHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccC-ChhHHHHhcccCCC---CCeeeeec----cccC
Q 044412           29 IIANQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFH-FIDYTILVFPQMQE---PNVFVYHA----FSSL  100 (311)
Q Consensus        29 ~~~~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g-~~~~a~~~~~~m~~---~~~~~~~~----~~~~  100 (311)
                      .+..++...++.+++..+++.+++.. +-+...|+..-.++ ...| ++++|...++...+   .+..+|+.    +.+.
T Consensus        48 ~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l-~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l  125 (315)
T d2h6fa1          48 YFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLL-KSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWL  125 (315)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHH-HHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhh
Confidence            45566677777788888888877763 12334556555565 5554 47777777766542   22333333    6666


Q ss_pred             CChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHH
Q 044412          101 RHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDA  180 (311)
Q Consensus       101 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~  180 (311)
                      |++++|++.|+...+.               -+-+...|..+...+.+.|++++    |...++...+.+          
T Consensus       126 ~~~~eAl~~~~kal~~---------------dp~n~~a~~~~~~~~~~~~~~~~----Al~~~~~al~~~----------  176 (315)
T d2h6fa1         126 RDPSQELEFIADILNQ---------------DAKNYHAWQHRQWVIQEFKLWDN----ELQYVDQLLKED----------  176 (315)
T ss_dssp             TCCTTHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHHTCCTT----HHHHHHHHHHHC----------
T ss_pred             ccHHHHHHHHhhhhhh---------------hhcchHHHHHHHHHHHHHHhhHH----HHHHHHHHHHHC----------
Confidence            7777777777777653               13446777777777777777777    444444422211          


Q ss_pred             HHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC------hhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHH
Q 044412          181 YARLAELLFNKMPAWDIRSWTTMITSYSQNKQ------FREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRG  253 (311)
Q Consensus       181 ~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~------~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~  253 (311)
                                   ..+...|+.+-..+.+.+.      +++|++.+....+.  .| +...|+-+-..+...| .+++..
T Consensus       177 -------------p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~--~P~~~~~~~~l~~ll~~~~-~~~~~~  240 (315)
T d2h6fa1         177 -------------VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRG-LSKYPN  240 (315)
T ss_dssp             -------------TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTC-GGGCHH
T ss_pred             -------------CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHh--CCCchHHHHHHHHHHHhcC-hHHHHH
Confidence                         2356677776666666555      56788888887775  45 4566776665544433 454444


Q ss_pred             HHHhhCChHHHHHHHhhcC-CCCchhHHHHHHHHHhc--CChHHHHHHHHHH
Q 044412          254 IQIYCRSLGRSLLVFFKLR-EKNLLCWNSITEALAIH--GFAHEALGMFDRM  302 (311)
Q Consensus       254 ~~~~~~~~~~a~~~~~~~~-~p~~~~~~~li~~~~~~--g~~~~a~~~~~~M  302 (311)
                      .++..      .   +..+ ..+...+..+...|...  ++.+.+...+++-
T Consensus       241 ~~~~~------~---~l~~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~~~ka  283 (315)
T d2h6fa1         241 LLNQL------L---DLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKA  283 (315)
T ss_dssp             HHHHH------H---HHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHH
T ss_pred             HHHHH------H---HhCCCcCCHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            33111      1   1111 12344566666766543  5556666666554

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=0.00018  Score=59.02  Aligned_cols=177  Identities=10%  Similarity=0.060  Sum_probs=110.0

Q ss_pred             HHHHHHHHHhhccCChhHHHHhcccCCC--CCe-eeeec----cccCC-ChhHHHHHHHHHHHCCCCchHHHHHHHHhcC
Q 044412           61 LAKQFISFCTSRFHFIDYTILVFPQMQE--PNV-FVYHA----FSSLR-HPLQAIAFYLYMLRAEVLLTTVHGQVWKNGF  132 (311)
Q Consensus        61 ~~~~ll~~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~----~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~  132 (311)
                      .++.+-..+ .+.+..++|.+++++..+  |+. ..|+.    +...+ ++++|++.++...+..               
T Consensus        45 a~~~~~~~~-~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~---------------  108 (315)
T d2h6fa1          45 VYDYFRAVL-QRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ---------------  108 (315)
T ss_dssp             HHHHHHHHH-HHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC---------------
T ss_pred             HHHHHHHHH-HhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH---------------
Confidence            444454556 778888999888888763  333 23333    34434 5788999988876531               


Q ss_pred             CCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC
Q 044412          133 SSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       133 ~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~  212 (311)
                      +-+..+|+.+-..+.+.|++++    |...++...+.+                       ..+...|+.+...+...|+
T Consensus       109 p~~~~a~~~~~~~~~~l~~~~e----Al~~~~kal~~d-----------------------p~n~~a~~~~~~~~~~~~~  161 (315)
T d2h6fa1         109 PKNYQVWHHRRVLVEWLRDPSQ----ELEFIADILNQD-----------------------AKNYHAWQHRQWVIQEFKL  161 (315)
T ss_dssp             TTCHHHHHHHHHHHHHHTCCTT----HHHHHHHHHHHC-----------------------TTCHHHHHHHHHHHHHHTC
T ss_pred             HhhhhHHHHHhHHHHhhccHHH----HHHHHhhhhhhh-----------------------hcchHHHHHHHHHHHHHHh
Confidence            3457888888888888999999    555555433211                       2367788888888888899


Q ss_pred             hhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHHHH
Q 044412          213 FREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITEAL  286 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~~~  286 (311)
                      +++|++.++...+.. +-+...|+.+-..+.+.+.......+.+.......|.++     .| +...|+.+...+
T Consensus       162 ~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~-----~P~~~~~~~~l~~ll  230 (315)
T d2h6fa1         162 WDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL-----VPHNESAWNYLKGIL  230 (315)
T ss_dssp             CTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH-----STTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHh-----CCCchHHHHHHHHHH
Confidence            999999999988853 224556665555555555543333222223333344443     24 344555554433

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.64  E-value=0.0017  Score=52.20  Aligned_cols=139  Identities=11%  Similarity=0.005  Sum_probs=79.2

Q ss_pred             hhHHHHHHHHHH-hCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC--cHhHHHHHHHHHHhCCC
Q 044412          136 VFVQTAMVDNYS-YSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW--DIRSWTTMITSYSQNKQ  212 (311)
Q Consensus       136 ~~~~~~ll~~~~-~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~--~~~~y~~li~~~~~~g~  212 (311)
                      ..++..+...|- ..|++++    |...+..                   |.+++.....+  -..+|..+...+...|+
T Consensus       117 ~~~~~~l~~~~~~~~~~~~~----A~~~~~~-------------------A~~l~~~~~~~~~~~~~~~~la~~~~~~g~  173 (290)
T d1qqea_         117 ANFKFELGEILENDLHDYAK----AIDCYEL-------------------AGEWYAQDQSVALSNKCFIKCADLKALDGQ  173 (290)
T ss_dssp             HHHHHHHHHHHHHTTCCHHH----HHHHHHH-------------------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhHhhHHHHHHH----HHHHHHH-------------------HHHHHHhcCchhhhhhHHHHHHHHHHHcCh
Confidence            445666666664 4699999    6666655                   33444444332  23468888999999999


Q ss_pred             hhHHHHHHHHHHhcCCC-----CCH-HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHH
Q 044412          213 FREALDAFNKTKKSGTG-----SDQ-VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEAL  286 (311)
Q Consensus       213 ~~~a~~~~~~m~~~g~~-----p~~-~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~  286 (311)
                      +++|+..|++.......     +.. ..+......+...|+.+.|...++.....+....-     .+.......++.++
T Consensus       174 y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~-----sre~~~l~~l~~a~  248 (290)
T d1qqea_         174 YIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFAD-----SRESNFLKSLIDAV  248 (290)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC--------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccc-----hHHHHHHHHHHHHH
Confidence            99999999998764211     111 12333444556678888776666654444322100     01122345555555


Q ss_pred             Hh--cCChHHHHHHHHHH
Q 044412          287 AI--HGFAHEALGMFDRM  302 (311)
Q Consensus       287 ~~--~g~~~~a~~~~~~M  302 (311)
                      -.  .+.+++|...|+++
T Consensus       249 ~~~d~e~~~eai~~y~~~  266 (290)
T d1qqea_         249 NEGDSEQLSEHCKEFDNF  266 (290)
T ss_dssp             HTTCTTTHHHHHHHHTTS
T ss_pred             HhcCHHHHHHHHHHHHHH
Confidence            44  23466666666543

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=97.48  E-value=0.0064  Score=48.96  Aligned_cols=191  Identities=11%  Similarity=-0.004  Sum_probs=119.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCc------hhHHHHHHHHHHhCCCCccchHHHHHHhccCCC-C
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSP------VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE-R  169 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~------~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~-~  169 (311)
                      +...|++++|++++++..+.                .|+      ...++.+-..|...|++++|.....+.....+. +
T Consensus        22 ~~~~g~~~~A~~~~~~aL~~----------------~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~   85 (366)
T d1hz4a_          22 AINDGNPDEAERLAKLALEE----------------LPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHD   85 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHT----------------CCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHCCCHHHHHHHHHHHHhh----------------CcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence            44678889999998886553                222      245677778899999999944443333322111 1


Q ss_pred             CH----hHHHHHHHHHHHH------------HHHHHhhCCCC----cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc---
Q 044412          170 KF----ATWNTMIDAYARL------------AELLFNKMPAW----DIRSWTTMITSYSQNKQFREALDAFNKTKKS---  226 (311)
Q Consensus       170 ~~----~~~~~li~~~~~~------------a~~~~~~m~~~----~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~---  226 (311)
                      +.    .++..+...+...            +..+......+    ....+..+-..+...|+++.+...+......   
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~  165 (366)
T d1hz4a_          86 VWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSS  165 (366)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhh
Confidence            11    1222232333221            33444333322    1234556667788889999999999887653   


Q ss_pred             -CCCCCHHHHHHHHHHHhccCChhhHHHHHHh----------------------------hCChHHHHHHHhhcCC--C-
Q 044412          227 -GTGSDQVTMATVLSACAHLGALDLGRGIQIY----------------------------CRSLGRSLLVFFKLRE--K-  274 (311)
Q Consensus       227 -g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~----------------------------~~~~~~a~~~~~~~~~--p-  274 (311)
                       +......++..+...+...++...+...+..                            .++.+.|...+.+..+  | 
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~  245 (366)
T d1hz4a_         166 YQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFA  245 (366)
T ss_dssp             SCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCT
T ss_pred             hhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccc
Confidence             2223344555666666677777776666554                            6778888888877652  1 


Q ss_pred             -C---chhHHHHHHHHHhcCChHHHHHHHHHHH
Q 044412          275 -N---LLCWNSITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       275 -~---~~~~~~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                       +   ...+..+...+...|++++|...+++..
T Consensus       246 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  278 (366)
T d1hz4a_         246 NNHFLQGQWRNIARAQILLGEFEPAEIVLEELN  278 (366)
T ss_dssp             TCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             1   2356667888999999999999998875

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.47  E-value=0.001  Score=49.90  Aligned_cols=98  Identities=7%  Similarity=-0.045  Sum_probs=72.2

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK  274 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p  274 (311)
                      |+....-..-..|.+.|++++|+..|.+..+.. +-+...|..+-.+|.+.|+++.|...|...-.+           .|
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l-----------~p   69 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL-----------DG   69 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-----------CT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh-----------CC
Confidence            444455555677888999999999999887753 345667888888889988888655554332221           24


Q ss_pred             -CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          275 -NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       275 -~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                       ++..|..+-.+|...|++++|...|++..+
T Consensus        70 ~~~~a~~~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          70 QSVKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             466888899999999999999999987653

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=0.0011  Score=45.47  Aligned_cols=94  Identities=14%  Similarity=0.039  Sum_probs=71.6

Q ss_pred             HHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHH
Q 044412          204 ITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSIT  283 (311)
Q Consensus       204 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li  283 (311)
                      -..+.+.|++++|+..|.+..+.. +-+...|..+-.++...|+++.|...+...-..          ...+...|..+-
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~----------~p~~~~~~~~~g   78 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL----------KPDWGKGYSRKA   78 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----------CTTCHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHh----------ccchhhHHHHHH
Confidence            345677899999999999998752 445677888888999989888666554321111          134678899999


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          284 EALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       284 ~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      .++...|++++|...|++..+  +.|+
T Consensus        79 ~~~~~~~~~~~A~~~~~~a~~--~~p~  103 (117)
T d1elwa_          79 AALEFLNRFEEAKRTYEEGLK--HEAN  103 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHT--TCTT
T ss_pred             HHHHHccCHHHHHHHHHHHHH--hCCC
Confidence            999999999999999999875  3454

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=0.00087  Score=46.46  Aligned_cols=97  Identities=9%  Similarity=-0.013  Sum_probs=73.7

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCC--CCc--
Q 044412          201 TTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLRE--KNL--  276 (311)
Q Consensus       201 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~--p~~--  276 (311)
                      ..+++.+...+++++|.+.|++..+.+ +.+..++..+-.++.+.++.+..          +.|..+|++..+  |+.  
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~----------~~Ai~~l~~~l~~~~~~~~   71 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDI----------RKGIVLLEELLPKGSKEEQ   71 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHH----------HHHHHHHHHHTTTSCHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHH----------HHHHHHHHHHHhccCCchH
Confidence            457788888999999999999988753 44667888888888876666532          256667776552  322  


Q ss_pred             -hhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          277 -LCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       277 -~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                       ..|..+-.+|.+.|++++|...|++..+  +.|+
T Consensus        72 ~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~--~~P~  104 (122)
T d1nzna_          72 RDYVFYLAVGNYRLKEYEKALKYVRGLLQ--TEPQ  104 (122)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTT
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHH--hCcC
Confidence             3677888899999999999999999987  4565

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=0.0011  Score=49.86  Aligned_cols=147  Identities=6%  Similarity=0.085  Sum_probs=96.3

Q ss_pred             hccCChhHHHHhcccCCCCCeeeeec----cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHH
Q 044412           71 SRFHFIDYTILVFPQMQEPNVFVYHA----FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNY  146 (311)
Q Consensus        71 ~~~g~~~~a~~~~~~m~~~~~~~~~~----~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~  146 (311)
                      ...|+++.|.+.|+++.+++...|.-    +...|++++|++.|++-.+..               +-+...|..+-.+|
T Consensus        16 ~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld---------------p~~~~a~~~~g~~~   80 (192)
T d1hh8a_          16 ADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD---------------KHLAVAYFQRGMLY   80 (192)
T ss_dssp             HHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh---------------hhhhhhHHHHHHHH
Confidence            67899999999999998877655543    889999999999999976632               34577888899999


Q ss_pred             HhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          147 SYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       147 ~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                      .+.|++++|..-..+.+...+......|.            .+...... ...++..+-.++.+.|++++|.+.|....+
T Consensus        81 ~~~g~~~~A~~~~~kAl~~~~~n~~~~~~------------~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_          81 YQTEKYDLAIKDLKEALIQLRGNQLIDYK------------ILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTTTCSEEECG------------GGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HhhccHHHHHHHHHHHHHhCccCchHHHH------------HhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            99999999443333333222211100000            00000001 124556677788999999999999998887


Q ss_pred             cCCCCCHHHHHHHHHHHhc
Q 044412          226 SGTGSDQVTMATVLSACAH  244 (311)
Q Consensus       226 ~g~~p~~~t~~~li~a~~~  244 (311)
                      ....|+.......+..+.+
T Consensus       149 ~~~~~~~~~~~~Al~~~~~  167 (192)
T d1hh8a_         149 MKSEPRHSKIDKAMECVWK  167 (192)
T ss_dssp             TCCSGGGGHHHHHHHHHHT
T ss_pred             cCCCcchHHHHHHHHHHHh
Confidence            6555544444444444433

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.21  E-value=0.00089  Score=50.42  Aligned_cols=115  Identities=8%  Similarity=-0.040  Sum_probs=83.6

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +...|++++|++.|+++                  ..|+..+|..+-.+|.+.|++++    |.+.|++..+.       
T Consensus        15 ~~~~~d~~~Al~~~~~i------------------~~~~~~~~~nlG~~~~~~g~~~~----A~~~~~kAl~l-------   65 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAV------------------QDPHSRICFNIGCMYTILKNMTE----AEKAFTRSINR-------   65 (192)
T ss_dssp             HHHTTCHHHHHHHHHTS------------------SSCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHCCCHHHHHHHHHhc------------------CCCCHHHHHHHHHHHHHcCCchh----HHHHHHHHHHH-------
Confidence            45778999999999765                  46778888899999999999999    77766653321       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcC------------C--CCC-HHHHHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSG------------T--GSD-QVTMATVLSA  241 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g------------~--~p~-~~t~~~li~a  241 (311)
                                      ...+...|+.+-.+|.+.|++++|++.|++-....            .  +++ ..++..+-.+
T Consensus        66 ----------------dp~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~  129 (192)
T d1hh8a_          66 ----------------DKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFM  129 (192)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHH
T ss_pred             ----------------hhhhhhhHHHHHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHH
Confidence                            12357789999999999999999999999875421            1  111 2445555666


Q ss_pred             HhccCChhhHHHHHH
Q 044412          242 CAHLGALDLGRGIQI  256 (311)
Q Consensus       242 ~~~~~~~~~a~~~~~  256 (311)
                      +.+.|+++.|...+.
T Consensus       130 ~~~~~~~~~A~~~l~  144 (192)
T d1hh8a_         130 YAKKEEWKKAEEQLA  144 (192)
T ss_dssp             HHHTTCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHH
Confidence            777788886665543

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.00088  Score=45.96  Aligned_cols=95  Identities=9%  Similarity=0.066  Sum_probs=70.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++..+.               -+-+...|..+-.+|.+.|++++|........+.           
T Consensus        13 ~~~~g~~~eAi~~~~~al~~---------------~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~-----------   66 (117)
T d1elwa_          13 ALSVGNIDDALQCYSEAIKL---------------DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL-----------   66 (117)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----------
T ss_pred             HHHcCCHHHHHHHHHHHHhc---------------CCcchhhhhcccccccccccccccchhhhhHHHh-----------
Confidence            45778999999999988664               2455778888888999999999944443333332           


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTM  235 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  235 (311)
                                      ...+...|..+-.++...|++++|+..|++-.+  ..|+...+
T Consensus        67 ----------------~p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~--~~p~~~~~  107 (117)
T d1elwa_          67 ----------------KPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLK--HEANNPQL  107 (117)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--TCTTCHHH
T ss_pred             ----------------ccchhhHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCCHHH
Confidence                            123677888899999999999999999999886  45655443

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.10  E-value=0.0056  Score=48.92  Aligned_cols=139  Identities=10%  Similarity=0.048  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCc--HhHHHHHHHHHHhCCChhH
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWD--IRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~--~~~y~~li~~~~~~g~~~~  215 (311)
                      .|...-+.|-..|++++    |.+.|.+                   |.++......+.  ..+|+.+-.+|.+.|++++
T Consensus        39 ~y~~aa~~y~~~~~~~~----A~~~y~k-------------------A~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~   95 (290)
T d1qqea_          39 LCVQAATIYRLRKELNL----AGDSFLK-------------------AADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVN   95 (290)
T ss_dssp             HHHHHHHHHHHTTCTHH----HHHHHHH-------------------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHCcCHHH----HHHHHHH-------------------HHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHH
Confidence            46666778889999999    7777666                   445555554432  4578999999999999999


Q ss_pred             HHHHHHHHHh----cCC-CCCHHHHHHHHHHHh-ccCChhhHHHHHHhhCChHHHHHHHhhcCCCC--chhHHHHHHHHH
Q 044412          216 ALDAFNKTKK----SGT-GSDQVTMATVLSACA-HLGALDLGRGIQIYCRSLGRSLLVFFKLREKN--LLCWNSITEALA  287 (311)
Q Consensus       216 a~~~~~~m~~----~g~-~p~~~t~~~li~a~~-~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~--~~~~~~li~~~~  287 (311)
                      |.+.+++..+    .|- .....++..+...|. ..|+++.|...+..      |.+++.....+.  ..+|..+...+.
T Consensus        96 A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~------A~~l~~~~~~~~~~~~~~~~la~~~~  169 (290)
T d1qqea_          96 AVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYEL------AGEWYAQDQSVALSNKCFIKCADLKA  169 (290)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH------HHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHH------HHHHHHhcCchhhhhhHHHHHHHHHH
Confidence            9999987554    221 111345556666664 46889988877643      444443333221  346888999999


Q ss_pred             hcCChHHHHHHHHHHHHc
Q 044412          288 IHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       288 ~~g~~~~a~~~~~~M~~~  305 (311)
                      ..|++++|..+|++....
T Consensus       170 ~~g~y~~A~~~~~~~~~~  187 (290)
T d1qqea_         170 LDGQYIEASDIYSKLIKS  187 (290)
T ss_dssp             HTTCHHHHHHHHHHHHHT
T ss_pred             HcChHHHHHHHHHHHHHh
Confidence            999999999999997753

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.08  E-value=0.0021  Score=46.48  Aligned_cols=86  Identities=12%  Similarity=0.147  Sum_probs=37.6

Q ss_pred             HHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHHHHHH
Q 044412          206 SYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWNSITE  284 (311)
Q Consensus       206 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~~li~  284 (311)
                      .|.+.|++++|+..|.+..+.. +-+...|..+-.+|...|+++.|...|+.      |.++     .| +...|..+..
T Consensus        19 ~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~k------al~~-----~p~~~~a~~~~g~   86 (159)
T d1a17a_          19 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATR------AIEL-----DKKYIKGYYRRAA   86 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTTCHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHH------HHHH-----cccchHHHHHHHH
Confidence            3444555555555555554432 12333444444455555555433333211      1110     12 2344555555


Q ss_pred             HHHhcCChHHHHHHHHHHH
Q 044412          285 ALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       285 ~~~~~g~~~~a~~~~~~M~  303 (311)
                      ++...|++++|...+++..
T Consensus        87 ~~~~~g~~~eA~~~~~~a~  105 (159)
T d1a17a_          87 SNMALGKFRAALRDYETVV  105 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            5555555555555554444

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.97  E-value=0.0014  Score=47.53  Aligned_cols=92  Identities=15%  Similarity=0.081  Sum_probs=71.6

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++..+..               +-+...|..+-.+|...|++++    |...|+...+.       
T Consensus        20 ~~~~~~y~~A~~~~~~al~~~---------------p~~~~~~~~lg~~~~~~~~~~~----A~~~~~kal~~-------   73 (159)
T d1a17a_          20 YFKAKDYENAIKFYSQAIELN---------------PSNAIYYGNRSLAYLRTECYGY----ALGDATRAIEL-------   73 (159)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---------------TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHcCCHHHHHHHhhhccccc---------------hhhhhhhhhhHHHHHhccccch----HHHHHHHHHHH-------
Confidence            557899999999999887642               4457888889999999999999    66666553221       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQ  232 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  232 (311)
                                      ...+...|..+..+|...|++++|++.|++..+.  .|+.
T Consensus        74 ----------------~p~~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~--~p~~  111 (159)
T d1a17a_          74 ----------------DKKYIKGYYRRAASNMALGKFRAALRDYETVVKV--KPHD  111 (159)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTC
T ss_pred             ----------------cccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCC
Confidence                            1235678999999999999999999999999875  4553

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.91  E-value=0.002  Score=48.25  Aligned_cols=87  Identities=10%  Similarity=-0.034  Sum_probs=68.8

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++..+.               -+-+...|+.+-.+|.+.|++++    |...|+...+-+      
T Consensus        14 ~~~~g~~~~Ai~~~~kal~~---------------~p~~~~~~~~lg~~y~~~~~~~~----Ai~~~~~al~l~------   68 (201)
T d2c2la1          14 LFVGRKYPEAAACYGRAITR---------------NPLVAVYYTNRALCYLKMQQPEQ----ALADCRRALELD------   68 (201)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---------------CSCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHTTSC------
T ss_pred             HHHcCCHHHHHHHHHHHHHh---------------CCCCHHHHHhHHHHHhhhhhhhh----hhHHHHHHHHhC------
Confidence            56789999999999887653               24567889999999999999999    666666544321      


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHh
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKK  225 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~  225 (311)
                                       ..+..+|..+-.+|...|++++|+..|++..+
T Consensus        69 -----------------p~~~~a~~~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          69 -----------------GQSVKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             -----------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----------------CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                             12577888999999999999999999998764

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=96.90  E-value=0.0021  Score=43.62  Aligned_cols=88  Identities=11%  Similarity=-0.030  Sum_probs=70.0

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-CchhHH
Q 044412          203 MITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NLLCWN  280 (311)
Q Consensus       203 li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~~~~~  280 (311)
                      +-..+-+.|++++|+..|++..+.  .| +...|..+-.++.+.|++++|...++.      |.++     .| +...|.
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~------al~~-----~p~~~~a~~   88 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNH------ARML-----DPKDIAVHA   88 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTTCHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccc--ccccchhhhhhhhhhhhhhhHHHhhccccc------cccc-----ccccccchH
Confidence            445677889999999999999875  45 577888888999999999977766533      2222     34 577899


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHH
Q 044412          281 SITEALAIHGFAHEALGMFDRMT  303 (311)
Q Consensus       281 ~li~~~~~~g~~~~a~~~~~~M~  303 (311)
                      .+-..|...|++++|.+.+++..
T Consensus        89 ~la~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          89 ALAVSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHh
Confidence            99999999999999999998753

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.80  E-value=0.0057  Score=45.24  Aligned_cols=71  Identities=21%  Similarity=0.201  Sum_probs=57.1

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC-cHhHHHHHHHHHHhCCChh
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW-DIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~-~~~~y~~li~~~~~~g~~~  214 (311)
                      ...+..+..++.+.|++++|...+.+.+..                            +| +...|..++.+|.+.|+..
T Consensus        67 ~~a~~~la~~~~~~g~~~~Al~~~~~al~~----------------------------~P~~e~~~~~l~~al~~~Gr~~  118 (179)
T d2ff4a2          67 VLAHTAKAEAEIACGRASAVIAELEALTFE----------------------------HPYREPLWTQLITAYYLSDRQS  118 (179)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------------------------STTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHCCCchHHHHHHHHHHHh----------------------------CCccHHHHHHHHHHHHHhcCHH
Confidence            356778899999999999955554444443                            23 6789999999999999999


Q ss_pred             HHHHHHHHHHh-----cCCCCCHHH
Q 044412          215 EALDAFNKTKK-----SGTGSDQVT  234 (311)
Q Consensus       215 ~a~~~~~~m~~-----~g~~p~~~t  234 (311)
                      +|++.|++..+     -|+.|...|
T Consensus       119 eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2         119 DALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            99999999744     599999876

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.69  E-value=0.0059  Score=49.70  Aligned_cols=228  Identities=11%  Similarity=-0.003  Sum_probs=111.1

Q ss_pred             hhhHHHHHHHHHHhccCcchhH-HHH---HHHHHhhc-------cCChhHHHHhcccCCC--C-Ceeeeec------ccc
Q 044412           40 IKELECVYATIVKTNANLDCFL-AKQ---FISFCTSR-------FHFIDYTILVFPQMQE--P-NVFVYHA------FSS   99 (311)
Q Consensus        40 ~~~~~~l~~~m~~~g~~p~~~~-~~~---ll~~~~~~-------~g~~~~a~~~~~~m~~--~-~~~~~~~------~~~   99 (311)
                      .+.+..++...++.  .|+..+ |+.   ++... ..       .|.+++|+.+++...+  | +...|..      ...
T Consensus        45 ~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l-~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~  121 (334)
T d1dcea1          45 DESVLELTSQILGA--NPDFATLWNCRREVLQHL-ETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLP  121 (334)
T ss_dssp             SHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH-HTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCS
T ss_pred             cHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHH-hhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhc
Confidence            35566677766654  355433 322   22222 22       2335666666666532  2 2222222      333


Q ss_pred             CCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHH-HHHHhCCCCccchHHHHHHhccCCCC---CHhHHH
Q 044412          100 LRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMV-DNYSYSNKFFESRRVSRRLFDEMPER---KFATWN  175 (311)
Q Consensus       100 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll-~~~~~~g~~~~a~~~a~~~~~~~~~~---~~~~~~  175 (311)
                      .++.++|+..++...+.               -+++...+...+ ..+...|..++    |...++...+.   +...|+
T Consensus       122 ~~~~~~a~~~~~~al~~---------------~~~~~~~~~~~~~~~~~~~~~~~~----Al~~~~~~i~~~p~~~~a~~  182 (334)
T d1dcea1         122 EPNWARELELCARFLEA---------------DERNFHCWDYRRFVAAQAAVAPAE----ELAFTDSLITRNFSNYSSWH  182 (334)
T ss_dssp             SCCHHHHHHHHHHHHHH---------------CTTCHHHHHHHHHHHHHTCCCHHH----HHHHHHTTTTTTCCCHHHHH
T ss_pred             cccHHHHHHHHHHHHhh---------------CchhhhhhhhHHHHHHHhccccHH----HHHHHHHHHHcCCCCHHHHH
Confidence            44567777777776543               133444444333 45556677777    66666555442   233343


Q ss_pred             HHHHHHHHH-----HHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          176 TMIDAYARL-----AELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       176 ~li~~~~~~-----a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                      .+-..+.+.     |...+.....-.. ........+...+..+++...+....... +++..++..+...+...+    
T Consensus       183 ~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~----  256 (334)
T d1dcea1         183 YRSCLLPQLHPQPDSGPQGRLPENVLL-KELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQ----  256 (334)
T ss_dssp             HHHHHHHHHSCCCCSSSCCSSCHHHHH-HHHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHH----
T ss_pred             HHHHHHHHhcCHHHHHHHHHHhHHhHH-HHHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHh----
Confidence            333332221     1110100000000 01112223334445555555555444321 222223333333333333    


Q ss_pred             HHHHHHhhCChHHHHHHHhhcCCCC---chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          251 GRGIQIYCRSLGRSLLVFFKLREKN---LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       251 a~~~~~~~~~~~~a~~~~~~~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                               +..+|...+.+..+.+   ...|..+...+.+.|+.++|.+++++..+
T Consensus       257 ---------~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~  304 (334)
T d1dcea1         257 ---------SELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKA  304 (334)
T ss_dssp             ---------HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHH
T ss_pred             ---------hHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                     4446666666655444   45677788889999999999999998876

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=96.51  E-value=0.0015  Score=44.41  Aligned_cols=86  Identities=10%  Similarity=-0.043  Sum_probs=66.2

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|+..|++.....               +-+...|..+-.+|.+.|++++    |...++...+.       
T Consensus        26 ~~~~g~~~~A~~~~~~al~~~---------------p~~~~a~~~lg~~~~~~~~~~~----A~~~~~~al~~-------   79 (112)
T d1hxia_          26 MLKLANLAEAALAFEAVCQKE---------------PEREEAWRSLGLTQAENEKDGL----AIIALNHARML-------   79 (112)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---------------TTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------
T ss_pred             HHHHhhhHHHHHHHhhhcccc---------------cccchhhhhhhhhhhhhhhHHH----hhccccccccc-------
Confidence            678899999999999886642               3357888889999999999999    66555542211       


Q ss_pred             HHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREALDAFNKTK  224 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~  224 (311)
                                      ...+...|..+-..|...|+.++|++.|++..
T Consensus        80 ----------------~p~~~~a~~~la~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          80 ----------------DPKDIAVHAALAVSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------ccccccchHHHHHHHHHCCCHHHHHHHHHHHh
Confidence                            12257788889999999999999999998753

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=96.45  E-value=0.016  Score=44.77  Aligned_cols=93  Identities=11%  Similarity=-0.122  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC-Cc
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK-NL  276 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p-~~  276 (311)
                      +|..+-..|-+.|++++|++.|++..+.  .| +..+|..+-.++.+.|++++|...|+.      +.++     .| +.
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~------al~~-----~p~~~  105 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDS------VLEL-----DPTYN  105 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHH------HHHH-----CTTCT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhH------HHHH-----Hhhhh
Confidence            4444455555566666666666665542  23 344555555556665655544443322      1111     12 23


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          277 LCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       277 ~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ..|..+-..|...|++++|...|++..+
T Consensus       106 ~a~~~lg~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_         106 YAHLNRGIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            3455555555555555555555555443

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.23  E-value=0.027  Score=41.36  Aligned_cols=93  Identities=15%  Similarity=0.207  Sum_probs=65.6

Q ss_pred             HHHHhCCChhHHHHHHHHHHhc--CC-CCC------------------HHHHHHHHHHHhccCChhhHHHHHHhhCChHH
Q 044412          205 TSYSQNKQFREALDAFNKTKKS--GT-GSD------------------QVTMATVLSACAHLGALDLGRGIQIYCRSLGR  263 (311)
Q Consensus       205 ~~~~~~g~~~~a~~~~~~m~~~--g~-~p~------------------~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~  263 (311)
                      ......|++++|.+.|.+-...  |- -++                  ...+..+..++...|++++|            
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~A------------   86 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAV------------   86 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHH------------
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHH------------
Confidence            4567789999999999987763  21 111                  13455566666666666644            


Q ss_pred             HHHHHhhcC--CC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH-----cCCCCC
Q 044412          264 SLLVFFKLR--EK-NLLCWNSITEALAIHGFAHEALGMFDRMTY-----ENVRPN  310 (311)
Q Consensus       264 a~~~~~~~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~-----~g~~P~  310 (311)
                       ...+++..  .| +...|..++.+|.+.|+..+|.+.|++...     -|+.|.
T Consensus        87 -l~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~  140 (179)
T d2ff4a2          87 -IAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPG  140 (179)
T ss_dssp             -HHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             -HHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcC
Confidence             44444443  34 567899999999999999999999999753     588885

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.99  E-value=0.034  Score=40.32  Aligned_cols=94  Identities=14%  Similarity=0.024  Sum_probs=65.3

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHhc-C----CCCC---------HHHHHHHHHHHhccCChhhHHHHHHhhCChHHHH
Q 044412          200 WTTMITSYSQNKQFREALDAFNKTKKS-G----TGSD---------QVTMATVLSACAHLGALDLGRGIQIYCRSLGRSL  265 (311)
Q Consensus       200 y~~li~~~~~~g~~~~a~~~~~~m~~~-g----~~p~---------~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~  265 (311)
                      +...-..+.+.|++++|+..|.+..+. .    ....         ..+|+.+-.+|.+.|+++.|...++.      |.
T Consensus        16 l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~------al   89 (170)
T d1p5qa1          16 VKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNK------AL   89 (170)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------HH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhh------hh
Confidence            444445677889999999999887653 1    1111         24556666777788888866554422      22


Q ss_pred             HHHhhcCCC-CchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          266 LVFFKLREK-NLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       266 ~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      ++     .| ++..|..+-.+|...|++++|...|++..+
T Consensus        90 ~~-----~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          90 EL-----DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hc-----cccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            11     34 677888899999999999999999998876

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.98  E-value=0.29  Score=39.48  Aligned_cols=62  Identities=3%  Similarity=-0.111  Sum_probs=29.9

Q ss_pred             HHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHH
Q 044412          239 LSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDR  301 (311)
Q Consensus       239 i~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  301 (311)
                      +..|-..+-++++.-++..++..+.|..+.=.- .++..-....++.+.+.++.+...++...
T Consensus       168 ~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~-~~~~~~~~~f~e~~~k~~N~e~~~~~i~~  229 (336)
T d1b89a_         168 LRAAEQAHLWAELVFLYDKYEEYDNAIITMMNH-PTDAWKEGQFKDIITKVANVELYYRAIQF  229 (336)
T ss_dssp             HHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHS-TTTTCCHHHHHHHHHHCSSTHHHHHHHHH
T ss_pred             HHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHc-chhhhhHHHHHHHHHccCChHHHHHHHHH
Confidence            444555555555555555555555543322111 12333445556666666666655554443

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=95.95  E-value=0.063  Score=38.02  Aligned_cols=96  Identities=10%  Similarity=0.023  Sum_probs=66.0

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHhcC----CCCC-----------HHHHHHHHHHHhccCChhhHHHHHHhhCChHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKKSG----TGSD-----------QVTMATVLSACAHLGALDLGRGIQIYCRSLGR  263 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~-----------~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~  263 (311)
                      .+...-..+.+.|++++|+..|.+....-    -.++           ..+|+.+-.+|.+.|+++.|...+..      
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~------   92 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASK------   92 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhc------
Confidence            44445567778899999999999876521    1112           23555666677777777766554322      


Q ss_pred             HHHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          264 SLLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       264 a~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      |.++    ...++..|..+-.++...|++++|...|++..+
T Consensus        93 al~~----~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          93 VLKI----DKNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHH----STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cccc----cchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            1111    133678999999999999999999999998776

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.95  E-value=0.0027  Score=43.84  Aligned_cols=89  Identities=7%  Similarity=0.042  Sum_probs=54.1

Q ss_pred             HHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCC---hhHH
Q 044412          140 TAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQ---FREA  216 (311)
Q Consensus       140 ~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~---~~~a  216 (311)
                      ..+++.+...+++++    |++.|+.....                       ...+..++..+-.++.+.++   .++|
T Consensus         3 ~~l~n~~~~~~~l~~----Ae~~Y~~aL~~-----------------------~p~~~~~~~n~a~~L~~s~~~~d~~~A   55 (122)
T d1nzna_           3 EAVLNELVSVEDLLK----FEKKFQSEKAA-----------------------GSVSKSTQFEYAWCLVRTRYNDDIRKG   55 (122)
T ss_dssp             HHHHHHHHHHHHHHH----HHHHHHHHHHH-----------------------SCCCHHHHHHHHHHHTTSSSHHHHHHH
T ss_pred             HHHHHHhcCHHHHHH----HHHHHHHHHhh-----------------------CCCCHHHHHHHHHHHHHhcchHHHHHH
Confidence            457777888888888    55555543221                       12245666666666666544   3457


Q ss_pred             HHHHHHHHhcCCCCCH-HHHHHHHHHHhccCChhhHHHHH
Q 044412          217 LDAFNKTKKSGTGSDQ-VTMATVLSACAHLGALDLGRGIQ  255 (311)
Q Consensus       217 ~~~~~~m~~~g~~p~~-~t~~~li~a~~~~~~~~~a~~~~  255 (311)
                      +.+|++..+..-.|+. .++..|-.+|.+.|+++.|...|
T Consensus        56 i~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~~~   95 (122)
T d1nzna_          56 IVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYV   95 (122)
T ss_dssp             HHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHhccCCchHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            7777777664433332 35666667777777777665554

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.94  E-value=0.0067  Score=44.34  Aligned_cols=69  Identities=7%  Similarity=-0.033  Sum_probs=52.2

Q ss_pred             hHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhHH
Q 044412          137 FVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFREA  216 (311)
Q Consensus       137 ~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~a  216 (311)
                      .+|+.+-.+|.+.|++++|+..+...+..                           ...++..|..+-.+|...|++++|
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~---------------------------~p~~~~a~~~~g~~~~~~g~~~~A  115 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALEL---------------------------DSNNEKGLSRRGEAHLAVNDFELA  115 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------------------CTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhc---------------------------cccchhhhHHHHHHHHHhhhHHHH
Confidence            46777888999999999955544444433                           122677888999999999999999


Q ss_pred             HHHHHHHHhcCCCCCHHH
Q 044412          217 LDAFNKTKKSGTGSDQVT  234 (311)
Q Consensus       217 ~~~~~~m~~~g~~p~~~t  234 (311)
                      +..|++..+.  .|+...
T Consensus       116 ~~~~~~al~l--~P~n~~  131 (170)
T d1p5qa1         116 RADFQKVLQL--YPNNKA  131 (170)
T ss_dssp             HHHHHHHHHH--CSSCHH
T ss_pred             HHHHHHHHHh--CCCCHH
Confidence            9999999874  564433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=95.92  E-value=0.012  Score=41.98  Aligned_cols=75  Identities=5%  Similarity=0.096  Sum_probs=54.6

Q ss_pred             hhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCCcHhHHHHHHHHHHhCCChhH
Q 044412          136 VFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAWDIRSWTTMITSYSQNKQFRE  215 (311)
Q Consensus       136 ~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~~~~~y~~li~~~~~~g~~~~  215 (311)
                      ..+|+.+-.+|.+.|++++|...+...+..                           ...++.+|..+..++...|++++
T Consensus        67 ~~~~~Nla~~~~~l~~~~~Al~~~~~al~~---------------------------~p~~~ka~~~~g~~~~~lg~~~~  119 (153)
T d2fbna1          67 ISCNLNLATCYNKNKDYPKAIDHASKVLKI---------------------------DKNNVKALYKLGVANMYFGFLEE  119 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------------------------STTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhhHHHHHHHhcccchhhhhhhccccc---------------------------cchhhhhhHHhHHHHHHcCCHHH
Confidence            357788888999999999954444444332                           12367889999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHH
Q 044412          216 ALDAFNKTKKSGTGSDQVTMATVL  239 (311)
Q Consensus       216 a~~~~~~m~~~g~~p~~~t~~~li  239 (311)
                      |+..|+.-.+.  .|+.......+
T Consensus       120 A~~~~~~al~l--~P~n~~~~~~l  141 (153)
T d2fbna1         120 AKENLYKAASL--NPNNLDIRNSY  141 (153)
T ss_dssp             HHHHHHHHHHH--STTCHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHH
Confidence            99999998874  56654443333

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.92  E-value=0.054  Score=37.06  Aligned_cols=100  Identities=12%  Similarity=0.141  Sum_probs=70.5

Q ss_pred             cccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHH
Q 044412           97 FSSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNT  176 (311)
Q Consensus        97 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~  176 (311)
                      +.+.|++++|++.|++..+..               +.+...|..+-.+|.+.|++++    |...++...+        
T Consensus        14 ~~~~~~y~~Ai~~y~~al~~~---------------p~~~~~~~~~a~~~~~~~~~~~----A~~~~~~al~--------   66 (128)
T d1elra_          14 AYKKKDFDTALKHYDKAKELD---------------PTNMTYITNQAAVYFEKGDYNK----CRELCEKAIE--------   66 (128)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHH--------
T ss_pred             HHHcCCHHHHHHHHHHHHHhC---------------cccHHHHHhHHHHHHHcCchHH----HHHHHHHHHH--------
Confidence            557899999999999887642               4458889999999999999999    5555554222        


Q ss_pred             HHHHHHHHHHHHHhhCCCC--c-HhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHH
Q 044412          177 MIDAYARLAELLFNKMPAW--D-IRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMA  236 (311)
Q Consensus       177 li~~~~~~a~~~~~~m~~~--~-~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  236 (311)
                                 +-......  + ..+|..+-..+...+++++|++.|..-...  .|+.....
T Consensus        67 -----------l~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~  116 (128)
T d1elra_          67 -----------VGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLK  116 (128)
T ss_dssp             -----------HHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHH
T ss_pred             -----------hCcccHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCHHHHH
Confidence                       11111111  1 246778888888999999999999887653  35554433

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=95.86  E-value=0.072  Score=37.76  Aligned_cols=101  Identities=18%  Similarity=0.125  Sum_probs=72.7

Q ss_pred             hHHHHHH--HHHHhCCChhHHHHHHHHHHhcC-CCCC----------HHHHHHHHHHHhccCChhhHHHHHHhhCChHHH
Q 044412          198 RSWTTMI--TSYSQNKQFREALDAFNKTKKSG-TGSD----------QVTMATVLSACAHLGALDLGRGIQIYCRSLGRS  264 (311)
Q Consensus       198 ~~y~~li--~~~~~~g~~~~a~~~~~~m~~~g-~~p~----------~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a  264 (311)
                      .+|..+-  ..+...|++++|+..|++-.+.. --|+          ...|+.+-.+|...|+++.|..-+      ..+
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~------~~a   81 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSA------DKA   81 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHH------HHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhh------hhh
Confidence            3566663  44556799999999999987621 1122          467888999999999999997654      456


Q ss_pred             HHHHhhcCCC--C-----chhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          265 LLVFFKLREK--N-----LLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       265 ~~~~~~~~~p--~-----~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+++.+....  +     ...|+.+-.+|...|++++|...|++..+
T Consensus        82 l~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          82 LHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            6665554422  1     23567788999999999999999998653

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.71  E-value=0.089  Score=35.88  Aligned_cols=97  Identities=14%  Similarity=0.190  Sum_probs=70.1

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCCC---ch
Q 044412          201 TTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREKN---LL  277 (311)
Q Consensus       201 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p~---~~  277 (311)
                      -.+=..+...|++++|+..|++..+.+ +-+...|..+-.+|.+.|+++.|...++..-.++.      ....+.   ..
T Consensus         8 k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~------~~~~~~~~~a~   80 (128)
T d1elra_           8 KELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR------ENREDYRQIAK   80 (128)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH------HSTTCHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCc------ccHHHHHHHHH
Confidence            344567888999999999999998853 34577888999999999999988776644322221      111110   13


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          278 CWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       278 ~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      +|..+-..+...+++++|.+.|++-..
T Consensus        81 ~~~~lg~~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          81 AYARIGNSYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHh
Confidence            677777788889999999999987654

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.52  E-value=0.0035  Score=51.13  Aligned_cols=194  Identities=8%  Similarity=-0.072  Sum_probs=119.2

Q ss_pred             hhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccC--ChhHHHHhcccCCC---CCeeeeec-----cccCCChhHHHHH
Q 044412           40 IKELECVYATIVKTNANLDCFLAKQFISFCTSRFH--FIDYTILVFPQMQE---PNVFVYHA-----FSSLRHPLQAIAF  109 (311)
Q Consensus        40 ~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g--~~~~a~~~~~~m~~---~~~~~~~~-----~~~~~~~~~a~~~  109 (311)
                      ..++..+++...+.. +-+...|..+..++ ...+  +.++|...++...+   ++...+..     +...+..++|++.
T Consensus        89 ~~~al~~~~~~l~~~-pk~~~~~~~~~~~~-~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~  166 (334)
T d1dcea1          89 VKAELGFLESCLRVN-PKSYGTWHHRCWLL-SRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAF  166 (334)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCcHHHHHHhhHHH-HHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHH
Confidence            444555666666543 23555666665555 5554  57888888888642   33333322     6678899999999


Q ss_pred             HHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHH-----
Q 044412          110 YLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARL-----  184 (311)
Q Consensus       110 ~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~-----  184 (311)
                      ++...+..               +-+...|+.+-..+.+.|+.++    |...+........... .....+...     
T Consensus       167 ~~~~i~~~---------------p~~~~a~~~l~~~~~~~~~~~~----A~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~  226 (334)
T d1dcea1         167 TDSLITRN---------------FSNYSSWHYRSCLLPQLHPQPD----SGPQGRLPENVLLKEL-ELVQNAFFTDPNDQ  226 (334)
T ss_dssp             HHTTTTTT---------------CCCHHHHHHHHHHHHHHSCCCC----SSSCCSSCHHHHHHHH-HHHHHHHHHCSSCS
T ss_pred             HHHHHHcC---------------CCCHHHHHHHHHHHHHhcCHHH----HHHHHHHhHHhHHHHH-HHHHHHHHhcchhH
Confidence            98876642               3457788888889999999999    5444443322111111 111111111     


Q ss_pred             HHHHHhh---CCCCcHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCChhhHHHHHHh
Q 044412          185 AELLFNK---MPAWDIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGALDLGRGIQIY  257 (311)
Q Consensus       185 a~~~~~~---m~~~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~  257 (311)
                      +...+..   ...++...+..+...+...|+.++|+..+.+....  .| +..++..+-.++...|+.++|...++.
T Consensus       227 a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~  301 (334)
T d1dcea1         227 SAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELESCKELQELEPE--NKWCLLTIILLMRALDPLLYEKETLQYFST  301 (334)
T ss_dssp             HHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHCTGGGHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhh--CchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            2222221   12234455666677777788999999999887653  33 445677788888898888877666543

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.36  E-value=0.13  Score=36.81  Aligned_cols=90  Identities=6%  Similarity=0.006  Sum_probs=49.4

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHhc--------------CCCC-CHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHH
Q 044412          202 TMITSYSQNKQFREALDAFNKTKKS--------------GTGS-DQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLL  266 (311)
Q Consensus       202 ~li~~~~~~g~~~~a~~~~~~m~~~--------------g~~p-~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~  266 (311)
                      ..-..+...|++++|++.|.+..+.              -+.| +...|..+-.++.+.|+++.|..             
T Consensus        32 ~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~-------------   98 (169)
T d1ihga1          32 NIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVD-------------   98 (169)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHH-------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhh-------------
Confidence            3444556667777777766665321              0111 22234444455555555554433             


Q ss_pred             HHhhcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 044412          267 VFFKLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTY  304 (311)
Q Consensus       267 ~~~~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~  304 (311)
                      .+++..   ..+...|..+-.+|...|++++|...|++..+
T Consensus        99 ~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          99 SCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            333222   23456677777777777777777777777665

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.18  E-value=1.1  Score=36.00  Aligned_cols=233  Identities=9%  Similarity=-0.051  Sum_probs=132.2

Q ss_pred             HHHhhccChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhccc-CCCCCeeeeec--cccCCChhHHHH
Q 044412           32 NQLKKCSSIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQ-MQEPNVFVYHA--FSSLRHPLQAIA  108 (311)
Q Consensus        32 ~~l~~~~~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~-m~~~~~~~~~~--~~~~~~~~~a~~  108 (311)
                      .++..+.+.++...+++...+.+   ++.+|..+...| .+......+.-+-.. ...++...--+  |-..|.+++...
T Consensus        45 rl~~~~v~l~~~~~avd~~~k~~---~~~~~k~~~~~l-~~~~e~~la~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~  120 (336)
T d1b89a_          45 RLASTLVHLGEYQAAVDGARKAN---STRTWKEVCFAC-VDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELIT  120 (336)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHT---CHHHHHHHHHHH-HHTTCHHHHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhhccHHHHHHHHHHcC---CHHHHHHHHHHH-HhCcHHHHHHHHHHHhhcCHHHHHHHHHHHHHcCChHHHHH
Confidence            33333344444444555555543   555777777777 666555544322111 11222111111  455556666666


Q ss_pred             HHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhcc-CCCCCHhHHHHHHHHHHHH---
Q 044412          109 FYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDE-MPERKFATWNTMIDAYARL---  184 (311)
Q Consensus       109 ~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~-~~~~~~~~~~~li~~~~~~---  184 (311)
                      +++.....               -..+...++-++.+|++.+. ++    ..+.+.. ...-+   ...++..|-+.   
T Consensus       121 ~Le~~~~~---------------~~~~~~~~~~L~~lyak~~~-~k----l~e~l~~~s~~y~---~~k~~~~c~~~~l~  177 (336)
T d1b89a_         121 MLEAALGL---------------ERAHMGMFTELAILYSKFKP-QK----MREHLELFWSRVN---IPKVLRAAEQAHLW  177 (336)
T ss_dssp             HHHHHTTS---------------TTCCHHHHHHHHHHHHTTCH-HH----HHHHHHHHSTTSC---HHHHHHHHHTTTCH
T ss_pred             HHHHHHcC---------------CccchHHHHHHHHHHHHhCh-HH----HHHHHHhccccCC---HHHHHHHHHHcCCh
Confidence            66544221               24566778888888888753 33    2222322 11111   12222222221   


Q ss_pred             --HHHHHhhCCCC------------cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhh
Q 044412          185 --AELLFNKMPAW------------DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDL  250 (311)
Q Consensus       185 --a~~~~~~m~~~------------~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~  250 (311)
                        +.-++.++...            +..-....++.+.+.++++...++.....+.  .|+  ..+.|+......-+..+
T Consensus       178 ~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~--~p~--~i~~lL~~v~~~~d~~r  253 (336)
T d1b89a_         178 AELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEF--KPL--LLNDLLMVLSPRLDHTR  253 (336)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH--CGG--GHHHHHHHHGGGCCHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHHHHHc--CHH--HHHHHHHHhccCCCHHH
Confidence              33344444332            2222334567778888888777777766653  353  44777888888888888


Q ss_pred             HHHHHHhhCChHHHHHHHhhcCC-CCchhHHHHHHHHHhcCChHHH
Q 044412          251 GRGIQIYCRSLGRSLLVFFKLRE-KNLLCWNSITEALAIHGFAHEA  295 (311)
Q Consensus       251 a~~~~~~~~~~~~a~~~~~~~~~-p~~~~~~~li~~~~~~g~~~~a  295 (311)
                      ..+.++..+++.....+++.... -+..+.+++.+.|....+++.-
T Consensus       254 ~V~~~~k~~~l~li~p~Le~v~~~n~~~vn~al~~lyie~~d~~~l  299 (336)
T d1b89a_         254 AVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQAL  299 (336)
T ss_dssp             HHHHHHHTTCTTTTHHHHHHHHTTCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHhcCCcHHHHHHHHHHHHcChHHHHHHHHHHHhCcchhHHH
Confidence            99999888888888888877653 4567899999999999987553

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=94.13  E-value=0.17  Score=39.49  Aligned_cols=110  Identities=5%  Similarity=0.033  Sum_probs=69.9

Q ss_pred             ccCCChhHHHHHHHHHHHCCCCchHHHHHHHHhcCCCchhHHHHHHHHHHhCCCCccchHHHHHHhccCCC--CCH-hHH
Q 044412           98 SSLRHPLQAIAFYLYMLRAEVLLTTVHGQVWKNGFSSPVFVQTAMVDNYSYSNKFFESRRVSRRLFDEMPE--RKF-ATW  174 (311)
Q Consensus        98 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~~g~~~~~~~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~--~~~-~~~  174 (311)
                      .+.|++++|+..|++-.+..               +-|...+..+...|+..|++++    |...++...+  |+. ..+
T Consensus         7 L~~G~l~eAl~~l~~al~~~---------------P~d~~ar~~La~lL~~~G~~e~----A~~~l~~a~~l~P~~~~~~   67 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKAS---------------PKDASLRSSFIELLCIDGDFER----ADEQLMQSIKLFPEYLPGA   67 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTC---------------TTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHCGGGHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHC---------------CCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHhCCCcHHHH
Confidence            46799999999999987752               5568999999999999999999    5555554432  322 222


Q ss_pred             HHHHHHHHHH--HHHHHhhCC------CC-cHhHHHHHHHHHHhCCChhHHHHHHHHHHhc
Q 044412          175 NTMIDAYARL--AELLFNKMP------AW-DIRSWTTMITSYSQNKQFREALDAFNKTKKS  226 (311)
Q Consensus       175 ~~li~~~~~~--a~~~~~~m~------~~-~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~  226 (311)
                      ..+-..+...  -.+.+....      .| +...+......+...|+.++|.+++.+..+.
T Consensus        68 ~~l~~ll~a~~~~~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          68 SQLRHLVKAAQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccHHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            2222222111  222333222      12 2333444455667779999999999887663

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=94.08  E-value=0.43  Score=33.94  Aligned_cols=100  Identities=15%  Similarity=0.060  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHh---cCCCCC-----------HHHHHHHHHHHhccCChhhHHHHHHhhCChHHH
Q 044412          199 SWTTMITSYSQNKQFREALDAFNKTKK---SGTGSD-----------QVTMATVLSACAHLGALDLGRGIQIYCRSLGRS  264 (311)
Q Consensus       199 ~y~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~-----------~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a  264 (311)
                      .+.-.-..+.+.|++++|++.|.+-..   ....++           ...|+.+-.+|.+.|++++|...++..-.    
T Consensus        17 ~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~----   92 (168)
T d1kt1a1          17 IVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG----   92 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH----
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhh----
Confidence            344455667788999999999877553   111111           12344455566677777755554332111    


Q ss_pred             HHHHhhcCCCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          265 LLVFFKLREKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       265 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                            +...++..|..+-.++...|++++|...|++..+  +.|+
T Consensus        93 ------l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~--l~P~  130 (168)
T d1kt1a1          93 ------LDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLE--VNPQ  130 (168)
T ss_dssp             ------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--SCTT
T ss_pred             ------cccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCC
Confidence                  1134667888888899999999999999988875  3454

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=93.82  E-value=0.17  Score=39.40  Aligned_cols=27  Identities=0%  Similarity=-0.305  Sum_probs=21.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHc
Q 044412          279 WNSITEALAIHGFAHEALGMFDRMTYE  305 (311)
Q Consensus       279 ~~~li~~~~~~g~~~~a~~~~~~M~~~  305 (311)
                      +......+...|+.++|...+++..+.
T Consensus       102 ~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1         102 SLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            344456677899999999999987653

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.47  E-value=0.3  Score=34.73  Aligned_cols=60  Identities=8%  Similarity=-0.010  Sum_probs=48.6

Q ss_pred             cHhHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          196 DIRSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       196 ~~~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      +...|+.+-.++.+.|++++|+..+.+..+.. +-+...|..+-.++.+.|+++.|...|+
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~  135 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLK  135 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHH
Confidence            45578888889999999999999999998742 3356688889999999999997766553

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.45  E-value=0.33  Score=32.85  Aligned_cols=113  Identities=11%  Similarity=0.034  Sum_probs=82.0

Q ss_pred             CcHhHHHHHHHHHHhCCChhHHHHHHHHHHh-cCCCCCHHHHHHHHHHHhccCC----hhhHHHHHHhhCChHHHHHHHh
Q 044412          195 WDIRSWTTMITSYSQNKQFREALDAFNKTKK-SGTGSDQVTMATVLSACAHLGA----LDLGRGIQIYCRSLGRSLLVFF  269 (311)
Q Consensus       195 ~~~~~y~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~li~a~~~~~~----~~~a~~~~~~~~~~~~a~~~~~  269 (311)
                      .+..-||-+|=.....-+.+-.+.+++..-+ ..+.|.. -...++.++.+.+.    ++.|..++-..++-+.-.++.+
T Consensus        32 s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~-Nlk~vv~C~~~~n~~se~vdlALd~lv~~~kkd~Ld~i~~  110 (161)
T d1wy6a1          32 STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQ-NLKSVVECGVINNTLNEHVNKALDILVIQGKRDKLEEIGR  110 (161)
T ss_dssp             SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCS-CTHHHHHHHHHTTCCCHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CCccccceeeeecccccchHHHHHHHHHHhhhcCchhhh-cHHHHHHHHHHhcchHHHHHHHHHHHHHhccHHHHHHHHH
Confidence            4566677777777777777777777777654 2222221 23455666666553    4667777777888888888877


Q ss_pred             hcC---CCCchhHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 044412          270 KLR---EKNLLCWNSITEALAIHGFAHEALGMFDRMTYENVR  308 (311)
Q Consensus       270 ~~~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~  308 (311)
                      .+.   +|++...-.+-.||-+-|...++.+++.+.-+.|++
T Consensus       111 ~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1         111 EILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            744   788888888899999999999999999999998874

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=93.41  E-value=0.68  Score=32.27  Aligned_cols=107  Identities=14%  Similarity=0.056  Sum_probs=69.6

Q ss_pred             hHHHHH--HHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCCC--------cHhHHHHHHHH
Q 044412          137 FVQTAM--VDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPAW--------DIRSWTTMITS  206 (311)
Q Consensus       137 ~~~~~l--l~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~~--------~~~~y~~li~~  206 (311)
                      ..|..+  -..+.+.|++++    |...|.+                   |.++....++.        ....|+.+-.+
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~----Ai~~y~~-------------------Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~   64 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDE----AAANCRR-------------------AMEISHTMPPEEAFDHAGFDAFCHAGLAEA   64 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHH----HHHHHHH-------------------HHHHHTTSCTTSCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHH----HHHHHHH-------------------HHHhChhhhhhhhcccchhHHHHHHHHHHH
Confidence            345555  445667799999    6666655                   33444444321        23578899999


Q ss_pred             HHhCCChhHHHHHHHHHHhc-----CCCCCH-----HHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC
Q 044412          207 YSQNKQFREALDAFNKTKKS-----GTGSDQ-----VTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR  272 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~-----g~~p~~-----~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~  272 (311)
                      |.+.|++++|...+++..+.     ...++.     ..|+.+-.+|...|++++|...|+      .|.+++.+..
T Consensus        65 ~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~------~Al~l~~~~~  134 (156)
T d2hr2a1          65 LAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFK------KVVEMIEERK  134 (156)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH------HHHHHHHHCC
T ss_pred             HHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHH------HHHHhhHHhh
Confidence            99999999999999887642     223322     245666788888899888876653      4444444443

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.94  E-value=0.64  Score=29.40  Aligned_cols=66  Identities=9%  Similarity=-0.027  Sum_probs=47.4

Q ss_pred             HHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcCCC--C-chhHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 044412          237 TVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLREK--N-LLCWNSITEALAIHGFAHEALGMFDRMTYENVRPN  310 (311)
Q Consensus       237 ~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~~p--~-~~~~~~li~~~~~~g~~~~a~~~~~~M~~~g~~P~  310 (311)
                      -+=..+.+.|+++.|...|+      +|.+++..-..+  + ..+++.+-.++.+.|++++|...+++..+  +.|+
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~------~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~--l~P~   78 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWME------QALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE--LDPE   78 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHH------HHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTT
T ss_pred             HHHHHHHHCCCHHHHHHHHH------HHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH--hCcC
Confidence            34455677888888877653      455555443322  2 35789999999999999999999999886  3465

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=91.76  E-value=1.4  Score=30.92  Aligned_cols=58  Identities=9%  Similarity=0.158  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHH
Q 044412          198 RSWTTMITSYSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQI  256 (311)
Q Consensus       198 ~~y~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~  256 (311)
                      ..|+.+-.+|.+.|++++|+..+++..+.. +.+...|..+-.++...|+++.|...|.
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~  122 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFE  122 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            457778888999999999999999988752 4467788888899999998886666553

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.96  E-value=0.78  Score=28.96  Aligned_cols=70  Identities=7%  Similarity=0.020  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHhCCCCccchHHHHHHhccCCCCCHhHHHHHHHHHHHHHHHHHhhCCC--C-cHhHHHHHHHHHHhCCChh
Q 044412          138 VQTAMVDNYSYSNKFFESRRVSRRLFDEMPERKFATWNTMIDAYARLAELLFNKMPA--W-DIRSWTTMITSYSQNKQFR  214 (311)
Q Consensus       138 ~~~~ll~~~~~~g~~~~a~~~a~~~~~~~~~~~~~~~~~li~~~~~~a~~~~~~m~~--~-~~~~y~~li~~~~~~g~~~  214 (311)
                      .+-.+-..+.+.|++++    |...|++                   |.++...-..  + ...+++.+-.++.+.|+++
T Consensus         7 dc~~lG~~~~~~g~y~~----A~~~~~~-------------------Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~   63 (95)
T d1tjca_           7 DSFELGKVAYTEADYYH----TELWMEQ-------------------ALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLD   63 (95)
T ss_dssp             HHHHHHHHHHHTTCHHH----HHHHHHH-------------------HHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHCCCHHH----HHHHHHH-------------------HHHHHhhhhccCccHHHHHHHHhhHHHhcCChH
Confidence            33456667889999999    6666665                   3334333322  2 2457889999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCH
Q 044412          215 EALDAFNKTKKSGTGSDQ  232 (311)
Q Consensus       215 ~a~~~~~~m~~~g~~p~~  232 (311)
                      +|++.+++..+.  .|+.
T Consensus        64 ~A~~~y~~aL~l--~P~~   79 (95)
T d1tjca_          64 KALLLTKKLLEL--DPEH   79 (95)
T ss_dssp             HHHHHHHHHHHH--CTTC
T ss_pred             HHHHHHHHHHHh--CcCC
Confidence            999999999874  5664

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=89.37  E-value=0.51  Score=32.69  Aligned_cols=83  Identities=11%  Similarity=0.099  Sum_probs=53.6

Q ss_pred             CChhHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhccCCh----hhHHHHHHhhCChHHHHHHHhhcC--CCCchhHHHHH
Q 044412          211 KQFREALDAFNKTKKSGTGS-DQVTMATVLSACAHLGAL----DLGRGIQIYCRSLGRSLLVFFKLR--EKNLLCWNSIT  283 (311)
Q Consensus       211 g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~a~~~~~~~----~~a~~~~~~~~~~~~a~~~~~~~~--~p~~~~~~~li  283 (311)
                      +.+++|+..|++..+.  .| +..+|..+=.+|...|.+    ..+.      +....|.+.|++..  .|+..+|..-+
T Consensus        55 ~~~~~Ai~~~~kAl~l--~P~~~~a~~~lG~~y~~~g~~~~~~~~~~------~~~~~A~~~~~kal~l~P~~~~~~~~L  126 (145)
T d1zu2a1          55 QMIQEAITKFEEALLI--DPKKDEAVWCIGNAYTSFAFLTPDETEAK------HNFDLATQFFQQAVDEQPDNTHYLKSL  126 (145)
T ss_dssp             HHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHCCCHHHHH------HHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHh--cchhhHHHhhHHHHHHHcccchhhHHHHH------HhHHHhhhhhhcccccCCCHHHHHHHH
Confidence            4568899999988874  45 456777777777665432    2222      22345666676655  78887777666


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCC
Q 044412          284 EALAIHGFAHEALGMFDRMTYENV  307 (311)
Q Consensus       284 ~~~~~~g~~~~a~~~~~~M~~~g~  307 (311)
                      .-+.      .|.+++.+..+.|+
T Consensus       127 ~~~~------ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         127 EMTA------KAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHH------THHHHHHHHHHSSS
T ss_pred             HHHH------HHHHHHHHHHHHhc
Confidence            5553      46777777777664

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=88.10  E-value=0.3  Score=33.98  Aligned_cols=94  Identities=13%  Similarity=0.045  Sum_probs=60.9

Q ss_pred             HHhCCChhHHHHHHHHHHhcCCCCCHHHHHHHHHHHhccCChhhHHHHHHhhCChHHHHHHHhhcC--CC-CchhHHHHH
Q 044412          207 YSQNKQFREALDAFNKTKKSGTGSDQVTMATVLSACAHLGALDLGRGIQIYCRSLGRSLLVFFKLR--EK-NLLCWNSIT  283 (311)
Q Consensus       207 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~a~~~~~~~~~a~~~~~~~~~~~~a~~~~~~~~--~p-~~~~~~~li  283 (311)
                      |-+.+.+++|+..|+.-.+.. +-+...+..+=.++...++...+..-   .+..++|...|++..  .| +...|+.+-
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~---~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG   82 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDA---KQMIQEAITKFEEALLIDPKKDEAVWCIG   82 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHH---HHHHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHH---HHHHHHHHHHHHHHHHhcchhhHHHhhHH
Confidence            345567899999999988753 33455666666666665555444322   234456777776655  44 567888887


Q ss_pred             HHHHhcCC-----------hHHHHHHHHHHHH
Q 044412          284 EALAIHGF-----------AHEALGMFDRMTY  304 (311)
Q Consensus       284 ~~~~~~g~-----------~~~a~~~~~~M~~  304 (311)
                      .+|...|+           +++|.+.|++..+
T Consensus        83 ~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~  114 (145)
T d1zu2a1          83 NAYTSFAFLTPDETEAKHNFDLATQFFQQAVD  114 (145)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcccchhhHHHHHHhHHHhhhhhhcccc
Confidence            77776543           5677777777664

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=81.65  E-value=1.7  Score=27.65  Aligned_cols=57  Identities=12%  Similarity=0.108  Sum_probs=43.7

Q ss_pred             HHHHHhhcc-ChhhHHHHHHHHHHhccCcchhHHHHHHHHHhhccCChhHHHHhcccCC
Q 044412           30 IANQLKKCS-SIKELECVYATIVKTNANLDCFLAKQFISFCTSRFHFIDYTILVFPQMQ   87 (311)
Q Consensus        30 ~~~~l~~~~-~~~~~~~l~~~m~~~g~~p~~~~~~~ll~~~~~~~g~~~~a~~~~~~m~   87 (311)
                      |...+..-. +.=++++-+..+....+.|++.+..+.+++| .|..++..|.++|+.++
T Consensus        11 y~~~F~~~~iD~we~rrgmN~l~~~DlVPeP~Ii~aALrAc-RRvND~alAVR~lE~vK   68 (105)
T d1v54e_          11 WVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRAC-RRLNDFASAVRILEVVK   68 (105)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHH-HHTTCHHHHHHHHHHHH
T ss_pred             HHHHhcCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHH-HHhhhHHHHHHHHHHHH
Confidence            344444332 3335567777777888999999999999999 99999999999997764